Revision ba5dcea5
Added by Andreas Müller almost 6 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/cdmLight/CdmLightClassificationExport.java | ||
|---|---|---|
| 76 | 76 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship; |
|
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
|
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException; |
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|
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/** |
| ... | ... | |
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|
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@SuppressWarnings("unchecked")
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TaxonNodeOutStreamPartitioner<XmlExportState> partitioner |
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= TaxonNodeOutStreamPartitioner.NewInstance( |
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this, state, state.getConfig().getTaxonNodeFilter(), |
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100, monitor, null); |
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= TaxonNodeOutStreamPartitioner.NewInstance(
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this, state, state.getConfig().getTaxonNodeFilter(),
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100, monitor, null);
|
|
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|
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|
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monitor.subTask("Start partitioning");
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|
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TaxonNode node = partitioner.next(); |
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while (node != null){
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handleTaxonNode(state, node); |
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node = partitioner.next(); |
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handleTaxonNode(state, node);
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node = partitioner.next();
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|
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} |
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|
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|
| ... | ... | |
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* @param classificationUuid |
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*/ |
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private void handleTaxonNode(CdmLightExportState state, TaxonNode taxonNode) {
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try {
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// TaxonNode taxonNode = getTaxonNodeService().find(taxonNodeUuid); |
|
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|
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if (taxonNode == null){
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String message = "TaxonNode for given taxon node UUID not found. "; |
| 183 | 183 |
//TODO |
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state.getResult().addWarning(message); |
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}else{
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TaxonNode root = taxonNode; |
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if (root.hasTaxon()){
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handleTaxon(state, root); |
|
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}else{
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// for (TaxonNode child : root.getChildNodes()){
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// handleTaxon(state, child); |
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// //TODO progress monitor |
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// } |
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try {
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TaxonNode root = taxonNode; |
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if (root.hasTaxon()){
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handleTaxon(state, root); |
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}else{
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// for (TaxonNode child : root.getChildNodes()){
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// handleTaxon(state, child); |
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// //TODO progress monitor |
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// } |
|
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} |
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} catch (Exception e) {
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state.getResult().addException(e, "An unexpected error occurred when handling classification " + |
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taxonNode.getUuid() + ": " + e.getMessage() + e.getStackTrace()); |
|
| 194 | 199 |
} |
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} |
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} catch (Exception e) {
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state.getResult().addException(e, "An unexpected error occurred when handling classification " + |
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taxonNode.getUuid() + ": " + e.getMessage() + e.getStackTrace()); |
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} |
|
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} |
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|
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/** |
| ... | ... | |
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for (Synonym syn : taxon.getSynonyms()){
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handleSynonym(state, syn); |
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} |
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|
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for (TaxonRelationship rel : taxon.getProParteAndPartialSynonymRelations()){
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handleProPartePartialMisapplied(state, rel); |
|
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} |
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for (TaxonRelationship rel : taxon.getMisappliedNameRelations()){
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handleProPartePartialMisapplied(state, rel); |
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} |
|
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|
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CdmLightExportTable table = CdmLightExportTable.TAXON; |
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String[] csvLine = new String[table.getSize()]; |
| ... | ... | |
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} |
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} |
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|
|
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/** |
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* @param state |
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* @param taxon |
| ... | ... | |
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csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name); |
| 705 | 712 |
csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, synonym.getSec()); |
| 706 | 713 |
csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(synonym.getSec()); |
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if (synonym.isProParte()) {
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csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = "1"; |
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}else {
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csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = "0"; |
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} |
|
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|
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state.getProcessor().put(table, synonym, csvLine); |
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} catch (Exception e) {
|
| ... | ... | |
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} |
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|
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/** |
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* Handles Misapplied names (including pro parte and partial as well as |
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* pro parte and partial synonyms |
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* @param state |
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* @param rel |
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*/ |
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private void handleProPartePartialMisapplied(CdmLightExportState state, TaxonRelationship rel) {
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try {
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Taxon ppSyonym = rel.getFromTaxon(); |
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if (isUnpublished(state.getConfig(), ppSyonym)){
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return; |
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} |
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TaxonName name = ppSyonym.getName(); |
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handleName(state, name); |
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|
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CdmLightExportTable table = CdmLightExportTable.SYNONYM; |
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String[] csvLine = new String[table.getSize()]; |
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|
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csvLine[table.getIndex(CdmLightExportTable.SYNONYM_ID)] = getId(state, rel); |
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csvLine[table.getIndex(CdmLightExportTable.TAXON_FK)] = getId(state, rel.getToTaxon()); |
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csvLine[table.getIndex(CdmLightExportTable.NAME_FK)] = getId(state, name); |
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|
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//TODO pro parte synonyms have to references, the synonym relationship reference |
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//and the sec reference of the Taxon representing the synonym. |
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//As we currently do have only 1 reference column in CDM light the synonym relationship |
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//reference is used here. This is according to how pro parte synonyms were mapped to |
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//concept relationships in #7334 |
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Reference secRef = rel.getCitation(); |
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csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, secRef); |
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csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(secRef); |
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|
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// Reference secRef = ppSyonym.getSec(); |
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// csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE_FK)] = getId(state, secRef); |
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// csvLine[table.getIndex(CdmLightExportTable.SEC_REFERENCE)] = getTitleCache(secRef); |
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// Reference synSecRef = rel.getCitation(); |
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// csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE_FK)] = getId(state, secRef); |
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// csvLine[table.getIndex(CdmLightExportTable.SYN_SEC_REFERENCE)] = getTitleCache(secRef); |
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| 760 |
|
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//pro parte type |
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TaxonRelationshipType type = rel.getType(); |
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csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = type.isProParte()? "1":"0"; |
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csvLine[table.getIndex(CdmLightExportTable.IS_PARTIAL)] = type.isPartial()? "1":"0"; |
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csvLine[table.getIndex(CdmLightExportTable.IS_MISAPPLIED)] = type.isAnyMisappliedName()? "1":"0"; |
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if (type.isPartial()) {
|
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String message = "Partial synonyms/misapplied names not yet handled by CDM light. Created " |
|
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+ "pro parte synonym/misapplied name instead for " + rel.getId(); |
|
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state.getResult().addWarning(message, "handleProParteSynonym", ppSyonym.getTitleCache()); |
|
| 770 |
csvLine[table.getIndex(CdmLightExportTable.IS_PRO_PARTE)] = "1"; |
|
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} |
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| 772 |
|
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state.getProcessor().put(table, ppSyonym, csvLine); |
|
| 774 |
} catch (Exception e) {
|
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| 775 |
state.getResult().addException(e, "An unexpected error occurred when handling " |
|
| 776 |
+ "pro parte/partial synonym relationship " + |
|
| 777 |
cdmBaseStr(rel) + ": " + e.getMessage()); |
|
| 778 |
} |
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| 779 |
|
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| 780 |
} |
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| 781 |
|
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| 782 |
|
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/** |
| 722 | 784 |
* @param state |
| 723 | 785 |
* @param name |
Also available in: Unified diff
ref #7334 adapt DwCA and CDM light export to new pro parte synonym handling, also add misapplied name handling to CDM light