Revision f8226169
Added by Andreas Müller over 4 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java | ||
|---|---|---|
| 698 | 698 |
return success; |
| 699 | 699 |
} |
| 700 | 700 |
|
| 701 |
private Integer findKingdomIdFromTreeIndex(TaxonBase<?> taxonBase,PesiExportState state) {
|
|
| 701 |
private static Integer findKingdomIdFromTreeIndex(TaxonBase<?> taxonBase,PesiExportState state) {
|
|
| 702 | 702 |
Taxon taxon; |
| 703 | 703 |
if (taxonBase instanceof Synonym){
|
| 704 | 704 |
taxon = ((Synonym) taxonBase).getAcceptedTaxon(); |
| ... | ... | |
| 727 | 727 |
kingdomID = state.getTreeIndexKingdomMap().get(treeIndexKingdom); |
| 728 | 728 |
} |
| 729 | 729 |
} |
| 730 |
if(Rank.DOMAIN().equals(taxon.getName().getRank())){
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|
| 731 |
return null; |
|
| 732 |
} |
|
| 730 | 733 |
if(kingdomID == null){
|
| 731 | 734 |
logger.warn("Kingdom could not be defined for treeindex " + treeIndex);
|
| 732 | 735 |
} |
| ... | ... | |
| 881 | 884 |
TaxonName taxonName = acceptedTaxon.getName(); |
| 882 | 885 |
|
| 883 | 886 |
if (taxonName.isZoological()) {
|
| 884 |
NomenclaturalCode nomenclaturalCode = taxonName.getNameType(); |
|
| 885 |
kingdomFk = PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode); |
|
| 887 |
kingdomFk = findKingdomIdFromTreeIndex(taxonBase, state); |
|
| 886 | 888 |
|
| 887 | 889 |
Set<TaxonNode> taxonNodes = acceptedTaxon.getTaxonNodes(); |
| 888 | 890 |
TaxonNode singleNode = null; |
| ... | ... | |
| 1316 | 1318 |
*/ |
| 1317 | 1319 |
private boolean invokeRankDataAndTypeNameFkAndKingdomFk(TaxonName taxonName, NomenclaturalCode nomenclaturalCode, |
| 1318 | 1320 |
Integer taxonFk, Integer typeNameFk, Integer kingdomFk, PesiExportState state) {
|
| 1319 |
try {
|
|
| 1321 |
|
|
| 1322 |
Integer rankFk = null; |
|
| 1323 |
try {
|
|
| 1320 | 1324 |
int index = 1; |
| 1321 |
Integer rankFk = getRankFk(taxonName, nomenclaturalCode);
|
|
| 1325 |
rankFk = getRankFk(taxonName, nomenclaturalCode); |
|
| 1322 | 1326 |
if (rankFk != null) {
|
| 1323 | 1327 |
rankTypeExpertsUpdateStmt.setInt(index++, rankFk); |
| 1324 | 1328 |
} else {
|
| ... | ... | |
| 1488 | 1492 |
* @see MethodMapper |
| 1489 | 1493 |
*/ |
| 1490 | 1494 |
private static String getRankCache(TaxonName taxonName, NomenclaturalCode nomenclaturalCode, PesiExportState state) {
|
| 1491 |
if (nomenclaturalCode != null) {
|
|
| 1492 |
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode)); |
|
| 1493 |
}else{
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|
| 1495 |
List<TaxonNode> nodes = getTaxonNodes(taxonName); |
|
| 1496 |
if (Rank.DOMAIN().equals(taxonName.getRank())){
|
|
| 1497 |
return state.getTransformer().getCacheByRankAndKingdom(Rank.DOMAIN(), null); |
|
| 1498 |
}else if (!nodes.isEmpty()) {
|
|
| 1499 |
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), findKingdomIdFromTreeIndex(nodes.iterator().next().getTaxon(), state)); //PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode)); |
|
| 1500 |
}else if (nomenclaturalCode != null){
|
|
| 1501 |
return state.getTransformer().getCacheByRankAndKingdom(taxonName.getRank(), PesiTransformer.nomenclaturalCode2Kingdom(nomenclaturalCode)); |
|
| 1502 |
}else{
|
|
| 1494 | 1503 |
logger.warn("No nomenclatural code defined for name " + taxonName.getUuid());
|
| 1495 | 1504 |
return null; |
| 1496 | 1505 |
} |
| 1497 | 1506 |
} |
| 1498 | 1507 |
|
| 1499 | 1508 |
/** |
| 1509 |
* @param taxonName |
|
| 1510 |
* @return |
|
| 1511 |
*/ |
|
| 1512 |
private static List<TaxonNode> getTaxonNodes(TaxonName taxonName) {
|
|
| 1513 |
List<TaxonNode> result = new ArrayList<>(); |
|
| 1514 |
for (TaxonBase<?> tb:taxonName.getTaxonBases()){
|
|
| 1515 |
Taxon taxon; |
|
| 1516 |
//TODO handle ERMS taxon relationships |
|
| 1517 |
if (tb.isInstanceOf(Taxon.class)){
|
|
| 1518 |
taxon = CdmBase.deproxy(tb, Taxon.class); |
|
| 1519 |
}else{
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|
| 1520 |
taxon = CdmBase.deproxy(tb, Synonym.class).getAcceptedTaxon(); |
|
| 1521 |
} |
|
| 1522 |
if (taxon != null){
|
|
| 1523 |
for (TaxonNode node : taxon.getTaxonNodes()){
|
|
| 1524 |
result.add(node); |
|
| 1525 |
} |
|
| 1526 |
} |
|
| 1527 |
} |
|
| 1528 |
return result; |
|
| 1529 |
} |
|
| 1530 |
|
|
| 1531 |
/** |
|
| 1500 | 1532 |
* Returns the <code>DisplayName</code> attribute. |
| 1501 | 1533 |
* @param taxon The {@link TaxonBase Taxon}.
|
| 1502 | 1534 |
* @return The <code>DisplayName</code> attribute. |
Also available in: Unified diff
ref #1444, ref #8508, ref #8509 improve rank handling in ERMS pipeline (II)