|
1
|
/**
|
|
2
|
* Copyright (C) 2013 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
|
package eu.etaxonomy.cdm.io.taxonx2013;
|
|
10
|
|
|
11
|
import java.util.Set;
|
|
12
|
|
|
13
|
import org.apache.log4j.Logger;
|
|
14
|
|
|
15
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
16
|
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
|
|
17
|
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
|
|
18
|
import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
|
|
19
|
import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
|
|
20
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
|
21
|
import eu.etaxonomy.cdm.model.description.TextData;
|
|
22
|
import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
|
|
23
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
|
24
|
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
|
|
25
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
|
26
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
|
27
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
28
|
|
|
29
|
/**
|
|
30
|
* @author pkelbert
|
|
31
|
* @date 20 déc. 2013
|
|
32
|
*
|
|
33
|
*/
|
|
34
|
public class TaxonXAddSources {
|
|
35
|
|
|
36
|
private Reference sourceUrlRef;
|
|
37
|
private TaxonXImport importer;
|
|
38
|
private TaxonXImportState configState;
|
|
39
|
@SuppressWarnings("unused")
|
|
40
|
private static final Logger logger = Logger.getLogger(TaxonXAddSources.class);
|
|
41
|
|
|
42
|
/**
|
|
43
|
* @param importer
|
|
44
|
*/
|
|
45
|
public void setImporter(TaxonXImport importer) {
|
|
46
|
this.importer=importer;
|
|
47
|
}
|
|
48
|
|
|
49
|
|
|
50
|
/**
|
|
51
|
* @param configState the configState to set
|
|
52
|
*/
|
|
53
|
public void setConfigState(TaxonXImportState configState) {
|
|
54
|
this.configState = configState;
|
|
55
|
}
|
|
56
|
|
|
57
|
|
|
58
|
/**
|
|
59
|
* @return the sourceUrlRef
|
|
60
|
*/
|
|
61
|
public Reference getSourceUrlRef() {
|
|
62
|
return sourceUrlRef;
|
|
63
|
}
|
|
64
|
|
|
65
|
/**
|
|
66
|
* @param sourceUrlRef the sourceUrlRef to set
|
|
67
|
*/
|
|
68
|
public void setSourceUrlRef(Reference sourceUrlRef) {
|
|
69
|
this.sourceUrlRef = sourceUrlRef;
|
|
70
|
}
|
|
71
|
|
|
72
|
|
|
73
|
protected IdentifiableSource getIdentifiableSource(Reference reference, Set<IdentifiableSource> sources, boolean original){
|
|
74
|
// logger.info("getIdentifiableSource");
|
|
75
|
boolean sourceExists=false;
|
|
76
|
IdentifiableSource source=null;
|
|
77
|
for (IdentifiableSource src : sources){
|
|
78
|
String micro = src.getCitationMicroReference();
|
|
79
|
Reference r = src.getCitation();
|
|
80
|
if (r.getTitleCache().equals(reference.getTitleCache())) {
|
|
81
|
sourceExists=true;
|
|
82
|
break;
|
|
83
|
}
|
|
84
|
}
|
|
85
|
if(!sourceExists) {
|
|
86
|
if(original) {
|
|
87
|
source = IdentifiableSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource,null,null,reference,null);
|
|
88
|
} else {
|
|
89
|
source = IdentifiableSource.NewInstance(OriginalSourceType.Import,null,null,reference,null);
|
|
90
|
}
|
|
91
|
}
|
|
92
|
return source;
|
|
93
|
}
|
|
94
|
|
|
95
|
protected DescriptionElementSource getDescriptionElementSource(Reference reference, Set<DescriptionElementSource> sources, boolean original){
|
|
96
|
//logger.info("getDescriptionElementSource");
|
|
97
|
boolean sourceExists=false;
|
|
98
|
DescriptionElementSource source=null;
|
|
99
|
for (DescriptionElementSource src : sources){
|
|
100
|
String micro = src.getCitationMicroReference();
|
|
101
|
Reference r = src.getCitation();
|
|
102
|
if (r.getTitleCache().equals(reference.getTitleCache())) {
|
|
103
|
sourceExists=true;
|
|
104
|
break;
|
|
105
|
}
|
|
106
|
}
|
|
107
|
if(!sourceExists) {
|
|
108
|
if(original) {
|
|
109
|
source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource,null,null,reference,null);
|
|
110
|
} else {
|
|
111
|
source = DescriptionElementSource.NewInstance(OriginalSourceType.Import,null,null,reference,null);
|
|
112
|
}
|
|
113
|
}
|
|
114
|
return source;
|
|
115
|
|
|
116
|
}
|
|
117
|
|
|
118
|
/**
|
|
119
|
* @param refMods
|
|
120
|
* @param synonym
|
|
121
|
*/
|
|
122
|
protected void addSource(Reference refMods, Synonym synonym) {
|
|
123
|
//logger.info("addSource");
|
|
124
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
125
|
Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
|
|
126
|
IdentifiableSource id = getIdentifiableSource(sourceUrlRef,synonym.getSources(), false);
|
|
127
|
IdentifiableSource id2 = getIdentifiableSource(refMods,synonym.getSources(), true);
|
|
128
|
IdentifiableSource id3 = getIdentifiableSource(sec,synonym.getSources(), false);
|
|
129
|
if( id!=null) {
|
|
130
|
synonym.addSource(id);
|
|
131
|
}
|
|
132
|
if( id2!=null) {
|
|
133
|
synonym.addSource(id2);
|
|
134
|
}
|
|
135
|
if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
|
|
136
|
synonym.addSource(id3);
|
|
137
|
}
|
|
138
|
}
|
|
139
|
|
|
140
|
|
|
141
|
/**
|
|
142
|
* @param refMods
|
|
143
|
* @param indAssociation
|
|
144
|
*/
|
|
145
|
protected IndividualsAssociation addSource(Reference refMods, IndividualsAssociation indAssociation) {
|
|
146
|
//logger.info("addSource");
|
|
147
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
148
|
Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
|
|
149
|
DescriptionElementSource id = getDescriptionElementSource(sourceUrlRef, indAssociation.getSources(), false);
|
|
150
|
DescriptionElementSource id2 = getDescriptionElementSource(refMods, indAssociation.getSources(), true);
|
|
151
|
DescriptionElementSource id3 = getDescriptionElementSource(sec, indAssociation.getSources(), false);
|
|
152
|
|
|
153
|
if(id!=null) {
|
|
154
|
indAssociation.addSource(id);
|
|
155
|
}
|
|
156
|
if( id2!=null) {
|
|
157
|
indAssociation.addSource(id2);
|
|
158
|
}
|
|
159
|
if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
|
|
160
|
indAssociation.addSource(id3);
|
|
161
|
}
|
|
162
|
return indAssociation;
|
|
163
|
}
|
|
164
|
|
|
165
|
/**
|
|
166
|
* @param refMods
|
|
167
|
* @param acceptedTaxon
|
|
168
|
*/
|
|
169
|
protected void addSource(Reference refMods, Taxon acceptedTaxon) {
|
|
170
|
//logger.info("addSource");
|
|
171
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
172
|
Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
|
|
173
|
IdentifiableSource id = getIdentifiableSource(sourceUrlRef, acceptedTaxon.getSources(), false);
|
|
174
|
IdentifiableSource id2 = getIdentifiableSource(refMods, acceptedTaxon.getSources(), true);
|
|
175
|
IdentifiableSource id3 = getIdentifiableSource(sec, acceptedTaxon.getSources(), false);
|
|
176
|
if( id!=null) {
|
|
177
|
acceptedTaxon.addSource(id);
|
|
178
|
}
|
|
179
|
if( id2!=null) {
|
|
180
|
acceptedTaxon.addSource(id2);
|
|
181
|
}
|
|
182
|
if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
|
|
183
|
acceptedTaxon.addSource(id3);
|
|
184
|
}
|
|
185
|
}
|
|
186
|
|
|
187
|
/**
|
|
188
|
* @param refMods
|
|
189
|
* @param nameToBeFilled
|
|
190
|
*/
|
|
191
|
protected void addSource(Reference refMods, ITaxonNameBase nameToBeFilled) {
|
|
192
|
//logger.info("addSource");
|
|
193
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
194
|
Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
|
|
195
|
IdentifiableSource id = getIdentifiableSource(sourceUrlRef, nameToBeFilled.getSources(), false);
|
|
196
|
IdentifiableSource id2 = getIdentifiableSource(refMods, nameToBeFilled.getSources(), true);
|
|
197
|
IdentifiableSource id3 = getIdentifiableSource(sec, nameToBeFilled.getSources(), false);
|
|
198
|
|
|
199
|
if( id!=null) {
|
|
200
|
nameToBeFilled.addSource(id);
|
|
201
|
}
|
|
202
|
if( id2!=null) {
|
|
203
|
nameToBeFilled.addSource(id2);
|
|
204
|
}
|
|
205
|
if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
|
|
206
|
nameToBeFilled.addSource(id3);
|
|
207
|
}
|
|
208
|
|
|
209
|
}
|
|
210
|
|
|
211
|
/**
|
|
212
|
* @param refMods
|
|
213
|
* @param textData
|
|
214
|
*/
|
|
215
|
protected void addSource(Reference refMods, TextData textData) {
|
|
216
|
//logger.info("addSource");
|
|
217
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
218
|
Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
|
|
219
|
DescriptionElementSource id = getDescriptionElementSource(sourceUrlRef, textData.getSources(), false);
|
|
220
|
DescriptionElementSource id2 = getDescriptionElementSource(refMods, textData.getSources(), true);
|
|
221
|
DescriptionElementSource id3 = getDescriptionElementSource(sec, textData.getSources(), false);
|
|
222
|
|
|
223
|
if( id!=null) {
|
|
224
|
textData.addSource(id);
|
|
225
|
}
|
|
226
|
if( id2!=null) {
|
|
227
|
textData.addSource(id2);
|
|
228
|
}
|
|
229
|
if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
|
|
230
|
textData.addSource(id3);
|
|
231
|
}
|
|
232
|
|
|
233
|
}
|
|
234
|
|
|
235
|
/**
|
|
236
|
* @param refMods
|
|
237
|
* @param taxonDescription
|
|
238
|
* @param currentRef
|
|
239
|
*/
|
|
240
|
protected void addAndSaveSource(Reference refMods, TaxonDescription taxonDescription, Reference currentRef) {
|
|
241
|
//logger.info("addAndSaveSource");
|
|
242
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
243
|
Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
|
|
244
|
IdentifiableSource id = getIdentifiableSource(sourceUrlRef, taxonDescription.getSources(), false);
|
|
245
|
IdentifiableSource id2 = getIdentifiableSource(refMods, taxonDescription.getSources(), true);
|
|
246
|
IdentifiableSource id3 = getIdentifiableSource(sec, taxonDescription.getSources(), false);
|
|
247
|
|
|
248
|
if( id!=null) {
|
|
249
|
taxonDescription.addSource(id);
|
|
250
|
}
|
|
251
|
if( id2!=null) {
|
|
252
|
taxonDescription.addSource(id2);
|
|
253
|
}
|
|
254
|
if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
|
|
255
|
taxonDescription.addSource(id3);
|
|
256
|
}
|
|
257
|
|
|
258
|
importer.getDescriptionService().saveOrUpdate(taxonDescription);
|
|
259
|
}
|
|
260
|
|
|
261
|
/**
|
|
262
|
* @param refMods
|
|
263
|
* @param derivedUnitBase
|
|
264
|
*/
|
|
265
|
protected void addAndSaveSource(Reference refMods, DerivedUnit derivedUnitBase) {
|
|
266
|
//logger.info("addAndSaveSource");
|
|
267
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
268
|
Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
|
|
269
|
IdentifiableSource id = getIdentifiableSource(sourceUrlRef, derivedUnitBase.getSources(), false);
|
|
270
|
IdentifiableSource id2 = getIdentifiableSource(refMods, derivedUnitBase.getSources(), true);
|
|
271
|
IdentifiableSource id3 = getIdentifiableSource(sec, derivedUnitBase.getSources(), false);
|
|
272
|
|
|
273
|
if( id!=null) {
|
|
274
|
derivedUnitBase.addSource(id);
|
|
275
|
}
|
|
276
|
if( id2!=null) {
|
|
277
|
derivedUnitBase.addSource(id2);
|
|
278
|
}
|
|
279
|
if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
|
|
280
|
derivedUnitBase.addSource(id3);
|
|
281
|
}
|
|
282
|
importer.getOccurrenceService().saveOrUpdate(derivedUnitBase);
|
|
283
|
derivedUnitBase= CdmBase.deproxy(derivedUnitBase, DerivedUnit.class);
|
|
284
|
}
|
|
285
|
|
|
286
|
|
|
287
|
/**
|
|
288
|
* @param refMods
|
|
289
|
* @param taxonDescription
|
|
290
|
*/
|
|
291
|
public void addSource(Reference refMods, TaxonDescription taxonDescription) {
|
|
292
|
//logger.info("addSource");
|
|
293
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
294
|
Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
|
|
295
|
IdentifiableSource id = getIdentifiableSource(sourceUrlRef, taxonDescription.getSources(), false);
|
|
296
|
IdentifiableSource id2 = getIdentifiableSource(refMods, taxonDescription.getSources(), true);
|
|
297
|
IdentifiableSource id3 = getIdentifiableSource(sec, taxonDescription.getSources(), false);
|
|
298
|
|
|
299
|
if( id!=null) {
|
|
300
|
taxonDescription.addSource(id);
|
|
301
|
}
|
|
302
|
if( id2!=null) {
|
|
303
|
taxonDescription.addSource(id2);
|
|
304
|
}
|
|
305
|
if(!configState.getConfig().doKeepOriginalSecundum() && id3!=null) {
|
|
306
|
taxonDescription.addSource(id3);
|
|
307
|
}
|
|
308
|
importer.getDescriptionService().saveOrUpdate(taxonDescription);
|
|
309
|
|
|
310
|
}
|
|
311
|
|
|
312
|
|
|
313
|
/**
|
|
314
|
* @param reference
|
|
315
|
* @param textData
|
|
316
|
* @param name
|
|
317
|
* @param ref
|
|
318
|
*/
|
|
319
|
public void addSource(Reference reference, TextData textData, TaxonName name, Reference refMods) {
|
|
320
|
//logger.info("addSource");
|
|
321
|
sourceUrlRef=CdmBase.deproxy(sourceUrlRef, Reference.class);
|
|
322
|
Reference sec = CdmBase.deproxy(configState.getConfig().getSecundum(), Reference.class);
|
|
323
|
DescriptionElementSource id1 = getDescriptionElementSource(refMods, textData.getSources(),name, true);
|
|
324
|
DescriptionElementSource id2 = getDescriptionElementSource(reference, textData.getSources(),name, false);
|
|
325
|
if( id1!=null) {
|
|
326
|
textData.addSource(id1);
|
|
327
|
}
|
|
328
|
|
|
329
|
if( id2!=null) {
|
|
330
|
textData.addSource(id2);
|
|
331
|
}
|
|
332
|
|
|
333
|
}
|
|
334
|
|
|
335
|
|
|
336
|
@SuppressWarnings({ "unused", "rawtypes" })
|
|
337
|
private DescriptionElementSource getDescriptionElementSource(Reference reference, Set<DescriptionElementSource> sources,
|
|
338
|
TaxonName originalname, boolean original){
|
|
339
|
//logger.info("getDescriptionElementSource");
|
|
340
|
boolean sourceExists=false;
|
|
341
|
DescriptionElementSource source=null;
|
|
342
|
for (DescriptionElementSource src : sources){
|
|
343
|
String micro = src.getCitationMicroReference();
|
|
344
|
Reference r = src.getCitation();
|
|
345
|
TaxonName oname = src.getNameUsedInSource();
|
|
346
|
try {
|
|
347
|
if (r.getTitleCache().equals(reference.getTitleCache())) {
|
|
348
|
if (oname.getTitleCache().equalsIgnoreCase(originalname.getTitleCache())) {
|
|
349
|
sourceExists=true;
|
|
350
|
break;
|
|
351
|
}
|
|
352
|
}
|
|
353
|
} catch (Exception e) {
|
|
354
|
// TODO Auto-generated catch block
|
|
355
|
e.printStackTrace();
|
|
356
|
}
|
|
357
|
}
|
|
358
|
if(!sourceExists) {
|
|
359
|
if(original) {
|
|
360
|
source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource, null,null, reference, null, originalname, null);
|
|
361
|
} else {
|
|
362
|
source = DescriptionElementSource.NewInstance(OriginalSourceType.Import, null,null, reference, null, originalname, null);
|
|
363
|
}
|
|
364
|
}
|
|
365
|
return source;
|
|
366
|
}
|
|
367
|
|
|
368
|
|
|
369
|
|
|
370
|
}
|