| 1 |
dfcd94fb
|
Andreas Kohlbecker
|
// $Id$
|
| 2 |
25663b56
|
Andreas Müller
|
/**
|
| 3 |
|
|
* Copyright (C) 2007 EDIT
|
| 4 |
|
|
* European Distributed Institute of Taxonomy
|
| 5 |
|
|
* http://www.e-taxonomy.eu
|
| 6 |
|
|
*
|
| 7 |
|
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
| 8 |
|
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
| 9 |
|
|
*/
|
| 10 |
|
|
|
| 11 |
2d993c6e
|
Andreas Müller
|
package eu.etaxonomy.cdm.api.service;
|
| 12 |
|
|
|
| 13 |
d57c0df0
|
ben.clark
|
import java.util.ArrayList;
|
| 14 |
d391964a
|
Andreas Kohlbecker
|
import java.util.Comparator;
|
| 15 |
d57c0df0
|
ben.clark
|
import java.util.List;
|
| 16 |
|
|
import java.util.Set;
|
| 17 |
|
|
import java.util.UUID;
|
| 18 |
|
|
|
| 19 |
2d993c6e
|
Andreas Müller
|
import org.apache.log4j.Logger;
|
| 20 |
|
|
import org.springframework.beans.factory.annotation.Autowired;
|
| 21 |
|
|
import org.springframework.stereotype.Service;
|
| 22 |
2a56d8c1
|
ben.clark
|
import org.springframework.transaction.annotation.Propagation;
|
| 23 |
2d993c6e
|
Andreas Müller
|
import org.springframework.transaction.annotation.Transactional;
|
| 24 |
|
|
|
| 25 |
24700eab
|
a.babadshanjan
|
import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;
|
| 26 |
a6f05c62
|
Andreas Müller
|
import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;
|
| 27 |
d57c0df0
|
ben.clark
|
import eu.etaxonomy.cdm.api.service.pager.Pager;
|
| 28 |
|
|
import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
|
| 29 |
f197a589
|
Andreas Müller
|
import eu.etaxonomy.cdm.common.IProgressMonitor;
|
| 30 |
b6cb1182
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
| 31 |
24700eab
|
a.babadshanjan
|
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
|
| 32 |
|
|
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
|
| 33 |
7a931ddb
|
a.babadshanjan
|
import eu.etaxonomy.cdm.model.common.RelationshipBase;
|
| 34 |
b6cb1182
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
|
| 35 |
2eecc314
|
n.hoffmann
|
import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
|
| 36 |
b79861eb
|
Katja Luther
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
| 37 |
02cf6cb7
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
| 38 |
b79861eb
|
Katja Luther
|
import eu.etaxonomy.cdm.model.media.Media;
|
| 39 |
|
|
import eu.etaxonomy.cdm.model.media.MediaRepresentation;
|
| 40 |
892efc69
|
Andreas Kohlbecker
|
import eu.etaxonomy.cdm.model.media.MediaUtils;
|
| 41 |
9b62c409
|
Andreas Kohlbecker
|
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
|
| 42 |
d57c0df0
|
ben.clark
|
import eu.etaxonomy.cdm.model.name.Rank;
|
| 43 |
02cf6cb7
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
| 44 |
1d36aa54
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
| 45 |
15ce3c9c
|
n.hoffmann
|
import eu.etaxonomy.cdm.model.taxon.Classification;
|
| 46 |
02cf6cb7
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
| 47 |
|
|
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
|
| 48 |
|
|
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
|
| 49 |
2d993c6e
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
| 50 |
|
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
| 51 |
a6f05c62
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
| 52 |
281bc0c7
|
Andreas Müller
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
|
| 53 |
|
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
|
| 54 |
24700eab
|
a.babadshanjan
|
import eu.etaxonomy.cdm.persistence.dao.common.IOrderedTermVocabularyDao;
|
| 55 |
|
|
import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;
|
| 56 |
2d993c6e
|
Andreas Müller
|
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
|
| 57 |
855f3dd0
|
Andreas Müller
|
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
|
| 58 |
65c22e25
|
Andreas Kohlbecker
|
import eu.etaxonomy.cdm.persistence.query.MatchMode;
|
| 59 |
d44277a9
|
ben.clark
|
import eu.etaxonomy.cdm.persistence.query.OrderHint;
|
| 60 |
f197a589
|
Andreas Müller
|
import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
|
| 61 |
2d993c6e
|
Andreas Müller
|
|
| 62 |
|
|
|
| 63 |
65c22e25
|
Andreas Kohlbecker
|
/**
|
| 64 |
|
|
* @author a.kohlbecker
|
| 65 |
|
|
* @date 10.09.2010
|
| 66 |
|
|
*
|
| 67 |
|
|
*/
|
| 68 |
2d993c6e
|
Andreas Müller
|
@Service
|
| 69 |
2a56d8c1
|
ben.clark
|
@Transactional(propagation = Propagation.SUPPORTS, readOnly = true)
|
| 70 |
01c21ead
|
n.hoffmann
|
public class TaxonServiceImpl extends IdentifiableServiceBase<TaxonBase,ITaxonDao> implements ITaxonService{
|
| 71 |
800cb472
|
Andreas Müller
|
private static final Logger logger = Logger.getLogger(TaxonServiceImpl.class);
|
| 72 |
2d993c6e
|
Andreas Müller
|
|
| 73 |
24700eab
|
a.babadshanjan
|
@Autowired
|
| 74 |
|
|
private ITaxonNameDao nameDao;
|
| 75 |
e0dbe59a
|
ben.clark
|
|
| 76 |
24700eab
|
a.babadshanjan
|
@Autowired
|
| 77 |
|
|
private IOrderedTermVocabularyDao orderedVocabularyDao;
|
| 78 |
7a1d87e3
|
a.babadshanjan
|
|
| 79 |
|
|
/**
|
| 80 |
|
|
* Constructor
|
| 81 |
|
|
*/
|
| 82 |
|
|
public TaxonServiceImpl(){
|
| 83 |
|
|
if (logger.isDebugEnabled()) { logger.debug("Load TaxonService Bean"); }
|
| 84 |
|
|
}
|
| 85 |
2d993c6e
|
Andreas Müller
|
|
| 86 |
e0dbe59a
|
ben.clark
|
/**
|
| 87 |
|
|
* FIXME Candidate for harmonization
|
| 88 |
|
|
* rename searchByName ?
|
| 89 |
|
|
*/
|
| 90 |
1d36aa54
|
Andreas Müller
|
public List<TaxonBase> searchTaxaByName(String name, Reference sec) {
|
| 91 |
d57c0df0
|
ben.clark
|
return dao.getTaxaByName(name, sec);
|
| 92 |
2d993c6e
|
Andreas Müller
|
}
|
| 93 |
c4e812bc
|
ben.clark
|
|
| 94 |
e0dbe59a
|
ben.clark
|
/**
|
| 95 |
|
|
* FIXME Candidate for harmonization
|
| 96 |
c4e812bc
|
ben.clark
|
* list(Synonym.class, ...)
|
| 97 |
e0dbe59a
|
ben.clark
|
* (non-Javadoc)
|
| 98 |
c4e812bc
|
ben.clark
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllSynonyms(int, int)
|
| 99 |
d93c0aaf
|
Andreas Müller
|
*/
|
| 100 |
c4e812bc
|
ben.clark
|
public List<Synonym> getAllSynonyms(int limit, int start) {
|
| 101 |
|
|
return dao.getAllSynonyms(limit, start);
|
| 102 |
07eb2b2b
|
a.babadshanjan
|
}
|
| 103 |
|
|
|
| 104 |
e0dbe59a
|
ben.clark
|
/**
|
| 105 |
|
|
* FIXME Candidate for harmonization
|
| 106 |
c4e812bc
|
ben.clark
|
* list(Taxon.class, ...)
|
| 107 |
e0dbe59a
|
ben.clark
|
* (non-Javadoc)
|
| 108 |
c4e812bc
|
ben.clark
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllTaxa(int, int)
|
| 109 |
d93c0aaf
|
Andreas Müller
|
*/
|
| 110 |
c4e812bc
|
ben.clark
|
public List<Taxon> getAllTaxa(int limit, int start) {
|
| 111 |
|
|
return dao.getAllTaxa(limit, start);
|
| 112 |
643cfd14
|
a.babadshanjan
|
}
|
| 113 |
d93c0aaf
|
Andreas Müller
|
|
| 114 |
e0dbe59a
|
ben.clark
|
/**
|
| 115 |
|
|
* FIXME Candidate for harmonization
|
| 116 |
1d36aa54
|
Andreas Müller
|
* merge with getRootTaxa(Reference sec, ..., ...)
|
| 117 |
e0dbe59a
|
ben.clark
|
* (non-Javadoc)
|
| 118 |
1d36aa54
|
Andreas Müller
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference, boolean)
|
| 119 |
855f3dd0
|
Andreas Müller
|
*/
|
| 120 |
1d36aa54
|
Andreas Müller
|
public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, boolean onlyWithChildren) {
|
| 121 |
855f3dd0
|
Andreas Müller
|
if (cdmFetch == null){
|
| 122 |
|
|
cdmFetch = CdmFetch.NO_FETCH();
|
| 123 |
|
|
}
|
| 124 |
d57c0df0
|
ben.clark
|
return dao.getRootTaxa(sec, cdmFetch, onlyWithChildren, false);
|
| 125 |
349fae93
|
Andreas Müller
|
}
|
| 126 |
1fce1de6
|
Andreas Müller
|
|
| 127 |
a400a105
|
m.doering
|
|
| 128 |
7a1d87e3
|
a.babadshanjan
|
/* (non-Javadoc)
|
| 129 |
1d36aa54
|
Andreas Müller
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.name.Rank, eu.etaxonomy.cdm.model.reference.Reference, boolean, boolean)
|
| 130 |
7a1d87e3
|
a.babadshanjan
|
*/
|
| 131 |
1fce1de6
|
Andreas Müller
|
public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren,boolean withMisapplications, List<String> propertyPaths) {
|
| 132 |
9b62c409
|
Andreas Kohlbecker
|
return dao.getRootTaxa(rank, sec, null, onlyWithChildren, withMisapplications, propertyPaths);
|
| 133 |
7a1d87e3
|
a.babadshanjan
|
}
|
| 134 |
|
|
|
| 135 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 136 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllRelationships(int, int)
|
| 137 |
|
|
*/
|
| 138 |
7a931ddb
|
a.babadshanjan
|
public List<RelationshipBase> getAllRelationships(int limit, int start){
|
| 139 |
d57c0df0
|
ben.clark
|
return dao.getAllRelationships(limit, start);
|
| 140 |
7a931ddb
|
a.babadshanjan
|
}
|
| 141 |
|
|
|
| 142 |
e0dbe59a
|
ben.clark
|
/**
|
| 143 |
|
|
* FIXME Candidate for harmonization
|
| 144 |
|
|
* is this the same as termService.getVocabulary(VocabularyEnum.TaxonRelationshipType) ?
|
| 145 |
|
|
*/
|
| 146 |
bb4f5701
|
n.hoffmann
|
@Deprecated
|
| 147 |
24700eab
|
a.babadshanjan
|
public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary() {
|
| 148 |
|
|
|
| 149 |
|
|
String taxonRelTypeVocabularyId = "15db0cf7-7afc-4a86-a7d4-221c73b0c9ac";
|
| 150 |
|
|
UUID uuid = UUID.fromString(taxonRelTypeVocabularyId);
|
| 151 |
|
|
OrderedTermVocabulary<TaxonRelationshipType> taxonRelTypeVocabulary =
|
| 152 |
|
|
(OrderedTermVocabulary)orderedVocabularyDao.findByUuid(uuid);
|
| 153 |
|
|
return taxonRelTypeVocabulary;
|
| 154 |
|
|
}
|
| 155 |
|
|
|
| 156 |
fd992c0d
|
n.hoffmann
|
|
| 157 |
02cf6cb7
|
Andreas Müller
|
|
| 158 |
f4cfc931
|
n.hoffmann
|
/*
|
| 159 |
|
|
* (non-Javadoc)
|
| 160 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#swapSynonymWithAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym)
|
| 161 |
|
|
*/
|
| 162 |
|
|
@Transactional(readOnly = false)
|
| 163 |
7d8e086d
|
n.hoffmann
|
public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon){
|
| 164 |
f4cfc931
|
n.hoffmann
|
|
| 165 |
7d8e086d
|
n.hoffmann
|
TaxonNameBase synonymName = synonym.getName();
|
| 166 |
|
|
synonymName.removeTaxonBase(synonym);
|
| 167 |
|
|
TaxonNameBase taxonName = acceptedTaxon.getName();
|
| 168 |
|
|
taxonName.removeTaxonBase(acceptedTaxon);
|
| 169 |
f4cfc931
|
n.hoffmann
|
|
| 170 |
7d8e086d
|
n.hoffmann
|
synonym.setName(taxonName);
|
| 171 |
|
|
acceptedTaxon.setName(synonymName);
|
| 172 |
8a433654
|
n.hoffmann
|
|
| 173 |
7d8e086d
|
n.hoffmann
|
// the accepted taxon needs a new uuid because the concept has changed
|
| 174 |
|
|
// FIXME this leads to an error "HibernateException: immutable natural identifier of an instance of eu.etaxonomy.cdm.model.taxon.Taxon was altered"
|
| 175 |
|
|
//acceptedTaxon.setUuid(UUID.randomUUID());
|
| 176 |
f4cfc931
|
n.hoffmann
|
}
|
| 177 |
892efc69
|
Andreas Kohlbecker
|
|
| 178 |
af8f90fb
|
n.hoffmann
|
|
| 179 |
0fe25ffd
|
Andreas Müller
|
/* (non-Javadoc)
|
| 180 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeSynonymToAcceptedTaxon(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.Taxon)
|
| 181 |
|
|
*/
|
| 182 |
ffa78fd4
|
Andreas Müller
|
//TODO correct delete handling still needs to be implemented / checked
|
| 183 |
aee5abae
|
Andreas Müller
|
@Override
|
| 184 |
ffa78fd4
|
Andreas Müller
|
@Transactional(readOnly = false)
|
| 185 |
aee5abae
|
Andreas Müller
|
public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym, boolean copyCitationInfo, Reference citation, String microCitation) throws IllegalArgumentException{
|
| 186 |
|
|
|
| 187 |
|
|
TaxonNameBase acceptedName = acceptedTaxon.getName();
|
| 188 |
|
|
TaxonNameBase synonymName = synonym.getName();
|
| 189 |
|
|
HomotypicalGroup synonymHomotypicGroup = synonymName.getHomotypicalGroup();
|
| 190 |
|
|
if (acceptedName.getHomotypicalGroup().equals(synonymHomotypicGroup)){
|
| 191 |
|
|
String message = "The accepted taxon and the synonym are part of the same homotypical group and therefore can not be both accepted.";
|
| 192 |
|
|
throw new IllegalArgumentException(message);
|
| 193 |
|
|
}
|
| 194 |
af8f90fb
|
n.hoffmann
|
|
| 195 |
ad3249f9
|
Katja Luther
|
Taxon newAcceptedTaxon = Taxon.NewInstance(synonymName, acceptedTaxon.getSec());
|
| 196 |
af8f90fb
|
n.hoffmann
|
|
| 197 |
aee5abae
|
Andreas Müller
|
SynonymRelationshipType relType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
|
| 198 |
|
|
List<Synonym> heteroSynonyms = synonymHomotypicGroup.getSynonymsInGroup(acceptedTaxon.getSec());
|
| 199 |
|
|
for (Synonym heteroSynonym : heteroSynonyms){
|
| 200 |
|
|
if (synonym.equals(heteroSynonym)){
|
| 201 |
|
|
acceptedTaxon.removeSynonym(heteroSynonym, false);
|
| 202 |
|
|
}else{
|
| 203 |
|
|
heteroSynonym.replaceAcceptedTaxon(newAcceptedTaxon, relType, copyCitationInfo, citation, microCitation);
|
| 204 |
|
|
}
|
| 205 |
|
|
}
|
| 206 |
|
|
|
| 207 |
ad3249f9
|
Katja Luther
|
//synonym.getName().removeTaxonBase(synonym);
|
| 208 |
ffa78fd4
|
Andreas Müller
|
//TODO correct delete handling still needs to be implemented / checked
|
| 209 |
aee5abae
|
Andreas Müller
|
if (deleteSynonym){
|
| 210 |
|
|
try {
|
| 211 |
ad3249f9
|
Katja Luther
|
this.dao.flush();
|
| 212 |
aee5abae
|
Andreas Müller
|
this.delete(synonym);
|
| 213 |
ad3249f9
|
Katja Luther
|
|
| 214 |
aee5abae
|
Andreas Müller
|
} catch (Exception e) {
|
| 215 |
|
|
logger.info("Can't delete old synonym from database");
|
| 216 |
|
|
}
|
| 217 |
|
|
}
|
| 218 |
|
|
|
| 219 |
ffa78fd4
|
Andreas Müller
|
|
| 220 |
af8f90fb
|
n.hoffmann
|
return newAcceptedTaxon;
|
| 221 |
|
|
}
|
| 222 |
636d99d1
|
n.hoffmann
|
|
| 223 |
1d36aa54
|
Andreas Müller
|
public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference citation, String microcitation){
|
| 224 |
636d99d1
|
n.hoffmann
|
|
| 225 |
|
|
// Get name from synonym
|
| 226 |
|
|
TaxonNameBase<?, ?> synonymName = synonym.getName();
|
| 227 |
|
|
|
| 228 |
|
|
// remove synonym from taxon
|
| 229 |
|
|
toTaxon.removeSynonym(synonym);
|
| 230 |
|
|
|
| 231 |
|
|
// Create a taxon with synonym name
|
| 232 |
|
|
Taxon fromTaxon = Taxon.NewInstance(synonymName, null);
|
| 233 |
|
|
|
| 234 |
|
|
// Add taxon relation
|
| 235 |
|
|
fromTaxon.addTaxonRelation(toTaxon, taxonRelationshipType, citation, microcitation);
|
| 236 |
|
|
|
| 237 |
|
|
// since we are swapping names, we have to detach the name from the synonym completely.
|
| 238 |
|
|
// Otherwise the synonym will still be in the list of typified names.
|
| 239 |
|
|
synonym.getName().removeTaxonBase(synonym);
|
| 240 |
|
|
|
| 241 |
|
|
return fromTaxon;
|
| 242 |
|
|
}
|
| 243 |
ffa78fd4
|
Andreas Müller
|
|
| 244 |
1188e04a
|
Andreas Müller
|
/* (non-Javadoc)
|
| 245 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#changeHomotypicalGroupOfSynonym(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.name.HomotypicalGroup, eu.etaxonomy.cdm.model.taxon.Taxon, boolean, boolean)
|
| 246 |
|
|
*/
|
| 247 |
|
|
@Transactional(readOnly = false)
|
| 248 |
|
|
@Override
|
| 249 |
|
|
public void changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup, Taxon targetTaxon,
|
| 250 |
|
|
boolean removeFromOtherTaxa, boolean setBasionymRelationIfApplicable){
|
| 251 |
|
|
// Get synonym name
|
| 252 |
|
|
TaxonNameBase synonymName = synonym.getName();
|
| 253 |
|
|
HomotypicalGroup oldHomotypicalGroup = synonymName.getHomotypicalGroup();
|
| 254 |
|
|
|
| 255 |
|
|
|
| 256 |
|
|
// Switch groups
|
| 257 |
|
|
oldHomotypicalGroup.removeTypifiedName(synonymName);
|
| 258 |
|
|
newHomotypicalGroup.addTypifiedName(synonymName);
|
| 259 |
|
|
|
| 260 |
|
|
//remove existing basionym relationships
|
| 261 |
|
|
synonymName.removeBasionyms();
|
| 262 |
|
|
|
| 263 |
|
|
//add basionym relationship
|
| 264 |
|
|
if (setBasionymRelationIfApplicable){
|
| 265 |
|
|
Set<TaxonNameBase> basionyms = newHomotypicalGroup.getBasionyms();
|
| 266 |
|
|
for (TaxonNameBase basionym : basionyms){
|
| 267 |
|
|
synonymName.addBasionym(basionym);
|
| 268 |
|
|
}
|
| 269 |
|
|
}
|
| 270 |
|
|
|
| 271 |
|
|
//set synonym relationship correctly
|
| 272 |
|
|
// SynonymRelationship relToTaxon = null;
|
| 273 |
|
|
boolean relToTargetTaxonExists = false;
|
| 274 |
|
|
Set<SynonymRelationship> existingRelations = synonym.getSynonymRelations();
|
| 275 |
|
|
for (SynonymRelationship rel : existingRelations){
|
| 276 |
|
|
Taxon acceptedTaxon = rel.getAcceptedTaxon();
|
| 277 |
|
|
boolean isTargetTaxon = acceptedTaxon != null && acceptedTaxon.equals(targetTaxon);
|
| 278 |
|
|
HomotypicalGroup acceptedGroup = acceptedTaxon.getHomotypicGroup();
|
| 279 |
|
|
boolean isHomotypicToTaxon = acceptedGroup.equals(newHomotypicalGroup);
|
| 280 |
|
|
SynonymRelationshipType newRelationType = isHomotypicToTaxon? SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF() : SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
|
| 281 |
|
|
rel.setType(newRelationType);
|
| 282 |
|
|
//TODO handle citation and microCitation
|
| 283 |
|
|
|
| 284 |
|
|
if (isTargetTaxon){
|
| 285 |
|
|
relToTargetTaxonExists = true;
|
| 286 |
|
|
}else{
|
| 287 |
|
|
if (removeFromOtherTaxa){
|
| 288 |
|
|
acceptedTaxon.removeSynonym(synonym, false);
|
| 289 |
|
|
}else{
|
| 290 |
|
|
//do nothing
|
| 291 |
|
|
}
|
| 292 |
|
|
}
|
| 293 |
|
|
}
|
| 294 |
|
|
if (targetTaxon != null && ! relToTargetTaxonExists ){
|
| 295 |
|
|
Taxon acceptedTaxon = targetTaxon;
|
| 296 |
|
|
HomotypicalGroup acceptedGroup = acceptedTaxon.getHomotypicGroup();
|
| 297 |
|
|
boolean isHomotypicToTaxon = acceptedGroup.equals(newHomotypicalGroup);
|
| 298 |
|
|
SynonymRelationshipType relType = isHomotypicToTaxon? SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF() : SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
|
| 299 |
|
|
//TODO handle citation and microCitation
|
| 300 |
|
|
Reference citation = null;
|
| 301 |
|
|
String microCitation = null;
|
| 302 |
|
|
acceptedTaxon.addSynonym(synonym, relType, citation, microCitation);
|
| 303 |
|
|
}
|
| 304 |
|
|
|
| 305 |
|
|
}
|
| 306 |
|
|
|
| 307 |
a400a105
|
m.doering
|
|
| 308 |
b17d9121
|
Andreas Müller
|
/* (non-Javadoc)
|
| 309 |
f197a589
|
Andreas Müller
|
* @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
|
| 310 |
b17d9121
|
Andreas Müller
|
*/
|
| 311 |
|
|
@Override
|
| 312 |
f197a589
|
Andreas Müller
|
public void updateTitleCache(Class<? extends TaxonBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<TaxonBase> cacheStrategy, IProgressMonitor monitor) {
|
| 313 |
|
|
if (clazz == null){
|
| 314 |
|
|
clazz = TaxonBase.class;
|
| 315 |
|
|
}
|
| 316 |
|
|
super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
|
| 317 |
a400a105
|
m.doering
|
}
|
| 318 |
f197a589
|
Andreas Müller
|
|
| 319 |
d57c0df0
|
ben.clark
|
@Autowired
|
| 320 |
|
|
protected void setDao(ITaxonDao dao) {
|
| 321 |
|
|
this.dao = dao;
|
| 322 |
|
|
}
|
| 323 |
|
|
|
| 324 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 325 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)
|
| 326 |
|
|
*/
|
| 327 |
a9e5cd74
|
ben.clark
|
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
| 328 |
|
|
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);
|
| 329 |
d57c0df0
|
ben.clark
|
|
| 330 |
|
|
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
| 331 |
|
|
if(numberOfResults > 0) { // no point checking again
|
| 332 |
a9e5cd74
|
ben.clark
|
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
|
| 333 |
d57c0df0
|
ben.clark
|
}
|
| 334 |
|
|
|
| 335 |
|
|
return new DefaultPagerImpl<TaxonBase>(pageNumber, numberOfResults, pageSize, results);
|
| 336 |
|
|
}
|
| 337 |
|
|
|
| 338 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 339 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listTaxaByName(java.lang.Class, java.lang.String, java.lang.String, java.lang.String, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, java.lang.Integer, java.lang.Integer)
|
| 340 |
|
|
*/
|
| 341 |
eaf661e6
|
em.lee
|
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize,Integer pageNumber) {
|
| 342 |
|
|
Integer numberOfResults = dao.countTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank);
|
| 343 |
|
|
|
| 344 |
|
|
List<TaxonBase> results = new ArrayList<TaxonBase>();
|
| 345 |
|
|
if(numberOfResults > 0) { // no point checking again
|
| 346 |
|
|
results = dao.findTaxaByName(clazz, uninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, rank, pageSize, pageNumber);
|
| 347 |
|
|
}
|
| 348 |
|
|
|
| 349 |
|
|
return results;
|
| 350 |
|
|
}
|
| 351 |
|
|
|
| 352 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 353 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
| 354 |
|
|
*/
|
| 355 |
d40f8755
|
Andreas Kohlbecker
|
public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
|
| 356 |
|
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);
|
| 357 |
d57c0df0
|
ben.clark
|
|
| 358 |
|
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
| 359 |
|
|
if(numberOfResults > 0) { // no point checking again
|
| 360 |
d40f8755
|
Andreas Kohlbecker
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo);
|
| 361 |
d57c0df0
|
ben.clark
|
}
|
| 362 |
d40f8755
|
Andreas Kohlbecker
|
return results;
|
| 363 |
|
|
}
|
| 364 |
|
|
|
| 365 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 366 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageToTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
| 367 |
|
|
*/
|
| 368 |
d40f8755
|
Andreas Kohlbecker
|
public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 369 |
cba96ea5
|
ben.clark
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedTo);
|
| 370 |
|
|
|
| 371 |
|
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
| 372 |
|
|
if(numberOfResults > 0) { // no point checking again
|
| 373 |
|
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedTo);
|
| 374 |
|
|
}
|
| 375 |
|
|
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results);
|
| 376 |
d40f8755
|
Andreas Kohlbecker
|
}
|
| 377 |
|
|
|
| 378 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 379 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
| 380 |
|
|
*/
|
| 381 |
d40f8755
|
Andreas Kohlbecker
|
public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths){
|
| 382 |
|
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom);
|
| 383 |
d57c0df0
|
ben.clark
|
|
| 384 |
d40f8755
|
Andreas Kohlbecker
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
| 385 |
|
|
if(numberOfResults > 0) { // no point checking again
|
| 386 |
|
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom);
|
| 387 |
|
|
}
|
| 388 |
|
|
return results;
|
| 389 |
|
|
}
|
| 390 |
|
|
|
| 391 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 392 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#pageFromTaxonRelationships(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
| 393 |
|
|
*/
|
| 394 |
d40f8755
|
Andreas Kohlbecker
|
public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 395 |
cba96ea5
|
ben.clark
|
Integer numberOfResults = dao.countTaxonRelationships(taxon, type, TaxonRelationship.Direction.relatedFrom);
|
| 396 |
|
|
|
| 397 |
|
|
List<TaxonRelationship> results = new ArrayList<TaxonRelationship>();
|
| 398 |
|
|
if(numberOfResults > 0) { // no point checking again
|
| 399 |
|
|
results = dao.getTaxonRelationships(taxon, type, pageSize, pageNumber, orderHints, propertyPaths, TaxonRelationship.Direction.relatedFrom);
|
| 400 |
|
|
}
|
| 401 |
|
|
return new DefaultPagerImpl<TaxonRelationship>(pageNumber, numberOfResults, pageSize, results);
|
| 402 |
d57c0df0
|
ben.clark
|
}
|
| 403 |
|
|
|
| 404 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 405 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getSynonyms(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
| 406 |
|
|
*/
|
| 407 |
d44277a9
|
ben.clark
|
public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 408 |
d57c0df0
|
ben.clark
|
Integer numberOfResults = dao.countSynonyms(taxon, type);
|
| 409 |
|
|
|
| 410 |
|
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
| 411 |
|
|
if(numberOfResults > 0) { // no point checking again
|
| 412 |
d44277a9
|
ben.clark
|
results = dao.getSynonyms(taxon, type, pageSize, pageNumber, orderHints, propertyPaths);
|
| 413 |
d57c0df0
|
ben.clark
|
}
|
| 414 |
|
|
|
| 415 |
|
|
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
| 416 |
|
|
}
|
| 417 |
9b62c409
|
Andreas Kohlbecker
|
|
| 418 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 419 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getSynonyms(eu.etaxonomy.cdm.model.taxon.Synonym, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
|
| 420 |
|
|
*/
|
| 421 |
219ab499
|
ben.clark
|
public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
| 422 |
|
|
Integer numberOfResults = dao.countSynonyms(synonym, type);
|
| 423 |
|
|
|
| 424 |
|
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
| 425 |
|
|
if(numberOfResults > 0) { // no point checking again
|
| 426 |
|
|
results = dao.getSynonyms(synonym, type, pageSize, pageNumber, orderHints, propertyPaths);
|
| 427 |
|
|
}
|
| 428 |
|
|
|
| 429 |
|
|
return new DefaultPagerImpl<SynonymRelationship>(pageNumber, numberOfResults, pageSize, results);
|
| 430 |
|
|
}
|
| 431 |
|
|
|
| 432 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 433 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHomotypicSynonymsByHomotypicGroup(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)
|
| 434 |
|
|
*/
|
| 435 |
9b62c409
|
Andreas Kohlbecker
|
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths){
|
| 436 |
|
|
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
| 437 |
|
|
return t.getHomotypicSynonymsByHomotypicGroup();
|
| 438 |
|
|
}
|
| 439 |
|
|
|
| 440 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 441 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getHeterotypicSynonymyGroups(eu.etaxonomy.cdm.model.taxon.Taxon, java.util.List)
|
| 442 |
|
|
*/
|
| 443 |
9b62c409
|
Andreas Kohlbecker
|
public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths){
|
| 444 |
|
|
Taxon t = (Taxon)dao.load(taxon.getUuid(), propertyPaths);
|
| 445 |
|
|
List<HomotypicalGroup> hsgl = t.getHeterotypicSynonymyGroups();
|
| 446 |
|
|
List<List<Synonym>> heterotypicSynonymyGroups = new ArrayList<List<Synonym>>(hsgl.size());
|
| 447 |
|
|
for(HomotypicalGroup hsg : hsgl){
|
| 448 |
|
|
heterotypicSynonymyGroups.add(hsg.getSynonymsInGroup(t.getSec()));
|
| 449 |
|
|
}
|
| 450 |
|
|
return heterotypicSynonymyGroups;
|
| 451 |
|
|
}
|
| 452 |
24700eab
|
a.babadshanjan
|
|
| 453 |
e66d9d39
|
Katja Luther
|
public List<UuidAndTitleCache<TaxonBase>> findTaxaAndNamesForEditor(ITaxonServiceConfigurator configurator){
|
| 454 |
|
|
|
| 455 |
|
|
List<UuidAndTitleCache<TaxonBase>> result = new ArrayList<UuidAndTitleCache<TaxonBase>>();
|
| 456 |
|
|
Class<? extends TaxonBase> clazz = null;
|
| 457 |
|
|
if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {
|
| 458 |
|
|
clazz = TaxonBase.class;
|
| 459 |
|
|
//propertyPath.addAll(configurator.getTaxonPropertyPath());
|
| 460 |
|
|
//propertyPath.addAll(configurator.getSynonymPropertyPath());
|
| 461 |
|
|
} else if(configurator.isDoTaxa()) {
|
| 462 |
|
|
clazz = Taxon.class;
|
| 463 |
|
|
//propertyPath = configurator.getTaxonPropertyPath();
|
| 464 |
|
|
} else if (configurator.isDoSynonyms()) {
|
| 465 |
|
|
clazz = Synonym.class;
|
| 466 |
|
|
//propertyPath = configurator.getSynonymPropertyPath();
|
| 467 |
|
|
}
|
| 468 |
|
|
|
| 469 |
5d8d15f2
|
Katja Luther
|
|
| 470 |
f77b32f4
|
n.hoffmann
|
result = dao.getTaxaByNameForEditor(clazz, configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());
|
| 471 |
e66d9d39
|
Katja Luther
|
return result;
|
| 472 |
|
|
}
|
| 473 |
65c22e25
|
Andreas Kohlbecker
|
/* (non-Javadoc)
|
| 474 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaAndNames(eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator)
|
| 475 |
|
|
*/
|
| 476 |
24700eab
|
a.babadshanjan
|
public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator) {
|
| 477 |
|
|
|
| 478 |
|
|
List<IdentifiableEntity> results = new ArrayList<IdentifiableEntity>();
|
| 479 |
7a9cb249
|
a.babadshanjan
|
int numberOfResults = 0; // overall number of results (as opposed to number of results per page)
|
| 480 |
|
|
List<TaxonBase> taxa = null;
|
| 481 |
24700eab
|
a.babadshanjan
|
|
| 482 |
7a9cb249
|
a.babadshanjan
|
// Taxa and synonyms
|
| 483 |
40ae36a4
|
Andreas Kohlbecker
|
long numberTaxaResults = 0L;
|
| 484 |
7a9cb249
|
a.babadshanjan
|
|
| 485 |
40ae36a4
|
Andreas Kohlbecker
|
Class<? extends TaxonBase> clazz = null;
|
| 486 |
892efc69
|
Andreas Kohlbecker
|
List<String> propertyPath = new ArrayList<String>();
|
| 487 |
e3def986
|
f.revilla
|
if(configurator.getTaxonPropertyPath() != null){
|
| 488 |
65c22e25
|
Andreas Kohlbecker
|
propertyPath.addAll(configurator.getTaxonPropertyPath());
|
| 489 |
|
|
}
|
| 490 |
829679d4
|
n.hoffmann
|
if ((configurator.isDoTaxa() && configurator.isDoSynonyms())) {
|
| 491 |
40ae36a4
|
Andreas Kohlbecker
|
clazz = TaxonBase.class;
|
| 492 |
892efc69
|
Andreas Kohlbecker
|
//propertyPath.addAll(configurator.getTaxonPropertyPath());
|
| 493 |
|
|
//propertyPath.addAll(configurator.getSynonymPropertyPath());
|
| 494 |
7a9cb249
|
a.babadshanjan
|
} else if(configurator.isDoTaxa()) {
|
| 495 |
a918f676
|
Andreas Kohlbecker
|
clazz = Taxon.class;
|
| 496 |
892efc69
|
Andreas Kohlbecker
|
//propertyPath = configurator.getTaxonPropertyPath();
|
| 497 |
7a9cb249
|
a.babadshanjan
|
} else if (configurator.isDoSynonyms()) {
|
| 498 |
a918f676
|
Andreas Kohlbecker
|
clazz = Synonym.class;
|
| 499 |
892efc69
|
Andreas Kohlbecker
|
//propertyPath = configurator.getSynonymPropertyPath();
|
| 500 |
40ae36a4
|
Andreas Kohlbecker
|
}
|
| 501 |
|
|
|
| 502 |
|
|
if(clazz != null){
|
| 503 |
65c22e25
|
Andreas Kohlbecker
|
if(configurator.getPageSize() != null){ // no point counting if we need all anyway
|
| 504 |
|
|
numberTaxaResults =
|
| 505 |
|
|
dao.countTaxaByName(clazz,
|
| 506 |
f77b32f4
|
n.hoffmann
|
configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(),
|
| 507 |
65c22e25
|
Andreas Kohlbecker
|
configurator.getNamedAreas());
|
| 508 |
|
|
}
|
| 509 |
e66d9d39
|
Katja Luther
|
|
| 510 |
65c22e25
|
Andreas Kohlbecker
|
if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){ // no point checking again if less results
|
| 511 |
40ae36a4
|
Andreas Kohlbecker
|
taxa = dao.getTaxaByName(clazz,
|
| 512 |
f77b32f4
|
n.hoffmann
|
configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(),
|
| 513 |
861721b1
|
Andreas Kohlbecker
|
configurator.getNamedAreas(), configurator.getPageSize(),
|
| 514 |
892efc69
|
Andreas Kohlbecker
|
configurator.getPageNumber(), propertyPath);
|
| 515 |
40ae36a4
|
Andreas Kohlbecker
|
}
|
| 516 |
24700eab
|
a.babadshanjan
|
}
|
| 517 |
|
|
|
| 518 |
7a9cb249
|
a.babadshanjan
|
if (logger.isDebugEnabled()) { logger.debug(numberTaxaResults + " matching taxa counted"); }
|
| 519 |
|
|
|
| 520 |
d40f8755
|
Andreas Kohlbecker
|
if(taxa != null){
|
| 521 |
|
|
results.addAll(taxa);
|
| 522 |
|
|
}
|
| 523 |
7a9cb249
|
a.babadshanjan
|
|
| 524 |
|
|
numberOfResults += numberTaxaResults;
|
| 525 |
e25724b6
|
em.lee
|
|
| 526 |
7a9cb249
|
a.babadshanjan
|
// Names without taxa
|
| 527 |
24700eab
|
a.babadshanjan
|
if (configurator.isDoNamesWithoutTaxa()) {
|
| 528 |
7a9cb249
|
a.babadshanjan
|
int numberNameResults = 0;
|
| 529 |
9cc4226b
|
Katja Luther
|
|
| 530 |
7a1d87e3
|
a.babadshanjan
|
List<? extends TaxonNameBase<?,?>> names =
|
| 531 |
f77b32f4
|
n.hoffmann
|
nameDao.findByName(configurator.getTitleSearchStringSqlized(), configurator.getMatchMode(),
|
| 532 |
e6555980
|
em.lee
|
configurator.getPageSize(), configurator.getPageNumber(), null, configurator.getTaxonNamePropertyPath());
|
| 533 |
7a1d87e3
|
a.babadshanjan
|
if (logger.isDebugEnabled()) { logger.debug(names.size() + " matching name(s) found"); }
|
| 534 |
|
|
if (names.size() > 0) {
|
| 535 |
24700eab
|
a.babadshanjan
|
for (TaxonNameBase<?,?> taxonName : names) {
|
| 536 |
|
|
if (taxonName.getTaxonBases().size() == 0) {
|
| 537 |
7a1d87e3
|
a.babadshanjan
|
results.add(taxonName);
|
| 538 |
|
|
numberNameResults++;
|
| 539 |
24700eab
|
a.babadshanjan
|
}
|
| 540 |
|
|
}
|
| 541 |
7a1d87e3
|
a.babadshanjan
|
if (logger.isDebugEnabled()) { logger.debug(numberNameResults + " matching name(s) without taxa found"); }
|
| 542 |
24700eab
|
a.babadshanjan
|
numberOfResults += numberNameResults;
|
| 543 |
|
|
}
|
| 544 |
|
|
}
|
| 545 |
7a1d87e3
|
a.babadshanjan
|
|
| 546 |
7a9cb249
|
a.babadshanjan
|
// Taxa from common names
|
| 547 |
9cc4226b
|
Katja Luther
|
|
| 548 |
7a1d87e3
|
a.babadshanjan
|
if (configurator.isDoTaxaByCommonNames()) {
|
| 549 |
9cc4226b
|
Katja Luther
|
taxa = null;
|
| 550 |
|
|
numberTaxaResults = 0;
|
| 551 |
65c22e25
|
Andreas Kohlbecker
|
if(configurator.getPageSize() != null){// no point counting if we need all anyway
|
| 552 |
f77b32f4
|
n.hoffmann
|
numberTaxaResults = dao.countTaxaByCommonName(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas());
|
| 553 |
65c22e25
|
Andreas Kohlbecker
|
}
|
| 554 |
|
|
if(configurator.getPageSize() == null || numberTaxaResults > configurator.getPageSize() * configurator.getPageNumber()){
|
| 555 |
f77b32f4
|
n.hoffmann
|
taxa = dao.getTaxaByCommonName(configurator.getTitleSearchStringSqlized(), configurator.getClassification(), configurator.getMatchMode(), configurator.getNamedAreas(), configurator.getPageSize(), configurator.getPageNumber(), configurator.getTaxonPropertyPath());
|
| 556 |
9cc4226b
|
Katja Luther
|
}
|
| 557 |
|
|
if(taxa != null){
|
| 558 |
|
|
results.addAll(taxa);
|
| 559 |
|
|
}
|
| 560 |
|
|
numberOfResults += numberTaxaResults;
|
| 561 |
|
|
|
| 562 |
7a1d87e3
|
a.babadshanjan
|
}
|
| 563 |
|
|
|
| 564 |
892efc69
|
Andreas Kohlbecker
|
return new DefaultPagerImpl<IdentifiableEntity>
|
| 565 |
24700eab
|
a.babadshanjan
|
(configurator.getPageNumber(), numberOfResults, configurator.getPageSize(), results);
|
| 566 |
|
|
}
|
| 567 |
b79861eb
|
Katja Luther
|
|
| 568 |
01c21ead
|
n.hoffmann
|
public List<UuidAndTitleCache<TaxonBase>> getTaxonUuidAndTitleCache(){
|
| 569 |
|
|
return dao.getUuidAndTitleCache();
|
| 570 |
b79861eb
|
Katja Luther
|
}
|
| 571 |
9cd8b927
|
Katja Luther
|
|
| 572 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 573 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getAllMedia(eu.etaxonomy.cdm.model.taxon.Taxon, int, int, int, java.lang.String[])
|
| 574 |
|
|
*/
|
| 575 |
a4e49cfa
|
Katja Luther
|
public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes){
|
| 576 |
9cd8b927
|
Katja Luther
|
List<MediaRepresentation> medRep = new ArrayList<MediaRepresentation>();
|
| 577 |
a4e49cfa
|
Katja Luther
|
taxon = (Taxon)dao.load(taxon.getUuid());
|
| 578 |
9cd8b927
|
Katja Luther
|
Set<TaxonDescription> descriptions = taxon.getDescriptions();
|
| 579 |
|
|
for (TaxonDescription taxDesc: descriptions){
|
| 580 |
|
|
Set<DescriptionElementBase> elements = taxDesc.getElements();
|
| 581 |
|
|
for (DescriptionElementBase descElem: elements){
|
| 582 |
|
|
for(Media media : descElem.getMedia()){
|
| 583 |
|
|
|
| 584 |
|
|
//find the best matching representation
|
| 585 |
d907eaa7
|
Andreas Kohlbecker
|
medRep.add(MediaUtils.findBestMatchingRepresentation(media, null, size, height, widthOrDuration, mimeTypes));
|
| 586 |
9cd8b927
|
Katja Luther
|
|
| 587 |
|
|
}
|
| 588 |
|
|
}
|
| 589 |
|
|
}
|
| 590 |
|
|
return medRep;
|
| 591 |
|
|
}
|
| 592 |
9cc4226b
|
Katja Luther
|
|
| 593 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 594 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findTaxaByID(java.util.Set)
|
| 595 |
|
|
*/
|
| 596 |
9cc4226b
|
Katja Luther
|
public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs) {
|
| 597 |
|
|
return this.dao.findById(listOfIDs);
|
| 598 |
|
|
}
|
| 599 |
|
|
|
| 600 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 601 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#countAllRelationships()
|
| 602 |
|
|
*/
|
| 603 |
9cc4226b
|
Katja Luther
|
public int countAllRelationships() {
|
| 604 |
|
|
return this.dao.countAllRelationships();
|
| 605 |
|
|
}
|
| 606 |
|
|
|
| 607 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 608 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#createAllInferredSynonyms(eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.model.taxon.Taxon)
|
| 609 |
|
|
*/
|
| 610 |
1d36aa54
|
Andreas Müller
|
public List<Synonym> createAllInferredSynonyms(Classification tree,
|
| 611 |
9cc4226b
|
Katja Luther
|
Taxon taxon) {
|
| 612 |
|
|
|
| 613 |
|
|
return this.dao.createAllInferredSynonyms(taxon, tree);
|
| 614 |
|
|
}
|
| 615 |
|
|
|
| 616 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 617 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#createInferredSynonyms(eu.etaxonomy.cdm.model.taxon.Classification, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType)
|
| 618 |
|
|
*/
|
| 619 |
1d36aa54
|
Andreas Müller
|
public List<Synonym> createInferredSynonyms(Classification tree, Taxon taxon, SynonymRelationshipType type) {
|
| 620 |
9cc4226b
|
Katja Luther
|
|
| 621 |
|
|
return this.dao.createInferredSynonyms(taxon, tree, type);
|
| 622 |
|
|
}
|
| 623 |
|
|
|
| 624 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 625 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNames(java.util.List)
|
| 626 |
|
|
*/
|
| 627 |
9cc4226b
|
Katja Luther
|
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath) {
|
| 628 |
|
|
|
| 629 |
|
|
return this.dao.findIdenticalTaxonNames(propertyPath);
|
| 630 |
|
|
}
|
| 631 |
|
|
|
| 632 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 633 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findIdenticalTaxonNameIds(java.util.List)
|
| 634 |
|
|
*/
|
| 635 |
892efc69
|
Andreas Kohlbecker
|
public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath) {
|
| 636 |
|
|
|
| 637 |
|
|
return this.dao.findIdenticalNamesNew(propertyPath);
|
| 638 |
|
|
}
|
| 639 |
|
|
|
| 640 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 641 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getPhylumName(eu.etaxonomy.cdm.model.name.TaxonNameBase)
|
| 642 |
|
|
*/
|
| 643 |
9cc4226b
|
Katja Luther
|
public String getPhylumName(TaxonNameBase name){
|
| 644 |
|
|
return this.dao.getPhylumName(name);
|
| 645 |
|
|
}
|
| 646 |
|
|
|
| 647 |
|
|
private class TaxonAndNameComparator implements Comparator{
|
| 648 |
|
|
|
| 649 |
|
|
public int compare(Object arg0, Object arg1) {
|
| 650 |
|
|
IdentifiableEntity castArg0 = (IdentifiableEntity) arg0;
|
| 651 |
|
|
IdentifiableEntity castArg1 = (IdentifiableEntity) arg1;
|
| 652 |
|
|
return castArg0.compareTo(castArg1);
|
| 653 |
|
|
}
|
| 654 |
|
|
|
| 655 |
|
|
}
|
| 656 |
892efc69
|
Andreas Kohlbecker
|
|
| 657 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 658 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#deleteSynonymRelationships(eu.etaxonomy.cdm.model.taxon.Synonym)
|
| 659 |
|
|
*/
|
| 660 |
892efc69
|
Andreas Kohlbecker
|
public long deleteSynonymRelationships(Synonym syn) {
|
| 661 |
|
|
|
| 662 |
|
|
return dao.deleteSynonymRelationships(syn);
|
| 663 |
|
|
}
|
| 664 |
|
|
|
| 665 |
|
|
|
| 666 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 667 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#listSynonymRelationships(eu.etaxonomy.cdm.model.taxon.TaxonBase, eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction)
|
| 668 |
|
|
*/
|
| 669 |
892efc69
|
Andreas Kohlbecker
|
public List<SynonymRelationship> listSynonymRelationships(
|
| 670 |
|
|
TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber,
|
| 671 |
|
|
List<OrderHint> orderHints, List<String> propertyPaths, Direction direction) {
|
| 672 |
|
|
Integer numberOfResults = dao.countSynonymRelationships(taxonBase, type, direction);
|
| 673 |
|
|
|
| 674 |
|
|
List<SynonymRelationship> results = new ArrayList<SynonymRelationship>();
|
| 675 |
|
|
if(numberOfResults > 0) { // no point checking again
|
| 676 |
|
|
results = dao.getSynonymRelationships(taxonBase, type, pageSize, pageNumber, orderHints, propertyPaths, direction);
|
| 677 |
|
|
}
|
| 678 |
|
|
return results;
|
| 679 |
|
|
}
|
| 680 |
65c22e25
|
Andreas Kohlbecker
|
|
| 681 |
|
|
/* (non-Javadoc)
|
| 682 |
ceec7c69
|
Andreas Müller
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingTaxon(java.lang.String)
|
| 683 |
65c22e25
|
Andreas Kohlbecker
|
*/
|
| 684 |
|
|
@Override
|
| 685 |
|
|
public Taxon findBestMatchingTaxon(String taxonName) {
|
| 686 |
a6f05c62
|
Andreas Müller
|
MatchingTaxonConfigurator config = MatchingTaxonConfigurator.NewInstance();
|
| 687 |
|
|
config.setTaxonNameTitle(taxonName);
|
| 688 |
|
|
return findBestMatchingTaxon(config);
|
| 689 |
|
|
}
|
| 690 |
|
|
|
| 691 |
|
|
|
| 692 |
|
|
|
| 693 |
|
|
@Override
|
| 694 |
|
|
public Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config) {
|
| 695 |
65c22e25
|
Andreas Kohlbecker
|
|
| 696 |
f34ca874
|
Andreas Müller
|
Taxon bestCandidate = null;
|
| 697 |
65c22e25
|
Andreas Kohlbecker
|
try{
|
| 698 |
3180d917
|
Andreas Kohlbecker
|
// 1. search for acceptet taxa
|
| 699 |
a6f05c62
|
Andreas Müller
|
List<TaxonBase> taxonList = dao.findByNameTitleCache(Taxon.class, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, null, null);
|
| 700 |
f34ca874
|
Andreas Müller
|
boolean bestCandidateMatchesSecUuid = false;
|
| 701 |
|
|
boolean bestCandidateIsInClassification = false;
|
| 702 |
a6f05c62
|
Andreas Müller
|
int countEqualCandidates = 0;
|
| 703 |
|
|
for(TaxonBase taxonBaseCandidate : taxonList){
|
| 704 |
65c22e25
|
Andreas Kohlbecker
|
if(taxonBaseCandidate instanceof Taxon){
|
| 705 |
a6f05c62
|
Andreas Müller
|
Taxon newCanditate = CdmBase.deproxy(taxonBaseCandidate, Taxon.class);
|
| 706 |
f34ca874
|
Andreas Müller
|
boolean newCandidateMatchesSecUuid = isMatchesSecUuid(newCanditate, config);
|
| 707 |
|
|
if (! newCandidateMatchesSecUuid && config.isOnlyMatchingSecUuid() ){
|
| 708 |
a6f05c62
|
Andreas Müller
|
continue;
|
| 709 |
f34ca874
|
Andreas Müller
|
}else if(newCandidateMatchesSecUuid && ! bestCandidateMatchesSecUuid){
|
| 710 |
|
|
bestCandidate = newCanditate;
|
| 711 |
a6f05c62
|
Andreas Müller
|
countEqualCandidates = 1;
|
| 712 |
f34ca874
|
Andreas Müller
|
bestCandidateMatchesSecUuid = true;
|
| 713 |
a6f05c62
|
Andreas Müller
|
continue;
|
| 714 |
65c22e25
|
Andreas Kohlbecker
|
}
|
| 715 |
a6f05c62
|
Andreas Müller
|
|
| 716 |
f34ca874
|
Andreas Müller
|
boolean newCandidateInClassification = isInClassification(newCanditate, config);
|
| 717 |
|
|
if (! newCandidateInClassification && config.isOnlyMatchingClassificationUuid()){
|
| 718 |
a6f05c62
|
Andreas Müller
|
continue;
|
| 719 |
f34ca874
|
Andreas Müller
|
}else if (newCandidateInClassification && ! bestCandidateIsInClassification){
|
| 720 |
|
|
bestCandidate = newCanditate;
|
| 721 |
|
|
countEqualCandidates = 1;
|
| 722 |
|
|
bestCandidateIsInClassification = true;
|
| 723 |
|
|
continue;
|
| 724 |
|
|
}
|
| 725 |
|
|
if (bestCandidate == null){
|
| 726 |
|
|
bestCandidate = newCanditate;
|
| 727 |
a6f05c62
|
Andreas Müller
|
countEqualCandidates = 1;
|
| 728 |
|
|
continue;
|
| 729 |
|
|
}
|
| 730 |
|
|
|
| 731 |
|
|
}else{ //not Taxon.class
|
| 732 |
|
|
continue;
|
| 733 |
|
|
}
|
| 734 |
|
|
countEqualCandidates++;
|
| 735 |
|
|
|
| 736 |
|
|
}
|
| 737 |
f34ca874
|
Andreas Müller
|
if (bestCandidate != null){
|
| 738 |
a6f05c62
|
Andreas Müller
|
if(countEqualCandidates > 1){
|
| 739 |
f34ca874
|
Andreas Müller
|
logger.info(countEqualCandidates + " equally matching TaxonBases found, using first accepted Taxon: " + bestCandidate.getTitleCache());
|
| 740 |
|
|
return bestCandidate;
|
| 741 |
a6f05c62
|
Andreas Müller
|
} else {
|
| 742 |
f34ca874
|
Andreas Müller
|
logger.info("using accepted Taxon: " + bestCandidate.getTitleCache());
|
| 743 |
|
|
return bestCandidate;
|
| 744 |
65c22e25
|
Andreas Kohlbecker
|
}
|
| 745 |
|
|
}
|
| 746 |
3180d917
|
Andreas Kohlbecker
|
|
| 747 |
a6f05c62
|
Andreas Müller
|
|
| 748 |
3180d917
|
Andreas Kohlbecker
|
// 2. search for synonyms
|
| 749 |
a6f05c62
|
Andreas Müller
|
if (config.isIncludeSynonyms()){
|
| 750 |
|
|
List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, config.getTaxonNameTitle(), null, MatchMode.EXACT, null, 0, null, null);
|
| 751 |
|
|
for(TaxonBase taxonBase : synonymList){
|
| 752 |
|
|
if(taxonBase instanceof Synonym){
|
| 753 |
|
|
Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
|
| 754 |
|
|
Set<Taxon> acceptetdCandidates = synonym.getAcceptedTaxa();
|
| 755 |
|
|
if(!acceptetdCandidates.isEmpty()){
|
| 756 |
f34ca874
|
Andreas Müller
|
bestCandidate = acceptetdCandidates.iterator().next();
|
| 757 |
a6f05c62
|
Andreas Müller
|
if(acceptetdCandidates.size() == 1){
|
| 758 |
f34ca874
|
Andreas Müller
|
logger.info(acceptetdCandidates.size() + " Accepted taxa found for synonym " + taxonBase.getTitleCache() + ", using first one: " + bestCandidate.getTitleCache());
|
| 759 |
|
|
return bestCandidate;
|
| 760 |
a6f05c62
|
Andreas Müller
|
} else {
|
| 761 |
f34ca874
|
Andreas Müller
|
logger.info("using accepted Taxon " + bestCandidate.getTitleCache() + "for synonym " + taxonBase.getTitleCache());
|
| 762 |
|
|
return bestCandidate;
|
| 763 |
a6f05c62
|
Andreas Müller
|
}
|
| 764 |
|
|
//TODO extend method: search using treeUUID, using SecUUID, first find accepted then include synonyms until a matching taxon is found
|
| 765 |
3180d917
|
Andreas Kohlbecker
|
}
|
| 766 |
|
|
}
|
| 767 |
|
|
}
|
| 768 |
|
|
}
|
| 769 |
|
|
|
| 770 |
65c22e25
|
Andreas Kohlbecker
|
} catch (Exception e){
|
| 771 |
|
|
logger.error(e);
|
| 772 |
|
|
}
|
| 773 |
|
|
|
| 774 |
f34ca874
|
Andreas Müller
|
return bestCandidate;
|
| 775 |
65c22e25
|
Andreas Kohlbecker
|
}
|
| 776 |
b6cb1182
|
Andreas Müller
|
|
| 777 |
a6f05c62
|
Andreas Müller
|
private boolean isInClassification(Taxon taxon, MatchingTaxonConfigurator config) {
|
| 778 |
|
|
UUID configClassificationUuid = config.getClassificationUuid();
|
| 779 |
|
|
if (configClassificationUuid == null){
|
| 780 |
|
|
return false;
|
| 781 |
|
|
}
|
| 782 |
|
|
for (TaxonNode node : taxon.getTaxonNodes()){
|
| 783 |
|
|
UUID classUuid = node.getClassification().getUuid();
|
| 784 |
|
|
if (configClassificationUuid.equals(classUuid)){
|
| 785 |
|
|
return true;
|
| 786 |
|
|
}
|
| 787 |
|
|
}
|
| 788 |
|
|
return false;
|
| 789 |
|
|
}
|
| 790 |
|
|
|
| 791 |
|
|
private boolean isMatchesSecUuid(Taxon taxon, MatchingTaxonConfigurator config) {
|
| 792 |
|
|
UUID configSecUuid = config.getSecUuid();
|
| 793 |
|
|
if (configSecUuid == null){
|
| 794 |
|
|
return false;
|
| 795 |
|
|
}
|
| 796 |
|
|
UUID taxonSecUuid = (taxon.getSec() == null)? null : taxon.getSec().getUuid();
|
| 797 |
|
|
return configSecUuid.equals(taxonSecUuid);
|
| 798 |
|
|
}
|
| 799 |
|
|
|
| 800 |
ceec7c69
|
Andreas Müller
|
/* (non-Javadoc)
|
| 801 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#findBestMatchingSynonym(java.lang.String)
|
| 802 |
|
|
*/
|
| 803 |
b6cb1182
|
Andreas Müller
|
@Override
|
| 804 |
|
|
public Synonym findBestMatchingSynonym(String taxonName) {
|
| 805 |
|
|
List<TaxonBase> synonymList = dao.findByNameTitleCache(Synonym.class, taxonName, null, MatchMode.EXACT, null, 0, null, null);
|
| 806 |
|
|
if(! synonymList.isEmpty()){
|
| 807 |
|
|
Synonym result = CdmBase.deproxy(synonymList.iterator().next(), Synonym.class);
|
| 808 |
|
|
if(synonymList.size() == 1){
|
| 809 |
|
|
logger.info(synonymList.size() + " Synonym found " + result.getTitleCache() );
|
| 810 |
|
|
return result;
|
| 811 |
|
|
} else {
|
| 812 |
|
|
logger.info("Several matching synonyms found. Using first: " + result.getTitleCache());
|
| 813 |
|
|
return result;
|
| 814 |
|
|
}
|
| 815 |
|
|
}
|
| 816 |
|
|
return null;
|
| 817 |
|
|
}
|
| 818 |
15ce3c9c
|
n.hoffmann
|
|
| 819 |
|
|
/* (non-Javadoc)
|
| 820 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#moveSynonymToAnotherTaxon(eu.etaxonomy.cdm.model.taxon.SynonymRelationship, eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.reference.Reference, java.lang.String)
|
| 821 |
|
|
*/
|
| 822 |
|
|
@Override
|
| 823 |
|
|
public Taxon moveSynonymToAnotherTaxon(SynonymRelationship synonymRelation,
|
| 824 |
|
|
Taxon toTaxon, SynonymRelationshipType synonymRelationshipType, Reference reference, String referenceDetail) {
|
| 825 |
|
|
Taxon fromTaxon = synonymRelation.getAcceptedTaxon();
|
| 826 |
fd992c0d
|
n.hoffmann
|
|
| 827 |
|
|
toTaxon.addSynonym(synonymRelation.getSynonym(), synonymRelationshipType, reference, referenceDetail);
|
| 828 |
15ce3c9c
|
n.hoffmann
|
|
| 829 |
|
|
fromTaxon.removeSynonymRelation(synonymRelation);
|
| 830 |
fd992c0d
|
n.hoffmann
|
|
| 831 |
15ce3c9c
|
n.hoffmann
|
return toTaxon;
|
| 832 |
|
|
}
|
| 833 |
7d399d75
|
n.hoffmann
|
|
| 834 |
|
|
/* (non-Javadoc)
|
| 835 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheTaxon()
|
| 836 |
|
|
*/
|
| 837 |
|
|
@Override
|
| 838 |
|
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon() {
|
| 839 |
|
|
return dao.getUuidAndTitleCacheTaxon();
|
| 840 |
|
|
}
|
| 841 |
|
|
|
| 842 |
|
|
/* (non-Javadoc)
|
| 843 |
|
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getUuidAndTitleCacheSynonym()
|
| 844 |
|
|
*/
|
| 845 |
|
|
@Override
|
| 846 |
|
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym() {
|
| 847 |
|
|
return dao.getUuidAndTitleCacheSynonym();
|
| 848 |
|
|
}
|
| 849 |
b6cb1182
|
Andreas Müller
|
|
| 850 |
|
|
|
| 851 |
2d993c6e
|
Andreas Müller
|
}
|