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package eu.etaxonomy.cdm.app.pesi.merging;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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import java.util.TreeSet;
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import java.util.UUID;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.app.pesi.FaunaEuropaeaSources;
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import eu.etaxonomy.cdm.app.util.TestDatabase;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaImportConfigurator;
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import eu.etaxonomy.cdm.io.pesi.merging.FaunaEuErmsMerging;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.TaxonNameComparator;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonComparator;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.HibernateProxyHelperExtended;
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public class FaunaEuErmsFindIdenticalNamesActivator {
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static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.cdm_test_jaxb2();
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//static final ICdmDataSource ermsSource = CdmDestinations.cdm_test_andreasM();
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//TODO hole aus beiden DB alle TaxonNameBases
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private CdmApplicationController initDb(ICdmDataSource db) {
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// Init source DB
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CdmApplicationController appCtrInit = null;
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appCtrInit = TestDatabase.initDb(db, DbSchemaValidation.VALIDATE, false);
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return appCtrInit;
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}
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/**
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* @param args
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*/
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public static void main(String[] args) {
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FaunaEuErmsFindIdenticalNamesActivator sc = new FaunaEuErmsFindIdenticalNamesActivator();
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CdmApplicationController appCtrFaunaEu = sc.initDb(faunaEuropaeaSource);
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String sFileName = "c:\\test";
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//CdmApplicationController appCtrErms = sc.initDb(ermsSource);
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List<String> propertyPaths = new ArrayList<String>();
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propertyPaths.add("sources.*");
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propertyPaths.add("sources.idInSource");
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propertyPaths.add("sources.idNamespace");
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propertyPaths.add("taxonBases.*");
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propertyPaths.add("taxonBases.relationsFromThisTaxon");
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propertyPaths.add("taxonBases.taxonNodes.*");
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propertyPaths.add("taxonBases.taxonNodes.parent.*");
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propertyPaths.add("taxonBases.taxonNodes.parent.taxon.name.*");
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System.err.println("Start getIdenticalNames...");
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List<TaxonNameBase> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(propertyPaths);
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//List<UUID> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(propertyPaths);
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System.err.println("first name: " + namesOfIdenticalTaxa.get(0) + " " + namesOfIdenticalTaxa.size());
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TaxonNameBase zooName = (TaxonNameBase)namesOfIdenticalTaxa.get(0);
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System.err.println(zooName + " nr of taxa " + namesOfIdenticalTaxa.size());
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//TaxonNameComparator taxComp = new TaxonNameComparator();
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//Collections.sort(namesOfIdenticalTaxa,taxComp);
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System.err.println(namesOfIdenticalTaxa.get(0) + " - " + namesOfIdenticalTaxa.get(1) + " - " + namesOfIdenticalTaxa.get(2));
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List<FaunaEuErmsMerging> mergingObjects = new ArrayList<FaunaEuErmsMerging>();
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FaunaEuErmsMerging mergeObject;
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TaxonNameBase faunaEuTaxName;
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TaxonNameBase ermsTaxName;
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mergingObjects= sc.createMergeObjects(namesOfIdenticalTaxa, appCtrFaunaEu);
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sc.writeSameNamesdifferentAuthorToCsv(mergingObjects, sFileName + "_authors.csv");
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sc.writeSameNamesdifferentStatusToCsv(mergingObjects, sFileName + "_status.csv");
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sc.writeSameNamesToCsVFile(mergingObjects, sFileName + "_names.csv");
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sc.writeSameNamesdifferentPhylumToCsv(mergingObjects, sFileName + "_phylum.csv");
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System.out.println("End merging Fauna Europaea and Erms");
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}
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private boolean writeSameNamesToCsVFile(
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List<FaunaEuErmsMerging> mergingObjects, String string) {
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try{
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FileWriter writer = new FileWriter(string);
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//create Header
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String firstLine = "same names";
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createHeader(writer, firstLine);
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for (FaunaEuErmsMerging merging : mergingObjects){
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writeCsvLine(writer, merging) ;
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}
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writer.flush();
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writer.close();
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}
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catch(IOException e)
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{
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return false;
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}
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return true;
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}
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private boolean writeSameNamesdifferentPhylumToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
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try
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{
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FileWriter writer = new FileWriter(sfileName);
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//create Header
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String firstLine = "same names but different phylum";
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createHeader(writer, firstLine);
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//write data
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for (FaunaEuErmsMerging merging : mergingObjects){
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//TODO
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if ((merging.getPhylumInErms()== null )^ (merging.getPhylumInFaunaEu()== null)){
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writeCsvLine(writer, merging) ;
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}else if(!((merging.getPhylumInErms()==null) && (merging.getPhylumInFaunaEu()==null))){
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if(!merging.getPhylumInErms().equals(merging.getPhylumInFaunaEu())){
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writeCsvLine(writer, merging) ;
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}
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}
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}
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writer.flush();
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writer.close();
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}
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catch(IOException e)
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{
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return false;
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}
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return true;
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}
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private boolean writeSameNamesdifferentRankToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
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try
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{
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FileWriter writer = new FileWriter(sfileName);
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String firstLine = "same names but different rank";
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//create Header
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createHeader(writer, firstLine);
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//write data
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for (FaunaEuErmsMerging merging : mergingObjects){
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if (!merging.getRankInErms().equals(merging.getRankInFaunaEu())){
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writeCsvLine(writer, merging);
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}
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}
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writer.flush();
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writer.close();
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}
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catch(IOException e)
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{
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return false;
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}
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return true;
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}
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private void createHeader(FileWriter writer, String firstLine) throws IOException{
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writer.append(firstLine);
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writer.append('\n');
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writer.append("uuid in Fauna Europaea");
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writer.append(';');
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writer.append("id in Fauna Europaea");
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writer.append(';');
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writer.append("name");
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writer.append(';');
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writer.append("author");
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writer.append(';');
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writer.append("rank");
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writer.append(';');
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writer.append("state");
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writer.append(';');
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writer.append("phylum");
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writer.append(';');
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writer.append("parent");
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writer.append(';');
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writer.append("parent rank");
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writer.append(';');
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writer.append("uuid in Erms");
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writer.append(';');
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writer.append("id in Erms");
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writer.append(';');
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writer.append("name");
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writer.append(';');
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writer.append("author");
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writer.append(';');
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writer.append("rank");
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writer.append(';');
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writer.append("state");
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writer.append(';');
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writer.append("phylum");
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writer.append(';');
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writer.append("parent");
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writer.append(';');
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writer.append("parent rank");
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writer.append('\n');
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}
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private boolean writeSameNamesdifferentStatusToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
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try
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{
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FileWriter writer = new FileWriter(sfileName);
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//create Header
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String firstLine = "same names but different status";
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createHeader(writer, firstLine);
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//write data
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for (FaunaEuErmsMerging merging : mergingObjects){
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if (merging.isStatInErms()^merging.isStatInFaunaEu()){
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writeCsvLine(writer, merging);
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}
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}
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writer.flush();
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writer.close();
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}
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catch(IOException e)
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{
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return false;
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}
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return true;
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}
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private boolean writeSameNamesdifferentAuthorToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
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try
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{
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FileWriter writer = new FileWriter(sfileName);
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//create Header
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String firstLine = "same names but different authors";
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createHeader(writer, firstLine);
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//write data
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for (FaunaEuErmsMerging merging : mergingObjects){
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if (!merging.getAuthorInErms().equals(merging.getAuthorInFaunaEu())){
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writeCsvLine(writer, merging);
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}
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}
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272
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writer.flush();
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writer.close();
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}
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catch(IOException e)
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{
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return false;
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279
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}
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return true;
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}
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282
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283
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private void writeCsvLine(FileWriter writer, FaunaEuErmsMerging merging) throws IOException{
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285
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writer.append(merging.getUuidFaunaEu());
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writer.append(';');
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writer.append(merging.getIdInFaunaEu());
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writer.append(';');
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writer.append(merging.getNameCacheInFaunaEu());
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writer.append(';');
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writer.append(merging.getAuthorInFaunaEu());
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writer.append(';');
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writer.append(merging.getRankInFaunaEu());
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writer.append(';');
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295
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if (merging.isStatInFaunaEu()){
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writer.append("accepted");
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297
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}else{
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writer.append("synonym");
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}
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300
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writer.append(';');
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writer.append(merging.getPhylumInFaunaEu());
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writer.append(';');
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writer.append(merging.getParentStringInFaunaEu());
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writer.append(';');
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writer.append(merging.getParentRankStringInFaunaEu());
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writer.append(';');
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307
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308
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writer.append(merging.getUuidErms());
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writer.append(';');
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writer.append(merging.getIdInErms());
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311
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writer.append(';');
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312
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writer.append(merging.getNameCacheInErms());
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313
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writer.append(';');
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314
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writer.append(merging.getAuthorInErms());
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writer.append(';');
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316
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writer.append(merging.getRankInErms());
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317
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writer.append(';');
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318
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if (merging.isStatInErms()){
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319
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writer.append("accepted");
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320
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}else{
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321
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writer.append("synonym");
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322
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}
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323
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324
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writer.append(';');
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325
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writer.append(merging.getPhylumInErms());
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writer.append(';');
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327
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writer.append(merging.getParentStringInErms());
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writer.append(';');
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329
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writer.append(merging.getParentRankStringInErms());
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writer.append('\n');
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}
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332
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333
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334
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private List<FaunaEuErmsMerging> createMergeObjects(List<TaxonNameBase> names, CdmApplicationController appCtr){
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335
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336
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List<FaunaEuErmsMerging> merge = new ArrayList<FaunaEuErmsMerging>();
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337
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ZoologicalName zooName, zooName2;
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338
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FaunaEuErmsMerging mergeObject;
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339
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String idInSource1;
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340
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for (int i = 0; i<names.size()-1; i=i+2){
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zooName = (ZoologicalName)names.get(i);
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zooName2 = (ZoologicalName)names.get(i+1);
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343
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mergeObject = new FaunaEuErmsMerging();
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344
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//TODO:?berpr?fen, ob die beiden Namen identisch sind und aus unterschiedlichen DB kommen
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345
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346
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//getPhylum
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347
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String phylum1 = null;
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348
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if (!zooName.getRank().isHigher(Rank.PHYLUM())){
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349
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phylum1 =appCtr.getTaxonService().getPhylumName(zooName);
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350
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}
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351
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352
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String phylum2 = null;
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353
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if (!zooName2.getRank().isHigher(Rank.PHYLUM())){
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354
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phylum2 = appCtr.getTaxonService().getPhylumName(zooName2);
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355
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}
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356
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mergeObject.setPhylumInErms(phylum1);
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357
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mergeObject.setPhylumInFaunaEu(phylum2);
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358
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359
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//getUuids
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360
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mergeObject.setUuidErms(zooName.getUuid().toString());
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361
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mergeObject.setUuidFaunaEu(zooName.getUuid().toString());
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362
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|
363
|
Iterator sources = zooName.getSources().iterator();
|
|
364
|
if (sources.hasNext()){
|
|
365
|
IdentifiableSource source = (IdentifiableSource)sources.next();
|
|
366
|
idInSource1 = source.getIdInSource();
|
|
367
|
mergeObject.setIdInErms(idInSource1);
|
|
368
|
}
|
|
369
|
sources = zooName2.getSources().iterator();
|
|
370
|
if (sources.hasNext()){
|
|
371
|
IdentifiableSource source = (IdentifiableSource)sources.next();
|
|
372
|
idInSource1 = source.getIdInSource();
|
|
373
|
mergeObject.setIdInFaunaEu(idInSource1);
|
|
374
|
}
|
|
375
|
|
|
376
|
mergeObject.setNameCacheInErms(zooName.getNameCache());
|
|
377
|
mergeObject.setNameCacheInFaunaEu(zooName2.getNameCache());
|
|
378
|
|
|
379
|
mergeObject.setAuthorInErms(zooName.getAuthorshipCache());
|
|
380
|
mergeObject.setAuthorInFaunaEu(zooName2.getAuthorshipCache());
|
|
381
|
Set<Taxon> taxa = zooName.getTaxa();
|
|
382
|
if (!taxa.isEmpty()){
|
|
383
|
mergeObject.setStatInErms(true);
|
|
384
|
Iterator taxaIterator = taxa.iterator();
|
|
385
|
Taxon taxon = null;
|
|
386
|
while (taxaIterator.hasNext()){
|
|
387
|
taxon = (Taxon) taxaIterator.next();
|
|
388
|
if (!taxon.isMisapplication()){
|
|
389
|
break;
|
|
390
|
}
|
|
391
|
}
|
|
392
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
|
393
|
Iterator taxonNodeIterator = nodes.iterator();
|
|
394
|
TaxonNode node, parentNode = null;
|
|
395
|
while (taxonNodeIterator.hasNext()){
|
|
396
|
node = (TaxonNode)taxonNodeIterator.next();
|
|
397
|
if (!node.isTopmostNode()){
|
|
398
|
parentNode = node.getParent();
|
|
399
|
}
|
|
400
|
}
|
|
401
|
//TODO: ?ndern mit erweitertem Initializer..
|
|
402
|
if (parentNode != null){
|
|
403
|
ZoologicalName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName(), ZoologicalName.class);
|
|
404
|
String parentNameCache = parentName.getNameCache();
|
|
405
|
mergeObject.setParentStringInErms(parentNameCache);
|
|
406
|
mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());
|
|
407
|
//System.err.println("parentName: " + parentNameCache);
|
|
408
|
}
|
|
409
|
}else{
|
|
410
|
mergeObject.setStatInErms(false);
|
|
411
|
}
|
|
412
|
taxa = zooName2.getTaxa();
|
|
413
|
if (!taxa.isEmpty()){
|
|
414
|
mergeObject.setStatInFaunaEu(true);
|
|
415
|
Iterator taxaIterator = taxa.iterator();
|
|
416
|
Taxon taxon = null;
|
|
417
|
while (taxaIterator.hasNext()){
|
|
418
|
taxon = (Taxon) taxaIterator.next();
|
|
419
|
if (!taxon.isMisapplication()){
|
|
420
|
break;
|
|
421
|
}
|
|
422
|
}
|
|
423
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
|
424
|
Iterator taxonNodeIterator = nodes.iterator();
|
|
425
|
TaxonNode node, parentNode = null;
|
|
426
|
while (taxonNodeIterator.hasNext()){
|
|
427
|
node = (TaxonNode)taxonNodeIterator.next();
|
|
428
|
if (!node.isTopmostNode()){
|
|
429
|
parentNode = node.getParent();
|
|
430
|
}
|
|
431
|
}
|
|
432
|
//TODO: ?ndern mit erweitertem Initializer..
|
|
433
|
if (parentNode != null){
|
|
434
|
if (parentNode.getTaxon().getName() instanceof ZoologicalName){
|
|
435
|
|
|
436
|
ZoologicalName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName(), ZoologicalName.class);
|
|
437
|
String parentNameCache = parentName.getNameCache();
|
|
438
|
mergeObject.setParentStringInFaunaEu(parentNameCache);
|
|
439
|
mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());
|
|
440
|
System.err.println("parentName: " + parentNameCache);
|
|
441
|
}else{
|
|
442
|
System.err.println("no zoologicalName: " + parentNode.getTaxon().getName().getTitleCache() +" . "+parentNode.getTaxon().getName().getUuid());
|
|
443
|
}
|
|
444
|
|
|
445
|
}
|
|
446
|
}else{
|
|
447
|
mergeObject.setStatInErms(false);
|
|
448
|
}
|
|
449
|
taxa = zooName2.getTaxa();
|
|
450
|
if (!taxa.isEmpty()){
|
|
451
|
mergeObject.setStatInFaunaEu(true);
|
|
452
|
}else{
|
|
453
|
mergeObject.setStatInFaunaEu(false);
|
|
454
|
|
|
455
|
}
|
|
456
|
|
|
457
|
mergeObject.setRankInErms(zooName.getRank().getLabel());
|
|
458
|
mergeObject.setRankInFaunaEu(zooName2.getRank().getLabel());
|
|
459
|
|
|
460
|
|
|
461
|
|
|
462
|
|
|
463
|
//set parent informations
|
|
464
|
|
|
465
|
|
|
466
|
/*
|
|
467
|
Set<HybridRelationship> parentRelations = zooName.getParentRelationships();
|
|
468
|
Iterator parentIterator = parentRelations.iterator();
|
|
469
|
HybridRelationship parentRel;
|
|
470
|
ZoologicalName parentName;
|
|
471
|
while (parentIterator.hasNext()){
|
|
472
|
parentRel = (HybridRelationship)parentIterator.next();
|
|
473
|
parentName = (ZoologicalName)parentRel.getParentName();
|
|
474
|
mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());
|
|
475
|
mergeObject.setParentStringInErms(parentName.getNameCache());
|
|
476
|
}
|
|
477
|
|
|
478
|
parentRelations = zooName2.getParentRelationships();
|
|
479
|
parentIterator = parentRelations.iterator();
|
|
480
|
|
|
481
|
while (parentIterator.hasNext()){
|
|
482
|
parentRel = (HybridRelationship)parentIterator.next();
|
|
483
|
parentName = (ZoologicalName)parentRel.getParentName();
|
|
484
|
mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());
|
|
485
|
mergeObject.setParentStringInFaunaEu(parentName.getNameCache());
|
|
486
|
}*/
|
|
487
|
merge.add(mergeObject);
|
|
488
|
}
|
|
489
|
|
|
490
|
return merge;
|
|
491
|
|
|
492
|
|
|
493
|
}
|
|
494
|
|
|
495
|
}
|