Revision 3faf7d1d
Added by Andreas Müller over 2 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/caryo/KewExcelTaxonImport.java | ||
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import eu.etaxonomy.cdm.model.taxon.SynonymType; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
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import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl; |
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|
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/** |
| ... | ... | |
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this.classification = null; |
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this.secReference = null; |
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this.sourceReference = null; |
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this.orphanedSynonymTaxon = null; |
|
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TransactionStatus tx = this.startTransaction(); |
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state.setTransactionStatus(tx); |
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logger.info(line + "New transaction started."); |
| ... | ... | |
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}else if (taxonBase.isInstanceOf(Synonym.class)){
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Taxon taxon = getAcceptedTaxon(record, line, kewId); |
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if (taxon == null){
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logger.warn(kewId + "Accepted taxon not found: " + getValue(record, Kew_Rel_Acc_Name_ID) + line); |
|
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taxon = getOrphanedSynonymTaxon(state); |
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}else{
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taxon.addSynonym(CdmBase.deproxy(taxonBase, Synonym.class), SynonymType.SYNONYM_OF()); |
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logger.warn(kewId + "Accepted taxon not found. Added synonym to 'orphaned synonym taxon': " + getValue(record, Kew_Rel_Acc_Name_ID) + line); |
|
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} |
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taxon.addSynonym(CdmBase.deproxy(taxonBase, Synonym.class), SynonymType.SYNONYM_OF()); |
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}else{
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logger.warn("Unhandled");
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} |
| ... | ... | |
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|
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} |
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Taxon orphanedSynonymTaxon; |
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private Taxon getOrphanedSynonymTaxon(SimpleExcelTaxonImportState<CONFIG> state) {
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UUID uuid = UUID.fromString(KEW_ORPHANED_PLACEHOLDER_TAXON); |
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Taxon placeholderTaxon = CdmBase.deproxy(getTaxonService().find(uuid), Taxon.class); |
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if (placeholderTaxon == null){
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if (orphanedSynonymTaxon != null) {
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return orphanedSynonymTaxon; |
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} |
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UUID orphanedTaxonUuid = UUID.fromString(KEW_ORPHANED_PLACEHOLDER_TAXON); |
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orphanedSynonymTaxon = CdmBase.deproxy(getTaxonService().find(orphanedTaxonUuid), Taxon.class); |
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if (orphanedSynonymTaxon == null){
|
|
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TaxonName placeholderName = TaxonNameFactory.NewBacterialInstance(Rank.SUBFAMILY()); |
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placeholderName.setTitleCache("Orphaned_Synonyms_KEW", true);
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placeholderTaxon = Taxon.NewInstance(placeholderName, getSecReference(state, state.getOriginalRecord())); |
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orphanedSynonymTaxon = Taxon.NewInstance(placeholderName, getSecReference(state, state.getOriginalRecord())); |
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orphanedSynonymTaxon.setUuid(orphanedTaxonUuid); |
|
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Taxon unplacedTaxon = CdmBase.deproxy(getTaxonService().find(UUID.fromString(KEW_UNPLACED_NODE)), Taxon.class); |
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getClassification(state).addParentChild(unplacedTaxon, placeholderTaxon, null, null); |
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TaxonNode orphandNode = getClassification(state).addParentChild(unplacedTaxon, orphanedSynonymTaxon, null, null); |
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getTaxonNodeService().save(orphandNode); |
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} |
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return placeholderTaxon;
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return orphanedSynonymTaxon;
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} |
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private Classification classification; |
Also available in: Unified diff
ref #9918 finetuning for caryophyllaceae import