Revision ae538f84
Added by Patrick Plitzner almost 8 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
|---|---|---|
| 38 | 38 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 40 | 40 |
import eu.etaxonomy.cdm.model.name.CultivarPlantName; |
| 41 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
|
| 41 | 42 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
| 42 | 43 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 43 | 44 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| ... | ... | |
| 234 | 235 |
addAnnotation(RedListUtil.WISSK+": "+wisskString, taxonBase); |
| 235 | 236 |
|
| 236 | 237 |
//check taxon name consistency |
| 237 |
checkTaxonNameConsistency(id, taxNameString, hybString, taxonBase);
|
|
| 238 |
checkTaxonConsistency(id, taxNameString, hybString, taxonBase); |
|
| 238 | 239 |
return taxonBase; |
| 239 | 240 |
} |
| 240 | 241 |
|
| ... | ... | |
| 252 | 253 |
String zusatzString = rs.getString(RedListUtil.ZUSATZ); |
| 253 | 254 |
String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB); |
| 254 | 255 |
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI); |
| 256 |
String hybString = rs.getString(RedListUtil.HYB); |
|
| 255 | 257 |
|
| 256 | 258 |
//combination author |
| 257 | 259 |
if(authorKombString.contains(RedListUtil.EX)){
|
| ... | ... | |
| 319 | 321 |
|
| 320 | 322 |
//check authorship consistency |
| 321 | 323 |
String authorString = rs.getString(RedListUtil.AUTOR); |
| 322 |
String authorshipCache = name.getAuthorshipCache(); |
|
| 323 |
checkAuthorShipConsistency(id, nomZusatzString, taxZusatzString, zusatzString, authorString, authorshipCache); |
|
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checkNameConsistency(id, nomZusatzString, taxZusatzString, zusatzString, authorString, hybString, name); |
|
| 324 | 325 |
} |
| 325 | 326 |
|
| 326 | 327 |
private NonViralName<?> importName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave) throws SQLException {
|
| ... | ... | |
| 366 | 367 |
name.setSpecificEpithet(ep2String); |
| 367 | 368 |
} |
| 368 | 369 |
} |
| 369 |
} |
|
| 370 |
//hybrid |
|
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if(CdmUtils.isNotBlank(hybString)){
|
|
| 372 |
//save hybrid formula |
|
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if(CdmUtils.isNotBlank(formelString)){
|
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Annotation annotation = Annotation.NewDefaultLanguageInstance(formelString); |
|
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annotation.setAnnotationType(AnnotationType.TECHNICAL()); |
|
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name.addAnnotation(annotation); |
|
| 370 |
if(CdmUtils.isNotBlank(ep3String)){
|
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name.setInfraSpecificEpithet(ep3String); |
|
| 377 | 372 |
} |
| 378 | 373 |
|
| 379 |
if(hybString.equals(RedListUtil.HYB_X)){
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name.setBinomHybrid(true); |
|
| 381 |
if(CdmUtils.isNotBlank(ep3String)){
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name.setInfraSpecificEpithet(ep3String); |
|
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} |
|
| 384 |
//nomenclatural status |
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if(CdmUtils.isNotBlank(nomZusatzString)){
|
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NomenclaturalStatusType statusType = makeNomenclaturalStatus(id, state, nomZusatzString); |
|
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if(statusType!=null){
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NomenclaturalStatus status = NomenclaturalStatus.NewInstance(statusType); |
|
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//special case for invalid names where the DB entry contains |
|
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//additional information in brackets e.g. "nom. inval. (sine basion.)" |
|
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if(statusType.equals(NomenclaturalStatusType.INVALID())){
|
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Pattern pattern = Pattern.compile("\\((.*?)\\)");
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Matcher matcher = pattern.matcher(nomZusatzString); |
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if (matcher.find()){
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status.setRuleConsidered(matcher.group(1)); |
|
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} |
|
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|
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//nomenclatural status |
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if(CdmUtils.isNotBlank(nomZusatzString)){
|
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NomenclaturalStatusType statusType = makeNomenclaturalStatus(id, state, nomZusatzString); |
|
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if(statusType!=null){
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NomenclaturalStatus status = NomenclaturalStatus.NewInstance(statusType); |
|
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//special case for invalid names where the DB entry contains |
|
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//additional information in brackets e.g. "nom. inval. (sine basion.)" |
|
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if(statusType.equals(NomenclaturalStatusType.INVALID())){
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Pattern pattern = Pattern.compile("\\((.*?)\\)");
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Matcher matcher = pattern.matcher(nomZusatzString); |
|
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if (matcher.find()){
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status.setRuleConsidered(matcher.group(1)); |
|
| 397 | 387 |
} |
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name.addStatus(status); |
|
| 399 | 388 |
} |
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name.addStatus(status); |
|
| 400 | 390 |
} |
| 401 |
//hybrid |
|
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if(CdmUtils.isNotBlank(hybString)){
|
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if(hybString.equals(RedListUtil.HYB_X)){
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name.setBinomHybrid(true); |
|
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} |
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else if(hybString.equals(RedListUtil.HYB_G)){
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name.setMonomHybrid(true); |
|
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} |
|
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//hybrid |
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if(CdmUtils.isNotBlank(hybString)){
|
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//save hybrid formula |
|
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if(CdmUtils.isNotBlank(formelString)){
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Annotation annotation = Annotation.NewDefaultLanguageInstance(formelString); |
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annotation.setAnnotationType(AnnotationType.TECHNICAL()); |
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name.addAnnotation(annotation); |
|
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} |
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|
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if(hybString.equals(RedListUtil.HYB_X)){
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name.setBinomHybrid(true); |
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} |
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else if(hybString.equals(RedListUtil.HYB_G)){
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name.setMonomHybrid(true); |
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} |
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else if(hybString.equals(RedListUtil.HYB_XF)){
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name.setHybridFormula(true); |
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if(ep1String.contains(RedListUtil.HYB_SIGN)){
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RedListUtil.logMessage(id, "EPI1 has hybrid signs but with flag: "+RedListUtil.HYB_XF, logger); |
|
| 408 | 411 |
} |
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else if(hybString.equals(RedListUtil.HYB_XF)){
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name.setHybridFormula(true); |
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if(ep1String.contains(RedListUtil.HYB_SIGN)){
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RedListUtil.logMessage(id, "EPI1 has hybrid signs but with flag: "+RedListUtil.HYB_XF, logger); |
|
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} |
|
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else if(ep2String.contains(RedListUtil.HYB_SIGN)){
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String[] split = ep2String.split(RedListUtil.HYB_SIGN); |
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if(split.length!=2){
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RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep2String, logger); |
|
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} |
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String hybridFormula1 = ep1String+" "+split[0].trim(); |
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String hybridFormula2 = ep1String+" "+split[1].trim(); |
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if(CdmUtils.isNotBlank(ep3String)){
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hybridFormula1 += " "+ep3String; |
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hybridFormula2 += " "+ep3String; |
|
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} |
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String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2; |
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name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula); |
|
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else if(ep2String.contains(RedListUtil.HYB_SIGN)){
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String[] split = ep2String.split(RedListUtil.HYB_SIGN); |
|
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if(split.length!=2){
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RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep2String, logger); |
|
| 427 | 416 |
} |
| 428 |
else if(ep3String.contains(RedListUtil.HYB_SIGN)){
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String[] split = ep3String.split(RedListUtil.HYB_SIGN); |
|
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if(split.length!=2){
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RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep3String, logger); |
|
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} |
|
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String hybridFormula1 = ep1String+" "+ep2String+" "+split[0]; |
|
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String hybridFormula2 = ep1String+" "+ep2String+" "+split[1]; |
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String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2; |
|
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name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula); |
|
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String hybridFormula1 = ep1String+" "+split[0].trim(); |
|
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String hybridFormula2 = ep1String+" "+split[1].trim(); |
|
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if(CdmUtils.isNotBlank(ep3String)){
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hybridFormula1 += " "+ep3String; |
|
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hybridFormula2 += " "+ep3String; |
|
| 437 | 422 |
} |
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String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2; |
|
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name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank); |
|
| 438 | 425 |
} |
| 439 |
else if(hybString.equals(RedListUtil.HYB_N)){
|
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name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String+" "+ep2String+" nothosubsp. "+ep3String); |
|
| 441 |
} |
|
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else if(hybString.equals(RedListUtil.HYB_GF)){
|
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if(ep1String.contains(RedListUtil.HYB_SIGN)){
|
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name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String); |
|
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} |
|
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else{
|
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RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger); |
|
| 426 |
else if(ep3String.contains(RedListUtil.HYB_SIGN)){
|
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String[] split = ep3String.split(RedListUtil.HYB_SIGN); |
|
| 428 |
if(split.length!=2){
|
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RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep3String, logger); |
|
| 448 | 430 |
} |
| 431 |
String hybridFormula1 = ep1String+" "+ep2String+" "+split[0]; |
|
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String hybridFormula2 = ep1String+" "+ep2String+" "+split[1]; |
|
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String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2; |
|
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name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula); |
|
| 449 | 435 |
} |
| 450 |
else if(hybString.equals(RedListUtil.HYB_XS)){
|
|
| 451 |
//nothing to do |
|
| 436 |
} |
|
| 437 |
else if(hybString.equals(RedListUtil.HYB_N)){
|
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| 438 |
name = NonViralNameParserImpl.NewInstance().parseFullName(taxNameString); |
|
| 439 |
} |
|
| 440 |
else if(hybString.equals(RedListUtil.HYB_GF)){
|
|
| 441 |
if(ep1String.contains(RedListUtil.HYB_SIGN)){
|
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name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String); |
|
| 452 | 443 |
} |
| 453 | 444 |
else{
|
| 454 |
logger.error("HYB value "+hybString+" not yet handled");
|
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| 445 |
RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
|
|
| 455 | 446 |
} |
| 456 | 447 |
} |
| 448 |
else if(hybString.equals(RedListUtil.HYB_XS)){
|
|
| 449 |
//nothing to do |
|
| 450 |
} |
|
| 457 | 451 |
else{
|
| 458 | 452 |
logger.error("HYB value "+hybString+" not yet handled");
|
| 459 | 453 |
} |
| ... | ... | |
| 466 | 460 |
return name; |
| 467 | 461 |
} |
| 468 | 462 |
|
| 469 |
private void checkAuthorShipConsistency(long id, String nomZusatzString, String taxZusatzString, |
|
| 470 |
String zusatzString, String authorString, String authorshipCache) {
|
|
| 463 |
private void checkNameConsistency(long id, String nomZusatzString, String taxZusatzString, |
|
| 464 |
String zusatzString, String authorString, String hybString, NonViralName<?> name) {
|
|
| 465 |
String authorshipCache = name.getAuthorshipCache(); |
|
| 466 |
if(hybString.equals(RedListUtil.HYB_XF)){
|
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| 467 |
if(name.getHybridChildRelations().isEmpty()){
|
|
| 468 |
RedListUtil.logMessage(id, "Hybrid formula but no hybrid child relations: "+name.getTitleCache(), logger); |
|
| 469 |
return; |
|
| 470 |
} |
|
| 471 |
return; |
|
| 472 |
} |
|
| 473 |
|
|
| 471 | 474 |
if(CdmUtils.isNotBlank(zusatzString)){
|
| 472 | 475 |
authorString = authorString.replace(", "+zusatzString, "");
|
| 473 | 476 |
} |
| ... | ... | |
| 492 | 495 |
} |
| 493 | 496 |
} |
| 494 | 497 |
|
| 495 |
private void checkTaxonNameConsistency(long id, String taxNameString, String hybString, TaxonBase<?> taxonBase) {
|
|
| 496 |
if(hybString.equals(RedListUtil.HYB_XF)){
|
|
| 497 |
if(HibernateProxyHelper.deproxy(taxonBase.getName(),NonViralName.class).getHybridChildRelations().isEmpty()){
|
|
| 498 |
RedListUtil.logMessage(id, "Hybrid name but no hybrid child relations: "+taxonBase.getTitleCache(), logger); |
|
| 499 |
return; |
|
| 500 |
} |
|
| 501 |
return; |
|
| 502 |
} |
|
| 503 |
|
|
| 504 |
|
|
| 498 |
private void checkTaxonConsistency(long id, String taxNameString, String hybString, TaxonBase<?> taxonBase) {
|
|
| 505 | 499 |
String nameCache = HibernateProxyHelper.deproxy(taxonBase.getName(), NonViralName.class).getNameCache().trim(); |
| 506 | 500 |
taxNameString = taxNameString.trim(); |
| 507 | 501 |
taxNameString.replaceAll(" +", " ");
|
| ... | ... | |
| 521 | 515 |
taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN, " x");
|
| 522 | 516 |
} |
| 523 | 517 |
|
| 524 |
if(taxNameString.endsWith("- Gruppe")){String a ="Festuca ×xx Lolium <-> Festuca ×× Lolium";
|
|
| 518 |
if(taxNameString.endsWith("- Gruppe")){
|
|
| 525 | 519 |
taxNameString = taxNameString.replaceAll("- Gruppe", "species group");
|
| 526 | 520 |
} |
| 527 | 521 |
if(taxNameString.endsWith("- group")){
|
| ... | ... | |
| 531 | 525 |
taxNameString = taxNameString.replace("[ranglos]", "[unranked]");
|
| 532 | 526 |
if(STRICT_TITLE_CHECK){
|
| 533 | 527 |
if(!taxNameString.trim().equals(nameCache)){
|
| 534 |
RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.titleCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
|
|
| 528 |
RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
|
|
| 535 | 529 |
} |
| 536 | 530 |
} |
| 537 | 531 |
else{
|
| 538 | 532 |
if(!taxNameString.startsWith(nameCache)){
|
| 539 |
RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.titleCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
|
|
| 533 |
RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
|
|
| 540 | 534 |
} |
| 541 | 535 |
} |
| 542 | 536 |
} |
Also available in: Unified diff
#5448 Fix import of hybrids due to merge conflicts