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         @Override
         public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
             ResultSet rs = partitioner.getResultSet();
             Classification classification = getClassificationService().load(state.getConfig().getClassificationUuid());
             Classification gesamtListeClassification = getClassificationService().load(state.getConfig().getClassificationUuid());
             Classification checklistClassification = getClassificationService().load(RedListUtil.checkListClassificationUuid);
             try {
                 while (rs.next()){
                     makeSingleTaxonNode(state, rs, classification);
                     makeSingleTaxonNode(state, rs, gesamtListeClassification, checklistClassification);
+                }
             } catch (SQLException e) {
-...
+            }
             logger.info("Update classification (1000 nodes)");
             getClassificationService().saveOrUpdate(classification);
             getClassificationService().saveOrUpdate(gesamtListeClassification);
             getClassificationService().saveOrUpdate(checklistClassification);
             return true;
+        }
         private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs, Classification classification)
         private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs, Classification gesamtListeClassification, Classification checklistClassification)
                 throws SQLException {
             long id = rs.getLong(RedListUtil.NAMNR);
             String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER));
             String gueltString = rs.getString(RedListUtil.GUELT);
             String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);
             TaxonBase taxonBase = state.getRelatedObject(RedListUtil.TAXON_NAMESPACE, String.valueOf(id), TaxonBase.class);
             Taxon parent = (Taxon) state.getRelatedObject(RedListUtil.TAXON_NAMESPACE, parentId, TaxonBase.class);
             //Gesamtliste
             TaxonBase taxonBaseGL = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);
             Taxon parentGL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, TaxonBase.class);
             createParentChildNodes(gesamtListeClassification, id, gueltString, taxZusatzString, taxonBaseGL, parentGL);
             //Checkliste
             TaxonBase taxonBaseCL = state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);
             Taxon parentCL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, parentId, TaxonBase.class);
             if(taxonBaseCL!=null && parentCL!=null){//null check necessary because not all taxa exist in the checklist
                 createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBaseCL, parentCL);
+            }
+        }
         private void createParentChildNodes(Classification classification, long id, String gueltString,
                 String taxZusatzString, TaxonBase taxonBase, Taxon parent) {
             if(parent==null){
                 RedListUtil.logMessage(id, "parent taxon of "+taxonBase+"  is null." , logger);
+            }
             if(taxonBase==null){
                 RedListUtil.logMessage(id, "child taxon/synonym of "+parent+"  is null." , logger);
+            }
             //taxon
             if(taxonBase.isInstanceOf(Taxon.class)){
                 //misapplied name
-...
+                    }
+                }
+            }
             //synonym
             else if(taxonBase.isInstanceOf(Synonym.class)){
                 //basionym
                 if(gueltString.equals(RedListUtil.GUELT_BASIONYM)){
-...
+                }
                 //regular synonym
                 else{
                     //TODO: how to correctly add a synonym?
                     SynonymRelationship synonymRelationship = parent.addSynonym((Synonym) taxonBase, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null);
                     //TAX_ZUSATZ
-...
                             taxonBase.setAppendedPhrase(taxZusatzString);
+                        }
                         else{
                             RedListUtil.logMessage(id, "unknown value for column "+RedListUtil.TAX_ZUSATZ, logger);
                             RedListUtil.logMessage(id, "unknown value "+taxZusatzString+" for column "+RedListUtil.TAX_ZUSATZ, logger);
+                        }
+                    }
+                }
-...
             } catch (SQLException e) {
                 e.printStackTrace();
+            }
             Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_NAMESPACE);
             result.put(RedListUtil.TAXON_NAMESPACE, taxonMap);
             Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);
             result.put(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, taxonMap);
             return result;
+        }
         private void makeClassification(RedListGefaesspflanzenImportState state) {
             //Gesamtliste
             Classification classification = Classification.NewInstance(state.getConfig().getClassificationName());
             classification.setUuid(state.getConfig().getClassificationUuid());
             getClassificationService().save(classification);
             //checkliste
             Classification checklistClassification = Classification.NewInstance("Checkliste");
             checklistClassification.setUuid(RedListUtil.checkListClassificationUuid);
             getClassificationService().save(checklistClassification);
+        }
         @Override

     import eu.etaxonomy.cdm.model.taxon.Synonym;
     import eu.etaxonomy.cdm.model.taxon.Taxon;
     import eu.etaxonomy.cdm.model.taxon.TaxonBase;
     import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
     import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
     /**
+     *
-...
                 RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);
                 return;
+            }
             taxaToSave.add(taxonBase);
             /*check if taxon/synonym is also in checklist
              * 1. create new taxon with the same name (in the checklist classification)
              * 2. create congruent concept relationship between both
              */
             String clTaxonString = rs.getString(RedListUtil.CL_TAXON);
             if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
                 TaxonBase clone = (TaxonBase) taxonBase.clone();
                 clone.setName(name);
                 if(taxonBase.isInstanceOf(Taxon.class)){
                     TaxonRelationship taxonRelation = ((Taxon) taxonBase).addTaxonRelation((Taxon) clone, TaxonRelationshipType.CONGRUENT_TO(), null, null);
                     taxonRelation.setDoubtful(true);//TODO Ist das mit " mit Fragezeichen" gemeint?
+                }
                 ImportHelper.setOriginalSource(clone, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);
                 state.getTaxonMap().put(id, clone.getUuid());
                 taxaToSave.add(clone);
+            }
             //id
             ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_NAMESPACE);
             ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);
             state.getTaxonMap().put(id, taxonBase.getUuid());
+        }

     	private final Map<String, UUID> authorMap = new HashMap<String, UUID>();
     	private final Map<Long, UUID> nameMap = new HashMap<Long, UUID>();
     	private final Map<Long, UUID> taxonMap = new HashMap<Long, UUID>();
     	private UUID checklistClassificationUuid;
         protected RedListGefaesspflanzenImportState(RedListGefaesspflanzenImportConfigurator config) {
             super(config);
-...
             return taxonMap;
+        }
         public void setChecklistClassificationUuid(UUID checklistClassificationUuid) {
             this.checklistClassificationUuid = checklistClassificationUuid;
+        }
         public UUID getChecklistClassificationUuid() {
             return checklistClassificationUuid;
+        }
+    }

     */
     package eu.etaxonomy.cdm.io.redlist.gefaesspflanzen;
     import java.util.UUID;
     import org.apache.log4j.Logger;
     /**
-...
      */
     public class RedListUtil {
         public static final UUID checkListClassificationUuid = UUID.fromString("928a4695-c055-465e-99da-07322384b0b7");
         public static final String NAME_NAMESPACE = "name";
         public static final String TAXON_NAMESPACE = "taxon";
         public static final String TAXON_GESAMTLISTE_NAMESPACE = "taxon_gesamt_liste";
         public static final String TAXON_CHECKLISTE_NAMESPACE = "taxon_checkliste";
         public static final String AUTHOR_NAMESPACE = "author";
         public static final String AUCT = "auct.";
-...
         public static final String RANG = "RANG";
         public static final String TAXNAME = "TAXNAME";
         public static final String AUTOR = "AUTOR";
         public static final String CL_TAXON = "CL_TAXON";
         public static void logMessage(long id, String message, Logger logger){
             logger.error(NAMNR+": "+id+" "+message);

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Revision 0873eb1c

Added by Patrick Plitzner about 8 years ago