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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.io.IOException;
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import java.util.ArrayList;
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import java.util.Collection;
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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.UUID;
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import org.apache.log4j.Logger;
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import org.apache.lucene.analysis.SimpleAnalyzer;
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import org.apache.lucene.index.CorruptIndexException;
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import org.apache.lucene.index.Term;
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import org.apache.lucene.queryParser.ParseException;
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import org.apache.lucene.search.BooleanQuery;
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import org.apache.lucene.search.Explanation;
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import org.apache.lucene.search.FuzzyLikeThisQuery;
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import org.apache.lucene.search.Query;
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import org.apache.lucene.search.SortField;
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import org.apache.lucene.search.BooleanClause.Occur;
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import org.apache.lucene.search.TermQuery;
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import org.apache.lucene.search.TopDocs;
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import org.apache.lucene.search.WildcardQuery;
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import org.apache.lucene.search.regex.RegexQuery;
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import org.apache.lucene.util.Version;
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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.Transactional;
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import eu.etaxonomy.cdm.api.service.config.NameDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;
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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.api.service.search.DocumentSearchResult;
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import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
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import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
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import eu.etaxonomy.cdm.api.service.search.QueryFactory;
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import eu.etaxonomy.cdm.api.service.search.SearchResult;
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import eu.etaxonomy.cdm.api.service.search.SearchResultBuilder;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.model.CdmBaseType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.common.Language;
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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.RelationshipBase.Direction;
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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.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.NameTypeDesignation;
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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.model.occurrence.DerivedUnitBase;
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import eu.etaxonomy.cdm.persistence.dao.common.ICdmGenericDao;
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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.cache.TaggedText;
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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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@Service
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@Transactional(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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@Autowired
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private ICdmGenericDao genericDao;
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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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.ServiceBase#delete(eu.etaxonomy.cdm.model.common.CdmBase)
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*/
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@Override
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public UUID delete(TaxonNameBase name){
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NameDeletionConfigurator config = new NameDeletionConfigurator();
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try {
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return delete(name, config);
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} catch (ReferencedObjectUndeletableException e) {
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//TODO throw DeleteException - current implementation is preliminary for testing
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throw new RuntimeException(e);
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}
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.INameService#delete(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.api.service.NameDeletionConfigurator)
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*/
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@Override
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public UUID delete(TaxonNameBase name, NameDeletionConfigurator config) throws ReferencedObjectUndeletableException{
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if (name == null){
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return null;
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}
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//remove references to this name
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removeNameRelationshipsByDeleteConfig(name, config);
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//check if this name is still used somewhere
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//name relationships
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if (! name.getNameRelations().isEmpty()){
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String message = "Name can't be deleted as it is used in name relationship(s). Remove name relationships prior to deletion.";
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throw new ReferencedObjectUndeletableException(message);
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// return null;
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}
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//concepts
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if (! name.getTaxonBases().isEmpty()){
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String message = "Name can't be deleted as it is used in concept(s). Remove or change concept prior to deletion.";
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throw new ReferencedObjectUndeletableException(message);
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}
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//hybrid relationships
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if (name.isInstanceOf(NonViralName.class)){
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NonViralName nvn = CdmBase.deproxy(name, NonViralName.class);
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// if (! nvn.getHybridChildRelations().isEmpty()){
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// String message = "Name can't be deleted as it is a child in (a) hybrid relationship(s). Remove hybrid relationships prior to deletion.";
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// throw new RuntimeException(message);
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// }
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if (! nvn.getHybridParentRelations().isEmpty()){
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String message = "Name can't be deleted as it is a parent in (a) hybrid relationship(s). Remove hybrid relationships prior to deletion.";
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throw new ReferencedObjectUndeletableException(message);
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}
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}
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//all type designation relationships are removed as they belong to the name
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deleteTypeDesignation(name, null);
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// //type designations
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// if (! name.getTypeDesignations().isEmpty()){
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// String message = "Name can't be deleted as it has types. Remove types prior to deletion.";
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// throw new ReferrencedObjectUndeletableException(message);
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// }
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//check references with only reverse mapping
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Set<CdmBase> referencingObjects = genericDao.getReferencingObjects(name);
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for (CdmBase referencingObject : referencingObjects){
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//DerivedUnitBase?.storedUnder
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if (referencingObject.isInstanceOf(DerivedUnitBase.class)){
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String message = "Name can't be deleted as it is used as derivedUnit#storedUnder by %s. Remove 'stored under' prior to deleting this name";
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message = String.format(message, CdmBase.deproxy(referencingObject, DerivedUnitBase.class).getTitleCache());
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throw new ReferencedObjectUndeletableException(message);
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}
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//DescriptionElementSource#nameUsedInSource
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if (referencingObject.isInstanceOf(DescriptionElementSource.class)){
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String message = "Name can't be deleted as it is used as descriptionElementSource#nameUsedInSource";
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throw new ReferencedObjectUndeletableException(message);
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}
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//NameTypeDesignation#typeName
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if (referencingObject.isInstanceOf(NameTypeDesignation.class)){
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String message = "Name can't be deleted as it is used as a name type in a NameTypeDesignation";
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throw new ReferencedObjectUndeletableException(message);
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}
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//TaxonNameDescriptions#taxonName
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//deleted via cascade?
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//NomenclaturalStatus
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//deleted via cascade?
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}
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//TODO inline references
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dao.delete(name);
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return name.getUuid();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.api.service.INameService#deleteTypeDesignation(eu.etaxonomy.cdm.model.name.TaxonNameBase, eu.etaxonomy.cdm.model.name.TypeDesignationBase)
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*/
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@Override
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public void deleteTypeDesignation(TaxonNameBase name, TypeDesignationBase typeDesignation){
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if (name == null && typeDesignation == null){
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return;
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}else if (name != null && typeDesignation != null){
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removeSingleDesignation(name, typeDesignation);
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}else if (name != null){
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Set<TypeDesignationBase> designationSet = new HashSet<TypeDesignationBase>(name.getTypeDesignations());
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for (Object o : designationSet){
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TypeDesignationBase desig = CdmBase.deproxy(o, TypeDesignationBase.class);
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removeSingleDesignation(name, desig);
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}
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}else if (typeDesignation != null){
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Set<TaxonNameBase> nameSet = new HashSet<TaxonNameBase>(typeDesignation.getTypifiedNames());
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for (Object o : nameSet){
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TaxonNameBase singleName = CdmBase.deproxy(o, TaxonNameBase.class);
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removeSingleDesignation(singleName, typeDesignation);
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}
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}
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}
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/**
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* @param name
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* @param typeDesignation
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*/
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private void removeSingleDesignation(TaxonNameBase name, TypeDesignationBase typeDesignation) {
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name.removeTypeDesignation(typeDesignation);
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if (typeDesignation.getTypifiedNames().isEmpty()){
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typeDesignation.removeType();
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typeDesignationDao.delete(typeDesignation);
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}
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}
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/**
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* @param name
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* @param config
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*/
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private void removeNameRelationshipsByDeleteConfig(TaxonNameBase name, NameDeletionConfigurator config) {
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if (config.isRemoveAllNameRelationships()){
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Set<NameRelationship> rels = name.getNameRelations();
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for (NameRelationship rel : rels){
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name.removeNameRelationship(rel);
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}
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}else{
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//relations to this name
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Set<NameRelationship> rels = name.getRelationsToThisName();
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for (NameRelationship rel : rels){
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if (config.isIgnoreHasBasionym() && NameRelationshipType.BASIONYM().equals(rel.getType() )){
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name.removeNameRelationship(rel);
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}else if (config.isIgnoreHasReplacedSynonym() && NameRelationshipType.REPLACED_SYNONYM().equals(rel.getType())){
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name.removeNameRelationship(rel);
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}
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}
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//relations from this name
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rels = name.getRelationsFromThisName();
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for (NameRelationship rel : rels){
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if (config.isIgnoreIsBasionymFor() && NameRelationshipType.BASIONYM().equals(rel.getType()) ){
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name.removeNameRelationship(rel);
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}else if (config.isIgnoreIsReplacedSynonymFor() && NameRelationshipType.REPLACED_SYNONYM().equals(rel.getType())){
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name.removeNameRelationship(rel);
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}
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}
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}
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}
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//********************* METHODS ****************************************************************//
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/**
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* @deprecated To be removed for harmonization see http://dev.e-taxonomy.eu/trac/wiki/CdmLibraryConventions
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* duplicate of findByName
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*/
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@Override
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@Deprecated
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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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/**
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* TODO candidate for harmonization
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* new name findByName
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*/
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@Override
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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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/**
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* TODO candidate for harmonization
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* new name saveHomotypicalGroups
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*
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* findByTitle
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*/
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@Override
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public List<NonViralName> findNamesByTitleCache(String titleCache, MatchMode matchMode, List<String> propertyPaths){
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List result = dao.findByTitle(titleCache, matchMode, null, null, null ,propertyPaths);
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return result;
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}
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/**
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* TODO candidate for harmonization
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* new name saveHomotypicalGroups
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*
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* findByTitle
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*/
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@Override
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public List<NonViralName> findNamesByNameCache(String nameCache, MatchMode matchMode, List<String> propertyPaths){
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336
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List result = dao.findByName(nameCache, matchMode, null, null, null ,propertyPaths);
|
|
337
|
return result;
|
|
338
|
}
|
|
339
|
|
|
340
|
/**
|
|
341
|
* @deprecated To be removed for harmonization see http://dev.e-taxonomy.eu/trac/wiki/CdmLibraryConventions
|
|
342
|
* Replace by load(UUID, propertyPaths)
|
|
343
|
*/
|
|
344
|
@Override
|
|
345
|
@Deprecated
|
|
346
|
public NonViralName findNameByUuid(UUID uuid, List<String> propertyPaths){
|
|
347
|
return (NonViralName)dao.findByUuid(uuid, null ,propertyPaths);
|
|
348
|
}
|
|
349
|
|
|
350
|
/**
|
|
351
|
* TODO candidate for harmonization
|
|
352
|
*/
|
|
353
|
@Override
|
|
354
|
public List getNamesByName(String name, CdmBase sessionObject){
|
|
355
|
return super.findCdmObjectsByTitle(name, sessionObject);
|
|
356
|
}
|
|
357
|
|
|
358
|
/**
|
|
359
|
* @deprecated To be removed for harmonization see http://dev.e-taxonomy.eu/trac/wiki/CdmLibraryConventions
|
|
360
|
* duplicate of findByTitle(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths)
|
|
361
|
*/
|
|
362
|
@Override
|
|
363
|
@Deprecated
|
|
364
|
public List findNamesByTitle(String title){
|
|
365
|
return super.findCdmObjectsByTitle(title);
|
|
366
|
}
|
|
367
|
|
|
368
|
/**
|
|
369
|
* @deprecated To be removed for harmonization see http://dev.e-taxonomy.eu/trac/wiki/CdmLibraryConventions
|
|
370
|
* duplicate of findByTitle()
|
|
371
|
*/
|
|
372
|
@Override
|
|
373
|
@Deprecated
|
|
374
|
public List findNamesByTitle(String title, CdmBase sessionObject){
|
|
375
|
return super.findCdmObjectsByTitle(title, sessionObject);
|
|
376
|
}
|
|
377
|
|
|
378
|
/**
|
|
379
|
* TODO candidate for harmonization
|
|
380
|
* new name saveHomotypicalGroups
|
|
381
|
*/
|
|
382
|
@Override
|
|
383
|
@Transactional(readOnly = false)
|
|
384
|
public Map<UUID, HomotypicalGroup> saveAllHomotypicalGroups(Collection<HomotypicalGroup> homotypicalGroups){
|
|
385
|
return homotypicalGroupDao.saveAll(homotypicalGroups);
|
|
386
|
}
|
|
387
|
|
|
388
|
/**
|
|
389
|
* TODO candidate for harmonization
|
|
390
|
* new name saveTypeDesignations
|
|
391
|
*/
|
|
392
|
@Override
|
|
393
|
@Transactional(readOnly = false)
|
|
394
|
public Map<UUID, TypeDesignationBase> saveTypeDesignationAll(Collection<TypeDesignationBase> typeDesignationCollection){
|
|
395
|
return typeDesignationDao.saveAll(typeDesignationCollection);
|
|
396
|
}
|
|
397
|
|
|
398
|
/**
|
|
399
|
* TODO candidate for harmonization
|
|
400
|
* new name saveReferencedEntities
|
|
401
|
*/
|
|
402
|
@Override
|
|
403
|
@Transactional(readOnly = false)
|
|
404
|
public Map<UUID, ReferencedEntityBase> saveReferencedEntitiesAll(Collection<ReferencedEntityBase> referencedEntityCollection){
|
|
405
|
return referencedEntityDao.saveAll(referencedEntityCollection);
|
|
406
|
}
|
|
407
|
|
|
408
|
/**
|
|
409
|
* TODO candidate for harmonization
|
|
410
|
* new name getNames
|
|
411
|
*/
|
|
412
|
public List<TaxonNameBase> getAllNames(int limit, int start){
|
|
413
|
return dao.list(limit, start);
|
|
414
|
}
|
|
415
|
|
|
416
|
/**
|
|
417
|
* TODO candidate for harmonization
|
|
418
|
* new name getNomenclaturalStatus
|
|
419
|
*/
|
|
420
|
@Override
|
|
421
|
public List<NomenclaturalStatus> getAllNomenclaturalStatus(int limit, int start){
|
|
422
|
return nomStatusDao.list(limit, start);
|
|
423
|
}
|
|
424
|
|
|
425
|
/**
|
|
426
|
* TODO candidate for harmonization
|
|
427
|
* new name getTypeDesignations
|
|
428
|
*/
|
|
429
|
@Override
|
|
430
|
public List<TypeDesignationBase> getAllTypeDesignations(int limit, int start){
|
|
431
|
return typeDesignationDao.getAllTypeDesignations(limit, start);
|
|
432
|
}
|
|
433
|
/**
|
|
434
|
* FIXME Candidate for harmonization
|
|
435
|
* homotypicalGroupService.list
|
|
436
|
*/
|
|
437
|
@Override
|
|
438
|
public List<HomotypicalGroup> getAllHomotypicalGroups(int limit, int start){
|
|
439
|
return homotypicalGroupDao.list(limit, start);
|
|
440
|
}
|
|
441
|
|
|
442
|
/**
|
|
443
|
* FIXME Candidate for harmonization
|
|
444
|
* remove
|
|
445
|
*/
|
|
446
|
@Override
|
|
447
|
@Deprecated
|
|
448
|
public List<RelationshipBase> getAllRelationships(int limit, int start){
|
|
449
|
return dao.getAllRelationships(limit, start);
|
|
450
|
}
|
|
451
|
|
|
452
|
/**
|
|
453
|
* FIXME Candidate for harmonization
|
|
454
|
* is this not the same as termService.getVocabulary(VocabularyEnum.Rank)
|
|
455
|
* since this returns OrderedTermVocabulary
|
|
456
|
*
|
|
457
|
* (non-Javadoc)
|
|
458
|
* @see eu.etaxonomy.cdm.api.service.INameService#getRankVocabulary()
|
|
459
|
*/
|
|
460
|
@Override
|
|
461
|
public OrderedTermVocabulary<Rank> getRankVocabulary() {
|
|
462
|
String uuidString = "ef0d1ce1-26e3-4e83-b47b-ca74eed40b1b";
|
|
463
|
UUID uuid = UUID.fromString(uuidString);
|
|
464
|
OrderedTermVocabulary<Rank> rankVocabulary =
|
|
465
|
(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid);
|
|
466
|
return rankVocabulary;
|
|
467
|
}
|
|
468
|
|
|
469
|
/**
|
|
470
|
* FIXME Candidate for harmonization
|
|
471
|
* is this the same as termService.getVocabulary(VocabularyEnum.NameRelationshipType)
|
|
472
|
* (non-Javadoc)
|
|
473
|
* @see eu.etaxonomy.cdm.api.service.INameService#getNameRelationshipTypeVocabulary()
|
|
474
|
*/
|
|
475
|
@Override
|
|
476
|
public TermVocabulary<NameRelationshipType> getNameRelationshipTypeVocabulary() {
|
|
477
|
String uuidString = "6878cb82-c1a4-4613-b012-7e73b413c8cd";
|
|
478
|
UUID uuid = UUID.fromString(uuidString);
|
|
479
|
TermVocabulary<NameRelationshipType> nameRelTypeVocabulary =
|
|
480
|
vocabularyDao.findByUuid(uuid);
|
|
481
|
return nameRelTypeVocabulary;
|
|
482
|
}
|
|
483
|
|
|
484
|
/**
|
|
485
|
* FIXME Candidate for harmonization
|
|
486
|
* is this the same as termService.getVocabulary(VocabularyEnum.StatusType)
|
|
487
|
* (non-Javadoc)
|
|
488
|
* @see eu.etaxonomy.cdm.api.service.INameService#getStatusTypeVocabulary()
|
|
489
|
*/
|
|
490
|
@Override
|
|
491
|
public TermVocabulary<NomenclaturalStatusType> getStatusTypeVocabulary() {
|
|
492
|
String uuidString = "bb28cdca-2f8a-4f11-9c21-517e9ae87f1f";
|
|
493
|
UUID uuid = UUID.fromString(uuidString);
|
|
494
|
TermVocabulary<NomenclaturalStatusType> nomStatusTypeVocabulary =
|
|
495
|
vocabularyDao.findByUuid(uuid);
|
|
496
|
return nomStatusTypeVocabulary;
|
|
497
|
}
|
|
498
|
|
|
499
|
/**
|
|
500
|
* FIXME Candidate for harmonization
|
|
501
|
* is this the same as termService.getVocabulary(VocabularyEnum.SpecimenTypeDesignationStatus)
|
|
502
|
* (non-Javadoc)
|
|
503
|
* @see eu.etaxonomy.cdm.api.service.INameService#getTypeDesignationStatusVocabulary()
|
|
504
|
*/
|
|
505
|
@Override
|
|
506
|
public TermVocabulary<SpecimenTypeDesignationStatus> getSpecimenTypeDesignationStatusVocabulary() {
|
|
507
|
String uuidString = "ab177bd7-d3c8-4e58-a388-226fff6ba3c2";
|
|
508
|
UUID uuid = UUID.fromString(uuidString);
|
|
509
|
TermVocabulary<SpecimenTypeDesignationStatus> typeDesigStatusVocabulary =
|
|
510
|
vocabularyDao.findByUuid(uuid);
|
|
511
|
return typeDesigStatusVocabulary;
|
|
512
|
}
|
|
513
|
|
|
514
|
/**
|
|
515
|
* FIXME Candidate for harmonization
|
|
516
|
* is this the same as termService.getVocabulary(VocabularyEnum.SpecimenTypeDesignationStatus)
|
|
517
|
* and also seems to duplicate the above method, differing only in the DAO used and the return type
|
|
518
|
* (non-Javadoc)
|
|
519
|
* @see eu.etaxonomy.cdm.api.service.INameService#getTypeDesignationStatusVocabulary()
|
|
520
|
*/
|
|
521
|
@Override
|
|
522
|
public OrderedTermVocabulary<SpecimenTypeDesignationStatus> getSpecimenTypeDesignationVocabulary() {
|
|
523
|
String uuidString = "ab177bd7-d3c8-4e58-a388-226fff6ba3c2";
|
|
524
|
UUID uuid = UUID.fromString(uuidString);
|
|
525
|
OrderedTermVocabulary<SpecimenTypeDesignationStatus> typeDesignationVocabulary =
|
|
526
|
(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid);
|
|
527
|
return typeDesignationVocabulary;
|
|
528
|
}
|
|
529
|
|
|
530
|
|
|
531
|
@Override
|
|
532
|
@Autowired
|
|
533
|
protected void setDao(ITaxonNameDao dao) {
|
|
534
|
this.dao = dao;
|
|
535
|
}
|
|
536
|
|
|
537
|
@Override
|
|
538
|
public Pager<HybridRelationship> getHybridNames(NonViralName name, HybridRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
539
|
Integer numberOfResults = dao.countHybridNames(name, type);
|
|
540
|
|
|
541
|
List<HybridRelationship> results = new ArrayList<HybridRelationship>();
|
|
542
|
if(AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)) { // no point checking again
|
|
543
|
results = dao.getHybridNames(name, type, pageSize, pageNumber,orderHints,propertyPaths);
|
|
544
|
}
|
|
545
|
|
|
546
|
return new DefaultPagerImpl<HybridRelationship>(pageNumber, numberOfResults, pageSize, results);
|
|
547
|
}
|
|
548
|
|
|
549
|
/* (non-Javadoc)
|
|
550
|
* @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)
|
|
551
|
*/
|
|
552
|
@Override
|
|
553
|
public List<NameRelationship> listNameRelationships(TaxonNameBase name, Direction direction, NameRelationshipType type, Integer pageSize,
|
|
554
|
Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
555
|
|
|
556
|
Integer numberOfResults = dao.countNameRelationships(name, NameRelationship.Direction.relatedFrom, type);
|
|
557
|
|
|
558
|
List<NameRelationship> results = new ArrayList<NameRelationship>();
|
|
559
|
if (AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)) { // no point checking again
|
|
560
|
results = dao.getNameRelationships(name, direction, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
561
|
}
|
|
562
|
return results;
|
|
563
|
}
|
|
564
|
|
|
565
|
|
|
566
|
protected LuceneSearch prepareFindByFuzzyNameSearch(Class<? extends CdmBase> clazz,
|
|
567
|
NonViralName nvn,
|
|
568
|
float accuracy,
|
|
569
|
List<Language> languages,
|
|
570
|
boolean highlightFragments) {
|
|
571
|
String similarity = Float.toString(accuracy);
|
|
572
|
String searchSuffix = "~" + similarity;
|
|
573
|
|
|
574
|
|
|
575
|
BooleanQuery finalQuery = new BooleanQuery();
|
|
576
|
BooleanQuery textQuery = new BooleanQuery();
|
|
577
|
|
|
578
|
LuceneSearch luceneSearch = new LuceneSearch(getSession(), TaxonNameBase.class);
|
|
579
|
QueryFactory queryFactory = new QueryFactory(luceneSearch);
|
|
580
|
|
|
581
|
SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};
|
|
582
|
luceneSearch.setSortFields(sortFields);
|
|
583
|
|
|
584
|
// ---- search criteria
|
|
585
|
luceneSearch.setClazz(clazz);
|
|
586
|
|
|
587
|
|
|
588
|
if(nvn.getGenusOrUninomial() != null && !nvn.getGenusOrUninomial().equals("")) {
|
|
589
|
textQuery.add(queryFactory.newTermQuery("genusOrUninomial", nvn.getGenusOrUninomial() + searchSuffix), Occur.SHOULD);
|
|
590
|
|
|
591
|
} else {
|
|
592
|
textQuery.add(new RegexQuery (new Term ("genusOrUninomial", "^[a-zA-Z]*")), Occur.MUST_NOT);
|
|
593
|
}
|
|
594
|
|
|
595
|
if(nvn.getInfraGenericEpithet() != null && !nvn.getInfraGenericEpithet().equals("")){
|
|
596
|
textQuery.add(queryFactory.newTermQuery("infraGenericEpithet", nvn.getInfraGenericEpithet() + searchSuffix), Occur.SHOULD);
|
|
597
|
} else {
|
|
598
|
textQuery.add(new RegexQuery (new Term ("infraGenericEpithet", "^[a-zA-Z]*")), Occur.MUST_NOT);
|
|
599
|
}
|
|
600
|
|
|
601
|
if(nvn.getSpecificEpithet() != null && !nvn.getSpecificEpithet().equals("")){
|
|
602
|
textQuery.add(queryFactory.newTermQuery("specificEpithet", nvn.getSpecificEpithet() + searchSuffix), Occur.SHOULD);
|
|
603
|
|
|
604
|
} else {
|
|
605
|
textQuery.add(new RegexQuery (new Term ("specificEpithet", "^[a-zA-Z]*")), Occur.MUST_NOT);
|
|
606
|
}
|
|
607
|
|
|
608
|
if(nvn.getInfraSpecificEpithet() != null && !nvn.getInfraSpecificEpithet().equals("")){
|
|
609
|
textQuery.add(queryFactory.newTermQuery("infraSpecificEpithet", nvn.getInfraSpecificEpithet() + searchSuffix), Occur.SHOULD);
|
|
610
|
} else {
|
|
611
|
textQuery.add(new RegexQuery (new Term ("infraSpecificEpithet", "^[a-zA-Z]*")), Occur.MUST_NOT);
|
|
612
|
}
|
|
613
|
|
|
614
|
if(nvn.getAuthorshipCache() != null && !nvn.getAuthorshipCache().equals("")){
|
|
615
|
textQuery.add(queryFactory.newTermQuery("authorshipCache", nvn.getAuthorshipCache() + searchSuffix), Occur.SHOULD);
|
|
616
|
} else {
|
|
617
|
//textQuery.add(new RegexQuery (new Term ("authorshipCache", "^[a-zA-Z]*")), Occur.MUST_NOT);
|
|
618
|
}
|
|
619
|
|
|
620
|
finalQuery.add(textQuery, Occur.MUST);
|
|
621
|
|
|
622
|
luceneSearch.setQuery(finalQuery);
|
|
623
|
|
|
624
|
if(highlightFragments){
|
|
625
|
luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
|
|
626
|
}
|
|
627
|
return luceneSearch;
|
|
628
|
}
|
|
629
|
|
|
630
|
protected LuceneSearch prepareFindByExactNameSearch(Class<? extends CdmBase> clazz,
|
|
631
|
String name,
|
|
632
|
boolean wildcard,
|
|
633
|
List<Language> languages,
|
|
634
|
boolean highlightFragments) {
|
|
635
|
BooleanQuery finalQuery = new BooleanQuery();
|
|
636
|
BooleanQuery textQuery = new BooleanQuery();
|
|
637
|
|
|
638
|
LuceneSearch luceneSearch = new LuceneSearch(getSession(), TaxonNameBase.class);
|
|
639
|
QueryFactory queryFactory = new QueryFactory(luceneSearch);
|
|
640
|
|
|
641
|
SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};
|
|
642
|
luceneSearch.setSortFields(sortFields);
|
|
643
|
|
|
644
|
// ---- search criteria
|
|
645
|
luceneSearch.setClazz(clazz);
|
|
646
|
|
|
647
|
|
|
648
|
|
|
649
|
if(name != null && !name.equals("")) {
|
|
650
|
if(wildcard) {
|
|
651
|
textQuery.add(new WildcardQuery(new Term("nameCache", name + "*")), Occur.MUST);
|
|
652
|
} else {
|
|
653
|
textQuery.add(queryFactory.newTermQuery("nameCache", name, false), Occur.MUST);
|
|
654
|
}
|
|
655
|
}
|
|
656
|
|
|
657
|
finalQuery.add(textQuery, Occur.MUST);
|
|
658
|
|
|
659
|
luceneSearch.setQuery(textQuery);
|
|
660
|
|
|
661
|
if(highlightFragments){
|
|
662
|
luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
|
|
663
|
}
|
|
664
|
return luceneSearch;
|
|
665
|
}
|
|
666
|
|
|
667
|
public List<SearchResult<TaxonNameBase>> findByNameFuzzySearch(
|
|
668
|
String name,
|
|
669
|
float accuracy,
|
|
670
|
List<Language> languages,
|
|
671
|
boolean highlightFragments,
|
|
672
|
List<String> propertyPaths,
|
|
673
|
int maxNoOfResults) throws CorruptIndexException, IOException, ParseException {
|
|
674
|
|
|
675
|
logger.info("Name to fuzzy search for : " + name);
|
|
676
|
// parse the input name
|
|
677
|
NonViralNameParserImpl parser = new NonViralNameParserImpl();
|
|
678
|
NonViralName nvn = parser.parseFullName(name);
|
|
679
|
if(name != null && !name.equals("") && nvn == null) {
|
|
680
|
throw new ParseException("Could not parse name " + name);
|
|
681
|
}
|
|
682
|
LuceneSearch luceneSearch = prepareFindByFuzzyNameSearch(null, nvn, accuracy, languages, highlightFragments);
|
|
683
|
|
|
684
|
// --- execute search
|
|
685
|
TopDocs topDocs = luceneSearch.executeSearch(maxNoOfResults);
|
|
686
|
|
|
687
|
|
|
688
|
Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
|
|
689
|
idFieldMap.put(CdmBaseType.NONVIRALNAME, "id");
|
|
690
|
|
|
691
|
// --- initialize taxa, highlight matches ....
|
|
692
|
ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
|
|
693
|
|
|
694
|
@SuppressWarnings("rawtypes")
|
|
695
|
List<SearchResult<TaxonNameBase>> searchResults = searchResultBuilder.createResultSet(
|
|
696
|
topDocs, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
|
|
697
|
|
|
698
|
return searchResults;
|
|
699
|
|
|
700
|
}
|
|
701
|
|
|
702
|
public List<DocumentSearchResult> findByNameFuzzySearch(
|
|
703
|
String name,
|
|
704
|
float accuracy,
|
|
705
|
List<Language> languages,
|
|
706
|
boolean highlightFragments,
|
|
707
|
int maxNoOfResults) throws CorruptIndexException, IOException, ParseException {
|
|
708
|
|
|
709
|
logger.info("Name to fuzzy search for : " + name);
|
|
710
|
// parse the input name
|
|
711
|
NonViralNameParserImpl parser = new NonViralNameParserImpl();
|
|
712
|
NonViralName nvn = parser.parseFullName(name);
|
|
713
|
if(name != null && !name.equals("") && nvn == null) {
|
|
714
|
throw new ParseException("Could not parse name " + name);
|
|
715
|
}
|
|
716
|
LuceneSearch luceneSearch = prepareFindByFuzzyNameSearch(null, nvn, accuracy, languages, highlightFragments);
|
|
717
|
|
|
718
|
// --- execute search
|
|
719
|
TopDocs topDocs = luceneSearch.executeSearch(maxNoOfResults);
|
|
720
|
// for(int i = 0; i < topDocs.scoreDocs.length ; i++) {
|
|
721
|
// Explanation exp = luceneSearch.getSearcher().explain(luceneSearch.getQuery(), topDocs.scoreDocs[i].doc);
|
|
722
|
// System.out.println("-----------------------");
|
|
723
|
// System.out.println(exp.toString());
|
|
724
|
// }
|
|
725
|
|
|
726
|
Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
|
|
727
|
|
|
728
|
// --- initialize taxa, highlight matches ....
|
|
729
|
ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
|
|
730
|
|
|
731
|
@SuppressWarnings("rawtypes")
|
|
732
|
List<DocumentSearchResult> searchResults = searchResultBuilder.createResultSet(topDocs, luceneSearch.getHighlightFields());
|
|
733
|
|
|
734
|
return searchResults;
|
|
735
|
}
|
|
736
|
|
|
737
|
public List<DocumentSearchResult> findByNameExactSearch(
|
|
738
|
String name,
|
|
739
|
boolean wildcard,
|
|
740
|
List<Language> languages,
|
|
741
|
boolean highlightFragments,
|
|
742
|
int maxNoOfResults) throws CorruptIndexException, IOException, ParseException {
|
|
743
|
|
|
744
|
logger.info("Name to fuzzy search for : " + name);
|
|
745
|
|
|
746
|
LuceneSearch luceneSearch = prepareFindByExactNameSearch(null, name, wildcard, languages, highlightFragments);
|
|
747
|
|
|
748
|
// --- execute search
|
|
749
|
TopDocs topDocs = luceneSearch.executeSearch(maxNoOfResults);
|
|
750
|
Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
|
|
751
|
|
|
752
|
// --- initialize taxa, highlight matches ....
|
|
753
|
ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
|
|
754
|
|
|
755
|
@SuppressWarnings("rawtypes")
|
|
756
|
List<DocumentSearchResult> searchResults = searchResultBuilder.createResultSet(topDocs, luceneSearch.getHighlightFields());
|
|
757
|
|
|
758
|
return searchResults;
|
|
759
|
}
|
|
760
|
|
|
761
|
/* (non-Javadoc)
|
|
762
|
* @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)
|
|
763
|
*/
|
|
764
|
@Override
|
|
765
|
public Pager<NameRelationship> pageNameRelationships(TaxonNameBase name, Direction direction, NameRelationshipType type, Integer pageSize,
|
|
766
|
Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
767
|
List<NameRelationship> results = listNameRelationships(name, direction, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
768
|
return new DefaultPagerImpl<NameRelationship>(pageNumber, results.size(), pageSize, results);
|
|
769
|
}
|
|
770
|
|
|
771
|
@Override
|
|
772
|
public List<NameRelationship> listFromNameRelationships(TaxonNameBase name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
773
|
return listNameRelationships(name, Direction.relatedFrom, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
774
|
}
|
|
775
|
|
|
776
|
@Override
|
|
777
|
public Pager<NameRelationship> pageFromNameRelationships(TaxonNameBase name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
778
|
List<NameRelationship> results = listNameRelationships(name, Direction.relatedFrom, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
779
|
return new DefaultPagerImpl<NameRelationship>(pageNumber, results.size(), pageSize, results);
|
|
780
|
}
|
|
781
|
|
|
782
|
@Override
|
|
783
|
public List<NameRelationship> listToNameRelationships(TaxonNameBase name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
784
|
return listNameRelationships(name, Direction.relatedTo, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
785
|
}
|
|
786
|
|
|
787
|
@Override
|
|
788
|
public Pager<NameRelationship> pageToNameRelationships(TaxonNameBase name, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
789
|
List<NameRelationship> results = listNameRelationships(name, Direction.relatedTo, type, pageSize, pageNumber, orderHints, propertyPaths);
|
|
790
|
return new DefaultPagerImpl<NameRelationship>(pageNumber, results.size(), pageSize, results);
|
|
791
|
}
|
|
792
|
|
|
793
|
@Override
|
|
794
|
public Pager<TypeDesignationBase> getTypeDesignations(TaxonNameBase name, SpecimenTypeDesignationStatus status,
|
|
795
|
Integer pageSize, Integer pageNumber) {
|
|
796
|
return getTypeDesignations(name, status, pageSize, pageNumber, null);
|
|
797
|
}
|
|
798
|
|
|
799
|
@Override
|
|
800
|
public Pager<TypeDesignationBase> getTypeDesignations(TaxonNameBase name, SpecimenTypeDesignationStatus status,
|
|
801
|
Integer pageSize, Integer pageNumber, List<String> propertyPaths){
|
|
802
|
Integer numberOfResults = dao.countTypeDesignations(name, status);
|
|
803
|
|
|
804
|
List<TypeDesignationBase> results = new ArrayList<TypeDesignationBase>();
|
|
805
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
806
|
results = dao.getTypeDesignations(name, status, pageSize, pageNumber, propertyPaths);
|
|
807
|
}
|
|
808
|
|
|
809
|
return new DefaultPagerImpl<TypeDesignationBase>(pageNumber, numberOfResults, pageSize, results);
|
|
810
|
}
|
|
811
|
|
|
812
|
/**
|
|
813
|
* FIXME Candidate for harmonization
|
|
814
|
* rename search
|
|
815
|
*/
|
|
816
|
@Override
|
|
817
|
public Pager<TaxonNameBase> searchNames(String uninomial,String infraGenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
|
818
|
List<String> propertyPaths) {
|
|
819
|
Integer numberOfResults = dao.countNames(uninomial, infraGenericEpithet, specificEpithet, infraspecificEpithet, rank);
|
|
820
|
|
|
821
|
List<TaxonNameBase> results = new ArrayList<TaxonNameBase>();
|
|
822
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
823
|
results = dao.searchNames(uninomial, infraGenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber, orderHints, propertyPaths);
|
|
824
|
}
|
|
825
|
|
|
826
|
return new DefaultPagerImpl<TaxonNameBase>(pageNumber, numberOfResults, pageSize, results);
|
|
827
|
}
|
|
828
|
|
|
829
|
/* (non-Javadoc)
|
|
830
|
* @see eu.etaxonomy.cdm.api.service.INameService#getUuidAndTitleCacheOfNames()
|
|
831
|
*/
|
|
832
|
@Override
|
|
833
|
public List<UuidAndTitleCache> getUuidAndTitleCacheOfNames() {
|
|
834
|
return dao.getUuidAndTitleCacheOfNames();
|
|
835
|
}
|
|
836
|
|
|
837
|
@Override
|
|
838
|
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) {
|
|
839
|
Integer numberOfResults = dao.countByName(clazz, queryString, matchmode, criteria);
|
|
840
|
|
|
841
|
List<TaxonNameBase> results = new ArrayList<TaxonNameBase>();
|
|
842
|
if(numberOfResults > 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
|
|
843
|
results = dao.findByName(clazz, queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
|
|
844
|
}
|
|
845
|
|
|
846
|
return new DefaultPagerImpl<TaxonNameBase>(pageNumber, numberOfResults, pageSize, results);
|
|
847
|
}
|
|
848
|
|
|
849
|
@Override
|
|
850
|
public HomotypicalGroup findHomotypicalGroup(UUID uuid) {
|
|
851
|
return homotypicalGroupDao.findByUuid(uuid);
|
|
852
|
}
|
|
853
|
|
|
854
|
|
|
855
|
/* (non-Javadoc)
|
|
856
|
* @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
|
|
857
|
*/
|
|
858
|
@Override
|
|
859
|
@Transactional(readOnly = false)
|
|
860
|
public void updateTitleCache(Class<? extends TaxonNameBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<TaxonNameBase> cacheStrategy, IProgressMonitor monitor) {
|
|
861
|
if (clazz == null){
|
|
862
|
clazz = TaxonNameBase.class;
|
|
863
|
}
|
|
864
|
super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
|
|
865
|
}
|
|
866
|
|
|
867
|
|
|
868
|
@Override
|
|
869
|
protected void setOtherCachesNull(TaxonNameBase name) {
|
|
870
|
if (name.isInstanceOf(NonViralName.class)){
|
|
871
|
NonViralName<?> nvn = CdmBase.deproxy(name, NonViralName.class);
|
|
872
|
if (! nvn.isProtectedNameCache()){
|
|
873
|
nvn.setNameCache(null, false);
|
|
874
|
}
|
|
875
|
if (! nvn.isProtectedAuthorshipCache()){
|
|
876
|
nvn.setAuthorshipCache(null, false);
|
|
877
|
}
|
|
878
|
if (! nvn.isProtectedFullTitleCache()){
|
|
879
|
nvn.setFullTitleCache(null, false);
|
|
880
|
}
|
|
881
|
}
|
|
882
|
}
|
|
883
|
|
|
884
|
/* (non-Javadoc)
|
|
885
|
* @see eu.etaxonomy.cdm.api.service.INameService#getTaggedName(eu.etaxonomy.cdm.model.name.TaxonNameBase)
|
|
886
|
*/
|
|
887
|
@Override
|
|
888
|
public List<TaggedText> getTaggedName(UUID uuid) {
|
|
889
|
TaxonNameBase taxonNameBase = dao.load(uuid);
|
|
890
|
List taggedName = taxonNameBase.getTaggedName();
|
|
891
|
return taggedName;
|
|
892
|
}
|
|
893
|
|
|
894
|
|
|
895
|
}
|