Revision ca169a1e
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 693 | 693 |
return success; |
| 694 | 694 |
} |
| 695 | 695 |
|
| 696 |
private Integer findKingdomIdFromTreeIndex(TaxonBase<?> taxon,PesiExportState state) {
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|
| 697 |
if (taxon instanceof Taxon){
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|
| 698 |
Set<TaxonNode> nodes = ((Taxon)taxon).getTaxonNodes(); |
|
| 696 |
private Integer findKingdomIdFromTreeIndex(TaxonBase<?> taxonBase,PesiExportState state) {
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|
| 697 |
Taxon taxon; |
|
| 698 |
if (taxonBase instanceof Synonym){
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| 699 |
taxon = ((Synonym) taxonBase).getAcceptedTaxon(); |
|
| 700 |
}else{
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| 701 |
taxon = (Taxon)taxonBase; |
|
| 702 |
} |
|
| 703 |
if (taxon != null){
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|
| 704 |
Set<TaxonNode> nodes = taxon.getTaxonNodes(); |
|
| 705 |
if (nodes.size()>1){
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| 706 |
logger.warn("The taxon has more then 1 taxon node: " + taxon.getTitleCache() + ". Take arbitrary one.");
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|
| 707 |
} |
|
| 699 | 708 |
if (!nodes.isEmpty()){
|
| 700 | 709 |
String treeIndex = nodes.iterator().next().treeIndex(); |
| 701 | 710 |
|
| 702 |
Pattern pattern = Pattern.compile("#t[0-9]+#[0-9]+#[0-9]+#");
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| 711 |
Pattern pattern = Pattern.compile("#t[0-9]+#([0-9]+#){3}");
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| 703 | 712 |
Matcher matcher = pattern.matcher(treeIndex); |
| 704 | 713 |
Integer kingdomID = null; |
| 705 | 714 |
if(matcher.find()) {
|
| 706 | 715 |
String treeIndexKingdom = matcher.group(0); |
| 707 | 716 |
kingdomID = state.getTreeIndexKingdomMap().get(treeIndexKingdom); |
| 717 |
}else{
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|
| 718 |
pattern = Pattern.compile("#t[0-9]+#([0-9]+#){2}");
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| 719 |
matcher = pattern.matcher(treeIndex); |
|
| 720 |
if(matcher.find()) {
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| 721 |
String treeIndexKingdom = matcher.group(0); |
|
| 722 |
kingdomID = state.getTreeIndexKingdomMap().get(treeIndexKingdom); |
|
| 723 |
} |
|
| 724 |
} |
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| 725 |
if(kingdomID == null){
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|
| 726 |
logger.warn("Kingdom could not be defined for treeindex " + treeIndex);
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|
| 708 | 727 |
} |
| 709 | 728 |
return kingdomID; |
| 710 | 729 |
} else {
|
| 711 |
logger.debug("The taxon has no nodes: " + taxon.getTitleCache() + " the kingdom is taken from the nomenclatural code: " + PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode));
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| 730 |
logger.warn("The taxon has no nodes: " + taxon.getTitleCache() + ". The kingdom is taken from the nomenclatural code: " + PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode));
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| 712 | 731 |
return PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode); |
| 713 |
}} else{
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| 714 |
return PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode); |
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| 732 |
} |
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| 733 |
} else{
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| 734 |
logger.warn("Taxon is synonym with no accepted taxon attached: " + taxonBase.getTitleCache() + ". The kingdom is taken from the nomenclatural code: " + PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode) );
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| 735 |
return PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode); |
|
| 715 | 736 |
} |
| 716 | 737 |
} |
| 717 | 738 |
|
Also available in: Unified diff
ref #8509 improve findKingdomIdFromTreeIndex