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.taxeditor.store;
|
11
|
|
12
|
import java.util.ArrayList;
|
13
|
import java.util.Arrays;
|
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
|
|
20
|
import eu.etaxonomy.cdm.api.service.ITermService;
|
21
|
import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;
|
22
|
import eu.etaxonomy.cdm.model.term.DefinedTermBase;
|
23
|
import eu.etaxonomy.cdm.model.common.MarkerType;
|
24
|
import eu.etaxonomy.cdm.model.term.TermType;
|
25
|
import eu.etaxonomy.cdm.model.term.TermVocabulary;
|
26
|
import eu.etaxonomy.cdm.model.description.Feature;
|
27
|
import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
|
28
|
import eu.etaxonomy.cdm.model.name.Rank;
|
29
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
|
30
|
import eu.etaxonomy.taxeditor.model.DefaultTermComparator;
|
31
|
import eu.etaxonomy.taxeditor.model.TaxonRelationshipTypeInverseContainer;
|
32
|
import eu.etaxonomy.taxeditor.preference.PreferencesUtil;
|
33
|
|
34
|
/**
|
35
|
* All terms may be accessed through this store.
|
36
|
* Note: This is for internal use. When using vocabularies in the UI, try to use the preferred terms from
|
37
|
* PreferenceUtil
|
38
|
*
|
39
|
* @author n.hoffmann
|
40
|
* @created 25.06.2009
|
41
|
* @version 1.0
|
42
|
*/
|
43
|
public class TermStore {
|
44
|
|
45
|
/**
|
46
|
* Returns an alphabetically sorted list of terms (anything that extends {@link DefinedTermBase}) of the given type currently available in the system.
|
47
|
*
|
48
|
* @param clazz a class that inherits from {@link DefinedTermBase}
|
49
|
* @return an alphabetically sorted list of terms
|
50
|
*/
|
51
|
public static <TERM extends DefinedTermBase> List<TERM> getTerms(Class<TERM> clazz){
|
52
|
return getTerms(clazz, null, true);
|
53
|
}
|
54
|
|
55
|
/**
|
56
|
* Returns an alphabetically sorted list of terms (anything that extends {@link DefinedTermBase}) of the given {@link TermType})
|
57
|
* currently available in the system.
|
58
|
*
|
59
|
* @param termType the term type
|
60
|
* @return an alphabetically sorted list of terms
|
61
|
*/
|
62
|
public static <TERM extends DefinedTermBase> List<TERM> getTerms(TermType termType, Comparator<TERM> comparator){
|
63
|
return getTermsFromService(termType, comparator);
|
64
|
}
|
65
|
|
66
|
/**
|
67
|
* Returns an alphabetically sorted list of terms (anything that extends {@link DefinedTermBase}) of the given {@link TermType})
|
68
|
* currently available in the system.
|
69
|
*
|
70
|
* @param termType the term type
|
71
|
* @return an alphabetically sorted list of terms
|
72
|
*/
|
73
|
public static <TERM extends DefinedTermBase> Set<TERM> getTerms(TermVocabulary<TERM> termVocabulary, Comparator<DefinedTermBase<?>> comparator){
|
74
|
return termVocabulary.getTerms();
|
75
|
}
|
76
|
|
77
|
/**
|
78
|
* Returns a list of terms of the given type currently available in the system.
|
79
|
* If <code>filtered</code> is set to <code>true</code>, all terms for certain types will be
|
80
|
* gathered from edge cases.
|
81
|
*
|
82
|
* @param clazz a class that inherits from {@link DefinedTermBase}
|
83
|
* @param comparator a {@link Comparator} that defines the sorting algorithm. If set to null, {@link DefaultTermComparator} will be used
|
84
|
* @param filtered if set to true, some terms are filtered from the result (according to definition in {@link ITermStoreEdgeCase}s)
|
85
|
* @return a sorted list of terms
|
86
|
*/
|
87
|
public static <TERM extends DefinedTermBase> List<TERM> getTerms(Class<TERM> clazz, Comparator<TERM> comparator, boolean filtered){
|
88
|
List<TERM> terms = new ArrayList<>();
|
89
|
|
90
|
ITermStoreEdgeCase<TERM> edgeCase = getEdgeCase(clazz);
|
91
|
if(filtered && edgeCase != null){
|
92
|
terms = edgeCase.getTerms();
|
93
|
}else{
|
94
|
terms = getTermsFromService(clazz, comparator);
|
95
|
}
|
96
|
|
97
|
return terms;
|
98
|
}
|
99
|
|
100
|
private static <T extends DefinedTermBase> List<T> getTermsFromService(TermType termType, Comparator<T> comparator){
|
101
|
if (comparator == null){
|
102
|
comparator = new DefaultTermComparator<T>();
|
103
|
}
|
104
|
|
105
|
List<T> terms = CdmStore.getService(ITermService.class).listByTermType(termType, null, null, null, null);
|
106
|
Collections.sort(terms, comparator);
|
107
|
return terms;
|
108
|
}
|
109
|
|
110
|
private static <T extends DefinedTermBase> List<T> getTermsFromService(Class<T> termClass, Comparator<T> comparator){
|
111
|
if (comparator == null){
|
112
|
comparator = new DefaultTermComparator<T>();
|
113
|
}
|
114
|
|
115
|
List<T> terms = CdmStore.getService(ITermService.class).list(termClass, null, null, null, null);
|
116
|
Collections.sort(terms, comparator);
|
117
|
return terms;
|
118
|
}
|
119
|
|
120
|
public static void saveTerm(DefinedTermBase term){
|
121
|
CdmStore.getService(ITermService.class).saveOrUpdate(term);
|
122
|
}
|
123
|
|
124
|
/**
|
125
|
* <p>delete</p>
|
126
|
*
|
127
|
* @param selected a {@link eu.etaxonomy.cdm.model.term.DefinedTermBase} object.
|
128
|
* @throws ReferencedObjectUndeletableException
|
129
|
*/
|
130
|
public static void delete(DefinedTermBase selected) throws ReferencedObjectUndeletableException {
|
131
|
CdmStore.getService(ITermService.class).delete(selected);
|
132
|
}
|
133
|
|
134
|
/**
|
135
|
* Save a vacabulary to data store
|
136
|
*
|
137
|
* @param term a {@link eu.etaxonomy.cdm.model.term.DefinedTermBase} object.
|
138
|
*/
|
139
|
public static void updateVocabulary(DefinedTermBase term) {
|
140
|
CdmStore.getService(ITermService.class).saveOrUpdate(term);
|
141
|
}
|
142
|
|
143
|
/**
|
144
|
* Handingling of special cases
|
145
|
*/
|
146
|
private static Set<ITermStoreEdgeCase<? extends DefinedTermBase>> termStoreEdgeCases = new HashSet<>();
|
147
|
|
148
|
static {
|
149
|
termStoreEdgeCases.add(new ITermStoreEdgeCase<Feature>() {
|
150
|
|
151
|
@Override
|
152
|
public Class<Feature> getTermClass() {
|
153
|
return Feature.class;
|
154
|
}
|
155
|
|
156
|
@Override
|
157
|
public List<Feature> getTerms() {
|
158
|
List<Feature> features = TermStore.getTermsFromService(Feature.class, null);
|
159
|
features.remove(Feature.IMAGE());
|
160
|
return features;
|
161
|
}
|
162
|
});
|
163
|
termStoreEdgeCases.add(new ITermStoreEdgeCase<MarkerType>(){
|
164
|
|
165
|
@Override
|
166
|
public Class<MarkerType> getTermClass() {
|
167
|
return MarkerType.class;
|
168
|
}
|
169
|
|
170
|
@Override
|
171
|
public List<MarkerType> getTerms() {
|
172
|
// filter out non technical markers
|
173
|
List<MarkerType> nonTechnicalMarkerTypes = new ArrayList<>();
|
174
|
List<MarkerType> markerTypes = TermStore.getTermsFromService(MarkerType.class, null);
|
175
|
|
176
|
for (Object type : markerTypes) {
|
177
|
if (((MarkerType) type).isTechnical() == false) {
|
178
|
nonTechnicalMarkerTypes.add((MarkerType) type);
|
179
|
}
|
180
|
}
|
181
|
|
182
|
return nonTechnicalMarkerTypes;
|
183
|
}
|
184
|
|
185
|
});
|
186
|
termStoreEdgeCases.add(new ITermStoreEdgeCase<Rank>() {
|
187
|
|
188
|
@Override
|
189
|
public Class<Rank> getTermClass() {
|
190
|
return Rank.class;
|
191
|
}
|
192
|
|
193
|
@Override
|
194
|
public List<Rank> getTerms() {
|
195
|
if(PreferencesUtil.getSortRanksHierarchichally()){
|
196
|
return TermStore.getTermsFromService(Rank.class, new Comparator<Rank>(){
|
197
|
@Override
|
198
|
public int compare(Rank o1, Rank o2) {
|
199
|
return o1.compareTo(o2);
|
200
|
}
|
201
|
});
|
202
|
}else{
|
203
|
return TermStore.getTermsFromService(Rank.class, null);
|
204
|
}
|
205
|
}
|
206
|
});
|
207
|
termStoreEdgeCases.add(new ITermStoreEdgeCase<PresenceAbsenceTerm>() {
|
208
|
@Override
|
209
|
public Class<PresenceAbsenceTerm> getTermClass() {
|
210
|
return PresenceAbsenceTerm.class;
|
211
|
}
|
212
|
@Override
|
213
|
public List<PresenceAbsenceTerm> getTerms() {
|
214
|
List<PresenceAbsenceTerm> presenceAbsenceTerms = TermStore.getTermsFromService(PresenceAbsenceTerm.class, null);
|
215
|
|
216
|
return presenceAbsenceTerms;
|
217
|
}
|
218
|
});
|
219
|
termStoreEdgeCases.add(new ITermStoreEdgeCase<TaxonRelationshipTypeInverseContainer>() {
|
220
|
@Override
|
221
|
public Class<TaxonRelationshipTypeInverseContainer> getTermClass() {
|
222
|
return TaxonRelationshipTypeInverseContainer.class;
|
223
|
}
|
224
|
@Override
|
225
|
public List<TaxonRelationshipTypeInverseContainer> getTerms() {
|
226
|
List<TaxonRelationshipType> excludeTaxonRelationshipTypes = Arrays.asList(new TaxonRelationshipType[]{
|
227
|
TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
228
|
TaxonRelationshipType.MISAPPLIED_NAME_FOR(),
|
229
|
TaxonRelationshipType.ALL_RELATIONSHIPS()
|
230
|
});
|
231
|
|
232
|
List<TaxonRelationshipTypeInverseContainer> relationshipTypeInverseContainers = new ArrayList<>();
|
233
|
|
234
|
List<TaxonRelationshipType> relationshipTypes = TermStore.getTerms(TaxonRelationshipType.class);
|
235
|
|
236
|
relationshipTypes.removeAll(excludeTaxonRelationshipTypes);
|
237
|
|
238
|
for (TaxonRelationshipType relationshipType : relationshipTypes){
|
239
|
if(!relationshipType.isSymmetric()){
|
240
|
TaxonRelationshipTypeInverseContainer inverseContainer = new TaxonRelationshipTypeInverseContainer(relationshipType, true);
|
241
|
relationshipTypeInverseContainers.add(inverseContainer);
|
242
|
}
|
243
|
TaxonRelationshipTypeInverseContainer container = new TaxonRelationshipTypeInverseContainer(relationshipType, false);
|
244
|
relationshipTypeInverseContainers.add(container);
|
245
|
}
|
246
|
|
247
|
return relationshipTypeInverseContainers;
|
248
|
}
|
249
|
});
|
250
|
}
|
251
|
|
252
|
private static <T extends DefinedTermBase> ITermStoreEdgeCase<T> getEdgeCase(Class<T> termClass) {
|
253
|
|
254
|
for (ITermStoreEdgeCase termStoreEdgeCase : termStoreEdgeCases){
|
255
|
if (termStoreEdgeCase.getTermClass().equals(termClass)){
|
256
|
return termStoreEdgeCase;
|
257
|
}
|
258
|
}
|
259
|
|
260
|
return null;
|
261
|
}
|
262
|
|
263
|
private interface ITermStoreEdgeCase<TERM> {
|
264
|
|
265
|
public abstract Class<TERM> getTermClass();
|
266
|
|
267
|
public abstract List<TERM> getTerms();
|
268
|
|
269
|
}
|
270
|
}
|