|
1
|
/**
|
|
2
|
* Copyright (C) 2007 EDIT
|
|
3
|
* European Distributed Institute of Taxonomy
|
|
4
|
* http://www.e-taxonomy.eu
|
|
5
|
*
|
|
6
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
|
7
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
|
8
|
*/
|
|
9
|
|
|
10
|
package eu.etaxonomy.cdm.api.service;
|
|
11
|
|
|
12
|
import org.apache.log4j.Logger;
|
|
13
|
import org.springframework.beans.factory.annotation.Autowired;
|
|
14
|
import org.springframework.stereotype.Service;
|
|
15
|
import org.springframework.transaction.TransactionStatus;
|
|
16
|
import org.springframework.transaction.annotation.Transactional;
|
|
17
|
|
|
18
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
|
19
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
20
|
import eu.etaxonomy.cdm.model.reference.ReferenceBase;
|
|
21
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
|
22
|
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
|
|
23
|
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
|
|
24
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
25
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
26
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
|
|
27
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
|
|
28
|
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
|
|
29
|
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
|
|
30
|
|
|
31
|
import java.util.Collection;
|
|
32
|
import java.util.List;
|
|
33
|
import java.util.Map;
|
|
34
|
import java.util.UUID;
|
|
35
|
|
|
36
|
|
|
37
|
@Service
|
|
38
|
@Transactional(readOnly = true)
|
|
39
|
public class TaxonServiceImpl extends ServiceBase<TaxonBase> implements ITaxonService {
|
|
40
|
static Logger logger = Logger.getLogger(TaxonServiceImpl.class);
|
|
41
|
|
|
42
|
private ITaxonDao taxonDao;
|
|
43
|
|
|
44
|
@Autowired
|
|
45
|
protected void setDao(ITaxonDao dao) {
|
|
46
|
this.dao = dao;
|
|
47
|
this.taxonDao = dao;
|
|
48
|
}
|
|
49
|
|
|
50
|
|
|
51
|
public TaxonBase getTaxonByUuid(UUID uuid) {
|
|
52
|
return super.getCdmObjectByUuid(uuid);
|
|
53
|
}
|
|
54
|
|
|
55
|
@Transactional(readOnly = false)
|
|
56
|
public UUID saveTaxon(TaxonBase taxon) {
|
|
57
|
return super.saveCdmObject(taxon);
|
|
58
|
}
|
|
59
|
|
|
60
|
//@Transactional(readOnly = false)
|
|
61
|
public UUID saveTaxon(TaxonBase taxon, TransactionStatus txStatus) {
|
|
62
|
|
|
63
|
return super.saveCdmObject(taxon);
|
|
64
|
}
|
|
65
|
|
|
66
|
|
|
67
|
@Transactional(readOnly = false)
|
|
68
|
public Map<UUID, TaxonBase> saveTaxonAll(Collection<TaxonBase> taxonCollection){
|
|
69
|
return saveCdmObjectAll(taxonCollection);
|
|
70
|
}
|
|
71
|
|
|
72
|
|
|
73
|
|
|
74
|
@Transactional(readOnly = false)
|
|
75
|
public UUID removeTaxon(TaxonBase taxon) {
|
|
76
|
return super.removeCdmObject(taxon);
|
|
77
|
}
|
|
78
|
|
|
79
|
public List<TaxonBase> searchTaxaByName(String name, ReferenceBase sec) {
|
|
80
|
return taxonDao.getTaxaByName(name, sec);
|
|
81
|
}
|
|
82
|
|
|
83
|
/* (non-Javadoc)
|
|
84
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase)
|
|
85
|
*/
|
|
86
|
public List<Taxon> getRootTaxa(ReferenceBase sec){
|
|
87
|
return getRootTaxa(sec, CdmFetch.FETCH_CHILDTAXA(), true);
|
|
88
|
}
|
|
89
|
|
|
90
|
|
|
91
|
|
|
92
|
/* (non-Javadoc)
|
|
93
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#getRootTaxa(eu.etaxonomy.cdm.model.reference.ReferenceBase, boolean)
|
|
94
|
*/
|
|
95
|
public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, boolean onlyWithChildren) {
|
|
96
|
if (cdmFetch == null){
|
|
97
|
cdmFetch = CdmFetch.NO_FETCH();
|
|
98
|
}
|
|
99
|
return taxonDao.getRootTaxa(sec, cdmFetch, onlyWithChildren);
|
|
100
|
}
|
|
101
|
|
|
102
|
/* (non-Javadoc)
|
|
103
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#makeTaxonSynonym(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.Taxon)
|
|
104
|
*/
|
|
105
|
@Transactional(readOnly = false)
|
|
106
|
public Synonym makeTaxonSynonym(Taxon oldTaxon, Taxon newAcceptedTaxon, SynonymRelationshipType synonymType, ReferenceBase citation, String citationMicroReference) {
|
|
107
|
if (oldTaxon == null || newAcceptedTaxon == null || oldTaxon.getName() == null){
|
|
108
|
return null;
|
|
109
|
}
|
|
110
|
|
|
111
|
// Move oldTaxon to newTaxon
|
|
112
|
TaxonNameBase synonymName = oldTaxon.getName();
|
|
113
|
if (synonymType == null){
|
|
114
|
if (synonymName.isHomotypic(newAcceptedTaxon.getName())){
|
|
115
|
synonymType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
|
|
116
|
}else{
|
|
117
|
//TODO synonymType
|
|
118
|
synonymType = SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
|
|
119
|
}
|
|
120
|
}
|
|
121
|
SynonymRelationship synRel = newAcceptedTaxon.addSynonymName(synonymName, synonymType, citation, citationMicroReference);
|
|
122
|
|
|
123
|
//Move Synonym Relations to new Taxon
|
|
124
|
for(SynonymRelationship synRelation : oldTaxon.getSynonymRelations()){
|
|
125
|
//TODO citation and microcitation
|
|
126
|
newAcceptedTaxon.addSynonym(synRelation.getSynonym(), synRelation.getType(), null, null);
|
|
127
|
}
|
|
128
|
|
|
129
|
//Move Taxon RelationShips to new Taxon
|
|
130
|
for(TaxonRelationship taxonRelation : oldTaxon.getTaxonRelations()){
|
|
131
|
//CHILDREN
|
|
132
|
if (taxonRelation.getType().equals(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN())){
|
|
133
|
if (taxonRelation.getFromTaxon() == oldTaxon){
|
|
134
|
oldTaxon.removeTaxonRelation(taxonRelation);
|
|
135
|
}else if(taxonRelation.getToTaxon() == oldTaxon){
|
|
136
|
newAcceptedTaxon.addTaxonomicChild(taxonRelation.getFromTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
|
|
137
|
oldTaxon.removeTaxonRelation(taxonRelation);
|
|
138
|
}else{
|
|
139
|
logger.warn("Taxon is not part of its own Taxonrelationship");
|
|
140
|
}
|
|
141
|
}
|
|
142
|
//MISAPPLIED NAMES
|
|
143
|
if (taxonRelation.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
|
|
144
|
if (taxonRelation.getFromTaxon() == oldTaxon){
|
|
145
|
newAcceptedTaxon.addMisappliedName(taxonRelation.getToTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
|
|
146
|
oldTaxon.removeTaxonRelation(taxonRelation);
|
|
147
|
}else if(taxonRelation.getToTaxon() == oldTaxon){
|
|
148
|
newAcceptedTaxon.addMisappliedName(taxonRelation.getFromTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
|
|
149
|
oldTaxon.removeTaxonRelation(taxonRelation);
|
|
150
|
}else{
|
|
151
|
logger.warn("Taxon is not part of its own Taxonrelationship");
|
|
152
|
}
|
|
153
|
}
|
|
154
|
//Concept Relationships
|
|
155
|
//FIXME implement
|
|
156
|
// if (taxonRelation.getType().equals(TaxonRelationshipType.MISAPPLIEDNAMEFOR())){
|
|
157
|
// if (taxonRelation.getFromTaxon() == oldTaxon){
|
|
158
|
// newAcceptedTaxon.addMisappliedName(taxonRelation.getToTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
|
|
159
|
// oldTaxon.removeTaxonRelation(taxonRelation);
|
|
160
|
// }else if(taxonRelation.getToTaxon() == oldTaxon){
|
|
161
|
// newAcceptedTaxon.addMisappliedName(taxonRelation.getFromTaxon(), taxonRelation.getCitation(), taxonRelation.getCitationMicroReference());
|
|
162
|
// oldTaxon.removeTaxonRelation(taxonRelation);
|
|
163
|
// }else{
|
|
164
|
// logger.warn("Taxon is not part of its own Taxonrelationship");
|
|
165
|
// }
|
|
166
|
// }
|
|
167
|
}
|
|
168
|
|
|
169
|
//Move Descriptions to new Taxon
|
|
170
|
for(TaxonDescription taxDescription : oldTaxon.getDescriptions()){
|
|
171
|
newAcceptedTaxon.addDescription(taxDescription);
|
|
172
|
}
|
|
173
|
//delete old Taxon
|
|
174
|
this.dao.saveOrUpdate(newAcceptedTaxon);
|
|
175
|
// FIXME implement
|
|
176
|
this.dao.delete(oldTaxon);
|
|
177
|
|
|
178
|
//return
|
|
179
|
this.dao.flush();
|
|
180
|
return synRel.getSynonym();
|
|
181
|
}
|
|
182
|
|
|
183
|
|
|
184
|
public void generateTitleCache() {
|
|
185
|
generateTitleCache(true);
|
|
186
|
}
|
|
187
|
//TODO
|
|
188
|
public void generateTitleCache(boolean forceProtected) {
|
|
189
|
logger.warn("generateTitleCache not yet fully implemented!");
|
|
190
|
// for (TaxonBase tb : taxonDao.getAllTaxa(null,null)){
|
|
191
|
// logger.warn("Old taxon title: " + tb.getTitleCache());
|
|
192
|
// if (forceProtected || !tb.isProtectedTitleCache() ){
|
|
193
|
// tb.setTitleCache(tb.generateTitle(), false);
|
|
194
|
// taxonDao.update(tb);
|
|
195
|
// logger.warn("New title: " + tb.getTitleCache());
|
|
196
|
// }
|
|
197
|
// }
|
|
198
|
|
|
199
|
}
|
|
200
|
}
|