1
|
// $Id$
|
2
|
/**
|
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
|
package eu.etaxonomy.cdm.api.service;
|
12
|
|
13
|
import java.util.ArrayList;
|
14
|
import java.util.Collections;
|
15
|
import java.util.Comparator;
|
16
|
import java.util.HashSet;
|
17
|
import java.util.List;
|
18
|
import java.util.Set;
|
19
|
import java.util.UUID;
|
20
|
|
21
|
import org.apache.log4j.Logger;
|
22
|
import org.springframework.beans.factory.annotation.Autowired;
|
23
|
import org.springframework.stereotype.Service;
|
24
|
import org.springframework.transaction.annotation.Propagation;
|
25
|
import org.springframework.transaction.annotation.Transactional;
|
26
|
|
27
|
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
|
28
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
29
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
30
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
31
|
import eu.etaxonomy.cdm.model.taxon.ITaxonNodeComparator;
|
32
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
33
|
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
|
34
|
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
|
35
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
36
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
37
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
|
38
|
import eu.etaxonomy.cdm.persistence.dao.BeanInitializer;
|
39
|
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
|
40
|
|
41
|
/**
|
42
|
* @author n.hoffmann
|
43
|
* @created Apr 9, 2010
|
44
|
* @version 1.0
|
45
|
*/
|
46
|
@Service
|
47
|
@Transactional(propagation = Propagation.SUPPORTS, readOnly = true)
|
48
|
public class TaxonNodeServiceImpl extends AnnotatableServiceBase<TaxonNode, ITaxonNodeDao> implements ITaxonNodeService{
|
49
|
private static final Logger logger = Logger.getLogger(TaxonNodeServiceImpl.class);
|
50
|
|
51
|
@Autowired
|
52
|
private BeanInitializer defaultBeanInitializer;
|
53
|
|
54
|
private Comparator<? super TaxonNode> taxonNodeComparator;
|
55
|
@Autowired
|
56
|
public void setTaxonNodeComparator(ITaxonNodeComparator<? super TaxonNode> taxonNodeComparator){
|
57
|
this.taxonNodeComparator = (Comparator<? super TaxonNode>) taxonNodeComparator;
|
58
|
}
|
59
|
|
60
|
public TaxonNode getTaxonNodeByUuid(UUID uuid) {
|
61
|
return dao.findByUuid(uuid);
|
62
|
}
|
63
|
|
64
|
public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode,
|
65
|
List<String> propertyPaths) {
|
66
|
taxonNode = dao.load(taxonNode.getUuid());
|
67
|
List<TaxonNode> childNodes = new ArrayList<TaxonNode>(taxonNode.getChildNodes());
|
68
|
Collections.sort(childNodes, taxonNodeComparator);
|
69
|
defaultBeanInitializer.initializeAll(childNodes, propertyPaths);
|
70
|
return childNodes;
|
71
|
}
|
72
|
|
73
|
/* (non-Javadoc)
|
74
|
* @see eu.etaxonomy.cdm.api.service.ServiceBase#setDao(eu.etaxonomy.cdm.persistence.dao.common.ICdmEntityDao)
|
75
|
*/
|
76
|
@Override
|
77
|
@Autowired
|
78
|
protected void setDao(ITaxonNodeDao dao) {
|
79
|
this.dao = dao;
|
80
|
}
|
81
|
|
82
|
/* (non-Javadoc)
|
83
|
* @see eu.etaxonomy.cdm.api.service.ITaxonService#makeTaxonSynonym(eu.etaxonomy.cdm.model.taxon.Taxon, eu.etaxonomy.cdm.model.taxon.Taxon)
|
84
|
*/
|
85
|
@Transactional(readOnly = false)
|
86
|
public Synonym makeTaxonNodeASynonymOfAnotherTaxonNode(TaxonNode oldTaxonNode, TaxonNode newAcceptedTaxonNode, SynonymRelationshipType synonymRelationshipType, Reference citation, String citationMicroReference) {
|
87
|
|
88
|
// TODO at the moment this method only moves synonym-, concept relations and descriptions to the new accepted taxon
|
89
|
// in a future version we also want to move cdm data like annotations, marker, so., but we will need a policy for that
|
90
|
if (oldTaxonNode == null || newAcceptedTaxonNode == null || oldTaxonNode.getTaxon().getName() == null){
|
91
|
throw new IllegalArgumentException("A mandatory parameter was null.");
|
92
|
}
|
93
|
|
94
|
if(oldTaxonNode.equals(newAcceptedTaxonNode)){
|
95
|
throw new IllegalArgumentException("Taxon can not be made synonym of its own.");
|
96
|
}
|
97
|
|
98
|
Taxon oldTaxon = (Taxon) HibernateProxyHelper.deproxy(oldTaxonNode.getTaxon());
|
99
|
Taxon newAcceptedTaxon = (Taxon) HibernateProxyHelper.deproxy(newAcceptedTaxonNode.getTaxon());
|
100
|
|
101
|
// Move oldTaxon to newTaxon
|
102
|
TaxonNameBase<?,?> synonymName = oldTaxon.getName();
|
103
|
if (synonymRelationshipType == null){
|
104
|
if (synonymName.isHomotypic(newAcceptedTaxon.getName())){
|
105
|
synonymRelationshipType = SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF();
|
106
|
}else{
|
107
|
synonymRelationshipType = SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF();
|
108
|
}
|
109
|
}
|
110
|
SynonymRelationship synonmyRelationship = newAcceptedTaxon.addSynonymName(synonymName, synonymRelationshipType, citation, citationMicroReference);
|
111
|
|
112
|
//Move Synonym Relations to new Taxon
|
113
|
for(SynonymRelationship synRelation : oldTaxon.getSynonymRelations()){
|
114
|
newAcceptedTaxon.addSynonym(synRelation.getSynonym(), synRelation.getType(),
|
115
|
synRelation.getCitation(), synRelation.getCitationMicroReference());
|
116
|
}
|
117
|
|
118
|
|
119
|
// CHILD NODES
|
120
|
if(oldTaxonNode.getChildNodes() != null && oldTaxonNode.getChildNodes().size() != 0){
|
121
|
for(TaxonNode childNode : oldTaxonNode.getChildNodes()){
|
122
|
newAcceptedTaxonNode.addChildNode(childNode, childNode.getReference(), childNode.getMicroReference(), childNode.getSynonymToBeUsed());
|
123
|
}
|
124
|
}
|
125
|
|
126
|
//Move Taxon RelationShips to new Taxon
|
127
|
Set<TaxonRelationship> obsoleteTaxonRelationships = new HashSet<TaxonRelationship>();
|
128
|
for(TaxonRelationship taxonRelationship : oldTaxon.getTaxonRelations()){
|
129
|
Taxon fromTaxon = (Taxon) HibernateProxyHelper.deproxy(taxonRelationship.getFromTaxon());
|
130
|
Taxon toTaxon = (Taxon) HibernateProxyHelper.deproxy(taxonRelationship.getToTaxon());
|
131
|
if (fromTaxon == oldTaxon){
|
132
|
newAcceptedTaxon.addTaxonRelation(taxonRelationship.getToTaxon(), taxonRelationship.getType(),
|
133
|
taxonRelationship.getCitation(), taxonRelationship.getCitationMicroReference());
|
134
|
|
135
|
}else if(toTaxon == oldTaxon){
|
136
|
taxonRelationship.getFromTaxon().addTaxonRelation(newAcceptedTaxon, taxonRelationship.getType(),
|
137
|
taxonRelationship.getCitation(), taxonRelationship.getCitationMicroReference());
|
138
|
|
139
|
}else{
|
140
|
logger.warn("Taxon is not part of its own Taxonrelationship");
|
141
|
}
|
142
|
// Remove old relationships
|
143
|
taxonRelationship.setToTaxon(null);
|
144
|
taxonRelationship.setFromTaxon(null);
|
145
|
}
|
146
|
|
147
|
//Move descriptions to new taxon
|
148
|
List<TaxonDescription> descriptions = new ArrayList<TaxonDescription>( oldTaxon.getDescriptions()); //to avoid concurrent modification errors (newAcceptedTaxon.addDescription() modifies also oldtaxon.descritpions())
|
149
|
for(TaxonDescription description : descriptions){
|
150
|
String message = "Description copied from former accepted taxon: %s (Old title: %s)";
|
151
|
message = String.format(message, oldTaxon.getTitleCache(), description.getTitleCache());
|
152
|
description.setTitleCache(message, true);
|
153
|
newAcceptedTaxon.addDescription(description);
|
154
|
}
|
155
|
|
156
|
oldTaxonNode.delete();
|
157
|
|
158
|
return synonmyRelationship.getSynonym();
|
159
|
}
|
160
|
}
|