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Revision c0c4c356

Added by Patrick Plitzner almost 8 years ago

#5448 Import cultivar as CultivarPlantName

View differences:

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
345
        if(rank!= null && rank.equals(Rank.CULTIVAR())){
346
            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

  
344
        //ep1 should always be present
345
        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);
352
            }
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            else{
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                name.setSpecificEpithet(ep2String);
356
            //ep1 should always be present
357
            if(CdmUtils.isBlank(ep1String)){
358
                RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
355 359
            }
356
        }
357
        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)){
362
            NomenclaturalStatusType statusType = makeNomenclaturalStatus(id, state, nomZusatzString);
363
            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
366
                //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);
370
                    if (matcher.find()){
371
                        status.setRuleConsidered(matcher.group(1));
372
                    }
360
            name.setGenusOrUninomial(ep1String);
361
            if(CdmUtils.isNotBlank(ep2String)){
362
                if(rank!=null && rank.isInfraGenericButNotSpeciesGroup()){
363
                    name.setInfraGenericEpithet(ep2String);
364
                }
365
                else{
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                    name.setSpecificEpithet(ep2String);
373 367
                }
374
                name.addStatus(status);
375 368
            }
376 369
        }
377 370
        //hybrid
......
385 378

  
386 379
            if(hybString.equals(RedListUtil.HYB_X)){
387 380
                name.setBinomHybrid(true);
388
            }
389
            else if(hybString.equals(RedListUtil.HYB_G)){
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                name.setMonomHybrid(true);
391
            }
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            else if(hybString.equals(RedListUtil.HYB_XF)){
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                name.setHybridFormula(true);
394
                if(ep1String.contains(RedListUtil.HYB_SIGN)){
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                    RedListUtil.logMessage(id, "EPI1 has hybrid signs but with flag: "+RedListUtil.HYB_XF, logger);
381
                if(CdmUtils.isNotBlank(ep3String)){
382
                    name.setInfraSpecificEpithet(ep3String);
396 383
                }
397
                else if(ep2String.contains(RedListUtil.HYB_SIGN)){
398
                    String[] split = ep2String.split(RedListUtil.HYB_SIGN);
399
                    if(split.length!=2){
400
                        RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep2String, logger);
401
                    }
402
                    String hybridFormula1 = ep1String+" "+split[0].trim();
403
                    String hybridFormula2 = ep1String+" "+split[1].trim();
404
                    if(CdmUtils.isNotBlank(ep3String)){
405
                        hybridFormula1 += " "+ep3String;
406
                        hybridFormula2 += " "+ep3String;
384
                //nomenclatural status
385
                if(CdmUtils.isNotBlank(nomZusatzString)){
386
                    NomenclaturalStatusType statusType = makeNomenclaturalStatus(id, state, nomZusatzString);
387
                    if(statusType!=null){
388
                        NomenclaturalStatus status = NomenclaturalStatus.NewInstance(statusType);
389
                        //special case for invalid names where the DB entry contains
390
                        //additional information in brackets e.g. "nom. inval. (sine basion.)"
391
                        if(statusType.equals(NomenclaturalStatusType.INVALID())){
392
                            Pattern pattern = Pattern.compile("\\((.*?)\\)");
393
                            Matcher matcher = pattern.matcher(nomZusatzString);
394
                            if (matcher.find()){
395
                                status.setRuleConsidered(matcher.group(1));
396
                            }
397
                        }
398
                        name.addStatus(status);
407 399
                    }
408
                    String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
409
                    name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula);
410 400
                }
411
                else if(ep3String.contains(RedListUtil.HYB_SIGN)){
412
                    String[] split = ep3String.split(RedListUtil.HYB_SIGN);
413
                    if(split.length!=2){
414
                        RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep3String, logger);
401
                //hybrid
402
                if(CdmUtils.isNotBlank(hybString)){
403
                    if(hybString.equals(RedListUtil.HYB_X)){
404
                        name.setBinomHybrid(true);
405
                    }
406
                    else if(hybString.equals(RedListUtil.HYB_G)){
407
                        name.setMonomHybrid(true);
408
                    }
409
                    else if(hybString.equals(RedListUtil.HYB_XF)){
410
                        name.setHybridFormula(true);
411
                        if(ep1String.contains(RedListUtil.HYB_SIGN)){
412
                            RedListUtil.logMessage(id, "EPI1 has hybrid signs but with flag: "+RedListUtil.HYB_XF, logger);
413
                        }
414
                        else if(ep2String.contains(RedListUtil.HYB_SIGN)){
415
                            String[] split = ep2String.split(RedListUtil.HYB_SIGN);
416
                            if(split.length!=2){
417
                                RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep2String, logger);
418
                            }
419
                            String hybridFormula1 = ep1String+" "+split[0].trim();
420
                            String hybridFormula2 = ep1String+" "+split[1].trim();
421
                            if(CdmUtils.isNotBlank(ep3String)){
422
                                hybridFormula1 += " "+ep3String;
423
                                hybridFormula2 += " "+ep3String;
424
                            }
425
                            String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
426
                            name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula);
427
                        }
428
                        else if(ep3String.contains(RedListUtil.HYB_SIGN)){
429
                            String[] split = ep3String.split(RedListUtil.HYB_SIGN);
430
                            if(split.length!=2){
431
                                RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep3String, logger);
432
                            }
433
                            String hybridFormula1 = ep1String+" "+ep2String+" "+split[0];
434
                            String hybridFormula2 = ep1String+" "+ep2String+" "+split[1];
435
                            String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
436
                            name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula);
437
                        }
438
                    }
439
                    else if(hybString.equals(RedListUtil.HYB_N)){
440
                        name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String+" "+ep2String+" nothosubsp. "+ep3String);
441
                    }
442
                    else if(hybString.equals(RedListUtil.HYB_GF)){
443
                        if(ep1String.contains(RedListUtil.HYB_SIGN)){
444
                            name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String);
445
                        }
446
                        else{
447
                            RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
448
                        }
449
                    }
450
                    else if(hybString.equals(RedListUtil.HYB_XS)){
451
                        //nothing to do
452
                    }
453
                    else{
454
                        logger.error("HYB value "+hybString+" not yet handled");
415 455
                    }
416
                    String hybridFormula1 = ep1String+" "+ep2String+" "+split[0];
417
                    String hybridFormula2 = ep1String+" "+ep2String+" "+split[1];
418
                    String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
419
                    name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula);
420
                }
421
            }
422
            else if(hybString.equals(RedListUtil.HYB_N)){
423
                name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String+" "+ep2String+" nothosubsp. "+ep3String);
424
            }
425
            else if(hybString.equals(RedListUtil.HYB_GF)){
426
                if(ep1String.contains(RedListUtil.HYB_SIGN)){
427
                    name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String);
428 456
                }
429 457
                else{
430
                    RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
458
                    logger.error("HYB value "+hybString+" not yet handled");
431 459
                }
432 460
            }
433
            else if(hybString.equals(RedListUtil.HYB_XS)){
434
                //nothing to do
435
            }
436
            else{
437
                logger.error("HYB value "+hybString+" not yet handled");
438
            }
439 461
        }
440 462
        //add source
441 463
        ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);

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