Revision d9ece393
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 330 | 330 |
String infraGenericEpithet = taxonName.getInfraGenericEpithet(); |
| 331 | 331 |
Rank rank = taxonName.getRank(); |
| 332 | 332 |
|
| 333 |
//as kingdomFk can not be defined in Phase 01 the below code was switched to use the CDM rank. This may be changed if we move validation to Phase03 or later |
|
| 333 |
//as kingdomFk can not be defined in Phase 01 the below code was switched to use the CDM rank. |
|
| 334 |
//This may be changed if we move validation to Phase03 or later |
|
| 334 | 335 |
// Integer rankFk = getRankFk(taxonName, taxonName.getNameType()); |
| 335 | 336 |
// if (rankFk == null) {
|
| 336 | 337 |
// logger.error("Rank was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
|
| ... | ... | |
| 341 | 342 |
// 2. Grandchilds of an accepted taxon of rank subgenus that are accepted taxa of rank subspecies have to have an infraGenericEpithet |
| 342 | 343 |
|
| 343 | 344 |
int ancestorLevel = 0; |
| 344 |
if (taxonName.getRank().equals(Rank.SUBSPECIES())) {
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| 345 |
if (rank == null){
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| 346 |
logger.warn("PhaseOne validation: Taxon name has no rank: " + taxonName.getTitleCache());
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| 347 |
}else if (rank.equals(Rank.SUBSPECIES())) {
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| 345 | 348 |
// The accepted taxon two rank levels above should be of rank subgenus |
| 346 | 349 |
ancestorLevel = 2; |
| 347 |
} |
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if (taxonName.getRank().equals(Rank.SPECIES())) {
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}else if (rank.equals(Rank.SPECIES())) {
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| 349 | 351 |
// The accepted taxon one rank level above should be of rank subgenus |
| 350 | 352 |
ancestorLevel = 1; |
| 351 | 353 |
} |
| ... | ... | |
| 359 | 361 |
} |
| 360 | 362 |
} |
| 361 | 363 |
|
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if (infraGenericEpithet == null && rank.isInfraGenericButNotSpeciesGroup()) {
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logger.warn("InfraGenericEpithet was not determined although it should exist for infra generic names: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
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} |
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if (specificEpithet != null && (rank.isInfraGenericButNotSpeciesGroup()||rank.isGenus()||rank.isSupraGeneric())) {
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logger.warn("SpecificEpithet was determined for rank " + rank.getTitleCache() + " although it should only exist for species aggregates, species or infraspecific taxa: TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
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} |
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if (infraSpecificEpithet != null && !rank.isInfraSpecific()) {
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String message = "InfraSpecificEpithet '" +infraSpecificEpithet + "' was determined for rank " + rank.getTitleCache() + " although it should only exist for rank species and higher: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")";
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if (StringUtils.isNotBlank(infraSpecificEpithet)){
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logger.warn(message); |
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}else{
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logger.warn(message); |
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} |
|
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if (rank != null){
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| 365 |
if (infraGenericEpithet == null && rank.isInfraGenericButNotSpeciesGroup()) {
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logger.warn("InfraGenericEpithet was not determined although it should exist for infra generic names: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");
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} |
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if (specificEpithet != null && (rank.isInfraGenericButNotSpeciesGroup()||rank.isGenus()||rank.isSupraGeneric())) {
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logger.warn("SpecificEpithet was determined for rank " + rank.getTitleCache() + " although it should only exist for species aggregates, species or infraspecific taxa: TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
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} |
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if (infraSpecificEpithet != null && !rank.isInfraSpecific()) {
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String message = "InfraSpecificEpithet '" +infraSpecificEpithet + "' was determined for rank " + rank.getTitleCache() + " although it should only exist for rank species and higher: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")";
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if (StringUtils.isNotBlank(infraSpecificEpithet)){
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logger.warn(message); |
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}else{
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logger.warn(message); |
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} |
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} |
|
| 375 | 379 |
} |
| 376 | 380 |
// } |
| 377 | 381 |
if (infraSpecificEpithet != null && specificEpithet == null) {
|
Also available in: Unified diff
ref #8587 handle null rank names in PESI export a bit better