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Revision 23336874

Added by Andreas Müller about 6 years ago

ID 2333687478d3e24d7b6ea4202ed61dc00908c5c4
Parent fd50d567
Child 53d7c437

cleanup BM import

     				Language language = getAndHandleLanguage(iso6392Map, iso639_2, iso639_1, languageString, originalLanguageString, state);
     				//CommonTaxonName
     				List<CommonTaxonName> commonTaxonNames = new ArrayList<CommonTaxonName>();
     				List<CommonTaxonName> commonTaxonNames = new ArrayList<>();
     				for (String regionFk : regionFkSplit){ //
     					CommonTaxonName commonTaxonName;
     					if (commonTaxonNames.size() == 0){

     					//detail
     					String detail = rs.getString("Detail");
     					if (StringUtils.isNotBlank(detail)){
     					if (isNotBlank(detail)){
     						ExtensionType detailExtensionType = getExtensionType(state, BerlinModelTransformer.DETAIL_EXT_UUID, "micro reference","micro reference","micro ref.");
     						Extension.NewInstance(taxonBase, detail, detailExtensionType);
+    					}
     					//idInSource
     					String idInSource = rs.getString("IdInSource");
     					if (StringUtils.isNotBlank(idInSource)){
     					if (isNotBlank(idInSource)){
     						ExtensionType detailExtensionType = getExtensionType(state, BerlinModelTransformer.ID_IN_SOURCE_EXT_UUID, "Berlin Model IdInSource","Berlin Model IdInSource","BM source id");
     						Extension.NewInstance(taxonBase, idInSource, detailExtensionType);
+    					}

     					if (rank == null){
     						//TODO rank should never be null or a more sophisticated algorithm has to be implemented for genus/supraGenericName
     						logger.warn("Rank is null. Genus epethiton was imported. May be wrong");
     						logger.warn("Rank is null. Genus epithet was imported. May be wrong");
     						success = false;
+    					}

     		//reference map
     		String nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
     		Class<?> cdmClass = Reference.class;
     		Map<String, Reference> refMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
     		@SuppressWarnings("unchecked")
             Map<String, Reference> refMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
     		String treeName = "Classification - No Name";
     		String classificationName = "Classification - No Name";
     		ResultSet rs = state.getConfig().getSource().getResultSet(getClassificationQuery(state)) ;
     		int i = 0;
     		//for each reference
     		try {
     			//TODO handle case useSingleClassification = true && sourceSecId = null, which returns no record
     			while (rs.next()){
     			boolean isFirst = true;
     		    while (rs.next()){
     				try {
     					if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("RelPTaxa handled: " + (i-1));}
-...
     					Reference ref = refMap.get(ptRefFk);
     					String refCache = rs.getString("RefCache");
     					if (StringUtils.isNotBlank(refCache)){
     						treeName = refCache;
     					if (isNotBlank(refCache)){
     						classificationName = refCache;
+    					}
     					if (ref != null && StringUtils.isNotBlank(ref.getTitleCache())){
     						treeName = ref.getTitleCache();
     						classificationName = ref.getTitleCache();
+    					}
     					if (isFirst && isNotBlank(state.getConfig().getClassificationName())){
     					    classificationName = state.getConfig().getClassificationName();
+    					}
     					Classification tree = Classification.NewInstance(treeName);
     					Classification tree = Classification.NewInstance(classificationName);
     					tree.setReference(ref);
     					if (i == 1 && state.getConfig().getClassificationUuid() != null){
     						tree.setUuid(state.getConfig().getClassificationUuid());
-...
     					getClassificationService().save(tree);
     					state.putClassificationUuidInt(ptRefFkInt, tree);
     					isFirst = false;
     				} catch (Exception e) {
     					logger.error("Error in BerlinModleTaxonRelationImport.makeClassifications: " + e.getMessage());
     					e.printStackTrace();
-...
     	@Override
     	protected String getRecordQuery(BerlinModelImportConfigurator config) {
     		String strQuery =
     			" SELECT RelPTaxon.*, FromTaxon.RIdentifier as taxon1Id, ToTaxon.RIdentifier as taxon2Id, ToTaxon.PTRefFk as treeRefFk, FromTaxon.PTRefFk as fromRefFk, q.is_concept_relation " +
     			" FROM PTaxon as FromTaxon " +
                   	" INNER JOIN RelPTaxon ON FromTaxon.PTNameFk = RelPTaxon.PTNameFk1 AND FromTaxon.PTRefFk = RelPTaxon.PTRefFk1 " +
                   	" INNER JOIN PTaxon AS ToTaxon ON RelPTaxon.PTNameFk2 = ToTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = ToTaxon.PTRefFk " +
     			" SELECT RelPTaxon.*, fromTaxon.RIdentifier as taxon1Id, toTaxon.RIdentifier as taxon2Id, toTaxon.PTRefFk as treeRefFk, fromTaxon.PTRefFk as fromRefFk, q.is_concept_relation " +
     			" FROM PTaxon as fromTaxon " +
                   	" INNER JOIN RelPTaxon ON fromTaxon.PTNameFk = relPTaxon.PTNameFk1 AND fromTaxon.PTRefFk = relPTaxon.PTRefFk1 " +
                   	" INNER JOIN PTaxon AS toTaxon ON RelPTaxon.PTNameFk2 = ToTaxon.PTNameFk AND RelPTaxon.PTRefFk2 = ToTaxon.PTRefFk " +
                   	" INNER JOIN RelPTQualifier q ON q.RelPTQualifierId = RelPTaxon.RelQualifierFk " +
                 " WHERE RelPTaxon.RelPTaxonId IN ("+ID_LIST_TOKEN+") ORDER BY RelPTaxon.RelPTaxonId ";
                 " WHERE RelPTaxon.RelPTaxonId IN ("+ID_LIST_TOKEN+") " +
                 " ORDER BY RelPTaxon.RelPTaxonId ";
     		return strQuery;
+    	}
     	@Override
     	public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
     		boolean success = true ;
     		BerlinModelImportConfigurator config = state.getConfig();
     		Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
     		Map<String, TaxonBase> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
     		Map<Integer, Classification> classificationMap = new HashMap<Integer, Classification>();
-...
     				int relPTaxonId = rs.getInt("RelPTaxonId");
     				Integer taxon1Id = nullSafeInt(rs, "taxon1Id");
     				Integer taxon2Id = nullSafeInt(rs, "taxon2Id");
     				int relQualifierFk = 0;
     				int relQualifierFk = -1;
     				try {
     					Integer relRefFk = nullSafeInt(rs,"relRefFk");
     					int treeRefFk = rs.getInt("treeRefFk");
-...
     							handleAllRelatedTaxa(state, toTaxon, classificationMap, treeRefFk);
     							Synonym synonym = (Synonym)taxon1;
     							if (synonym.getAcceptedTaxon()!= null){
     							    logger.warn("Synonym already has an accepted taxon. Create clone.");
     							    logger.warn("RelID: " + relPTaxonId + ". Synonym ("+taxon1Id +") already has an accepted taxon. Create clone.");
     							    synonym = (Synonym)synonym.clone();
+    							}
     							makeSynRel(relQualifierFk, toTaxon, synonym, citation, microcitation);
     							if (isNotBlank(notes)){
     	                            logger.warn("Notes for synonym relationship or unknown taxon relationship not handled");
+    	                        }
     							if (relQualifierFk == TAX_REL_IS_SYNONYM_OF ||
     									relQualifierFk == TAX_REL_IS_HOMOTYPIC_SYNONYM_OF ||
-...
     							        synonym.setPartial(true);
     							}else{
     								success = false;
     								logger.warn("Proparte/Partial not yet implemented for TaxonRelationShipType " + relQualifierFk);
     								logger.warn("Synonym relationship type not yet implemented: " + relQualifierFk);
+    							}
     						}else if (isConceptRelationship){
     							ResultWrapper<Boolean> isInverse = ResultWrapper.NewInstance(false);
-...
     						if (taxonRelationship != null){
     						    doNotes(taxonRelationship, notes);
     						}else if (isNotBlank(notes)){
     						    logger.warn("Notes for synonym relationship or unknown taxon relationship not handled");
     						    logger.warn("Notes for synonym relationship or unknown taxon relationship not handled. RelID: " + relPTaxonId + ". Note: " + notes);
+    						}
     						taxaToSave.add(taxon2);

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Revision 23336874

Added by Andreas Müller about 6 years ago