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8
9
10 package eu.etaxonomy.cdm.io.specimen.abcd206.in;
11
12 import java.io.IOException;
13 import java.io.InputStream;
14 import java.net.URL;
15 import java.util.ArrayList;
16 import java.util.HashMap;
17 import java.util.Iterator;
18 import java.util.List;
19 import java.util.Set;
20 import java.util.UUID;
21
22 import javax.xml.parsers.DocumentBuilder;
23 import javax.xml.parsers.DocumentBuilderFactory;
24 import javax.xml.parsers.ParserConfigurationException;
25
26 import org.apache.log4j.Logger;
27 import org.springframework.stereotype.Component;
28 import org.springframework.transaction.TransactionStatus;
29 import org.w3c.dom.Document;
30 import org.w3c.dom.Element;
31 import org.w3c.dom.Node;
32 import org.w3c.dom.NodeList;
33 import org.xml.sax.SAXException;
34
35 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
36 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType;
37 import eu.etaxonomy.cdm.common.mediaMetaData.ImageMetaData;
38 import eu.etaxonomy.cdm.io.common.ICdmIO;
39 import eu.etaxonomy.cdm.io.specimen.SpecimenIoBase;
40 import eu.etaxonomy.cdm.io.specimen.UnitsGatheringArea;
41 import eu.etaxonomy.cdm.io.specimen.UnitsGatheringEvent;
42 import eu.etaxonomy.cdm.model.agent.Institution;
43 import eu.etaxonomy.cdm.model.agent.Team;
44 import eu.etaxonomy.cdm.model.common.DescriptionElementSource;
45 import eu.etaxonomy.cdm.model.description.Feature;
46 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
47 import eu.etaxonomy.cdm.model.description.TaxonDescription;
48 import eu.etaxonomy.cdm.model.location.NamedArea;
49 import eu.etaxonomy.cdm.model.media.ImageFile;
50 import eu.etaxonomy.cdm.model.media.Media;
51 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
52 import eu.etaxonomy.cdm.model.name.BacterialName;
53 import eu.etaxonomy.cdm.model.name.BotanicalName;
54 import eu.etaxonomy.cdm.model.name.CultivarPlantName;
55 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
56 import eu.etaxonomy.cdm.model.name.NonViralName;
57 import eu.etaxonomy.cdm.model.name.Rank;
58 import eu.etaxonomy.cdm.model.name.ZoologicalName;
59 import eu.etaxonomy.cdm.model.occurrence.Collection;
60 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
61 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
62 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
63 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
64 import eu.etaxonomy.cdm.model.taxon.Taxon;
65 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
66 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
67
68
69
70
71
72
73
74 @Component
75 public class Abcd206Import extends SpecimenIoBase<Abcd206ImportConfigurator, Abcd206ImportState> implements ICdmIO<Abcd206ImportState> {
76 private static final Logger logger = Logger.getLogger(Abcd206Import.class);
77
78
79 public Abcd206Import() {
80 super();
81 }
82
83
84 @Override
85 protected boolean doCheck(Abcd206ImportState state) {
86 logger.warn("Checking not yet implemented for " + this.getClass().getSimpleName());
87 return true;
88 }
89
90
91 @Override
92 public boolean doInvoke(Abcd206ImportState state){
93 logger.info("INVOKE Specimen Import from ABCD2.06 XML File");
94 boolean result = true;
95
96 String sourceName = state.getConfig().getSource();
97 NodeList unitsList = getUnitsNodeList(sourceName);
98 if (unitsList != null){
99 String message = "nb units to insert: "+unitsList.getLength();
100 logger.info(message);
101 updateProgress(state, message);
102
103 Abcd206DataHolder dataHolder = new Abcd206DataHolder();
104
105 for (int i=0 ; i<unitsList.getLength() ; i++){
106 this.setUnitPropertiesXML((Element)unitsList.item(i), dataHolder);
107 result &= this.handleSingleUnit(state, dataHolder);
108
109
110 compareABCDtoCDM(sourceName, dataHolder.knownABCDelements, dataHolder);
111
112
113
114 dataHolder.allABCDelements = new HashMap<String,String>();
115 }
116 }
117
118 return result;
119
120 }
121
122
123
124
125 private boolean handleSingleUnit(Abcd206ImportState state, Abcd206DataHolder dataHolder){
126 boolean result = true;
127
128 Abcd206ImportConfigurator config = state.getConfig();
129
130 TransactionStatus tx = startTransaction();
131 try {
132 updateProgress(state, "Importing data for unit: " + dataHolder.unitID);
133
134
135
136 ReferenceBase sec = config.getTaxonReference();
137
138
139 DerivedUnitFacade derivedUnitFacade = getFacade(dataHolder);
140
141
142
143 handleIdentifications(config, derivedUnitFacade, sec, dataHolder);
144
145
146 setCollectionData(config, dataHolder, derivedUnitFacade);
147
148
149
150
151
152
153 UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(
154 getTermService(), dataHolder.locality, dataHolder.languageIso, dataHolder.longitude,
155 dataHolder.latitude, dataHolder.gatheringAgentList);
156
157
158 UnitsGatheringArea unitsGatheringArea =
159 new UnitsGatheringArea(dataHolder.isocountry, dataHolder.country, getOccurrenceService());
160 NamedArea areaCountry = unitsGatheringArea.getArea();
161
162
163 unitsGatheringArea = new UnitsGatheringArea(dataHolder.namedAreaList);
164 ArrayList<NamedArea> nas = unitsGatheringArea.getAreas();
165 for (NamedArea namedArea : nas){
166 unitsGatheringEvent.addArea(namedArea);
167 }
168
169
170 GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();
171 derivedUnitFacade.setLocality(gatheringEvent.getLocality());
172 derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());
173 derivedUnitFacade.setCollector(gatheringEvent.getCollector());
174 derivedUnitFacade.setCountry(areaCountry);
175 derivedUnitFacade.addCollectingAreas(unitsGatheringArea.getAreas());
176
177
178
179
180
181 derivedUnitFacade.setFieldNumber(dataHolder.fieldNumber);
182
183
184
185
186 if(dataHolder.multimediaObjects.size() > 0){
187 MediaRepresentation representation;
188 Media media;
189 ImageMetaData imd ;
190 URL url ;
191 ImageFile imf;
192 for (String multimediaObject : dataHolder.multimediaObjects){
193 if( multimediaObject != null){
194 imd = ImageMetaData.newInstance();
195 url = new URL(multimediaObject);
196 try {
197 imd.readMetaData(url.toURI(), 0);
198 } catch (Exception e) {
199 String message = "An error occurred when trying to read image meta data: " + e.getMessage();
200 logger.warn(message);
201 }
202
203 if (imd != null){
204 imf = ImageFile.NewInstance(multimediaObject, null, imd);
205 representation = MediaRepresentation.NewInstance();
206 representation.addRepresentationPart(imf);
207 media = Media.NewInstance();
208 media.addRepresentation(representation);
209
210 derivedUnitFacade.addFieldObjectMedia(media);
211 }
212 }
213 }
214 }
215
216
217
218
219 getTermService().save(areaCountry);
220 for (NamedArea area : nas){
221 getTermService().save(area);
222 }
223 getTermService().saveLanguageData(unitsGatheringEvent.getLocality());
224
225 getOccurrenceService().save(derivedUnitFacade.getDerivedUnit());
226 logger.info("saved ABCD specimen ...");
227
228
229 } catch (Exception e) {
230 logger.warn("Error when reading record!!");
231 e.printStackTrace();
232 result = false;
233 }
234 commitTransaction(tx);
235
236 return result;
237 }
238
239
240 private void setCollectionData(Abcd206ImportConfigurator config,
241 Abcd206DataHolder dataHolder, DerivedUnitFacade derivedUnitFacade) {
242
243 derivedUnitFacade.setCatalogNumber(dataHolder.unitID);
244 derivedUnitFacade.setAccessionNumber(dataHolder.accessionNumber);
245 derivedUnitFacade.setCollectorsNumber(dataHolder.collectorsNumber);
246
247
248
249
250
251
252 Institution institution = this.getInstitution(dataHolder.institutionCode, config, dataHolder);
253
254 Collection collection = this.getCollection(dataHolder.collectionCode, institution, config, dataHolder);
255
256 derivedUnitFacade.setCollection(collection);
257 }
258
259
260 private DerivedUnitFacade getFacade(Abcd206DataHolder dataHolder) {
261
262
263
264
265 DerivedUnitType type = null;
266
267
268 if (dataHolder.recordBasis != null){
269 if (dataHolder.recordBasis.toLowerCase().startsWith("s")) {
270 type = DerivedUnitType.Specimen;
271 }else if (dataHolder.recordBasis.toLowerCase().startsWith("o")) {
272 type = DerivedUnitType.Observation;
273 }else if (dataHolder.recordBasis.toLowerCase().startsWith("l")) {
274 type = DerivedUnitType.LivingBeing;
275 }
276 if (type == null){
277 logger.info("The basis of record does not seem to be known: " + dataHolder.recordBasis);
278 type = DerivedUnitType.DerivedUnit;
279 }
280
281 }else{
282 logger.info("The basis of record is null");
283 type = DerivedUnitType.DerivedUnit;
284 }
285 DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
286 return derivedUnitFacade;
287 }
288
289
290
291
292
293
294
295 private static NodeList getUnitsNodeList(String urlFileName){
296 NodeList unitList = null;
297 try {
298 DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
299 DocumentBuilder builder = factory.newDocumentBuilder();
300 URL url = new URL(urlFileName);
301 Object o = url.getContent();
302 InputStream is = (InputStream)o;
303 Document document = builder.parse(is);
304 Element root = document.getDocumentElement();
305 unitList = root.getElementsByTagName("Unit");
306
307 }catch(Exception e){
308 logger.warn(e);
309 }
310 return unitList;
311 }
312
313
314
315
316
317
318
319
320 private void setUnitPropertiesXML(Element root, Abcd206DataHolder dataHolder){
321 try{
322 NodeList group;
323
324
325 group = root.getChildNodes();
326
327 for (int i = 0; i < group.getLength(); i++){
328 if (group.item(i).getNodeName().equals("Identifications")){
329 group = group.item(i).getChildNodes();
330 break;
331 }
332 }
333 dataHolder.identificationList = new ArrayList<String>();
334 dataHolder.atomisedIdentificationList = new ArrayList<HashMap<String, String>>();
335 dataHolder.referenceList = new ArrayList<String>();
336 dataHolder.multimediaObjects = new ArrayList<String>();
337
338 this.getScientificNames(group, dataHolder);
339
340
341 this.getIDs(root, dataHolder);
342 this.getRecordBasis(root, dataHolder);
343 this.getMultimedia(root, dataHolder);
344 this.getNumbers(root, dataHolder);
345 this.getGeolocation(root, dataHolder);
346 this.getGatheringPeople(root, dataHolder);
347
348 } catch (Exception e) {
349 logger.info("Error occured while parsing XML file"+e);
350 }
351 }
352
353 String path= "";
354 private void getHierarchie(Node node){
355 while (node != null && node.getNodeName() != "DataSets"){
356
357 path = node.getParentNode().getNodeName()+"/"+path;
358 node = node.getParentNode();
359 }
360
361 }
362
363 private void getScientificNames(NodeList group, Abcd206DataHolder dataHolder){
364 NodeList identifications,results;
365 String tmpName = null;
366 for (int j=0; j< group.getLength(); j++){
367 if(group.item(j).getNodeName().equals("Identification")){
368 dataHolder.nomenclatureCode ="";
369 identifications = group.item(j).getChildNodes();
370 for (int m=0; m<identifications.getLength();m++){
371 if(identifications.item(m).getNodeName().equals("Result")){
372 results = identifications.item(m).getChildNodes();
373 for(int k=0; k<results.getLength();k++){
374 if (results.item(k).getNodeName().equals("TaxonIdentified")){
375 tmpName=this.getScientificName(results.item(k), dataHolder);
376 }
377 }
378 }else if(identifications.item(m).getNodeName().equals("PreferredFlag")){
379 if (dataHolder.nomenclatureCode != null && dataHolder.nomenclatureCode !=""){
380 dataHolder.identificationList.add(tmpName+"_preferred_"+identifications.item(m).getTextContent()+"_code_" + dataHolder.nomenclatureCode);
381 }else{
382 dataHolder.identificationList.add(tmpName+"_preferred_"+identifications.item(m).getTextContent());
383 }
384 path=identifications.item(m).getNodeName();
385 getHierarchie(identifications.item(m));
386 dataHolder.knownABCDelements.add(path);
387 path="";
388 }else if (identifications.item(m).getNodeName().equals("References")){
389 this.getReferences(identifications.item(m), dataHolder);
390 }
391 }
392 }
393 }
394 boolean hasPref=false;
395 for (int j=0; j< group.getLength(); j++){
396 if(group.item(j).getNodeName().equals("Identification")){
397 dataHolder.nomenclatureCode ="";
398 identifications = group.item(j).getChildNodes();
399 for (int m=0; m<identifications.getLength();m++){
400 if(identifications.item(m).getNodeName().equals("Result")){
401 results = identifications.item(m).getChildNodes();
402 for(int k=0; k<results.getLength();k++){
403 if (results.item(k).getNodeName().equals("TaxonIdentified")){
404 tmpName=this.getScientificName(results.item(k), dataHolder);
405 }
406 }
407 }
408 if(identifications.item(m).getNodeName().equals("PreferredFlag")){
409 hasPref=true;
410 }
411 }
412 if ( !hasPref && tmpName != null){
413 if (dataHolder.nomenclatureCode != null && dataHolder.nomenclatureCode !=""){
414 dataHolder.identificationList.add(tmpName+"_preferred_"+"0"+"_code_" + dataHolder.nomenclatureCode);
415 } else {
416 dataHolder.identificationList.add(tmpName+"_preferred_"+"0");
417 }
418 }
419 }
420 }
421 }
422
423
424
425 private void getReferences(Node result, Abcd206DataHolder dataHolder){
426 NodeList results,reference;
427 results = result.getChildNodes();
428 for(int k=0; k<results.getLength();k++){
429 if (results.item(k).getNodeName().equals("Reference")){
430 reference = results.item(k).getChildNodes();
431 for(int l=0;l<reference.getLength();l++){
432 if (reference.item(l).getNodeName().equals("TitleCitation")){
433 path = reference.item(l).getNodeName();
434 dataHolder.referenceList.add(reference.item(l).getTextContent());
435 getHierarchie(reference.item(l));
436 dataHolder.knownABCDelements.add(path);
437 path="";
438 }
439 }
440 }
441 }
442 }
443
444 private String getScientificName(Node result, Abcd206DataHolder dataHolder){
445 NodeList taxonsIdentified, scnames, atomised;
446 String tmpName = "";
447 dataHolder.atomisedStr = "";
448 taxonsIdentified = result.getChildNodes();
449 for (int l=0; l<taxonsIdentified.getLength(); l++){
450 if (taxonsIdentified.item(l).getNodeName().equals("ScientificName")){
451 scnames = taxonsIdentified.item(l).getChildNodes();
452 for (int n=0;n<scnames.getLength();n++){
453 if (scnames.item(n).getNodeName().equals("FullScientificNameString")){
454 path=scnames.item(n).getNodeName();
455 tmpName = scnames.item(n).getTextContent();
456 getHierarchie(scnames.item(n));
457 dataHolder.knownABCDelements.add(path);
458 path="";
459 }
460 if (scnames.item(n).getNodeName().equals("NameAtomised")){
461 try {
462 if (scnames.item(n).hasChildNodes()){
463 dataHolder.nomenclatureCode = scnames.item(n).getChildNodes().item(1).getNodeName();
464 }
465 } catch (Exception e) {
466 dataHolder.nomenclatureCode ="";
467 }
468 atomised = scnames.item(n).getChildNodes().item(1).getChildNodes();
469 dataHolder.atomisedIdentificationList.add(this.getAtomisedNames(dataHolder.nomenclatureCode, atomised, dataHolder));
470 }
471 }
472 }
473 }
474 return tmpName;
475 }
476
477 private HashMap<String,String> getAtomisedNames(String code, NodeList atomised, Abcd206DataHolder dataHolder){
478 if (code.equals("Botanical")){
479 return this.getAtomisedBotanical(atomised, dataHolder);
480 }
481 if (code.equals("Bacterial")){
482 return this.getAtomisedBacterial(atomised, dataHolder);
483 }
484 if (code.equals("NameViral")){
485 return this.getAtomisedViral(atomised, dataHolder);
486 }
487 if (code.equals("NameZoological")){
488 return this.getAtomisedZoological(atomised,dataHolder);
489 }
490 return new HashMap<String,String>();
491 }
492
493 private HashMap<String,String> getAtomisedZoological(NodeList atomised, Abcd206DataHolder dataHolder){
494 HashMap<String,String> atomisedMap = new HashMap<String,String>();
495 for (int i=0;i<atomised.getLength();i++){
496 if(atomised.item(i).getNodeName().equals("GenusOrMonomial")){
497 atomisedMap.put("Genus",atomised.item(i).getTextContent());
498 path=atomised.item(i).getNodeName();
499 getHierarchie(atomised.item(i));
500 dataHolder.knownABCDelements.add(path);
501 path="";
502 }
503 if(atomised.item(i).getNodeName().equals("Subgenus")){
504 atomisedMap.put("Subgenus",atomised.item(i).getTextContent());
505 path=atomised.item(i).getNodeName();
506 getHierarchie(atomised.item(i));
507 dataHolder.knownABCDelements.add(path);
508 path="";
509 }
510 if(atomised.item(i).getNodeName().equals("SpeciesEpithet")){
511 atomisedMap.put("SpeciesEpithet",atomised.item(i).getTextContent());
512 path=atomised.item(i).getNodeName();
513 getHierarchie(atomised.item(i));
514 dataHolder.knownABCDelements.add(path);
515 path="";
516 }
517 if(atomised.item(i).getNodeName().equals("SubspeciesEpithet")){
518 atomisedMap.put("SubspeciesEpithet",atomised.item(i).getTextContent());
519 path=atomised.item(i).getNodeName();
520 getHierarchie(atomised.item(i));
521 dataHolder.knownABCDelements.add(path);
522 path="";
523 }
524 if(atomised.item(i).getNodeName().equals("AuthorTeamOriginalAndYear")){
525 atomisedMap.put("AuthorTeamOriginalAndYear",atomised.item(i).getTextContent());
526 path=atomised.item(i).getNodeName();
527 getHierarchie(atomised.item(i));
528 dataHolder.knownABCDelements.add(path);
529 path="";
530 }
531 if(atomised.item(i).getNodeName().equals("AuthorTeamParenthesisAndYear")){
532 atomisedMap.put("AuthorTeamParenthesisAndYear",atomised.item(i).getTextContent());
533 path=atomised.item(i).getNodeName();
534 getHierarchie(atomised.item(i));
535 dataHolder.knownABCDelements.add(path);
536 path="";
537 }
538 if(atomised.item(i).getNodeName().equals("CombinationAuthorTeamAndYear")){
539 atomisedMap.put("CombinationAuthorTeamAndYear",atomised.item(i).getTextContent());
540 path=atomised.item(i).getNodeName();
541 getHierarchie(atomised.item(i));
542 dataHolder.knownABCDelements.add(path);
543 path="";
544 }
545 if(atomised.item(i).getNodeName().equals("Breed")){
546 atomisedMap.put("Breed",atomised.item(i).getTextContent());
547 path=atomised.item(i).getNodeName();
548 getHierarchie(atomised.item(i));
549 dataHolder.knownABCDelements.add(path);
550 path="";
551 }
552 if(atomised.item(i).getNodeName().equals("NamedIndividual")){
553 atomisedMap.put("NamedIndividual",atomised.item(i).getTextContent());
554 path=atomised.item(i).getNodeName();
555 getHierarchie(atomised.item(i));
556 dataHolder.knownABCDelements.add(path);
557 path="";
558 }
559 }
560 return atomisedMap;
561 }
562
563 private HashMap<String,String> getAtomisedViral(NodeList atomised, Abcd206DataHolder dataHolder){
564 HashMap<String,String> atomisedMap = new HashMap<String,String>();
565 for (int i=0;i<atomised.getLength();i++){
566 if(atomised.item(i).getNodeName().equals("GenusOrMonomial")){
567 atomisedMap.put("Genus",atomised.item(i).getTextContent());
568 path=atomised.item(i).getNodeName();
569 getHierarchie(atomised.item(i));
570 dataHolder.knownABCDelements.add(path);
571 path="";
572 }
573 if(atomised.item(i).getNodeName().equals("ViralSpeciesDesignation")){
574 atomisedMap.put("ViralSpeciesDesignation", atomised.item(i).getTextContent());
575 path=atomised.item(i).getNodeName();
576 getHierarchie(atomised.item(i));
577 dataHolder.knownABCDelements.add(path);
578 path="";
579 }
580 if(atomised.item(i).getNodeName().equals("Acronym")){
581 atomisedMap.put("Acronym",atomised.item(i).getTextContent());
582 path=atomised.item(i).getNodeName();
583 getHierarchie(atomised.item(i));
584 dataHolder.knownABCDelements.add(path);
585 path="";
586 }
587 }
588 return atomisedMap;
589 }
590
591 private HashMap<String,String> getAtomisedBotanical(NodeList atomised, Abcd206DataHolder dataHolder){
592 HashMap<String,String> atomisedMap = new HashMap<String,String>();
593 for (int i=0;i<atomised.getLength();i++){
594 if(atomised.item(i).getNodeName().equals("GenusOrMonomial")){
595 atomisedMap.put("Genus",atomised.item(i).getTextContent());
596 path=atomised.item(i).getNodeName();
597 getHierarchie(atomised.item(i));
598 dataHolder.knownABCDelements.add(path);
599 path="";
600 }
601 if(atomised.item(i).getNodeName().equals("FirstEpithet")){
602 atomisedMap.put("FirstEpithet",atomised.item(i).getTextContent());
603 path=atomised.item(i).getNodeName();
604 getHierarchie(atomised.item(i));
605 dataHolder.knownABCDelements.add(path);
606 path="";
607 }
608 if(atomised.item(i).getNodeName().equals("InfraspecificEpithet")){
609 atomisedMap.put("InfraSpeEpithet", atomised.item(i).getTextContent());
610 path=atomised.item(i).getNodeName();
611 getHierarchie(atomised.item(i));
612 dataHolder.knownABCDelements.add(path);
613 path="";
614 }
615 if(atomised.item(i).getNodeName().equals("Rank")){
616 atomisedMap.put("Rank",atomised.item(i).getTextContent());
617 path=atomised.item(i).getNodeName();
618 getHierarchie(atomised.item(i));
619 dataHolder.knownABCDelements.add(path);
620 path="";
621 }
622 if(atomised.item(i).getNodeName().equals("HybridFlag")){
623 atomisedMap.put("HybridFlag",atomised.item(i).getTextContent());
624 path=atomised.item(i).getNodeName();
625 getHierarchie(atomised.item(i));
626 dataHolder.knownABCDelements.add(path);
627 path="";
628 }
629 if(atomised.item(i).getNodeName().equals("AuthorTeamParenthesis")){
630 atomisedMap.put("AuthorTeamParenthesis",atomised.item(i).getTextContent());
631 path=atomised.item(i).getNodeName();
632 getHierarchie(atomised.item(i));
633 dataHolder.knownABCDelements.add(path);
634 path="";
635 }
636 if(atomised.item(i).getNodeName().equals("AuthorTeam")){
637 atomisedMap.put("AuthorTeam",atomised.item(i).getTextContent());
638 path=atomised.item(i).getNodeName();
639 getHierarchie(atomised.item(i));
640 dataHolder.knownABCDelements.add(path);
641 path="";
642 }
643 if(atomised.item(i).getNodeName().equals("CultivarGroupName")){
644 atomisedMap.put("CultivarGroupName",atomised.item(i).getTextContent());
645 path=atomised.item(i).getNodeName();
646 getHierarchie(atomised.item(i));
647 dataHolder.knownABCDelements.add(path);
648 path="";
649 }
650 if(atomised.item(i).getNodeName().equals("CultivarName")){
651 atomisedMap.put("CultivarName",atomised.item(i).getTextContent());
652 path=atomised.item(i).getNodeName();
653 getHierarchie(atomised.item(i));
654 dataHolder.knownABCDelements.add(path);
655 path="";
656 }
657 if(atomised.item(i).getNodeName().equals("TradeDesignationNames")){
658 atomisedMap.put("Trade",atomised.item(i).getTextContent());
659 path=atomised.item(i).getNodeName();
660 getHierarchie(atomised.item(i));
661 dataHolder.knownABCDelements.add(path);
662 path="";
663 }
664 }
665 return atomisedMap;
666 }
667
668 private HashMap<String,String> getAtomisedBacterial(NodeList atomised, Abcd206DataHolder dataHolder){
669 HashMap<String,String> atomisedMap = new HashMap<String,String>();
670 for (int i=0;i<atomised.getLength();i++){
671 if(atomised.item(i).getNodeName().equals("GenusOrMonomial")){
672 atomisedMap.put("Genus",atomised.item(i).getTextContent());
673 path=atomised.item(i).getNodeName();
674 getHierarchie(atomised.item(i));
675 dataHolder.knownABCDelements.add(path);
676 path="";
677 }
678 if(atomised.item(i).getNodeName().equals("Subgenus")){
679 atomisedMap.put("SubGenus",atomised.item(i).getTextContent());
680 path=atomised.item(i).getNodeName();
681 getHierarchie(atomised.item(i));
682 dataHolder.knownABCDelements.add(path);
683 path="";
684 }
685 if(atomised.item(i).getNodeName().equals("SubgenusAuthorAndYear")){
686 atomisedMap.put("SubgenusAuthorAndYear",atomised.item(i).getTextContent());
687 path=atomised.item(i).getNodeName();
688 getHierarchie(atomised.item(i));
689 dataHolder.knownABCDelements.add(path);
690 path="";
691 }
692 if(atomised.item(i).getNodeName().equals("SpeciesEpithet")){
693 atomisedMap.put("SpeciesEpithet",atomised.item(i).getTextContent());
694 path=atomised.item(i).getNodeName();
695 getHierarchie(atomised.item(i));
696 dataHolder.knownABCDelements.add(path);
697 path="";
698 }
699 if(atomised.item(i).getNodeName().equals("SubspeciesEpithet")){
700 atomisedMap.put("SubspeciesEpithet",atomised.item(i).getTextContent());
701 path=atomised.item(i).getNodeName();
702 getHierarchie(atomised.item(i));
703 dataHolder.knownABCDelements.add(path);
704 path="";
705 }
706 if(atomised.item(i).getNodeName().equals("ParentheticalAuthorTeamAndYear")){
707 atomisedMap.put("ParentheticalAuthorTeamAndYear",atomised.item(i).getTextContent());
708 path=atomised.item(i).getNodeName();
709 getHierarchie(atomised.item(i));
710 dataHolder.knownABCDelements.add(path);
711 path="";
712 }
713 if(atomised.item(i).getNodeName().equals("AuthorTeamAndYear")){
714 atomisedMap.put("AuthorTeamAndYear",atomised.item(i).getTextContent());
715 path=atomised.item(i).getNodeName();
716 getHierarchie(atomised.item(i));
717 dataHolder.knownABCDelements.add(path);
718 path="";
719 }
720 if(atomised.item(i).getNodeName().equals("NameApprobation")){
721 atomisedMap.put("NameApprobation",atomised.item(i).getTextContent());
722 path=atomised.item(i).getNodeName();
723 getHierarchie(atomised.item(i));
724 dataHolder.knownABCDelements.add(path);
725 path="";
726 }
727 }
728 return atomisedMap;
729 }
730
731 private void getIDs(Element root, Abcd206DataHolder dataHolder){
732 NodeList group;
733 try {
734 group = root.getElementsByTagName("SourceInstitutionID");
735 path=group.item(0).getNodeName();
736 getHierarchie(group.item(0));
737 dataHolder.knownABCDelements.add(path);
738 path="";
739 dataHolder.institutionCode = group.item(0).getTextContent();
740 } catch (NullPointerException e) {
741 dataHolder.institutionCode= "";
742 }
743 try {
744 group = root.getElementsByTagName("SourceID");
745 path=group.item(0).getNodeName();
746 getHierarchie(group.item(0));
747 dataHolder.knownABCDelements.add(path);
748 path="";
749 dataHolder.collectionCode = group.item(0).getTextContent();
750 } catch (NullPointerException e) {
751 dataHolder.collectionCode = "";
752 }
753 try {
754 group = root.getElementsByTagName("UnitID");
755 path=group.item(0).getNodeName();
756 getHierarchie(group.item(0));
757 dataHolder.knownABCDelements.add(path);
758 path="";
759 dataHolder.unitID = group.item(0).getTextContent();
760 } catch (NullPointerException e) {
761 dataHolder.unitID = "";
762 }
763 }
764
765 private void getRecordBasis(Element root, Abcd206DataHolder dataHolder){
766 NodeList group;
767 try {
768 group = root.getElementsByTagName("RecordBasis");
769 path=group.item(0).getNodeName();
770 getHierarchie(group.item(0));
771 dataHolder.knownABCDelements.add(path);
772 path="";
773 dataHolder.recordBasis = group.item(0).getTextContent();
774 } catch (NullPointerException e) {
775 dataHolder.recordBasis = "";
776 }
777 }
778
779 private void getMultimedia(Element root, Abcd206DataHolder dataHolder){
780 NodeList group, multimedias, multimedia;
781 try {
782 group = root.getElementsByTagName("MultiMediaObjects");
783 for(int i=0;i<group.getLength();i++){
784 multimedias = group.item(i).getChildNodes();
785 for (int j=0;j<multimedias.getLength();j++){
786 if (multimedias.item(j).getNodeName().equals("MultiMediaObject")){
787 multimedia = multimedias.item(j).getChildNodes();
788 for (int k=0;k<multimedia.getLength();k++){
789 if(multimedia.item(k).getNodeName().equals("FileURI")){
790 dataHolder.multimediaObjects.add(multimedia.item(k).getTextContent());
791 path = multimedia.item(k).getNodeName();
792 getHierarchie(multimedia.item(k));
793 dataHolder.knownABCDelements.add(path);
794 path="";
795 }
796 }
797 }
798 }
799 }
800 } catch (NullPointerException e) {
801 logger.info(e);
802 }
803 }
804
805 private void getNumbers(Element root, Abcd206DataHolder dataHolder){
806 NodeList group;
807 try {
808 group = root.getElementsByTagName("AccessionNumber");
809 path=group.item(0).getNodeName();
810 getHierarchie(group.item(0));
811 dataHolder.knownABCDelements.add(path);
812 path="";
813 dataHolder.accessionNumber = group.item(0).getTextContent();
814 } catch (NullPointerException e) {
815 dataHolder.accessionNumber = "";
816 }
817 try {
818 group = root.getElementsByTagName("CollectorsFieldNumber");
819 path=group.item(0).getNodeName();
820 getHierarchie(group.item(0));
821 dataHolder.knownABCDelements.add(path);
822 path="";
823 dataHolder.fieldNumber = group.item(0).getTextContent();
824 } catch (NullPointerException e) {
825 dataHolder.fieldNumber = "";
826 }
827
828 try {
829 group = root.getElementsByTagName("CollectorsNumber");
830 path=group.item(0).getNodeName();
831 getHierarchie(group.item(0));
832 dataHolder.knownABCDelements.add(path);
833 path="";
834 dataHolder.collectorsNumber = group.item(0).getTextContent();
835 } catch (NullPointerException e) {
836 dataHolder.collectorsNumber = "";
837 }
838
839 try {
840 group = root.getElementsByTagName("AccessionNumber");
841 path=group.item(0).getNodeName();
842 getHierarchie(group.item(0));
843 dataHolder.knownABCDelements.add(path);
844 path="";
845 dataHolder.accessionNumber = group.item(0).getTextContent();
846 } catch (NullPointerException e) {
847 dataHolder.accessionNumber = "";
848 }
849 }
850
851 private void getGeolocation(Element root, Abcd206DataHolder dataHolder){
852 NodeList group, childs;
853 try {
854 group = root.getElementsByTagName("LocalityText");
855 path=group.item(0).getNodeName();
856 getHierarchie(group.item(0));
857 dataHolder.knownABCDelements.add(path);
858 path="";
859 dataHolder.locality = group.item(0).getTextContent();
860 if (group.item(0).hasAttributes())
861 if (group.item(0).getAttributes().getNamedItem("lang") != null)
862 dataHolder.languageIso = group.item(0).getAttributes().getNamedItem("lang").getTextContent();
863 } catch (NullPointerException e) {
864 dataHolder.locality = "";
865 }
866 try {
867 group = root.getElementsByTagName("LongitudeDecimal");
868 path=group.item(0).getNodeName();
869 getHierarchie(group.item(0));
870 dataHolder.knownABCDelements.add(path);
871 path="";
872 dataHolder.longitude = Double.valueOf(group.item(0).getTextContent());
873 } catch (NullPointerException e) {
874 dataHolder.longitude=0.0;
875 }
876 try {
877 group = root.getElementsByTagName("LatitudeDecimal");
878 path=group.item(0).getNodeName();
879 getHierarchie(group.item(0));
880 dataHolder.knownABCDelements.add(path);
881 path="";
882 dataHolder.latitude = Double.valueOf(group.item(0).getTextContent());
883 } catch (NullPointerException e) {
884 dataHolder.latitude=0.0;
885 }
886 try {
887 group = root.getElementsByTagName("Country");
888 childs = group.item(0).getChildNodes();
889 for (int i=0;i<childs.getLength(); i++){
890 if(childs.item(i).getNodeName() == "Name"){
891 path=childs.item(i).getNodeName();
892 getHierarchie(childs.item(i));
893 dataHolder.knownABCDelements.add(path);
894 path="";
895 dataHolder.country = childs.item(i).getTextContent();
896 }
897 }
898 } catch (NullPointerException e) {
899 dataHolder.country = "";
900 }
901 try {
902 group = root.getElementsByTagName("Country");
903 childs = group.item(0).getChildNodes();
904 for (int i=0;i<childs.getLength(); i++){
905 if(childs.item(i).getNodeName() == "ISO3166Code"){
906 path=childs.item(i).getNodeName();
907 getHierarchie(childs.item(i));
908 dataHolder.knownABCDelements.add(path);
909 path="";
910 dataHolder.isocountry = childs.item(i).getTextContent();
911 }
912 }
913 } catch (NullPointerException e) {
914 dataHolder.isocountry = "";
915 }
916 try {
917 group = root.getElementsByTagName("Altitude");
918 for (int i=0;i<group.getLength();i++){
919 childs = group.item(i).getChildNodes();
920 for (int j=0;j<childs.getLength();j++){
921 if (childs.item(j).getNodeName().equals("MeasurementOrFactText")){
922 path=childs.item(j).getNodeName();
923 getHierarchie(childs.item(j));
924 dataHolder.knownABCDelements.add(path);
925 path="";
926 dataHolder.altitude = Integer.valueOf(childs.item(j).getTextContent());
927 }
928 }
929 }
930 } catch (NullPointerException e) {
931 dataHolder.altitude = -9999;
932 }
933
934 try {
935 group = root.getElementsByTagName("Depth");
936 path=group.item(0).getNodeName();
937 getHierarchie(group.item(0));
938 dataHolder.knownABCDelements.add(path);
939 path="";
940 dataHolder.depth = Integer.valueOf(group.item(0).getTextContent());
941 } catch (NullPointerException e) {
942 dataHolder.depth = -9999;
943 }
944
945 try{
946 group = root.getElementsByTagName("NamedArea");
947 dataHolder.namedAreaList = new ArrayList<String>();
948 for (int i=0;i<group.getLength();i++){
949 childs = group.item(i).getChildNodes();
950 for (int j=0; j<childs.getLength();j++){
951 if (childs.item(j).getNodeName().equals("AreaName")){
952 path = childs.item(j).getNodeName();
953 getHierarchie(childs.item(j));
954 dataHolder.knownABCDelements.add(path);
955 path="";
956 dataHolder.namedAreaList.add(childs.item(j).getTextContent());
957 }
958 }
959 }
960 }catch(NullPointerException e){
961 dataHolder.namedAreaList = new ArrayList<String>();
962 }
963 }
964
965 private void getGatheringPeople(Element root, Abcd206DataHolder dataHolder){
966 NodeList group, childs, person;
967 try {
968 group = root.getElementsByTagName("GatheringAgent");
969 dataHolder.gatheringAgentList = new ArrayList<String>();
970 for (int i=0; i< group.getLength(); i++){
971 childs = group.item(i).getChildNodes();
972 for (int j=0; j<childs.getLength();j++){
973 if (childs.item(j).getNodeName().equals("Person")){
974 person = childs.item(j).getChildNodes();
975 for (int k=0; k<person.getLength(); k++){
976 if (person.item(k).getNodeName().equals("FullName")){
977 path=person.item(k).getNodeName();
978 getHierarchie(person.item(k));
979 dataHolder.knownABCDelements.add(path);
980 path="";
981 dataHolder.gatheringAgentList.add(person.item(k).getTextContent());
982 }
983 }
984 }
985
986 }
987 }
988 } catch (NullPointerException e) {
989 dataHolder.gatheringAgentList = new ArrayList<String>();
990 }
991 }
992
993 private Institution getInstitution(String institutionCode, Abcd206ImportConfigurator config, Abcd206DataHolder dataHolder){
994 Institution institution;
995 List<Institution> institutions;
996 try{
997 logger.info(dataHolder.institutionCode);
998 institutions = getAgentService().searchInstitutionByCode(dataHolder.institutionCode);
999 }catch(Exception e){
1000 institutions=new ArrayList<Institution>();
1001 }
1002 if (institutions.size() ==0 || !config.isReUseExistingMetadata()){
1003 logger.info("Institution (agent) unknown or not allowed to reuse existing metadata");
1004
1005 institution = Institution.NewInstance();
1006 institution.setCode(dataHolder.institutionCode);
1007 }
1008 else{
1009 logger.info("Institution (agent) already in the db");
1010 institution = institutions.get(0);
1011 }
1012 return institution;
1013 }
1014
1015
1016
1017
1018
1019
1020
1021
1022 private Collection getCollection(String collectionCode, Institution institution, Abcd206ImportConfigurator config, Abcd206DataHolder dataHolder){
1023 Collection collection = Collection.NewInstance();
1024 List<Collection> collections;
1025 try{
1026 collections = getCollectionService().searchByCode(dataHolder.collectionCode);
1027 }catch(Exception e){
1028 collections=new ArrayList<Collection>();
1029 }
1030 if (collections.size() ==0 || !config.isReUseExistingMetadata()){
1031 logger.info("Collection not found or do not reuse existing metadata " + dataHolder.collectionCode);
1032
1033 collection.setCode(dataHolder.collectionCode);
1034 collection.setCodeStandard("GBIF");
1035 collection.setInstitute(institution);
1036 }
1037 else{
1038 boolean collectionFound=false;
1039 for (int i=0; i<collections.size(); i++){
1040 collection = collections.get(i);
1041 try {
1042 if (collection.getInstitute().getCode().equalsIgnoreCase(institution.getCode())){
1043
1044 collectionFound=true;
1045 }
1046 } catch (NullPointerException e) {}
1047 }
1048 if (!collectionFound){
1049 collection.setCode(dataHolder.collectionCode);
1050 collection.setCodeStandard("GBIF");
1051 collection.setInstitute(institution);
1052 }
1053
1054 }
1055 return collection;
1056 }
1057
1058
1059
1060
1061
1062
1063
1064 private void handleIdentifications(Abcd206ImportConfigurator config, DerivedUnitFacade facade, ReferenceBase sec, Abcd206DataHolder dataHolder){
1065 NonViralName<?> taxonName = null;
1066 String fullScientificNameString;
1067 Taxon taxon = null;
1068 DeterminationEvent determinationEvent = null;
1069 List<TaxonBase> names = null;
1070
1071 String scientificName="";
1072 boolean preferredFlag=false;
1073
1074 for (int i = 0; i < dataHolder.identificationList.size(); i++) {
1075 fullScientificNameString = dataHolder.identificationList.get(i);
1076 fullScientificNameString = fullScientificNameString.replaceAll(" et ", " & ");
1077 if (fullScientificNameString.indexOf("_preferred_") != -1){
1078 scientificName = fullScientificNameString.split("_preferred_")[0];
1079 String pTmp = fullScientificNameString.split("_preferred_")[1].split("_code_")[0];
1080 if (pTmp.equals("1") || pTmp.toLowerCase().indexOf("true") != -1){
1081 preferredFlag=true;
1082 } else {
1083 preferredFlag=false;
1084 }
1085 }
1086 else{
1087 scientificName = fullScientificNameString;
1088 }
1089 logger.info(fullScientificNameString);
1090 if (fullScientificNameString.indexOf("_code_") != -1){
1091 dataHolder.nomenclatureCode = fullScientificNameString.split("_code_")[1];
1092 }
1093 if (config.isDoAutomaticParsing() || dataHolder.atomisedIdentificationList == null || dataHolder.atomisedIdentificationList.size()==0){
1094 taxonName = this.parseScientificName(scientificName, dataHolder);
1095 } else {
1096 if (dataHolder.atomisedIdentificationList != null || dataHolder.atomisedIdentificationList.size()>0){
1097 taxonName = this.setTaxonNameByType(dataHolder.atomisedIdentificationList.get(i), scientificName, dataHolder);
1098 }
1099 }
1100 if(taxonName == null){
1101 taxonName = NonViralName.NewInstance(null);
1102 taxonName.setFullTitleCache(scientificName);
1103 }
1104
1105
1106
1107 if (config.isDoMatchTaxa()){
1108 taxon = getTaxonService().findBestMatchingTaxon(scientificName);
1109 }
1110 if (taxon == null && config.isDoReUseTaxon()){
1111 try{
1112 names = getTaxonService().searchTaxaByName(scientificName, sec);
1113 taxon = (Taxon)names.get(0);
1114 } catch(Exception e){
1115 taxon=null;
1116 }
1117 } else {
1118 logger.info("Matching to existing Taxon : " + taxon.getTitleCache());
1119 }
1120
1121 if (!config.isDoReUseTaxon() || taxon == null){
1122 getNameService().save(taxonName);
1123 taxon = Taxon.NewInstance(taxonName, sec);
1124 }
1125
1126
1127
1128
1129
1130
1131 determinationEvent = DeterminationEvent.NewInstance();
1132 determinationEvent.setTaxon(taxon);
1133 determinationEvent.setPreferredFlag(preferredFlag);
1134
1135 for (String strReference : dataHolder.referenceList){
1136
1137 ReferenceBase reference = ReferenceFactory.newGeneric();
1138 reference.setTitleCache(strReference, true);
1139 determinationEvent.addReference(reference);
1140 }
1141 facade.addDetermination(determinationEvent);
1142
1143 if(config.isDoCreateIndividualsAssociations()){
1144 TaxonDescription taxonDescription = null;
1145 if(config.isDoMatchToExistingDescription()){
1146 logger.error("The import option 'DoMatchToExistingDescription' is not yet implemented.");
1147 } else {
1148 UUID taxonDescriptionUUID = config.getTaxonToDescriptionMap().get(taxon.getUuid());
1149 taxonDescription = (TaxonDescription) getDescriptionService().load(taxonDescriptionUUID);
1150 if(taxonDescription == null){
1151 taxonDescription = TaxonDescription.NewInstance(taxon);
1152 config.getTaxonToDescriptionMap().put(taxon.getUuid(), taxonDescription.getUuid());
1153 if(taxonDescriptionUUID == null){
1154 logger.info("Creating new TaxonDescription for " + taxon.getTitleCache());
1155 } else {
1156 logger.fatal("TaxonDescription with UUID " + taxonDescriptionUUID + " not found --> creating a new one.");
1157 }
1158 }
1159 }
1160 IndividualsAssociation individualsAssociation = IndividualsAssociation.NewInstance();
1161 individualsAssociation.setAssociatedSpecimenOrObservation(facade.getDerivedUnit());
1162 individualsAssociation.setFeature(Feature.INDIVIDUALS_ASSOCIATION());
1163 for(ReferenceBase citation : determinationEvent.getReferences()){
1164 individualsAssociation.addSource(DescriptionElementSource.NewInstance(null, null, citation, null));
1165 }
1166 taxonDescription.addElement(individualsAssociation);
1167 getDescriptionService().saveOrUpdate(taxonDescription);
1168 }
1169 }
1170
1171 }
1172
1173 private NonViralName<?> parseScientificName(String scientificName, Abcd206DataHolder dataHolder){
1174 NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
1175 NonViralName<?>taxonName = null;
1176 boolean problem=false;
1177
1178 if (dataHolder.nomenclatureCode.toString().equals("Zoological")){
1179 taxonName = (ZoologicalName)nvnpi.parseFullName(scientificName,NomenclaturalCode.ICZN,null);
1180 if (taxonName.hasProblem()){
1181 problem=true;
1182 }
1183 }
1184 if (dataHolder.nomenclatureCode.toString().equals("Botanical")){
1185 taxonName = (BotanicalName)nvnpi.parseFullName(scientificName,NomenclaturalCode.ICBN,null);
1186 if (taxonName.hasProblem()){
1187 problem=true;;
1188 }
1189 }
1190 if (dataHolder.nomenclatureCode.toString().equals("Bacterial")){
1191 taxonName = (BacterialName)nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNB, null);
1192 if (taxonName.hasProblem()){
1193 problem=true;
1194 }
1195 }
1196 if (dataHolder.nomenclatureCode.toString().equals("Cultivar")){
1197 taxonName = (CultivarPlantName)nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNCP, null);
1198 if (taxonName.hasProblem()){
1199 problem=true;
1200 }
1201 }
1202
1203
1204
1205
1206
1207
1208 if(problem){
1209 taxonName = NonViralName.NewInstance(null);
1210 taxonName.setTitleCache(scientificName, true);
1211 }
1212 return taxonName;
1213
1214 }
1215
1216 private NonViralName<?> setTaxonNameByType(HashMap<String, String> atomisedMap,String fullName, Abcd206DataHolder dataHolder){
1217 if (dataHolder.nomenclatureCode.equals("Zoological")){
1218 NonViralName<ZoologicalName> taxonName = ZoologicalName.NewInstance(null);
1219 taxonName.setFullTitleCache(fullName, true);
1220 taxonName.setGenusOrUninomial(getFromMap(atomisedMap,"Genus"));
1221 taxonName.setInfraGenericEpithet(getFromMap(atomisedMap,"SubGenus"));
1222 taxonName.setSpecificEpithet(getFromMap(atomisedMap,"SpeciesEpithet"));
1223 taxonName.setInfraSpecificEpithet(getFromMap(atomisedMap,"SubspeciesEpithet"));
1224 Team team = null;
1225 if(getFromMap(atomisedMap,"AuthorTeamParenthesis") != null){
1226 team = Team.NewInstance();
1227 team.setTitleCache(getFromMap(atomisedMap,"AuthorTeamParenthesis"), true);
1228 }else{
1229 if (getFromMap(atomisedMap,"AuthorTeamAndYear") != null){
1230 team = Team.NewInstance();
1231 team.setTitleCache(getFromMap(atomisedMap,"AuthorTeamAndYear"), true);
1232 }
1233 }
1234 if(team != null){
1235 taxonName.setBasionymAuthorTeam(team);
1236 }else{
1237 if(getFromMap(atomisedMap,"AuthorTeamParenthesis") != null){
1238 taxonName.setAuthorshipCache(getFromMap(atomisedMap,"AuthorTeamParenthesis"));
1239 } else if (getFromMap(atomisedMap,"AuthorTeamAndYear") != null){
1240 taxonName.setAuthorshipCache(getFromMap(atomisedMap,"AuthorTeamAndYear"));
1241 }
1242 }
1243 if(getFromMap(atomisedMap,"CombinationAuthorTeamAndYear") != null){
1244 team = Team.NewInstance();
1245 team.setTitleCache(getFromMap(atomisedMap,"CombinationAuthorTeamAndYear"), true);
1246 taxonName.setCombinationAuthorTeam(team);
1247 }
1248 if (taxonName.hasProblem()){
1249 logger.info("pb ICZN");
1250 }else{
1251 return taxonName;
1252 }
1253 }
1254 if (dataHolder.nomenclatureCode.equals("Botanical")){
1255 NonViralName<BotanicalName> taxonName = BotanicalName.NewInstance(null);
1256 taxonName.setFullTitleCache(fullName, true);
1257 taxonName.setGenusOrUninomial(getFromMap(atomisedMap,"Genus"));
1258 taxonName.setInfraGenericEpithet(getFromMap(atomisedMap,"FirstEpithet"));
1259 taxonName.setInfraSpecificEpithet(getFromMap(atomisedMap,"InfraSpeEpithet"));
1260 try{taxonName.setRank(Rank.getRankByName(getFromMap(atomisedMap,"Rank")));
1261 }catch(Exception e){}
1262 Team team = null;
1263 if(getFromMap(atomisedMap,"AuthorTeamParenthesis") != null){
1264 team = Team.NewInstance();
1265 team.setTitleCache(getFromMap(atomisedMap,"AuthorTeamParenthesis"), true);
1266 if(team != null){
1267 taxonName.setBasionymAuthorTeam(team);
1268 }
1269 }
1270 if (getFromMap(atomisedMap,"AuthorTeam") != null){
1271 team = Team.NewInstance();
1272 team.setTitleCache(getFromMap(atomisedMap,"AuthorTeam"), true);
1273 if(team != null){
1274 taxonName.setCombinationAuthorTeam(team);
1275 }
1276 }
1277 if (team == null) {
1278 if(getFromMap(atomisedMap,"AuthorTeamParenthesis") != null){
1279 taxonName.setAuthorshipCache(getFromMap(atomisedMap,"AuthorTeamParenthesis"));
1280 }else if (getFromMap(atomisedMap,"AuthorTeam") != null){
1281 taxonName.setAuthorshipCache(getFromMap(atomisedMap,"AuthorTeam"));
1282 }
1283 }
1284 if(getFromMap(atomisedMap,"CombinationAuthorTeamAndYear") != null){
1285 team = Team.NewInstance();
1286 team.setTitleCache(getFromMap(atomisedMap,"CombinationAuthorTeamAndYear"), true);
1287 taxonName.setCombinationAuthorTeam(team);
1288 }
1289 if (taxonName.hasProblem()){
1290 logger.info("pb ICBN");
1291 }else {
1292 return taxonName;
1293 }
1294 }
1295 if (dataHolder.nomenclatureCode.equals("Bacterial")){
1296 NonViralName<BacterialName> taxonName = BacterialName.NewInstance(null);
1297 taxonName.setFullTitleCache(fullName, true);
1298 taxonName.setGenusOrUninomial(getFromMap(atomisedMap,"Genus"));
1299 taxonName.setInfraGenericEpithet(getFromMap(atomisedMap,"SubGenus"));
1300 taxonName.setSpecificEpithet(getFromMap(atomisedMap,"Species"));
1301 taxonName.setInfraSpecificEpithet(getFromMap(atomisedMap,"SubspeciesEpithet"));
1302 if(getFromMap(atomisedMap,"AuthorTeamAndYear") != null){
1303 Team team = Team.NewInstance();
1304 team.setTitleCache(getFromMap(atomisedMap,"AuthorTeamAndYear"), true);
1305 taxonName.setCombinationAuthorTeam(team);
1306 }
1307 if(getFromMap(atomisedMap,"ParentheticalAuthorTeamAndYear") != null){
1308 Team team = Team.NewInstance();
1309 team.setTitleCache(getFromMap(atomisedMap,"ParentheticalAuthorTeamAndYear"), true);
1310 taxonName.setBasionymAuthorTeam(team);
1311 }
1312 if (taxonName.hasProblem()){
1313 logger.info("pb ICNB");
1314 }else{
1315 return taxonName;
1316 }
1317 }
1318 if (dataHolder.nomenclatureCode.equals("Cultivar")){
1319 CultivarPlantName taxonName = CultivarPlantName.NewInstance(null);
1320
1321 if (taxonName.hasProblem()){
1322 logger.info("pb ICNCP");
1323 }else {
1324 return taxonName;
1325 }
1326 }
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336 NonViralName<?>taxonName = NonViralName.NewInstance(null);
1337 taxonName.setFullTitleCache(fullName, true);
1338 return taxonName;
1339 }
1340
1341 private String getFromMap(HashMap<String, String> atomisedMap, String key){
1342 String value = null;
1343 if (atomisedMap.containsKey(key)){
1344 value = atomisedMap.get(key);
1345 }
1346 try{
1347 if (value != null && key.matches(".*Year.*")){
1348 value=value.trim();
1349 if (value.matches("[a-z A-Z ]*[0-9]{4}$")){
1350 String tmp=value.split("[0-9]{4}$")[0];
1351 int year = Integer.parseInt(value.split(tmp)[1]);
1352 if (year >= 1752){
1353 value=tmp;
1354 }else{
1355 value=null;
1356 }
1357 }else{
1358 value=null;
1359 }
1360 }
1361 }catch(Exception e){value=null;}
1362
1363 return value;
1364 }
1365
1366 private void compareABCDtoCDM(String urlFileName, ArrayList<String> knownElts, Abcd206DataHolder dataHolder){
1367
1368 try {
1369 DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
1370 DocumentBuilder constructeur = factory.newDocumentBuilder();
1371 URL url = new URL(urlFileName);
1372 Object o = url.getContent();
1373 InputStream is = (InputStream)o;
1374 Document document = constructeur.parse(is);
1375 Element root = document.getDocumentElement();
1376 traverse(root, dataHolder);
1377 } catch (ParserConfigurationException e) {
1378 e.printStackTrace();
1379 } catch (SAXException e) {
1380 e.printStackTrace();
1381 } catch (IOException e) {
1382 e.printStackTrace();
1383 }
1384 Set<String> elts = dataHolder.allABCDelements.keySet();
1385 Iterator< String>it = elts.iterator();
1386 String elt;
1387 while (it.hasNext()){
1388 elt = it.next();
1389 if (knownElts.indexOf(elt) == -1){
1390 logger.info("Unsaved ABCD element: " + elt + " - " + dataHolder.allABCDelements.get(elt));
1391 }
1392 }
1393 }
1394
1395
1396
1397
1398
1399
1400
1401
1402 private void traverse(Node node, Abcd206DataHolder dataHolder){
1403
1404 String test = node.getTextContent();
1405
1406
1407 if(test != null && test != "#text" && node.getNodeName() != "#text" && test.split("\n").length==1 && test.length()>0){
1408 path=node.getNodeName();
1409 getHierarchie(node);
1410 dataHolder.allABCDelements.put(path,test);
1411 path="";
1412 }
1413
1414 if (node.hasChildNodes()) {
1415
1416 NodeList nl = node.getChildNodes();
1417
1418 int size = nl.getLength();
1419 for (int i=0; i<size; i++){
1420
1421 traverse (nl.item(i), dataHolder);
1422 }
1423 }
1424 }
1425
1426
1427
1428 @Override
1429 protected boolean isIgnore(Abcd206ImportState state) {
1430
1431 return false;
1432 }
1433
1434
1435
1436 }