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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.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.TreeMap;
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import java.util.UUID;
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import javax.persistence.EntityNotFoundException;
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import org.apache.commons.collections.CollectionUtils;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Service;
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import org.springframework.transaction.annotation.Transactional;
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import eu.etaxonomy.cdm.api.service.config.CreateHierarchyForClassificationConfigurator;
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import eu.etaxonomy.cdm.api.service.config.NodeDeletionConfigurator.ChildHandling;
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import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.dto.EntityDTO;
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import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
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import eu.etaxonomy.cdm.api.service.dto.MarkedEntityDTO;
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import eu.etaxonomy.cdm.api.service.dto.TaxonInContextDTO;
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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.IProgressMonitor;
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import eu.etaxonomy.cdm.exception.UnpublishedException;
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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.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.ITreeNode;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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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.TaxonDescription;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.media.MediaUtils;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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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.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.ITaxonNodeComparator;
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import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.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.TaxonRelationshipType;
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import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
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import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
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import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
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import eu.etaxonomy.cdm.persistence.dto.ClassificationLookupDTO;
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
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import eu.etaxonomy.cdm.persistence.dto.TaxonStatus;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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/**
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* @author n.hoffmann
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* @since Sep 21, 2009
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*/
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@Service
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@Transactional(readOnly = true)
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public class ClassificationServiceImpl
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extends IdentifiableServiceBase<Classification, IClassificationDao>
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implements IClassificationService {
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private static final Logger logger = Logger.getLogger(ClassificationServiceImpl.class);
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@Autowired
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private ITaxonNodeDao taxonNodeDao;
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@Autowired
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private ITaxonDao taxonDao;
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@Autowired
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private ITaxonNodeService taxonNodeService;
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@Autowired
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private IDefinedTermDao termDao;
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@Autowired
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private IBeanInitializer defaultBeanInitializer;
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@Override
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@Autowired
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protected void setDao(IClassificationDao dao) {
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this.dao = dao;
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}
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private Comparator<? super TaxonNode> taxonNodeComparator;
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@Autowired
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public void setTaxonNodeComparator(ITaxonNodeComparator<? super TaxonNode> taxonNodeComparator){
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this.taxonNodeComparator = (Comparator<? super TaxonNode>) taxonNodeComparator;
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}
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@Override
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public TaxonNode loadTaxonNodeByTaxon(Taxon taxon, UUID classificationUuid, List<String> propertyPaths){
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Classification tree = dao.load(classificationUuid);
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TaxonNode node = tree.getNode(taxon);
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return loadTaxonNode(node.getUuid(), propertyPaths);
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}
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@Override
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@Deprecated // use loadTaxonNode(UUID, List<String>) instead
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public TaxonNode loadTaxonNode(TaxonNode taxonNode, List<String> propertyPaths){
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return taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);
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}
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public TaxonNode loadTaxonNode(UUID taxonNodeUuid, List<String> propertyPaths){
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return taxonNodeDao.load(taxonNodeUuid, propertyPaths);
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}
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@Override
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@Transactional(readOnly = false)
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public UpdateResult cloneClassification(UUID classificationUuid,
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String name, Reference sec, TaxonRelationshipType relationshipType) {
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UpdateResult result = new UpdateResult();
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Classification classification = load(classificationUuid);
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Classification clone = Classification.NewInstance(name);
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clone.setReference(sec);
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//clone taxa and taxon nodes
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List<TaxonNode> childNodes = classification.getRootNode().getChildNodes();
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for (TaxonNode taxonNode : childNodes) {
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addChildTaxa(taxonNode, null, clone, relationshipType);
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}
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dao.saveOrUpdate(clone);
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result.setCdmEntity(clone);
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return result;
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}
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private void addChildTaxa(TaxonNode originalParentNode, TaxonNode cloneParentNode, Classification classification, TaxonRelationshipType relationshipType){
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Reference reference = classification.getReference();
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Taxon cloneTaxon = (Taxon) HibernateProxyHelper.deproxy(originalParentNode.getTaxon(), Taxon.class).clone();
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cloneTaxon.setSec(reference);
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String microReference = null;
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List<TaxonNode> originalChildNodes = originalParentNode.getChildNodes();
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HHH_9751_Util.removeAllNull(originalChildNodes);
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//add relation between taxa
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if (relationshipType != null){
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cloneTaxon.addTaxonRelation(originalParentNode.getTaxon(), relationshipType, reference, microReference);
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}
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TaxonNode cloneChildNode = null;
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//add taxon node to either parent node or classification (no parent node)
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if(cloneParentNode==null){
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cloneChildNode = classification.addChildTaxon(cloneTaxon, reference, microReference);
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}
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else{
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cloneChildNode = cloneParentNode.addChildTaxon(cloneTaxon, reference, microReference);
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}
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taxonNodeDao.saveOrUpdate(cloneChildNode);
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//add children
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for (TaxonNode originalChildNode : originalChildNodes) {
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addChildTaxa(originalChildNode, cloneChildNode, classification, relationshipType);
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}
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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<TaxonNode> listRankSpecificRootNodes(Classification classification, Rank rank,
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boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
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return pageRankSpecificRootNodes(classification, rank, includeUnpublished, pageSize, pageIndex, propertyPaths).getRecords();
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}
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@Override
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public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, Rank rank,
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boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
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long[] numberOfResults = dao.countRankSpecificRootNodes(classification, includeUnpublished, rank);
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long totalNumberOfResults = numberOfResults[0] + (numberOfResults.length > 1 ? numberOfResults[1] : 0);
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List<TaxonNode> results = new ArrayList<>();
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if (AbstractPagerImpl.hasResultsInRange(totalNumberOfResults, pageIndex, pageSize)) { // no point checking again
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Integer limit = PagerUtils.limitFor(pageSize);
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Integer start = PagerUtils.startFor(pageSize, pageIndex);
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Integer remainingLimit = limit;
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int[] queryIndexes = rank == null ? new int[]{0} : new int[]{0,1};
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for(int queryIndex: queryIndexes) {
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if(start != null && start > numberOfResults[queryIndex]) {
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// start in next query with new start value
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start = start - (int)numberOfResults[queryIndex];
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continue;
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}
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List<TaxonNode> perQueryResults = dao.listRankSpecificRootNodes(classification,
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rank, includeUnpublished, remainingLimit, start, propertyPaths, queryIndex);
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results.addAll(perQueryResults);
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if(remainingLimit != null ){
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remainingLimit = remainingLimit - results.size();
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if(remainingLimit <= 0) {
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// no need to run further queries if first query returned enough items!
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break;
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}
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// start at with fist item of next query to fetch the remaining items
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start = 0;
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}
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}
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}
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// long start_t = System.currentTimeMillis();
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Collections.sort(results, taxonNodeComparator); // TODO is ordering during the hibernate query in the dao possible?
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// System.err.println("service.pageRankSpecificRootNodes() - Collections.sort(results, taxonNodeComparator) " + (System.currentTimeMillis() - start_t));
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return new DefaultPagerImpl<TaxonNode>(pageIndex, totalNumberOfResults, pageSize, results);
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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<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank,
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boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
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TaxonNode thisNode = taxonNodeDao.load(taxonNode.getUuid(), propertyPaths);
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if(baseRank != null){
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baseRank = (Rank) termDao.load(baseRank.getUuid());
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}
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if (!includeUnpublished && thisNode.getTaxon() != null && !thisNode.getTaxon().isPublish()){
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throw new UnpublishedException("Final taxon in tree branch is unpublished.");
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}
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List<TaxonNode> pathToRoot = new ArrayList<>();
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pathToRoot.add(thisNode);
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while(!thisNode.isTopmostNode()){
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//TODO why do we need to deproxy here?
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// without this thisNode.getParent() will return NULL in
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// some cases (environment dependend?) even if the parent exits
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TaxonNode parentNode = CdmBase.deproxy(thisNode).getParent();
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if(parentNode == null){
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throw new NullPointerException("Taxon node " + thisNode + " must have a parent since it is not top most");
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}
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if(parentNode.getTaxon() == null){
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throw new NullPointerException("The taxon associated with taxon node " + parentNode + " is NULL");
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}
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if(!includeUnpublished && !parentNode.getTaxon().isPublish()){
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throw new UnpublishedException("Some taxon in tree branch is unpublished.");
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}
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if(parentNode.getTaxon().getName() == null){
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throw new NullPointerException("The name of the taxon associated with taxonNode " + parentNode + " is NULL");
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}
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Rank parentNodeRank = (parentNode.getTaxon().getName() == null) ? null : parentNode.getTaxon().getName().getRank();
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// stop if the next parent is higher than the baseRank
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if(baseRank != null && parentNodeRank != null && baseRank.isLower(parentNodeRank)){
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break;
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}
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pathToRoot.add(parentNode);
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thisNode = parentNode;
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}
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// initialize and invert order of nodes in list
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defaultBeanInitializer.initializeAll(pathToRoot, propertyPaths);
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Collections.reverse(pathToRoot);
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return pathToRoot;
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}
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@Override
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public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification, Rank baseRank,
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boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
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UUID nodeUuid = getTaxonNodeUuidByTaxonUuid(classification.getUuid(), taxon.getUuid());
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TaxonNode node = taxonNodeService.find(nodeUuid);
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if(node == null){
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logger.warn("The specified taxon is not found in the given tree.");
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return null;
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}
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return loadTreeBranch(node, baseRank, includeUnpublished, propertyPaths);
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}
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@Override
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public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,
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List<String> propertyPaths) {
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taxonNode = taxonNodeDao.load(taxonNode.getUuid());
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List<TaxonNode> childNodes = new ArrayList<TaxonNode>(taxonNode.getChildNodes());
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defaultBeanInitializer.initializeAll(childNodes, propertyPaths);
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Collections.sort(childNodes, taxonNodeComparator);
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return childNodes;
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}
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@Override
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public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid,
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boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths){
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Classification classification = dao.load(classificationUuid);
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Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
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List<TaxonNode> results = dao.listChildrenOf(
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taxon, classification, includeUnpublished, pageSize, pageIndex, propertyPaths);
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Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
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return results;
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}
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@Override
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public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
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Integer pageSize, Integer pageIndex, List<String> propertyPaths){
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Classification classification = dao.load(classificationUuid);
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Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
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long numberOfResults = dao.countSiblingsOf(taxon, classification, includeUnpublished);
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List<TaxonNode> results;
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if(PagerUtils.hasResultsInRange(numberOfResults, pageIndex, pageSize)) {
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results = dao.listSiblingsOf(taxon, classification, includeUnpublished, pageSize, pageIndex, propertyPaths);
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Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
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} else {
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results = new ArrayList<>();
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}
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return new DefaultPagerImpl<TaxonNode>(pageIndex, numberOfResults, pageSize, results);
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}
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@Override
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public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
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Integer pageSize, Integer pageIndex, List<String> propertyPaths){
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Pager<TaxonNode> pager = pageSiblingsOfTaxon(taxonUuid, classificationUuid, includeUnpublished, pageSize, pageIndex, propertyPaths);
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return pager.getRecords();
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}
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@Override
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public ITaxonTreeNode getTreeNodeByUuid(UUID uuid){
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ITaxonTreeNode treeNode = taxonNodeDao.findByUuid(uuid);
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if(treeNode == null){
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treeNode = dao.findByUuid(uuid);
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}
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return treeNode;
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}
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@Override
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public TaxonNode getRootNode(UUID classificationUuid){
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return dao.getRootNode(classificationUuid);
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}
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@Override
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public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
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return dao.list(limit, start, orderHints, propertyPaths);
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}
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@Override
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public UUID removeTaxonNode(TaxonNode taxonNode) {
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return taxonNodeDao.delete(taxonNode);
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}
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|
@Override
|
385
|
public UUID removeTreeNode(ITaxonTreeNode treeNode) {
|
386
|
if(treeNode instanceof Classification){
|
387
|
return dao.delete((Classification) treeNode);
|
388
|
}else if(treeNode instanceof TaxonNode){
|
389
|
return taxonNodeDao.delete((TaxonNode)treeNode);
|
390
|
}
|
391
|
return null;
|
392
|
}
|
393
|
@Override
|
394
|
public UUID saveTaxonNode(TaxonNode taxonNode) {
|
395
|
return taxonNodeDao.save(taxonNode).getUuid();
|
396
|
}
|
397
|
|
398
|
@Override
|
399
|
public Map<UUID, TaxonNode> saveTaxonNodeAll(
|
400
|
Collection<TaxonNode> taxonNodeCollection) {
|
401
|
return taxonNodeDao.saveAll(taxonNodeCollection);
|
402
|
}
|
403
|
|
404
|
@Override
|
405
|
public UUID saveClassification(Classification classification) {
|
406
|
|
407
|
taxonNodeDao.saveOrUpdateAll(classification.getAllNodes());
|
408
|
UUID result =dao.saveOrUpdate(classification);
|
409
|
return result;
|
410
|
}
|
411
|
|
412
|
@Override
|
413
|
public UUID saveTreeNode(ITaxonTreeNode treeNode) {
|
414
|
if(treeNode instanceof Classification){
|
415
|
return dao.save((Classification) treeNode).getUuid();
|
416
|
}else if(treeNode instanceof TaxonNode){
|
417
|
return taxonNodeDao.save((TaxonNode)treeNode).getUuid();
|
418
|
}
|
419
|
return null;
|
420
|
}
|
421
|
|
422
|
@Override
|
423
|
public List<TaxonNode> getAllNodes(){
|
424
|
return taxonNodeDao.list(null,null);
|
425
|
}
|
426
|
|
427
|
@Override
|
428
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications) {
|
429
|
return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), limit, pattern, searchForClassifications);
|
430
|
}
|
431
|
|
432
|
@Override
|
433
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, Integer limit, String pattern, boolean searchForClassifications) {
|
434
|
return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern, searchForClassifications);
|
435
|
}
|
436
|
|
437
|
@Override
|
438
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, boolean searchForClassifications ) {
|
439
|
return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), null, null, searchForClassifications);
|
440
|
}
|
441
|
|
442
|
@Override
|
443
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, boolean searchForClassifications ) {
|
444
|
return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, null, null, searchForClassifications);
|
445
|
}
|
446
|
|
447
|
@Override
|
448
|
public List<UuidAndTitleCache<Classification>> getUuidAndTitleCache(Integer limit, String pattern) {
|
449
|
return dao.getUuidAndTitleCache(limit, pattern);
|
450
|
}
|
451
|
|
452
|
@Override
|
453
|
public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(
|
454
|
TaxonNode taxonNode, List<String> propertyPaths, int size,
|
455
|
int height, int widthOrDuration, String[] mimeTypes) {
|
456
|
|
457
|
TreeMap<UUID, List<MediaRepresentation>> result = new TreeMap<UUID, List<MediaRepresentation>>();
|
458
|
List<Media> taxonMedia = new ArrayList<Media>();
|
459
|
List<MediaRepresentation> mediaRepresentations = new ArrayList<MediaRepresentation>();
|
460
|
|
461
|
//add all media of the children to the result map
|
462
|
if (taxonNode != null){
|
463
|
|
464
|
List<TaxonNode> nodes = new ArrayList<TaxonNode>();
|
465
|
|
466
|
nodes.add(loadTaxonNode(taxonNode, propertyPaths));
|
467
|
nodes.addAll(loadChildNodesOfTaxonNode(taxonNode, propertyPaths));
|
468
|
|
469
|
if (nodes != null){
|
470
|
for(TaxonNode node : nodes){
|
471
|
Taxon taxon = node.getTaxon();
|
472
|
for (TaxonDescription taxonDescription: taxon.getDescriptions()){
|
473
|
for (DescriptionElementBase descriptionElement: taxonDescription.getElements()){
|
474
|
for(Media media : descriptionElement.getMedia()){
|
475
|
taxonMedia.add(media);
|
476
|
|
477
|
//find the best matching representation
|
478
|
mediaRepresentations.add(MediaUtils.findBestMatchingRepresentation(media,null, size, height, widthOrDuration, mimeTypes));
|
479
|
|
480
|
}
|
481
|
}
|
482
|
}
|
483
|
result.put(taxon.getUuid(), mediaRepresentations);
|
484
|
|
485
|
}
|
486
|
}
|
487
|
|
488
|
}
|
489
|
|
490
|
return result;
|
491
|
|
492
|
}
|
493
|
|
494
|
|
495
|
@Override
|
496
|
@Transactional(readOnly = false)
|
497
|
public void updateTitleCache(Class<? extends Classification> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<Classification> cacheStrategy, IProgressMonitor monitor) {
|
498
|
if (clazz == null){
|
499
|
clazz = Classification.class;
|
500
|
}
|
501
|
super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
|
502
|
}
|
503
|
|
504
|
/**
|
505
|
*
|
506
|
* @param allNodesOfClassification
|
507
|
* @return null - if allNodesOfClassification is empty <br>
|
508
|
*/
|
509
|
|
510
|
private Map<String, List<TaxonNode>> getSortedGenusList(Collection<TaxonNode> allNodesOfClassification){
|
511
|
|
512
|
if(allNodesOfClassification == null || allNodesOfClassification.isEmpty()){
|
513
|
return null;
|
514
|
}
|
515
|
Map<String, List<TaxonNode>> sortedGenusMap = new HashMap<>();
|
516
|
for(TaxonNode node:allNodesOfClassification){
|
517
|
final TaxonNode tn = node;
|
518
|
Taxon taxon = node.getTaxon();
|
519
|
INonViralName name = taxon.getName();
|
520
|
String genusOrUninomial = name.getGenusOrUninomial();
|
521
|
//if rank unknown split string and take first word
|
522
|
if(genusOrUninomial == null){
|
523
|
String titleCache = taxon.getTitleCache();
|
524
|
String[] split = titleCache.split("\\s+");
|
525
|
for(String s:split){
|
526
|
genusOrUninomial = s;
|
527
|
break;
|
528
|
}
|
529
|
}
|
530
|
//if node has children
|
531
|
|
532
|
//retrieve list from map if not create List
|
533
|
if(sortedGenusMap.containsKey(genusOrUninomial)){
|
534
|
List<TaxonNode> list = sortedGenusMap.get(genusOrUninomial);
|
535
|
list.add(node);
|
536
|
sortedGenusMap.put(genusOrUninomial, list);
|
537
|
}else{
|
538
|
//create List for genus
|
539
|
List<TaxonNode> list = new ArrayList<TaxonNode>();
|
540
|
list.add(node);
|
541
|
sortedGenusMap.put(genusOrUninomial, list);
|
542
|
}
|
543
|
}
|
544
|
return sortedGenusMap;
|
545
|
}
|
546
|
|
547
|
/**
|
548
|
*
|
549
|
* creates new Classification and parent TaxonNodes at genus level
|
550
|
*
|
551
|
*
|
552
|
* @param map GenusMap which holds a name (Genus) and all the same Taxa as a list
|
553
|
* @param classification you want to improve the hierarchy (will not be modified)
|
554
|
* @param configurator to change certain settings, if null then standard settings will be taken
|
555
|
* @return new classification with parentNodes for each entry in the map
|
556
|
*/
|
557
|
@SuppressWarnings({ "unchecked" })
|
558
|
@Transactional(readOnly = false)
|
559
|
@Override
|
560
|
public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator){
|
561
|
UpdateResult result = new UpdateResult();
|
562
|
classification = dao.findByUuid(classification.getUuid());
|
563
|
Map<String, List<TaxonNode>> map = getSortedGenusList(classification.getAllNodes());
|
564
|
|
565
|
final String APPENDIX = "repaired";
|
566
|
String titleCache = StringUtils.isBlank(classification.getTitleCache()) ? " " : classification.getTitleCache() ;
|
567
|
//TODO classification clone???
|
568
|
Classification newClassification = Classification.NewInstance(titleCache +" "+ APPENDIX);
|
569
|
newClassification.setReference(classification.getReference());
|
570
|
|
571
|
for(Map.Entry<String, List<TaxonNode>> entry:map.entrySet()){
|
572
|
String genus = entry.getKey();
|
573
|
List<TaxonNode> listOfTaxonNodes = entry.getValue();
|
574
|
TaxonNode parentNode = null;
|
575
|
//Search for genus in list
|
576
|
for(TaxonNode tNode:listOfTaxonNodes){
|
577
|
//take that taxonNode as parent and remove from list with all it possible children
|
578
|
//FIXME NPE for name
|
579
|
TaxonName name = tNode.getTaxon().getName();
|
580
|
if(name.getNameCache().equalsIgnoreCase(genus)){
|
581
|
TaxonNode clone = (TaxonNode) tNode.clone();
|
582
|
if(!tNode.hasChildNodes()){
|
583
|
//FIXME remove classification
|
584
|
// parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
|
585
|
parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
|
586
|
//remove taxonNode from list because just added to classification
|
587
|
result.addUpdatedObject(tNode);
|
588
|
listOfTaxonNodes.remove(tNode);
|
589
|
}else{
|
590
|
//get all childNodes
|
591
|
//save prior Hierarchy and remove them from the list
|
592
|
List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tNode, clone, result);
|
593
|
// parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
|
594
|
//FIXME remove classification
|
595
|
parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
|
596
|
//remove taxonNode from list because just added to classification
|
597
|
result.addUpdatedObject(tNode);
|
598
|
listOfTaxonNodes.remove(tNode);
|
599
|
if(copyAllChildrenToTaxonNode != null){
|
600
|
listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
|
601
|
}
|
602
|
}
|
603
|
break;
|
604
|
}
|
605
|
}
|
606
|
if(parentNode == null){
|
607
|
//if no match found in list, create parentNode
|
608
|
NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
|
609
|
TaxonName TaxonName = (TaxonName)parser.parseFullName(genus);
|
610
|
//TODO Sec via configurator
|
611
|
Taxon taxon = Taxon.NewInstance(TaxonName, null);
|
612
|
parentNode = newClassification.addChildTaxon(taxon, 0, null, null);
|
613
|
result.addUpdatedObject(parentNode);
|
614
|
}
|
615
|
//iterate over the rest of the list
|
616
|
for(TaxonNode tn : listOfTaxonNodes){
|
617
|
//if TaxonNode has a parent and this is not the classification then skip it
|
618
|
//and add to new classification via the parentNode as children of it
|
619
|
//this should assures to keep the already existing hierarchy
|
620
|
//FIXME: Assert is not rootnode --> entrypoint is not classification in future but rather rootNode
|
621
|
|
622
|
if(!tn.isTopmostNode()){
|
623
|
continue; //skip to next taxonNode
|
624
|
}
|
625
|
|
626
|
TaxonNode clone = (TaxonNode) tn.clone();
|
627
|
//FIXME: citation from node
|
628
|
//TODO: addchildNode without citation and references
|
629
|
// TaxonNode taxonNode = parentNode.addChildNode(clone, classification.getCitation(), classification.getMicroReference());
|
630
|
TaxonNode taxonNode = parentNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
|
631
|
result.addUnChangedObject(clone);
|
632
|
if(tn.hasChildNodes()){
|
633
|
//save hierarchy in new classification
|
634
|
List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tn, taxonNode, result);
|
635
|
if(copyAllChildrenToTaxonNode != null){
|
636
|
listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
|
637
|
}
|
638
|
}
|
639
|
}
|
640
|
}
|
641
|
dao.saveOrUpdate(newClassification);
|
642
|
result.setCdmEntity(newClassification);
|
643
|
return result;
|
644
|
}
|
645
|
|
646
|
/**
|
647
|
*
|
648
|
* recursive method to get all childnodes of taxonNode in classification.
|
649
|
*
|
650
|
* @param classification just for References and Citation, can be null
|
651
|
* @param copyFromNode TaxonNode with Children
|
652
|
* @param copyToNode TaxonNode which will receive the children
|
653
|
* @return List of ChildNode which has been added. If node has no children returns null
|
654
|
*/
|
655
|
private List<TaxonNode> copyAllChildrenToTaxonNode(TaxonNode copyFromNode, TaxonNode copyToNode, UpdateResult result) {
|
656
|
List<TaxonNode> childNodes;
|
657
|
if(!copyFromNode.hasChildNodes()){
|
658
|
return null;
|
659
|
}else{
|
660
|
childNodes = copyFromNode.getChildNodes();
|
661
|
}
|
662
|
for(TaxonNode childNode:childNodes){
|
663
|
TaxonNode clone = (TaxonNode) childNode.clone();
|
664
|
result.addUnChangedObject(clone);
|
665
|
if(childNode.hasChildNodes()){
|
666
|
copyAllChildrenToTaxonNode(childNode, clone, result);
|
667
|
}
|
668
|
//FIXME: citation from node instead of classification
|
669
|
// copyToNode.addChildNode(clone,classification.getCitation(), classification.getMicroReference());
|
670
|
copyToNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
|
671
|
}
|
672
|
return childNodes;
|
673
|
}
|
674
|
|
675
|
/**
|
676
|
* {@inheritDoc}
|
677
|
*/
|
678
|
@Override
|
679
|
public ClassificationLookupDTO classificationLookup(Classification classification) {
|
680
|
return dao.classificationLookup(classification);
|
681
|
}
|
682
|
|
683
|
|
684
|
@Override
|
685
|
@Transactional
|
686
|
public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config){
|
687
|
DeleteResult result = new DeleteResult();
|
688
|
Classification classification = dao.findByUuid(classificationUuid);
|
689
|
if (classification == null){
|
690
|
result.addException(new IllegalArgumentException("The classification does not exist in database."));
|
691
|
result.setAbort();
|
692
|
return result;
|
693
|
}
|
694
|
if (!classification.hasChildNodes()){
|
695
|
dao.delete(classification);
|
696
|
result.addDeletedObject(classification);
|
697
|
return result;
|
698
|
}
|
699
|
if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE)){
|
700
|
// TaxonNode root = classification.getRootNode();
|
701
|
// result.includeResult(taxonNodeService.deleteTaxonNode(HibernateProxyHelper.deproxy(root), config));
|
702
|
// result.addDeletedObject(classification);
|
703
|
dao.delete(classification);
|
704
|
result.addDeletedObject(classification);
|
705
|
return result;
|
706
|
}
|
707
|
|
708
|
|
709
|
return result;
|
710
|
}
|
711
|
|
712
|
@Override
|
713
|
public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> originalTaxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank){
|
714
|
List<GroupedTaxonDTO> result = new ArrayList<>();
|
715
|
|
716
|
//get treeindex for each taxonUUID
|
717
|
Map<UUID, TreeIndex> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
|
718
|
|
719
|
//build treeindex list (or tree)
|
720
|
//TODO make it work with TreeIndex or move there
|
721
|
List<String> treeIndexClosureStr = new ArrayList<>();
|
722
|
for (TreeIndex treeIndex : taxonIdTreeIndexMap.values()){
|
723
|
String[] splits = treeIndex.toString().substring(1).split(ITreeNode.separator);
|
724
|
String currentIndex = ITreeNode.separator;
|
725
|
for (String split : splits){
|
726
|
if (split.equals("")){
|
727
|
continue;
|
728
|
}
|
729
|
currentIndex += split + ITreeNode.separator;
|
730
|
if (!treeIndexClosureStr.contains(currentIndex) && !split.startsWith(ITreeNode.treePrefix)){
|
731
|
treeIndexClosureStr.add(currentIndex);
|
732
|
}
|
733
|
}
|
734
|
}
|
735
|
|
736
|
//get rank sortindex for all parent taxa with sortindex <= minRank and sortIndex >= maxRank (if available)
|
737
|
Integer minRankOrderIndex = minRank == null ? null : minRank.getOrderIndex();
|
738
|
Integer maxRankOrderIndex = maxRank == null ? null : maxRank.getOrderIndex();
|
739
|
List<TreeIndex> treeIndexClosure = TreeIndex.NewListInstance(treeIndexClosureStr);
|
740
|
|
741
|
Map<TreeIndex, Integer> treeIndexSortIndexMapTmp = taxonNodeDao.rankOrderIndexForTreeIndex(treeIndexClosure, minRankOrderIndex, maxRankOrderIndex);
|
742
|
|
743
|
//remove all treeindex with "exists child in above map(and child.sortindex > xxx)
|
744
|
List<TreeIndex> treeIndexList = TreeIndex.sort(treeIndexSortIndexMapTmp.keySet());
|
745
|
|
746
|
Map<TreeIndex, Integer> treeIndexSortIndexMap = new HashMap<>();
|
747
|
TreeIndex lastTreeIndex = null;
|
748
|
for (TreeIndex treeIndex : treeIndexList){
|
749
|
if (lastTreeIndex != null && lastTreeIndex.hasChild(treeIndex)){
|
750
|
treeIndexSortIndexMap.remove(lastTreeIndex);
|
751
|
}
|
752
|
treeIndexSortIndexMap.put(treeIndex, treeIndexSortIndexMapTmp.get(treeIndex));
|
753
|
lastTreeIndex = treeIndex;
|
754
|
}
|
755
|
|
756
|
//get taxonID for treeIndexes
|
757
|
Map<TreeIndex, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(treeIndexSortIndexMap.keySet());
|
758
|
|
759
|
//fill result list
|
760
|
for (UUID originalTaxonUuid : originalTaxonUuids){
|
761
|
GroupedTaxonDTO item = new GroupedTaxonDTO();
|
762
|
result.add(item);
|
763
|
item.setTaxonUuid(originalTaxonUuid);
|
764
|
TreeIndex groupTreeIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);
|
765
|
String groupIndexX = TreeIndex.toString(groupTreeIndex);
|
766
|
while (groupTreeIndex != null){
|
767
|
if (treeIndexTaxonIdMap.get(groupTreeIndex) != null){
|
768
|
UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupTreeIndex);
|
769
|
item.setGroupTaxonUuid(uuidAndLabel.getUuid());
|
770
|
item.setGroupTaxonName(uuidAndLabel.getTitleCache());
|
771
|
break;
|
772
|
}else{
|
773
|
groupTreeIndex = groupTreeIndex.parent();
|
774
|
// int index = groupIndex.substring(0, groupIndex.length()-1).lastIndexOf(ITreeNode.separator);
|
775
|
// groupIndex = index < 0 ? null : groupIndex.substring(0, index+1);
|
776
|
}
|
777
|
}
|
778
|
}
|
779
|
|
780
|
return result;
|
781
|
}
|
782
|
|
783
|
/**
|
784
|
* {@inheritDoc}
|
785
|
*/
|
786
|
@Override
|
787
|
public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> originalTaxonUuids, UUID classificationUuid,
|
788
|
MarkerType markerType, Boolean flag) {
|
789
|
|
790
|
List<GroupedTaxonDTO> result = new ArrayList<>();
|
791
|
|
792
|
//get treeindex for each taxonUUID
|
793
|
Map<UUID, TreeIndex> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
|
794
|
|
795
|
//get all marked tree indexes
|
796
|
Set<TreeIndex> markedTreeIndexes = dao.getMarkedTreeIndexes(markerType, flag);
|
797
|
|
798
|
|
799
|
Map<TreeIndex, TreeIndex> groupedMap = TreeIndex.group(markedTreeIndexes, taxonIdTreeIndexMap.values());
|
800
|
Set<TreeIndex> notNullGroups = new HashSet<>(groupedMap.values());
|
801
|
notNullGroups.remove(null);
|
802
|
|
803
|
//get taxonInfo for treeIndexes
|
804
|
Map<TreeIndex, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(notNullGroups);
|
805
|
|
806
|
//fill result list
|
807
|
for (UUID originalTaxonUuid : originalTaxonUuids){
|
808
|
GroupedTaxonDTO item = new GroupedTaxonDTO();
|
809
|
result.add(item);
|
810
|
item.setTaxonUuid(originalTaxonUuid);
|
811
|
|
812
|
TreeIndex toBeGroupedTreeIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);
|
813
|
TreeIndex groupTreeIndex = groupedMap.get(toBeGroupedTreeIndex);
|
814
|
UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupTreeIndex);
|
815
|
if (uuidAndLabel != null){
|
816
|
item.setGroupTaxonUuid(uuidAndLabel.getUuid());
|
817
|
item.setGroupTaxonName(uuidAndLabel.getTitleCache());
|
818
|
}
|
819
|
}
|
820
|
|
821
|
return result;
|
822
|
}
|
823
|
|
824
|
/**
|
825
|
* {@inheritDoc}
|
826
|
*/
|
827
|
@Override
|
828
|
public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid) {
|
829
|
Map<UUID, UUID> map = dao.getTaxonNodeUuidByTaxonUuid(classificationUuid, Arrays.asList(taxonUuid));
|
830
|
UUID taxonNodeUuid = map.get(taxonUuid);
|
831
|
return taxonNodeUuid;
|
832
|
}
|
833
|
|
834
|
/**
|
835
|
* {@inheritDoc}
|
836
|
*/
|
837
|
@Override
|
838
|
public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonBaseUuid,
|
839
|
Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
|
840
|
NodeSortMode sortMode) {
|
841
|
TaxonInContextDTO result = new TaxonInContextDTO();
|
842
|
|
843
|
TaxonBase<?> taxonBase = taxonDao.load(taxonBaseUuid);
|
844
|
if (taxonBase == null){
|
845
|
throw new EntityNotFoundException("Taxon with uuid " + taxonBaseUuid + " not found in datasource");
|
846
|
}
|
847
|
boolean isSynonym = false;
|
848
|
Taxon acceptedTaxon;
|
849
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
850
|
isSynonym = true;
|
851
|
Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
|
852
|
acceptedTaxon = synonym.getAcceptedTaxon();
|
853
|
if (acceptedTaxon == null) {
|
854
|
throw new EntityNotFoundException("Accepted taxon not found for synonym" );
|
855
|
}
|
856
|
TaxonStatus taxonStatus = TaxonStatus.Synonym;
|
857
|
if (synonym.getName()!= null && acceptedTaxon.getName() != null
|
858
|
&& synonym.getName().getHomotypicalGroup().equals(acceptedTaxon.getName().getHomotypicalGroup())){
|
859
|
taxonStatus = TaxonStatus.SynonymObjective;
|
860
|
}
|
861
|
result.setTaxonStatus(taxonStatus);
|
862
|
|
863
|
}else{
|
864
|
acceptedTaxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
865
|
result.setTaxonStatus(TaxonStatus.Accepted);
|
866
|
}
|
867
|
UUID acceptedTaxonUuid = acceptedTaxon.getUuid();
|
868
|
|
869
|
UUID taxonNodeUuid = getTaxonNodeUuidByTaxonUuid(classificationUuid, acceptedTaxonUuid);
|
870
|
if (taxonNodeUuid == null) {
|
871
|
throw new EntityNotFoundException("Taxon not found in classficiation with uuid " + classificationUuid + ". Either classification does not exist or does not contain taxon/synonym with uuid " + taxonBaseUuid );
|
872
|
}
|
873
|
result.setTaxonNodeUuid(taxonNodeUuid);
|
874
|
|
875
|
//TODO make it a dao call
|
876
|
Taxon parentTaxon = getParentTaxon(classificationUuid, acceptedTaxon);
|
877
|
if (parentTaxon != null){
|
878
|
result.setParentTaxonUuid(parentTaxon.getUuid());
|
879
|
result.setParentTaxonLabel(parentTaxon.getTitleCache());
|
880
|
if (parentTaxon.getName() != null){
|
881
|
result.setParentNameLabel(parentTaxon.getName().getTitleCache());
|
882
|
}
|
883
|
}
|
884
|
|
885
|
result.setTaxonUuid(taxonBaseUuid);
|
886
|
result.setClassificationUuid(classificationUuid);
|
887
|
if (taxonBase.getSec() != null){
|
888
|
result.setSecundumUuid(taxonBase.getSec().getUuid());
|
889
|
result.setSecundumLabel(taxonBase.getSec().getTitleCache());
|
890
|
}
|
891
|
result.setTaxonLabel(taxonBase.getTitleCache());
|
892
|
|
893
|
TaxonName name = taxonBase.getName();
|
894
|
result.setNameUuid(name.getUuid());
|
895
|
result.setNameLabel(name.getTitleCache());
|
896
|
result.setNameWithoutAuthor(name.getNameCache());
|
897
|
result.setGenusOrUninomial(name.getGenusOrUninomial());
|
898
|
result.setInfraGenericEpithet(name.getInfraGenericEpithet());
|
899
|
result.setSpeciesEpithet(name.getSpecificEpithet());
|
900
|
result.setInfraSpecificEpithet(name.getInfraSpecificEpithet());
|
901
|
|
902
|
result.setAuthorship(name.getAuthorshipCache());
|
903
|
|
904
|
Rank rank = name.getRank();
|
905
|
if (rank != null){
|
906
|
result.setRankUuid(rank.getUuid());
|
907
|
String rankLabel = rank.getAbbreviation();
|
908
|
if (StringUtils.isBlank(rankLabel)){
|
909
|
rankLabel = rank.getLabel();
|
910
|
}
|
911
|
result.setRankLabel(rankLabel);
|
912
|
}
|
913
|
|
914
|
boolean recursive = false;
|
915
|
Integer pageSize = null;
|
916
|
Integer pageIndex = null;
|
917
|
Pager<TaxonNodeDto> children = taxonNodeService.pageChildNodesDTOs(taxonNodeUuid, recursive, includeUnpublished, doSynonyms,
|
918
|
sortMode, pageSize, pageIndex);
|
919
|
|
920
|
//children
|
921
|
if(! isSynonym) {
|
922
|
for (TaxonNodeDto childDto : children.getRecords()){
|
923
|
if (doChildren && childDto.getStatus().equals(TaxonStatus.Accepted)){
|
924
|
EntityDTO<Taxon> child = new EntityDTO<Taxon>(childDto.getTaxonUuid(), childDto.getTitleCache());
|
925
|
result.addChild(child);
|
926
|
}else if (doSynonyms && childDto.getStatus().isSynonym()){
|
927
|
EntityDTO<Synonym> child = new EntityDTO<Synonym>(childDto.getTaxonUuid(), childDto.getTitleCache());
|
928
|
result.addSynonym(child);
|
929
|
}
|
930
|
}
|
931
|
}else{
|
932
|
result.setAcceptedTaxonUuid(acceptedTaxonUuid);
|
933
|
String nameTitel = acceptedTaxon.getName() == null ? null : acceptedTaxon.getName().getTitleCache();
|
934
|
result.setAcceptedTaxonLabel(acceptedTaxon.getTitleCache());
|
935
|
result.setAcceptedNameLabel(nameTitel);
|
936
|
}
|
937
|
|
938
|
//marked ancestors
|
939
|
if (ancestorMarkers != null && !ancestorMarkers.isEmpty()){
|
940
|
List<DefinedTermBase> markerTypesTerms = termDao.list(ancestorMarkers, pageSize, null, null, null);
|
941
|
List<MarkerType> markerTypes = new ArrayList<>();
|
942
|
for (DefinedTermBase<?> term : markerTypesTerms){
|
943
|
if (term.isInstanceOf(MarkerType.class)){
|
944
|
markerTypes.add(CdmBase.deproxy(term, MarkerType.class));
|
945
|
}
|
946
|
}
|
947
|
if (! markerTypes.isEmpty()){
|
948
|
TaxonNode node = taxonNodeDao.findByUuid(taxonNodeUuid);
|
949
|
handleAncestorsForMarkersRecursive(result, markerTypes, node);
|
950
|
}
|
951
|
}
|
952
|
|
953
|
return result;
|
954
|
}
|
955
|
|
956
|
/**
|
957
|
* @param classificationUuid
|
958
|
* @param acceptedTaxon
|
959
|
* @return
|
960
|
*/
|
961
|
private Taxon getParentTaxon(UUID classificationUuid, Taxon acceptedTaxon) {
|
962
|
if (classificationUuid == null){
|
963
|
return null;
|
964
|
}
|
965
|
TaxonNode parent = null;
|
966
|
for (TaxonNode node : acceptedTaxon.getTaxonNodes()){
|
967
|
if (classificationUuid.equals(node.getClassification().getUuid())){
|
968
|
parent = node.getParent();
|
969
|
}
|
970
|
}
|
971
|
if (parent != null){
|
972
|
return parent.getTaxon();
|
973
|
}
|
974
|
return null;
|
975
|
}
|
976
|
|
977
|
/**
|
978
|
* @param result
|
979
|
* @param markerTypes
|
980
|
* @param node
|
981
|
*/
|
982
|
private void handleAncestorsForMarkersRecursive(TaxonInContextDTO result, List<MarkerType> markerTypes, TaxonNode node) {
|
983
|
for (MarkerType type : markerTypes){
|
984
|
Taxon taxon = node.getTaxon();
|
985
|
if (taxon != null && taxon.hasMarker(type, true)){
|
986
|
String label = taxon.getName() == null? taxon.getTitleCache() : taxon.getName().getTitleCache();
|
987
|
MarkedEntityDTO<Taxon> dto = new MarkedEntityDTO<>(type, true, taxon.getUuid(), label);
|
988
|
result.addMarkedAncestor(dto);
|
989
|
}
|
990
|
}
|
991
|
TaxonNode parentNode = node.getParent();
|
992
|
if (parentNode != null){
|
993
|
handleAncestorsForMarkersRecursive(result, markerTypes, parentNode);
|
994
|
}
|
995
|
}
|
996
|
|
997
|
/**
|
998
|
* {@inheritDoc}
|
999
|
*/
|
1000
|
@Override
|
1001
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
1002
|
Classification classification) {
|
1003
|
return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, false);
|
1004
|
}
|
1005
|
|
1006
|
/**
|
1007
|
* {@inheritDoc}
|
1008
|
*/
|
1009
|
@Override
|
1010
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
1011
|
UUID classificationUuid) {
|
1012
|
return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid, false);
|
1013
|
}
|
1014
|
|
1015
|
/**
|
1016
|
* {@inheritDoc}
|
1017
|
*/
|
1018
|
@Override
|
1019
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
1020
|
UUID classificationUuid, Integer limit, String pattern) {
|
1021
|
return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid, limit, pattern, false);
|
1022
|
}
|
1023
|
|
1024
|
/**
|
1025
|
* {@inheritDoc}
|
1026
|
*/
|
1027
|
@Override
|
1028
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
1029
|
Classification classification, Integer limit, String pattern) {
|
1030
|
return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern, false);
|
1031
|
}
|
1032
|
|
1033
|
|
1034
|
}
|