Revision 16c76ded
Added by Patrick Plitzner over 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
|---|---|---|
| 197 | 197 |
long id = rs.getLong(RedListUtil.NAMNR); |
| 198 | 198 |
String taxNameString = rs.getString(RedListUtil.TAXNAME); |
| 199 | 199 |
String epi1String = rs.getString(RedListUtil.EPI1); |
| 200 |
String epi2String = rs.getString(RedListUtil.EPI2); |
|
| 201 |
String epi3String = rs.getString(RedListUtil.EPI3); |
|
| 200 | 202 |
String gueltString = rs.getString(RedListUtil.GUELT); |
| 201 | 203 |
String trivialString = rs.getString(RedListUtil.TRIVIAL); |
| 202 | 204 |
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI); |
| ... | ... | |
| 239 | 241 |
addAnnotation(RedListUtil.WISSK+": "+wisskString, taxonBase); |
| 240 | 242 |
|
| 241 | 243 |
//check taxon name consistency |
| 242 |
checkTaxonConsistency(id, taxNameString, hybString, epi1String, taxonBase, state); |
|
| 244 |
checkTaxonConsistency(id, taxNameString, hybString, epi1String, epi2String, epi3String, taxonBase, state);
|
|
| 243 | 245 |
return taxonBase; |
| 244 | 246 |
} |
| 245 | 247 |
|
| ... | ... | |
| 415 | 417 |
} |
| 416 | 418 |
else if(hybString.equals(RedListUtil.HYB_XF) || hybString.equals(RedListUtil.HYB_XU)){
|
| 417 | 419 |
name.setHybridFormula(true); |
| 418 |
if(ep1String.contains(RedListUtil.HYB_SIGN)){
|
|
| 419 |
name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String, NomenclaturalCode.ICNAFP, rank); |
|
| 420 |
} |
|
| 421 |
else if(ep2String.contains(RedListUtil.HYB_SIGN)){
|
|
| 422 |
String[] split = ep2String.split(RedListUtil.HYB_SIGN); |
|
| 423 |
String hybridFormula1 = ep1String+" "+split[0].trim(); |
|
| 424 |
String hybridFormula2 = ep1String+" "+split[1].trim(); |
|
| 425 |
//check if the genus is mentioned in EP2 or not |
|
| 426 |
String[] secondHybrid = split[1].trim().split(" ");
|
|
| 427 |
//check if the genus is abbreviated like e.g. Centaurea jacea × C. decipiens |
|
| 428 |
if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z]\\.")){
|
|
| 429 |
hybridFormula2 = ep1String+" "+split[1].trim().substring(2); |
|
| 430 |
} |
|
| 431 |
else if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
|
|
| 432 |
hybridFormula2 = split[1]; |
|
| 433 |
} |
|
| 434 |
if(CdmUtils.isNotBlank(ep3String)){
|
|
| 435 |
hybridFormula1 += " "+rank.getAbbreviation()+" "+ep3String; |
|
| 436 |
hybridFormula2 += " "+rank.getAbbreviation()+" "+ep3String; |
|
| 437 |
} |
|
| 438 |
String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2; |
|
| 439 |
name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank); |
|
| 440 |
} |
|
| 441 |
else if(ep3String.contains(RedListUtil.HYB_SIGN)){
|
|
| 442 |
String[] split = ep3String.split(RedListUtil.HYB_SIGN); |
|
| 443 |
String hybridFormula1 = ep1String+" "+ep2String+" "+rank.getAbbreviation()+" "+split[0]; |
|
| 444 |
String hybridFormula2 = ep1String+" "+ep2String+" "+rank.getAbbreviation()+" "+split[1]; |
|
| 445 |
//check if the genus is mentioned in EP3 or not |
|
| 446 |
String[] secondHybrid = split[1].trim().split(" ");
|
|
| 447 |
//check if the genus is abbreviated like e.g. Centaurea jacea jacea × C. jacea subsp. decipiens |
|
| 448 |
if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z]\\.")){
|
|
| 449 |
hybridFormula2 = ep1String+" "+split[1].trim().substring(2); |
|
| 450 |
} |
|
| 451 |
else if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
|
|
| 452 |
hybridFormula2 = split[1]; |
|
| 453 |
} |
|
| 454 |
String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2; |
|
| 455 |
name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank); |
|
| 456 |
} |
|
| 420 |
String fullFormula = buildHybridFormula(ep1String, ep2String, ep3String, rank); |
|
| 421 |
name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank); |
|
| 457 | 422 |
} |
| 458 | 423 |
else if(hybString.equals(RedListUtil.HYB_N)){
|
| 459 | 424 |
name = NonViralNameParserImpl.NewInstance().parseFullName(taxNameString, NomenclaturalCode.ICNAFP, rank); |
| ... | ... | |
| 482 | 447 |
return name; |
| 483 | 448 |
} |
| 484 | 449 |
|
| 450 |
private String buildHybridFormula(String ep1String, String ep2String, String ep3String, Rank rank) {
|
|
| 451 |
String fullFormula = null; |
|
| 452 |
if(ep1String.contains(RedListUtil.HYB_SIGN)){
|
|
| 453 |
fullFormula = ep1String; |
|
| 454 |
} |
|
| 455 |
else if(ep2String.contains(RedListUtil.HYB_SIGN)){
|
|
| 456 |
String[] split = ep2String.split(RedListUtil.HYB_SIGN); |
|
| 457 |
String hybridFormula1 = ep1String+" "+split[0].trim(); |
|
| 458 |
String hybridFormula2 = ep1String+" "+split[1].trim(); |
|
| 459 |
//check if the genus is mentioned in EP2 or not |
|
| 460 |
String[] secondHybrid = split[1].trim().split(" ");
|
|
| 461 |
//check if the genus is abbreviated like e.g. Centaurea jacea × C. decipiens |
|
| 462 |
if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z]\\.")){
|
|
| 463 |
hybridFormula2 = ep1String+" "+split[1].trim().substring(3); |
|
| 464 |
} |
|
| 465 |
else if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
|
|
| 466 |
hybridFormula2 = split[1].trim(); |
|
| 467 |
} |
|
| 468 |
if(CdmUtils.isNotBlank(ep3String)){
|
|
| 469 |
hybridFormula1 += " "+rank.getAbbreviation()+" "+ep3String; |
|
| 470 |
hybridFormula2 += " "+rank.getAbbreviation()+" "+ep3String; |
|
| 471 |
} |
|
| 472 |
fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2; |
|
| 473 |
} |
|
| 474 |
else if(ep3String.contains(RedListUtil.HYB_SIGN)){
|
|
| 475 |
String[] split = ep3String.split(RedListUtil.HYB_SIGN); |
|
| 476 |
String hybridFormula1 = ep1String+" "+ep2String+" "+rank.getAbbreviation()+" "+split[0].trim(); |
|
| 477 |
String hybridFormula2 = ep1String+" "+ep2String+" "+rank.getAbbreviation()+" "+split[1].trim(); |
|
| 478 |
//check if the genus is mentioned in EP3 or not |
|
| 479 |
String[] secondHybrid = split[1].trim().split(" ");
|
|
| 480 |
//check if the genus is abbreviated like e.g. Centaurea jacea jacea × C. jacea subsp. decipiens |
|
| 481 |
if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z]\\.")){
|
|
| 482 |
hybridFormula2 = ep1String+" "+split[1].trim().substring(3); |
|
| 483 |
} |
|
| 484 |
else if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
|
|
| 485 |
hybridFormula2 = split[1].trim(); |
|
| 486 |
} |
|
| 487 |
fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2; |
|
| 488 |
} |
|
| 489 |
return fullFormula; |
|
| 490 |
} |
|
| 491 |
|
|
| 485 | 492 |
private void checkNameConsistency(long id, String nomZusatzString, String taxZusatzString, |
| 486 | 493 |
String zusatzString, String authorString, String hybString, NonViralName<?> name) {
|
| 487 | 494 |
String authorshipCache = name.getAuthorshipCache(); |
| ... | ... | |
| 518 | 525 |
} |
| 519 | 526 |
} |
| 520 | 527 |
|
| 521 |
private void checkTaxonConsistency(long id, String taxNameString, String hybString, String epi1String, TaxonBase<?> taxonBase, RedListGefaesspflanzenImportState state) {
|
|
| 528 |
private void checkTaxonConsistency(long id, String taxNameString, String hybString, String epi1String, String epi2String, String epi3String, TaxonBase<?> taxonBase, RedListGefaesspflanzenImportState state) {
|
|
| 522 | 529 |
if(taxNameString.split(RedListUtil.HYB_SIGN).length>2){
|
| 523 | 530 |
RedListUtil.logInfoMessage(id, "multiple hybrid signs. No name check for "+taxNameString, logger); |
| 524 | 531 |
return; |
| ... | ... | |
| 544 | 551 |
if(nameCache.contains("sec")){
|
| 545 | 552 |
nameCache = nameCache.substring(0, nameCache.indexOf("sec"));
|
| 546 | 553 |
} |
| 547 |
if(taxNameString.matches((".*[A-Z]\\..*"))){
|
|
| 548 |
taxNameString = taxNameString.replaceAll("[A-Z]\\.", epi1String);
|
|
| 554 |
if(!STRICT_TITLE_CHECK){
|
|
| 555 |
taxNameString = buildHybridFormula(epi1String, epi2String, epi3String, taxonBase.getName().getRank());
|
|
| 549 | 556 |
} |
| 550 |
if(taxNameString.matches((".*"+RedListUtil.HYB_SIGN+"\\s[a-z].*"))){
|
|
| 551 |
taxNameString = taxNameString.replaceAll(RedListUtil.HYB_SIGN+" ", RedListUtil.HYB_SIGN+" "+epi1String+" ");
|
|
| 557 |
if(taxNameString.split(RedListUtil.HYB_SIGN).length==1){
|
|
| 558 |
taxNameString = taxNameString.replace(RedListUtil.HYB_SIGN+" ", RedListUtil.HYB_SIGN);
|
|
| 552 | 559 |
} |
| 553 | 560 |
} |
| 554 | 561 |
|
Also available in: Unified diff
#5448 Refactor hybrid name import/check