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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.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.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.stereotype.Service;
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import org.springframework.transaction.TransactionStatus;
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import org.springframework.transaction.annotation.Transactional;
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import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.persistence.dao.common.IOrderedTermVocabularyDao;
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import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;
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import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
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import eu.etaxonomy.cdm.persistence.query.SelectMode;
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@Service
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@Transactional(readOnly = true)
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public class TaxonServiceImpl extends IdentifiableServiceBase<TaxonBase,ITaxonDao> implements ITaxonService {
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private static final Logger logger = Logger.getLogger(TaxonServiceImpl.class);
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@Autowired
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private ITaxonNameDao nameDao;
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// @Autowired
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// @Qualifier("nonViralNameDaoHibernateImpl")
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// private INonViralNameDao nonViralNameDao;
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@Autowired
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private IOrderedTermVocabularyDao orderedVocabularyDao;
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@Autowired
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private IDescriptionDao descriptionDao;
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/**
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* Constructor
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*/
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public TaxonServiceImpl(){
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if (logger.isDebugEnabled()) { logger.debug("Load TaxonService Bean"); }
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}
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public TaxonBase getTaxonByUuid(UUID uuid) {
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return super.getCdmObjectByUuid(uuid);
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}
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@Transactional(readOnly = false)
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public UUID saveTaxon(TaxonBase taxon) {
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return super.saveCdmObject(taxon);
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}
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//@Transactional(readOnly = false)
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public UUID saveTaxon(TaxonBase taxon, TransactionStatus txStatus) {
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//return super.saveCdmObject(taxon, txStatus);
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return super.saveCdmObject(taxon);
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}
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@Transactional(readOnly = false)
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public Map<UUID, ? extends TaxonBase> saveTaxonAll(Collection<? extends TaxonBase> taxonCollection){
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return saveCdmObjectAll(taxonCollection);
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}
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@Transactional(readOnly = false)
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public UUID removeTaxon(TaxonBase taxon) {
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return super.removeCdmObject(taxon);
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}
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public List<TaxonBase> searchTaxaByName(String name, ReferenceBase sec) {
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return dao.getTaxaByName(name, sec);
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}
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public List<TaxonBase> getAllTaxonBases(int limit, int start){
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return dao.list(limit, start);
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}
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public List<Taxon> getAllTaxa(int limit, int start){
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return dao.getAllTaxa(limit, start);
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}
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public List<Synonym> getAllSynonyms(int limit, int start) {
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return dao.getAllSynonyms(limit, start);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase)
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*/
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public List<Taxon> getRootTaxa(ReferenceBase sec){
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return getRootTaxa(sec, CdmFetch.FETCH_CHILDTAXA(), true);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase, boolean)
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*/
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public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, boolean onlyWithChildren) {
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if (cdmFetch == null){
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cdmFetch = CdmFetch.NO_FETCH();
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}
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return dao.getRootTaxa(sec, cdmFetch, onlyWithChildren, false);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase, boolean, boolean)
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*/
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public List<Taxon> getRootTaxa(ReferenceBase sec, boolean onlyWithChildren,
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boolean withMisapplications) {
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return dao.getRootTaxa(sec, null, onlyWithChildren, withMisapplications);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.ReferenceBase, boolean, boolean)
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*/
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public List<Taxon> getRootTaxa(Rank rank, ReferenceBase sec, boolean onlyWithChildren,
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boolean withMisapplications) {
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return dao.getRootTaxa(rank, sec, null, onlyWithChildren, withMisapplications);
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}
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public List<RelationshipBase> getAllRelationships(int limit, int start){
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return dao.getAllRelationships(limit, start);
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}
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public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary() {
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String taxonRelTypeVocabularyId = "15db0cf7-7afc-4a86-a7d4-221c73b0c9ac";
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UUID uuid = UUID.fromString(taxonRelTypeVocabularyId);
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OrderedTermVocabulary<TaxonRelationshipType> taxonRelTypeVocabulary =
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(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid);
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return taxonRelTypeVocabulary;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ITaxonService#makeTaxonSynonym(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.Taxon)
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*/
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@Transactional(readOnly = false)
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public Synonym makeTaxonSynonym(Taxon oldTaxon, Taxon newAcceptedTaxon, SynonymRelationshipType synonymType, ReferenceBase citation, String citationMicroReference) {
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if (oldTaxon == null || newAcceptedTaxon == null || oldTaxon.getName() == null){
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return null;
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}
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// Move oldTaxon to newTaxon
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TaxonNameBase<?,?> synonymName = oldTaxon.getName();
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if (synonymType == null){
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if (synonymName.isHomotypic(newAcceptedTaxon.getName())){
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synonymType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
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}else{
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//TODO synonymType
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synonymType = SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
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}
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}
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SynonymRelationship synRel = newAcceptedTaxon.addSynonymName(synonymName, synonymType, citation, citationMicroReference);
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//Move Synonym Relations to new Taxon
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for(SynonymRelationship synRelation : oldTaxon.getSynonymRelations()){
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newAcceptedTaxon.addSynonym(synRelation.getSynonym(), synRelation.getType(),
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synRelation.getCitation(), synRelation.getCitationMicroReference());
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}
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//Move Taxon RelationShips to new Taxon
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Set<TaxonRelationship> removableTaxonRels = new HashSet<TaxonRelationship>();
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for(TaxonRelationship taxonRelation : oldTaxon.getTaxonRelations()){
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//CHILDREN
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if (taxonRelation.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())){
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if (taxonRelation.getFromTaxon() == oldTaxon){
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removableTaxonRels.add(taxonRelation);
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// oldTaxon.removeTaxonRelation(taxonRelation);
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}else if(taxonRelation.getToTaxon() == oldTaxon){
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newAcceptedTaxon.addTaxonomicChild(taxonRelation.getFromTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
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removableTaxonRels.add(taxonRelation);
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// oldTaxon.removeTaxonRelation(taxonRelation);
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}else{
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logger.warn("Taxon is not part of its own Taxonrelationship");
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}
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}
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//MISAPPLIED NAMES
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if (taxonRelation.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
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if (taxonRelation.getFromTaxon() == oldTaxon){
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newAcceptedTaxon.addMisappliedName(taxonRelation.getToTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
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removableTaxonRels.add(taxonRelation);
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// oldTaxon.removeTaxonRelation(taxonRelation);
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}else if(taxonRelation.getToTaxon() == oldTaxon){
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newAcceptedTaxon.addMisappliedName(taxonRelation.getFromTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
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removableTaxonRels.add(taxonRelation);
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// oldTaxon.removeTaxonRelation(taxonRelation);
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}else{
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logger.warn("Taxon is not part of its own Taxonrelationship");
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}
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}
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//Concept Relationships
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//FIXME implement
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// if (taxonRelation.getType().equals(TaxonRelationshipType.MISAPPLIEDNAMEFOR())){
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// if (taxonRelation.getFromTaxon() == oldTaxon){
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// newAcceptedTaxon.addMisappliedName(taxonRelation.getToTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
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// removableTaxonRels.add(taxonRelation);
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// }else if(taxonRelation.getToTaxon() == oldTaxon){
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// newAcceptedTaxon.addMisappliedName(taxonRelation.getFromTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
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// removableTaxonRels.add(taxonRelation);
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// }else{
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// logger.warn("Taxon is not part of its own Taxonrelationship");
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// }
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// }
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}
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for(TaxonRelationship taxonRel : removableTaxonRels) {
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oldTaxon.removeTaxonRelation(taxonRel);
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}
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//Move Descriptions to new Taxon
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for(TaxonDescription taxDescription : oldTaxon.getDescriptions()){
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newAcceptedTaxon.addDescription(taxDescription);
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}
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//delete old Taxon
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this.dao.saveOrUpdate(newAcceptedTaxon);
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// FIXME implement
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// this.dao.delete(oldTaxon);
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//return
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// this.dao.flush();
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return synRel.getSynonym();
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}
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public void generateTitleCache() {
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generateTitleCache(true);
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}
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//TODO
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public void generateTitleCache(boolean forceProtected) {
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logger.warn("generateTitleCache not yet fully implemented!");
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// for (TaxonBase tb : taxonDao.getAllTaxa(null,null)){
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// logger.warn("Old taxon title: " + tb.getTitleCache());
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// if (forceProtected || !tb.isProtectedTitleCache() ){
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// tb.setTitleCache(tb.generateTitle(), false);
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// taxonDao.update(tb);
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// logger.warn("New title: " + tb.getTitleCache());
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// }
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// }
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}
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@Autowired
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protected void setDao(ITaxonDao dao) {
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this.dao = dao;
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}
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public Pager<TaxonBase> findTaxaByName(Boolean accepted, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
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Integer numberOfResults = dao.countTaxaByName(accepted, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);
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List<TaxonBase> results = new ArrayList<TaxonBase>();
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if(numberOfResults > 0) { // no point checking again
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results = dao.findTaxaByName(accepted, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
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}
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return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);
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}
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public Pager<TaxonRelationship> getRelatedTaxa(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber) {
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Integer numberOfResults = dao.countRelatedTaxa(taxon, type);
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List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
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if(numberOfResults > 0) { // no point checking again
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results = dao.getRelatedTaxa(taxon, type, pageSize, pageNumber);
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}
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return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results);
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}
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public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber) {
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Integer numberOfResults = dao.countSynonyms(taxon, type);
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List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
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if(numberOfResults > 0) { // no point checking again
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results = dao.getSynonyms(taxon, type, pageSize, pageNumber);
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}
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return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
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}
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public Pager<TaxonBase> searchTaxa(String queryString, Boolean accepted, Integer pageSize, Integer pageNumber) {
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Integer numberOfResults = dao.countTaxa(queryString, accepted);
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List<TaxonBase> results = new ArrayList<TaxonBase>();
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if(numberOfResults > 0) { // no point checking again
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results = dao.searchTaxa(queryString, accepted, pageSize, pageNumber);
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}
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return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);
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|
323
|
}
|
|
324
|
|
|
325
|
|
|
326
|
public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator) {
|
|
327
|
|
|
328
|
List<IdentifiableEntity> results = new ArrayList<IdentifiableEntity>();
|
|
329
|
int numberOfResults = 0;
|
|
330
|
List<TaxonBase> taxa = null;
|
|
331
|
int taxaCount = 0;
|
|
332
|
int numberTaxaResults = 0;
|
|
333
|
boolean isMisappliedName = false;
|
|
334
|
|
|
335
|
// Taxa and synonyms
|
|
336
|
|
|
337
|
if (configurator.isDoTaxa() && configurator.isDoSynonyms()) {
|
|
338
|
taxa = dao.getTaxaByName(configurator.getSearchString(), configurator.getMatchMode(),
|
|
339
|
SelectMode.ALL, configurator.getPageSize(), configurator.getPageNumber());
|
|
340
|
numberTaxaResults = dao.countTaxaByName(configurator.getSearchString(), configurator.getMatchMode(), true);
|
|
341
|
|
|
342
|
} else if(configurator.isDoTaxa()) {
|
|
343
|
taxa = dao.getTaxaByName(configurator.getSearchString(), configurator.getMatchMode(),
|
|
344
|
true, configurator.getPageSize(), configurator.getPageNumber());
|
|
345
|
numberTaxaResults = dao.countTaxaByName(configurator.getSearchString(), configurator.getMatchMode(), true);
|
|
346
|
|
|
347
|
} else if (configurator.isDoSynonyms()) {
|
|
348
|
taxa = dao.getTaxaByName(configurator.getSearchString(), configurator.getMatchMode(),
|
|
349
|
false, configurator.getPageSize(), configurator.getPageNumber());
|
|
350
|
numberTaxaResults = dao.countTaxaByName(configurator.getSearchString(), configurator.getMatchMode(), false);
|
|
351
|
}
|
|
352
|
|
|
353
|
if (logger.isDebugEnabled()) { logger.debug(numberTaxaResults + " matching taxa counted"); }
|
|
354
|
|
|
355
|
results.addAll(taxa);
|
|
356
|
|
|
357
|
numberOfResults += numberTaxaResults;
|
|
358
|
|
|
359
|
// Names without taxa
|
|
360
|
|
|
361
|
if (configurator.isDoNamesWithoutTaxa()) {
|
|
362
|
int numberNameResults = 0;
|
|
363
|
List<? extends TaxonNameBase<?,?>> names =
|
|
364
|
nameDao.findByName(configurator.getSearchString(), configurator.getMatchMode(),
|
|
365
|
configurator.getPageSize(), configurator.getPageNumber(), null);
|
|
366
|
if (logger.isDebugEnabled()) { logger.debug(names.size() + " matching name(s) found"); }
|
|
367
|
if (names.size() > 0) {
|
|
368
|
for (TaxonNameBase<?,?> taxonName : names) {
|
|
369
|
if (taxonName.getTaxonBases().size() == 0) {
|
|
370
|
results.add(taxonName);
|
|
371
|
numberNameResults++;
|
|
372
|
}
|
|
373
|
}
|
|
374
|
if (logger.isDebugEnabled()) { logger.debug(numberNameResults + " matching name(s) without taxa found"); }
|
|
375
|
numberOfResults += numberNameResults;
|
|
376
|
}
|
|
377
|
}
|
|
378
|
|
|
379
|
// Taxa from common names
|
|
380
|
|
|
381
|
if (configurator.isDoTaxaByCommonNames()) {
|
|
382
|
int numberCommonNameResults = 0;
|
|
383
|
List<CommonTaxonName> commonTaxonNames =
|
|
384
|
descriptionDao.searchDescriptionByCommonName(configurator.getSearchString(),
|
|
385
|
configurator.getMatchMode(), configurator.getPageSize(), configurator.getPageNumber());
|
|
386
|
if (logger.isDebugEnabled()) { logger.debug(commonTaxonNames.size() + " matching common name(s) found"); }
|
|
387
|
if (commonTaxonNames.size() > 0) {
|
|
388
|
for (CommonTaxonName commonTaxonName : commonTaxonNames) {
|
|
389
|
DescriptionBase description = commonTaxonName.getInDescription();
|
|
390
|
description = HibernateProxyHelper.deproxy(description, DescriptionBase.class);
|
|
391
|
if (description instanceof TaxonDescription) {
|
|
392
|
TaxonDescription taxonDescription = HibernateProxyHelper.deproxy(description, TaxonDescription.class);
|
|
393
|
Taxon taxon = taxonDescription.getTaxon();
|
|
394
|
taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
|
|
395
|
if (!results.contains(taxon) && !taxon.isMisappliedName()) {
|
|
396
|
results.add(taxon);
|
|
397
|
numberCommonNameResults++;
|
|
398
|
}
|
|
399
|
} else {
|
|
400
|
logger.warn("Description of " + commonTaxonName.getName() + " is not an instance of TaxonDescription");
|
|
401
|
}
|
|
402
|
}
|
|
403
|
numberOfResults += numberCommonNameResults;
|
|
404
|
}
|
|
405
|
}
|
|
406
|
|
|
407
|
Collections.sort(results);
|
|
408
|
return new DefaultPagerImpl<IdentifiableEntity>
|
|
409
|
(configurator.getPageNumber(), numberOfResults, configurator.getPageSize(), results);
|
|
410
|
}
|
|
411
|
|
|
412
|
}
|