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// $Id$
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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.List;
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import java.util.Map;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.hibernate.criterion.Criterion;
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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.annotation.Propagation;
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import org.springframework.transaction.annotation.Transactional;
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import eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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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.IProgressMonitor;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.persistence.dao.common.IOrderedTermVocabularyDao;
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import eu.etaxonomy.cdm.persistence.dao.common.IReferencedEntityDao;
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import eu.etaxonomy.cdm.persistence.dao.common.ITermVocabularyDao;
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import eu.etaxonomy.cdm.persistence.dao.name.IHomotypicalGroupDao;
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import eu.etaxonomy.cdm.persistence.dao.name.INomenclaturalStatusDao;
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import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;
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import eu.etaxonomy.cdm.persistence.dao.name.ITypeDesignationDao;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.strategy.TaggedText;
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import eu.etaxonomy.cdm.strategy.TaggedTextGenerator;
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import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
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@Service
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@Transactional(propagation = Propagation.SUPPORTS, readOnly = true)
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public class NameServiceImpl extends IdentifiableServiceBase<TaxonNameBase,ITaxonNameDao> implements INameService {
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static private final Logger logger = Logger.getLogger(NameServiceImpl.class);
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@Autowired
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protected ITermVocabularyDao vocabularyDao;
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@Autowired
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protected IOrderedTermVocabularyDao orderedVocabularyDao;
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@Autowired
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@Qualifier("refEntDao")
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protected IReferencedEntityDao<ReferencedEntityBase> referencedEntityDao;
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@Autowired
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private INomenclaturalStatusDao nomStatusDao;
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@Autowired
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private ITypeDesignationDao typeDesignationDao;
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@Autowired
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private IHomotypicalGroupDao homotypicalGroupDao;
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/**
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* Constructor
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*/
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public NameServiceImpl(){
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if (logger.isDebugEnabled()) { logger.debug("Load NameService Bean"); }
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}
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//********************* METHODS ****************************************************************//
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public List getNamesByName(String name){
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return super.findCdmObjectsByTitle(name);
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}
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public List<NonViralName> getNamesByNameCache(String nameCache){
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List result = dao.findByName(nameCache, MatchMode.EXACT, null, null, null, null);
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return result;
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}
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public List getNamesByName(String name, CdmBase sessionObject){
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return super.findCdmObjectsByTitle(name, sessionObject);
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}
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public List findNamesByTitle(String title){
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return super.findCdmObjectsByTitle(title);
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}
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public List findNamesByTitle(String title, CdmBase sessionObject){
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return super.findCdmObjectsByTitle(title, sessionObject);
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}
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@Transactional(readOnly = false)
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public Map<UUID, HomotypicalGroup> saveAllHomotypicalGroups(Collection<HomotypicalGroup> homotypicalGroups){
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return homotypicalGroupDao.saveAll(homotypicalGroups);
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}
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@Transactional(readOnly = false)
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public Map<UUID, TypeDesignationBase> saveTypeDesignationAll(Collection<TypeDesignationBase> typeDesignationCollection){
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return typeDesignationDao.saveAll(typeDesignationCollection);
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}
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@Transactional(readOnly = false)
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public Map<UUID, ReferencedEntityBase> saveReferencedEntitiesAll(Collection<ReferencedEntityBase> referencedEntityCollection){
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return referencedEntityDao.saveAll(referencedEntityCollection);
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}
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public List<TaxonNameBase> getAllNames(int limit, int start){
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return dao.list(limit, start);
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}
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public List<NomenclaturalStatus> getAllNomenclaturalStatus(int limit, int start){
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return nomStatusDao.list(limit, start);
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}
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public List<TypeDesignationBase> getAllTypeDesignations(int limit, int start){
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return typeDesignationDao.getAllTypeDesignations(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* homotypicalGroupService.list
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*/
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public List<HomotypicalGroup> getAllHomotypicalGroups(int limit, int start){
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return homotypicalGroupDao.list(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* remove
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*/
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@Deprecated
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public List<RelationshipBase> getAllRelationships(int limit, int start){
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return dao.getRelationships(limit, start);
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}
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/**
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* FIXME Candidate for harmonization
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* is this the same as termService.getVocabulary(VocabularyEnum.Rank)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.INameService#getRankVocabulary()
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*/
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public OrderedTermVocabulary<Rank> getRankVocabulary() {
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String uuidString = "ef0d1ce1-26e3-4e83-b47b-ca74eed40b1b";
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UUID uuid = UUID.fromString(uuidString);
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OrderedTermVocabulary<Rank> rankVocabulary =
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(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid);
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return rankVocabulary;
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}
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/**
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* FIXME Candidate for harmonization
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* is this the same as termService.getVocabulary(VocabularyEnum.NameRelationshipType)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.INameService#getNameRelationshipTypeVocabulary()
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*/
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public TermVocabulary<NameRelationshipType> getNameRelationshipTypeVocabulary() {
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String uuidString = "6878cb82-c1a4-4613-b012-7e73b413c8cd";
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UUID uuid = UUID.fromString(uuidString);
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TermVocabulary<NameRelationshipType> nameRelTypeVocabulary =
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(TermVocabulary)vocabularyDao.findByUuid(uuid);
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return nameRelTypeVocabulary;
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}
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/**
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* FIXME Candidate for harmonization
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* is this the same as termService.getVocabulary(VocabularyEnum.StatusType)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.INameService#getStatusTypeVocabulary()
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*/
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public TermVocabulary<NomenclaturalStatusType> getStatusTypeVocabulary() {
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String uuidString = "bb28cdca-2f8a-4f11-9c21-517e9ae87f1f";
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UUID uuid = UUID.fromString(uuidString);
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TermVocabulary<NomenclaturalStatusType> nomStatusTypeVocabulary =
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(TermVocabulary)vocabularyDao.findByUuid(uuid);
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return nomStatusTypeVocabulary;
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}
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/**
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* FIXME Candidate for harmonization
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* is this the same as termService.getVocabulary(VocabularyEnum.SpecimenTypeDesignationStatus)
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.INameService#getTypeDesignationStatusVocabulary()
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*/
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public TermVocabulary<SpecimenTypeDesignationStatus> getSpecimenTypeDesignationStatusVocabulary() {
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String uuidString = "ab177bd7-d3c8-4e58-a388-226fff6ba3c2";
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UUID uuid = UUID.fromString(uuidString);
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TermVocabulary<SpecimenTypeDesignationStatus> typeDesigStatusVocabulary =
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(TermVocabulary)vocabularyDao.findByUuid(uuid);
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return typeDesigStatusVocabulary;
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}
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/**
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* FIXME Candidate for harmonization
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* is this the same as termService.getVocabulary(VocabularyEnum.SpecimenTypeDesignationStatus)
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* and also seems to duplicate the above method, differing only in the DAO used and the return type
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* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.INameService#getTypeDesignationStatusVocabulary()
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*/
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public OrderedTermVocabulary<SpecimenTypeDesignationStatus> getSpecimenTypeDesignationVocabulary() {
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String uuidString = "ab177bd7-d3c8-4e58-a388-226fff6ba3c2";
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UUID uuid = UUID.fromString(uuidString);
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OrderedTermVocabulary<SpecimenTypeDesignationStatus> typeDesignationVocabulary =
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(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid);
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return typeDesignationVocabulary;
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}
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@Autowired
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protected void setDao(ITaxonNameDao dao) {
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this.dao = dao;
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}
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public Pager<HybridRelationship> getHybridNames(NonViralName name, HybridRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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Integer numberOfResults = dao.countHybridNames(name, type);
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List<HybridRelationship> results = new ArrayList<HybridRelationship>();
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if(AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)) { // no point checking again
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results = dao.getHybridNames(name, type, pageSize, pageNumber,orderHints,propertyPaths);
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}
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return new DefaultPagerImpl<HybridRelationship>(pageNumber, numberOfResults, pageSize, results);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.INameService#listNameRelationships(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction, eu.etaxonomy.cdm.model.name.NameRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
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*/
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@Override
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public List<NameRelationship> listNameRelationships(TaxonNameBase name, Direction direction, NameRelationshipType type, Integer pageSize,
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Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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Integer numberOfResults = dao.countNameRelationships(name, NameRelationship.Direction.relatedFrom, type);
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List<NameRelationship> results = new ArrayList<NameRelationship>();
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if (AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)) { // no point checking again
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results = dao.getNameRelationships(name, direction, type, pageSize, pageNumber, orderHints, propertyPaths);
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}
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return results;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.INameService#pageNameRelationships(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction, eu.etaxonomy.cdm.model.name.NameRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
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*/
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@Override
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public Pager<NameRelationship> pageNameRelationships(TaxonNameBase name, Direction direction, NameRelationshipType type, Integer pageSize,
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Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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List<NameRelationship> results = listNameRelationships(name, direction, type, pageSize, pageNumber, orderHints, propertyPaths);
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return new DefaultPagerImpl<NameRelationship>(pageNumber, results.size(), pageSize, results);
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}
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public List<NameRelationship> listFromNameRelationships(TaxonNameBase name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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return listNameRelationships(name, Direction.relatedFrom, type, pageSize, pageNumber, orderHints, propertyPaths);
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}
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public Pager<NameRelationship> pageFromNameRelationships(TaxonNameBase name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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List<NameRelationship> results = listNameRelationships(name, Direction.relatedFrom, type, pageSize, pageNumber, orderHints, propertyPaths);
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return new DefaultPagerImpl<NameRelationship>(pageNumber, results.size(), pageSize, results);
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}
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public List<NameRelationship> listToNameRelationships(TaxonNameBase name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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return listNameRelationships(name, Direction.relatedTo, type, pageSize, pageNumber, orderHints, propertyPaths);
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}
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public Pager<NameRelationship> pageToNameRelationships(TaxonNameBase name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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List<NameRelationship> results = listNameRelationships(name, Direction.relatedTo, type, pageSize, pageNumber, orderHints, propertyPaths);
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return new DefaultPagerImpl<NameRelationship>(pageNumber, results.size(), pageSize, results);
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}
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public Pager<TypeDesignationBase> getTypeDesignations(TaxonNameBase name, SpecimenTypeDesignationStatus status,
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Integer pageSize, Integer pageNumber) {
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return getTypeDesignations(name, status, pageSize, pageNumber, null);
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}
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public Pager<TypeDesignationBase> getTypeDesignations(TaxonNameBase name, SpecimenTypeDesignationStatus status,
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Integer pageSize, Integer pageNumber, List<String> propertyPaths){
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Integer numberOfResults = dao.countTypeDesignations(name, status);
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List<TypeDesignationBase> results = new ArrayList<TypeDesignationBase>();
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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results = dao.getTypeDesignations(name, status, pageSize, pageNumber, propertyPaths);
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}
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return new DefaultPagerImpl<TypeDesignationBase>(pageNumber, numberOfResults, pageSize, results);
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}
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/**
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* FIXME Candidate for harmonization
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310
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* rename search
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311
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*/
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312
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public Pager<TaxonNameBase> searchNames(String uninomial,String infraGenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
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313
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List<String> propertyPaths) {
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314
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Integer numberOfResults = dao.countNames(uninomial, infraGenericEpithet, specificEpithet, infraspecificEpithet, rank);
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315
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316
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List<TaxonNameBase> results = new ArrayList<TaxonNameBase>();
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317
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if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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318
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results = dao.searchNames(uninomial, infraGenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber, orderHints, propertyPaths);
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319
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}
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320
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321
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return new DefaultPagerImpl<TaxonNameBase>(pageNumber, numberOfResults, pageSize, results);
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322
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}
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323
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324
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/* (non-Javadoc)
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325
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* @see eu.etaxonomy.cdm.api.service.INameService#getUuidAndTitleCacheOfNames()
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326
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*/
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327
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public List<UuidAndTitleCache> getUuidAndTitleCacheOfNames() {
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328
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return dao.getUuidAndTitleCacheOfNames();
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329
|
}
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330
|
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331
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public Pager<TaxonNameBase> findByName(Class<? extends TaxonNameBase> clazz, String queryString, MatchMode matchmode, List<Criterion> criteria, Integer pageSize,Integer pageNumber, List<OrderHint> orderHints,List<String> propertyPaths) {
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332
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Integer numberOfResults = dao.countByName(clazz, queryString, matchmode, criteria);
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333
|
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334
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List<TaxonNameBase> results = new ArrayList<TaxonNameBase>();
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335
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
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336
|
results = dao.findByName(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
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337
|
}
|
|
338
|
|
|
339
|
return new DefaultPagerImpl<TaxonNameBase>(pageNumber, numberOfResults, pageSize, results);
|
|
340
|
}
|
|
341
|
|
|
342
|
public HomotypicalGroup findHomotypicalGroup(UUID uuid) {
|
|
343
|
return homotypicalGroupDao.findByUuid(uuid);
|
|
344
|
}
|
|
345
|
|
|
346
|
|
|
347
|
/* (non-Javadoc)
|
|
348
|
* @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
|
|
349
|
*/
|
|
350
|
@Override
|
|
351
|
public void updateTitleCache(Class<? extends TaxonNameBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<TaxonNameBase> cacheStrategy, IProgressMonitor monitor) {
|
|
352
|
if (clazz == null){
|
|
353
|
clazz = TaxonNameBase.class;
|
|
354
|
}
|
|
355
|
super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
|
|
356
|
}
|
|
357
|
|
|
358
|
|
|
359
|
@Override
|
|
360
|
protected void setOtherCachesNull(TaxonNameBase name) {
|
|
361
|
if (name.isInstanceOf(NonViralName.class)){
|
|
362
|
NonViralName nvn = CdmBase.deproxy(name, NonViralName.class);
|
|
363
|
if (! nvn.isProtectedNameCache()){
|
|
364
|
nvn.setNameCache(null, false);
|
|
365
|
}
|
|
366
|
if (! nvn.isProtectedAuthorshipCache()){
|
|
367
|
nvn.setAuthorshipCache(null, false);
|
|
368
|
}
|
|
369
|
if (! nvn.isProtectedFullTitleCache()){
|
|
370
|
nvn.setFullTitleCache(null, false);
|
|
371
|
}
|
|
372
|
}
|
|
373
|
}
|
|
374
|
|
|
375
|
/* (non-Javadoc)
|
|
376
|
* @see eu.etaxonomy.cdm.api.service.INameService#getTaggedName(eu.etaxonomy.cdm.model.name.TaxonNameBase)
|
|
377
|
*/
|
|
378
|
@Override
|
|
379
|
public List<TaggedText> getTaggedName(UUID uuid) {
|
|
380
|
TaxonNameBase taxonNameBase = dao.load(uuid);
|
|
381
|
return TaggedTextGenerator.getTaggedName(taxonNameBase);
|
|
382
|
}
|
|
383
|
|
|
384
|
|
|
385
|
}
|