/ - Diff - EDIT - EDIT Project Management

     package eu.etaxonomy.cdm.io.pesi.indexFungorum;
     import java.util.ArrayList;
     import java.util.HashMap;
     import java.util.List;
     import java.util.Map;
     import java.util.UUID;
-...
     	private Map<String, TaxonBase> speciesMap;
     	private List<UUID> infraspecificTaxaUUIDs = new ArrayList<>();
     	private Map<UUID,Integer> infraspecificTaxaUUIDs = new HashMap<>();
-...
     //		super(config);
+    	}
         public List<UUID> getInfraspecificTaxaUUIDs() {
         public Map<UUID,Integer> getInfraspecificTaxaUUIDs() {
             return infraspecificTaxaUUIDs;
+        }
         public void setInfraspecificTaxaUUIDs(List<UUID> infraspecificTaxaUUIDs) {
         public void setInfraspecificTaxaUUIDs(Map<UUID, Integer> infraspecificTaxaUUIDs) {
             this.infraspecificTaxaUUIDs = infraspecificTaxaUUIDs;
+        }

     import java.util.HashSet;
     import java.util.Map;
     import java.util.Set;
     import java.util.UUID;
     import org.apache.commons.lang.StringUtils;
     import org.apache.log4j.Logger;
     import org.springframework.stereotype.Component;
-...
     				String phylumName = rs.getString("Phylum name");
     				String preferredName = rs.getString("PreferredName");
     				if (StringUtils.isBlank(preferredName)){
     					logger.warn("Preferred name is blank. This case is not yet handled by IF import. RECORD UMBER" + CdmUtils.Nz(id));
     				if (isBlank(preferredName)){
     					logger.warn("Preferred name is blank. This case is not yet handled by IF import. RECORD NUMBER" + CdmUtils.Nz(id));
+    				}
     				//Rank rank = Rank.SPECIES();
-...
     				INonViralName name = parser.parseSimpleName(preferredName, NomenclaturalCode.ICNAFP, null);
     				Taxon taxon = Taxon.NewInstance(name, sourceReference);
     				//if name is infraspecific the parent should be the species not the genus
     				Taxon parent;
     				if (!name.isInfraSpecific()){
     				    parent = getParentTaxon(state, rs);
     				//if name is infra-specific the parent should be the species not the genus
     				Integer genusId = rs.getInt("PreferredNameFDCnumber");
     		        if (!name.isInfraSpecific()){
     				    Taxon parent = getParentTaxon(state, genusId);
     				    if (parent == null){
     	                    logger.warn("parent not found for name:" +preferredName);
     	                    logger.warn("parent not found for name:" + preferredName + "ID(PreferredNameIFnumber)" +id+ "; GenusId(PreferredNameFDCnumber): ");
     	                }else{
     	                    classification.addParentChild(parent, taxon, null, null);
+    	                }
     				    classification.addParentChild(parent, taxon, null, null);
+    				}
     				}else {
                         state.getInfraspecificTaxaUUIDs().put(taxon.getUuid(), genusId);
+                    }
     				//author + publication
     				makeAuthorAndPublication(state, rs, name);
-...
     					ExtensionType fossilExtType = getExtensionType(state, ErmsTransformer.uuidExtFossilStatus, "fossil status", "fossil status", "fos. stat.");
     					Extension.NewInstance(taxon, PesiTransformer.STR_FOSSIL_ONLY, fossilExtType);
+    				}
     				//save
     				getTaxonService().saveOrUpdate(taxon);
     				UUID uuidTaxon = getTaxonService().saveOrUpdate(taxon);
     				//getNameService().saveOrUpdate(name);
     				if (name.isInfraSpecific()){
                         state.getInfraspecificTaxaUUIDs().add(uuidTaxon);
+                    }
+    			}
     		} catch (Exception e) {
     			e.printStackTrace();
-...
     		return success;
+    	}
         private Taxon getParentTaxon(IndexFungorumImportState state, ResultSet rs) throws SQLException {
     		Integer genusId = rs.getInt("PreferredNameFDCnumber");
     		Taxon taxon = state.getRelatedObject(NAMESPACE_GENERA, String.valueOf(genusId), Taxon.class);
     		if (taxon == null){
     			logger.warn("Taxon not found for " + genusId);
+    		}
     		return taxon;
         private Taxon getParentTaxon(IndexFungorumImportState state, Integer genusId) {
             return state.getRelatedObject(NAMESPACE_GENERA, String.valueOf(genusId), Taxon.class);
+    	}
     	@Override
     	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, IndexFungorumImportState state) {
     		String nameSpace;
     		Class<?> cdmClass;
     	    String nameSpace;
     		Set<String> idSet;
     		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();

              propertyPaths.add("taxonNodes.parent.*");
              propertyPaths.add("taxonNodes.parent.taxon.*");
              Classification classification = getClassification(state);
             for (UUID infraspecificTaxonUUID: state.getInfraspecificTaxaUUIDs()){
             for (UUID infraspecificTaxonUUID: state.getInfraspecificTaxaUUIDs().keySet()){
             	TransactionStatus txStatus = startTransaction();
             	Taxon infraspecificTaxon = (Taxon)getTaxonService().load(infraspecificTaxonUUID, propertyPaths);
-...
                 List<TaxonBase> potentialParents = getTaxonService().findTaxaByName(matchingConfig);
                         //Taxon.class, parentNameString + "sec. ", MatchMode.BEGINNING, , pageSize, pageNumber, orderHints, propertyPaths)
                         //.searchNames(String uninomial,String infraGenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
                 boolean matched = false;
                 if (potentialParents.size()>1){
                     for (@SuppressWarnings("rawtypes") TaxonBase potentialParent : potentialParents){
                         if (potentialParent.getTitleCache().equals(parentNameString + " sec*")){
                             classification.addParentChild((Taxon)potentialParent, infraspecificTaxon, null, null);
                             matched = true;
                             break;
+                        }
+                    }
                     if (matched == false){
                         logger.warn("Multiple match candidates but no match for " + name.getTitleCache());
+                    }
                 }else if (!potentialParents.isEmpty()){
                     Taxon parent = HibernateProxyHelper.deproxy(potentialParents.get(0), Taxon.class);
                     Taxon child = (Taxon)getTaxonService().load(infraspecificTaxon.getUuid(), propertyPaths);
                     classification.addParentChild(parent, child, null, null);
                     classification.addParentChild(parent, infraspecificTaxon, null, null);
                     matched = true;
                 } else{
                     Integer genusId = state.getInfraspecificTaxaUUIDs().get(infraspecificTaxonUUID);
                     Taxon genusParent = getParentGenus(state, genusId);
     //                Taxon genusParent = state.getRelatedObject(NAMESPACE_GENERA, String.valueOf(genusId), Taxon.class);
                     classification.addParentChild(genusParent, infraspecificTaxon, null, null);
                     logger.warn("Added infraspecific taxon to genus because species does not exist: " + infraspecificTaxon.getTitleCache());
                     matched = true;
+                }
                 if (!matched){
                     System.out.println("No parent for: " + name.getTitleCache());
+                }
                 getTaxonService().saveOrUpdate(infraspecificTaxon);
-...
+            }
+    	}
         private Taxon getParentGenus(IndexFungorumImportState state, Integer genusId) {
             Taxon result = getCommonService().getSourcedObjectByIdInSource(Taxon.class, String.valueOf(genusId), NAMESPACE_GENERA);
             return result;
+        }
         private String getParentNameInfraSpecific(TaxonName taxonName){
             String parentName = taxonName.getGenusOrUninomial() + " " + taxonName.getSpecificEpithet();
             return parentName;

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Revision 02bf7c25

Added by Andreas Müller over 4 years ago