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Revision 87bd976a

Added by Andreas Müller about 4 years ago

ID 87bd976a8d20db39b35d1b5115462e87172a9845
Parent fbdb38bb
Child 6720d336

ref #1447 further improve findIdenticalNames for PESI

     import java.util.Set;
     import java.util.UUID;
     import org.apache.commons.lang3.StringUtils;
     import org.apache.log4j.Logger;
     import org.springframework.transaction.TransactionStatus;
-...
     import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
     import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
     /**
      * Finds taxa with identical {@link TaxonName#getNameCache() name cache} but from different
      * sources (import source) and writes them into multiple csv file.
      * All cases are stored in file xxx_namesAll, some prefiltered files are created for e.g.
      * those having different parents or different authors.
      * Taxa are pairwise compared. If a name appears in 3 sources for each of the 3 pairs 1 record
      * is created below each other. Also if a name appears multiple times (e.g. homonyms) in 1
      * DB and 1 time in another. Each of the multiple names is compared to the other databases
      * record.
      * <BR><BR>
+     *
      * TODO is is necessary to create these extra files? Filters can also be appied in Excel.
+     *
      * @author a.mueller
      * @since 22.01.2020
      */
     public class PesiFindIdenticalNamesActivator {
         private static final Logger logger = Logger.getLogger(PesiFindIdenticalNamesActivator.class);
-...
+            }
+        }
         //old method when all sources were in 1 line
         private boolean isDifferent(Map<UUID, PesiMergeObject> merging, Method method)
                 throws IllegalAccessException, IllegalArgumentException, InvocationTargetException {
             if (method == null){
                 return true;
+            }
             Object value = null;
             boolean isFirst = true;
             for (UUID sourceUuid: merging.keySet()){
                 if (isFirst){
                     value = method.invoke(merging.get(sourceUuid));
                     isFirst = false;
                 }else{
                     Object newValue = method.invoke(merging.get(sourceUuid));
                     if (!CdmUtils.nullSafeEqual(newValue, value)){
                         return true;
+                    }
+                }
+            }
             return false;
+        }
     	private void createHeader(Writer writer, String firstLine){
     	 	try {
                 writer.append(firstLine);
                 writer.append('\n');
                 writeHeaderPair(writer, "taxon uuid");
                 writeHeaderPair(writer, "taxon id");
                 writer.append("next name cache").append(";");
                 writer.append("diff").append(";");
                 writeHeaderPair(writer, "source");
                 writeHeaderPair(writer, "name uuid");
                 writeHeaderPair(writer, "idInSource");
                 writeHeaderPair(writer, "nameCache");
                 writeHeaderPair(writer, "tid");
                 writer.append("use;");
                 writer.append("nameUse;");
                 writer.append("next;");
                 writer.append("diff;");
                 writeHeaderPair(writer, "src");
     //            writeHeaderPair(writer, "nuuid");
     //            writeHeaderPair(writer, "idInSource");
                 writer.append("nameCache;");
                 writeHeaderPair(writer, "author");
                 writeHeaderPair(writer, "nom.ref.");
                 writeHeaderPair(writer, "rank");
                 writeHeaderPair(writer, "kingdom");
                 writeHeaderPair(writer, "phylum");
-...
                 writeHeaderPair(writer, "parentString");
                 writeHeaderPair(writer, "parentRankString");
                 writeHeaderPair(writer, "status");
                 writeHeaderPair(writer, "tuuid");
                 writer.append('\n');
             } catch (IOException e) {
                 e.printStackTrace();
-...
                PesiMergeObject merge1, PesiMergeObject merge2,
                Method method, boolean isNextNameCache){
             writePair(writer, merge1, merge2, "UuidTaxon");
             writePair(writer, merge1, merge2, "IdTaxon");
             writePair(writer, merge1, merge2, "IdTaxon", Compare.NO);
             writeSingleValue(writer, "");
             writeSingleValue(writer, "");
             writeSingleValue(writer, isNextNameCache?"1":"0");
             boolean different = isDifferent(merge1,  merge2, method);
             writeSingleValue(writer, different?"1":"0");
             writeSingleValue(writer, sourcesLabels.get(UUID.fromString(merge1.getUuidSource())));
             writeSingleValue(writer, sourcesLabels.get(UUID.fromString(merge2.getUuidSource())));
             writePair(writer, merge1, merge2, "UuidName");
             writePair(writer, merge1, merge2, "IdInSource");
             writePair(writer, merge1, merge2, "NameCache");
             writePair(writer, merge1, merge2, "Author");
             writePair(writer, merge1, merge2, "Rank");
             writePairNode(writer, merge1, merge2, "Kingdom");
             writePairNode(writer, merge1, merge2, "Phylum");
             writePairNode(writer, merge1, merge2, "Family");
             writePair(writer, merge1, merge2, "ParentString");
             writePair(writer, merge1, merge2, "ParentRankString");
             writeSingleValue(writer, merge1.isStatus()?"accepted":"synonym");
             writeSingleValue(writer, merge2.isStatus()?"accepted":"synonym");
     //        writePair(writer, merge1, merge2, "UuidName");
     //        writePair(writer, merge1, merge2, "IdInSource");
             writeSingleValue(writer, merge1.getNameCache());
     //        writePair(writer, merge1, merge2, "NameCache");
             writePair(writer, merge1, merge2, "Author", Compare.YES);
             writePair(writer, merge1, merge2, "NomenclaturalReference", Compare.YES);
             writePair(writer, merge1, merge2, "Rank", Compare.YES);
             writePair(writer, merge1, merge2, "KingdomCache", Compare.KEEP_FIRST);
             writePair(writer, merge1, merge2, "PhylumCache", Compare.YES);
             writePair(writer, merge1, merge2, "FamilyCache", Compare.YES);
             writePair(writer, merge1, merge2, "ParentString", Compare.YES);
             writePair(writer, merge1, merge2, "ParentRankString", Compare.YES);
             writePair(writer, merge1, merge2, "StatusStr", Compare.YES);
             writePair(writer, merge1, merge2, "UuidTaxon", Compare.YES);
             try {
                 writer.append('\n');
             } catch (IOException e) {
-...
+            }
+        }
         private void writePairNode(Writer writer, PesiMergeObject merge1, PesiMergeObject merge2, String methodName) {
             try {
                 Method method = PesiMergeObject.class.getDeclaredMethod("get"+methodName);
                 TaxonNodeDto value = (TaxonNodeDto) method.invoke(merge1);
                 writer.append(value==null?"":value.getTitleCache()).append(";");
                 value = (TaxonNodeDto) method.invoke(merge2);
                 writer.append(value==null?"":value.getTitleCache()).append(";");
             } catch (Exception e) {
                 e.printStackTrace();
         private enum Compare{
             NO,
             YES,
             KEEP_FIRST;
             boolean isAnyCompare(){
                 return this == NO;
+            }
+        }
         private void writePair(Writer writer, PesiMergeObject merge1, PesiMergeObject merge2, String methodName) {
         private void writePair(Writer writer, PesiMergeObject merge1, PesiMergeObject merge2, String methodName, Compare compare) {
             try {
                 Method method = PesiMergeObject.class.getDeclaredMethod("get"+methodName);
                 String value1 = (String) method.invoke(merge1);
                 writer.append(normalize(value1)).append(";");
                 String value2 = (String) method.invoke(merge2);
                 if (compare.isAnyCompare() && CdmUtils.nullSafeEqual(value1, value2)){
                     value2 = StringUtils.isBlank(value2)? "":"-";
                     if (compare == Compare.YES){
                         value1 = value2;
+                    }
+                }
                 writer.append(normalize(value1)).append(";");
                 writer.append(normalize(value2)).append(";");
             } catch (Exception e) {
                 e.printStackTrace();
-...
             return CdmUtils.Nz(val).replace(";", "@");
+        }
         private void writeCsvLine(Writer writer, Map<UUID,PesiMergeObject> mergeObjects, Map<UUID,String> sources) throws IOException{
             for (UUID uuid : sourceRefUuids){
     	        PesiMergeObject merging = mergeObjects.get(uuid);
     	        if(merging == null){
     	            continue;
+    	        }
     	        writer.append(Nz(sources.get(uuid))).append(";");
                 writer.append(Nz(merging.getUuidName())).append(";");
     	        writer.append(Nz(merging.getIdInSource())).append(";");
     	        writer.append(Nz(merging.getNameCache())).append(";");
     	        writer.append(Nz(merging.getAuthor())).append(";");
     	        writer.append(Nz(merging.getRank())).append(";");
     	        if (merging.isStatus()){
     	            writer.append("accepted").append(";");
     	        }else{
     	            writer.append("synonym").append(";");
+    	        }
     	        writer.append(Nz(merging.getPhylum() != null? merging.getPhylum().getTitleCache(): "")).append(";");
     	        writer.append(Nz(merging.getParentString())).append(";");
     	        writer.append(Nz(merging.getParentRankString())).append(";");
+    	    }
             writer.append('\n');
+    	}
         private List<Map<UUID,List<PesiMergeObject>>> createMergeObjects(
                 Map<String, Map<UUID, Set<TaxonName>>> identicalNames,
     	        CdmApplicationController appCtr){
-...
                         //authorship
                         mergeObject.setAuthor(name.getAuthorshipCache());
                         //nom.ref.
                         mergeObject.setNomenclaturalReference(name.getNomenclaturalReference()== null?null: name.getNomenclaturalReference().getAbbrevTitleCache());
                         //rank
                         mergeObject.setRank(name.getRank().getLabel());

     	private String nameCache;
     	private boolean status;
     	private boolean isStatus;
     	private String author;
     	private String rank;
     	private String nomenclaturalReference;
     	private TaxonNodeDto phylum;
     	private TaxonNodeDto kingdom;
-...
     		this.rank = rank;
+    	}
     	public TaxonNodeDto getPhylum() {
     		return phylum;
+    	}
     	public void setPhylum(TaxonNodeDto phylum) {
     		this.phylum = phylum;
+    	}
     	public boolean isStatus() {
     		return status;
     		return isStatus;
+    	}
         public String getStatusStr() {
             return isStatus? "accepted":"synonym";
+        }
     	public void setStatus(boolean status) {
     		this.status = status;
     		this.isStatus = status;
+    	}
     	public String getAuthor() {
-...
         public TaxonNodeDto getKingdom() {
             return kingdom;
+        }
         public String getKingdomCache() {
             return kingdom == null? null : kingdom.getNameCache();
+        }
         public void setKingdom(TaxonNodeDto kingdom) {
             this.kingdom = kingdom;
+        }
         public TaxonNodeDto getPhylum() {
             return phylum;
+        }
         public String getPhylumCache() {
             return phylum == null? null : phylum.getNameCache();
+        }
         public void setPhylum(TaxonNodeDto phylum) {
             this.phylum = phylum;
+        }
         public TaxonNodeDto getFamily() {
             return family;
+        }
         public String getFamilyCache() {
             return family == null? null : family.getNameCache();
+        }
         public void setFamily(TaxonNodeDto family) {
             this.family = family;
+        }
-...
         public void setUuidSource(String uuidSource) {
             this.uuidSource = uuidSource;
+        }
         public String getNomenclaturalReference() {
             return nomenclaturalReference;
+        }
         public void setNomenclaturalReference(String nomenclaturalReference) {
             this.nomenclaturalReference = nomenclaturalReference;
+        }
+    }

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Revision 87bd976a

Added by Andreas Müller about 4 years ago