|
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.specimen.abcd206.in;
|
|
11
|
|
|
12
|
import java.io.InputStream;
|
|
13
|
import java.net.MalformedURLException;
|
|
14
|
import java.net.URI;
|
|
15
|
import java.util.ArrayList;
|
|
16
|
import java.util.HashMap;
|
|
17
|
import java.util.List;
|
|
18
|
import java.util.Map;
|
|
19
|
import java.util.Set;
|
|
20
|
import java.util.UUID;
|
|
21
|
|
|
22
|
import org.apache.commons.lang.StringUtils;
|
|
23
|
import org.apache.log4j.Logger;
|
|
24
|
import org.springframework.stereotype.Component;
|
|
25
|
import org.w3c.dom.Element;
|
|
26
|
import org.w3c.dom.NodeList;
|
|
27
|
|
|
28
|
import eu.etaxonomy.cdm.api.application.ICdmRepository;
|
|
29
|
import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
|
|
30
|
import eu.etaxonomy.cdm.ext.occurrence.bioCase.BioCaseQueryServiceWrapper;
|
|
31
|
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
|
|
32
|
import eu.etaxonomy.cdm.io.common.ICdmIO;
|
|
33
|
import eu.etaxonomy.cdm.io.common.MapWrapper;
|
|
34
|
import eu.etaxonomy.cdm.io.specimen.SpecimenImportBase;
|
|
35
|
import eu.etaxonomy.cdm.io.specimen.SpecimenUserInteraction;
|
|
36
|
import eu.etaxonomy.cdm.io.specimen.UnitsGatheringArea;
|
|
37
|
import eu.etaxonomy.cdm.io.specimen.UnitsGatheringEvent;
|
|
38
|
import eu.etaxonomy.cdm.io.specimen.abcd206.in.molecular.AbcdDnaParser;
|
|
39
|
import eu.etaxonomy.cdm.model.agent.Institution;
|
|
40
|
import eu.etaxonomy.cdm.model.agent.Person;
|
|
41
|
import eu.etaxonomy.cdm.model.agent.Team;
|
|
42
|
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
|
|
43
|
import eu.etaxonomy.cdm.model.common.Annotation;
|
|
44
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
45
|
import eu.etaxonomy.cdm.model.common.DefinedTerm;
|
|
46
|
import eu.etaxonomy.cdm.model.common.DefinedTermBase;
|
|
47
|
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
|
|
48
|
import eu.etaxonomy.cdm.model.common.Language;
|
|
49
|
import eu.etaxonomy.cdm.model.common.LanguageString;
|
|
50
|
import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
|
|
51
|
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
|
|
52
|
import eu.etaxonomy.cdm.model.location.NamedArea;
|
|
53
|
import eu.etaxonomy.cdm.model.media.Media;
|
|
54
|
import eu.etaxonomy.cdm.model.molecular.DnaSample;
|
|
55
|
import eu.etaxonomy.cdm.model.occurrence.Collection;
|
|
56
|
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
|
|
57
|
import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
|
|
58
|
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
|
|
59
|
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
|
|
60
|
import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
|
|
61
|
import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
|
|
62
|
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
|
|
63
|
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
|
|
64
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
|
65
|
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
|
|
66
|
import eu.etaxonomy.cdm.model.taxon.Classification;
|
|
67
|
|
|
68
|
/**
|
|
69
|
* @author p.kelbert
|
|
70
|
* @author p.plitzner
|
|
71
|
* @created 20.10.2008
|
|
72
|
*/
|
|
73
|
@Component
|
|
74
|
public class Abcd206Import extends SpecimenImportBase<Abcd206ImportConfigurator, Abcd206ImportState> {
|
|
75
|
|
|
76
|
private static final long serialVersionUID = 3918095362150986307L;
|
|
77
|
|
|
78
|
private static final UUID SPECIMEN_SCAN_TERM = UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03");
|
|
79
|
|
|
80
|
private static final Logger logger = Logger.getLogger(Abcd206Import.class);
|
|
81
|
|
|
82
|
|
|
83
|
public Abcd206Import() {
|
|
84
|
super();
|
|
85
|
}
|
|
86
|
|
|
87
|
|
|
88
|
@Override
|
|
89
|
// @SuppressWarnings("rawtypes")
|
|
90
|
public void doInvoke(Abcd206ImportState state) {
|
|
91
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
92
|
Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
|
|
93
|
MapWrapper<TeamOrPersonBase<?>> authorStore = (MapWrapper<TeamOrPersonBase<?>>)stores.get(ICdmIO.TEAM_STORE);
|
|
94
|
state.setPersonStore(authorStore);
|
|
95
|
MapWrapper<Reference> referenceStore = (MapWrapper<Reference>)stores.get(ICdmIO.REFERENCE_STORE);
|
|
96
|
URI sourceUri = config.getSourceUri();
|
|
97
|
try{
|
|
98
|
state.setTx(startTransaction());
|
|
99
|
logger.info("INVOKE Specimen Import from ABCD2.06 XML ");
|
|
100
|
InputStream response = null;
|
|
101
|
//init cd repository
|
|
102
|
if(state.getCdmRepository()==null){
|
|
103
|
state.setCdmRepository(this);
|
|
104
|
}
|
|
105
|
if (config.getOccurenceQuery() != null){
|
|
106
|
BioCaseQueryServiceWrapper queryService = new BioCaseQueryServiceWrapper();
|
|
107
|
try {
|
|
108
|
|
|
109
|
response = queryService.query(config.getOccurenceQuery(), sourceUri);
|
|
110
|
state.setActualAccessPoint(sourceUri);
|
|
111
|
|
|
112
|
}catch(Exception e){
|
|
113
|
logger.error("An error during ABCD import");
|
|
114
|
}
|
|
115
|
}
|
|
116
|
SpecimenUserInteraction sui = state.getConfig().getSpecimenUserInteraction();
|
|
117
|
|
|
118
|
//init import reference
|
|
119
|
// List<Reference> references = getReferenceService().list(Reference.class, null, null, null, null);
|
|
120
|
// List<Reference> references = new ArrayList<Reference>();
|
|
121
|
|
|
122
|
// if (state.getConfig().isInteractWithUser()){
|
|
123
|
// Map<String,Reference> refMap = new HashMap<String, Reference>();
|
|
124
|
// for (Reference reference : references) {
|
|
125
|
// if (! StringUtils.isBlank(reference.getTitleCache())) {
|
|
126
|
// refMap.put(reference.getTitleCache(),reference);
|
|
127
|
// }
|
|
128
|
// }
|
|
129
|
// state.setRef(sui.askForReference(refMap));
|
|
130
|
//
|
|
131
|
// if (state.getRef() == null){
|
|
132
|
// String cla = sui.createNewReference();
|
|
133
|
// if (refMap.get(cla)!= null) {
|
|
134
|
// state.setRef(refMap.get(cla));
|
|
135
|
// } else {
|
|
136
|
// state.setRef(ReferenceFactory.newGeneric());
|
|
137
|
// state.getRef().setTitle(cla);
|
|
138
|
// }
|
|
139
|
// }
|
|
140
|
// else{
|
|
141
|
// state.setRef(getReferenceService().find(state.getRef().getUuid()));
|
|
142
|
// }
|
|
143
|
// }else{
|
|
144
|
if (state.getRef()==null){
|
|
145
|
String name = NB(state.getConfig().getSourceReferenceTitle());
|
|
146
|
for (Reference reference : referenceStore.getAllValues()) {
|
|
147
|
if (! StringUtils.isBlank(reference.getTitleCache())) {
|
|
148
|
if (reference.getTitleCache().equalsIgnoreCase(name)) {
|
|
149
|
state.setRef(reference);
|
|
150
|
}
|
|
151
|
}
|
|
152
|
}
|
|
153
|
if (state.getRef() == null){
|
|
154
|
if (state.getConfig().getSourceReference() != null){
|
|
155
|
state.setRef(state.getConfig().getSourceReference());
|
|
156
|
}else{
|
|
157
|
state.setRef(ReferenceFactory.newGeneric());
|
|
158
|
|
|
159
|
if (state.getConfig().getSourceReferenceTitle() != null){
|
|
160
|
state.getRef().setTitle(state.getConfig().getSourceReferenceTitle());
|
|
161
|
} else{
|
|
162
|
state.getRef().setTitle("ABCD Import Source Reference");
|
|
163
|
}
|
|
164
|
}
|
|
165
|
|
|
166
|
}
|
|
167
|
}
|
|
168
|
//}
|
|
169
|
|
|
170
|
save(state.getRef(), state);
|
|
171
|
state.getConfig().setSourceReference(state.getRef());
|
|
172
|
|
|
173
|
if(state.getConfig().getClassificationUuid()!=null){
|
|
174
|
//load classification from config if it exists
|
|
175
|
state.setClassification(getClassificationService().load(state.getConfig().getClassificationUuid()));
|
|
176
|
}
|
|
177
|
if(state.getClassification()==null){//no existing classification was set in config
|
|
178
|
List<Classification> classificationList = getClassificationService().list(Classification.class, null, null, null, null);
|
|
179
|
//get classification via user interaction
|
|
180
|
if (state.getConfig().isUseClassification() && state.getConfig().isInteractWithUser()){
|
|
181
|
Map<String,Classification> classMap = new HashMap<>();
|
|
182
|
for (Classification tree : classificationList) {
|
|
183
|
if (! StringUtils.isBlank(tree.getTitleCache())) {
|
|
184
|
classMap.put(tree.getTitleCache(),tree);
|
|
185
|
}
|
|
186
|
}
|
|
187
|
state.setClassification(sui.askForClassification(classMap));
|
|
188
|
if (state.getClassification() == null){
|
|
189
|
String cla = sui.createNewClassification();
|
|
190
|
if (classMap.get(cla)!= null) {
|
|
191
|
state.setClassification(classMap.get(cla));
|
|
192
|
} else {
|
|
193
|
state.setClassification(Classification.NewInstance(cla, state.getRef(), Language.DEFAULT()));
|
|
194
|
}
|
|
195
|
}
|
|
196
|
save(state.getClassification(), state);
|
|
197
|
}
|
|
198
|
// use default classification as the classification to import into
|
|
199
|
if (state.getClassification() == null) {
|
|
200
|
String name = NB(state.getConfig().getClassificationName());
|
|
201
|
for (Classification classif : classificationList){
|
|
202
|
if (classif.getTitleCache() != null && classif.getTitleCache().equalsIgnoreCase(name)) {
|
|
203
|
state.setClassification(classif);
|
|
204
|
}
|
|
205
|
}
|
|
206
|
if (state.getClassification() == null){
|
|
207
|
state.setClassification(Classification.NewInstance(name, state.getRef(), Language.DEFAULT()));
|
|
208
|
//we do not need a default classification when creating an empty new one
|
|
209
|
state.setDefaultClassification(state.getClassification());
|
|
210
|
save(state.getDefaultClassification(false), state);
|
|
211
|
}
|
|
212
|
save(state.getClassification(), state);
|
|
213
|
}
|
|
214
|
}
|
|
215
|
|
|
216
|
if (response == null){
|
|
217
|
response =state.getConfig().getSource();
|
|
218
|
}
|
|
219
|
UnitAssociationWrapper unitAssociationWrapper = AbcdParseUtility.parseUnitsNodeList(response, state.getReport());
|
|
220
|
NodeList unitsList = unitAssociationWrapper.getAssociatedUnits();
|
|
221
|
state.setPrefix(unitAssociationWrapper.getPrefix());
|
|
222
|
|
|
223
|
if (unitsList != null) {
|
|
224
|
String message = "nb units to insert: " + unitsList.getLength();
|
|
225
|
logger.info(message);
|
|
226
|
state.getConfig().getProgressMonitor().beginTask("Importing ABCD file", unitsList.getLength() + 3);
|
|
227
|
updateProgress(state, message);
|
|
228
|
|
|
229
|
state.setDataHolder(new Abcd206DataHolder());
|
|
230
|
state.getDataHolder().reset();
|
|
231
|
|
|
232
|
Abcd206XMLFieldGetter abcdFieldGetter = new Abcd206XMLFieldGetter(state.getDataHolder(), state.getPrefix());
|
|
233
|
if (config.getNomenclaturalCode() != null){
|
|
234
|
state.getDataHolder().setNomenclatureCode(config.getNomenclaturalCode().getKey());
|
|
235
|
}
|
|
236
|
prepareCollectors(state, unitsList, abcdFieldGetter);
|
|
237
|
|
|
238
|
|
|
239
|
// save authors
|
|
240
|
getAgentService().saveOrUpdate((java.util.Collection)state.getPersonStore().objects());
|
|
241
|
|
|
242
|
commitTransaction(state.getTx());
|
|
243
|
state.setTx(startTransaction());
|
|
244
|
if (state.getDefaultClassification(false) != null){
|
|
245
|
state.setDefaultClassification(getClassificationService().load(state.getDefaultClassification(false).getUuid()));
|
|
246
|
}
|
|
247
|
if (state.getClassification() != null){
|
|
248
|
state.setClassification(getClassificationService().load(state.getClassification().getUuid()));
|
|
249
|
}
|
|
250
|
state.setAssociationRefs(new ArrayList<>());
|
|
251
|
state.setDescriptionRefs(new ArrayList<>());
|
|
252
|
state.setDerivedUnitSources(new ArrayList<>());
|
|
253
|
for (int i = 0; i < unitsList.getLength(); i++) {
|
|
254
|
if(state.getConfig().getProgressMonitor().isCanceled()){
|
|
255
|
break;
|
|
256
|
}
|
|
257
|
|
|
258
|
state.reset();
|
|
259
|
|
|
260
|
Element item = (Element) unitsList.item(i);
|
|
261
|
Abcd206ImportParser.setUnitPropertiesXML( item, abcdFieldGetter, state);
|
|
262
|
updateProgress(state, "Importing data for unit "+state.getDataHolder().getUnitID()+" ("+i+"/"+unitsList.getLength()+")");
|
|
263
|
|
|
264
|
//import unit + field unit data
|
|
265
|
state.setAssociatedUnitIds(state.getDataHolder().getAssociatedUnitIds());
|
|
266
|
this.handleSingleUnit(state, item, true);
|
|
267
|
|
|
268
|
}
|
|
269
|
if(state.getConfig().isDeduplicateReferences()){
|
|
270
|
getReferenceService().deduplicate(Reference.class, null, null);
|
|
271
|
}
|
|
272
|
if(state.getConfig().isDeduplicateClassifications()){
|
|
273
|
getClassificationService().deduplicate(Classification.class, null, null);
|
|
274
|
}
|
|
275
|
}
|
|
276
|
commitTransaction(state.getTx());
|
|
277
|
}
|
|
278
|
catch(Exception e){
|
|
279
|
String errorDuringImport = "Exception during import!";
|
|
280
|
logger.error(errorDuringImport, e);
|
|
281
|
state.getReport().addException(errorDuringImport, e);
|
|
282
|
}
|
|
283
|
finally{
|
|
284
|
state.getReport().printReport(state.getConfig().getReportUri());
|
|
285
|
}
|
|
286
|
return;
|
|
287
|
}
|
|
288
|
|
|
289
|
|
|
290
|
/**
|
|
291
|
* @param state
|
|
292
|
* @param item
|
|
293
|
*/
|
|
294
|
private void getSiblings(Abcd206ImportState state, Object item, DerivedUnitFacade facade) {
|
|
295
|
String unitId = facade.getCatalogNumber();
|
|
296
|
|
|
297
|
UnitAssociationParser unitParser = new UnitAssociationParser(state.getPrefix(), state.getReport(), state.getCdmRepository());
|
|
298
|
UnitAssociationWrapper unitAssociationWrapper = null;
|
|
299
|
for (URI accessPoint: state.getActualAccesPoint()){
|
|
300
|
unitAssociationWrapper = unitParser.parseSiblings(unitId, accessPoint);
|
|
301
|
if (unitAssociationWrapper.getAssociatedUnits() != null){
|
|
302
|
break;
|
|
303
|
}
|
|
304
|
}
|
|
305
|
|
|
306
|
DerivedUnit currentUnit = state.getDerivedUnitBase();
|
|
307
|
// DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();
|
|
308
|
FieldUnit currentFieldUnit = facade.getFieldUnit(false);
|
|
309
|
if(unitAssociationWrapper!=null){
|
|
310
|
NodeList associatedUnits = unitAssociationWrapper.getAssociatedUnits();
|
|
311
|
if(associatedUnits!=null){
|
|
312
|
for(int m=0;m<associatedUnits.getLength();m++){
|
|
313
|
if(associatedUnits.item(m) instanceof Element){
|
|
314
|
state.reset();
|
|
315
|
String associationType = AbcdParseUtility.parseFirstTextContent(((Element) associatedUnits.item(m)).getElementsByTagName(state.getPrefix()+"AssociationType"));
|
|
316
|
|
|
317
|
Abcd206ImportParser.setUnitPropertiesXML((Element) associatedUnits.item(m), new Abcd206XMLFieldGetter(state.getDataHolder(), unitAssociationWrapper.getPrefix()), state);
|
|
318
|
// logger.debug("derived unit: " + state.getDerivedUnitBase().toString() + " associated unit: " +state.getDataHolder().getKindOfUnit() + ", " + state.getDataHolder().accessionNumber + ", " + state.getDataHolder().getRecordBasis() + ", " + state.getDataHolder().getUnitID());
|
|
319
|
|
|
320
|
handleSingleUnit(state, associatedUnits.item(m), false);
|
|
321
|
|
|
322
|
DerivedUnit associatedUnit = state.getDerivedUnitBase();
|
|
323
|
FieldUnit associatedFieldUnit = null;
|
|
324
|
java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository().getOccurrenceService().getFieldUnits(associatedUnit.getUuid());
|
|
325
|
//ignore field unit if associated unit has more than one
|
|
326
|
if(associatedFieldUnits.size()>1){
|
|
327
|
state.getReport().addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));
|
|
328
|
}
|
|
329
|
else if(associatedFieldUnits.size()==1){
|
|
330
|
associatedFieldUnit = associatedFieldUnits.iterator().next();
|
|
331
|
}
|
|
332
|
//parent-child relation:
|
|
333
|
if(associationType.contains("individual") || associationType.contains("culture") || associationType.contains("sample")){
|
|
334
|
DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(currentUnit, associatedUnit, DerivationEventType.ACCESSIONING());
|
|
335
|
if(associatedFieldUnit!=null && associatedFieldUnit != currentFieldUnit){
|
|
336
|
associatedFieldUnit.removeDerivationEvent(updatedDerivationEvent);
|
|
337
|
state.getCdmRepository().getOccurrenceService().delete(associatedFieldUnit);
|
|
338
|
}
|
|
339
|
state.getReport().addDerivate(associatedUnit, currentUnit, state.getConfig());
|
|
340
|
}
|
|
341
|
save(associatedUnit, state);
|
|
342
|
|
|
343
|
}
|
|
344
|
}
|
|
345
|
}
|
|
346
|
}
|
|
347
|
state.reset();
|
|
348
|
state.setDerivedUnitBase(currentUnit);
|
|
349
|
|
|
350
|
}
|
|
351
|
|
|
352
|
/**
|
|
353
|
* Handle a single unit
|
|
354
|
* @param state
|
|
355
|
* @param item
|
|
356
|
*/
|
|
357
|
@Override
|
|
358
|
public void handleSingleUnit(Abcd206ImportState state, Object itemObject){
|
|
359
|
handleSingleUnit(state, itemObject, true);
|
|
360
|
}
|
|
361
|
|
|
362
|
|
|
363
|
@SuppressWarnings("rawtypes")
|
|
364
|
public void handleSingleUnit(Abcd206ImportState state, Object itemObject, boolean handleAssociatedUnits) {
|
|
365
|
Element item = (Element) itemObject;
|
|
366
|
|
|
367
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
368
|
if (logger.isDebugEnabled()) {
|
|
369
|
logger.info("handleSingleUnit "+state.getRef());
|
|
370
|
}
|
|
371
|
try {
|
|
372
|
ICdmRepository cdmAppController = state.getConfig().getCdmAppController();
|
|
373
|
if(cdmAppController==null){
|
|
374
|
cdmAppController = this;
|
|
375
|
}
|
|
376
|
//check if unit already exists
|
|
377
|
DerivedUnitFacade derivedUnitFacade = null;
|
|
378
|
if(state.getConfig().isIgnoreImportOfExistingSpecimen()){
|
|
379
|
SpecimenOrObservationBase<?> existingSpecimen = findExistingSpecimen(state.getDataHolder().getUnitID(), state);
|
|
380
|
if(existingSpecimen!=null && existingSpecimen.isInstanceOf(DerivedUnit.class)){
|
|
381
|
DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(existingSpecimen, DerivedUnit.class);
|
|
382
|
state.setDerivedUnitBase(derivedUnit);
|
|
383
|
derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
|
|
384
|
if (handleAssociatedUnits){
|
|
385
|
importAssociatedUnits(state, item, derivedUnitFacade);
|
|
386
|
}
|
|
387
|
|
|
388
|
state.getReport().addAlreadyExistingSpecimen(SpecimenImportUtility.getUnitID(derivedUnit, config), derivedUnit);
|
|
389
|
|
|
390
|
return;
|
|
391
|
}
|
|
392
|
}
|
|
393
|
// TODO: implement overwrite/merge specimen
|
|
394
|
// else if(state.getConfig().isOverwriteExistingSpecimens()){
|
|
395
|
// Pager<SpecimenOrObservationBase> existingSpecimens = cdmAppController.getOccurrenceService().findByTitle(config);
|
|
396
|
// if(!existingSpecimens.getRecords().isEmpty()){
|
|
397
|
// derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit);
|
|
398
|
// derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
|
|
399
|
// fieldUnit = derivedUnitFacade.getFieldUnit(true);
|
|
400
|
// }
|
|
401
|
// }
|
|
402
|
//import new specimen
|
|
403
|
|
|
404
|
// import DNA unit
|
|
405
|
if(state.getDataHolder().getKindOfUnit() !=null && state.getDataHolder().getKindOfUnit().equalsIgnoreCase("dna")){
|
|
406
|
AbcdDnaParser dnaParser = new AbcdDnaParser(state.getPrefix(), state.getReport(), state.getCdmRepository());
|
|
407
|
DnaSample dnaSample = dnaParser.parse(item, state);
|
|
408
|
save(dnaSample, state);
|
|
409
|
//set dna as derived unit to avoid creating an extra specimen for this dna sample (instead just the field unit will be created)
|
|
410
|
state.setDerivedUnitBase(dnaSample);
|
|
411
|
derivedUnitFacade = DerivedUnitFacade.NewInstance(state.getDerivedUnitBase());
|
|
412
|
}
|
|
413
|
else{
|
|
414
|
// create facade
|
|
415
|
derivedUnitFacade = getFacade(state);
|
|
416
|
state.setDerivedUnitBase(derivedUnitFacade.innerDerivedUnit());
|
|
417
|
|
|
418
|
}
|
|
419
|
|
|
420
|
/**
|
|
421
|
* GATHERING EVENT
|
|
422
|
*/
|
|
423
|
|
|
424
|
//look for existing fieldUnit
|
|
425
|
|
|
426
|
FieldUnit fieldUnit = state.getFieldUnit(state.getDataHolder().getFieldNumber());
|
|
427
|
|
|
428
|
|
|
429
|
// gathering event
|
|
430
|
UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(cdmAppController.getTermService(),
|
|
431
|
state.getDataHolder().locality, state.getDataHolder().languageIso, state.getDataHolder().longitude,
|
|
432
|
state.getDataHolder().latitude, state.getDataHolder().getGatheringElevationText(),
|
|
433
|
state.getDataHolder().getGatheringElevationMin(), state.getDataHolder().getGatheringElevationMax(),
|
|
434
|
state.getDataHolder().getGatheringElevationUnit(), state.getDataHolder().getGatheringDateText(),
|
|
435
|
state.getDataHolder().getGatheringNotes(), state.getDataHolder().getGatheringMethod(), state.getTransformer().getReferenceSystemByKey(
|
|
436
|
state.getDataHolder().getGatheringSpatialDatum()),
|
|
437
|
state.getConfig());
|
|
438
|
|
|
439
|
unitsGatheringEvent.setGatheringDepth(state.getDataHolder().getGatheringDepthText(),state.getDataHolder().getGatheringDepthMin(), state.getDataHolder().getGatheringDepthMax(), state.getDataHolder().getGatheringDepthUnit());
|
|
440
|
//unitsGatheringEvent.setHeight(heightText, heightMin, heightMax, heightUnit);
|
|
441
|
if(state.getDataHolder().gatheringAgentsList.isEmpty()) {
|
|
442
|
unitsGatheringEvent.setCollector(state.getPersonStore().get(state.getDataHolder().gatheringAgentsText), config);
|
|
443
|
}else{
|
|
444
|
unitsGatheringEvent.setCollector(state.getPersonStore().get(state.getDataHolder().gatheringAgentsList.toString()), config);
|
|
445
|
}
|
|
446
|
// count
|
|
447
|
UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea();
|
|
448
|
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(), getTermService());
|
|
449
|
unitsGatheringArea.setParams(state.getDataHolder().isocountry, state.getDataHolder().country, (state.getConfig()), cdmAppController.getTermService(), cdmAppController.getOccurrenceService(), cdmAppController.getVocabularyService());
|
|
450
|
|
|
451
|
DefinedTermBase<?> areaCountry = unitsGatheringArea.getCountry();
|
|
452
|
|
|
453
|
// other areas
|
|
454
|
unitsGatheringArea = new UnitsGatheringArea();
|
|
455
|
// unitsGatheringArea.setConfig(state.getConfig(),getOccurrenceService(),getTermService());
|
|
456
|
|
|
457
|
unitsGatheringArea.setAreas(state.getDataHolder().getNamedAreaList(),(state.getConfig()), cdmAppController.getTermService(), cdmAppController.getVocabularyService());
|
|
458
|
|
|
459
|
ArrayList<DefinedTermBase> nas = unitsGatheringArea.getAreas();
|
|
460
|
for (DefinedTermBase namedArea : nas) {
|
|
461
|
unitsGatheringEvent.addArea(namedArea);
|
|
462
|
}
|
|
463
|
|
|
464
|
// copy gathering event to facade
|
|
465
|
GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();
|
|
466
|
if (fieldUnit != null){
|
|
467
|
derivedUnitFacade.setFieldUnit(fieldUnit);
|
|
468
|
}
|
|
469
|
|
|
470
|
derivedUnitFacade.setLocality(gatheringEvent.getLocality());
|
|
471
|
derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());
|
|
472
|
derivedUnitFacade.setCollector(gatheringEvent.getCollector());
|
|
473
|
derivedUnitFacade.setCountry((NamedArea)areaCountry);
|
|
474
|
derivedUnitFacade.setAbsoluteElevationText(gatheringEvent.getAbsoluteElevationText());
|
|
475
|
derivedUnitFacade.setAbsoluteElevation(gatheringEvent.getAbsoluteElevation());
|
|
476
|
derivedUnitFacade.setAbsoluteElevationMax(gatheringEvent.getAbsoluteElevationMax());
|
|
477
|
derivedUnitFacade.setDistanceToGroundText(gatheringEvent.getDistanceToGroundText());
|
|
478
|
derivedUnitFacade.setDistanceToGroundMax(gatheringEvent.getDistanceToGroundMax());
|
|
479
|
derivedUnitFacade.setDistanceToGround(gatheringEvent.getDistanceToGround());
|
|
480
|
derivedUnitFacade.setDistanceToWaterSurfaceText(gatheringEvent.getDistanceToWaterSurfaceText());
|
|
481
|
derivedUnitFacade.setDistanceToWaterSurfaceMax(gatheringEvent.getDistanceToWaterSurfaceMax());
|
|
482
|
derivedUnitFacade.setDistanceToWaterSurface(gatheringEvent.getDistanceToWaterSurface());
|
|
483
|
derivedUnitFacade.setGatheringPeriod(gatheringEvent.getTimeperiod());
|
|
484
|
derivedUnitFacade.setCollectingMethod(gatheringEvent.getCollectingMethod());
|
|
485
|
|
|
486
|
for(DefinedTermBase<?> area:unitsGatheringArea.getAreas()){
|
|
487
|
derivedUnitFacade.addCollectingArea((NamedArea) area);
|
|
488
|
}
|
|
489
|
// derivedUnitFacade.addCollectingAreas(unitsGatheringArea.getAreas());
|
|
490
|
// TODO exsiccatum
|
|
491
|
|
|
492
|
// add fieldNumber
|
|
493
|
derivedUnitFacade.setFieldNumber(NB(state.getDataHolder().getFieldNumber()));
|
|
494
|
save(unitsGatheringEvent.getLocality(), state);
|
|
495
|
|
|
496
|
// add unitNotes
|
|
497
|
if (state.getDataHolder().getUnitNotes() != null){
|
|
498
|
derivedUnitFacade.addAnnotation(Annotation.NewDefaultLanguageInstance(NB(state.getDataHolder().getUnitNotes())));
|
|
499
|
}
|
|
500
|
|
|
501
|
|
|
502
|
|
|
503
|
// //add Multimedia URLs
|
|
504
|
if (state.getDataHolder().getMultimediaObjects().size() != -1) {
|
|
505
|
for (String multimediaObject : state.getDataHolder().getMultimediaObjects().keySet()) {
|
|
506
|
Media media;
|
|
507
|
try {
|
|
508
|
media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
|
|
509
|
Map<String, String> attributes = state.getDataHolder().getMultimediaObjects().get(multimediaObject);
|
|
510
|
if (attributes.containsKey("Context")){
|
|
511
|
LanguageString description = LanguageString.NewInstance(attributes.get("Context"), Language.ENGLISH());
|
|
512
|
media.addDescription(description);
|
|
513
|
}
|
|
514
|
if (attributes.containsKey("Comment")){
|
|
515
|
LanguageString description = LanguageString.NewInstance(attributes.get("Comment"), Language.ENGLISH());
|
|
516
|
media.addDescription(description);
|
|
517
|
}
|
|
518
|
if (attributes.containsKey("Creators")){
|
|
519
|
String creators = attributes.get("Creators");
|
|
520
|
Person artist;
|
|
521
|
Team artistTeam;
|
|
522
|
String[] artists;
|
|
523
|
if (creators != null){
|
|
524
|
if (creators.contains("&")){
|
|
525
|
artists = creators.split("&");
|
|
526
|
artistTeam = new Team();
|
|
527
|
for (String creator:artists){
|
|
528
|
artist = Person.NewTitledInstance(creator);
|
|
529
|
artistTeam.addTeamMember(artist);
|
|
530
|
}
|
|
531
|
media.setArtist(artistTeam);
|
|
532
|
} else{
|
|
533
|
|
|
534
|
artist = Person.NewTitledInstance(creators);
|
|
535
|
media.setArtist(artist);
|
|
536
|
}
|
|
537
|
}
|
|
538
|
|
|
539
|
|
|
540
|
|
|
541
|
}
|
|
542
|
|
|
543
|
derivedUnitFacade.addDerivedUnitMedia(media);
|
|
544
|
if(state.getConfig().isAddMediaAsMediaSpecimen()){
|
|
545
|
//add media also as specimen scan
|
|
546
|
MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.StillImage);
|
|
547
|
mediaSpecimen.setMediaSpecimen(media);
|
|
548
|
//do it only once!!
|
|
549
|
DefinedTermBase specimenScanTerm = getTermService().load(SPECIMEN_SCAN_TERM);
|
|
550
|
if(specimenScanTerm instanceof DefinedTerm){
|
|
551
|
mediaSpecimen.setKindOfUnit((DefinedTerm) specimenScanTerm);
|
|
552
|
}
|
|
553
|
DerivationEvent derivationEvent = DerivationEvent.NewInstance(DerivationEventType.PREPARATION());
|
|
554
|
derivationEvent.addDerivative(mediaSpecimen);
|
|
555
|
derivedUnitFacade.innerDerivedUnit().addDerivationEvent(derivationEvent);
|
|
556
|
}
|
|
557
|
|
|
558
|
} catch (MalformedURLException e) {
|
|
559
|
// TODO Auto-generated catch block
|
|
560
|
e.printStackTrace();
|
|
561
|
}
|
|
562
|
|
|
563
|
}
|
|
564
|
}
|
|
565
|
//multimedia for fieldUnit
|
|
566
|
if (state.getDataHolder().getGatheringMultimediaObjects().size() != -1) {
|
|
567
|
for (String multimediaObject : state.getDataHolder().getGatheringMultimediaObjects().keySet()) {
|
|
568
|
Media media;
|
|
569
|
try {
|
|
570
|
media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
|
|
571
|
Map<String, String> attributes = state.getDataHolder().getGatheringMultimediaObjects().get(multimediaObject);
|
|
572
|
if (attributes.containsKey("Context")){
|
|
573
|
LanguageString description = LanguageString.NewInstance(attributes.get("Context"), Language.ENGLISH());
|
|
574
|
media.addDescription(description);
|
|
575
|
}
|
|
576
|
if (attributes.containsKey("Comment")){
|
|
577
|
LanguageString description = LanguageString.NewInstance(attributes.get("Comment"), Language.ENGLISH());
|
|
578
|
media.addDescription(description);
|
|
579
|
}
|
|
580
|
if (attributes.containsKey("Creators")){
|
|
581
|
String creators = attributes.get("Creators");
|
|
582
|
Person artist;
|
|
583
|
Team artistTeam;
|
|
584
|
String[] artists;
|
|
585
|
if (creators != null){
|
|
586
|
if (creators.contains("&")){
|
|
587
|
artists = creators.split("&");
|
|
588
|
artistTeam = new Team();
|
|
589
|
for (String creator:artists){
|
|
590
|
artist = Person.NewTitledInstance(creator);
|
|
591
|
artistTeam.addTeamMember(artist);
|
|
592
|
}
|
|
593
|
media.setArtist(artistTeam);
|
|
594
|
} else{
|
|
595
|
|
|
596
|
artist = Person.NewTitledInstance(creators);
|
|
597
|
media.setArtist(artist);
|
|
598
|
}
|
|
599
|
}
|
|
600
|
|
|
601
|
|
|
602
|
|
|
603
|
}
|
|
604
|
|
|
605
|
derivedUnitFacade.addFieldObjectMedia(media);
|
|
606
|
|
|
607
|
|
|
608
|
} catch (MalformedURLException e) {
|
|
609
|
// TODO Auto-generated catch block
|
|
610
|
e.printStackTrace();
|
|
611
|
}
|
|
612
|
|
|
613
|
}
|
|
614
|
}
|
|
615
|
|
|
616
|
// /*
|
|
617
|
// * merge AND STORE DATA
|
|
618
|
// */
|
|
619
|
// getTermService().saveOrUpdate(areaCountry);// TODO save area sooner
|
|
620
|
//
|
|
621
|
// for (NamedArea area : otherAreas) {
|
|
622
|
// getTermService().saveOrUpdate(area);// merge it sooner (foreach area)
|
|
623
|
// }
|
|
624
|
// save(derivedUnitFacade.getFieldUnit(false), state);
|
|
625
|
if (derivedUnitFacade.getFieldUnit(false) != null){
|
|
626
|
state.setFieldUnit(derivedUnitFacade.getFieldUnit(false));
|
|
627
|
}
|
|
628
|
|
|
629
|
// handle collection data
|
|
630
|
setCollectionData(state, derivedUnitFacade);
|
|
631
|
|
|
632
|
//Reference stuff
|
|
633
|
SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
|
|
634
|
Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<>();
|
|
635
|
|
|
636
|
state.getDataHolder().setDocSources(new ArrayList<>());
|
|
637
|
for (String[] fullReference : state.getDataHolder().getReferenceList()) {
|
|
638
|
String strReference=fullReference[0];
|
|
639
|
String citationDetail = fullReference[1];
|
|
640
|
String citationURL = fullReference[2];
|
|
641
|
|
|
642
|
if (!citationURL.isEmpty()) {
|
|
643
|
citationDetail+=", "+citationURL;
|
|
644
|
}
|
|
645
|
|
|
646
|
Reference reference;
|
|
647
|
if(strReference.equals(state.getRef().getTitleCache())){
|
|
648
|
reference = state.getRef();
|
|
649
|
}
|
|
650
|
else{
|
|
651
|
reference = ReferenceFactory.newGeneric();
|
|
652
|
reference.setTitle(strReference);
|
|
653
|
}
|
|
654
|
|
|
655
|
|
|
656
|
save(reference, state);
|
|
657
|
IdentifiableSource sour = getIdentifiableSource(reference, citationDetail);
|
|
658
|
sour.getCitation().setUri(state.getActualAccessPoint());
|
|
659
|
sour.setType(OriginalSourceType.PrimaryTaxonomicSource);
|
|
660
|
try{
|
|
661
|
if (sour.getCitation() != null){
|
|
662
|
if(StringUtils.isNotBlank(sour.getCitationMicroReference())) {
|
|
663
|
state.getDataHolder().getDocSources().add(sour.getCitation().getTitleCache()+ "---"+sour.getCitationMicroReference());
|
|
664
|
} else {
|
|
665
|
state.getDataHolder().getDocSources().add(sour.getCitation().getTitleCache());
|
|
666
|
}
|
|
667
|
}
|
|
668
|
}catch(Exception e){
|
|
669
|
logger.warn("oups");
|
|
670
|
}
|
|
671
|
derivedUnitFacade.addSource(sour);
|
|
672
|
|
|
673
|
}
|
|
674
|
// List<IdentifiableSource> issTmp = new ArrayList<IdentifiableSource>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
|
|
675
|
// List<DescriptionElementSource> issTmp2 = new ArrayList<DescriptionElementSource>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
|
|
676
|
//
|
|
677
|
// Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
|
|
678
|
// if(issTmp2!=null) {
|
|
679
|
// osbSet.addAll(issTmp2);
|
|
680
|
// }
|
|
681
|
// if(issTmp!=null) {
|
|
682
|
// osbSet.addAll(issTmp);
|
|
683
|
// }
|
|
684
|
|
|
685
|
IdentifiableSource sour = getIdentifiableSource(state.getRef(),null);
|
|
686
|
String idInSource = derivedUnitFacade.getAccessionNumber() != null? derivedUnitFacade.getAccessionNumber():derivedUnitFacade.getCatalogNumber();
|
|
687
|
sour.getCitation().setUri(state.getActualAccessPoint());
|
|
688
|
sour.setIdInSource(idInSource);
|
|
689
|
try{
|
|
690
|
if (sour.getCitation() != null){
|
|
691
|
if(StringUtils.isNotBlank(sour.getCitationMicroReference())) {
|
|
692
|
state.getDataHolder().getDocSources().add(sour.getCitation().getTitleCache()+ "---"+sour.getCitationMicroReference());
|
|
693
|
} else {
|
|
694
|
state.getDataHolder().getDocSources().add(sour.getCitation().getTitleCache());
|
|
695
|
}
|
|
696
|
}
|
|
697
|
}catch(Exception e){
|
|
698
|
logger.warn("oups");
|
|
699
|
}
|
|
700
|
|
|
701
|
derivedUnitFacade.addSource(sour);
|
|
702
|
// sourceMap.put(sour.getCitation().getTitleCache()+ "---"+sour.getCitationMicroReference(),sour);
|
|
703
|
|
|
704
|
// if( state.getConfig().isInteractWithUser()){
|
|
705
|
// List<OriginalSourceBase<?>>sources=null;
|
|
706
|
// if(!state.isDerivedUnitSourcesSet()){
|
|
707
|
// sources= sui.askForSource(sourceMap, "the unit itself","",getReferenceService(), state.getDataHolder().getDocSources());
|
|
708
|
// state.setDerivedUnitSources(sources);
|
|
709
|
// state.setDerivedUnitSourcesSet(true);
|
|
710
|
// }
|
|
711
|
// else{
|
|
712
|
// sources=state.getDerivedUnitSources();
|
|
713
|
// }
|
|
714
|
//// for (OriginalSourceBase<?> source:sources){
|
|
715
|
//// if(source.isInstanceOf(IdentifiableSource.class)){
|
|
716
|
//// if(sourceNotLinkedToElement(derivedUnitFacade,source)) {
|
|
717
|
//// derivedUnitFacade.addSource((IdentifiableSource)source.clone());
|
|
718
|
//// }
|
|
719
|
//// }else{
|
|
720
|
//// if(sourceNotLinkedToElement(derivedUnitFacade,sour)) {
|
|
721
|
//// derivedUnitFacade.addSource(OriginalSourceType.Import,source.getCitation(),source.getCitationMicroReference(), ioName);
|
|
722
|
//// }
|
|
723
|
//// }
|
|
724
|
//// }
|
|
725
|
// }else{
|
|
726
|
// for (OriginalSourceBase<?> sr : sourceMap.values()){
|
|
727
|
// if(sr.isInstanceOf(IdentifiableSource.class)){
|
|
728
|
// if(sourceNotLinkedToElement(derivedUnitFacade,sr)) {
|
|
729
|
// derivedUnitFacade.addSource((IdentifiableSource)sr.clone());
|
|
730
|
// }
|
|
731
|
// }else{
|
|
732
|
// if(sourceNotLinkedToElement(derivedUnitFacade,sr)) {
|
|
733
|
// derivedUnitFacade.addSource(OriginalSourceType.Import,sr.getCitation(),sr.getCitationMicroReference(), ioName);
|
|
734
|
// }
|
|
735
|
// }
|
|
736
|
// }
|
|
737
|
// }
|
|
738
|
|
|
739
|
save(state.getDerivedUnitBase(), state);
|
|
740
|
|
|
741
|
if(logger.isDebugEnabled()) {
|
|
742
|
logger.info("saved ABCD specimen ...");
|
|
743
|
}
|
|
744
|
|
|
745
|
// handle identifications
|
|
746
|
handleIdentifications(state, derivedUnitFacade);
|
|
747
|
|
|
748
|
//associatedUnits
|
|
749
|
if (handleAssociatedUnits){
|
|
750
|
importAssociatedUnits(state, item, derivedUnitFacade);
|
|
751
|
}
|
|
752
|
//siblings/ other children
|
|
753
|
if (derivedUnitFacade.getType() != null && (derivedUnitFacade.getType().equals(SpecimenOrObservationType.LivingSpecimen) || derivedUnitFacade.getType().equals(SpecimenOrObservationType.TissueSample) || derivedUnitFacade.getType().equals(SpecimenOrObservationType.OtherSpecimen)) &&state.getConfig().isGetSiblings()){
|
|
754
|
getSiblings(state, item, derivedUnitFacade);
|
|
755
|
}
|
|
756
|
|
|
757
|
|
|
758
|
} catch (Exception e) {
|
|
759
|
String message = "Error when reading record!";
|
|
760
|
logger.warn(message);
|
|
761
|
state.getReport().addException(message, e);
|
|
762
|
e.printStackTrace();
|
|
763
|
state.setUnsuccessfull();
|
|
764
|
}
|
|
765
|
|
|
766
|
return;
|
|
767
|
}
|
|
768
|
|
|
769
|
@Override
|
|
770
|
protected void importAssociatedUnits(Abcd206ImportState state, Object itemObject, DerivedUnitFacade derivedUnitFacade) {
|
|
771
|
|
|
772
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
773
|
//import associated units
|
|
774
|
FieldUnit currentFieldUnit = derivedUnitFacade.innerFieldUnit();
|
|
775
|
//TODO: push state (think of implementing stack architecture for state
|
|
776
|
DerivedUnit currentUnit = state.getDerivedUnitBase();
|
|
777
|
DerivationEvent currentDerivedFrom = currentUnit.getDerivedFrom();
|
|
778
|
URI currentAccessPoint = state.getActualAccessPoint();
|
|
779
|
String currentPrefix = state.getPrefix();
|
|
780
|
Element item = null;
|
|
781
|
if (itemObject instanceof Element){
|
|
782
|
item = (Element)itemObject;
|
|
783
|
}
|
|
784
|
NodeList unitAssociationList = null;
|
|
785
|
if (item != null){
|
|
786
|
unitAssociationList = item.getElementsByTagName(currentPrefix+"UnitAssociation");
|
|
787
|
for(int k=0;k<unitAssociationList.getLength();k++){
|
|
788
|
if(unitAssociationList.item(k) instanceof Element){
|
|
789
|
Element unitAssociation = (Element)unitAssociationList.item(k);
|
|
790
|
UnitAssociationParser unitAssociationParser = new UnitAssociationParser(currentPrefix, state.getReport(), state.getCdmRepository());
|
|
791
|
UnitAssociationWrapper associationWrapper = unitAssociationParser.parse(unitAssociation);
|
|
792
|
|
|
793
|
state.setActualAccessPoint(associationWrapper.getAccesPoint());
|
|
794
|
if(associationWrapper!=null){
|
|
795
|
NodeList associatedUnits = associationWrapper.getAssociatedUnits();
|
|
796
|
if(associatedUnits!=null){
|
|
797
|
for(int m=0;m<associatedUnits.getLength();m++){
|
|
798
|
if(associatedUnits.item(m) instanceof Element){
|
|
799
|
state.reset();
|
|
800
|
state.setPrefix(associationWrapper.getPrefix());
|
|
801
|
Abcd206ImportParser.setUnitPropertiesXML((Element) associatedUnits.item(m), new Abcd206XMLFieldGetter(state.getDataHolder(), state.getPrefix()), state);
|
|
802
|
logger.debug("derived unit: " + state.getDerivedUnitBase().toString() + " associated unit: " +state.getDataHolder().getKindOfUnit() + ", " + state.getDataHolder().accessionNumber + ", " + state.getDataHolder().getRecordBasis() + ", " + state.getDataHolder().getUnitID());
|
|
803
|
handleSingleUnit(state, associatedUnits.item(m), true);
|
|
804
|
|
|
805
|
DerivedUnit associatedUnit = state.getDerivedUnitBase();
|
|
806
|
FieldUnit associatedFieldUnit = null;
|
|
807
|
java.util.Collection<FieldUnit> associatedFieldUnits = state.getCdmRepository().getOccurrenceService().getFieldUnits(associatedUnit.getUuid());
|
|
808
|
//ignore field unit if associated unit has more than one
|
|
809
|
if(associatedFieldUnits.size()>1){
|
|
810
|
state.getReport().addInfoMessage(String.format("%s has more than one field unit.", associatedUnit));
|
|
811
|
}
|
|
812
|
else if(associatedFieldUnits.size()==1){
|
|
813
|
associatedFieldUnit = associatedFieldUnits.iterator().next();
|
|
814
|
}
|
|
815
|
|
|
816
|
//attach current unit and associated unit depending on association type
|
|
817
|
|
|
818
|
//parent-child relation:
|
|
819
|
//copy derivation event and connect parent and sub derivative
|
|
820
|
// if(associationWrapper.getAssociationType().contains("individual") || associationWrapper.getAssociationType().contains("culture") || associationWrapper.getAssociationType().contains("sample") || associationWrapper.getAssociationType().contains("same in situ")){
|
|
821
|
if(currentDerivedFrom==null){
|
|
822
|
state.getReport().addInfoMessage(String.format("No derivation event found for unit %s. Defaulting to ACCESSIONING event.",SpecimenImportUtility.getUnitID(currentUnit, config)));
|
|
823
|
DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, DerivationEventType.ACCESSIONING());
|
|
824
|
}
|
|
825
|
else{
|
|
826
|
DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedUnit, currentUnit, currentDerivedFrom.getType());
|
|
827
|
updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
|
|
828
|
updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
|
|
829
|
updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
|
|
830
|
updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
|
|
831
|
|
|
832
|
}
|
|
833
|
state.getReport().addDerivate(associatedUnit, currentUnit, config);
|
|
834
|
// }
|
|
835
|
//siblings relation
|
|
836
|
//connect current unit to field unit of associated unit
|
|
837
|
// else if(associationWrapper.getAssociationType().contains("population")|| associationWrapper.getAssociationType().contains("sample")){
|
|
838
|
// //no associated field unit -> using current one
|
|
839
|
// if(associatedFieldUnit==null){
|
|
840
|
// if(currentFieldUnit!=null){
|
|
841
|
// DerivationEvent.NewSimpleInstance(currentFieldUnit, associatedUnit, DerivationEventType.ACCESSIONING());
|
|
842
|
// }
|
|
843
|
// }
|
|
844
|
// else{
|
|
845
|
// if(currentDerivedFrom==null){
|
|
846
|
// state.getReport().addInfoMessage("No derivation event found for unit "+SpecimenImportUtility.getUnitID(currentUnit, config)+". Defaulting to ACCESIONING event.");
|
|
847
|
// DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, DerivationEventType.ACCESSIONING());
|
|
848
|
// }
|
|
849
|
// if(currentDerivedFrom!=null && associatedFieldUnit==currentFieldUnit){
|
|
850
|
// DerivationEvent updatedDerivationEvent = DerivationEvent.NewSimpleInstance(associatedFieldUnit, currentUnit, currentDerivedFrom.getType());
|
|
851
|
// updatedDerivationEvent.setActor(currentDerivedFrom.getActor());
|
|
852
|
// updatedDerivationEvent.setDescription(currentDerivedFrom.getDescription());
|
|
853
|
// updatedDerivationEvent.setInstitution(currentDerivedFrom.getInstitution());
|
|
854
|
// updatedDerivationEvent.setTimeperiod(currentDerivedFrom.getTimeperiod());
|
|
855
|
// }
|
|
856
|
// }
|
|
857
|
// }
|
|
858
|
|
|
859
|
//delete current field unit if replaced
|
|
860
|
if(currentFieldUnit!=null && currentDerivedFrom!=null
|
|
861
|
&& currentFieldUnit.getDerivationEvents().size()==1 && currentFieldUnit.getDerivationEvents().contains(currentDerivedFrom) //making sure that the field unit
|
|
862
|
&& currentDerivedFrom.getDerivatives().size()==1 && currentDerivedFrom.getDerivatives().contains(currentUnit) //is not attached to other derived units
|
|
863
|
&& currentDerivedFrom!=currentUnit.getDerivedFrom() // <- derivation has been replaced and can be deleted
|
|
864
|
){
|
|
865
|
currentFieldUnit.removeDerivationEvent(currentDerivedFrom);
|
|
866
|
state.getCdmRepository().getOccurrenceService().delete(currentFieldUnit);
|
|
867
|
}
|
|
868
|
|
|
869
|
save(associatedUnit, state);
|
|
870
|
}
|
|
871
|
}
|
|
872
|
}
|
|
873
|
}
|
|
874
|
}
|
|
875
|
}
|
|
876
|
}
|
|
877
|
//TODO: pop state
|
|
878
|
state.reset();
|
|
879
|
state.setDerivedUnitBase(currentUnit);
|
|
880
|
state.setActualAccessPoint(currentAccessPoint);
|
|
881
|
state.setPrefix(currentPrefix);
|
|
882
|
}
|
|
883
|
|
|
884
|
|
|
885
|
|
|
886
|
|
|
887
|
/**
|
|
888
|
* @param derivedUnitFacade
|
|
889
|
* @param sour
|
|
890
|
* @return
|
|
891
|
*/
|
|
892
|
private boolean sourceNotLinkedToElement(DerivedUnitFacade derivedUnitFacade, OriginalSourceBase<?> source) {
|
|
893
|
Set<IdentifiableSource> linkedSources = derivedUnitFacade.getSources();
|
|
894
|
for (IdentifiableSource is:linkedSources){
|
|
895
|
if (is.getCitation()!=null && source.getCitation()!=null &&
|
|
896
|
is.getCitation().getTitleCache().equalsIgnoreCase(source.getCitation().getTitleCache())){
|
|
897
|
String isDetail = is.getCitationMicroReference();
|
|
898
|
if ((StringUtils.isBlank(isDetail) && StringUtils.isBlank(source.getCitationMicroReference()))
|
|
899
|
|| (isDetail != null && isDetail.equalsIgnoreCase(source.getCitationMicroReference())) ) {
|
|
900
|
return false;
|
|
901
|
}
|
|
902
|
}
|
|
903
|
}
|
|
904
|
return true;
|
|
905
|
}
|
|
906
|
|
|
907
|
|
|
908
|
|
|
909
|
// /**
|
|
910
|
// * @param reference
|
|
911
|
// * @param citationDetail
|
|
912
|
// * @return
|
|
913
|
// */
|
|
914
|
// private DescriptionElementSource getDescriptionSource(Reference reference, String citationDetail) {
|
|
915
|
//
|
|
916
|
// List<OriginalSourceBase> issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
|
|
917
|
//
|
|
918
|
// try {
|
|
919
|
// for (OriginalSourceBase<?> osb:issTmp2){
|
|
920
|
// if (osb.getCitation().equals(reference) && osb.getCitationMicroReference().equalsIgnoreCase(citationDetail)) {
|
|
921
|
// return (DescriptionElementSource) osb.clone();
|
|
922
|
// }
|
|
923
|
// }
|
|
924
|
// } catch (CloneNotSupportedException e) {
|
|
925
|
// // TODO Auto-generated catch block
|
|
926
|
// e.printStackTrace();
|
|
927
|
// }
|
|
928
|
//
|
|
929
|
// DescriptionElementSource sour = DescriptionElementSource.NewInstance(OriginalSourceType.Import,null,null, reference,citationDetail);
|
|
930
|
// return sour;
|
|
931
|
// }
|
|
932
|
|
|
933
|
|
|
934
|
|
|
935
|
|
|
936
|
/**
|
|
937
|
* setCollectionData : store the collection object into the
|
|
938
|
* derivedUnitFacade
|
|
939
|
*
|
|
940
|
* @param state
|
|
941
|
*/
|
|
942
|
protected void setCollectionData(Abcd206ImportState state, DerivedUnitFacade derivedUnitFacade) {
|
|
943
|
Abcd206ImportConfigurator config = state.getConfig();
|
|
944
|
SpecimenImportUtility.setUnitID(derivedUnitFacade.innerDerivedUnit(), state.getDataHolder().getUnitID(), config);
|
|
945
|
if(!config.isMapUnitIdToAccessionNumber()){
|
|
946
|
derivedUnitFacade.setAccessionNumber(NB(state.getDataHolder().accessionNumber));
|
|
947
|
}
|
|
948
|
// derivedUnitFacade.setCollectorsNumber(NB(state.getDataHolder().collectorsNumber));
|
|
949
|
|
|
950
|
/*
|
|
951
|
* INSTITUTION & COLLECTION
|
|
952
|
*/
|
|
953
|
// manage institution
|
|
954
|
Institution institution = this.getInstitution(NB(state.getDataHolder().institutionCode), state);
|
|
955
|
// manage collection
|
|
956
|
Collection collection = this.getCollection(institution, NB(state.getDataHolder().collectionCode), state);
|
|
957
|
// link specimen & collection
|
|
958
|
derivedUnitFacade.setCollection(collection);
|
|
959
|
}
|
|
960
|
|
|
961
|
/**
|
|
962
|
* getFacade : get the DerivedUnitFacade based on the recordBasis
|
|
963
|
* @param state
|
|
964
|
*
|
|
965
|
* @return DerivedUnitFacade
|
|
966
|
*/
|
|
967
|
@Override
|
|
968
|
protected DerivedUnitFacade getFacade(Abcd206ImportState state) {
|
|
969
|
if(logger.isDebugEnabled()) {
|
|
970
|
logger.info("getFacade()");
|
|
971
|
}
|
|
972
|
SpecimenOrObservationType type = null;
|
|
973
|
DefinedTerm kindOfUnit = null;
|
|
974
|
|
|
975
|
// create specimen
|
|
976
|
if (NB((state.getDataHolder()).getRecordBasis()) != null) {
|
|
977
|
if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("living")>-1) {
|
|
978
|
type = SpecimenOrObservationType.LivingSpecimen;
|
|
979
|
}
|
|
980
|
else if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("s") || state.getDataHolder().getRecordBasis().toLowerCase().indexOf("specimen")>-1) {// specimen
|
|
981
|
type = SpecimenOrObservationType.PreservedSpecimen;
|
|
982
|
}
|
|
983
|
else if (state.getDataHolder().getRecordBasis().toLowerCase().startsWith("o") ||state.getDataHolder().getRecordBasis().toLowerCase().indexOf("observation")>-1 ) {
|
|
984
|
type = SpecimenOrObservationType.Observation;
|
|
985
|
}
|
|
986
|
else if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("fossil")>-1){
|
|
987
|
type = SpecimenOrObservationType.Fossil;
|
|
988
|
}else if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("materialsample")>-1){
|
|
989
|
type = SpecimenOrObservationType.OtherSpecimen;
|
|
990
|
}
|
|
991
|
else if (state.getDataHolder().getRecordBasis().toLowerCase().indexOf("sample")>-1){
|
|
992
|
type = SpecimenOrObservationType.TissueSample;
|
|
993
|
}
|
|
994
|
|
|
995
|
if (type == null) {
|
|
996
|
logger.info("The basis of record does not seem to be known: " + state.getDataHolder().getRecordBasis());
|
|
997
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
998
|
}
|
|
999
|
} else {
|
|
1000
|
logger.info("The basis of record is null");
|
|
1001
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
1002
|
}
|
|
1003
|
|
|
1004
|
if (NB((state.getDataHolder()).getKindOfUnit()) != null) {
|
|
1005
|
if (state.getDataHolder().getKindOfUnit().toLowerCase().indexOf("clone")>-1) {
|
|
1006
|
kindOfUnit = getKindOfUnit(state, null, "clone culture", "clone culture", "cc", null);
|
|
1007
|
}
|
|
1008
|
else if (state.getDataHolder().getKindOfUnit().toLowerCase().startsWith("live")) {
|
|
1009
|
kindOfUnit = getKindOfUnit(state, null, "live sample", "live sample", "ls", null);
|
|
1010
|
}
|
|
1011
|
|
|
1012
|
|
|
1013
|
if (kindOfUnit == null) {
|
|
1014
|
logger.info("The kind of unit does not seem to be known: " + state.getDataHolder().getKindOfUnit());
|
|
1015
|
|
|
1016
|
}
|
|
1017
|
} else {
|
|
1018
|
logger.info("The kind of unit is null");
|
|
1019
|
|
|
1020
|
}
|
|
1021
|
DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
|
|
1022
|
derivedUnitFacade.setFieldUnit(state.getFieldUnit(state.getDataHolder().getFieldNumber()));
|
|
1023
|
derivedUnitFacade.setKindOfUnit(kindOfUnit);
|
|
1024
|
return derivedUnitFacade;
|
|
1025
|
}
|
|
1026
|
|
|
1027
|
private void getCollectorsFromXML(Element root, Abcd206XMLFieldGetter abcdFieldGetter, Abcd206ImportState state) {
|
|
1028
|
NodeList group;
|
|
1029
|
|
|
1030
|
group = root.getChildNodes();
|
|
1031
|
for (int i = 0; i < group.getLength(); i++) {
|
|
1032
|
if (group.item(i).getNodeName().equals(state.getPrefix() + "Identifications")) {
|
|
1033
|
group = group.item(i).getChildNodes();
|
|
1034
|
break;
|
|
1035
|
}
|
|
1036
|
}
|
|
1037
|
//state.getDataHolder().gatheringAgents = "";
|
|
1038
|
|
|
1039
|
abcdFieldGetter.getType(root);
|
|
1040
|
abcdFieldGetter.getGatheringPeople(root);
|
|
1041
|
}
|
|
1042
|
|
|
1043
|
|
|
1044
|
|
|
1045
|
// private void compareABCDtoCDM(URI urlFileName, List<String> knownElts, Abcd206XMLFieldGetter abcdFieldGetter) {
|
|
1046
|
// try {
|
|
1047
|
// DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
|
|
1048
|
// DocumentBuilder constructeur = factory.newDocumentBuilder();
|
|
1049
|
// URL url = urlFileName.toURL();
|
|
1050
|
// Object o = url.getContent();
|
|
1051
|
// InputStream is = (InputStream) o;
|
|
1052
|
// Document document = constructeur.parse(is);
|
|
1053
|
// Element root = document.getDocumentElement();
|
|
1054
|
// abcdFieldGetter.traverse(root);
|
|
1055
|
// }
|
|
1056
|
// catch (ParserConfigurationException e){
|
|
1057
|
// e.printStackTrace();
|
|
1058
|
// }
|
|
1059
|
// catch (SAXException e) {
|
|
1060
|
// e.printStackTrace();
|
|
1061
|
// }
|
|
1062
|
// catch (IOException e) {
|
|
1063
|
// e.printStackTrace();
|
|
1064
|
// }
|
|
1065
|
// Set<String> elts = state.getDataHolder().allABCDelements.keySet();
|
|
1066
|
// Iterator<String> it = elts.iterator();
|
|
1067
|
// String elt;
|
|
1068
|
// while (it.hasNext()) {
|
|
1069
|
// elt = it.next();
|
|
1070
|
// if (knownElts.indexOf(elt) == -1) {
|
|
1071
|
// if(DEBUG) {
|
|
1072
|
// logger.info("Unmerged ABCD element: " + elt + " - "+ state.getDataHolder().allABCDelements.get(elt));
|
|
1073
|
// }
|
|
1074
|
// }
|
|
1075
|
// }
|
|
1076
|
// }
|
|
1077
|
|
|
1078
|
/**
|
|
1079
|
* Load the list of names from the ABCD file and save them
|
|
1080
|
* @param state : the current ABCD import state
|
|
1081
|
* @param unitsList : the unit list from the ABCD file
|
|
1082
|
* @param abcdFieldGetter : the ABCD parser
|
|
1083
|
*/
|
|
1084
|
private void prepareCollectors(Abcd206ImportState state, NodeList unitsList, Abcd206XMLFieldGetter abcdFieldGetter) {
|
|
1085
|
|
|
1086
|
TeamOrPersonBase<?> teamOrPerson = null;
|
|
1087
|
Team team = null;
|
|
1088
|
//ImportHelper.setOriginalSource(teamOrPerson, state.getConfig().getSourceReference(), collector, "Collector");
|
|
1089
|
for (int i = 0; i < unitsList.getLength(); i++) {
|
|
1090
|
this.getCollectorsFromXML((Element) unitsList.item(i), abcdFieldGetter, state);
|
|
1091
|
if (!(state.getDataHolder().gatheringAgentsList.isEmpty())){
|
|
1092
|
if (state.getDataHolder().gatheringAgentsList.size() == 1){
|
|
1093
|
teamOrPerson = parseAuthorString(state.getDataHolder().gatheringAgentsList.get(0));
|
|
1094
|
}else{
|
|
1095
|
team = new Team();
|
|
1096
|
for(String collector: state.getDataHolder().gatheringAgentsList){
|
|
1097
|
teamOrPerson = parseAuthorString(collector);
|
|
1098
|
if (teamOrPerson instanceof Person){
|
|
1099
|
team.addTeamMember((Person)teamOrPerson);
|
|
1100
|
}else{
|
|
1101
|
for (Person person: ((Team)teamOrPerson).getTeamMembers()){
|
|
1102
|
team.addTeamMember(person);
|
|
1103
|
}
|
|
1104
|
}
|
|
1105
|
}
|
|
1106
|
}
|
|
1107
|
if (!state.getPersonStore().containsId(state.getDataHolder().gatheringAgentsList.toString())) {
|
|
1108
|
state.getPersonStore().put(state.getDataHolder().gatheringAgentsList.toString(), teamOrPerson);
|
|
1109
|
if (logger.isDebugEnabled()) { logger.debug("Stored author " + state.getDataHolder().gatheringAgentsList.toString());}
|
|
1110
|
logger.warn("Not imported author with duplicated aut_id " + state.getDataHolder().gatheringAgentsList.toString() );
|
|
1111
|
}
|
|
1112
|
}
|
|
1113
|
if (!StringUtils.isBlank(state.getDataHolder().gatheringAgentsText) && state.getDataHolder().gatheringAgentsList.isEmpty()){
|
|
1114
|
teamOrPerson = parseAuthorString(state.getDataHolder().gatheringAgentsText);
|
|
1115
|
}
|
|
1116
|
|
|
1117
|
}
|
|
1118
|
|
|
1119
|
|
|
1120
|
|
|
1121
|
|
|
1122
|
// List<String> collectorsU = new ArrayList<String>(new HashSet<String>(collectors));
|
|
1123
|
// List<String> teamsU = new ArrayList<String>(new HashSet<String>(teams));
|
|
1124
|
//
|
|
1125
|
//
|
|
1126
|
// //existing teams in DB
|
|
1127
|
// Map<String,Team> titleCacheTeam = new HashMap<String, Team>();
|
|
1128
|
// List<UuidAndTitleCache<Team>> hiberTeam = new ArrayList<UuidAndTitleCache<Team>>();//getAgentService().getTeamUuidAndTitleCache();
|
|
1129
|
|
|
1130
|
// Set<UUID> uuids = new HashSet<UUID>();
|
|
1131
|
// for (UuidAndTitleCache<Team> hibernateT:hiberTeam){
|
|
1132
|
// uuids.add(hibernateT.getUuid());
|
|
1133
|
// }
|
|
1134
|
// if (!uuids.isEmpty()){
|
|
1135
|
// List<AgentBase> existingTeams = getAgentService().find(uuids);
|
|
1136
|
// for (AgentBase<?> existingP:existingTeams){
|
|
1137
|
// titleCacheTeam.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Team.class));
|
|
1138
|
// }
|
|
1139
|
// }
|
|
1140
|
|
|
1141
|
|
|
1142
|
// Map<String,UUID> teamMap = new HashMap<String, UUID>();
|
|
1143
|
// for (UuidAndTitleCache<Team> uuidt:hiberTeam){
|
|
1144
|
// teamMap.put(uuidt.getTitleCache(), uuidt.getUuid());
|
|
1145
|
// }
|
|
1146
|
|
|
1147
|
//existing persons in DB
|
|
1148
|
// List<UuidAndTitleCache<Person>> hiberPersons = new ArrayList<UuidAndTitleCache<Person>>();//getAgentService().getPersonUuidAndTitleCache();
|
|
1149
|
// Map<String,Person> titleCachePerson = new HashMap<String, Person>();
|
|
1150
|
// uuids = new HashSet<UUID>();
|
|
1151
|
// for (UuidAndTitleCache<Person> hibernateP:hiberPersons){
|
|
1152
|
// uuids.add(hibernateP.getUuid());
|
|
1153
|
// }
|
|
1154
|
//
|
|
1155
|
// if (!uuids.isEmpty()){
|
|
1156
|
// List<AgentBase> existingPersons = getAgentService().find(uuids);
|
|
1157
|
// for (AgentBase<?> existingP:existingPersons){
|
|
1158
|
// titleCachePerson.put(existingP.getTitleCache(),CdmBase.deproxy(existingP,Person.class));
|
|
1159
|
// }
|
|
1160
|
// }
|
|
1161
|
//
|
|
1162
|
// Map<String,UUID> personMap = new HashMap<String, UUID>();
|
|
1163
|
// for (UuidAndTitleCache<Person> person:hiberPersons){
|
|
1164
|
// personMap.put(person.getTitleCache(), person.getUuid());
|
|
1165
|
// }
|
|
1166
|
//
|
|
1167
|
// java.util.Collection<Person> personToadd = new ArrayList<Person>();
|
|
1168
|
// java.util.Collection<Team> teamToAdd = new ArrayList<Team>();
|
|
1169
|
//
|
|
1170
|
// for (String collector:collectorsU){
|
|
1171
|
// Person p = Person.NewInstance();
|
|
1172
|
// p.setTitleCache(collector,true);
|
|
1173
|
// if (!personMap.containsKey(p.getTitleCache())){
|
|
1174
|
// personToadd.add(p);
|
|
1175
|
// }
|
|
1176
|
// }
|
|
1177
|
// for (String team:teamsU){
|
|
1178
|
// Team p = Team.NewInstance();
|
|
1179
|
// p.setTitleCache(team,true);
|
|
1180
|
// if (!teamMap.containsKey(p.getTitleCache())){
|
|
1181
|
// teamToAdd.add(p);
|
|
1182
|
// }
|
|
1183
|
// }
|
|
1184
|
//
|
|
1185
|
// if(!personToadd.isEmpty()){
|
|
1186
|
// for (Person agent: personToadd){
|
|
1187
|
// save(agent, state);
|
|
1188
|
// titleCachePerson.put(agent.getTitleCache(),CdmBase.deproxy(agent, Person.class) );
|
|
1189
|
// }
|
|
1190
|
// }
|
|
1191
|
//
|
|
1192
|
// Person ptmp ;
|
|
1193
|
// Map <String,Integer>teamdone = new HashMap<String, Integer>();
|
|
1194
|
// for (List<String> collteam: collectorinteams){
|
|
1195
|
// if (!teamdone.containsKey(StringUtils.join(collteam.toArray(),"-"))){
|
|
1196
|
// Team team = new Team();
|
|
1197
|
// boolean em =true;
|
|
1198
|
// for (String collector:collteam){
|
|
1199
|
// ptmp = Person.NewInstance();
|
|
1200
|
// ptmp.setTitleCache(collector,true);
|
|
1201
|
// Person p2 = titleCachePerson.get(ptmp.getTitleCache());
|
|
1202
|
// team.addTeamMember(p2);
|
|
1203
|
// em=false;
|
|
1204
|
// }
|
|
1205
|
// if (!em) {
|
|
1206
|
// teamToAdd.add(team);
|
|
1207
|
// }
|
|
1208
|
// teamdone.put(StringUtils.join(collteam.toArray(),"-"),0);
|
|
1209
|
// }
|
|
1210
|
// }
|
|
1211
|
//
|
|
1212
|
// if(!teamToAdd.isEmpty()){
|
|
1213
|
// for (Team agent: teamToAdd){
|
|
1214
|
// save(agent, state);
|
|
1215
|
// titleCacheTeam.put(agent.getTitleCache(), CdmBase.deproxy( agent,Team.class) );
|
|
1216
|
// }
|
|
1217
|
// }
|
|
1218
|
|
|
1219
|
// ((Abcd206ImportConfigurator) state.getConfig()).setTeams(titleCacheTeam);
|
|
1220
|
// ((Abcd206ImportConfigurator) state.getConfig()).setPersons(titleCachePerson);
|
|
1221
|
}
|
|
1222
|
|
|
1223
|
|
|
1224
|
@Override
|
|
1225
|
protected boolean doCheck(Abcd206ImportState state) {
|
|
1226
|
logger.warn("Checking not yet implemented for " + this.getClass().getSimpleName());
|
|
1227
|
return true;
|
|
1228
|
}
|
|
1229
|
|
|
1230
|
@Override
|
|
1231
|
protected boolean isIgnore(Abcd206ImportState state) {
|
|
1232
|
return false;
|
|
1233
|
}
|
|
1234
|
|
|
1235
|
}
|