Revision c0c4c356
Added by Patrick Plitzner almost 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
|---|---|---|
| 37 | 37 |
import eu.etaxonomy.cdm.model.description.CommonTaxonName; |
| 38 | 38 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
| 39 | 39 |
import eu.etaxonomy.cdm.model.name.BotanicalName; |
| 40 |
import eu.etaxonomy.cdm.model.name.CultivarPlantName; |
|
| 40 | 41 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus; |
| 41 | 42 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 42 | 43 |
import eu.etaxonomy.cdm.model.name.NonViralName; |
| ... | ... | |
| 338 | 339 |
RedListUtil.logMessage(id, "No name found!", logger); |
| 339 | 340 |
} |
| 340 | 341 |
|
| 342 |
NonViralName<?> name = null; |
|
| 341 | 343 |
Rank rank = makeRank(id, state, rangString, ep3String!=null); |
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NonViralName<?> name = BotanicalName.NewInstance(rank); |
|
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//cultivar |
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if(rank!= null && rank.equals(Rank.CULTIVAR())){
|
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CultivarPlantName cultivar = CultivarPlantName.NewInstance(rank); |
|
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cultivar.setGenusOrUninomial(ep1String); |
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cultivar.setSpecificEpithet(ep2String); |
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cultivar.setCultivarName(ep3String); |
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name = cultivar; |
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} |
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//botanical names |
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else{
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name = BotanicalName.NewInstance(rank); |
|
| 343 | 355 |
|
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//ep1 should always be present |
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if(CdmUtils.isBlank(ep1String)){
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RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger); |
|
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} |
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name.setGenusOrUninomial(ep1String); |
|
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if(CdmUtils.isNotBlank(ep2String)){
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if(rank!=null && rank.isInfraGenericButNotSpeciesGroup()){
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name.setInfraGenericEpithet(ep2String); |
|
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} |
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else{
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name.setSpecificEpithet(ep2String); |
|
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//ep1 should always be present |
|
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if(CdmUtils.isBlank(ep1String)){
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RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger); |
|
| 355 | 359 |
} |
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} |
|
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if(CdmUtils.isNotBlank(ep3String)){
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name.setInfraSpecificEpithet(ep3String); |
|
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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)); |
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} |
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name.setGenusOrUninomial(ep1String); |
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if(CdmUtils.isNotBlank(ep2String)){
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if(rank!=null && rank.isInfraGenericButNotSpeciesGroup()){
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name.setInfraGenericEpithet(ep2String); |
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} |
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else{
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name.setSpecificEpithet(ep2String); |
|
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} |
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name.addStatus(status); |
|
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} |
| 376 | 369 |
} |
| 377 | 370 |
//hybrid |
| ... | ... | |
| 385 | 378 |
|
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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); |
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if(CdmUtils.isNotBlank(ep3String)){
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name.setInfraSpecificEpithet(ep3String); |
|
| 396 | 383 |
} |
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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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//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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name.addStatus(status); |
|
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} |
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String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2; |
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name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula); |
|
| 410 | 400 |
} |
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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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//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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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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} |
|
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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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} |
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} |
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else if(hybString.equals(RedListUtil.HYB_N)){
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name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String+" "+ep2String+" nothosubsp. "+ep3String); |
|
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} |
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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); |
|
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} |
|
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} |
|
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else if(hybString.equals(RedListUtil.HYB_XS)){
|
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//nothing to do |
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} |
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else{
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logger.error("HYB value "+hybString+" not yet handled");
|
|
| 415 | 455 |
} |
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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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} |
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} |
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else if(hybString.equals(RedListUtil.HYB_N)){
|
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name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String+" "+ep2String+" nothosubsp. "+ep3String); |
|
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} |
|
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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); |
|
| 428 | 456 |
} |
| 429 | 457 |
else{
|
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RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
|
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logger.error("HYB value "+hybString+" not yet handled");
|
|
| 431 | 459 |
} |
| 432 | 460 |
} |
| 433 |
else if(hybString.equals(RedListUtil.HYB_XS)){
|
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//nothing to do |
|
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} |
|
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else{
|
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logger.error("HYB value "+hybString+" not yet handled");
|
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} |
|
| 439 | 461 |
} |
| 440 | 462 |
//add source |
| 441 | 463 |
ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE); |
Also available in: Unified diff
#5448 Import cultivar as CultivarPlantName