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10 package eu.etaxonomy.cdm.io.tcsxml.in;
11
12 import java.util.ArrayList;
13 import java.util.Collection;
14 import java.util.List;
15 import java.util.Map;
16
17 import org.apache.log4j.Logger;
18 import org.jdom.Element;
19 import org.jdom.Namespace;
20 import org.springframework.stereotype.Component;
21
22 import eu.etaxonomy.cdm.common.ResultWrapper;
23 import eu.etaxonomy.cdm.common.XmlHelp;
24 import eu.etaxonomy.cdm.io.common.ICdmIO;
25 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
26 import eu.etaxonomy.cdm.io.common.ImportHelper;
27 import eu.etaxonomy.cdm.io.common.MapWrapper;
28 import eu.etaxonomy.cdm.io.tcsxml.TcsXmlTransformer;
29 import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;
30 import eu.etaxonomy.cdm.model.agent.Person;
31 import eu.etaxonomy.cdm.model.agent.Team;
32 import eu.etaxonomy.cdm.model.common.CdmBase;
33 import eu.etaxonomy.cdm.model.name.CultivarPlantName;
34 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
35 import eu.etaxonomy.cdm.model.name.NonViralName;
36 import eu.etaxonomy.cdm.model.name.Rank;
37 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
38 import eu.etaxonomy.cdm.model.name.ZoologicalName;
39 import eu.etaxonomy.cdm.model.reference.IGeneric;
40 import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
41 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
42 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
43
44 @Component("tcsXmlTaxonNameIO")
45 public class TcsXmlTaxonNameImport extends TcsXmlImportBase implements ICdmIO<TcsXmlImportState> {
46 private static final Logger logger = Logger.getLogger(TcsXmlTaxonNameImport.class);
47
48 private static int modCount = 5000;
49
50 public TcsXmlTaxonNameImport(){
51 super();
52 }
53
54 @Override
55 public boolean doCheck(TcsXmlImportState state){
56 boolean result = true;
57 logger.warn("BasionymRelations not yet implemented");
58 logger.warn("Checking for TaxonNames not yet implemented");
59
60
61
62 return result;
63 }
64
65
66 @Override
67 public boolean doInvoke(TcsXmlImportState state){
68
69 logger.info("start make TaxonNames ...");
70 MapWrapper<Person> authorMap = (MapWrapper<Person>)state.getStore(ICdmIO.TEAM_STORE);
71 MapWrapper<TaxonNameBase> taxonNameMap = (MapWrapper<TaxonNameBase>)state.getStore(ICdmIO.TAXONNAME_STORE);
72 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)state.getStore(ICdmIO.REFERENCE_STORE);
73
74 ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true);
75 String childName;
76 boolean obligatory;
77 String idNamespace = "TaxonName";
78
79 TcsXmlImportConfigurator config = state.getConfig();
80 Element elDataSet = getDataSetElement(config);
81 Namespace tcsNamespace = config.getTcsXmlNamespace();
82
83 childName = "TaxonNames";
84 obligatory = false;
85 Element elTaxonNames = XmlHelp.getSingleChildElement(success, elDataSet, childName, tcsNamespace, obligatory);
86
87 String tcsElementName = "TaxonName";
88 List<Element> elTaxonNameList = (List<Element>)elTaxonNames.getChildren(tcsElementName, tcsNamespace);
89
90 int i = 0;
91
92 for (Element elTaxonName : elTaxonNameList){
93 if ((++i % modCount) == 0){ logger.info("Names handled: " + (i-1));}
94 List<String> elementList = new ArrayList<String>();
95
96
97 String strId = elTaxonName.getAttributeValue("id");
98 String strNomenclaturalCode = elTaxonName.getAttributeValue("nomenclaturalCode");
99
100 childName = "Rank";
101 obligatory = false;
102 Element elRank = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
103 Rank rank = makeRank(elRank);
104 elementList.add(childName.toString());
105
106
107 try {
108 TaxonNameBase<?,?> nameBase;
109 NomenclaturalCode nomCode = TcsXmlTransformer.nomCodeString2NomCode(strNomenclaturalCode);
110 if (nomCode != null){
111 nameBase = nomCode.getNewTaxonNameInstance(rank);
112 }else{
113 nameBase = NonViralName.NewInstance(rank);
114 }
115 childName = "Simple";
116 obligatory = true;
117 Element elSimple = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
118 String simple = (elSimple == null)? "" : elSimple.getTextNormalize();
119 nameBase.setTitleCache(simple, false);
120 elementList.add(childName.toString());
121
122 childName = "CanonicalName";
123 obligatory = false;
124 Element elCanonicalName = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
125 makeCanonicalName(nameBase, elCanonicalName, taxonNameMap, success);
126 elementList.add(childName.toString());
127
128 childName = "CanonicalAuthorship";
129 obligatory = false;
130 Element elCanonicalAuthorship = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
131 makeCanonicalAuthorship(nameBase, elCanonicalAuthorship, authorMap, success);
132 elementList.add(childName.toString());
133
134 childName = "PublishedIn";
135 obligatory = false;
136 Element elPublishedIn = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
137 makePublishedIn(nameBase, elPublishedIn, referenceMap, success);
138 elementList.add(childName.toString());
139
140 childName = "Year";
141 obligatory = false;
142 Element elYear = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
143 makeYear(nameBase, elYear, success);
144 elementList.add(childName.toString());
145
146 childName = "MicroReference";
147 obligatory = false;
148 Element elMicroReference = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
149 makeMicroReference(nameBase, elMicroReference, success);
150 elementList.add(childName.toString());
151
152 childName = "Typification";
153 obligatory = false;
154 Element elTypification = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
155 makeTypification(nameBase, elTypification, success);
156 elementList.add(childName.toString());
157
158 childName = "PublicationStatus";
159 obligatory = false;
160 Element elPublicationStatus = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
161 makePublicationStatus(nameBase, elPublicationStatus, success);
162 elementList.add(childName.toString());
163
164 childName = "ProviderLink";
165 obligatory = false;
166 Element elProviderLink = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
167 makeProviderLink(nameBase, elProviderLink, success);
168 elementList.add(childName.toString());
169
170 childName = "ProviderSpecificData";
171 obligatory = false;
172 Element elProviderSpecificData = XmlHelp.getSingleChildElement(success, elTaxonName, childName, tcsNamespace, obligatory);
173 makeProviderSpecificData(nameBase, elProviderSpecificData, success);
174 elementList.add(childName.toString());
175
176
177 ImportHelper.setOriginalSource(nameBase, config.getSourceReference(), strId, idNamespace);
178
179 taxonNameMap.put(strId, nameBase);
180
181 } catch (UnknownCdmTypeException e) {
182 logger.warn("Name with id " + strId + " has unknown nomenclatural code.");
183 success.setValue(false);
184 }
185 }
186 logger.info(i + " names handled");
187 Collection<? extends TaxonNameBase> col = taxonNameMap.objects();
188 getNameService().save((Collection)col);
189
190 logger.info("end makeTaxonNames ...");
191 return success.getValue();
192
193 }
194
195
196
197
198
199
200
201
202
203
204
205 protected static Rank makeRank(Element elRank){
206 Rank result;
207 if (elRank == null){
208 return null;
209 }
210 String strRankCode = elRank.getAttributeValue("code");
211 String strRankString = elRank.getTextNormalize();
212 if (strRankCode == null || "".equals(strRankCode.trim()) &&
213 strRankString == null || "".equals(strRankString.trim())
214 ){
215 return null;
216 }
217
218 Rank codeRank = null;
219 try {
220 codeRank = TcsXmlTransformer.rankCode2Rank(strRankCode);
221 } catch (UnknownCdmTypeException e1) {
222 codeRank = Rank.UNKNOWN_RANK();
223 }
224 Rank stringRank = null;
225 try {
226 boolean useUnknown = true;
227 stringRank = Rank.getRankByNameOrAbbreviation(strRankString, useUnknown);
228 } catch (UnknownCdmTypeException e1) {
229
230 }
231
232
233 if (! (codeRank == null) && ! codeRank.equals(Rank.UNKNOWN_RANK())){
234 result = codeRank;
235 if (! codeRank.equals(stringRank) && ! stringRank.equals(Rank.UNKNOWN_RANK())){
236 logger.warn("code rank and string rank are unequal. code: " + codeRank.getLabel() + stringRank.getLabel());
237 }
238 }
239
240 else{
241 result = stringRank;
242 logger.warn("string rank used, because code rank does not exist or was not recognized: " + stringRank.getLabel());
243 }
244 return result;
245 }
246
247 private void makeCanonicalName(TaxonNameBase name, Element elCanonicalName, MapWrapper<TaxonNameBase> taxonNameMap, ResultWrapper<Boolean> success){
248 boolean cacheProtected = false;
249
250 if (elCanonicalName == null){
251 return;
252 }
253 Namespace ns = elCanonicalName.getNamespace();
254
255 String childName = "Simple";
256 boolean obligatory = true;
257 Element elSimple = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
258 String simple = (elSimple == null)? "" : elSimple.getTextNormalize();
259 name.setFullTitleCache(simple, cacheProtected);
260
261 if (name instanceof NonViralName<?>){
262 NonViralName<?> nonViralName = (NonViralName<?>)name;
263 childName = "Uninomial";
264 obligatory = false;
265 Element elUninomial = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
266 String uninomial = (elUninomial == null)? "" : elUninomial.getTextNormalize();
267 if (! uninomial.trim().equals("")){
268 nonViralName.setGenusOrUninomial(uninomial);
269 if (nonViralName.getRank() != null && nonViralName.getRank().isLower(Rank.GENUS())){
270 logger.warn("Name " + simple + " lower then 'genus' but has a canonical name part 'Uninomial'.");
271 }
272 }
273 testNoMoreElements();
274
275 childName = "Genus";
276 obligatory = false;
277 Element elGenus = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
278 String genus = (elGenus == null)? "" : elGenus.getTextNormalize();
279
280 makeGenusReferenceType(name, elGenus, taxonNameMap, success);
281 if (! genus.trim().equals("")){
282 nonViralName.setGenusOrUninomial(genus);
283 if (nonViralName.getRank() != null && ! nonViralName.getRank().isLower(Rank.GENUS() )){
284 logger.warn("Name " + simple + " is not lower then 'genus' but has canonical name part 'Genus'.");
285 }
286 }
287
288 childName = "InfragenericEpithet";
289 obligatory = false;
290 Element elInfrageneric = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
291 String infraGenericEpithet = (elInfrageneric == null)? "" : elInfrageneric.getTextNormalize();
292 if (! infraGenericEpithet.trim().equals("")){
293 nonViralName.setInfraGenericEpithet(infraGenericEpithet);
294 if (nonViralName.getRank() != null && ! name.getRank().isInfraGeneric()){
295 logger.warn("Name " + simple + " is not infra generic but has canonical name part 'InfragenericEpithet'.");
296 }
297 }
298 testNoMoreElements();
299
300 childName = "SpecificEpithet";
301 obligatory = false;
302 Element elSpecificEpithet = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
303 String specificEpithet = (elSpecificEpithet == null)? "" : elSpecificEpithet.getTextNormalize();
304 if (! specificEpithet.trim().equals("")){
305 nonViralName.setSpecificEpithet(specificEpithet);
306 if (nonViralName.getRank() != null && name.getRank().isHigher(Rank.SPECIES()) ){
307 logger.warn("Name " + simple + " is not species or below but has canonical name part 'SpecificEpithet'.");
308 }
309 }
310 testNoMoreElements();
311
312 childName = "InfraspecificEpithet";
313 obligatory = false;
314 Element elInfraspecificEpithet = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
315 String infraspecificEpithet = (elInfraspecificEpithet == null)? "" : elInfraspecificEpithet.getTextNormalize();
316 if (! infraspecificEpithet.trim().equals("")){
317 nonViralName.setInfraSpecificEpithet(infraspecificEpithet);
318 if (nonViralName.getRank() != null && ! name.isInfraSpecific() ){
319 logger.warn("Name " + simple + " is not infraspecific but has canonical name part 'InfraspecificEpithet'.");
320 }
321 }
322 testNoMoreElements();
323
324
325 }else{
326
327 }
328
329
330 childName = "CultivarNameGroup";
331 obligatory = false;
332 Element elCultivarNameGroup = XmlHelp.getSingleChildElement(success, elCanonicalName, childName, ns, obligatory);
333 String cultivarNameGroup = (elCultivarNameGroup == null)? "" : elCultivarNameGroup.getTextNormalize();
334 if (! "".equals(cultivarNameGroup.trim())){
335 if (name instanceof CultivarPlantName){
336 makeCultivarName();
337 }else{
338 logger.warn("Non cultivar name has 'cultivar name group' element. Omitted");
339 }
340 }
341 return;
342 }
343
344 protected void testNoMoreElements(){
345
346
347 }
348
349 private void makeCultivarName(){
350
351
352 }
353
354 private void makeGenusReferenceType(TaxonNameBase name, Element elGenus, MapWrapper<TaxonNameBase> taxonNameMap, ResultWrapper<Boolean> success){
355 if(name instanceof NonViralName){
356 NonViralName nonViralName = (NonViralName)name;
357 if (elGenus != null && name != null){
358 TaxonNameBase genusReferenceName;
359
360 Class<? extends NonViralName> clazz = NonViralName.class;
361 genusReferenceName = makeReferenceType(elGenus, clazz, taxonNameMap, success);
362 NonViralName nvGenusReference = (NonViralName)genusReferenceName;
363
364 String genus = nvGenusReference.getGenusOrUninomial()!= null ? nvGenusReference.getGenusOrUninomial(): genusReferenceName.getTitleCache();
365 nonViralName.setGenusOrUninomial(genus);
366 }else{
367 logger.warn("Missing Genus information");
368 }
369 }else{
370
371
372 }
373
374 }
375
376
377 @SuppressWarnings("unchecked")
378 private INomenclaturalAuthor makeNameCitation(Element elNameCitation, MapWrapper<Person> authorMap, ResultWrapper<Boolean> success){
379 INomenclaturalAuthor result = null;
380 String childName;
381 boolean obligatory;
382 if (elNameCitation != null){
383 Namespace ns = elNameCitation.getNamespace();
384
385 childName = "Authors";
386 obligatory = false;
387 Element elAuthors = XmlHelp.getSingleChildElement(success, elNameCitation, childName, ns, obligatory);
388 testNoMoreElements();
389
390 if (elAuthors != null){
391 childName = "AgentName";
392 List<Element> elAgentList = elAuthors.getChildren(childName, ns);
393 Team team = Team.NewInstance();
394 result = team;
395 if (elAgentList.size() > 1){
396 for(Element elAgent : elAgentList){
397 Person teamMember = makeAgent(elAgent, ns, authorMap, success);
398 team.addTeamMember(teamMember);
399 }
400 }else if(elAgentList.size() == 1){
401 result = makeAgent(elAgentList.get(0), ns, authorMap, success);
402 }
403 }else{
404 childName = "Simple";
405 obligatory = true;
406 Element elSimple = XmlHelp.getSingleChildElement(success, elNameCitation, childName, ns, obligatory);
407 String simple = (elSimple == null)? "" : elSimple.getTextNormalize();
408 result = Team.NewInstance();
409 result.setNomenclaturalTitle(simple);
410 }
411 }
412 return result;
413 }
414
415 private Person makeAgent(Element elAgentName, Namespace ns, MapWrapper<Person> agentMap, ResultWrapper<Boolean> success){
416 Person result = null;
417 if (elAgentName != null){
418 String authorTitle = elAgentName.getTextNormalize();
419 result = Person.NewTitledInstance(authorTitle);
420 Class<? extends Person> clazz = Person.class;
421 result = makeReferenceType(elAgentName, clazz, agentMap, success);
422 return result;
423 }else{
424 return null;
425 }
426 }
427
428 private void makeCanonicalAuthorship(TaxonNameBase name, Element elCanonicalAuthorship, MapWrapper<Person> authorMap, ResultWrapper<Boolean> success){
429 if (elCanonicalAuthorship != null){
430 Namespace ns = elCanonicalAuthorship.getNamespace();
431
432 if (name instanceof NonViralName){
433 NonViralName nonViralName = (NonViralName)name;
434
435 String childName = "Simple";
436 boolean obligatory = true;
437 Element elSimple = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory);
438 String simple = (elSimple == null)? "" : elSimple.getTextNormalize();
439
440
441
442
443 childName = "Authorship";
444 obligatory = false;
445 Element elAuthorship = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory);
446 INomenclaturalAuthor author = makeNameCitation(elAuthorship, authorMap, success);
447 nonViralName.setCombinationAuthorTeam(author);
448 testNoMoreElements();
449
450 childName = "BasionymAuthorship";
451 obligatory = false;
452 Element elBasionymAuthorship = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory);
453 INomenclaturalAuthor basionymAuthor = makeNameCitation(elBasionymAuthorship, authorMap, success);
454 nonViralName.setBasionymAuthorTeam(basionymAuthor);
455 testNoMoreElements();
456
457 childName = "CombinationAuthorship";
458 obligatory = false;
459 Element elCombinationAuthorship = XmlHelp.getSingleChildElement(success, elCanonicalAuthorship, childName, ns, obligatory);
460 INomenclaturalAuthor combinationAuthor = makeNameCitation(elCombinationAuthorship, authorMap ,success);
461 nonViralName.setCombinationAuthorTeam(combinationAuthor);
462 testNoMoreElements();
463
464 if (elAuthorship != null && (elBasionymAuthorship != null || elCombinationAuthorship != null) ){
465 logger.warn("Authorship and (BasionymAuthorship or CombinationAuthorship) must not exist at the same time in CanonicalAuthorship");
466 success.setValue(false);
467 }
468 }
469 }
470 }
471
472
473 private void makePublishedIn(TaxonNameBase name, Element elPublishedIn, MapWrapper<ReferenceBase> referenceMap, ResultWrapper<Boolean> success){
474 if (elPublishedIn != null && name != null){
475 Class<? extends ReferenceBase> clazz = ReferenceBase.class;
476 ReferenceBase ref = makeReferenceType(elPublishedIn, clazz, referenceMap, success);
477 if (ref instanceof INomenclaturalReference){
478 name.setNomenclaturalReference(ref);
479 }else{
480 logger.warn("Reference is not of type INomenclaturalReference and could not be added to the name " + name.getTitleCache());
481 }
482 }else if (name == null){
483 logger.warn("TaxonName must not be 'null'");
484 success.setValue(false);
485 }
486 }
487
488
489 private void makeYear(TaxonNameBase name, Element elYear, ResultWrapper<Boolean> success){
490 if (elYear != null){
491 String year = elYear.getTextNormalize();
492 if (name instanceof ZoologicalName){
493 ((ZoologicalName)name).setPublicationYear(getIntegerYear(year));
494 }else{
495 logger.warn("Year can be set only for a zoological name");
496 }
497 }
498 }
499
500 private Integer getIntegerYear(String year){
501 try {
502 Integer result = Integer.valueOf(year);
503 return result;
504 } catch (NumberFormatException e) {
505 logger.warn("Year string could not be parsed. Set = 9999 instead");
506 return 9999;
507 }
508 }
509
510
511 private void makeMicroReference(TaxonNameBase name, Element elMicroReference, ResultWrapper<Boolean> success){
512 if (elMicroReference != null){
513 String microReference = elMicroReference.getTextNormalize();
514 name.setNomenclaturalMicroReference(microReference);
515 }
516 }
517
518
519 private void makeTypification(TaxonNameBase name, Element elTypifiacation, ResultWrapper<Boolean> success){
520 if (elTypifiacation != null){
521
522
523 }
524 }
525
526
527 private void makePublicationStatus(TaxonNameBase name, Element elPublicationStatus, ResultWrapper<Boolean> success){
528
529
530 if (elPublicationStatus != null){
531
532
533 }
534 }
535
536 private void makeProviderLink(TaxonNameBase name, Element elProviderLink, ResultWrapper<Boolean> success){
537 if (elProviderLink != null){
538
539
540 }
541 }
542
543
544 private void makeProviderSpecificData(TaxonNameBase name, Element elProviderSpecificData, ResultWrapper<Boolean> success){
545 if (elProviderSpecificData != null){
546
547
548 }
549 }
550
551
552
553
554
555 protected boolean isIgnore(TcsXmlImportState state){
556 return ! state.getConfig().isDoTaxonNames();
557 }
558
559 }