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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 java.util.stream.Collectors;
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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.SubtreeCloneConfigurator;
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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.FilterException;
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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.model.common.CdmBase;
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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.TaxonRelationship;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
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import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
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import eu.etaxonomy.cdm.persistence.dao.term.IDefinedTermDao;
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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 IReferenceDao referenceDao;
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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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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(SubtreeCloneConfigurator config) {
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UpdateResult result = new UpdateResult();
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if (config.getSubTreeUuids().isEmpty()){
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return result;
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}
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//TODO error handling
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Reference taxonSecundum = config.isReuseTaxa() || config.isReuseTaxonSecundum() || config.getTaxonSecundumUuid() == null ?
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null : referenceDao.findByUuid(config.getTaxonSecundumUuid());
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config.setTaxonSecundum(taxonSecundum);
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Reference parentChildReference = config.isReuseParentChildReference() || config.getParentChildReferenceUuid() == null ?
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null : referenceDao.findByUuid(config.getParentChildReferenceUuid());
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config.setParentChildReference(parentChildReference);
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Reference taxonRelationshipReference = config.getRelationTypeToOldTaxon() == null ?
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null : referenceDao.findByUuid(config.getRelationshipReferenceUuid());
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config.setRelationshipReference(taxonRelationshipReference);
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Classification classificationClone = Classification.NewInstance(config.getClassificationName());
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if (config.isReuseClassificationReference()){
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TaxonNode anyNode = taxonNodeDao.findByUuid(config.getSubTreeUuids().iterator().next());
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if (anyNode != null){
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Reference oldClassificationRef = anyNode.getClassification().getReference();
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classificationClone.setReference(oldClassificationRef);
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}
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}else if (config.getClassificationReferenceUuid() != null) {
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Reference classificationReference = referenceDao.findByUuid(config.getClassificationReferenceUuid());
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classificationClone.setReference(classificationReference);
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}
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//clone taxa and taxon nodes
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// List<Integer> childNodeIds = taxonNodeService.idList(taxonNodeFilter);
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// List<TaxonNode> childNodes = taxonNodeService.loadByIds(childNodeIds, null);
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List<TaxonNode> rootNodes = taxonNodeService.find(config.getSubTreeUuids());
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for (TaxonNode taxonNode : rootNodes) {
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addChildTaxaToClone(taxonNode, classificationClone.getRootNode(), config);
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}
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dao.saveOrUpdate(classificationClone);
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result.setCdmEntity(classificationClone);
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return result;
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}
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private void addChildTaxaToClone(TaxonNode originalParentNode, TaxonNode parentNodeClone,
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SubtreeCloneConfigurator config){
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Taxon originalTaxon = CdmBase.deproxy(originalParentNode.getTaxon());
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if (originalTaxon == null){
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for (TaxonNode originalChildChildNode : originalParentNode.getChildNodes()) {
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addChildTaxaToClone(originalChildChildNode, parentNodeClone, config);
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}
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}else{
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TaxonNode childNodeClone;
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String microReference = null;
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if (config.isReuseTaxa()){
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childNodeClone = parentNodeClone.addChildTaxon(originalTaxon, config.getParentChildReference(), microReference);
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}else{
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Taxon cloneTaxon = originalTaxon.clone(config.isIncludeSynonymsIncludingManAndProParte(),
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config.isIncludeTaxonRelationshipsExcludingManAndProParte(),
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config.isIncludeDescriptiveData(), config.isIncludeMedia());
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//name
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if (!config.isReuseNames()){
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cloneTaxon.setName(cloneTaxon.getName().clone());
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}
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if (!config.isReuseTaxonSecundum()){
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cloneTaxon.setSec(config.getTaxonSecundum());
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}
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//add relation between taxa
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if (config.getRelationTypeToOldTaxon() != null){
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TaxonRelationship rel = cloneTaxon.addTaxonRelation(originalParentNode.getTaxon(), config.getRelationTypeToOldTaxon(),
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config.getRelationshipReference(), microReference);
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rel.setDoubtful(config.isRelationDoubtful());
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}
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childNodeClone = parentNodeClone.addChildTaxon(cloneTaxon, config.getParentChildReference(), microReference);
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}
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//probably necessary as taxon nodes do not cascade
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taxonNodeDao.saveOrUpdate(childNodeClone);
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//add children
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List<TaxonNode> originalChildNodes = originalParentNode.getChildNodes();
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HHH_9751_Util.removeAllNull(originalChildNodes);
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for (TaxonNode originalChildNode : originalChildNodes) {
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addChildTaxaToClone(originalChildNode, childNodeClone, config);
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}
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}
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}
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@Override
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public List<TaxonNode> listRankSpecificRootNodes(Classification classification,
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TaxonNode subtree, Rank rank,
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boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
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return pageRankSpecificRootNodes(classification, subtree, rank, includeUnpublished, pageSize, pageIndex, propertyPaths).getRecords();
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}
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@Override
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public List<TaxonNodeDto> listRankSpecificRootNodeDtos(Classification classification, TaxonNode subtree,
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Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode,
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List<String> propertyPaths) {
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List<TaxonNode> list = listRankSpecificRootNodes(classification, subtree, rank, includeUnpublished, pageSize, pageIndex, propertyPaths);
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return list.stream().filter(e -> e != null).map(e -> new TaxonNodeDto(e)).sorted(sortMode.newComparator()).collect(Collectors.toList());
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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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return pageRankSpecificRootNodes(classification, null, rank, includeUnpublished, pageSize, pageIndex, propertyPaths);
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}
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@Override
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public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, TaxonNode subtree, Rank rank,
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boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) {
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long[] numberOfResults = dao.countRankSpecificRootNodes(classification, subtree, 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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subtree, rank, includeUnpublished, remainingLimit,
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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<>(pageIndex, totalNumberOfResults, pageSize, results);
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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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return loadTreeBranch(taxonNode, null, baseRank, includeUnpublished, propertyPaths);
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}
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@Override
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public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, TaxonNode subtree, 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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if((subtree!= null && !subtree.isAncestor(parentNode) )){
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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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return loadTreeBranchToTaxon(taxon, classification, null, baseRank, includeUnpublished, propertyPaths);
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}
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@Override
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public List<TaxonNodeDto> loadTreeBranchDTOsToTaxon(Taxon taxon, Classification classification,
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TaxonNode subtree, Rank baseRank,
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boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException {
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372
|
List<TaxonNode> list = loadTreeBranchToTaxon(taxon, classification, subtree, baseRank, includeUnpublished, propertyPaths);
|
373
|
return list.stream().map(e -> new TaxonNodeDto(e)).collect(Collectors.toList());
|
374
|
}
|
375
|
|
376
|
@Override
|
377
|
public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
|
378
|
TaxonNode subtree, Rank baseRank,
|
379
|
boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException{
|
380
|
|
381
|
UUID nodeUuid = getTaxonNodeUuidByTaxonUuid(classification.getUuid(), taxon.getUuid());
|
382
|
TaxonNode node = taxonNodeService.find(nodeUuid);
|
383
|
if(node == null){
|
384
|
logger.warn("The specified taxon is not found in the given tree.");
|
385
|
return null;
|
386
|
}else if (subtree != null && !node.isDescendant(subtree)){
|
387
|
//TODO handle as exception? E.g. FilterException, AccessDeniedException?
|
388
|
logger.warn("The specified taxon is not found for the given subtree.");
|
389
|
return null;
|
390
|
}
|
391
|
|
392
|
return loadTreeBranch(node, subtree, baseRank, includeUnpublished, propertyPaths);
|
393
|
}
|
394
|
|
395
|
|
396
|
@Override
|
397
|
public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,
|
398
|
List<String> propertyPaths) {
|
399
|
taxonNode = taxonNodeDao.load(taxonNode.getUuid());
|
400
|
List<TaxonNode> childNodes = new ArrayList<TaxonNode>(taxonNode.getChildNodes());
|
401
|
defaultBeanInitializer.initializeAll(childNodes, propertyPaths);
|
402
|
Collections.sort(childNodes, taxonNodeComparator);
|
403
|
return childNodes;
|
404
|
}
|
405
|
|
406
|
@Override
|
407
|
public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid,
|
408
|
boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths){
|
409
|
try {
|
410
|
return listChildNodesOfTaxon(taxonUuid, classificationUuid, null, includeUnpublished, pageSize, pageIndex, propertyPaths);
|
411
|
} catch (FilterException e) {
|
412
|
throw new RuntimeException(e); //this should not happen as filter is null
|
413
|
}
|
414
|
}
|
415
|
|
416
|
@Override
|
417
|
public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid,
|
418
|
boolean includeUnpublished, Integer pageSize, Integer pageIndex, List<String> propertyPaths) throws FilterException{
|
419
|
|
420
|
Classification classification = dao.load(classificationUuid);
|
421
|
Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
|
422
|
TaxonNode subtree = taxonNodeDao.load(subtreeUuid);
|
423
|
if (subtreeUuid != null && subtree == null){
|
424
|
throw new FilterException("Taxon node for subtree filter can not be found in database", true);
|
425
|
}
|
426
|
|
427
|
List<TaxonNode> results = dao.listChildrenOf(
|
428
|
taxon, classification, subtree, includeUnpublished, pageSize, pageIndex, propertyPaths);
|
429
|
Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
|
430
|
return results;
|
431
|
}
|
432
|
|
433
|
@Override
|
434
|
public List<TaxonNodeDto> listChildNodeDtosOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
|
435
|
Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode, List<String> propertyPaths) throws FilterException{
|
436
|
Classification classification = dao.load(classificationUuid);
|
437
|
Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
|
438
|
TaxonNode subtree = taxonNodeDao.load(subtreeUuid);
|
439
|
if (subtreeUuid != null && subtree == null){
|
440
|
throw new FilterException("Taxon node for subtree filter can not be found in database", true);
|
441
|
}
|
442
|
|
443
|
List<TaxonNode> results = dao.listChildrenOf(
|
444
|
taxon, classification, subtree, includeUnpublished, pageSize, pageIndex, propertyPaths);
|
445
|
Comparator<TaxonNodeDto> comparator = sortMode.newComparator();
|
446
|
// TODO order during the hibernate query in the dao?
|
447
|
List<TaxonNodeDto> dtos = results.stream().map(e -> new TaxonNodeDto(e)).sorted(comparator).collect(Collectors.toList());
|
448
|
return dtos;
|
449
|
}
|
450
|
|
451
|
@Override
|
452
|
public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
|
453
|
Integer pageSize, Integer pageIndex, List<String> propertyPaths){
|
454
|
|
455
|
Classification classification = dao.load(classificationUuid);
|
456
|
Taxon taxon = (Taxon) taxonDao.load(taxonUuid);
|
457
|
|
458
|
long numberOfResults = dao.countSiblingsOf(taxon, classification, includeUnpublished);
|
459
|
|
460
|
List<TaxonNode> results;
|
461
|
if(PagerUtils.hasResultsInRange(numberOfResults, pageIndex, pageSize)) {
|
462
|
results = dao.listSiblingsOf(taxon, classification, includeUnpublished, pageSize, pageIndex, propertyPaths);
|
463
|
Collections.sort(results, taxonNodeComparator); // FIXME this is only a HACK, order during the hibernate query in the dao
|
464
|
} else {
|
465
|
results = new ArrayList<>();
|
466
|
}
|
467
|
|
468
|
return new DefaultPagerImpl<>(pageIndex, numberOfResults, pageSize, results);
|
469
|
}
|
470
|
|
471
|
@Override
|
472
|
public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
|
473
|
Integer pageSize, Integer pageIndex, List<String> propertyPaths){
|
474
|
|
475
|
Pager<TaxonNode> pager = pageSiblingsOfTaxon(taxonUuid, classificationUuid, includeUnpublished, pageSize, pageIndex, propertyPaths);
|
476
|
return pager.getRecords();
|
477
|
}
|
478
|
|
479
|
@Override
|
480
|
public ITaxonTreeNode getTreeNodeByUuid(UUID uuid){
|
481
|
ITaxonTreeNode treeNode = taxonNodeDao.findByUuid(uuid);
|
482
|
if(treeNode == null){
|
483
|
treeNode = dao.findByUuid(uuid);
|
484
|
}
|
485
|
|
486
|
return treeNode;
|
487
|
}
|
488
|
|
489
|
@Override
|
490
|
public TaxonNode getRootNode(UUID classificationUuid){
|
491
|
return dao.getRootNode(classificationUuid);
|
492
|
}
|
493
|
|
494
|
@Override
|
495
|
public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
496
|
return dao.list(limit, start, orderHints, propertyPaths);
|
497
|
}
|
498
|
|
499
|
@Override
|
500
|
public UUID removeTreeNode(ITaxonTreeNode treeNode) {
|
501
|
if(treeNode instanceof Classification){
|
502
|
return dao.delete((Classification) treeNode);
|
503
|
}else if(treeNode instanceof TaxonNode){
|
504
|
return taxonNodeDao.delete((TaxonNode)treeNode);
|
505
|
}
|
506
|
return null;
|
507
|
}
|
508
|
|
509
|
@Override
|
510
|
public Map<UUID, TaxonNode> saveTaxonNodeAll(
|
511
|
Collection<TaxonNode> taxonNodeCollection) {
|
512
|
return taxonNodeDao.saveAll(taxonNodeCollection);
|
513
|
}
|
514
|
|
515
|
@Override
|
516
|
public UUID saveClassification(Classification classification) {
|
517
|
|
518
|
taxonNodeDao.saveOrUpdateAll(classification.getAllNodes());
|
519
|
UUID result =dao.saveOrUpdate(classification);
|
520
|
return result;
|
521
|
}
|
522
|
|
523
|
@Override
|
524
|
public UUID saveTreeNode(ITaxonTreeNode treeNode) {
|
525
|
if(treeNode instanceof Classification){
|
526
|
return dao.save((Classification) treeNode).getUuid();
|
527
|
}else if(treeNode instanceof TaxonNode){
|
528
|
return taxonNodeDao.save((TaxonNode)treeNode).getUuid();
|
529
|
}
|
530
|
return null;
|
531
|
}
|
532
|
|
533
|
@Override
|
534
|
public List<TaxonNode> getAllNodes(){
|
535
|
return taxonNodeDao.list(null,null);
|
536
|
}
|
537
|
|
538
|
@Override
|
539
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications, boolean includeDoubtful) {
|
540
|
return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), limit, pattern, searchForClassifications, includeDoubtful);
|
541
|
}
|
542
|
|
543
|
@Override
|
544
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, Integer limit, String pattern, boolean searchForClassifications) {
|
545
|
return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern, searchForClassifications);
|
546
|
}
|
547
|
|
548
|
@Override
|
549
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid, boolean searchForClassifications ) {
|
550
|
return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(dao.load(classificationUuid), null, null, searchForClassifications);
|
551
|
}
|
552
|
|
553
|
@Override
|
554
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification, boolean searchForClassifications ) {
|
555
|
return taxonNodeDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, null, null, searchForClassifications);
|
556
|
}
|
557
|
|
558
|
@Override
|
559
|
public List<UuidAndTitleCache<Classification>> getUuidAndTitleCache(Integer limit, String pattern) {
|
560
|
return dao.getUuidAndTitleCache(limit, pattern);
|
561
|
}
|
562
|
|
563
|
@Override
|
564
|
public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(
|
565
|
TaxonNode taxonNode, List<String> propertyPaths, int size,
|
566
|
int height, int widthOrDuration, String[] mimeTypes) {
|
567
|
|
568
|
TreeMap<UUID, List<MediaRepresentation>> result = new TreeMap<>();
|
569
|
List<MediaRepresentation> mediaRepresentations = new ArrayList<>();
|
570
|
|
571
|
//add all media of the children to the result map
|
572
|
if (taxonNode != null){
|
573
|
|
574
|
List<TaxonNode> nodes = new ArrayList<>();
|
575
|
|
576
|
nodes.add(loadTaxonNode(taxonNode.getUuid(), propertyPaths));
|
577
|
nodes.addAll(loadChildNodesOfTaxonNode(taxonNode, propertyPaths));
|
578
|
|
579
|
for(TaxonNode node : nodes){
|
580
|
Taxon taxon = node.getTaxon();
|
581
|
for (TaxonDescription taxonDescription: taxon.getDescriptions()){
|
582
|
for (DescriptionElementBase descriptionElement: taxonDescription.getElements()){
|
583
|
for(Media media : descriptionElement.getMedia()){
|
584
|
//find the best matching representation
|
585
|
mediaRepresentations.add(MediaUtils.findBestMatchingRepresentation(media,null, size, height, widthOrDuration, mimeTypes, MediaUtils.MissingValueStrategy.MAX));
|
586
|
}
|
587
|
}
|
588
|
}
|
589
|
result.put(taxon.getUuid(), mediaRepresentations);
|
590
|
}
|
591
|
}
|
592
|
|
593
|
return result;
|
594
|
}
|
595
|
|
596
|
@Override
|
597
|
@Transactional(readOnly = false)
|
598
|
public UpdateResult updateCaches(Class<? extends Classification> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<Classification> cacheStrategy, IProgressMonitor monitor) {
|
599
|
if (clazz == null){
|
600
|
clazz = Classification.class;
|
601
|
}
|
602
|
return super.updateCachesImpl(clazz, stepSize, cacheStrategy, monitor);
|
603
|
}
|
604
|
|
605
|
/**
|
606
|
*
|
607
|
* @param allNodesOfClassification
|
608
|
* @return null - if allNodesOfClassification is empty <br>
|
609
|
*/
|
610
|
|
611
|
private Map<String, List<TaxonNode>> getSortedGenusList(Collection<TaxonNode> allNodesOfClassification){
|
612
|
|
613
|
if(allNodesOfClassification == null || allNodesOfClassification.isEmpty()){
|
614
|
return null;
|
615
|
}
|
616
|
Map<String, List<TaxonNode>> sortedGenusMap = new HashMap<>();
|
617
|
for(TaxonNode node:allNodesOfClassification){
|
618
|
Taxon taxon = node.getTaxon();
|
619
|
INonViralName name = taxon.getName();
|
620
|
String genusOrUninomial = name.getGenusOrUninomial();
|
621
|
//if rank unknown split string and take first word
|
622
|
if(genusOrUninomial == null){
|
623
|
String titleCache = taxon.getTitleCache();
|
624
|
String[] split = titleCache.split("\\s+");
|
625
|
for(String s:split){
|
626
|
genusOrUninomial = s;
|
627
|
break;
|
628
|
}
|
629
|
}
|
630
|
//if node has children
|
631
|
|
632
|
//retrieve list from map if not create List
|
633
|
if(sortedGenusMap.containsKey(genusOrUninomial)){
|
634
|
List<TaxonNode> list = sortedGenusMap.get(genusOrUninomial);
|
635
|
list.add(node);
|
636
|
sortedGenusMap.put(genusOrUninomial, list);
|
637
|
}else{
|
638
|
//create List for genus
|
639
|
List<TaxonNode> list = new ArrayList<>();
|
640
|
list.add(node);
|
641
|
sortedGenusMap.put(genusOrUninomial, list);
|
642
|
}
|
643
|
}
|
644
|
return sortedGenusMap;
|
645
|
}
|
646
|
|
647
|
/**
|
648
|
*
|
649
|
* creates new Classification and parent TaxonNodes at genus level
|
650
|
*
|
651
|
*
|
652
|
* @param map GenusMap which holds a name (Genus) and all the same Taxa as a list
|
653
|
* @param classification you want to improve the hierarchy (will not be modified)
|
654
|
* @param configurator to change certain settings, if null then standard settings will be taken
|
655
|
* @return new classification with parentNodes for each entry in the map
|
656
|
*/
|
657
|
@SuppressWarnings({ "unchecked" })
|
658
|
@Transactional(readOnly = false)
|
659
|
@Override
|
660
|
public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator){
|
661
|
UpdateResult result = new UpdateResult();
|
662
|
classification = dao.findByUuid(classification.getUuid());
|
663
|
Map<String, List<TaxonNode>> map = getSortedGenusList(classification.getAllNodes());
|
664
|
|
665
|
final String APPENDIX = "repaired";
|
666
|
String titleCache = StringUtils.isBlank(classification.getTitleCache()) ? " " : classification.getTitleCache() ;
|
667
|
//TODO classification clone???
|
668
|
Classification newClassification = Classification.NewInstance(titleCache +" "+ APPENDIX);
|
669
|
newClassification.setReference(classification.getReference());
|
670
|
|
671
|
for(Map.Entry<String, List<TaxonNode>> entry:map.entrySet()){
|
672
|
String genus = entry.getKey();
|
673
|
List<TaxonNode> listOfTaxonNodes = entry.getValue();
|
674
|
TaxonNode parentNode = null;
|
675
|
//Search for genus in list
|
676
|
for(TaxonNode tNode:listOfTaxonNodes){
|
677
|
//take that taxonNode as parent and remove from list with all it possible children
|
678
|
//FIXME NPE for name
|
679
|
TaxonName name = tNode.getTaxon().getName();
|
680
|
if(name.getNameCache().equalsIgnoreCase(genus)){
|
681
|
TaxonNode clone = tNode.clone();
|
682
|
if(!tNode.hasChildNodes()){
|
683
|
//FIXME remove classification
|
684
|
// parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
|
685
|
parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
|
686
|
//remove taxonNode from list because just added to classification
|
687
|
result.addUpdatedObject(tNode);
|
688
|
listOfTaxonNodes.remove(tNode);
|
689
|
}else{
|
690
|
//get all childNodes
|
691
|
//save prior Hierarchy and remove them from the list
|
692
|
List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tNode, clone, result);
|
693
|
// parentNode = newClassification.addChildNode(clone, 0, classification.getCitation(), classification.getMicroReference());
|
694
|
//FIXME remove classification
|
695
|
parentNode = newClassification.addChildNode(clone, 0, clone.getReference(), clone.getMicroReference());
|
696
|
//remove taxonNode from list because just added to classification
|
697
|
result.addUpdatedObject(tNode);
|
698
|
listOfTaxonNodes.remove(tNode);
|
699
|
if(copyAllChildrenToTaxonNode != null){
|
700
|
listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
|
701
|
}
|
702
|
}
|
703
|
break;
|
704
|
}
|
705
|
}
|
706
|
if(parentNode == null){
|
707
|
//if no match found in list, create parentNode
|
708
|
NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
|
709
|
TaxonName TaxonName = (TaxonName)parser.parseFullName(genus);
|
710
|
//TODO Sec via configurator
|
711
|
Taxon taxon = Taxon.NewInstance(TaxonName, null);
|
712
|
parentNode = newClassification.addChildTaxon(taxon, 0, null, null);
|
713
|
result.addUpdatedObject(parentNode);
|
714
|
}
|
715
|
//iterate over the rest of the list
|
716
|
for(TaxonNode tn : listOfTaxonNodes){
|
717
|
//if TaxonNode has a parent and this is not the classification then skip it
|
718
|
//and add to new classification via the parentNode as children of it
|
719
|
//this should assures to keep the already existing hierarchy
|
720
|
//FIXME: Assert is not rootnode --> entrypoint is not classification in future but rather rootNode
|
721
|
|
722
|
if(!tn.isTopmostNode()){
|
723
|
continue; //skip to next taxonNode
|
724
|
}
|
725
|
|
726
|
TaxonNode clone = tn.clone();
|
727
|
//FIXME: citation from node
|
728
|
//TODO: addchildNode without citation and references
|
729
|
// TaxonNode taxonNode = parentNode.addChildNode(clone, classification.getCitation(), classification.getMicroReference());
|
730
|
TaxonNode taxonNode = parentNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
|
731
|
result.addUnChangedObject(clone);
|
732
|
if(tn.hasChildNodes()){
|
733
|
//save hierarchy in new classification
|
734
|
List<TaxonNode> copyAllChildrenToTaxonNode = copyAllChildrenToTaxonNode(tn, taxonNode, result);
|
735
|
if(copyAllChildrenToTaxonNode != null){
|
736
|
listOfTaxonNodes = (List<TaxonNode>) CollectionUtils.removeAll(listOfTaxonNodes, copyAllChildrenToTaxonNode);
|
737
|
}
|
738
|
}
|
739
|
}
|
740
|
}
|
741
|
dao.saveOrUpdate(newClassification);
|
742
|
result.setCdmEntity(newClassification);
|
743
|
return result;
|
744
|
}
|
745
|
|
746
|
/**
|
747
|
*
|
748
|
* recursive method to get all childnodes of taxonNode in classification.
|
749
|
*
|
750
|
* @param classification just for References and Citation, can be null
|
751
|
* @param copyFromNode TaxonNode with Children
|
752
|
* @param copyToNode TaxonNode which will receive the children
|
753
|
* @return List of ChildNode which has been added. If node has no children returns null
|
754
|
*/
|
755
|
private List<TaxonNode> copyAllChildrenToTaxonNode(TaxonNode copyFromNode, TaxonNode copyToNode, UpdateResult result) {
|
756
|
List<TaxonNode> childNodes;
|
757
|
if(!copyFromNode.hasChildNodes()){
|
758
|
return null;
|
759
|
}else{
|
760
|
childNodes = copyFromNode.getChildNodes();
|
761
|
}
|
762
|
for(TaxonNode childNode:childNodes){
|
763
|
TaxonNode clone = childNode.clone();
|
764
|
result.addUnChangedObject(clone);
|
765
|
if(childNode.hasChildNodes()){
|
766
|
copyAllChildrenToTaxonNode(childNode, clone, result);
|
767
|
}
|
768
|
//FIXME: citation from node instead of classification
|
769
|
// copyToNode.addChildNode(clone,classification.getCitation(), classification.getMicroReference());
|
770
|
copyToNode.addChildNode(clone, clone.getReference(), clone.getMicroReference());
|
771
|
}
|
772
|
return childNodes;
|
773
|
}
|
774
|
|
775
|
@Override
|
776
|
public ClassificationLookupDTO classificationLookup(Classification classification) {
|
777
|
return dao.classificationLookup(classification);
|
778
|
}
|
779
|
|
780
|
@Override
|
781
|
@Transactional
|
782
|
public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config){
|
783
|
DeleteResult result = new DeleteResult();
|
784
|
Classification classification = dao.findByUuid(classificationUuid);
|
785
|
if (classification == null){
|
786
|
result.addException(new IllegalArgumentException("The classification does not exist in database."));
|
787
|
result.setAbort();
|
788
|
return result;
|
789
|
}
|
790
|
if (!classification.hasChildNodes()){
|
791
|
dao.delete(classification);
|
792
|
result.addDeletedObject(classification);
|
793
|
return result;
|
794
|
}
|
795
|
if (config.getTaxonNodeConfig().getChildHandling().equals(ChildHandling.DELETE)){
|
796
|
// TaxonNode root = classification.getRootNode();
|
797
|
// result.includeResult(taxonNodeService.deleteTaxonNode(HibernateProxyHelper.deproxy(root), config));
|
798
|
// result.addDeletedObject(classification);
|
799
|
dao.delete(classification);
|
800
|
result.addDeletedObject(classification);
|
801
|
return result;
|
802
|
}
|
803
|
|
804
|
|
805
|
return result;
|
806
|
}
|
807
|
|
808
|
@Override
|
809
|
public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> originalTaxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank){
|
810
|
List<GroupedTaxonDTO> result = new ArrayList<>();
|
811
|
|
812
|
//get treeindex for each taxonUUID
|
813
|
Map<UUID, TreeIndex> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
|
814
|
|
815
|
//build treeindex list (or tree)
|
816
|
//TODO make it work with TreeIndex or move there
|
817
|
List<String> treeIndexClosureStr = new ArrayList<>();
|
818
|
for (TreeIndex treeIndex : taxonIdTreeIndexMap.values()){
|
819
|
String[] splits = treeIndex.toString().substring(1).split(ITreeNode.separator);
|
820
|
String currentIndex = ITreeNode.separator;
|
821
|
for (String split : splits){
|
822
|
if (split.equals("")){
|
823
|
continue;
|
824
|
}
|
825
|
currentIndex += split + ITreeNode.separator;
|
826
|
if (!treeIndexClosureStr.contains(currentIndex) && !split.startsWith(ITreeNode.treePrefix)){
|
827
|
treeIndexClosureStr.add(currentIndex);
|
828
|
}
|
829
|
}
|
830
|
}
|
831
|
|
832
|
//get rank sortindex for all parent taxa with sortindex <= minRank and sortIndex >= maxRank (if available)
|
833
|
Integer minRankOrderIndex = minRank == null ? null : minRank.getOrderIndex();
|
834
|
Integer maxRankOrderIndex = maxRank == null ? null : maxRank.getOrderIndex();
|
835
|
List<TreeIndex> treeIndexClosure = TreeIndex.NewListInstance(treeIndexClosureStr);
|
836
|
|
837
|
Map<TreeIndex, Integer> treeIndexSortIndexMapTmp = taxonNodeDao.rankOrderIndexForTreeIndex(treeIndexClosure, minRankOrderIndex, maxRankOrderIndex);
|
838
|
|
839
|
//remove all treeindex with "exists child in above map(and child.sortindex > xxx)
|
840
|
List<TreeIndex> treeIndexList = TreeIndex.sort(treeIndexSortIndexMapTmp.keySet());
|
841
|
|
842
|
Map<TreeIndex, Integer> treeIndexSortIndexMap = new HashMap<>();
|
843
|
TreeIndex lastTreeIndex = null;
|
844
|
for (TreeIndex treeIndex : treeIndexList){
|
845
|
if (lastTreeIndex != null && lastTreeIndex.hasChild(treeIndex)){
|
846
|
treeIndexSortIndexMap.remove(lastTreeIndex);
|
847
|
}
|
848
|
treeIndexSortIndexMap.put(treeIndex, treeIndexSortIndexMapTmp.get(treeIndex));
|
849
|
lastTreeIndex = treeIndex;
|
850
|
}
|
851
|
|
852
|
//get taxonID for treeIndexes
|
853
|
Map<TreeIndex, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(treeIndexSortIndexMap.keySet());
|
854
|
|
855
|
//fill result list
|
856
|
for (UUID originalTaxonUuid : originalTaxonUuids){
|
857
|
GroupedTaxonDTO item = new GroupedTaxonDTO();
|
858
|
result.add(item);
|
859
|
item.setTaxonUuid(originalTaxonUuid);
|
860
|
TreeIndex groupTreeIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);
|
861
|
String groupIndexX = TreeIndex.toString(groupTreeIndex);
|
862
|
while (groupTreeIndex != null){
|
863
|
if (treeIndexTaxonIdMap.get(groupTreeIndex) != null){
|
864
|
UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupTreeIndex);
|
865
|
item.setGroupTaxonUuid(uuidAndLabel.getUuid());
|
866
|
item.setGroupTaxonName(uuidAndLabel.getTitleCache());
|
867
|
break;
|
868
|
}else{
|
869
|
groupTreeIndex = groupTreeIndex.parent();
|
870
|
// int index = groupIndex.substring(0, groupIndex.length()-1).lastIndexOf(ITreeNode.separator);
|
871
|
// groupIndex = index < 0 ? null : groupIndex.substring(0, index+1);
|
872
|
}
|
873
|
}
|
874
|
}
|
875
|
|
876
|
return result;
|
877
|
}
|
878
|
|
879
|
@Override
|
880
|
public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> originalTaxonUuids, UUID classificationUuid,
|
881
|
MarkerType markerType, Boolean flag) {
|
882
|
|
883
|
List<GroupedTaxonDTO> result = new ArrayList<>();
|
884
|
|
885
|
//get treeindex for each taxonUUID
|
886
|
Map<UUID, TreeIndex> taxonIdTreeIndexMap = dao.treeIndexForTaxonUuids(classificationUuid, originalTaxonUuids);
|
887
|
|
888
|
//get all marked tree indexes
|
889
|
Set<TreeIndex> markedTreeIndexes = dao.getMarkedTreeIndexes(markerType, flag);
|
890
|
|
891
|
Map<TreeIndex, TreeIndex> groupedMap = TreeIndex.group(markedTreeIndexes, taxonIdTreeIndexMap.values());
|
892
|
Set<TreeIndex> notNullGroups = new HashSet<>(groupedMap.values());
|
893
|
notNullGroups.remove(null);
|
894
|
|
895
|
//get taxonInfo for treeIndexes
|
896
|
Map<TreeIndex, UuidAndTitleCache<?>> treeIndexTaxonIdMap = taxonNodeDao.taxonUuidsForTreeIndexes(notNullGroups);
|
897
|
|
898
|
//fill result list
|
899
|
for (UUID originalTaxonUuid : originalTaxonUuids){
|
900
|
GroupedTaxonDTO item = new GroupedTaxonDTO();
|
901
|
result.add(item);
|
902
|
item.setTaxonUuid(originalTaxonUuid);
|
903
|
|
904
|
TreeIndex toBeGroupedTreeIndex = taxonIdTreeIndexMap.get(originalTaxonUuid);
|
905
|
TreeIndex groupTreeIndex = groupedMap.get(toBeGroupedTreeIndex);
|
906
|
UuidAndTitleCache<?> uuidAndLabel = treeIndexTaxonIdMap.get(groupTreeIndex);
|
907
|
if (uuidAndLabel != null){
|
908
|
item.setGroupTaxonUuid(uuidAndLabel.getUuid());
|
909
|
item.setGroupTaxonName(uuidAndLabel.getTitleCache());
|
910
|
}
|
911
|
}
|
912
|
|
913
|
return result;
|
914
|
}
|
915
|
|
916
|
@Override
|
917
|
public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid) {
|
918
|
Map<UUID, UUID> map = dao.getTaxonNodeUuidByTaxonUuid(classificationUuid, Arrays.asList(taxonUuid));
|
919
|
UUID taxonNodeUuid = map.get(taxonUuid);
|
920
|
return taxonNodeUuid;
|
921
|
}
|
922
|
|
923
|
@Override
|
924
|
public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonBaseUuid,
|
925
|
Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
|
926
|
TaxonNodeSortMode sortMode) {
|
927
|
|
928
|
TaxonInContextDTO result = new TaxonInContextDTO();
|
929
|
|
930
|
TaxonBase<?> taxonBase = taxonDao.load(taxonBaseUuid);
|
931
|
if (taxonBase == null){
|
932
|
throw new EntityNotFoundException("Taxon with uuid " + taxonBaseUuid + " not found in datasource");
|
933
|
}
|
934
|
boolean isSynonym = false;
|
935
|
Taxon acceptedTaxon;
|
936
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
937
|
isSynonym = true;
|
938
|
Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
|
939
|
acceptedTaxon = synonym.getAcceptedTaxon();
|
940
|
if (acceptedTaxon == null) {
|
941
|
throw new EntityNotFoundException("Accepted taxon not found for synonym" );
|
942
|
}
|
943
|
TaxonStatus taxonStatus = TaxonStatus.Synonym;
|
944
|
if (synonym.getName()!= null && acceptedTaxon.getName() != null
|
945
|
&& synonym.getName().getHomotypicalGroup().equals(acceptedTaxon.getName().getHomotypicalGroup())){
|
946
|
taxonStatus = TaxonStatus.SynonymObjective;
|
947
|
}
|
948
|
result.setTaxonStatus(taxonStatus);
|
949
|
|
950
|
}else{
|
951
|
acceptedTaxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
952
|
result.setTaxonStatus(TaxonStatus.Accepted);
|
953
|
}
|
954
|
UUID acceptedTaxonUuid = acceptedTaxon.getUuid();
|
955
|
|
956
|
UUID taxonNodeUuid = getTaxonNodeUuidByTaxonUuid(classificationUuid, acceptedTaxonUuid);
|
957
|
if (taxonNodeUuid == null) {
|
958
|
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 );
|
959
|
}
|
960
|
result.setTaxonNodeUuid(taxonNodeUuid);
|
961
|
|
962
|
//TODO make it a dao call
|
963
|
Taxon parentTaxon = getParentTaxon(classificationUuid, acceptedTaxon);
|
964
|
if (parentTaxon != null){
|
965
|
result.setParentTaxonUuid(parentTaxon.getUuid());
|
966
|
result.setParentTaxonLabel(parentTaxon.getTitleCache());
|
967
|
if (parentTaxon.getName() != null){
|
968
|
result.setParentNameLabel(parentTaxon.getName().getTitleCache());
|
969
|
}
|
970
|
}
|
971
|
|
972
|
result.setTaxonUuid(taxonBaseUuid);
|
973
|
result.setClassificationUuid(classificationUuid);
|
974
|
if (taxonBase.getSec() != null){
|
975
|
result.setSecundumUuid(taxonBase.getSec().getUuid());
|
976
|
result.setSecundumLabel(taxonBase.getSec().getTitleCache());
|
977
|
}
|
978
|
result.setTaxonLabel(taxonBase.getTitleCache());
|
979
|
|
980
|
TaxonName name = taxonBase.getName();
|
981
|
result.setNameUuid(name.getUuid());
|
982
|
result.setNameLabel(name.getTitleCache());
|
983
|
result.setNameWithoutAuthor(name.getNameCache());
|
984
|
result.setGenusOrUninomial(name.getGenusOrUninomial());
|
985
|
result.setInfraGenericEpithet(name.getInfraGenericEpithet());
|
986
|
result.setSpeciesEpithet(name.getSpecificEpithet());
|
987
|
result.setInfraSpecificEpithet(name.getInfraSpecificEpithet());
|
988
|
|
989
|
result.setAuthorship(name.getAuthorshipCache());
|
990
|
|
991
|
Rank rank = name.getRank();
|
992
|
if (rank != null){
|
993
|
result.setRankUuid(rank.getUuid());
|
994
|
String rankLabel = rank.getAbbreviation();
|
995
|
if (StringUtils.isBlank(rankLabel)){
|
996
|
rankLabel = rank.getLabel();
|
997
|
}
|
998
|
result.setRankLabel(rankLabel);
|
999
|
}
|
1000
|
|
1001
|
boolean recursive = false;
|
1002
|
Integer pageSize = null;
|
1003
|
Integer pageIndex = null;
|
1004
|
Pager<TaxonNodeDto> children = taxonNodeService.pageChildNodesDTOs(taxonNodeUuid, recursive, includeUnpublished, doSynonyms,
|
1005
|
sortMode, pageSize, pageIndex);
|
1006
|
|
1007
|
//children
|
1008
|
if(! isSynonym) {
|
1009
|
for (TaxonNodeDto childDto : children.getRecords()){
|
1010
|
if (doChildren && childDto.getTaxonStatus().equals(TaxonStatus.Accepted)){
|
1011
|
EntityDTO<Taxon> child = new EntityDTO<Taxon>(childDto.getTaxonUuid(), childDto.getTitleCache());
|
1012
|
result.addChild(child);
|
1013
|
}else if (doSynonyms && childDto.getTaxonStatus().isSynonym()){
|
1014
|
EntityDTO<Synonym> child = new EntityDTO<>(childDto.getTaxonUuid(), childDto.getTitleCache());
|
1015
|
result.addSynonym(child);
|
1016
|
}
|
1017
|
}
|
1018
|
}else{
|
1019
|
result.setAcceptedTaxonUuid(acceptedTaxonUuid);
|
1020
|
String nameTitel = acceptedTaxon.getName() == null ? null : acceptedTaxon.getName().getTitleCache();
|
1021
|
result.setAcceptedTaxonLabel(acceptedTaxon.getTitleCache());
|
1022
|
result.setAcceptedNameLabel(nameTitel);
|
1023
|
}
|
1024
|
|
1025
|
//marked ancestors
|
1026
|
if (ancestorMarkers != null && !ancestorMarkers.isEmpty()){
|
1027
|
@SuppressWarnings("rawtypes")
|
1028
|
List<DefinedTermBase> markerTypesTerms = termDao.list(ancestorMarkers, pageSize, null, null, null);
|
1029
|
List<MarkerType> markerTypes = new ArrayList<>();
|
1030
|
for (DefinedTermBase<?> term : markerTypesTerms){
|
1031
|
if (term.isInstanceOf(MarkerType.class)){
|
1032
|
markerTypes.add(CdmBase.deproxy(term, MarkerType.class));
|
1033
|
}
|
1034
|
}
|
1035
|
if (! markerTypes.isEmpty()){
|
1036
|
TaxonNode node = taxonNodeDao.findByUuid(taxonNodeUuid);
|
1037
|
handleAncestorsForMarkersRecursive(result, markerTypes, node);
|
1038
|
}
|
1039
|
}
|
1040
|
|
1041
|
return result;
|
1042
|
}
|
1043
|
|
1044
|
private Taxon getParentTaxon(UUID classificationUuid, Taxon acceptedTaxon) {
|
1045
|
if (classificationUuid == null){
|
1046
|
return null;
|
1047
|
}
|
1048
|
TaxonNode parent = null;
|
1049
|
for (TaxonNode node : acceptedTaxon.getTaxonNodes()){
|
1050
|
if (classificationUuid.equals(node.getClassification().getUuid())){
|
1051
|
parent = node.getParent();
|
1052
|
}
|
1053
|
}
|
1054
|
if (parent != null){
|
1055
|
return parent.getTaxon();
|
1056
|
}
|
1057
|
return null;
|
1058
|
}
|
1059
|
|
1060
|
private void handleAncestorsForMarkersRecursive(TaxonInContextDTO result, List<MarkerType> markerTypes, TaxonNode node) {
|
1061
|
for (MarkerType type : markerTypes){
|
1062
|
Taxon taxon = node.getTaxon();
|
1063
|
if (taxon != null && taxon.hasMarker(type, true)){
|
1064
|
String label = taxon.getName() == null? taxon.getTitleCache() : taxon.getName().getTitleCache();
|
1065
|
MarkedEntityDTO<Taxon> dto = new MarkedEntityDTO<>(type, true, taxon.getUuid(), label);
|
1066
|
result.addMarkedAncestor(dto);
|
1067
|
}
|
1068
|
}
|
1069
|
TaxonNode parentNode = node.getParent();
|
1070
|
if (parentNode != null){
|
1071
|
handleAncestorsForMarkersRecursive(result, markerTypes, parentNode);
|
1072
|
}
|
1073
|
}
|
1074
|
|
1075
|
@Override
|
1076
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
1077
|
Classification classification) {
|
1078
|
return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, false);
|
1079
|
}
|
1080
|
|
1081
|
@Override
|
1082
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
1083
|
UUID classificationUuid) {
|
1084
|
return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid, false);
|
1085
|
}
|
1086
|
|
1087
|
@Override
|
1088
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
1089
|
UUID classificationUuid, Integer limit, String pattern) {
|
1090
|
return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classificationUuid, limit, pattern, false);
|
1091
|
}
|
1092
|
|
1093
|
@Override
|
1094
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
1095
|
Classification classification, Integer limit, String pattern) {
|
1096
|
return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, limit, pattern, false);
|
1097
|
}
|
1098
|
|
1099
|
@Override
|
1100
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
1101
|
UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications) {
|
1102
|
return getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
1103
|
classificationUuid, limit, pattern, searchForClassifications, false);
|
1104
|
}
|
1105
|
}
|