|
1
|
/**
|
|
2
|
* Copyright (C) 2007 EDIT
|
|
3
|
* European Distributed Institute of Taxonomy
|
|
4
|
* http://www.e-taxonomy.eu
|
|
5
|
*
|
|
6
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
|
7
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
|
8
|
*/
|
|
9
|
|
|
10
|
package eu.etaxonomy.cdm.io.globis;
|
|
11
|
|
|
12
|
import java.sql.ResultSet;
|
|
13
|
import java.sql.SQLException;
|
|
14
|
import java.util.HashMap;
|
|
15
|
import java.util.HashSet;
|
|
16
|
import java.util.List;
|
|
17
|
import java.util.Map;
|
|
18
|
import java.util.Set;
|
|
19
|
import java.util.UUID;
|
|
20
|
import java.util.regex.Matcher;
|
|
21
|
import java.util.regex.Pattern;
|
|
22
|
|
|
23
|
import org.apache.log4j.Logger;
|
|
24
|
import org.springframework.stereotype.Component;
|
|
25
|
|
|
26
|
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
|
|
27
|
import eu.etaxonomy.cdm.common.CdmUtils;
|
|
28
|
import eu.etaxonomy.cdm.io.common.IOValidator;
|
|
29
|
import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
|
|
30
|
import eu.etaxonomy.cdm.io.common.mapping.IMappingImport;
|
|
31
|
import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
|
|
32
|
import eu.etaxonomy.cdm.io.globis.validation.GlobisSpecTaxaImportValidator;
|
|
33
|
import eu.etaxonomy.cdm.model.agent.AgentBase;
|
|
34
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
35
|
import eu.etaxonomy.cdm.model.common.ExtensionType;
|
|
36
|
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
|
|
37
|
import eu.etaxonomy.cdm.model.common.Marker;
|
|
38
|
import eu.etaxonomy.cdm.model.common.MarkerType;
|
|
39
|
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
|
|
40
|
import eu.etaxonomy.cdm.model.description.Feature;
|
|
41
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
|
42
|
import eu.etaxonomy.cdm.model.name.IZoologicalName;
|
|
43
|
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
|
|
44
|
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
|
|
45
|
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
|
|
46
|
import eu.etaxonomy.cdm.model.name.Rank;
|
|
47
|
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
|
|
48
|
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
|
|
49
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
|
50
|
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
|
|
51
|
import eu.etaxonomy.cdm.model.occurrence.Collection;
|
|
52
|
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
|
|
53
|
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
|
|
54
|
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
|
|
55
|
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
|
|
56
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
|
57
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
|
58
|
import eu.etaxonomy.cdm.model.taxon.SynonymType;
|
|
59
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
60
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
61
|
import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
|
|
62
|
|
|
63
|
|
|
64
|
/**
|
|
65
|
* @author a.mueller
|
|
66
|
* @created 20.02.2010
|
|
67
|
*/
|
|
68
|
@Component
|
|
69
|
public class GlobisSpecTaxImport extends GlobisImportBase<Reference> implements IMappingImport<Reference, GlobisImportState>{
|
|
70
|
private static final Logger logger = Logger.getLogger(GlobisSpecTaxImport.class);
|
|
71
|
|
|
72
|
private int modCount = 10000;
|
|
73
|
private static final String pluralString = "taxa";
|
|
74
|
private static final String dbTableName = "specTax";
|
|
75
|
private static final Class<?> cdmTargetClass = Reference.class;
|
|
76
|
|
|
77
|
private static UUID uuidCitedTypeLocality = UUID.fromString("ca431e0a-84ec-4828-935f-df4c8f5cf880");
|
|
78
|
private static UUID uuidCitedTypeMaterial = UUID.fromString("8395021a-e596-4a55-9794-8c03aaad9e16");
|
|
79
|
|
|
80
|
public GlobisSpecTaxImport(){
|
|
81
|
super(pluralString, dbTableName, cdmTargetClass);
|
|
82
|
}
|
|
83
|
|
|
84
|
@Override
|
|
85
|
protected String getIdQuery() {
|
|
86
|
String strRecordQuery =
|
|
87
|
" SELECT specTaxId " +
|
|
88
|
" FROM " + dbTableName;
|
|
89
|
return strRecordQuery;
|
|
90
|
}
|
|
91
|
|
|
92
|
@Override
|
|
93
|
protected String getRecordQuery(GlobisImportConfigurator config) {
|
|
94
|
String strRecordQuery =
|
|
95
|
" SELECT t.*, t.DateCreated as Created_When, t.CreatedBy as Created_Who," +
|
|
96
|
" t.ModifiedBy as Updated_who, t.DateModified as Updated_When, t.SpecRemarks as Notes " +
|
|
97
|
" FROM " + getTableName() + " t " +
|
|
98
|
" WHERE ( t.specTaxId IN (" + ID_LIST_TOKEN + ") )";
|
|
99
|
return strRecordQuery;
|
|
100
|
}
|
|
101
|
|
|
102
|
|
|
103
|
@Override
|
|
104
|
public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {
|
|
105
|
boolean success = true;
|
|
106
|
|
|
107
|
Set<TaxonBase> objectsToSave = new HashSet<>();
|
|
108
|
Set<TaxonName> namesToSave = new HashSet<>();
|
|
109
|
|
|
110
|
Map<String, Taxon> taxonMap = partitioner.getObjectMap(TAXON_NAMESPACE);
|
|
111
|
Map<String, Reference> referenceMap = partitioner.getObjectMap(REFERENCE_NAMESPACE);
|
|
112
|
|
|
113
|
ResultSet rs = partitioner.getResultSet();
|
|
114
|
|
|
115
|
try {
|
|
116
|
|
|
117
|
int i = 0;
|
|
118
|
|
|
119
|
//for each reference
|
|
120
|
while (rs.next()){
|
|
121
|
|
|
122
|
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}
|
|
123
|
|
|
124
|
Integer specTaxId = rs.getInt("SpecTaxId");
|
|
125
|
Integer acceptedTaxonId = nullSafeInt(rs, "SpecCurrspecID");
|
|
126
|
String specSystaxRank = rs.getString("SpecSystaxRank");
|
|
127
|
|
|
128
|
//ignore: CountryDummy, currentSpecies, DepositoryDisplay, DepositoryDummy, ReferenceDisplay,
|
|
129
|
// SpecDescriptionImageFile, all *Valid*
|
|
130
|
|
|
131
|
try {
|
|
132
|
|
|
133
|
//source ref
|
|
134
|
Reference sourceRef = state.getTransactionalSourceReference();
|
|
135
|
|
|
136
|
Taxon acceptedTaxon = taxonMap.get(String.valueOf(acceptedTaxonId));
|
|
137
|
TaxonBase<?> thisTaxon = null;
|
|
138
|
|
|
139
|
IZoologicalName name = null;
|
|
140
|
if (isBlank(specSystaxRank) ){
|
|
141
|
name = makeName(state, rs, specTaxId);
|
|
142
|
}else if (specSystaxRank.equals("synonym")){
|
|
143
|
Synonym synonym = getSynonym(state, rs, specTaxId);
|
|
144
|
if (acceptedTaxon == null){
|
|
145
|
if (acceptedTaxonId == null){
|
|
146
|
logger.warn("Synonym has no accepted taxon defined. SpecTaxId: "+ specTaxId);
|
|
147
|
}else{
|
|
148
|
logger.warn("Accepted taxon (" + acceptedTaxonId + ") not found for synonym "+ specTaxId);
|
|
149
|
}
|
|
150
|
}else{
|
|
151
|
acceptedTaxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
|
|
152
|
thisTaxon = synonym;
|
|
153
|
}
|
|
154
|
}else if (specSystaxRank.equals("species")){
|
|
155
|
validateAcceptedTaxon(acceptedTaxon, rs, specTaxId, acceptedTaxonId);
|
|
156
|
thisTaxon = acceptedTaxon;
|
|
157
|
}else{
|
|
158
|
logger.warn(String.format("Unhandled specSystaxRank %s in specTaxId %d", specSystaxRank, specTaxId));
|
|
159
|
name = makeName(state, rs, specTaxId);
|
|
160
|
}
|
|
161
|
|
|
162
|
if (thisTaxon != null){
|
|
163
|
name = CdmBase.deproxy(thisTaxon.getName(), TaxonName.class);
|
|
164
|
}else{
|
|
165
|
if (name == null){
|
|
166
|
name = makeName(state, rs, specTaxId);
|
|
167
|
}
|
|
168
|
|
|
169
|
thisTaxon = Taxon.NewInstance(name, sourceRef);
|
|
170
|
objectsToSave.add(thisTaxon);
|
|
171
|
}
|
|
172
|
if (name == null){
|
|
173
|
throw new RuntimeException("Name is still null");
|
|
174
|
}
|
|
175
|
|
|
176
|
handleNomRef(state, referenceMap, rs, name, specTaxId);
|
|
177
|
|
|
178
|
handleTypeInformation(state,rs, name, specTaxId);
|
|
179
|
|
|
180
|
|
|
181
|
// this.doIdCreatedUpdatedNotes(state, ref, rs, refId, REFERENCE_NAMESPACE);
|
|
182
|
|
|
183
|
if (acceptedTaxon != null){
|
|
184
|
objectsToSave.add(acceptedTaxon);
|
|
185
|
}
|
|
186
|
|
|
187
|
//makeMarker1(state, rs, name); //ignore!
|
|
188
|
|
|
189
|
//make not available
|
|
190
|
makeNotAvailable(state, rs, name, specTaxId);
|
|
191
|
|
|
192
|
//maken invalid
|
|
193
|
//TODO
|
|
194
|
|
|
195
|
//SpecCitedTypeLocality
|
|
196
|
String citedTypeLocality = rs.getString("SpecCitedTypeLocality");
|
|
197
|
if (isNotBlank(citedTypeLocality)){
|
|
198
|
// ExtensionType exTypeCitedTypeLoc = getExtensionType(state, uuidCitedTypeLocality, "Type locality as cited in original description", "Type locality as cited in original description", null, ExtensionType.DOI().getVocabulary());
|
|
199
|
// name.addExtension(citedTypeLocality, exTypeCitedTypeLoc);
|
|
200
|
addNameDescription(state, name, uuidCitedTypeLocality, citedTypeLocality, "Type locality as cited in original description");
|
|
201
|
}
|
|
202
|
|
|
203
|
//SpecCitedTypeMaterial
|
|
204
|
String citedTypeMaterial = rs.getString("SpecCitedTypeMaterial");
|
|
205
|
if (isNotBlank(citedTypeMaterial)){
|
|
206
|
ExtensionType exTypeCitedTypeLoc = getExtensionType(state, uuidCitedTypeMaterial, "Type material as cited in original description", "Type material as cited in original description", null, ExtensionType.DOI().getVocabulary());
|
|
207
|
name.addExtension(citedTypeLocality, exTypeCitedTypeLoc);
|
|
208
|
}
|
|
209
|
|
|
210
|
name.addSource(OriginalSourceType.Import, String.valueOf(specTaxId), SPEC_TAX_NAMESPACE, state.getTransactionalSourceReference(), null);
|
|
211
|
|
|
212
|
namesToSave.add(TaxonName.castAndDeproxy(name));
|
|
213
|
|
|
214
|
|
|
215
|
} catch (Exception e) {
|
|
216
|
logger.warn("Exception in specTax: SpecTaxId " + specTaxId + ". " + e.getMessage());
|
|
217
|
e.printStackTrace();
|
|
218
|
}
|
|
219
|
|
|
220
|
}
|
|
221
|
|
|
222
|
logger.warn(pluralString + " to save: " + objectsToSave.size());
|
|
223
|
getTaxonService().save(objectsToSave);
|
|
224
|
getNameService().save(namesToSave);
|
|
225
|
|
|
226
|
return success;
|
|
227
|
} catch (Exception e) {
|
|
228
|
logger.error("Exception: " + e);
|
|
229
|
return false;
|
|
230
|
}
|
|
231
|
}
|
|
232
|
|
|
233
|
|
|
234
|
private void makeNotAvailable(GlobisImportState state, ResultSet rs, IZoologicalName name, int id) throws SQLException {
|
|
235
|
String notAvailableStr = rs.getString("SpecNotAvailable");
|
|
236
|
String notAvailableReason = rs.getString("SpecNotAvailableReason");
|
|
237
|
|
|
238
|
if (isNotBlank(notAvailableStr) && notAvailableStr.contains("not available")){
|
|
239
|
if (isBlank(notAvailableReason)){
|
|
240
|
logger.warn("Blank notAvailableReason has available: " + id);
|
|
241
|
}
|
|
242
|
NomenclaturalStatus nomStatus = getNomStatus(state, notAvailableReason, id);
|
|
243
|
if (nomStatus != null){
|
|
244
|
name.addStatus(nomStatus);
|
|
245
|
}
|
|
246
|
}else{
|
|
247
|
if (isNotBlank(notAvailableReason)){
|
|
248
|
logger.warn("Blank notAvailable has reason: " + id);
|
|
249
|
}
|
|
250
|
//Do nothing
|
|
251
|
}
|
|
252
|
|
|
253
|
|
|
254
|
//OLD
|
|
255
|
// if (notAvailableStr.contains("not available") ){
|
|
256
|
// UUID uuidNotAvailableMarkerType = state.getTransformer().getMarkerTypeUuid("not available");
|
|
257
|
//
|
|
258
|
// MarkerType markerType = getMarkerType(state, uuidNotAvailableMarkerType, "not available", "not available", null);
|
|
259
|
// name.addMarker(Marker.NewInstance(markerType, true));
|
|
260
|
// }
|
|
261
|
// //Not available reason
|
|
262
|
// String notAvailableReason = rs.getString("SpecNotAvailableReason");
|
|
263
|
// if (isNotBlank(notAvailableReason)){
|
|
264
|
// UUID uuidNotAvailableReason;
|
|
265
|
// try {
|
|
266
|
// uuidNotAvailableReason = state.getTransformer().getExtensionTypeUuid("not available reason");
|
|
267
|
// ExtensionType notAvailableReasonExtType = getExtensionType(state, uuidNotAvailableReason, "Not available reason", "Not available reason", null, null);
|
|
268
|
// name.addExtension(notAvailableReason, notAvailableReasonExtType);
|
|
269
|
// } catch (UndefinedTransformerMethodException e) {
|
|
270
|
// e.printStackTrace();
|
|
271
|
// }
|
|
272
|
// }
|
|
273
|
|
|
274
|
}
|
|
275
|
|
|
276
|
|
|
277
|
|
|
278
|
|
|
279
|
|
|
280
|
private NomenclaturalStatus getNomStatus(GlobisImportState state, String notAvailableReason, int id) {
|
|
281
|
NomenclaturalStatus status = NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ZOO_NOT_AVAILABLE());
|
|
282
|
status.setRuleConsidered(notAvailableReason);
|
|
283
|
if (notAvailableReason.equalsIgnoreCase("hybrid")){
|
|
284
|
logger.warn("Check hybrid for correctnes. Is there a better status?");
|
|
285
|
}else if (notAvailableReason.equalsIgnoreCase("infrasubspecific name") || notAvailableReason.equalsIgnoreCase("infrasubspeciic name")){
|
|
286
|
logger.warn("Check infrasubspecific name for correctnes. Is there a better status?");
|
|
287
|
}else if (notAvailableReason.equalsIgnoreCase("by ruling of the Commission")){
|
|
288
|
logger.warn("Check by ruling of the Commission for correctnes. Is there a better status?");
|
|
289
|
}else{
|
|
290
|
logger.warn("Unknown non available reason. ");
|
|
291
|
}
|
|
292
|
return status;
|
|
293
|
}
|
|
294
|
|
|
295
|
/**
|
|
296
|
* This method is not used anymore as according to Alexander Marker1 should be ignored.
|
|
297
|
* @param state
|
|
298
|
* @param rs
|
|
299
|
* @param name
|
|
300
|
* @throws SQLException
|
|
301
|
*/
|
|
302
|
@SuppressWarnings("unused")
|
|
303
|
private void makeMarker1(GlobisImportState state, ResultSet rs, IZoologicalName name) throws SQLException {
|
|
304
|
String marker1Str = rs.getString("Marker1");
|
|
305
|
try {
|
|
306
|
if (isNotBlank(marker1Str)){
|
|
307
|
marker1Str = marker1Str.trim();
|
|
308
|
if (marker1Str.contains("checked") || marker1Str.contains("berpr") ){ //überprüft
|
|
309
|
UUID uuidCheckedMarkerType;
|
|
310
|
uuidCheckedMarkerType = state.getTransformer().getMarkerTypeUuid("checked");
|
|
311
|
|
|
312
|
MarkerType markerType = getMarkerType(state, uuidCheckedMarkerType, "checked", "checked", null);
|
|
313
|
name.addMarker(Marker.NewInstance(markerType, true));
|
|
314
|
}
|
|
315
|
if (marker1Str.contains("old record") || marker1Str.contains("alte Angabe") ){
|
|
316
|
UUID uuidOldRecordMarkerType = state.getTransformer().getMarkerTypeUuid("old record");
|
|
317
|
MarkerType markerType = getMarkerType(state, uuidOldRecordMarkerType, "checked", "checked", null);
|
|
318
|
name.addMarker(Marker.NewInstance(markerType, true));
|
|
319
|
}
|
|
320
|
}
|
|
321
|
} catch (UndefinedTransformerMethodException e) {
|
|
322
|
e.printStackTrace();
|
|
323
|
}
|
|
324
|
|
|
325
|
}
|
|
326
|
|
|
327
|
|
|
328
|
private void addNameDescription(GlobisImportState state, IZoologicalName name, UUID featureUuid,
|
|
329
|
String citedTypeLocality, String featureLabel) {
|
|
330
|
Feature feature = getFeature(state, featureUuid,featureLabel,featureLabel, null, null);
|
|
331
|
getTaxonNameDescription((TaxonName<?,?>)name, false, true);
|
|
332
|
|
|
333
|
}
|
|
334
|
|
|
335
|
|
|
336
|
private Pattern patternAll = Pattern.compile("(.+,\\s.+)(\\(.+\\))");
|
|
337
|
|
|
338
|
|
|
339
|
private void handleTypeInformation(GlobisImportState state, ResultSet rs, IZoologicalName name, Integer specTaxId) throws SQLException {
|
|
340
|
if (! hasTypeInformation(rs)){
|
|
341
|
return;
|
|
342
|
}
|
|
343
|
|
|
344
|
FieldUnit fieldObservation = makeTypeFieldObservation(state, rs);
|
|
345
|
|
|
346
|
//typeDepository
|
|
347
|
String specTypeDepositoriesStr = rs.getString("SpecTypeDepository");
|
|
348
|
String[] specTypeDepositories;
|
|
349
|
if (isNotBlank(specTypeDepositoriesStr) ){
|
|
350
|
specTypeDepositories = specTypeDepositoriesStr.trim().split(";");
|
|
351
|
}else{
|
|
352
|
specTypeDepositories = new String[0];
|
|
353
|
}
|
|
354
|
|
|
355
|
//TODO several issues
|
|
356
|
if (specTypeDepositories.length == 0){
|
|
357
|
DerivedUnit specimen = makeSingleTypeSpecimen(fieldObservation);
|
|
358
|
makeTypeDesignation(name, rs, specimen, specTaxId);
|
|
359
|
makeTypeIdInSource(state, specimen, "null", specTaxId);
|
|
360
|
}else{
|
|
361
|
for (String specTypeDepositoryStr : specTypeDepositories){
|
|
362
|
specTypeDepositoryStr = specTypeDepositoryStr.trim();
|
|
363
|
|
|
364
|
//Specimen
|
|
365
|
DerivedUnit specimen = makeSingleTypeSpecimen(fieldObservation);
|
|
366
|
|
|
367
|
if (specTypeDepositoryStr.equals("??")){
|
|
368
|
//unknown
|
|
369
|
//TODO marker unknown ?
|
|
370
|
specimen.setTitleCache("??", true);
|
|
371
|
makeTypeIdInSource(state, specimen, "??", specTaxId);
|
|
372
|
}else if (specTypeDepositoryStr.equals("[lost]")){
|
|
373
|
//lost
|
|
374
|
//TODO marker lost ?
|
|
375
|
specimen.setTitleCache("lost", true);
|
|
376
|
makeTypeIdInSource(state, specimen, "[lost]", specTaxId);
|
|
377
|
}else{
|
|
378
|
specTypeDepositoryStr = makeAdditionalSpecimenInformation(
|
|
379
|
specTypeDepositoryStr, specimen, specTaxId);
|
|
380
|
|
|
381
|
Collection collection = makeCollection(state, specTypeDepositoryStr, specimen, specTaxId);
|
|
382
|
String collectionCode = collection.getCode();
|
|
383
|
if (isBlank(collectionCode)){
|
|
384
|
collectionCode = collection.getName();
|
|
385
|
}
|
|
386
|
if (isBlank(collectionCode)){
|
|
387
|
logger.warn("Collection has empty representation: " + specTypeDepositoryStr + ", specTaxId" + specTaxId);
|
|
388
|
}
|
|
389
|
makeTypeIdInSource(state, specimen, collectionCode , specTaxId);
|
|
390
|
}
|
|
391
|
|
|
392
|
//type Designation
|
|
393
|
makeTypeDesignation(name, rs, specimen, specTaxId);
|
|
394
|
}
|
|
395
|
}
|
|
396
|
|
|
397
|
|
|
398
|
}
|
|
399
|
|
|
400
|
|
|
401
|
private void makeTypeIdInSource(GlobisImportState state, DerivedUnit specimen, String collectionCode, Integer specTaxId) {
|
|
402
|
String namespace = TYPE_NAMESPACE;
|
|
403
|
String id = getTypeId(specTaxId, collectionCode);
|
|
404
|
IdentifiableSource source = IdentifiableSource.NewInstance(OriginalSourceType.Import, id, namespace, state.getTransactionalSourceReference(), null);
|
|
405
|
specimen.addSource(source);
|
|
406
|
}
|
|
407
|
|
|
408
|
|
|
409
|
|
|
410
|
|
|
411
|
public static String getTypeId(Integer specTaxId, String collectionCode) {
|
|
412
|
String result = String.valueOf(specTaxId) + "@" + collectionCode;
|
|
413
|
return result;
|
|
414
|
}
|
|
415
|
|
|
416
|
|
|
417
|
|
|
418
|
|
|
419
|
private boolean hasTypeInformation(ResultSet rs) throws SQLException {
|
|
420
|
String specTypeDepositoriesStr = rs.getString("SpecTypeDepository");
|
|
421
|
String countryString = rs.getString("SpecTypeCountry");
|
|
422
|
String specType = rs.getString("SpecType");
|
|
423
|
boolean result = false;
|
|
424
|
result |= isNotBlank(specTypeDepositoriesStr) || isNotBlank(countryString)
|
|
425
|
|| isNotBlank(specType);
|
|
426
|
return result;
|
|
427
|
}
|
|
428
|
|
|
429
|
|
|
430
|
|
|
431
|
/**
|
|
432
|
* @param state
|
|
433
|
* @param specTypeDepositoryStr
|
|
434
|
* @param specimen
|
|
435
|
* @param specTaxId
|
|
436
|
*/
|
|
437
|
protected Collection makeCollection(GlobisImportState state, String specTypeDepositoryStr, DerivedUnit specimen, Integer specTaxId) {
|
|
438
|
|
|
439
|
//Collection
|
|
440
|
specTypeDepositoryStr = specTypeDepositoryStr.replace("Washington, D.C.", "Washington@ D.C.")
|
|
441
|
.replace("St.-Raymond, Quebec", "St.-Raymond@ Quebec")
|
|
442
|
.replace("St.Petersburg", "St. Petersburg");
|
|
443
|
|
|
444
|
|
|
445
|
Collection collection = handleSpecialCase(specTypeDepositoryStr, state, specimen);
|
|
446
|
if (collection == null){
|
|
447
|
String[] split = specTypeDepositoryStr.split(",");
|
|
448
|
if (split.length != 2){
|
|
449
|
if (split.length == 1 && (split[0].startsWith("coll.")|| split[0].startsWith("Coll.") )){
|
|
450
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, split[0], Collection.class);
|
|
451
|
if (collection == null){
|
|
452
|
collection = Collection.NewInstance();
|
|
453
|
collection.setName(split[0]);
|
|
454
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
455
|
}
|
|
456
|
specimen.setCollection(collection);
|
|
457
|
}else{
|
|
458
|
logger.warn("Split size in SpecTypeDepository is not 2: " + specTypeDepositoryStr + " (specTaxID:" + specTaxId + ")");
|
|
459
|
collection = Collection.NewInstance();
|
|
460
|
collection.setCode("??");
|
|
461
|
//TODO deduplicate ??
|
|
462
|
}
|
|
463
|
|
|
464
|
}else{
|
|
465
|
String collectionStr = split[0];
|
|
466
|
String location = split[1].replace("@", ",").trim();
|
|
467
|
|
|
468
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, collectionStr, Collection.class);
|
|
469
|
if (collection == null){
|
|
470
|
collection = Collection.NewInstance();
|
|
471
|
if (collectionStr != null && collectionStr.startsWith("coll.")){
|
|
472
|
collection.setName(collectionStr);
|
|
473
|
}else{
|
|
474
|
collection.setCode(collectionStr);
|
|
475
|
}
|
|
476
|
collection.setTownOrLocation(location);
|
|
477
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getCode(), collection);
|
|
478
|
|
|
479
|
}else if (! CdmUtils.nullSafeEqual(location, collection.getTownOrLocation())){
|
|
480
|
if (! normalizeTownOrLocation(location, collection)){
|
|
481
|
String message = "Location (%s) is not equal to location (%s) of existing collection, specTaxId: " + specTaxId;
|
|
482
|
logger.warn(String.format(message, location, collection.getTownOrLocation(), collection.getCode()));
|
|
483
|
}
|
|
484
|
|
|
485
|
}
|
|
486
|
|
|
487
|
specimen.setCollection(collection);
|
|
488
|
}
|
|
489
|
}
|
|
490
|
return collection;
|
|
491
|
}
|
|
492
|
|
|
493
|
|
|
494
|
private boolean normalizeTownOrLocation(String location, Collection collection) {
|
|
495
|
boolean result = false;
|
|
496
|
if (location != null){
|
|
497
|
if ("coll. C. G. Treadaway".equals(collection.getName())){
|
|
498
|
if (! "Frankfurt am Main".equals(collection.getTownOrLocation())){
|
|
499
|
collection.setTownOrLocation("Frankfurt am Main");
|
|
500
|
getCollectionService().saveOrUpdate(collection);
|
|
501
|
}
|
|
502
|
return true;
|
|
503
|
} else if ("coll. K. Rose".equals(collection.getName())){
|
|
504
|
if (! "Mainz-Bretzenheim".equals(collection.getTownOrLocation())){
|
|
505
|
collection.setTownOrLocation("Mainz-Bretzenheim");
|
|
506
|
getCollectionService().saveOrUpdate(collection);
|
|
507
|
}
|
|
508
|
return true;
|
|
509
|
} else if ("NMPN".equals(collection.getCode())){
|
|
510
|
if (! "Prague".equals(collection.getTownOrLocation())){
|
|
511
|
collection.setTownOrLocation("Prague");
|
|
512
|
getCollectionService().saveOrUpdate(collection);
|
|
513
|
}
|
|
514
|
return true;
|
|
515
|
} else if ("USNM".equals(collection.getCode())){
|
|
516
|
if (! "Washington, D.C.".equals(collection.getTownOrLocation())){
|
|
517
|
collection.setTownOrLocation("Washington, D.C.");
|
|
518
|
getCollectionService().saveOrUpdate(collection);
|
|
519
|
}
|
|
520
|
return true;
|
|
521
|
} else if ("coll. S. Kocman".equals(collection.getName())){
|
|
522
|
if (! "Ostrava-Zabreh".equals(collection.getTownOrLocation())){
|
|
523
|
collection.setTownOrLocation("Ostrava-Zabreh");
|
|
524
|
getCollectionService().saveOrUpdate(collection);
|
|
525
|
}
|
|
526
|
return true;
|
|
527
|
} else if ("ZSSM".equals(collection.getCode())){
|
|
528
|
if (! "Munich".equals(collection.getTownOrLocation())){
|
|
529
|
collection.setTownOrLocation("Munich");
|
|
530
|
getCollectionService().saveOrUpdate(collection);
|
|
531
|
}
|
|
532
|
return true;
|
|
533
|
} else if ("coll. R. H. Anken".equals(collection.getName())){
|
|
534
|
if (! "Stuttgart".equals(collection.getTownOrLocation())){
|
|
535
|
collection.setTownOrLocation("Stuttgart");
|
|
536
|
getCollectionService().saveOrUpdate(collection);
|
|
537
|
}
|
|
538
|
return true;
|
|
539
|
} else if ("coll. S.-I. Murayama".equals(collection.getName())){
|
|
540
|
if (! "Aichi-Gakuin".equals(collection.getTownOrLocation())){
|
|
541
|
collection.setTownOrLocation("Aichi-Gakuin");
|
|
542
|
getCollectionService().saveOrUpdate(collection);
|
|
543
|
}
|
|
544
|
return true;
|
|
545
|
} else if ("coll. Y. Sorimachi".equals(collection.getName())){
|
|
546
|
if (! "Saitama".equals(collection.getTownOrLocation())){
|
|
547
|
collection.setTownOrLocation("Saitama");
|
|
548
|
getCollectionService().saveOrUpdate(collection);
|
|
549
|
}
|
|
550
|
return true;
|
|
551
|
} else if ("coll. K. Yoshino".equals(collection.getName())){
|
|
552
|
if (! "Saitama".equals(collection.getTownOrLocation())){
|
|
553
|
collection.setTownOrLocation("Saitama");
|
|
554
|
getCollectionService().saveOrUpdate(collection);
|
|
555
|
}
|
|
556
|
return true;
|
|
557
|
} else if ("coll. U. Eitschberger".equals(collection.getName())){
|
|
558
|
if (! "Marktleuthen".equals(collection.getTownOrLocation())){
|
|
559
|
collection.setTownOrLocation("Marktleuthen");
|
|
560
|
getCollectionService().saveOrUpdate(collection);
|
|
561
|
}
|
|
562
|
return true;
|
|
563
|
} else if ("coll. G. Sala".equals(collection.getName())){
|
|
564
|
if (! "Sal\u00f2".equals(collection.getTownOrLocation())){
|
|
565
|
collection.setTownOrLocation("Sal\u00f2"); //LATIN SMALL LETTER O WITH GRAVE
|
|
566
|
getCollectionService().saveOrUpdate(collection);
|
|
567
|
}
|
|
568
|
return true;
|
|
569
|
} else if ("coll. Dantchenko".equals(collection.getName())){
|
|
570
|
if (! "Moscow".equals(collection.getTownOrLocation())){
|
|
571
|
collection.setTownOrLocation("Moscow");
|
|
572
|
getCollectionService().saveOrUpdate(collection);
|
|
573
|
}
|
|
574
|
return true;
|
|
575
|
} else if ("coll. S. Nakano".equals(collection.getName())){
|
|
576
|
if (! "Tokyo".equals(collection.getTownOrLocation())){
|
|
577
|
collection.setTownOrLocation("Tokyo");
|
|
578
|
getCollectionService().saveOrUpdate(collection);
|
|
579
|
}
|
|
580
|
return true;
|
|
581
|
} else if ("coll. A. Yagishita".equals(collection.getName())){
|
|
582
|
if (! "Toride Ibaraki".equals(collection.getTownOrLocation())){
|
|
583
|
collection.setTownOrLocation("Toride Ibaraki");
|
|
584
|
getCollectionService().saveOrUpdate(collection);
|
|
585
|
}
|
|
586
|
return true;
|
|
587
|
} else if ("coll. H. Sugiyama".equals(collection.getName())){
|
|
588
|
if (! "Gifu".equals(collection.getTownOrLocation())){
|
|
589
|
collection.setTownOrLocation("Gifu");
|
|
590
|
getCollectionService().saveOrUpdate(collection);
|
|
591
|
}
|
|
592
|
return true;
|
|
593
|
} else if ("MDMO".equals(collection.getCode())){
|
|
594
|
if (! "Moscow".equals(collection.getTownOrLocation())){
|
|
595
|
collection.setTownOrLocation("Moscow");
|
|
596
|
getCollectionService().saveOrUpdate(collection);
|
|
597
|
}
|
|
598
|
return true;
|
|
599
|
} else if ("coll. W. Eckweiler".equals(collection.getName())){
|
|
600
|
if (! "Frankfurt am Main".equals(collection.getTownOrLocation())){
|
|
601
|
collection.setTownOrLocation("Frankfurt am Main");
|
|
602
|
getCollectionService().saveOrUpdate(collection);
|
|
603
|
}
|
|
604
|
return true;
|
|
605
|
} else if ("coll. T. Frankenbach".equals(collection.getName())){
|
|
606
|
if (! "Wangen".equals(collection.getTownOrLocation())){
|
|
607
|
collection.setTownOrLocation("Wangen");
|
|
608
|
getCollectionService().saveOrUpdate(collection);
|
|
609
|
}
|
|
610
|
return true;
|
|
611
|
}
|
|
612
|
}
|
|
613
|
|
|
614
|
return result;
|
|
615
|
}
|
|
616
|
|
|
617
|
private Collection handleSpecialCase(String specTypeDepositoryStr, GlobisImportState state, DerivedUnit specimen) {
|
|
618
|
Collection collection;
|
|
619
|
if (specTypeDepositoryStr.equals("BMNH, London and/or MNHN, Paris")){
|
|
620
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, specTypeDepositoryStr, Collection.class);
|
|
621
|
if (collection == null){
|
|
622
|
collection = Collection.NewInstance();
|
|
623
|
collection.setName(specTypeDepositoryStr);
|
|
624
|
collection.setTownOrLocation("London or Paris");
|
|
625
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
626
|
}
|
|
627
|
specimen.setCollection(collection);
|
|
628
|
}else if (specTypeDepositoryStr.equals("ZISP, St. Petersburg, and/or BMNH, London ?")){
|
|
629
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, specTypeDepositoryStr, Collection.class);
|
|
630
|
if (collection == null){
|
|
631
|
collection = Collection.NewInstance();
|
|
632
|
collection.setName(specTypeDepositoryStr);
|
|
633
|
collection.setTownOrLocation("St. Petersburg or London");
|
|
634
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
635
|
}
|
|
636
|
specimen.setCollection(collection);
|
|
637
|
}else if (specTypeDepositoryStr.equals("MFNB, Berlin or SMTD, Dresden")){
|
|
638
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, specTypeDepositoryStr, Collection.class);
|
|
639
|
if (collection == null){
|
|
640
|
collection = Collection.NewInstance();
|
|
641
|
collection.setName(specTypeDepositoryStr);
|
|
642
|
collection.setTownOrLocation("Berlin or Dresden");
|
|
643
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
644
|
}
|
|
645
|
specimen.setCollection(collection);
|
|
646
|
}else if (specTypeDepositoryStr.equals("coll. S. Ianoka, Yamanashi, coll. A. Shinkai, Tokyo or coll. S. Morita")){
|
|
647
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, specTypeDepositoryStr, Collection.class);
|
|
648
|
if (collection == null){
|
|
649
|
collection = Collection.NewInstance();
|
|
650
|
collection.setName(specTypeDepositoryStr);
|
|
651
|
collection.setTownOrLocation("Yamanashi or Tokyo or ?");
|
|
652
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
653
|
}
|
|
654
|
specimen.setCollection(collection);
|
|
655
|
}else if (specTypeDepositoryStr.equals("coll. S. Inaoka, Yamanashi, coll. A. Shinkai, Tokyo, coll. H. Mikami, coll. S. Koiwaya, coll S. Morita or coll. Y. Nose")){
|
|
656
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, specTypeDepositoryStr, Collection.class);
|
|
657
|
if (collection == null){
|
|
658
|
collection = Collection.NewInstance();
|
|
659
|
collection.setName(specTypeDepositoryStr);
|
|
660
|
collection.setTownOrLocation("Yamanashi or Tokyo or ?");
|
|
661
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
662
|
}
|
|
663
|
specimen.setCollection(collection);
|
|
664
|
}else if (specTypeDepositoryStr.equals("S. Morita, Tokyo or coll. Y. Sorimachi, Saitama")){
|
|
665
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, specTypeDepositoryStr, Collection.class);
|
|
666
|
if (collection == null){
|
|
667
|
collection = Collection.NewInstance();
|
|
668
|
collection.setName(specTypeDepositoryStr);
|
|
669
|
collection.setTownOrLocation("Tokyo or Saitama");
|
|
670
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
671
|
}
|
|
672
|
specimen.setCollection(collection);
|
|
673
|
|
|
674
|
}else if (specTypeDepositoryStr.equals("coll. L. V. Kaabak, A .V. Sotshivko & V. V. Titov, Moscow")){
|
|
675
|
String colName = "coll. L. V. Kaabak, A .V. Sotshivko & V. V. Titov";
|
|
676
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, colName, Collection.class);
|
|
677
|
if (collection == null){
|
|
678
|
collection = Collection.NewInstance();
|
|
679
|
collection.setName(colName);
|
|
680
|
collection.setTownOrLocation("Moscow");
|
|
681
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
682
|
}
|
|
683
|
specimen.setCollection(collection);
|
|
684
|
}else if (specTypeDepositoryStr.matches("coll. R. E. Parrott?, Port Hope, Ontario")){
|
|
685
|
String colName = "coll. R. E. Parrott";
|
|
686
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, colName, Collection.class);
|
|
687
|
if (collection == null){
|
|
688
|
collection = Collection.NewInstance();
|
|
689
|
collection.setName(colName);
|
|
690
|
collection.setTownOrLocation("Port Hope, Ontario");
|
|
691
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
692
|
}
|
|
693
|
specimen.setCollection(collection);
|
|
694
|
}else if (specTypeDepositoryStr.matches("coll. O. Slaby, Plzen, Tschechei")){
|
|
695
|
String colName = "coll. O. Slaby";
|
|
696
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, colName, Collection.class);
|
|
697
|
if (collection == null){
|
|
698
|
collection = Collection.NewInstance();
|
|
699
|
collection.setName(colName);
|
|
700
|
collection.setTownOrLocation("Plzen, Tschechei");
|
|
701
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
702
|
}
|
|
703
|
specimen.setCollection(collection);
|
|
704
|
}else if (specTypeDepositoryStr.matches("coll. K. Okubo")){
|
|
705
|
String colName = "coll. K. Okubo";
|
|
706
|
collection = state.getRelatedObject(COLLECTION_NAMESPACE, colName, Collection.class);
|
|
707
|
if (collection == null){
|
|
708
|
collection = Collection.NewInstance();
|
|
709
|
collection.setName(colName);
|
|
710
|
collection.setTownOrLocation("Nichinomiya city, Hyogo");
|
|
711
|
state.addRelatedObject(COLLECTION_NAMESPACE, collection.getName(), collection);
|
|
712
|
}
|
|
713
|
specimen.setCollection(collection);
|
|
714
|
}else{
|
|
715
|
collection = null;
|
|
716
|
}
|
|
717
|
|
|
718
|
|
|
719
|
return collection;
|
|
720
|
}
|
|
721
|
|
|
722
|
/**
|
|
723
|
* @param specTypeDepositoriesStr
|
|
724
|
* @param specTypeDepositoryStr
|
|
725
|
* @param specimen
|
|
726
|
* @param specTaxId
|
|
727
|
* @return
|
|
728
|
*/
|
|
729
|
protected String makeAdditionalSpecimenInformation( String specTypeDepositoryStr, DerivedUnit specimen, Integer specTaxId) {
|
|
730
|
//doubful
|
|
731
|
if (specTypeDepositoryStr.endsWith("?")){
|
|
732
|
Marker.NewInstance(specimen, true, MarkerType.IS_DOUBTFUL());
|
|
733
|
specTypeDepositoryStr = specTypeDepositoryStr.substring(0, specTypeDepositoryStr.length() -1).trim();
|
|
734
|
}
|
|
735
|
|
|
736
|
//brackets
|
|
737
|
Matcher matcher = patternAll.matcher(specTypeDepositoryStr);
|
|
738
|
if (matcher.find()){
|
|
739
|
//has brackets
|
|
740
|
String brackets = matcher.group(2);
|
|
741
|
brackets = brackets.substring(1, brackets.length()-1);
|
|
742
|
|
|
743
|
//TODO this is unwanted according to Alexander
|
|
744
|
brackets = brackets.replace("[mm]", "\u2642\u2642");
|
|
745
|
brackets = brackets.replace("[m]", "\u2642");
|
|
746
|
brackets = brackets.replace("[ff]", "\u2640\u2640");
|
|
747
|
brackets = brackets.replace("[f]", "\u2640");
|
|
748
|
brackets = brackets.replace("[m/f]", "\u26a5");
|
|
749
|
|
|
750
|
if (brackets.contains("[") || brackets.contains("]")){
|
|
751
|
logger.warn ("There are still '[', ']' in the bracket part: " + brackets + "; specTaxId: " + specTaxId);
|
|
752
|
}
|
|
753
|
|
|
754
|
//TODO replace mm/ff by Unicode male
|
|
755
|
specimen.setTitleCache(brackets, true);
|
|
756
|
specTypeDepositoryStr = matcher.group(1).trim();
|
|
757
|
}
|
|
758
|
return specTypeDepositoryStr;
|
|
759
|
}
|
|
760
|
|
|
761
|
|
|
762
|
|
|
763
|
|
|
764
|
/**
|
|
765
|
* @param fieldObservation
|
|
766
|
* @return
|
|
767
|
*/
|
|
768
|
protected DerivedUnit makeSingleTypeSpecimen(FieldUnit fieldObservation) {
|
|
769
|
DerivationEvent derivEvent = DerivationEvent.NewInstance();
|
|
770
|
// derivEvent.setType(DerivationEventType.ACCESSIONING());
|
|
771
|
fieldObservation.addDerivationEvent(derivEvent);
|
|
772
|
DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
|
|
773
|
specimen.setDerivedFrom(derivEvent);
|
|
774
|
return specimen;
|
|
775
|
}
|
|
776
|
|
|
777
|
|
|
778
|
|
|
779
|
|
|
780
|
/**
|
|
781
|
* @param state
|
|
782
|
* @return
|
|
783
|
* @throws SQLException
|
|
784
|
*/
|
|
785
|
protected FieldUnit makeTypeFieldObservation(GlobisImportState state,
|
|
786
|
ResultSet rs) throws SQLException {
|
|
787
|
|
|
788
|
String countryString = rs.getString("SpecTypeCountry");
|
|
789
|
|
|
790
|
SpecimenOrObservationType unitType = SpecimenOrObservationType.PreservedSpecimen;
|
|
791
|
DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(unitType);
|
|
792
|
|
|
793
|
NamedArea typeCountry = getCountry(state, countryString);
|
|
794
|
facade.setCountry(typeCountry);
|
|
795
|
FieldUnit fieldObservation = facade.innerFieldUnit();
|
|
796
|
return fieldObservation;
|
|
797
|
}
|
|
798
|
|
|
799
|
|
|
800
|
|
|
801
|
|
|
802
|
/**
|
|
803
|
* @param name
|
|
804
|
* @param rs
|
|
805
|
* @param status
|
|
806
|
* @param specimen
|
|
807
|
* @param specTaxId
|
|
808
|
* @throws SQLException
|
|
809
|
*/
|
|
810
|
protected void makeTypeDesignation(IZoologicalName name, ResultSet rs, DerivedUnit specimen, Integer specTaxId) throws SQLException {
|
|
811
|
//type
|
|
812
|
String specType = rs.getString("SpecType");
|
|
813
|
SpecimenTypeDesignationStatus status = getTypeDesigType(specType, specTaxId);
|
|
814
|
|
|
815
|
SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance();
|
|
816
|
typeDesignation.setTypeStatus(status);
|
|
817
|
typeDesignation.setTypeSpecimen(specimen);
|
|
818
|
|
|
819
|
name.addTypeDesignation(typeDesignation, true);
|
|
820
|
}
|
|
821
|
|
|
822
|
|
|
823
|
|
|
824
|
|
|
825
|
private SpecimenTypeDesignationStatus getTypeDesigType(String specType, Integer specTaxId) {
|
|
826
|
if (isBlank(specType) ){
|
|
827
|
return null;
|
|
828
|
}else if (specType.matches("Holotype(\r*\n*Holotypus)?")){
|
|
829
|
return SpecimenTypeDesignationStatus.HOLOTYPE();
|
|
830
|
}else if (specType.matches("Neotype")){
|
|
831
|
return SpecimenTypeDesignationStatus.NEOTYPE();
|
|
832
|
}else if (specType.matches("Syntype(\\(s\\))?") || specType.matches("Syntype.*Syntype\\(s\\)\\s*") ){
|
|
833
|
return SpecimenTypeDesignationStatus.SYNTYPE();
|
|
834
|
}else if (specType.matches("Syntype\r*\n*Syntype.*") ){
|
|
835
|
return SpecimenTypeDesignationStatus.SYNTYPE();
|
|
836
|
}else if (specType.matches("Lectotype")){
|
|
837
|
return SpecimenTypeDesignationStatus.LECTOTYPE();
|
|
838
|
}else{
|
|
839
|
logger.warn("SpecimenTypeDesignationStatus does not match: " + specType + " in specTaxId " + specTaxId);
|
|
840
|
return null;
|
|
841
|
}
|
|
842
|
}
|
|
843
|
|
|
844
|
|
|
845
|
|
|
846
|
|
|
847
|
/**
|
|
848
|
* @param state
|
|
849
|
* @param referenceMap
|
|
850
|
* @param rs
|
|
851
|
* @param name
|
|
852
|
* @param specTaxId
|
|
853
|
* @return
|
|
854
|
* @throws SQLException
|
|
855
|
*/
|
|
856
|
private Reference handleNomRef(GlobisImportState state, Map<String, Reference> referenceMap, ResultSet rs,
|
|
857
|
IZoologicalName name, Integer specTaxId) throws SQLException {
|
|
858
|
//ref
|
|
859
|
Integer refId = nullSafeInt(rs, "fiSpecRefID");
|
|
860
|
Reference nomRef = null;
|
|
861
|
if (refId != null){
|
|
862
|
nomRef = referenceMap.get(String.valueOf(refId));
|
|
863
|
if (nomRef == null && state.getConfig().getDoReferences().equals(state.getConfig().getDoReferences().ALL)){
|
|
864
|
logger.warn("Reference " + refId + " could not be found. SpecTaxId: " + specTaxId);
|
|
865
|
}else if (nomRef != null){
|
|
866
|
name.setNomenclaturalReference(nomRef);
|
|
867
|
}
|
|
868
|
}
|
|
869
|
|
|
870
|
//refDetail
|
|
871
|
String refDetail = rs.getString("SpecPage");
|
|
872
|
if (isNotBlank(refDetail)){
|
|
873
|
name.setNomenclaturalMicroReference(refDetail);
|
|
874
|
}
|
|
875
|
return nomRef;
|
|
876
|
}
|
|
877
|
|
|
878
|
|
|
879
|
|
|
880
|
|
|
881
|
private void validateAcceptedTaxon(Taxon acceptedTaxon, ResultSet rs, Integer specTaxId, Integer acceptedTaxonId) throws SQLException {
|
|
882
|
if (acceptedTaxon == null){
|
|
883
|
logger.warn("Accepted taxon is null for taxon taxon to validate. SpecTaxId " + specTaxId + ", accTaxonId: " + acceptedTaxonId);
|
|
884
|
return;
|
|
885
|
}
|
|
886
|
|
|
887
|
//TODO
|
|
888
|
IZoologicalName name = acceptedTaxon.getName();
|
|
889
|
|
|
890
|
String specName = rs.getString("SpecName");
|
|
891
|
if (! name.getSpecificEpithet().equals(specName)){
|
|
892
|
logger.warn(String.format("Species epithet is not equal for accepted taxon: %s - %s. SpecTaxId: %d", name.getSpecificEpithet(), specName, specTaxId));
|
|
893
|
}
|
|
894
|
//TODO
|
|
895
|
}
|
|
896
|
|
|
897
|
|
|
898
|
|
|
899
|
|
|
900
|
private Synonym getSynonym(GlobisImportState state, ResultSet rs, Integer specTaxId) throws SQLException {
|
|
901
|
TaxonName<?,?> name = (TaxonName<?,?>)makeName(state, rs, specTaxId);
|
|
902
|
|
|
903
|
Synonym synonym = Synonym.NewInstance(name, state.getTransactionalSourceReference());
|
|
904
|
|
|
905
|
return synonym;
|
|
906
|
}
|
|
907
|
|
|
908
|
|
|
909
|
|
|
910
|
|
|
911
|
/**
|
|
912
|
* @param state
|
|
913
|
* @param rs
|
|
914
|
* @param specTaxId
|
|
915
|
* @return
|
|
916
|
* @throws SQLException
|
|
917
|
*/
|
|
918
|
protected IZoologicalName makeName(GlobisImportState state, ResultSet rs, Integer specTaxId)
|
|
919
|
throws SQLException {
|
|
920
|
//rank
|
|
921
|
String rankStr = rs.getString("SpecRank");
|
|
922
|
Rank rank = null;
|
|
923
|
if (isNotBlank(rankStr)){
|
|
924
|
try {
|
|
925
|
rank = Rank.getRankByNameOrIdInVoc(rankStr, NomenclaturalCode.ICZN, true);
|
|
926
|
} catch (UnknownCdmTypeException e) {
|
|
927
|
e.printStackTrace();
|
|
928
|
}
|
|
929
|
}
|
|
930
|
|
|
931
|
//name
|
|
932
|
IZoologicalName name = TaxonNameFactory.NewZoologicalInstance(rank);
|
|
933
|
makeNamePartsAndCache(state, rs, rankStr, name);
|
|
934
|
|
|
935
|
|
|
936
|
// name.setGenusOrUninomial(genusOrUninomial);
|
|
937
|
String authorStr = rs.getString("SpecAuthor");
|
|
938
|
String yearStr = rs.getString("SpecYear");
|
|
939
|
String authorAndYearStr = CdmUtils.concat(", ", authorStr, yearStr);
|
|
940
|
handleAuthorAndYear(authorAndYearStr, name, specTaxId, state);
|
|
941
|
|
|
942
|
return name;
|
|
943
|
}
|
|
944
|
|
|
945
|
|
|
946
|
|
|
947
|
|
|
948
|
private void makeNamePartsAndCache(GlobisImportState state, ResultSet rs, String rank, IZoologicalName name) throws SQLException {
|
|
949
|
String citedFamily = rs.getString("SpecCitedFamily");
|
|
950
|
String citedGenus = rs.getString("SpecCitedGenus");
|
|
951
|
String citedSpecies = rs.getString("SpecCitedSpecies");
|
|
952
|
String citedSubspecies = rs.getString("SpecCitedSubspecies");
|
|
953
|
String lastEpithet = rs.getString("SpecName");
|
|
954
|
|
|
955
|
|
|
956
|
String cache = CdmUtils.concat(" ", new String[]{citedFamily, citedGenus, citedSpecies, citedSubspecies, rank, lastEpithet});
|
|
957
|
name.setGenusOrUninomial(citedGenus);
|
|
958
|
//TODO separate authors
|
|
959
|
if (isBlank(citedSpecies)){
|
|
960
|
name.setSpecificEpithet(lastEpithet);
|
|
961
|
}else{
|
|
962
|
name.setSpecificEpithet(citedSpecies);
|
|
963
|
if (isBlank(citedSubspecies)){
|
|
964
|
name.setInfraSpecificEpithet(lastEpithet);
|
|
965
|
}
|
|
966
|
}
|
|
967
|
|
|
968
|
//TODO check if cache needs protection
|
|
969
|
name.setNameCache(cache, true);
|
|
970
|
}
|
|
971
|
|
|
972
|
@Override
|
|
973
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, GlobisImportState state) {
|
|
974
|
String nameSpace;
|
|
975
|
Class<?> cdmClass;
|
|
976
|
Set<String> idSet;
|
|
977
|
|
|
978
|
Set<AgentBase> agents = state.getAgents();
|
|
979
|
getAgentService().saveOrUpdate(agents);
|
|
980
|
|
|
981
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
982
|
try{
|
|
983
|
Set<String> taxonIdSet = new HashSet<String>();
|
|
984
|
Set<String> referenceIdSet = new HashSet<String>();
|
|
985
|
|
|
986
|
while (rs.next()){
|
|
987
|
handleForeignKey(rs, taxonIdSet, "SpecCurrspecID");
|
|
988
|
handleForeignKey(rs, referenceIdSet, "fiSpecRefID");
|
|
989
|
}
|
|
990
|
|
|
991
|
//taxon map
|
|
992
|
nameSpace = TAXON_NAMESPACE;
|
|
993
|
cdmClass = Taxon.class;
|
|
994
|
idSet = taxonIdSet;
|
|
995
|
Map<String, Taxon> objectMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
996
|
result.put(nameSpace, objectMap);
|
|
997
|
|
|
998
|
//reference map
|
|
999
|
nameSpace = REFERENCE_NAMESPACE;
|
|
1000
|
cdmClass = Reference.class;
|
|
1001
|
idSet = referenceIdSet;
|
|
1002
|
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
1003
|
result.put(nameSpace, referenceMap);
|
|
1004
|
|
|
1005
|
//collection map
|
|
1006
|
nameSpace = COLLECTION_NAMESPACE;
|
|
1007
|
List<Collection> listCollection = getCollectionService().list(Collection.class, null, null, null, null);
|
|
1008
|
Map<String, Collection> collectionMap = new HashMap<String, Collection>();
|
|
1009
|
for (Collection collection : listCollection){
|
|
1010
|
if (isNotBlank(collection.getCode())){
|
|
1011
|
collectionMap.put(collection.getCode(), collection);
|
|
1012
|
}else if (isNotBlank(collection.getName())){
|
|
1013
|
collectionMap.put(collection.getName(), collection);
|
|
1014
|
}else{
|
|
1015
|
logger.warn("Collection code and name are blank: " + collection);
|
|
1016
|
}
|
|
1017
|
}
|
|
1018
|
result.put(nameSpace, collectionMap);
|
|
1019
|
|
|
1020
|
} catch (SQLException e) {
|
|
1021
|
throw new RuntimeException(e);
|
|
1022
|
}
|
|
1023
|
return result;
|
|
1024
|
}
|
|
1025
|
|
|
1026
|
/* (non-Javadoc)
|
|
1027
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
1028
|
*/
|
|
1029
|
@Override
|
|
1030
|
protected boolean doCheck(GlobisImportState state){
|
|
1031
|
IOValidator<GlobisImportState> validator = new GlobisSpecTaxaImportValidator();
|
|
1032
|
return validator.validate(state);
|
|
1033
|
}
|
|
1034
|
|
|
1035
|
|
|
1036
|
/* (non-Javadoc)
|
|
1037
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
1038
|
*/
|
|
1039
|
@Override
|
|
1040
|
protected boolean isIgnore(GlobisImportState state){
|
|
1041
|
return ! state.getConfig().isDoSpecTaxa();
|
|
1042
|
}
|
|
1043
|
|
|
1044
|
|
|
1045
|
|
|
1046
|
|
|
1047
|
@Override
|
|
1048
|
public Reference createObject(ResultSet rs, GlobisImportState state)
|
|
1049
|
throws SQLException {
|
|
1050
|
// not needed
|
|
1051
|
return null;
|
|
1052
|
}
|
|
1053
|
|
|
1054
|
}
|