1
|
package eu.etaxonomy.cdm.io.csv.caryophyllales.out;
|
2
|
|
3
|
import java.io.ByteArrayOutputStream;
|
4
|
import java.io.FileOutputStream;
|
5
|
import java.io.OutputStream;
|
6
|
import java.io.OutputStreamWriter;
|
7
|
import java.io.PrintWriter;
|
8
|
import java.util.ArrayList;
|
9
|
import java.util.Collections;
|
10
|
import java.util.HashMap;
|
11
|
import java.util.HashSet;
|
12
|
import java.util.Iterator;
|
13
|
import java.util.List;
|
14
|
import java.util.Set;
|
15
|
import java.util.TreeMap;
|
16
|
import java.util.UUID;
|
17
|
|
18
|
import org.apache.log4j.Logger;
|
19
|
import org.springframework.beans.factory.annotation.Autowired;
|
20
|
import org.springframework.stereotype.Component;
|
21
|
|
22
|
import eu.etaxonomy.cdm.api.service.dto.CondensedDistribution;
|
23
|
import eu.etaxonomy.cdm.api.service.pager.Pager;
|
24
|
import eu.etaxonomy.cdm.ext.geo.CondensedDistributionRecipe;
|
25
|
import eu.etaxonomy.cdm.ext.geo.IEditGeoService;
|
26
|
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
|
27
|
import eu.etaxonomy.cdm.model.common.DefinedTermBase;
|
28
|
import eu.etaxonomy.cdm.model.common.Language;
|
29
|
import eu.etaxonomy.cdm.model.description.DescriptionBase;
|
30
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
31
|
import eu.etaxonomy.cdm.model.description.Distribution;
|
32
|
import eu.etaxonomy.cdm.model.description.Feature;
|
33
|
import eu.etaxonomy.cdm.model.description.TextData;
|
34
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
35
|
import eu.etaxonomy.cdm.model.name.BotanicalName;
|
36
|
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
|
37
|
import eu.etaxonomy.cdm.model.name.HomotypicalGroupComparator;
|
38
|
import eu.etaxonomy.cdm.model.name.IBotanicalName;
|
39
|
import eu.etaxonomy.cdm.model.name.INonViralName;
|
40
|
import eu.etaxonomy.cdm.model.name.NameRelationship;
|
41
|
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
|
42
|
import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
|
43
|
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
|
44
|
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
|
45
|
import eu.etaxonomy.cdm.model.name.Rank;
|
46
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
47
|
import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
|
48
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
49
|
import eu.etaxonomy.cdm.model.taxon.Classification;
|
50
|
import eu.etaxonomy.cdm.model.taxon.HomotypicGroupTaxonComparator;
|
51
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
52
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
53
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
54
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
55
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
|
56
|
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
|
57
|
import eu.etaxonomy.cdm.persistence.query.MatchMode;
|
58
|
|
59
|
|
60
|
|
61
|
@Component
|
62
|
public class CsvNameExport extends CsvNameExportBase {
|
63
|
private static final long serialVersionUID = 7289805663701807425L;
|
64
|
|
65
|
private static final Logger logger = Logger.getLogger(CsvNameExport.class);
|
66
|
|
67
|
@Autowired
|
68
|
IEditGeoService geoService;
|
69
|
|
70
|
public CsvNameExport() {
|
71
|
super();
|
72
|
this.ioName = this.getClass().getSimpleName();
|
73
|
|
74
|
}
|
75
|
|
76
|
@Override
|
77
|
protected void doInvoke(CsvNameExportState state) {
|
78
|
CsvNameExportConfigurator config = state.getConfig();
|
79
|
|
80
|
|
81
|
PrintWriter writer = null;
|
82
|
|
83
|
try {
|
84
|
|
85
|
switch(config.getTarget()) {
|
86
|
case FILE :
|
87
|
OutputStream os = new FileOutputStream(config.getDestination());
|
88
|
os.write(239);
|
89
|
os.write(187);
|
90
|
os.write(191);
|
91
|
writer = new PrintWriter(new OutputStreamWriter(os, "UTF-8"));
|
92
|
break;
|
93
|
case EXPORT_DATA :
|
94
|
exportStream = new ByteArrayOutputStream();
|
95
|
writer = new PrintWriter(exportStream);
|
96
|
break;
|
97
|
default:
|
98
|
break;
|
99
|
|
100
|
}
|
101
|
|
102
|
List<HashMap<String, String>> result;
|
103
|
if (config.getRank() == null){
|
104
|
config.setRank(Rank.GENUS());
|
105
|
}
|
106
|
if (config.isNamesOnly()){
|
107
|
txStatus = startTransaction();
|
108
|
result = getNameService().getNameRecords();
|
109
|
} else {
|
110
|
result = getRecordsForPrintPub(state);
|
111
|
}
|
112
|
NameRecord nameRecord;
|
113
|
int count = 0;
|
114
|
boolean isFirst = true;
|
115
|
for (HashMap<String,String> record:result){
|
116
|
if (count > 0){
|
117
|
isFirst = false;
|
118
|
}
|
119
|
count++;
|
120
|
nameRecord = new NameRecord(record, isFirst);
|
121
|
nameRecord.print(writer, config);
|
122
|
|
123
|
}
|
124
|
writer.flush();
|
125
|
|
126
|
writer.close();
|
127
|
|
128
|
} catch (Exception e) {
|
129
|
// TODO Auto-generated catch block
|
130
|
e.printStackTrace();
|
131
|
}
|
132
|
if (txStatus != null ){
|
133
|
commitTransaction(txStatus);
|
134
|
}
|
135
|
return;
|
136
|
|
137
|
|
138
|
}
|
139
|
|
140
|
@Override
|
141
|
protected boolean doCheck(CsvNameExportState state) {
|
142
|
boolean result = true;
|
143
|
logger.warn("No check implemented for " + this.ioName);
|
144
|
return result;
|
145
|
}
|
146
|
|
147
|
@Override
|
148
|
protected boolean isIgnore(CsvNameExportState state) {
|
149
|
return false;
|
150
|
}
|
151
|
|
152
|
|
153
|
public List<HashMap<String,String>> getRecordsForPrintPub(CsvNameExportState state){
|
154
|
List<String> propertyPaths = new ArrayList<String>();
|
155
|
propertyPaths.add("childNodes");
|
156
|
txStatus = startTransaction();
|
157
|
Classification classification = getClassificationService().load(state.getConfig().getClassificationUUID());
|
158
|
TaxonNode rootNode = classification.getRootNode();
|
159
|
rootNode = getTaxonNodeService().load(rootNode.getUuid(), propertyPaths);
|
160
|
Set<UUID> childrenUuids = new HashSet<UUID>();
|
161
|
|
162
|
|
163
|
rootNode = HibernateProxyHelper.deproxy(rootNode, TaxonNode.class);
|
164
|
rootNode.removeNullValueFromChildren();
|
165
|
for (TaxonNode child: rootNode.getChildNodes()){
|
166
|
child = HibernateProxyHelper.deproxy(child, TaxonNode.class);
|
167
|
childrenUuids.add(child.getUuid());
|
168
|
}
|
169
|
Set<UUID> parentsNodesUUID = new HashSet<UUID>(childrenUuids);
|
170
|
childrenUuids.clear();
|
171
|
List<TaxonNode> childrenNodes = new ArrayList<TaxonNode>();
|
172
|
TaxonNameBase name;
|
173
|
|
174
|
|
175
|
findChildren(state, childrenUuids, parentsNodesUUID);
|
176
|
|
177
|
|
178
|
List<HashMap<String,String>> nameRecords = new ArrayList<HashMap<String,String>>();
|
179
|
HashMap<String,String> nameRecord = new HashMap<String,String>();
|
180
|
|
181
|
childrenNodes = getTaxonNodeService().find(childrenUuids);
|
182
|
for(TaxonNode genusNode : childrenNodes) {
|
183
|
|
184
|
nameRecords.add(createNewRecord(genusNode, state));
|
185
|
|
186
|
refreshTransaction();
|
187
|
|
188
|
}
|
189
|
|
190
|
return nameRecords;
|
191
|
|
192
|
}
|
193
|
|
194
|
/**
|
195
|
* @param state
|
196
|
* @param childrenUuids
|
197
|
* @param parentsNodesUUID
|
198
|
* @param familyNode
|
199
|
*/
|
200
|
private void findChildren(CsvNameExportState state, Set<UUID> childrenUuids, Set<UUID> parentsNodesUUID) {
|
201
|
TaxonNameBase name;
|
202
|
List<TaxonNode> familyNodes = getTaxonNodeService().find(parentsNodesUUID);
|
203
|
parentsNodesUUID =new HashSet<UUID>();
|
204
|
for (TaxonNode familyNode: familyNodes){
|
205
|
familyNode = HibernateProxyHelper.deproxy(familyNode, TaxonNode.class);
|
206
|
familyNode.removeNullValueFromChildren();
|
207
|
for (TaxonNode child: familyNode.getChildNodes()){
|
208
|
child = HibernateProxyHelper.deproxy(child, TaxonNode.class);
|
209
|
name = HibernateProxyHelper.deproxy(child.getTaxon().getName(), TaxonNameBase.class);
|
210
|
if (child.getTaxon().getName().getRank().isLower(state.getConfig().getRank()) ) {
|
211
|
childrenUuids.add(child.getUuid());
|
212
|
if (child.hasChildNodes()){
|
213
|
parentsNodesUUID.add(child.getUuid());
|
214
|
}
|
215
|
}else{
|
216
|
parentsNodesUUID.add(child.getUuid());
|
217
|
}
|
218
|
}
|
219
|
//refreshTransaction();
|
220
|
if (!parentsNodesUUID.isEmpty()){
|
221
|
findChildren(state, childrenUuids, parentsNodesUUID);
|
222
|
}
|
223
|
}
|
224
|
|
225
|
}
|
226
|
|
227
|
|
228
|
|
229
|
|
230
|
private String createSynonymNameString(IBotanicalName synonymName, boolean isInvalid) {
|
231
|
String synonymString = null;
|
232
|
|
233
|
synonymString= createTaggedNameString(synonymName, isInvalid);
|
234
|
Set<NameRelationship> nameRelations = synonymName.getNameRelations();
|
235
|
|
236
|
INonViralName relatedName = null;
|
237
|
String nameRelType = null;
|
238
|
boolean first = true;
|
239
|
boolean isInvalidRel = false;
|
240
|
for (NameRelationship nameRel: nameRelations){
|
241
|
// NameRelationship nameRel = nameRelations.iterator().next();
|
242
|
BotanicalName fromName = HibernateProxyHelper.deproxy(nameRel.getFromName(), BotanicalName.class);
|
243
|
|
244
|
nameRel = HibernateProxyHelper.deproxy(nameRel, NameRelationship.class);
|
245
|
nameRelType = nameRel.getType().getTitleCache();
|
246
|
String relatedNameString = "";
|
247
|
if (fromName.equals(synonymName)){
|
248
|
relatedName = nameRel.getToName();
|
249
|
}else{
|
250
|
relatedName = nameRel.getFromName();
|
251
|
}
|
252
|
if (!nameRel.getType().equals(NameRelationshipType.BASIONYM())){
|
253
|
isInvalidRel = getStatus(relatedName);
|
254
|
relatedNameString = createTaggedNameString(relatedName, isInvalidRel&&isInvalid);
|
255
|
|
256
|
if (nameRel.getType().equals(NameRelationshipType.LATER_HOMONYM())){
|
257
|
if (synonymName.equals(nameRel.getFromName())){
|
258
|
if (first){
|
259
|
synonymString = synonymString + " [non " + relatedNameString ;
|
260
|
first = false;
|
261
|
} else{
|
262
|
synonymString = synonymString + " nec " + relatedNameString ;
|
263
|
}
|
264
|
}
|
265
|
} else if (nameRel.getType().equals(NameRelationshipType.REPLACED_SYNONYM())){
|
266
|
//synonymString = synonymString + " [non " + relatedNameString + "]";
|
267
|
} else if (nameRel.getType().equals(NameRelationshipType.BLOCKING_NAME_FOR())){
|
268
|
if (synonymName.equals(nameRel.getToName())){
|
269
|
if (first){
|
270
|
synonymString = synonymString + " [non " + relatedNameString ;
|
271
|
first = false;
|
272
|
} else{
|
273
|
synonymString = synonymString + " nec " + relatedNameString ;
|
274
|
}
|
275
|
|
276
|
}
|
277
|
} else if (nameRel.getType().equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())){
|
278
|
if (first){
|
279
|
synonymString = synonymString + " [non " + relatedNameString ;
|
280
|
first = false;
|
281
|
} else{
|
282
|
synonymString = synonymString + " nec " + relatedNameString ;
|
283
|
}
|
284
|
} else if (nameRel.getType().equals(NameRelationshipType.ALTERNATIVE_NAME())){
|
285
|
if (first){
|
286
|
synonymString = synonymString + " [non " + relatedNameString ;
|
287
|
first = false;
|
288
|
} else{
|
289
|
synonymString = synonymString + " nec " + relatedNameString ;
|
290
|
}
|
291
|
} else if (nameRel.getType().equals(NameRelationshipType.CONSERVED_AGAINST())) {
|
292
|
|
293
|
}else if (nameRel.getType().equals(NameRelationshipType.ORTHOGRAPHIC_VARIANT())){
|
294
|
|
295
|
}
|
296
|
|
297
|
|
298
|
}
|
299
|
}
|
300
|
if (!first){
|
301
|
synonymString = synonymString + "]";
|
302
|
}
|
303
|
|
304
|
|
305
|
|
306
|
return synonymString;
|
307
|
}
|
308
|
|
309
|
/**
|
310
|
* @param relatedName
|
311
|
* @return
|
312
|
*/
|
313
|
private boolean getStatus(INonViralName relatedName) {
|
314
|
boolean result;
|
315
|
if (!relatedName.getStatus().isEmpty()){
|
316
|
NomenclaturalStatus status = HibernateProxyHelper.deproxy(relatedName.getStatus().iterator().next(),NomenclaturalStatus.class);
|
317
|
if (status.getType().isInvalidType()){
|
318
|
result = true;
|
319
|
}else{
|
320
|
result = false;
|
321
|
}
|
322
|
}else{
|
323
|
result = false;
|
324
|
}
|
325
|
return result;
|
326
|
}
|
327
|
|
328
|
private String createTaggedNameString(INonViralName name, boolean isInvalid){
|
329
|
String nameString = null;
|
330
|
if (name == null){
|
331
|
return nameString;
|
332
|
}
|
333
|
|
334
|
nameString = name.generateFullTitle();
|
335
|
if (isInvalid){
|
336
|
nameString = nameString.replace(name.getTitleCache(), "\""+name.getTitleCache()+"\"");
|
337
|
}
|
338
|
if (name.getGenusOrUninomial() != null){
|
339
|
nameString = nameString.replaceAll(name.getGenusOrUninomial(), "<i>"+ name.getGenusOrUninomial() + "</i>");
|
340
|
}
|
341
|
if (name.getInfraGenericEpithet() != null){
|
342
|
nameString = nameString.replaceAll(name.getInfraGenericEpithet(), "<i>"+ name.getInfraGenericEpithet() + "</i>");
|
343
|
}
|
344
|
if (name.getSpecificEpithet() != null){
|
345
|
nameString = nameString.replaceAll(name.getSpecificEpithet(), "<i>"+ name.getSpecificEpithet() + "</i>");
|
346
|
}
|
347
|
if (name.getInfraSpecificEpithet() != null && !name.isAutonym()){
|
348
|
nameString = nameString.replaceAll(name.getInfraSpecificEpithet(), "<i>"+ name.getInfraSpecificEpithet() + "</i>");
|
349
|
}
|
350
|
|
351
|
return nameString;
|
352
|
}
|
353
|
|
354
|
|
355
|
|
356
|
private List<TaxonNode> getGenusNodes (UUID classificationUUID){
|
357
|
Classification classification = getClassificationService().load(classificationUUID);
|
358
|
TaxonNode rootNode = classification.getRootNode();
|
359
|
rootNode = getTaxonNodeService().load(rootNode.getUuid());
|
360
|
Set<UUID> childrenUuids = new HashSet<UUID>();
|
361
|
|
362
|
for (TaxonNode child: rootNode.getChildNodes()){
|
363
|
child = HibernateProxyHelper.deproxy(child, TaxonNode.class);
|
364
|
childrenUuids.add(child.getUuid());
|
365
|
}
|
366
|
|
367
|
List<TaxonNode> familyNodes = getTaxonNodeService().find(childrenUuids);
|
368
|
childrenUuids.clear();
|
369
|
List<TaxonNode> genusNodes = new ArrayList<TaxonNode>();
|
370
|
for (TaxonNode familyNode: familyNodes){
|
371
|
for (TaxonNode child: familyNode.getChildNodes()){
|
372
|
child = HibernateProxyHelper.deproxy(child, TaxonNode.class);
|
373
|
childrenUuids.add(child.getUuid());
|
374
|
}
|
375
|
|
376
|
genusNodes = getTaxonNodeService().find(childrenUuids);
|
377
|
}
|
378
|
return genusNodes;
|
379
|
}
|
380
|
|
381
|
private TaxonNode getHigherNode(TaxonNode node, Rank rank){
|
382
|
|
383
|
Rank nodeRank = node.getTaxon().getName().getRank();
|
384
|
if (nodeRank.isKindOf(rank)){
|
385
|
return null;
|
386
|
|
387
|
}else if (nodeRank.isHigher(rank)){
|
388
|
return null;
|
389
|
} else {
|
390
|
return node.getAncestorOfRank(rank);
|
391
|
}
|
392
|
}
|
393
|
|
394
|
private void extractDescriptions(HashMap<String, String> nameRecord, Taxon taxon, Feature feature, String columnName, CsvNameExportState state){
|
395
|
StringBuffer descriptionsString = new StringBuffer();
|
396
|
TextData textElement;
|
397
|
Set<Distribution> distributions = new HashSet<Distribution>();
|
398
|
if (taxon.getDescriptions().isEmpty()){
|
399
|
nameRecord.put(columnName, null);
|
400
|
return;
|
401
|
}
|
402
|
for (DescriptionBase<?> descriptionBase: taxon.getDescriptions()){
|
403
|
if (!descriptionBase.isImageGallery()){
|
404
|
Set<DescriptionElementBase> elements = descriptionBase.getElements();
|
405
|
for (DescriptionElementBase element: elements){
|
406
|
if (element.getFeature().equals(feature)){
|
407
|
if (element instanceof TextData){
|
408
|
textElement = HibernateProxyHelper.deproxy(element, TextData.class);
|
409
|
descriptionsString.append(textElement.getText(Language.ENGLISH()));
|
410
|
|
411
|
}else if (element instanceof Distribution ){
|
412
|
|
413
|
Distribution distribution = HibernateProxyHelper.deproxy(element, Distribution.class);
|
414
|
distributions.add(distribution);
|
415
|
|
416
|
|
417
|
}
|
418
|
|
419
|
}
|
420
|
}
|
421
|
}
|
422
|
|
423
|
|
424
|
|
425
|
}
|
426
|
if (state.getConfig().isCondensedDistribution()){
|
427
|
List<Language> langs = new ArrayList<Language>();
|
428
|
langs.add(Language.ENGLISH());
|
429
|
|
430
|
|
431
|
CondensedDistribution conDis = geoService.getCondensedDistribution(distributions, true, null,null,CondensedDistributionRecipe.FloraCuba, langs );
|
432
|
|
433
|
nameRecord.put(columnName, conDis.toString());
|
434
|
|
435
|
} else{
|
436
|
NamedArea area ;
|
437
|
for (Distribution distribution:distributions){
|
438
|
|
439
|
if (descriptionsString.length()> 0 ){
|
440
|
descriptionsString.append(", ");
|
441
|
}
|
442
|
area = HibernateProxyHelper.deproxy(distribution.getArea(), NamedArea.class);
|
443
|
if (area.getIdInVocabulary() != null){
|
444
|
descriptionsString.append(area.getIdInVocabulary());
|
445
|
}else if (area.getSymbol() != null){
|
446
|
descriptionsString.append(area.getSymbol());
|
447
|
}else{
|
448
|
descriptionsString.append(area.getLabel());
|
449
|
}
|
450
|
|
451
|
}
|
452
|
nameRecord.put(columnName, descriptionsString.toString());
|
453
|
}
|
454
|
|
455
|
}
|
456
|
|
457
|
private Feature getNotesFeature(CsvNameExportState state){
|
458
|
if (state.getNotesFeature() != null){
|
459
|
return state.getNotesFeature();
|
460
|
} else{
|
461
|
Pager<DefinedTermBase> notesFeature = getTermService().findByTitle(Feature.class, "Notes" ,MatchMode.EXACT, null, null, null, null, null);
|
462
|
if (notesFeature.getRecords().size() == 0){
|
463
|
return null;
|
464
|
}else{
|
465
|
DefinedTermBase feature= notesFeature.getRecords().iterator().next();
|
466
|
if (feature instanceof Feature){
|
467
|
state.setNotesFeature((Feature)feature);
|
468
|
return (Feature) feature;
|
469
|
} else{
|
470
|
return null;
|
471
|
}
|
472
|
}
|
473
|
}
|
474
|
|
475
|
}
|
476
|
|
477
|
private HashMap<String, String> createNewRecord(TaxonNode childNode, CsvNameExportState state){
|
478
|
HashMap<String, String> nameRecord = new HashMap<String,String>();
|
479
|
nameRecord.put("classification", childNode.getClassification().getTitleCache());
|
480
|
TaxonNode familyNode = getHigherNode(childNode, Rank.FAMILY());
|
481
|
Taxon taxon;
|
482
|
String nameString;
|
483
|
BotanicalName name;
|
484
|
if (familyNode == null){
|
485
|
nameRecord.put("familyTaxon", null);
|
486
|
nameRecord.put("familyName", null);
|
487
|
nameRecord.put("descriptionsFam", null);
|
488
|
}else{
|
489
|
familyNode = HibernateProxyHelper.deproxy(familyNode, TaxonNode.class);
|
490
|
familyNode.getTaxon().setProtectedTitleCache(true);
|
491
|
nameRecord.put("familyTaxon", familyNode.getTaxon().getTitleCache());
|
492
|
|
493
|
taxon = (Taxon)getTaxonService().load(familyNode.getTaxon().getUuid());
|
494
|
taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
|
495
|
//if publish flag is set
|
496
|
|
497
|
// if (taxon.isPublish()){
|
498
|
name = HibernateProxyHelper.deproxy(taxon.getName(), BotanicalName.class);
|
499
|
nameRecord.put("familyName", name.getNameCache());
|
500
|
extractDescriptions(nameRecord, taxon, Feature.INTRODUCTION(), "descriptionsFam", state);
|
501
|
}
|
502
|
TaxonNode genusNode = getHigherNode(childNode, Rank.GENUS());
|
503
|
if (genusNode!= null){
|
504
|
genusNode = HibernateProxyHelper.deproxy(genusNode, TaxonNode.class);
|
505
|
genusNode.getTaxon().setProtectedTitleCache(true);
|
506
|
nameRecord.put("genusTaxon", genusNode.getTaxon().getTitleCache());
|
507
|
|
508
|
taxon = (Taxon)getTaxonService().load(genusNode.getTaxon().getUuid());
|
509
|
taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
|
510
|
//if publish flag is set
|
511
|
|
512
|
// if (taxon.isPublish()){
|
513
|
name = HibernateProxyHelper.deproxy(taxon.getName(), BotanicalName.class);
|
514
|
if (name.getNameCache() != null){
|
515
|
nameRecord.put("genusName", name.getNameCache());
|
516
|
}else{
|
517
|
nameRecord.put("genusName", name.getGenusOrUninomial());
|
518
|
}
|
519
|
extractDescriptions(nameRecord, taxon,getNotesFeature(state), "descriptionsGen", state);
|
520
|
}else{
|
521
|
nameRecord.put("genusTaxon", null);
|
522
|
nameRecord.put("genusName", null);
|
523
|
nameRecord.put("descriptionsGen", null);
|
524
|
}
|
525
|
|
526
|
taxon = (Taxon) getTaxonService().load(childNode.getTaxon().getUuid());
|
527
|
taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
|
528
|
// if (taxon.isPublish()){
|
529
|
|
530
|
INonViralName nonViralName = taxon.getName();
|
531
|
|
532
|
nameString = createTaggedNameString(nonViralName, false);
|
533
|
nameRecord.put("childTaxon", taxon.getTitleCache());
|
534
|
if (taxon.getSec()!= null){
|
535
|
nameRecord.put("secRef", taxon.getSec().getTitleCache());
|
536
|
}else{
|
537
|
nameRecord.put("secRef", null);
|
538
|
}
|
539
|
|
540
|
getTaxonRelations(nameRecord, taxon);
|
541
|
|
542
|
name = HibernateProxyHelper.deproxy(getNameService().load(taxon.getName().getUuid()), BotanicalName.class);
|
543
|
nameRecord.put("childName",nameString);
|
544
|
nameRecord.put("nameId", String.valueOf(name.getId()));
|
545
|
nameRecord.put("nameCache", name.getNameCache());
|
546
|
nameRecord.put("titleName", name.getTitleCache());
|
547
|
if (name.getNomenclaturalReference() != null){
|
548
|
nameRecord.put("NomRefTitleCache", name.getNomenclaturalReference().getTitleCache());
|
549
|
} else{
|
550
|
nameRecord.put("NomRefTitleCache",null);
|
551
|
}
|
552
|
nameRecord.put("fullName", name.getNameCache());
|
553
|
nameRecord.put("fullTitleCache", name.getFullTitleCache());
|
554
|
Set<TypeDesignationBase> typeDesSet = name.getTypeDesignations();
|
555
|
Iterator<TypeDesignationBase> it = typeDesSet.iterator();
|
556
|
String typeNameString = NOT_DESIGNATED;
|
557
|
String statusString = null;
|
558
|
if (it.hasNext()){
|
559
|
|
560
|
TypeDesignationBase typeDes = HibernateProxyHelper.deproxy(it.next(), TypeDesignationBase.class);
|
561
|
|
562
|
if (typeDes instanceof NameTypeDesignation){
|
563
|
NameTypeDesignation nameTypeDes = HibernateProxyHelper.deproxy(typeDes, NameTypeDesignation.class);
|
564
|
|
565
|
BotanicalName typeName = HibernateProxyHelper.deproxy(nameTypeDes.getTypeName(), BotanicalName.class);
|
566
|
if (typeName != null){
|
567
|
|
568
|
typeNameString = "<i>" + typeName.getNameCache() +"</i> " + typeName.getAuthorshipCache();
|
569
|
if (nameTypeDes.getTypeStatus() != null){
|
570
|
NameTypeDesignationStatus status = HibernateProxyHelper.deproxy(nameTypeDes.getTypeStatus(), NameTypeDesignationStatus.class);
|
571
|
statusString = status.getTitleCache();
|
572
|
}
|
573
|
}
|
574
|
}
|
575
|
}
|
576
|
nameRecord.put("typeName", typeNameString);
|
577
|
StringBuffer homotypicalSynonyms = new StringBuffer();
|
578
|
TreeMap<HomotypicalGroup,List<Synonym>> heterotypicSynonymsList = new TreeMap<HomotypicalGroup,List<Synonym>>(new HomotypicalGroupComparator());
|
579
|
|
580
|
List<Synonym> homotypicSynonymsList = new ArrayList<Synonym>();
|
581
|
StringBuffer heterotypicalSynonyms = new StringBuffer();
|
582
|
List<Synonym> homotypicSynonyms;
|
583
|
|
584
|
HomotypicalGroup group;
|
585
|
BotanicalName synonymName;
|
586
|
String doubtfulTitleCache;
|
587
|
for (Synonym synonym: taxon.getSynonyms()){
|
588
|
synonymName = HibernateProxyHelper.deproxy(synonym.getName(), BotanicalName.class);
|
589
|
group = HibernateProxyHelper.deproxy(synonymName.getHomotypicalGroup(), HomotypicalGroup.class);
|
590
|
synonymName.generateFullTitle();
|
591
|
if (synonym.isDoubtful()){
|
592
|
if (!synonymName.getFullTitleCache().startsWith("?")){
|
593
|
doubtfulTitleCache = "?" + synonymName.getFullTitleCache();
|
594
|
synonymName = (BotanicalName) synonymName.clone();
|
595
|
synonymName.setFullTitleCache(doubtfulTitleCache, true);
|
596
|
}
|
597
|
}
|
598
|
if (!group.equals(name.getHomotypicalGroup())){
|
599
|
if (heterotypicSynonymsList.containsKey(group)){
|
600
|
heterotypicSynonymsList.get(group).add(synonym);
|
601
|
}else{
|
602
|
homotypicSynonyms = new ArrayList<Synonym>();
|
603
|
homotypicSynonyms.add(synonym);
|
604
|
heterotypicSynonymsList.put(group, homotypicSynonyms);
|
605
|
homotypicSynonyms= null;
|
606
|
}
|
607
|
} else{
|
608
|
synonymName.generateFullTitle();
|
609
|
homotypicSynonymsList.add(synonym);
|
610
|
}
|
611
|
}
|
612
|
|
613
|
|
614
|
|
615
|
String synonymString;
|
616
|
boolean first = true;
|
617
|
|
618
|
for (List<Synonym> list: heterotypicSynonymsList.values()){
|
619
|
Collections.sort(list, new HomotypicGroupTaxonComparator(null));
|
620
|
first = true;
|
621
|
for (TaxonBase<?> synonym : list){
|
622
|
NomenclaturalStatus status = null;
|
623
|
if (!synonym.getName().getStatus().isEmpty()){
|
624
|
status = HibernateProxyHelper.deproxy(synonym.getName().getStatus().iterator().next(),NomenclaturalStatus.class);
|
625
|
if (status.getType().isInvalidType()){
|
626
|
heterotypicalSynonyms.append(" <invalid> ");
|
627
|
synonymName = HibernateProxyHelper.deproxy(synonym.getName(), BotanicalName.class);
|
628
|
|
629
|
synonymString = createSynonymNameString(synonymName, state.getConfig().isInvalidNamesQuoted()) ;
|
630
|
heterotypicalSynonyms.append(synonymString);
|
631
|
continue;
|
632
|
}
|
633
|
}
|
634
|
if (first){
|
635
|
heterotypicalSynonyms.append(" <heterotypic> ");
|
636
|
}else{
|
637
|
heterotypicalSynonyms.append(" <homonym> ");
|
638
|
}
|
639
|
first = false;
|
640
|
synonymName = HibernateProxyHelper.deproxy(synonym.getName(), BotanicalName.class);
|
641
|
synonymString = createSynonymNameString(synonymName, false);
|
642
|
heterotypicalSynonyms.append(synonymString);
|
643
|
}
|
644
|
}
|
645
|
|
646
|
first = true;
|
647
|
Collections.sort(homotypicSynonymsList, new HomotypicGroupTaxonComparator(null) );
|
648
|
NomenclaturalStatus status = null;
|
649
|
for (TaxonBase<?> synonym : homotypicSynonymsList){
|
650
|
|
651
|
if (!synonym.getName().getStatus().isEmpty()){
|
652
|
status = HibernateProxyHelper.deproxy(synonym.getName().getStatus().iterator().next(),NomenclaturalStatus.class);
|
653
|
if (status.getType().isInvalidType()){
|
654
|
homotypicalSynonyms.append(" <invalid> ");
|
655
|
synonymName = HibernateProxyHelper.deproxy(synonym.getName(), BotanicalName.class);
|
656
|
synonymString = createSynonymNameString(synonymName, true);
|
657
|
homotypicalSynonyms.append(synonymString);
|
658
|
continue;
|
659
|
}else if (!first){
|
660
|
homotypicalSynonyms.append(" <homonym> ");
|
661
|
}
|
662
|
|
663
|
}else if (!first){
|
664
|
homotypicalSynonyms.append(" <homonym> ");
|
665
|
}
|
666
|
first = false;
|
667
|
synonymName = HibernateProxyHelper.deproxy(synonym.getName(), BotanicalName.class);
|
668
|
|
669
|
synonymString = createSynonymNameString(synonymName, false);
|
670
|
|
671
|
homotypicalSynonyms.append(synonymString);
|
672
|
|
673
|
}
|
674
|
|
675
|
nameRecord.put("synonyms_homotypic", homotypicalSynonyms.toString());
|
676
|
nameRecord.put("synonyms_heterotypic", heterotypicalSynonyms.toString());
|
677
|
nameRecord.put("status", statusString);
|
678
|
|
679
|
Set<NameRelationship> nameRelations = name.getNameRelations();
|
680
|
|
681
|
INonViralName relatedName = null;
|
682
|
String nameRelType = null;
|
683
|
String relNameString = null;
|
684
|
if (nameRelations.size()>0){
|
685
|
NameRelationship nameRel = nameRelations.iterator().next();
|
686
|
BotanicalName fromName = HibernateProxyHelper.deproxy(nameRel.getFromName(), BotanicalName.class);
|
687
|
if (fromName.equals(taxon.getName())){
|
688
|
relatedName = nameRel.getToName();
|
689
|
|
690
|
}else{
|
691
|
relatedName = nameRel.getFromName();
|
692
|
}
|
693
|
nameRel = HibernateProxyHelper.deproxy(nameRel, NameRelationship.class);
|
694
|
nameRelType = nameRel.getType().getTitleCache();
|
695
|
relNameString = createTaggedNameString(relatedName, getStatus(relatedName));
|
696
|
}
|
697
|
|
698
|
|
699
|
nameRecord.put("relatedName", relNameString);
|
700
|
nameRecord.put("nameRelType", nameRelType);
|
701
|
|
702
|
extractDescriptions(nameRecord, taxon, Feature.DISTRIBUTION(), "descriptions", state);
|
703
|
return nameRecord;
|
704
|
}
|
705
|
|
706
|
/**
|
707
|
* @param nameRecord
|
708
|
* @param taxon
|
709
|
*/
|
710
|
private void getTaxonRelations(HashMap<String, String> nameRecord, Taxon taxon) {
|
711
|
Set<TaxonRelationship> relations = new HashSet<TaxonRelationship>();
|
712
|
relations =taxon.getTaxonRelations();
|
713
|
if (relations.isEmpty()){
|
714
|
nameRecord.put("missappliedNames", null);
|
715
|
}else{
|
716
|
Taxon relatedTaxon = null;
|
717
|
StringBuffer nameString = new StringBuffer();
|
718
|
for (TaxonRelationship rel : relations){
|
719
|
if (rel.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
|
720
|
relatedTaxon = rel.getFromTaxon();
|
721
|
Reference secRef = relatedTaxon.getSec();
|
722
|
String appendedPhrase = "";
|
723
|
if (relatedTaxon.getAppendedPhrase() != null){
|
724
|
appendedPhrase = relatedTaxon.getAppendedPhrase();
|
725
|
}
|
726
|
if (secRef == null){
|
727
|
nameString.append("<misapplied>\"" + createTaggedNameString(relatedTaxon.getName(), false) + "\" " + appendedPhrase);
|
728
|
} else if (secRef.getAuthorship() == null){
|
729
|
nameString.append("<misapplied>\"" + createTaggedNameString(relatedTaxon.getName(), false) + "\" " + appendedPhrase + " sensu " + secRef.getTitleCache());
|
730
|
} else {
|
731
|
nameString.append("<misapplied>\"" + createTaggedNameString(relatedTaxon.getName(), false) + "\" " + appendedPhrase + " sensu " + secRef.getAuthorship().getNomenclaturalTitle());
|
732
|
}
|
733
|
|
734
|
}
|
735
|
}
|
736
|
nameRecord.put("missappliedNames", nameString.toString());
|
737
|
}
|
738
|
|
739
|
}
|
740
|
|
741
|
|
742
|
}
|
743
|
|