|
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.common.monitor.IProgressMonitor;
|
|
25
|
import eu.etaxonomy.cdm.ext.geo.CondensedDistributionRecipe;
|
|
26
|
import eu.etaxonomy.cdm.ext.geo.IEditGeoService;
|
|
27
|
import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
|
|
28
|
import eu.etaxonomy.cdm.io.common.TaxonNodeOutStreamPartitioner;
|
|
29
|
import eu.etaxonomy.cdm.io.common.XmlExportState;
|
|
30
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
31
|
import eu.etaxonomy.cdm.model.common.Language;
|
|
32
|
import eu.etaxonomy.cdm.model.description.DescriptionBase;
|
|
33
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
|
34
|
import eu.etaxonomy.cdm.model.description.Distribution;
|
|
35
|
import eu.etaxonomy.cdm.model.description.Feature;
|
|
36
|
import eu.etaxonomy.cdm.model.description.TextData;
|
|
37
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
|
38
|
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
|
|
39
|
import eu.etaxonomy.cdm.model.name.HomotypicalGroupComparator;
|
|
40
|
import eu.etaxonomy.cdm.model.name.IBotanicalName;
|
|
41
|
import eu.etaxonomy.cdm.model.name.INonViralName;
|
|
42
|
import eu.etaxonomy.cdm.model.name.NameRelationship;
|
|
43
|
import eu.etaxonomy.cdm.model.name.NameRelationshipType;
|
|
44
|
import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
|
|
45
|
import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
|
|
46
|
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
|
|
47
|
import eu.etaxonomy.cdm.model.name.Rank;
|
|
48
|
import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
|
|
49
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
|
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.persistence.query.MatchMode;
|
|
57
|
|
|
58
|
|
|
59
|
|
|
60
|
@Component
|
|
61
|
public class CsvNameExport extends CsvNameExportBase {
|
|
62
|
private static final long serialVersionUID = 7289805663701807425L;
|
|
63
|
|
|
64
|
private static final Logger logger = Logger.getLogger(CsvNameExport.class);
|
|
65
|
|
|
66
|
@Autowired
|
|
67
|
IEditGeoService geoService;
|
|
68
|
|
|
69
|
HashMap<UUID, HashMap<String,String>> familyMap = new HashMap();
|
|
70
|
HashMap<UUID, HashMap<String,String>> genusMap = new HashMap();
|
|
71
|
|
|
72
|
List<HashMap<String,String>> nameRecords = new ArrayList<>();
|
|
73
|
|
|
74
|
public CsvNameExport() {
|
|
75
|
super();
|
|
76
|
this.ioName = this.getClass().getSimpleName();
|
|
77
|
}
|
|
78
|
|
|
79
|
@Override
|
|
80
|
protected void doInvoke(CsvNameExportState state) {
|
|
81
|
CsvNameExportConfigurator config = state.getConfig();
|
|
82
|
|
|
83
|
|
|
84
|
PrintWriter writer = null;
|
|
85
|
|
|
86
|
try {
|
|
87
|
|
|
88
|
switch(config.getTarget()) {
|
|
89
|
case FILE :
|
|
90
|
OutputStream os = new FileOutputStream(config.getDestination());
|
|
91
|
os.write(239);
|
|
92
|
os.write(187);
|
|
93
|
os.write(191);
|
|
94
|
writer = new PrintWriter(new OutputStreamWriter(os, "UTF-8"));
|
|
95
|
break;
|
|
96
|
case EXPORT_DATA :
|
|
97
|
exportStream = new ByteArrayOutputStream();
|
|
98
|
writer = new PrintWriter(exportStream);
|
|
99
|
break;
|
|
100
|
default:
|
|
101
|
break;
|
|
102
|
|
|
103
|
}
|
|
104
|
|
|
105
|
List<HashMap<String, String>> result;
|
|
106
|
if (config.getRank() == null){
|
|
107
|
config.setRank(Rank.GENUS());
|
|
108
|
}
|
|
109
|
if (config.isNamesOnly()){
|
|
110
|
txStatus = startTransaction();
|
|
111
|
result = getNameService().getNameRecords();
|
|
112
|
} else {
|
|
113
|
result = getRecordsForPrintPub(state);
|
|
114
|
}
|
|
115
|
CsvRecord nameRecord;
|
|
116
|
int count = 0;
|
|
117
|
boolean isFirst = true;
|
|
118
|
for (HashMap<String,String> record:result){
|
|
119
|
if (count > 0){
|
|
120
|
isFirst = false;
|
|
121
|
}
|
|
122
|
count++;
|
|
123
|
nameRecord = new CsvRecord(record, isFirst);
|
|
124
|
nameRecord.print(writer, config);
|
|
125
|
|
|
126
|
}
|
|
127
|
if (exportStream != null){
|
|
128
|
state.getResult().addExportData(getByteArray());
|
|
129
|
//this.exportData.addExportData(exportStream.toByteArray());
|
|
130
|
}
|
|
131
|
writer.flush();
|
|
132
|
|
|
133
|
writer.close();
|
|
134
|
|
|
135
|
} catch (Exception e) {
|
|
136
|
// TODO Auto-generated catch block
|
|
137
|
e.printStackTrace();
|
|
138
|
}
|
|
139
|
if (txStatus != null ){
|
|
140
|
commitTransaction(txStatus);
|
|
141
|
}
|
|
142
|
return;
|
|
143
|
|
|
144
|
|
|
145
|
}
|
|
146
|
|
|
147
|
@Override
|
|
148
|
public long countSteps(CsvNameExportState state) {
|
|
149
|
TaxonNodeFilter filter = state.getConfig().getTaxonNodeFilter();
|
|
150
|
return taxonNodeService.count(filter);
|
|
151
|
}
|
|
152
|
|
|
153
|
|
|
154
|
@Override
|
|
155
|
protected boolean doCheck(CsvNameExportState state) {
|
|
156
|
boolean result = true;
|
|
157
|
logger.warn("No check implemented for " + this.ioName);
|
|
158
|
return result;
|
|
159
|
}
|
|
160
|
|
|
161
|
@Override
|
|
162
|
protected boolean isIgnore(CsvNameExportState state) {
|
|
163
|
return false;
|
|
164
|
}
|
|
165
|
|
|
166
|
|
|
167
|
public List<HashMap<String,String>> getRecordsForPrintPub(CsvNameExportState state){
|
|
168
|
// List<String> propertyPaths = new ArrayList<String>();
|
|
169
|
// propertyPaths.add("childNodes");
|
|
170
|
// txStatus = startTransaction();
|
|
171
|
// Classification classification = getClassificationService().load(state.getConfig().getClassificationUUID());
|
|
172
|
// TaxonNode rootNode;
|
|
173
|
// if (classification != null){
|
|
174
|
// rootNode = classification.getRootNode();
|
|
175
|
// }else{
|
|
176
|
// List<Classification> classifications = getClassificationService().list(Classification.class, 10, 0, null, null);
|
|
177
|
// if (classifications.isEmpty()){
|
|
178
|
// return null;
|
|
179
|
// }
|
|
180
|
// classification = classifications.get(0);
|
|
181
|
// rootNode = classification.getRootNode();
|
|
182
|
// }
|
|
183
|
// rootNode = getTaxonNodeService().load(rootNode.getUuid(), propertyPaths);
|
|
184
|
// Set<UUID> childrenUuids = new HashSet<UUID>();
|
|
185
|
//
|
|
186
|
//
|
|
187
|
// rootNode = CdmBase.deproxy(rootNode);
|
|
188
|
// rootNode.removeNullValueFromChildren();
|
|
189
|
// for (TaxonNode child: rootNode.getChildNodes()){
|
|
190
|
// child = CdmBase.deproxy(child);
|
|
191
|
// childrenUuids.add(child.getUuid());
|
|
192
|
// }
|
|
193
|
// Set<UUID> parentsNodesUUID = new HashSet<UUID>(childrenUuids);
|
|
194
|
// childrenUuids.clear();
|
|
195
|
// List<TaxonNode> childrenNodes = new ArrayList<TaxonNode>();
|
|
196
|
//
|
|
197
|
// findChildren(state, childrenUuids, parentsNodesUUID);
|
|
198
|
|
|
199
|
IProgressMonitor monitor = state.getConfig().getProgressMonitor();
|
|
200
|
@SuppressWarnings("unchecked")
|
|
201
|
TaxonNodeOutStreamPartitioner<XmlExportState> partitioner
|
|
202
|
= TaxonNodeOutStreamPartitioner.NewInstance(
|
|
203
|
this, state, state.getConfig().getTaxonNodeFilter(),
|
|
204
|
100, monitor, null);
|
|
205
|
|
|
206
|
|
|
207
|
monitor.subTask("Start partitioning");
|
|
208
|
// List<HashMap<String,String>> nameRecords = new ArrayList<>();
|
|
209
|
TaxonNode node = partitioner.next();
|
|
210
|
while (node != null){
|
|
211
|
HashMap<String, String> nameRecord = createNewRecord(node, state);
|
|
212
|
if (nameRecord != null){
|
|
213
|
nameRecords.add(nameRecord);
|
|
214
|
}
|
|
215
|
node = partitioner.next();
|
|
216
|
}
|
|
217
|
|
|
218
|
|
|
219
|
|
|
220
|
|
|
221
|
// List<HashMap<String,String>> nameRecords = new ArrayList<>();
|
|
222
|
//
|
|
223
|
// childrenNodes = getTaxonNodeService().find(childrenUuids);
|
|
224
|
// for(TaxonNode genusNode : childrenNodes) {
|
|
225
|
// nameRecords.add(createNewRecord(genusNode, state));
|
|
226
|
// refreshTransaction();
|
|
227
|
// }
|
|
228
|
|
|
229
|
return nameRecords;
|
|
230
|
|
|
231
|
}
|
|
232
|
|
|
233
|
// /**
|
|
234
|
// * @param state
|
|
235
|
// * @param childrenUuids
|
|
236
|
// * @param parentsNodesUUID
|
|
237
|
// * @param familyNode
|
|
238
|
// */
|
|
239
|
// private void findChildren(CsvNameExportState state, Set<UUID> childrenUuids, Set<UUID> parentsNodesUUID) {
|
|
240
|
// TaxonName name;
|
|
241
|
// List<TaxonNode> familyNodes = getTaxonNodeService().find(parentsNodesUUID);
|
|
242
|
// parentsNodesUUID =new HashSet<>();
|
|
243
|
// for (TaxonNode familyNode: familyNodes){
|
|
244
|
// familyNode = CdmBase.deproxy(familyNode);
|
|
245
|
// familyNode.removeNullValueFromChildren();
|
|
246
|
// for (TaxonNode child: familyNode.getChildNodes()){
|
|
247
|
// child = CdmBase.deproxy(child);
|
|
248
|
// Taxon taxon = CdmBase.deproxy(child.getTaxon());
|
|
249
|
// if (taxon != null){
|
|
250
|
// name = CdmBase.deproxy(taxon.getName());
|
|
251
|
// if (child.getTaxon().getName().getRank().isLower(state.getConfig().getRank()) ) {
|
|
252
|
// childrenUuids.add(child.getUuid());
|
|
253
|
// if (child.hasChildNodes()){
|
|
254
|
// parentsNodesUUID.add(child.getUuid());
|
|
255
|
// }
|
|
256
|
// }else{
|
|
257
|
// parentsNodesUUID.add(child.getUuid());
|
|
258
|
// }
|
|
259
|
// }
|
|
260
|
// }
|
|
261
|
// //refreshTransaction();
|
|
262
|
// if (!parentsNodesUUID.isEmpty()){
|
|
263
|
// findChildren(state, childrenUuids, parentsNodesUUID);
|
|
264
|
// }
|
|
265
|
// }
|
|
266
|
//
|
|
267
|
// }
|
|
268
|
|
|
269
|
|
|
270
|
|
|
271
|
|
|
272
|
private String createSynonymNameString(IBotanicalName synonymName, boolean isInvalid) {
|
|
273
|
String synonymString = null;
|
|
274
|
|
|
275
|
synonymString= createTaggedNameString(synonymName, isInvalid);
|
|
276
|
Set<NameRelationship> nameRelations = synonymName.getNameRelations();
|
|
277
|
|
|
278
|
INonViralName relatedName = null;
|
|
279
|
String nameRelType = null;
|
|
280
|
boolean first = true;
|
|
281
|
boolean isInvalidRel = false;
|
|
282
|
for (NameRelationship nameRel: nameRelations){
|
|
283
|
// NameRelationship nameRel = nameRelations.iterator().next();
|
|
284
|
if (!nameRel.getType().equals(NameRelationshipType.BASIONYM())){
|
|
285
|
IBotanicalName fromName = CdmBase.deproxy(nameRel.getFromName());
|
|
286
|
|
|
287
|
nameRel = CdmBase.deproxy(nameRel);
|
|
288
|
nameRelType = nameRel.getType().getTitleCache();
|
|
289
|
String relatedNameString = "";
|
|
290
|
if (fromName.equals(synonymName)){
|
|
291
|
relatedName = nameRel.getToName();
|
|
292
|
}else{
|
|
293
|
relatedName = nameRel.getFromName();
|
|
294
|
}
|
|
295
|
|
|
296
|
isInvalidRel = getStatus(relatedName);
|
|
297
|
relatedNameString = createTaggedNameString(relatedName, isInvalidRel&&isInvalid);
|
|
298
|
|
|
299
|
if (nameRel.getType().equals(NameRelationshipType.LATER_HOMONYM())){
|
|
300
|
if (synonymName.equals(nameRel.getFromName())){
|
|
301
|
if (first){
|
|
302
|
synonymString = synonymString + " [non " + relatedNameString ;
|
|
303
|
first = false;
|
|
304
|
} else{
|
|
305
|
synonymString = synonymString + " nec " + relatedNameString ;
|
|
306
|
}
|
|
307
|
}
|
|
308
|
} else if (nameRel.getType().equals(NameRelationshipType.REPLACED_SYNONYM())){
|
|
309
|
//synonymString = synonymString + " [non " + relatedNameString + "]";
|
|
310
|
} else if (nameRel.getType().equals(NameRelationshipType.BLOCKING_NAME_FOR())){
|
|
311
|
if (synonymName.equals(nameRel.getToName())){
|
|
312
|
if (first){
|
|
313
|
synonymString = synonymString + " [non " + relatedNameString ;
|
|
314
|
first = false;
|
|
315
|
} else{
|
|
316
|
synonymString = synonymString + " nec " + relatedNameString ;
|
|
317
|
}
|
|
318
|
|
|
319
|
}
|
|
320
|
} else if (nameRel.getType().equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())){
|
|
321
|
if (first){
|
|
322
|
synonymString = synonymString + " [non " + relatedNameString ;
|
|
323
|
first = false;
|
|
324
|
} else{
|
|
325
|
synonymString = synonymString + " nec " + relatedNameString ;
|
|
326
|
}
|
|
327
|
} else if (nameRel.getType().equals(NameRelationshipType.ALTERNATIVE_NAME())){
|
|
328
|
if (first){
|
|
329
|
synonymString = synonymString + " [non " + relatedNameString ;
|
|
330
|
first = false;
|
|
331
|
} else{
|
|
332
|
synonymString = synonymString + " nec " + relatedNameString ;
|
|
333
|
}
|
|
334
|
} else if (nameRel.getType().equals(NameRelationshipType.CONSERVED_AGAINST())) {
|
|
335
|
|
|
336
|
}else if (nameRel.getType().equals(NameRelationshipType.ORTHOGRAPHIC_VARIANT())){
|
|
337
|
|
|
338
|
}
|
|
339
|
}
|
|
340
|
}
|
|
341
|
if (!first){
|
|
342
|
synonymString = synonymString + "]";
|
|
343
|
}
|
|
344
|
|
|
345
|
return synonymString;
|
|
346
|
}
|
|
347
|
|
|
348
|
/**
|
|
349
|
* @param relatedName
|
|
350
|
* @return
|
|
351
|
*/
|
|
352
|
private boolean getStatus(INonViralName relatedName) {
|
|
353
|
boolean result;
|
|
354
|
if (!relatedName.getStatus().isEmpty()){
|
|
355
|
NomenclaturalStatus status = CdmBase.deproxy(relatedName.getStatus().iterator().next());
|
|
356
|
if (status.getType().isInvalidType()){
|
|
357
|
result = true;
|
|
358
|
}else{
|
|
359
|
result = false;
|
|
360
|
}
|
|
361
|
}else{
|
|
362
|
result = false;
|
|
363
|
}
|
|
364
|
return result;
|
|
365
|
}
|
|
366
|
|
|
367
|
private String createTaggedNameString(INonViralName name, boolean isInvalid){
|
|
368
|
String nameString = null;
|
|
369
|
if (name == null){
|
|
370
|
return nameString;
|
|
371
|
}
|
|
372
|
|
|
373
|
nameString = name.generateFullTitle();
|
|
374
|
if (isInvalid){
|
|
375
|
nameString = nameString.replace(name.getTitleCache(), "\""+name.getTitleCache()+"\"");
|
|
376
|
}
|
|
377
|
if (name.getGenusOrUninomial() != null){
|
|
378
|
nameString = nameString.replaceAll(name.getGenusOrUninomial(), "<i>"+ name.getGenusOrUninomial() + "</i>");
|
|
379
|
}
|
|
380
|
if (name.getInfraGenericEpithet() != null){
|
|
381
|
nameString = nameString.replaceAll(name.getInfraGenericEpithet(), "<i>"+ name.getInfraGenericEpithet() + "</i>");
|
|
382
|
}
|
|
383
|
if (name.getSpecificEpithet() != null){
|
|
384
|
nameString = nameString.replaceAll(name.getSpecificEpithet(), "<i>"+ name.getSpecificEpithet() + "</i>");
|
|
385
|
}
|
|
386
|
if (name.getInfraSpecificEpithet() != null && !name.isAutonym()){
|
|
387
|
nameString = nameString.replaceAll(name.getInfraSpecificEpithet(), "<i>"+ name.getInfraSpecificEpithet() + "</i>");
|
|
388
|
}
|
|
389
|
|
|
390
|
return nameString;
|
|
391
|
}
|
|
392
|
|
|
393
|
|
|
394
|
|
|
395
|
// private List<TaxonNode> getGenusNodes (UUID classificationUUID){
|
|
396
|
// Classification classification = getClassificationService().load(classificationUUID);
|
|
397
|
// TaxonNode rootNode = classification.getRootNode();
|
|
398
|
// rootNode = getTaxonNodeService().load(rootNode.getUuid());
|
|
399
|
// Set<UUID> childrenUuids = new HashSet<>();
|
|
400
|
//
|
|
401
|
// for (TaxonNode child: rootNode.getChildNodes()){
|
|
402
|
// child = CdmBase.deproxy(child);
|
|
403
|
// childrenUuids.add(child.getUuid());
|
|
404
|
// }
|
|
405
|
//
|
|
406
|
// List<TaxonNode> familyNodes = getTaxonNodeService().find(childrenUuids);
|
|
407
|
// childrenUuids.clear();
|
|
408
|
// List<TaxonNode> genusNodes = new ArrayList<>();
|
|
409
|
// for (TaxonNode familyNode: familyNodes){
|
|
410
|
// for (TaxonNode child: familyNode.getChildNodes()){
|
|
411
|
// child = CdmBase.deproxy(child);
|
|
412
|
// childrenUuids.add(child.getUuid());
|
|
413
|
// }
|
|
414
|
//
|
|
415
|
// genusNodes = getTaxonNodeService().find(childrenUuids);
|
|
416
|
// }
|
|
417
|
// return genusNodes;
|
|
418
|
// }
|
|
419
|
|
|
420
|
private TaxonNode getHigherNode(TaxonNode node, Rank rank){
|
|
421
|
|
|
422
|
Rank nodeRank = node.getTaxon().getName().getRank();
|
|
423
|
if (nodeRank.isKindOf(rank)){
|
|
424
|
return null;
|
|
425
|
|
|
426
|
}else if (nodeRank.isHigher(rank)){
|
|
427
|
return null;
|
|
428
|
} else {
|
|
429
|
return node.getAncestorOfRank(rank);
|
|
430
|
}
|
|
431
|
}
|
|
432
|
|
|
433
|
private void extractDescriptions(HashMap<String, String> nameRecord, Taxon taxon, Feature feature, String columnName, CsvNameExportState state){
|
|
434
|
StringBuffer descriptionsString = new StringBuffer();
|
|
435
|
TextData textElement;
|
|
436
|
Set<Distribution> distributions = new HashSet<>();
|
|
437
|
if (taxon.getDescriptions().isEmpty()){
|
|
438
|
nameRecord.put(columnName, null);
|
|
439
|
return;
|
|
440
|
}
|
|
441
|
for (DescriptionBase<?> descriptionBase: taxon.getDescriptions()){
|
|
442
|
if (!descriptionBase.isImageGallery()){
|
|
443
|
Set<DescriptionElementBase> elements = descriptionBase.getElements();
|
|
444
|
for (DescriptionElementBase element: elements){
|
|
445
|
if (element.getFeature().equals(feature)){
|
|
446
|
if (element instanceof TextData){
|
|
447
|
textElement = CdmBase.deproxy(element, TextData.class);
|
|
448
|
descriptionsString.append(textElement.getText(Language.ENGLISH()));
|
|
449
|
|
|
450
|
}else if (element instanceof Distribution ){
|
|
451
|
|
|
452
|
Distribution distribution = CdmBase.deproxy(element, Distribution.class);
|
|
453
|
distributions.add(distribution);
|
|
454
|
}
|
|
455
|
|
|
456
|
}
|
|
457
|
}
|
|
458
|
}
|
|
459
|
}
|
|
460
|
if (state.getConfig().isCondensedDistribution()){
|
|
461
|
List<Language> langs = new ArrayList<Language>();
|
|
462
|
langs.add(Language.ENGLISH());
|
|
463
|
|
|
464
|
CondensedDistribution conDis = geoService.getCondensedDistribution(distributions, true, null,null,CondensedDistributionRecipe.FloraCuba, langs );
|
|
465
|
|
|
466
|
nameRecord.put(columnName, conDis.toString());
|
|
467
|
|
|
468
|
} else{
|
|
469
|
NamedArea area ;
|
|
470
|
for (Distribution distribution:distributions){
|
|
471
|
|
|
472
|
if (descriptionsString.length()> 0 ){
|
|
473
|
descriptionsString.append(", ");
|
|
474
|
}
|
|
475
|
area = CdmBase.deproxy(distribution.getArea());
|
|
476
|
if (area.getIdInVocabulary() != null){
|
|
477
|
descriptionsString.append(area.getIdInVocabulary());
|
|
478
|
}else if (area.getSymbol() != null){
|
|
479
|
descriptionsString.append(area.getSymbol());
|
|
480
|
}else{
|
|
481
|
descriptionsString.append(area.getLabel());
|
|
482
|
}
|
|
483
|
|
|
484
|
}
|
|
485
|
nameRecord.put(columnName, descriptionsString.toString());
|
|
486
|
}
|
|
487
|
|
|
488
|
}
|
|
489
|
|
|
490
|
private Feature getNotesFeature(CsvNameExportState state){
|
|
491
|
if (state.getNotesFeature() != null){
|
|
492
|
return state.getNotesFeature();
|
|
493
|
} else{
|
|
494
|
Pager<Feature> notesFeature = getTermService().findByTitleWithRestrictions(Feature.class, "Notes" ,MatchMode.EXACT, null, null, null, null, null);
|
|
495
|
if (notesFeature.getRecords().size() == 0){
|
|
496
|
return null;
|
|
497
|
}else{
|
|
498
|
Feature feature= notesFeature.getRecords().iterator().next();
|
|
499
|
state.setNotesFeature(feature);
|
|
500
|
return feature;
|
|
501
|
}
|
|
502
|
}
|
|
503
|
|
|
504
|
}
|
|
505
|
|
|
506
|
private HashMap<String, String> createNewRecord(TaxonNode childNode, CsvNameExportState state){
|
|
507
|
HashMap<String, String> nameRecord = new HashMap<>();
|
|
508
|
nameRecord.put("classification", childNode.getClassification().getTitleCache());
|
|
509
|
if (!childNode.getTaxon().getName().getRank().isLower(Rank.GENUS())){
|
|
510
|
return null;
|
|
511
|
}
|
|
512
|
TaxonNode familyNode = getHigherNode(childNode, Rank.FAMILY());
|
|
513
|
Taxon taxon;
|
|
514
|
String nameString;
|
|
515
|
IBotanicalName name;
|
|
516
|
if (familyNode == null){
|
|
517
|
nameRecord.put("familyTaxon", null);
|
|
518
|
nameRecord.put("familyName", null);
|
|
519
|
nameRecord.put("descriptionsFam", null);
|
|
520
|
}else{
|
|
521
|
familyNode = CdmBase.deproxy(familyNode);
|
|
522
|
familyNode.getTaxon().setProtectedTitleCache(true);
|
|
523
|
nameRecord.put("familyTaxon", familyNode.getTaxon().getTitleCache());
|
|
524
|
if (familyMap.get(familyNode.getTaxon().getUuid()) != null){
|
|
525
|
nameRecord.putAll(familyMap.get(familyNode.getTaxon().getUuid()));
|
|
526
|
}else{
|
|
527
|
taxon = (Taxon)getTaxonService().load(familyNode.getTaxon().getUuid());
|
|
528
|
taxon = CdmBase.deproxy(taxon);
|
|
529
|
name = CdmBase.deproxy(taxon.getName());
|
|
530
|
nameRecord.put("familyName", name.getNameCache());
|
|
531
|
extractDescriptions(nameRecord, taxon, Feature.INTRODUCTION(), "descriptionsFam", state);
|
|
532
|
familyMap.put(familyNode.getTaxon().getUuid(), nameRecord);
|
|
533
|
}
|
|
534
|
|
|
535
|
}
|
|
536
|
TaxonNode genusNode = getHigherNode(childNode, Rank.GENUS());
|
|
537
|
if (genusNode!= null){
|
|
538
|
genusNode = CdmBase.deproxy(genusNode);
|
|
539
|
genusNode.getTaxon().setProtectedTitleCache(true);
|
|
540
|
nameRecord.put("genusTaxon", genusNode.getTaxon().getTitleCache());
|
|
541
|
if (genusMap.get(genusNode.getTaxon().getUuid()) != null){
|
|
542
|
nameRecord.putAll(genusMap.get(genusNode.getTaxon().getUuid()));
|
|
543
|
}else{
|
|
544
|
taxon = (Taxon)getTaxonService().load(genusNode.getTaxon().getUuid());
|
|
545
|
taxon = CdmBase.deproxy(taxon);
|
|
546
|
name = CdmBase.deproxy(taxon.getName());
|
|
547
|
if (name.getNameCache() != null){
|
|
548
|
nameRecord.put("genusName", name.getNameCache());
|
|
549
|
}else{
|
|
550
|
nameRecord.put("genusName", name.getGenusOrUninomial());
|
|
551
|
}
|
|
552
|
extractDescriptions(nameRecord, taxon,getNotesFeature(state), "descriptionsGen", state);
|
|
553
|
genusMap.put(genusNode.getTaxon().getUuid(), nameRecord);
|
|
554
|
}
|
|
555
|
|
|
556
|
|
|
557
|
}else{
|
|
558
|
nameRecord.put("genusTaxon", null);
|
|
559
|
nameRecord.put("genusName", null);
|
|
560
|
nameRecord.put("descriptionsGen", null);
|
|
561
|
}
|
|
562
|
|
|
563
|
// taxon = (Taxon) getTaxonService().load(childNode.getTaxon().getUuid());
|
|
564
|
taxon = CdmBase.deproxy(childNode.getTaxon());
|
|
565
|
// if (taxon.isPublish()){
|
|
566
|
|
|
567
|
INonViralName nonViralName = taxon.getName();
|
|
568
|
|
|
569
|
nameString = createTaggedNameString(nonViralName, false);
|
|
570
|
nameRecord.put("childTaxon", taxon.getTitleCache());
|
|
571
|
if (taxon.getSec()!= null){
|
|
572
|
nameRecord.put("secRef", taxon.getSec().getTitleCache());
|
|
573
|
}else{
|
|
574
|
nameRecord.put("secRef", null);
|
|
575
|
}
|
|
576
|
|
|
577
|
getTaxonRelations(nameRecord, taxon);
|
|
578
|
|
|
579
|
name = CdmBase.deproxy(taxon.getName());
|
|
580
|
nameRecord.put("childName",nameString);
|
|
581
|
nameRecord.put("nameId", String.valueOf(name.getId()));
|
|
582
|
nameRecord.put("nameCache", name.getNameCache());
|
|
583
|
nameRecord.put("titleName", name.getTitleCache());
|
|
584
|
if (name.getNomenclaturalReference() != null){
|
|
585
|
nameRecord.put("NomRefTitleCache", name.getNomenclaturalReference().getTitleCache());
|
|
586
|
} else{
|
|
587
|
nameRecord.put("NomRefTitleCache",null);
|
|
588
|
}
|
|
589
|
nameRecord.put("fullName", name.getNameCache());
|
|
590
|
nameRecord.put("fullTitleCache", name.getFullTitleCache());
|
|
591
|
Set<TypeDesignationBase<?>> typeDesSet = name.getTypeDesignations();
|
|
592
|
Iterator<TypeDesignationBase<?>> it = typeDesSet.iterator();
|
|
593
|
String typeNameString = NOT_DESIGNATED;
|
|
594
|
String statusString = null;
|
|
595
|
if (it.hasNext()){
|
|
596
|
|
|
597
|
TypeDesignationBase<?> typeDes = CdmBase.deproxy(it.next());
|
|
598
|
|
|
599
|
if (typeDes instanceof NameTypeDesignation){
|
|
600
|
NameTypeDesignation nameTypeDes = CdmBase.deproxy(typeDes, NameTypeDesignation.class);
|
|
601
|
|
|
602
|
IBotanicalName typeName = CdmBase.deproxy(nameTypeDes.getTypeName());
|
|
603
|
if (typeName != null){
|
|
604
|
|
|
605
|
typeNameString = "<i>" + typeName.getNameCache() +"</i> " + typeName.getAuthorshipCache();
|
|
606
|
if (nameTypeDes.getTypeStatus() != null){
|
|
607
|
NameTypeDesignationStatus status = CdmBase.deproxy(nameTypeDes.getTypeStatus());
|
|
608
|
statusString = status.getTitleCache();
|
|
609
|
}
|
|
610
|
}
|
|
611
|
}
|
|
612
|
}
|
|
613
|
nameRecord.put("typeName", typeNameString);
|
|
614
|
StringBuffer homotypicalSynonyms = new StringBuffer();
|
|
615
|
TreeMap<HomotypicalGroup,List<Synonym>> heterotypicSynonymsList = new TreeMap<>(new HomotypicalGroupComparator());
|
|
616
|
|
|
617
|
List<Synonym> homotypicSynonymsList = new ArrayList<>();
|
|
618
|
StringBuffer heterotypicalSynonyms = new StringBuffer();
|
|
619
|
List<Synonym> homotypicSynonyms;
|
|
620
|
|
|
621
|
HomotypicalGroup group;
|
|
622
|
IBotanicalName synonymName;
|
|
623
|
String doubtfulTitleCache;
|
|
624
|
for (Synonym synonym: taxon.getSynonyms()){
|
|
625
|
synonymName = CdmBase.deproxy(synonym.getName());
|
|
626
|
group = CdmBase.deproxy(synonymName.getHomotypicalGroup());
|
|
627
|
synonymName.generateFullTitle();
|
|
628
|
if (synonym.isDoubtful()){
|
|
629
|
if (!synonymName.getFullTitleCache().startsWith("?")){
|
|
630
|
doubtfulTitleCache = "?" + synonymName.getFullTitleCache();
|
|
631
|
synonymName = (IBotanicalName) synonymName.clone();
|
|
632
|
synonymName.setFullTitleCache(doubtfulTitleCache, true);
|
|
633
|
}
|
|
634
|
}
|
|
635
|
if (!group.equals(name.getHomotypicalGroup())){
|
|
636
|
if (heterotypicSynonymsList.containsKey(group)){
|
|
637
|
heterotypicSynonymsList.get(group).add(synonym);
|
|
638
|
}else{
|
|
639
|
homotypicSynonyms = new ArrayList<>();
|
|
640
|
homotypicSynonyms.add(synonym);
|
|
641
|
heterotypicSynonymsList.put(group, homotypicSynonyms);
|
|
642
|
homotypicSynonyms= null;
|
|
643
|
}
|
|
644
|
} else{
|
|
645
|
synonymName.generateFullTitle();
|
|
646
|
homotypicSynonymsList.add(synonym);
|
|
647
|
}
|
|
648
|
}
|
|
649
|
|
|
650
|
|
|
651
|
|
|
652
|
String synonymString;
|
|
653
|
boolean first = true;
|
|
654
|
|
|
655
|
for (List<Synonym> list: heterotypicSynonymsList.values()){
|
|
656
|
Collections.sort(list, new HomotypicGroupTaxonComparator(null));
|
|
657
|
first = true;
|
|
658
|
for (TaxonBase<?> synonym : list){
|
|
659
|
NomenclaturalStatus status = null;
|
|
660
|
if (!synonym.getName().getStatus().isEmpty()){
|
|
661
|
status = CdmBase.deproxy(synonym.getName().getStatus().iterator().next());
|
|
662
|
if (status.getType().isInvalidType()){
|
|
663
|
heterotypicalSynonyms.append(" <invalid> ");
|
|
664
|
synonymName = CdmBase.deproxy(synonym.getName());
|
|
665
|
|
|
666
|
synonymString = createSynonymNameString(synonymName, state.getConfig().isInvalidNamesQuoted()) ;
|
|
667
|
heterotypicalSynonyms.append(synonymString);
|
|
668
|
continue;
|
|
669
|
}
|
|
670
|
}
|
|
671
|
if (first){
|
|
672
|
heterotypicalSynonyms.append(" <heterotypic> ");
|
|
673
|
}else{
|
|
674
|
heterotypicalSynonyms.append(" <homonym> ");
|
|
675
|
}
|
|
676
|
first = false;
|
|
677
|
synonymName = CdmBase.deproxy(synonym.getName());
|
|
678
|
synonymString = createSynonymNameString(synonymName, false);
|
|
679
|
heterotypicalSynonyms.append(synonymString);
|
|
680
|
}
|
|
681
|
}
|
|
682
|
|
|
683
|
first = true;
|
|
684
|
Collections.sort(homotypicSynonymsList, new HomotypicGroupTaxonComparator(null) );
|
|
685
|
NomenclaturalStatus status = null;
|
|
686
|
for (TaxonBase<?> synonym : homotypicSynonymsList){
|
|
687
|
|
|
688
|
if (!synonym.getName().getStatus().isEmpty()){
|
|
689
|
status = CdmBase.deproxy(synonym.getName().getStatus().iterator().next());
|
|
690
|
if (status.getType().isInvalidType()){
|
|
691
|
homotypicalSynonyms.append(" <invalid> ");
|
|
692
|
synonymName = CdmBase.deproxy(synonym.getName());
|
|
693
|
synonymString = createSynonymNameString(synonymName, true);
|
|
694
|
homotypicalSynonyms.append(synonymString);
|
|
695
|
continue;
|
|
696
|
}else if (!first){
|
|
697
|
homotypicalSynonyms.append(" <homonym> ");
|
|
698
|
}
|
|
699
|
|
|
700
|
}else if (!first){
|
|
701
|
homotypicalSynonyms.append(" <homonym> ");
|
|
702
|
}
|
|
703
|
first = false;
|
|
704
|
synonymName = CdmBase.deproxy(synonym.getName());
|
|
705
|
|
|
706
|
synonymString = createSynonymNameString(synonymName, false);
|
|
707
|
|
|
708
|
homotypicalSynonyms.append(synonymString);
|
|
709
|
|
|
710
|
}
|
|
711
|
|
|
712
|
nameRecord.put("synonyms_homotypic", homotypicalSynonyms.toString());
|
|
713
|
nameRecord.put("synonyms_heterotypic", heterotypicalSynonyms.toString());
|
|
714
|
nameRecord.put("status", statusString);
|
|
715
|
|
|
716
|
Set<NameRelationship> nameRelations = name.getNameRelations();
|
|
717
|
|
|
718
|
INonViralName relatedName = null;
|
|
719
|
String nameRelType = null;
|
|
720
|
String relNameString = null;
|
|
721
|
if (nameRelations.size()>0){
|
|
722
|
NameRelationship nameRel = nameRelations.iterator().next();
|
|
723
|
IBotanicalName fromName = CdmBase.deproxy(nameRel.getFromName());
|
|
724
|
if (fromName.equals(taxon.getName())){
|
|
725
|
relatedName = nameRel.getToName();
|
|
726
|
|
|
727
|
}else{
|
|
728
|
relatedName = nameRel.getFromName();
|
|
729
|
}
|
|
730
|
nameRel = CdmBase.deproxy(nameRel);
|
|
731
|
nameRelType = nameRel.getType().getTitleCache();
|
|
732
|
relNameString = createTaggedNameString(relatedName, getStatus(relatedName));
|
|
733
|
}
|
|
734
|
|
|
735
|
|
|
736
|
nameRecord.put("relatedName", relNameString);
|
|
737
|
nameRecord.put("nameRelType", nameRelType);
|
|
738
|
|
|
739
|
extractDescriptions(nameRecord, taxon, Feature.DISTRIBUTION(), "descriptions", state);
|
|
740
|
return nameRecord;
|
|
741
|
}
|
|
742
|
|
|
743
|
/**
|
|
744
|
* @param nameRecord
|
|
745
|
* @param taxon
|
|
746
|
*/
|
|
747
|
private void getTaxonRelations(HashMap<String, String> nameRecord, Taxon taxon) {
|
|
748
|
Set<TaxonRelationship> relations = new HashSet<>();
|
|
749
|
relations =taxon.getTaxonRelations();
|
|
750
|
if (relations.isEmpty()){
|
|
751
|
nameRecord.put("missappliedNames", null);
|
|
752
|
}else{
|
|
753
|
Taxon relatedTaxon = null;
|
|
754
|
StringBuffer nameString = new StringBuffer();
|
|
755
|
for (TaxonRelationship rel : relations){
|
|
756
|
if (rel.getType().isAnyMisappliedName()){
|
|
757
|
relatedTaxon = rel.getFromTaxon();
|
|
758
|
Reference secRef = relatedTaxon.getSec();
|
|
759
|
String appendedPhrase = "";
|
|
760
|
if (relatedTaxon.getAppendedPhrase() != null){
|
|
761
|
appendedPhrase = relatedTaxon.getAppendedPhrase();
|
|
762
|
}
|
|
763
|
if (appendedPhrase.equals("sphalm.")){
|
|
764
|
String relNameString = createTaggedNameString(relatedTaxon.getName(), getStatus(relatedTaxon.getName()));
|
|
765
|
|
|
766
|
nameRecord.put("relatedName", relNameString);
|
|
767
|
nameRecord.put("nameRelType", NameRelationshipType.ORTHOGRAPHIC_VARIANT().getTitleCache());
|
|
768
|
return;
|
|
769
|
}
|
|
770
|
if (secRef == null){
|
|
771
|
nameString.append("<misapplied>" +"\u201C" + createTaggedNameString(relatedTaxon.getName(), false) + "\u201D " + appendedPhrase);
|
|
772
|
} else if (secRef.getAuthorship() == null){
|
|
773
|
nameString.append("<misapplied>"+"\u201C" + createTaggedNameString(relatedTaxon.getName(), false) + "\u201D " + appendedPhrase + " sensu " + secRef.getTitleCache());
|
|
774
|
} else {
|
|
775
|
nameString.append("<misapplied>\"" + createTaggedNameString(relatedTaxon.getName(), false) + "\" " + appendedPhrase + " sensu " + secRef.getAuthorship().getFullTitle());
|
|
776
|
}
|
|
777
|
|
|
778
|
}
|
|
779
|
}
|
|
780
|
nameRecord.put("missappliedNames", nameString.toString());
|
|
781
|
}
|
|
782
|
}
|
|
783
|
|
|
784
|
}
|
|
785
|
|