|
1
|
/**
|
|
2
|
* Copyright (C) 2009 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.pesi.out;
|
|
10
|
|
|
11
|
import java.util.ArrayList;
|
|
12
|
import java.util.EnumSet;
|
|
13
|
import java.util.HashSet;
|
|
14
|
import java.util.Iterator;
|
|
15
|
import java.util.List;
|
|
16
|
import java.util.Set;
|
|
17
|
import java.util.UUID;
|
|
18
|
|
|
19
|
import org.apache.log4j.Logger;
|
|
20
|
|
|
21
|
import eu.etaxonomy.cdm.api.service.pager.Pager;
|
|
22
|
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
|
|
23
|
import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
|
|
24
|
import eu.etaxonomy.cdm.io.common.DbExportBase;
|
|
25
|
import eu.etaxonomy.cdm.io.common.mapping.out.DbLastActionMapper;
|
|
26
|
import eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer;
|
|
27
|
import eu.etaxonomy.cdm.model.common.AnnotationType;
|
|
28
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
29
|
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
|
|
30
|
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
|
|
31
|
import eu.etaxonomy.cdm.model.common.Marker;
|
|
32
|
import eu.etaxonomy.cdm.model.common.MarkerType;
|
|
33
|
import eu.etaxonomy.cdm.model.common.RelationshipBase;
|
|
34
|
import eu.etaxonomy.cdm.model.description.Feature;
|
|
35
|
import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
|
|
36
|
import eu.etaxonomy.cdm.model.description.TextData;
|
|
37
|
import eu.etaxonomy.cdm.model.name.HybridRelationship;
|
|
38
|
import eu.etaxonomy.cdm.model.name.INonViralName;
|
|
39
|
import eu.etaxonomy.cdm.model.name.NameRelationship;
|
|
40
|
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
|
|
41
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
|
42
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
|
43
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
|
44
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
45
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
46
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
|
47
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
|
|
48
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
|
|
49
|
import eu.etaxonomy.cdm.persistence.query.OrderHint;
|
|
50
|
import eu.etaxonomy.cdm.strategy.cache.name.TaxonNameDefaultCacheStrategy;
|
|
51
|
import eu.etaxonomy.cdm.strategy.cache.name.ZooNameNoMarkerCacheStrategy;
|
|
52
|
|
|
53
|
/**
|
|
54
|
* @author e.-m.lee
|
|
55
|
* @since 12.02.2010
|
|
56
|
*/
|
|
57
|
public abstract class PesiExportBase
|
|
58
|
extends DbExportBase<PesiExportConfigurator, PesiExportState, PesiTransformer> {
|
|
59
|
|
|
60
|
private static final long serialVersionUID = 6226747017958138156L;
|
|
61
|
private static final Logger logger = Logger.getLogger(PesiExportBase.class);
|
|
62
|
|
|
63
|
protected static final boolean IS_CACHE = true;
|
|
64
|
|
|
65
|
private static Set<NameRelationshipType> excludedRelTypes = new HashSet<>();
|
|
66
|
|
|
67
|
private static TaxonNameDefaultCacheStrategy zooNameStrategy = ZooNameNoMarkerCacheStrategy.NewInstance();
|
|
68
|
private static TaxonNameDefaultCacheStrategy botanicalNameStrategy = TaxonNameDefaultCacheStrategy.NewInstance();
|
|
69
|
|
|
70
|
public PesiExportBase() {
|
|
71
|
super();
|
|
72
|
}
|
|
73
|
|
|
74
|
protected <CLASS extends TaxonBase> List<CLASS> getNextTaxonPartition(Class<CLASS> clazz, int limit,
|
|
75
|
int partitionCount, List<String> propertyPath) {
|
|
76
|
|
|
77
|
List<OrderHint> orderHints = new ArrayList<>();
|
|
78
|
orderHints.add(new OrderHint("id", OrderHint.SortOrder.ASCENDING ));
|
|
79
|
|
|
80
|
List<CLASS> list = getTaxonService().list(clazz, limit, partitionCount * limit, orderHints, propertyPath);
|
|
81
|
|
|
82
|
if (list.isEmpty()){
|
|
83
|
return null;
|
|
84
|
}
|
|
85
|
|
|
86
|
Iterator<CLASS> it = list.iterator();
|
|
87
|
while (it.hasNext()){
|
|
88
|
TaxonBase<?> taxonBase = it.next();
|
|
89
|
if (! isPesiTaxon(taxonBase)){
|
|
90
|
it.remove();
|
|
91
|
}
|
|
92
|
taxonBase = null;
|
|
93
|
}
|
|
94
|
it = null;
|
|
95
|
return list;
|
|
96
|
}
|
|
97
|
|
|
98
|
protected List<TaxonNameDescription> getNextNameDescriptionPartition(int limit, int partitionCount, List<String> propertyPath) {
|
|
99
|
List<OrderHint> orderHints = new ArrayList<>();
|
|
100
|
orderHints.add(new OrderHint("id", OrderHint.SortOrder.ASCENDING ));
|
|
101
|
Pager<TaxonNameDescription> l = getDescriptionService().getTaxonNameDescriptions(null, limit, partitionCount, propertyPath);
|
|
102
|
List<TaxonNameDescription> list = l.getRecords();
|
|
103
|
if (list.isEmpty()){
|
|
104
|
return null;
|
|
105
|
}
|
|
106
|
|
|
107
|
Iterator<TaxonNameDescription> it = list.iterator();
|
|
108
|
while (it.hasNext()){
|
|
109
|
TaxonNameDescription nameDescription = it.next();
|
|
110
|
if (! isPesiNameDescriptionTaxon(nameDescription)){
|
|
111
|
it.remove();
|
|
112
|
}
|
|
113
|
}
|
|
114
|
return list;
|
|
115
|
}
|
|
116
|
|
|
117
|
private boolean isPesiNameDescriptionTaxon(TaxonNameDescription nameDescription) {
|
|
118
|
TaxonName name = nameDescription.getTaxonName();
|
|
119
|
if (isPurePesiName(name)){
|
|
120
|
return true;
|
|
121
|
}else{
|
|
122
|
Set<TaxonBase> taxa = name.getTaxonBases();
|
|
123
|
for (TaxonBase<?> taxonBase : taxa){
|
|
124
|
if (isPesiTaxon(taxonBase)){
|
|
125
|
return true;
|
|
126
|
}
|
|
127
|
}
|
|
128
|
}
|
|
129
|
return false;
|
|
130
|
}
|
|
131
|
|
|
132
|
/**
|
|
133
|
* Returns the next list of pure names. If finished result will be null. If list is empty there may be result in further partitions.
|
|
134
|
*/
|
|
135
|
protected List<TaxonName> getNextPureNamePartition(Class<TaxonName> clazz,int limit, int partitionCount) {
|
|
136
|
List<OrderHint> orderHints = new ArrayList<>();
|
|
137
|
orderHints.add(new OrderHint("id", OrderHint.SortOrder.ASCENDING ));
|
|
138
|
// List<String> propPath = Arrays.asList(new String[]{"taxonBases"});
|
|
139
|
|
|
140
|
List<TaxonName> list = getNameService().list(clazz, limit, partitionCount * limit, orderHints, null);
|
|
141
|
if (list.isEmpty()){
|
|
142
|
return null;
|
|
143
|
}
|
|
144
|
Iterator<TaxonName> it = list.iterator();
|
|
145
|
while (it.hasNext()){
|
|
146
|
TaxonName taxonName = HibernateProxyHelper.deproxy(it.next());
|
|
147
|
if (! isPurePesiName(taxonName)){
|
|
148
|
it.remove();
|
|
149
|
}
|
|
150
|
}
|
|
151
|
return list;
|
|
152
|
}
|
|
153
|
|
|
154
|
protected <CLASS extends RelationshipBase> List<CLASS> getNextNameRelationshipPartition(
|
|
155
|
Class<CLASS> clazz, int pageSize, int partitionCount, List<String> propertyPaths) {
|
|
156
|
|
|
157
|
List<CLASS> result = new ArrayList<>();
|
|
158
|
List<OrderHint> orderHints = null;
|
|
159
|
List<CLASS> list;
|
|
160
|
if (NameRelationship.class.isAssignableFrom(clazz)){
|
|
161
|
list = (List<CLASS>)getNameService().listNameRelationships(null, pageSize, partitionCount, orderHints, propertyPaths);
|
|
162
|
}else if (HybridRelationship.class.isAssignableFrom(clazz)){
|
|
163
|
list = (List<CLASS>)getNameService().listHybridRelationships(null, pageSize, partitionCount, orderHints, propertyPaths);
|
|
164
|
}else{
|
|
165
|
throw new RuntimeException("Only NameRelationship or HybridRelationship allowed here");
|
|
166
|
}
|
|
167
|
if (list.isEmpty()){
|
|
168
|
return null;
|
|
169
|
}
|
|
170
|
for (CLASS rel : list){
|
|
171
|
if (isPesiNameRelationship(rel)){
|
|
172
|
result.add(rel);
|
|
173
|
}
|
|
174
|
}
|
|
175
|
return result;
|
|
176
|
}
|
|
177
|
|
|
178
|
protected <CLASS extends RelationshipBase> List<CLASS> getNextTaxonRelationshipPartition( int limit, int partitionCount, List<String> propertyPaths) {
|
|
179
|
|
|
180
|
List<CLASS> result = new ArrayList<>();
|
|
181
|
|
|
182
|
List<OrderHint> orderHints = null;
|
|
183
|
@SuppressWarnings("unchecked")
|
|
184
|
List<CLASS> list = (List<CLASS>)this.getTaxonService()
|
|
185
|
.listTaxonRelationships(null, limit, partitionCount, orderHints, propertyPaths);
|
|
186
|
|
|
187
|
if (list.isEmpty()){
|
|
188
|
return null;
|
|
189
|
}
|
|
190
|
|
|
191
|
for (CLASS rel : list){
|
|
192
|
if (isPesiTaxonOrSynonymRelationship(rel)){
|
|
193
|
result.add(rel);
|
|
194
|
}
|
|
195
|
}
|
|
196
|
return result;
|
|
197
|
}
|
|
198
|
|
|
199
|
protected List<TaxonNode> getNextTaxonNodePartition( int limit, int partitionCount, List<String> propertyPaths) {
|
|
200
|
|
|
201
|
List<TaxonNode> result = new ArrayList<>();
|
|
202
|
|
|
203
|
List<OrderHint> orderHints = null;
|
|
204
|
List<TaxonNode> list = this.getTaxonNodeService()
|
|
205
|
.list(TaxonNode.class, limit, limit * partitionCount, orderHints, propertyPaths);
|
|
206
|
|
|
207
|
if (list.isEmpty()){
|
|
208
|
return null;
|
|
209
|
}
|
|
210
|
|
|
211
|
for (TaxonNode tn : list){
|
|
212
|
if (isPesiTaxonNode(tn)){
|
|
213
|
result.add(tn);
|
|
214
|
}
|
|
215
|
}
|
|
216
|
return result;
|
|
217
|
}
|
|
218
|
|
|
219
|
protected boolean isPesiTaxonNode(TaxonNode tn){
|
|
220
|
TaxonBase<?> fromTaxon;
|
|
221
|
Taxon toTaxon;
|
|
222
|
|
|
223
|
fromTaxon = tn.getTaxon();
|
|
224
|
toTaxon = tn.getParent()== null? null: tn.getParent().getTaxon();
|
|
225
|
|
|
226
|
return (isPesiTaxon(fromTaxon, true) && isPesiTaxon(toTaxon, true));
|
|
227
|
}
|
|
228
|
|
|
229
|
protected boolean isPesiNameRelationship(RelationshipBase<?,?,?> rel){
|
|
230
|
TaxonName name1;
|
|
231
|
TaxonName name2;
|
|
232
|
if (rel.isInstanceOf(HybridRelationship.class)){
|
|
233
|
HybridRelationship hybridRel = CdmBase.deproxy(rel, HybridRelationship.class);
|
|
234
|
name1 = hybridRel.getParentName();
|
|
235
|
name2 = hybridRel.getHybridName();
|
|
236
|
}else if (rel.isInstanceOf(NameRelationship.class)){
|
|
237
|
NameRelationship nameRel = CdmBase.deproxy(rel, NameRelationship.class);
|
|
238
|
name1 = nameRel.getFromName();
|
|
239
|
name2 = nameRel.getToName();
|
|
240
|
}else{
|
|
241
|
logger.warn ("Only hybrid- and name-relationships alowed here");
|
|
242
|
return false;
|
|
243
|
}
|
|
244
|
return (isPesiName(name1) && isPesiName(name2));
|
|
245
|
}
|
|
246
|
|
|
247
|
private boolean isPesiName(TaxonName name) {
|
|
248
|
return hasPesiTaxon(name) || isPurePesiName(name);
|
|
249
|
}
|
|
250
|
|
|
251
|
protected boolean isPesiTaxonOrSynonymRelationship(RelationshipBase rel){
|
|
252
|
TaxonBase<?> fromTaxon;
|
|
253
|
Taxon toTaxon;
|
|
254
|
// TODO:fix!!!
|
|
255
|
// if (rel.isInstanceOf(SynonymRelationship.class)){
|
|
256
|
// SynonymRelationship synRel = CdmBase.deproxy(rel, SynonymRelationship.class);
|
|
257
|
// fromTaxon = synRel.getSynonym();
|
|
258
|
// toTaxon = synRel.getAcceptedTaxon();
|
|
259
|
// synRel = null;
|
|
260
|
// }else
|
|
261
|
if (rel.isInstanceOf(TaxonRelationship.class)){
|
|
262
|
TaxonRelationship taxRel = CdmBase.deproxy(rel, TaxonRelationship.class);
|
|
263
|
fromTaxon = taxRel.getFromTaxon();
|
|
264
|
toTaxon = taxRel.getToTaxon();
|
|
265
|
taxRel = null;
|
|
266
|
}else{
|
|
267
|
logger.warn ("Only synonym - and taxon-relationships allowed here");
|
|
268
|
return false;
|
|
269
|
}
|
|
270
|
return (isPesiTaxon(fromTaxon, false) && isPesiTaxon(toTaxon, true));
|
|
271
|
}
|
|
272
|
|
|
273
|
/**
|
|
274
|
* Decides if a name is not used as the name part of a PESI taxon (and therefore is
|
|
275
|
* exported to PESI as taxon already) but is related to a name used as a PESI taxon
|
|
276
|
* (e.g. as basionym, orthographic variant, etc.) and therefore should be exported
|
|
277
|
* to PESI as part of the name relationship.
|
|
278
|
* @param taxonName
|
|
279
|
* @return
|
|
280
|
*/
|
|
281
|
protected boolean isPurePesiName(TaxonName taxonName){
|
|
282
|
if (hasPesiTaxon(taxonName)){
|
|
283
|
return false;
|
|
284
|
}
|
|
285
|
|
|
286
|
//from names
|
|
287
|
for (NameRelationship rel :taxonName.getRelationsFromThisName()){
|
|
288
|
TaxonName relatedName = rel.getToName();
|
|
289
|
if (hasPesiTaxon(relatedName)){
|
|
290
|
return true;
|
|
291
|
}
|
|
292
|
}
|
|
293
|
|
|
294
|
//excluded relationships on to-side
|
|
295
|
initExcludedRelTypes();
|
|
296
|
|
|
297
|
//to names
|
|
298
|
for (NameRelationship rel :taxonName.getRelationsToThisName()){
|
|
299
|
//exclude certain types
|
|
300
|
if (excludedRelTypes.contains(rel.getType())){
|
|
301
|
continue;
|
|
302
|
}
|
|
303
|
TaxonName relatedName = rel.getFromName();
|
|
304
|
if (hasPesiTaxon(relatedName)){
|
|
305
|
return true;
|
|
306
|
}
|
|
307
|
}
|
|
308
|
|
|
309
|
//include hybrid parents, but no childs
|
|
310
|
|
|
311
|
for (HybridRelationship rel : taxonName.getHybridParentRelations()){
|
|
312
|
INonViralName child = rel.getHybridName();
|
|
313
|
if (hasPesiTaxon(child)){
|
|
314
|
return true;
|
|
315
|
}
|
|
316
|
}
|
|
317
|
|
|
318
|
return false;
|
|
319
|
}
|
|
320
|
|
|
321
|
|
|
322
|
private void initExcludedRelTypes() {
|
|
323
|
if (excludedRelTypes.isEmpty()){
|
|
324
|
excludedRelTypes.add(NameRelationshipType.BASIONYM());
|
|
325
|
excludedRelTypes.add(NameRelationshipType.REPLACED_SYNONYM());
|
|
326
|
excludedRelTypes.add(NameRelationshipType.ORTHOGRAPHIC_VARIANT());
|
|
327
|
}
|
|
328
|
}
|
|
329
|
|
|
330
|
|
|
331
|
/**
|
|
332
|
* Decides if a given name has "PESI taxa" attached.
|
|
333
|
*
|
|
334
|
* @see #getPesiTaxa(TaxonNameBase)
|
|
335
|
* @see #isPesiTaxon(TaxonBase)
|
|
336
|
* @param taxonName
|
|
337
|
* @return
|
|
338
|
*/
|
|
339
|
protected boolean hasPesiTaxon(INonViralName taxonName) {
|
|
340
|
for (TaxonBase<?> taxon : taxonName.getTaxonBases()){
|
|
341
|
if (isPesiTaxon(taxon)){
|
|
342
|
return true;
|
|
343
|
}
|
|
344
|
}
|
|
345
|
return false;
|
|
346
|
}
|
|
347
|
|
|
348
|
/**
|
|
349
|
* Returns those concepts (taxon bases) for the given name that
|
|
350
|
* are pesi taxa.
|
|
351
|
*
|
|
352
|
* @see #isPesiTaxon(TaxonBase)
|
|
353
|
* @param name
|
|
354
|
* @return
|
|
355
|
*/
|
|
356
|
protected Set<TaxonBase<?>> getPesiTaxa(TaxonName name){
|
|
357
|
Set<TaxonBase<?>> result = new HashSet<>();
|
|
358
|
for (TaxonBase<?> taxonBase : name.getTaxonBases()){
|
|
359
|
if (isPesiTaxon(taxonBase)){
|
|
360
|
result.add(taxonBase);
|
|
361
|
}
|
|
362
|
}
|
|
363
|
return result;
|
|
364
|
}
|
|
365
|
|
|
366
|
/**
|
|
367
|
* @see #isPesiTaxon(TaxonBase, boolean)
|
|
368
|
* @return
|
|
369
|
*/
|
|
370
|
protected static boolean isPesiTaxon(TaxonBase taxonBase) {
|
|
371
|
return isPesiTaxon(taxonBase, false);
|
|
372
|
}
|
|
373
|
|
|
374
|
/**
|
|
375
|
* Checks if this taxon base is a taxon that is to be exported to PESI. This is generally the case
|
|
376
|
* but not for taxa that are marked as "unpublish". Synonyms and misapplied names are exported if they are
|
|
377
|
* related at least to one accepted taxon that is also exported, except for those misapplied names
|
|
378
|
* marked as misapplied names created by Euro+Med common names ({@linkplain http://dev.e-taxonomy.eu/trac/ticket/2786} ).
|
|
379
|
* The list of conditions may change in future.
|
|
380
|
* @param taxonBase
|
|
381
|
* @return
|
|
382
|
*/
|
|
383
|
protected static boolean isPesiTaxon(TaxonBase<?> taxonBase, boolean excludeMisappliedNames) {
|
|
384
|
if (taxonBase == null){
|
|
385
|
return false;
|
|
386
|
}
|
|
387
|
//handle accepted taxa
|
|
388
|
if (taxonBase.isInstanceOf(Taxon.class)){
|
|
389
|
Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
390
|
return isPesiAcceptedTaxon(excludeMisappliedNames, taxon);
|
|
391
|
//handle synonyms
|
|
392
|
}else if (taxonBase.isInstanceOf(Synonym.class)){
|
|
393
|
Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
|
|
394
|
return isPesiSynonym(synonym);
|
|
395
|
}else {
|
|
396
|
throw new RuntimeException("Unknown taxon base type: " + taxonBase.getClass());
|
|
397
|
}
|
|
398
|
}
|
|
399
|
|
|
400
|
private static boolean isPesiSynonym(Synonym synonym) {
|
|
401
|
boolean hasAcceptedPesiTaxon = false;
|
|
402
|
|
|
403
|
hasAcceptedPesiTaxon = isPesiTaxon(synonym.getAcceptedTaxon());
|
|
404
|
if (!hasAcceptedPesiTaxon) {if (logger.isDebugEnabled()){logger.debug("Synonym has no accepted PESI taxon: " + synonym.getUuid() + ", (" + synonym.getTitleCache() + ")");}}
|
|
405
|
|
|
406
|
return hasAcceptedPesiTaxon && synonym.isPublish();
|
|
407
|
}
|
|
408
|
|
|
409
|
private static boolean isPesiAcceptedTaxon(boolean excludeMisappliedNames, Taxon taxon) {
|
|
410
|
if (! taxon.isPublish()){
|
|
411
|
return false;
|
|
412
|
}
|
|
413
|
for (Marker marker : taxon.getMarkers()){
|
|
414
|
//probably not needed anymore after #1780 was fixed, also #4046 interesting
|
|
415
|
if (marker.getValue() == false && marker.getMarkerType().equals(MarkerType.PUBLISH())){
|
|
416
|
return false;
|
|
417
|
//probably not needed any more after #2786 was fixed
|
|
418
|
}else if (marker.getValue() == true && marker.getMarkerType().getUuid().equals(BerlinModelTransformer.uuidMisappliedCommonName)){
|
|
419
|
logger.warn("Misapplied common name still exists");
|
|
420
|
return false;
|
|
421
|
}
|
|
422
|
}
|
|
423
|
|
|
424
|
//handle PESI accepted taxa
|
|
425
|
if (! taxon.isMisapplication()){
|
|
426
|
for (Marker marker : taxon.getMarkers()){
|
|
427
|
if (marker.getValue() == false && marker.getMarkerType().equals(MarkerType.PUBLISH())){
|
|
428
|
return false;
|
|
429
|
}
|
|
430
|
}
|
|
431
|
return true;
|
|
432
|
//handle misapplied names
|
|
433
|
}else{
|
|
434
|
if (excludeMisappliedNames){
|
|
435
|
return false;
|
|
436
|
}
|
|
437
|
for (Marker marker : taxon.getMarkers()){
|
|
438
|
//probably not needed any more after #2786 was fixed
|
|
439
|
if (marker.getValue() == true && marker.getMarkerType().getUuid().equals(BerlinModelTransformer.uuidMisappliedCommonName)){
|
|
440
|
logger.warn("Misapplied common name still exists");
|
|
441
|
return false;
|
|
442
|
}
|
|
443
|
}
|
|
444
|
for (TaxonRelationship taxRel : taxon.getRelationsFromThisTaxon()){
|
|
445
|
if (taxRel.getType().isAnyMisappliedName()){
|
|
446
|
// logger.warn(taxRel.getUuid() + "; " + taxRel.getToTaxon().getUuid() + " + " + taxRel.getToTaxon().getTitleCache());
|
|
447
|
if (isPesiTaxon(taxRel.getToTaxon(), true)){
|
|
448
|
return true;
|
|
449
|
}
|
|
450
|
}
|
|
451
|
}
|
|
452
|
if (logger.isDebugEnabled()){ logger.debug("Misapplied name has no accepted PESI taxon: " + taxon.getUuid() + ", (" + taxon.getTitleCache() + ")");}
|
|
453
|
return false;
|
|
454
|
}
|
|
455
|
}
|
|
456
|
|
|
457
|
@Override
|
|
458
|
protected Object getDbIdCdmWithExceptions(CdmBase cdmBase, PesiExportState state) {
|
|
459
|
if (cdmBase.isInstanceOf(TaxonName.class)){
|
|
460
|
TaxonName name = CdmBase.deproxy(cdmBase, TaxonName.class);
|
|
461
|
if (name.getTaxonBases().size()>1){
|
|
462
|
logger.warn("Name has multiple taxa. Can't define correct ID. Use first one." + name.getUuid());
|
|
463
|
}
|
|
464
|
if (!name.getTaxonBases().isEmpty()){
|
|
465
|
TaxonBase<?> tb = name.getTaxonBases().iterator().next();
|
|
466
|
return this.getDbId(tb, state);
|
|
467
|
}else{
|
|
468
|
return ( cdmBase.getId() + state.getConfig().getNameIdStart() );
|
|
469
|
}
|
|
470
|
}else if (isAdditionalSource(cdmBase) ){
|
|
471
|
return ( cdmBase.getId() + 2 * state.getConfig().getNameIdStart() ); //make it a separate variable if conflicts occur.
|
|
472
|
}else{
|
|
473
|
return super.getDbIdCdmWithExceptions(cdmBase, state);
|
|
474
|
}
|
|
475
|
}
|
|
476
|
|
|
477
|
private boolean isAdditionalSource(CdmBase cdmBase) {
|
|
478
|
if (cdmBase.isInstanceOf(TextData.class)){
|
|
479
|
TextData textData = CdmBase.deproxy(cdmBase, TextData.class);
|
|
480
|
if (textData.getFeature().equals(Feature.ADDITIONAL_PUBLICATION()) ||
|
|
481
|
textData.getFeature().equals(Feature.CITATION())){
|
|
482
|
return true;
|
|
483
|
}
|
|
484
|
}
|
|
485
|
return false;
|
|
486
|
}
|
|
487
|
|
|
488
|
protected MarkerType getUuidMarkerType(UUID uuid, PesiExportState state){
|
|
489
|
if (uuid == null){
|
|
490
|
uuid = UUID.randomUUID();
|
|
491
|
}
|
|
492
|
|
|
493
|
MarkerType markerType = state.getMarkerType(uuid);
|
|
494
|
if (markerType == null){
|
|
495
|
if (uuid.equals(PesiTransformer.uuidMarkerGuidIsMissing)){
|
|
496
|
markerType = MarkerType.NewInstance("Uuid is Missing", "Uuid is missing", null);
|
|
497
|
markerType.setUuid(uuid);
|
|
498
|
} else if (uuid.equals(PesiTransformer.uuidMarkerTypeHasNoLastAction)){
|
|
499
|
markerType = MarkerType.NewInstance("Has no last Action", "Has no last action", null);
|
|
500
|
markerType.setUuid(uuid);
|
|
501
|
}
|
|
502
|
}
|
|
503
|
|
|
504
|
state.putMarkerType(markerType);
|
|
505
|
return markerType;
|
|
506
|
}
|
|
507
|
|
|
508
|
protected static TaxonNameDefaultCacheStrategy getCacheStrategy(TaxonName taxonName) {
|
|
509
|
TaxonNameDefaultCacheStrategy cacheStrategy;
|
|
510
|
if (taxonName.isZoological()){
|
|
511
|
cacheStrategy = zooNameStrategy;
|
|
512
|
}else if (taxonName.isBotanical()) {
|
|
513
|
cacheStrategy = botanicalNameStrategy;
|
|
514
|
}else{
|
|
515
|
logger.error("Unhandled taxon name type. Can't define strategy class");
|
|
516
|
cacheStrategy = botanicalNameStrategy;
|
|
517
|
}
|
|
518
|
return cacheStrategy;
|
|
519
|
}
|
|
520
|
|
|
521
|
/**
|
|
522
|
* Checks whether a given taxon is a misapplied name.
|
|
523
|
* @param taxon The {@link TaxonBase Taxon}.
|
|
524
|
* @return Whether the given TaxonName is a misapplied name or not.
|
|
525
|
*/
|
|
526
|
protected static boolean isMisappliedName(TaxonBase<?> taxon) {
|
|
527
|
return getAcceptedTaxonForMisappliedName(taxon) != null;
|
|
528
|
}
|
|
529
|
|
|
530
|
/**
|
|
531
|
* Returns the first accepted taxon for this misapplied name.
|
|
532
|
* If this misapplied name is not a misapplied name, <code>null</code> is returned.
|
|
533
|
* @param taxon The {@link TaxonBase Taxon}.
|
|
534
|
*/
|
|
535
|
private static Taxon getAcceptedTaxonForMisappliedName(TaxonBase<?> taxon) {
|
|
536
|
if (! taxon.isInstanceOf(Taxon.class)){
|
|
537
|
return null;
|
|
538
|
}
|
|
539
|
Set<TaxonRelationship> taxonRelations = CdmBase.deproxy(taxon, Taxon.class).getRelationsFromThisTaxon();
|
|
540
|
for (TaxonRelationship taxonRelationship : taxonRelations) {
|
|
541
|
TaxonRelationshipType taxonRelationshipType = taxonRelationship.getType();
|
|
542
|
if (taxonRelationshipType.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())) {
|
|
543
|
return taxonRelationship.getToTaxon();
|
|
544
|
}
|
|
545
|
}
|
|
546
|
return null;
|
|
547
|
}
|
|
548
|
|
|
549
|
protected List<AnnotationType> getLastActionAnnotationTypes() {
|
|
550
|
Set<UUID> uuidSet = new HashSet<>();
|
|
551
|
uuidSet.add(DbLastActionMapper.uuidAnnotationTypeLastActionDate);
|
|
552
|
uuidSet.add(DbLastActionMapper.uuidAnnotationTypeLastAction);
|
|
553
|
uuidSet.add(ErmsTransformer.uuidAnnSpeciesExpertName);
|
|
554
|
@SuppressWarnings({"unchecked","rawtypes"})
|
|
555
|
List<AnnotationType> result = (List)getTermService().find(uuidSet);
|
|
556
|
return result;
|
|
557
|
}
|
|
558
|
|
|
559
|
protected enum PesiSource{
|
|
560
|
EM,
|
|
561
|
FE,
|
|
562
|
ERMS,
|
|
563
|
IF;
|
|
564
|
|
|
565
|
private PesiSource(){
|
|
566
|
|
|
567
|
}
|
|
568
|
}
|
|
569
|
|
|
570
|
/**
|
|
571
|
* Returns the source (E+M, Fauna Europaea, Index Fungorum, ERMS) of a given
|
|
572
|
* Identifiable Entity as an {@link EnumSet enum set}
|
|
573
|
*/
|
|
574
|
protected static EnumSet<PesiSource> getSources(IdentifiableEntity<?> entity){
|
|
575
|
EnumSet<PesiSource> result = EnumSet.noneOf(PesiSource.class);
|
|
576
|
|
|
577
|
Set<IdentifiableSource> sources = getPesiSources(entity);
|
|
578
|
for (IdentifiableSource source : sources) {
|
|
579
|
Reference ref = source.getCitation();
|
|
580
|
UUID refUuid = ref.getUuid();
|
|
581
|
if (refUuid.equals(PesiTransformer.uuidSourceRefEuroMed)){
|
|
582
|
result.add(PesiSource.EM);
|
|
583
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefFaunaEuropaea)){
|
|
584
|
result.add(PesiSource.FE);
|
|
585
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefErms)){
|
|
586
|
result.add(PesiSource.ERMS);
|
|
587
|
}else if (refUuid.equals(PesiTransformer.uuidSourceRefIndexFungorum)){
|
|
588
|
result.add(PesiSource.IF);
|
|
589
|
}else{
|
|
590
|
if (logger.isDebugEnabled()){logger.debug("Not a PESI source");};
|
|
591
|
}
|
|
592
|
}
|
|
593
|
return result;
|
|
594
|
}
|
|
595
|
|
|
596
|
/**
|
|
597
|
* Returns the Sources for a given TaxonName only.
|
|
598
|
* @param identifiableEntity
|
|
599
|
* @return The Sources.
|
|
600
|
*/
|
|
601
|
protected static Set<IdentifiableSource> getPesiSources(IdentifiableEntity<?> identifiableEntity) {
|
|
602
|
Set<IdentifiableSource> sources = new HashSet<>();
|
|
603
|
|
|
604
|
//Taxon Names
|
|
605
|
if (identifiableEntity.isInstanceOf(TaxonName.class)){
|
|
606
|
// Sources from TaxonName
|
|
607
|
TaxonName taxonName = CdmBase.deproxy(identifiableEntity, TaxonName.class);
|
|
608
|
Set<IdentifiableSource> testSources = identifiableEntity.getSources();
|
|
609
|
sources = filterPesiSources(testSources);
|
|
610
|
|
|
611
|
if (sources.size() == 0 && testSources.size()>0){
|
|
612
|
IdentifiableSource source = testSources.iterator().next();
|
|
613
|
logger.warn("There are sources, but they are no pesi sources!!!" + source.getIdInSource() + " - " + source.getIdNamespace() + " - " + source.getCitation().getTitleCache());
|
|
614
|
}
|
|
615
|
if (sources.size() > 1) {
|
|
616
|
logger.warn("This TaxonName has more than one Source: " + identifiableEntity.getUuid() + " (" + identifiableEntity.getTitleCache() + ")");
|
|
617
|
}
|
|
618
|
|
|
619
|
// name has no PESI source, take sources from TaxonBase
|
|
620
|
if (sources == null || sources.isEmpty()) {
|
|
621
|
Set<TaxonBase> taxa = taxonName.getTaxonBases();
|
|
622
|
for (TaxonBase<?> taxonBase: taxa){
|
|
623
|
sources.addAll(filterPesiSources(taxonBase.getSources()));
|
|
624
|
}
|
|
625
|
}
|
|
626
|
|
|
627
|
//for TaxonBases
|
|
628
|
}else if (identifiableEntity.isInstanceOf(TaxonBase.class)){
|
|
629
|
sources = filterPesiSources(identifiableEntity.getSources());
|
|
630
|
} else {
|
|
631
|
sources = filterPesiSources(identifiableEntity.getSources());
|
|
632
|
}
|
|
633
|
|
|
634
|
return sources;
|
|
635
|
}
|
|
636
|
|
|
637
|
// return all sources with a PESI reference
|
|
638
|
protected static Set<IdentifiableSource> filterPesiSources(Set<? extends IdentifiableSource> sources) {
|
|
639
|
Set<IdentifiableSource> result = new HashSet<>();
|
|
640
|
for (IdentifiableSource source : sources){
|
|
641
|
Reference ref = source.getCitation();
|
|
642
|
if (ref != null){
|
|
643
|
UUID refUuid = ref.getUuid();
|
|
644
|
if (refUuid.equals(PesiTransformer.uuidSourceRefEuroMed) ||
|
|
645
|
refUuid.equals(PesiTransformer.uuidSourceRefFaunaEuropaea)||
|
|
646
|
refUuid.equals(PesiTransformer.uuidSourceRefErms)||
|
|
647
|
refUuid.equals(PesiTransformer.uuidSourceRefIndexFungorum) ||
|
|
648
|
refUuid.equals(PesiTransformer.uuidSourceRefAuct)){
|
|
649
|
result.add(source);
|
|
650
|
}
|
|
651
|
}
|
|
652
|
}
|
|
653
|
return result;
|
|
654
|
}
|
|
655
|
|
|
656
|
}
|