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Revision 8b256be0

Added by Andreas Müller over 3 years ago

ID 8b256be0d8ec26a61f3fb35069df5c8fc3dbe975
Parent 45c2e0b4
Child cd156f0a

ref #6591 adapt PESI import to new original spellings handling

     import eu.etaxonomy.cdm.model.name.INonViralName;
     import eu.etaxonomy.cdm.model.name.NameRelationship;
     import eu.etaxonomy.cdm.model.name.NameRelationshipType;
     import eu.etaxonomy.cdm.model.name.NomenclaturalSource;
     import eu.etaxonomy.cdm.model.name.TaxonName;
     import eu.etaxonomy.cdm.model.reference.Reference;
     import eu.etaxonomy.cdm.model.taxon.Synonym;
-...
     		return list;
+    	}
     	protected List<NomenclaturalSource> getNextOriginalSpellingPartition(
     	        int pageSize, int partitionCount, List<String> propertyPaths) {
            List<NomenclaturalSource> result = new ArrayList<>();
            List<OrderHint> orderHints = null;
            List<NomenclaturalSource> list;
            list = getNameService().listOriginalSpellings(pageSize, partitionCount, orderHints, propertyPaths);
            if (list.isEmpty()){
                return null;
+           }
            for (NomenclaturalSource rel : list){
                if (isPesiOriginalSpelling(rel)){
                    result.add(rel);
+               }
+           }
            return result;
+        }
     	protected <CLASS extends RelationshipBase> List<CLASS> getNextNameRelationshipPartition(
     	                Class<CLASS> clazz, int pageSize, int partitionCount, List<String> propertyPaths) {
-...
     		return (isPesiName(name1) && isPesiName(name2));
+    	}
     	protected boolean isPesiOriginalSpelling(NomenclaturalSource nomSource){
             TaxonName name1 = nomSource.getNameUsedInSource();
             TaxonName name2 = nomSource.getSourcedName();
             return (isPesiName(name1) && isPesiName(name2));
+        }
     	private boolean isPesiName(TaxonName name) {
     		return hasPesiTaxon(name) || isPurePesiName(name);
+    	}

     import eu.etaxonomy.cdm.model.name.HybridRelationship;
     import eu.etaxonomy.cdm.model.name.NameRelationship;
     import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
     import eu.etaxonomy.cdm.model.name.NomenclaturalSource;
     import eu.etaxonomy.cdm.model.name.TaxonName;
     import eu.etaxonomy.cdm.model.taxon.Synonym;
     import eu.etaxonomy.cdm.model.taxon.Taxon;
-...
     	private PesiExportMapping mapping;
     	private PesiExportMapping synonymMapping;
     	private PesiExportMapping taxonNodeMapping;
     	private PesiExportMapping originalSpellingMapping;
     	public PesiRelTaxonExport() {
     		super();
-...
                 taxonNodeMapping = getTaxonNodeMapping();
                 taxonNodeMapping.initialize(state);
     			//Export taxon relations
     			success &= doPhase01(state, mapping);
-...
             while ((hybridList = getNextNameRelationshipPartition(HybridRelationship.class, limit, partitionCount++, null)) != null   ) {
                 txStatus = handleNameRelationList(state, txStatus, hybridList);
+            }
             //original spellings
             List<NomenclaturalSource> originalSpellingList;
             partitionCount = 0;
             while ((originalSpellingList = getNextOriginalSpellingPartition(limit, partitionCount++, null)) != null   ) {
                 txStatus = handleOriginalSpellingList(state, txStatus, originalSpellingList);
+            }
             commitTransaction(txStatus);
     		logger.info("End PHASE 2: Name Relationships ...");
     		state.setCurrentFromObject(null);
-...
             				mapping.invoke(rel);
+            			}
+            		}
             		fromList = null;
             		toList = null;
             	} catch (Exception e) {
             		logger.error(e.getMessage() + ". Relationship: " +  rel.getUuid());
             		e.printStackTrace();
-...
             return txStatus;
+        }
         private TransactionStatus handleOriginalSpellingList(PesiExportState state, TransactionStatus txStatus,
                 List<NomenclaturalSource> list) {
             for (NomenclaturalSource nomSource : list){
                 try {
                     TaxonName name1 = nomSource.getNameUsedInSource();
                     TaxonName name2 = nomSource.getSourcedName();
                     List<IdentifiableEntity> fromList = new ArrayList<>();
                     List<IdentifiableEntity> toList = new ArrayList<>();
                     makeList(name1, fromList);
                     makeList(name2, toList);
                     for (IdentifiableEntity<?> fromEntity : fromList){
                         for (IdentifiableEntity<?> toEntity : toList){
                             //TODO set entities to state
                             state.setCurrentFromObject(fromEntity);
                             state.setCurrentToObject(toEntity);
                             originalSpellingMapping.invoke(nomSource);
+                        }
+                    }
                 } catch (Exception e) {
                     logger.error(e.getMessage() + ". NomenclaturalSource: " +  nomSource.getUuid());
                     e.printStackTrace();
+                }
+            }
             commitTransaction(txStatus);
             txStatus = startTransaction();
             return txStatus;
+        }
     	private void makeList(TaxonName name, List<IdentifiableEntity> list) {
     		if (! hasPesiTaxon(name)){
     			list.add(name);
     		}else{
     			for (TaxonBase<?> taxon:  getPesiTaxa(name)){
     			for (TaxonBase<?> taxon: getPesiTaxa(name)){
     				list.add(taxon);
+    			}
+    		}
-...
             return state.getDbId(parentTaxon);
+        }
         /**
          * Returns the id of the previously defined fromObject.
          * @see MethodMapper
          */
         @SuppressWarnings("unused")
         private static Integer getFromObject(PesiExportState state) {
             return state.getDbId(state.getCurrentFromObject());
+        }
         /**
          * Returns the id of the previously defined fromObject.
          * @see MethodMapper
          */
         @SuppressWarnings("unused")
         private static Integer getToObject(PesiExportState state) {
             return state.getDbId(state.getCurrentToObject());
+        }
     	/**
     	 * Returns the <code>TaxonFk2</code> attribute. It corresponds to a CDM <code>SynonymRelationship</code>.
     	 * @param relationship The {@link RelationshipBase Relationship}.
-...
     		if (relationship.isInstanceOf(TaxonRelationship.class)) {
     			TaxonRelationship tr = (TaxonRelationship)relationship;
     			taxonBase = (isFrom) ? tr.getFromTaxon():  tr.getToTaxon();
     		} else if (relationship.isInstanceOf(NameRelationship.class) ||  relationship.isInstanceOf(HybridRelationship.class)) {
     		} else if (relationship.isInstanceOf(NameRelationship.class)
     		        || relationship.isInstanceOf(HybridRelationship.class)) {
     			if (isFrom){
     				return state.getDbId(state.getCurrentFromObject());
     			}else{
-...
     		return null;
+    	}
        private static Integer getObjectFk(NomenclaturalSource nomSource, PesiExportState state, boolean isFrom) {
             if (isFrom){
                 return state.getDbId(state.getCurrentFromObject());
             }else{
                 return state.getDbId(state.getCurrentToObject());
+            }
+        }
         @SuppressWarnings("unused")  //for synonym mapping
         private static String getSynonymTypeCache(Synonym synonym, PesiExportState state) {
             String result = null;
-...
     		return mapping;
+    	}
     	   /**
     	/**
          * Returns the CDM to PESI specific export mappings.
          * @return The {@link PesiExportMapping PesiExportMapping}.
          */
-...
             mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getParent", TaxonNode.class, PesiExportState.class));
             mapping.addMapper(DbObjectMapper.NewInstance("taxon", "TaxonFk1"));
             mapping.addMapper(DbFixedIntegerMapper.NewInstance(101, "RelTaxonQualifierFk"));
             mapping.addMapper(DbFixedIntegerMapper.NewInstance(PesiTransformer.IS_TAXONOMICALLY_INCLUDED_IN, "RelTaxonQualifierFk"));
             mapping.addMapper(DbFixedStringMapper.NewInstance("is taxonomically included in", "RelQualifierCache"));
     //        mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes"));
             return mapping;
+        }
         PesiExportMapping getOriginalSpellingMapping() {
             PesiExportMapping mapping = new PesiExportMapping(dbTableName);
             mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getFromObject", PesiExportState.class));
             mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getToObject", PesiExportState.class));
             mapping.addMapper(DbFixedIntegerMapper.NewInstance(PesiTransformer.IS_ORIGINAL_SPELLING_FOR, "RelTaxonQualifierFk"));
             mapping.addMapper(DbFixedStringMapper.NewInstance("is original spelling for", "RelQualifierCache"));
     //        mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes"));
             return mapping;
+        }
         @Override
         protected boolean doCheck(PesiExportState state) {
-...
         protected boolean isIgnore(PesiExportState state) {
             return ! state.getConfig().isDoRelTaxa();
+        }
+    }
+    }

     	private static int IS_ORTHOGRAPHIC_VARIANT_OF = 16;
     	private static int IS_ALTERNATIVE_NAME_FOR = 17;
     	private static int HAS_SAME_TYPE_AS = 18;
     	private static int IS_ORIGINAL_SPELLING_FOR = 19;
     	public static int IS_ORIGINAL_SPELLING_FOR = 19;
     	private static int IS_BLOCKING_NAME_FOR = 20;
     	private static int IS_LECTOTYPE_OF = 61;
     	private static int TYPE_NOT_DESIGNATED = 62;
-...
     			return IS_TREATED_AS_LATER_HOMONYM_OF;
     		} else if (type.equals(NameRelationshipType.ORTHOGRAPHIC_VARIANT())) {
     			return IS_ORTHOGRAPHIC_VARIANT_OF;
     	    } else if (type.equals(NameRelationshipType.ORIGINAL_SPELLING())) {
     	        return IS_ORIGINAL_SPELLING_FOR;
     //	    } else if (type.equals(NameRelationshipType.ORIGINAL_SPELLING())) {
     //	        return IS_ORIGINAL_SPELLING_FOR;
             } else if (type.equals(NameRelationshipType.BLOCKING_NAME_FOR())) {
                 return IS_BLOCKING_NAME_FOR;
     		} else if (type.equals(NameRelationshipType.ALTERNATIVE_NAME())) {

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Revision 8b256be0

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Added by Andreas Müller over 3 years ago

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