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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.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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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.ErmsImportActivator;
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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.api.application.CdmIoApplicationController;
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import eu.etaxonomy.cdm.io.pesi.merging.FaunaEuErmsMerging;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.name.IZoologicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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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.TaxonNode;
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
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public class FaunaEuErmsFindIdenticalNamesActivator {
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private static final Logger logger = Logger.getLogger(FaunaEuErmsFindIdenticalNamesActivator.class);
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//static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.localH2();
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static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.cdm_test_local_faunaEu_mysql();
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static Reference faunaSec;
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static Reference ermsSec;
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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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CdmApplicationController appCtrInit = CdmIoApplicationController.NewInstance(db, DbSchemaValidation.VALIDATE, false);
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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:\\Users\\k.luther\\test";
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//CdmApplicationController appCtrErms = sc.initDb(ermsSource);
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List<String> propertyPaths = new ArrayList<>();
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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.childNodes.*");
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propertyPaths.add("taxonBases.taxonNodes.childNodes.classification.rootNode.childNodes.*");
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propertyPaths.add("taxonBases.taxonNodes.parent.taxon.name.*");
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propertyPaths.add("taxonBases.acceptedTaxon.taxonNodes.*");
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propertyPaths.add("taxonBases.acceptedTaxon.taxonNodes.childNodes.*");
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propertyPaths.add("taxonBases.acceptedTaxon.taxonNodes.childNodes.classification.rootNode.childNodes.*");
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System.err.println("Start getIdenticalNames...");
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faunaSec = appCtrFaunaEu.getReferenceService().load(UUID.fromString("6786d863-75d4-4796-b916-c1c3dff4cb70"));
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ermsSec = appCtrFaunaEu.getReferenceService().load(UUID.fromString("7744bc26-f914-42c4-b54a-dd2a030a8bb7"));
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Map<String, List<TaxonName>> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(ermsSec, faunaSec, propertyPaths);
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List<FaunaEuErmsMerging> mergingObjects = new ArrayList<>();
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FaunaEuErmsMerging mergeObject;
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TaxonName faunaEuTaxName;
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TaxonName ermsTaxName;
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System.err.println("Start creating merging objects");
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mergingObjects= sc.createMergeObjects(namesOfIdenticalTaxa, appCtrFaunaEu);
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boolean resultOK = true;
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System.err.println("Start creating csv files");
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resultOK = resultOK && sc.writeSameNamesdifferentAuthorToCsv(mergingObjects, sFileName + "_authors.csv");
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resultOK = resultOK &&sc.writeSameNamesdifferentStatusToCsv(mergingObjects, sFileName + "_status.csv");
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resultOK = resultOK &&sc.writeSameNamesToCsVFile(mergingObjects, sFileName + "_names.csv");
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resultOK = resultOK &&sc.writeSameNamesdifferentPhylumToCsv(mergingObjects, sFileName + "_phylum.csv");
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resultOK = resultOK &&sc.writeSameNamesDifferentParentToCsv(mergingObjects, sFileName + "parent.csv");
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System.err.println("End merging Fauna Europaea and Erms" + resultOK);
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System.exit(0);
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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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}catch(IOException e){
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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 writeSameNamesDifferentParentToCsv(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 parent";
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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.getParentStringInErms()== null )^ (merging.getParentStringInFaunaEu()== null)){
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writeCsvLine(writer, merging) ;
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}else if(!((merging.getParentStringInErms()==null) && (merging.getParentStringInFaunaEu()==null))){
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if(!merging.getParentStringInErms().equals(merging.getParentStringInFaunaEu())){
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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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256
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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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264
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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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268
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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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274
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return false;
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275
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}
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276
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return true;
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277
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}
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278
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279
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private boolean writeSameNamesdifferentAuthorToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){
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280
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try
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281
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{
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282
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FileWriter writer = new FileWriter(sfileName);
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283
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284
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//create Header
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285
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String firstLine = "same names but different authors";
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286
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createHeader(writer, firstLine);
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287
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288
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//write data
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289
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for (FaunaEuErmsMerging merging : mergingObjects){
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290
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291
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if (merging.getAuthorInErms() != null && merging.getAuthorInFaunaEu() != null && !merging.getAuthorInErms().equals(merging.getAuthorInFaunaEu())){
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writeCsvLine(writer, merging);
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}else if ((merging.getAuthorInErms() == null && merging.getAuthorInFaunaEu() != null) || (merging.getAuthorInErms() != null && merging.getAuthorInFaunaEu() == null)) {
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294
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writeCsvLine(writer, merging);
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295
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}
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296
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}
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297
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298
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299
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writer.flush();
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300
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writer.close();
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301
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}
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302
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catch(IOException e)
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303
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{
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304
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return false;
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305
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}
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306
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return true;
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307
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}
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308
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309
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private void writeCsvLine(FileWriter writer, FaunaEuErmsMerging merging) throws IOException{
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310
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311
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writer.append(merging.getUuidFaunaEu());
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312
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writer.append(';');
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313
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writer.append(merging.getIdInFaunaEu());
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314
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writer.append(';');
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315
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writer.append(merging.getNameCacheInFaunaEu());
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316
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writer.append(';');
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317
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writer.append(merging.getAuthorInFaunaEu());
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318
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writer.append(';');
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319
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writer.append(merging.getRankInFaunaEu());
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320
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writer.append(';');
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321
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if (merging.isStatInFaunaEu()){
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322
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writer.append("accepted");
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323
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}else{
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324
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writer.append("synonym");
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325
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}
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326
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writer.append(';');
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327
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writer.append(merging.getPhylumInFaunaEu() != null? merging.getPhylumInFaunaEu().getTaxonTitleCache(): "");
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328
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writer.append(';');
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329
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writer.append(merging.getParentStringInFaunaEu());
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writer.append(';');
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331
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writer.append(merging.getParentRankStringInFaunaEu());
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writer.append(';');
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333
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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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writer.append(';');
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writer.append(merging.getNameCacheInErms());
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writer.append(';');
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340
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writer.append(merging.getAuthorInErms());
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writer.append(';');
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342
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writer.append(merging.getRankInErms());
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343
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writer.append(';');
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344
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if (merging.isStatInErms()){
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345
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writer.append("accepted");
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346
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}else{
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347
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writer.append("synonym");
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348
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}
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349
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350
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writer.append(';');
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351
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writer.append(merging.getPhylumInErms() != null? merging.getPhylumInErms().getTaxonTitleCache():"");
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352
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writer.append(';');
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353
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writer.append(merging.getParentStringInErms());
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writer.append(';');
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355
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writer.append(merging.getParentRankStringInErms());
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356
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writer.append('\n');
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357
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}
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358
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359
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360
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private List<FaunaEuErmsMerging> createMergeObjects(Map<String,List<TaxonName>> names, CdmApplicationController appCtr){
|
|
361
|
Classification faunaEuClassification = appCtr.getClassificationService().load(UUID.fromString("44d8605e-a7ce-41e1-bee9-99edfec01e7c"));
|
|
362
|
Classification ermsClassification = appCtr.getClassificationService().load(UUID.fromString("6fa988a9-10b7-48b0-a370-2586fbc066eb"));
|
|
363
|
List<FaunaEuErmsMerging> merge = new ArrayList<>();
|
|
364
|
|
|
365
|
FaunaEuErmsMerging mergeObject;
|
|
366
|
String idInSource1;
|
|
367
|
List<TaxonName> identicalNames;
|
|
368
|
|
|
369
|
for (String nameCache: names.keySet()){
|
|
370
|
identicalNames = names.get(nameCache);
|
|
371
|
|
|
372
|
mergeObject = new FaunaEuErmsMerging();
|
|
373
|
|
|
374
|
|
|
375
|
//getPhylum
|
|
376
|
TaxonNodeDto phylum1 = null;
|
|
377
|
TaxonName faunaEuName = null;
|
|
378
|
TaxonName ermsName = null;
|
|
379
|
TaxonBase tempName = null;
|
|
380
|
if (identicalNames.size() == 2) {
|
|
381
|
Set<TaxonBase> taxonBases = identicalNames.get(0).getTaxonBases();
|
|
382
|
if (taxonBases.size()==1) {
|
|
383
|
Iterator<TaxonBase> it = taxonBases.iterator();
|
|
384
|
tempName = it.next();
|
|
385
|
if (tempName.getSec().equals(faunaSec)) {
|
|
386
|
faunaEuName = identicalNames.get(0);
|
|
387
|
ermsName = identicalNames.get(1);
|
|
388
|
}else {
|
|
389
|
faunaEuName = identicalNames.get(1);
|
|
390
|
ermsName = identicalNames.get(0);
|
|
391
|
}
|
|
392
|
}else {
|
|
393
|
//TODO: find the two correct names
|
|
394
|
}
|
|
395
|
}else {
|
|
396
|
logger.debug(nameCache + " has more than two identical namecaches");
|
|
397
|
continue;
|
|
398
|
}
|
|
399
|
phylum1 = null;
|
|
400
|
if (faunaEuName.getRank().equals(Rank.PHYLUM())) {
|
|
401
|
Taxon taxon = null;
|
|
402
|
taxon = getAcceptedTaxon(faunaEuName);
|
|
403
|
if (taxon != null) {
|
|
404
|
phylum1 = new TaxonNodeDto(taxon.getTaxonNode(faunaEuClassification));
|
|
405
|
}
|
|
406
|
|
|
407
|
}
|
|
408
|
if (phylum1 == null && faunaEuName != null && !faunaEuName.getRank().isHigher(Rank.PHYLUM())){
|
|
409
|
phylum1 =appCtr.getTaxonNodeService().taxonNodeDtoParentRank(faunaEuClassification, Rank.PHYLUM(), faunaEuName);
|
|
410
|
}
|
|
411
|
|
|
412
|
TaxonNodeDto phylum2 = null;
|
|
413
|
if (ermsName.getRank().equals(Rank.PHYLUM())) {
|
|
414
|
Taxon taxon = null;
|
|
415
|
taxon = getAcceptedTaxon(ermsName);
|
|
416
|
if (taxon != null) {
|
|
417
|
phylum2 = new TaxonNodeDto(taxon.getTaxonNode(ermsClassification));
|
|
418
|
}
|
|
419
|
|
|
420
|
}
|
|
421
|
if (phylum2 == null && ermsName != null && !ermsName.getRank().isHigher(Rank.PHYLUM())){
|
|
422
|
phylum2 = appCtr.getTaxonNodeService().taxonNodeDtoParentRank(ermsClassification, Rank.PHYLUM(), ermsName);
|
|
423
|
}
|
|
424
|
mergeObject.setPhylumInErms(phylum1);
|
|
425
|
mergeObject.setPhylumInFaunaEu(phylum2);
|
|
426
|
|
|
427
|
//getUuids
|
|
428
|
mergeObject.setUuidErms(ermsName.getUuid().toString());
|
|
429
|
mergeObject.setUuidFaunaEu(faunaEuName.getUuid().toString());
|
|
430
|
|
|
431
|
Iterator<IdentifiableSource> sources = ermsName.getSources().iterator();
|
|
432
|
if (sources.hasNext()){
|
|
433
|
IdentifiableSource source = sources.next();
|
|
434
|
idInSource1 = source.getIdInSource();
|
|
435
|
mergeObject.setIdInErms(idInSource1);
|
|
436
|
}
|
|
437
|
sources = faunaEuName.getSources().iterator();
|
|
438
|
if (sources.hasNext()){
|
|
439
|
IdentifiableSource source = sources.next();
|
|
440
|
idInSource1 = source.getIdInSource();
|
|
441
|
mergeObject.setIdInFaunaEu(idInSource1);
|
|
442
|
}
|
|
443
|
|
|
444
|
mergeObject.setNameCacheInErms(ermsName.getNameCache());
|
|
445
|
mergeObject.setNameCacheInFaunaEu(faunaEuName.getNameCache());
|
|
446
|
|
|
447
|
mergeObject.setAuthorInErms(ermsName.getAuthorshipCache());
|
|
448
|
mergeObject.setAuthorInFaunaEu(faunaEuName.getAuthorshipCache());
|
|
449
|
Set<Taxon> taxa = ermsName.getTaxa();
|
|
450
|
if (!taxa.isEmpty()){
|
|
451
|
mergeObject.setStatInErms(true);
|
|
452
|
Iterator<Taxon> taxaIterator = taxa.iterator();
|
|
453
|
Taxon taxon = null;
|
|
454
|
while (taxaIterator.hasNext()){
|
|
455
|
taxon = taxaIterator.next();
|
|
456
|
if (!taxon.isMisapplication()){
|
|
457
|
break;
|
|
458
|
}
|
|
459
|
}
|
|
460
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
|
461
|
Iterator<TaxonNode> taxonNodeIterator = nodes.iterator();
|
|
462
|
TaxonNode node, parentNode = null;
|
|
463
|
while (taxonNodeIterator.hasNext()){
|
|
464
|
node = taxonNodeIterator.next();
|
|
465
|
if (!node.isTopmostNode()){
|
|
466
|
parentNode = node.getParent();
|
|
467
|
}
|
|
468
|
}
|
|
469
|
//TODO: ändern mit erweitertem Initializer..
|
|
470
|
if (parentNode != null){
|
|
471
|
TaxonName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName());
|
|
472
|
String parentNameCache = parentName.getNameCache();
|
|
473
|
mergeObject.setParentStringInErms(parentNameCache);
|
|
474
|
mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());
|
|
475
|
|
|
476
|
}
|
|
477
|
}else{
|
|
478
|
mergeObject.setStatInErms(false);
|
|
479
|
TaxonNode parentNode = getAcceptedNode(ermsName);
|
|
480
|
//TODO: ändern mit erweitertem Initializer..
|
|
481
|
if (parentNode != null){
|
|
482
|
TaxonName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName());
|
|
483
|
String parentNameCache = parentName.getNameCache();
|
|
484
|
mergeObject.setParentStringInErms(parentNameCache);
|
|
485
|
mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());
|
|
486
|
|
|
487
|
}
|
|
488
|
}
|
|
489
|
taxa = faunaEuName.getTaxa();
|
|
490
|
if (!taxa.isEmpty()){
|
|
491
|
mergeObject.setStatInFaunaEu(true);
|
|
492
|
Iterator<Taxon> taxaIterator = taxa.iterator();
|
|
493
|
Taxon taxon = null;
|
|
494
|
while (taxaIterator.hasNext()){
|
|
495
|
taxon = taxaIterator.next();
|
|
496
|
if (!taxon.isMisapplication()){
|
|
497
|
break;
|
|
498
|
}
|
|
499
|
}
|
|
500
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
|
501
|
Iterator<TaxonNode> taxonNodeIterator = nodes.iterator();
|
|
502
|
TaxonNode node, parentNode = null;
|
|
503
|
while (taxonNodeIterator.hasNext()){
|
|
504
|
node = taxonNodeIterator.next();
|
|
505
|
if (!node.isTopmostNode()){
|
|
506
|
parentNode = node.getParent();
|
|
507
|
}
|
|
508
|
}
|
|
509
|
//TODO: ändern mit erweitertem Initializer..
|
|
510
|
if (parentNode != null){
|
|
511
|
if (parentNode.getTaxon().getName().isZoological()){
|
|
512
|
|
|
513
|
IZoologicalName parentName = CdmBase.deproxy(parentNode.getTaxon().getName());
|
|
514
|
String parentNameCache = parentName.getNameCache();
|
|
515
|
mergeObject.setParentStringInFaunaEu(parentNameCache);
|
|
516
|
mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());
|
|
517
|
|
|
518
|
}else{
|
|
519
|
logger.debug("no zoologicalName: " + parentNode.getTaxon().getName().getTitleCache() +" . "+parentNode.getTaxon().getName().getUuid());
|
|
520
|
}
|
|
521
|
|
|
522
|
}
|
|
523
|
}else{
|
|
524
|
mergeObject.setStatInFaunaEu(false);
|
|
525
|
TaxonNode parentNode = getAcceptedNode(faunaEuName);
|
|
526
|
//TODO: ändern mit erweitertem Initializer..
|
|
527
|
if (parentNode != null){
|
|
528
|
TaxonName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName());
|
|
529
|
String parentNameCache = parentName.getNameCache();
|
|
530
|
mergeObject.setParentStringInFaunaEu(parentNameCache);
|
|
531
|
mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());
|
|
532
|
|
|
533
|
}
|
|
534
|
}
|
|
535
|
|
|
536
|
|
|
537
|
mergeObject.setRankInErms(ermsName.getRank().getLabel());
|
|
538
|
mergeObject.setRankInFaunaEu(faunaEuName.getRank().getLabel());
|
|
539
|
|
|
540
|
//set parent informations
|
|
541
|
|
|
542
|
|
|
543
|
/*
|
|
544
|
Set<HybridRelationship> parentRelations = zooName.getParentRelationships();
|
|
545
|
Iterator parentIterator = parentRelations.iterator();
|
|
546
|
HybridRelationship parentRel;
|
|
547
|
ZoologicalName parentName;
|
|
548
|
while (parentIterator.hasNext()){
|
|
549
|
parentRel = (HybridRelationship)parentIterator.next();
|
|
550
|
parentName = (ZoologicalName)parentRel.getParentName();
|
|
551
|
mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());
|
|
552
|
mergeObject.setParentStringInErms(parentName.getNameCache());
|
|
553
|
}
|
|
554
|
|
|
555
|
parentRelations = zooName2.getParentRelationships();
|
|
556
|
parentIterator = parentRelations.iterator();
|
|
557
|
|
|
558
|
while (parentIterator.hasNext()){
|
|
559
|
parentRel = (HybridRelationship)parentIterator.next();
|
|
560
|
parentName = (ZoologicalName)parentRel.getParentName();
|
|
561
|
mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());
|
|
562
|
mergeObject.setParentStringInFaunaEu(parentName.getNameCache());
|
|
563
|
}*/
|
|
564
|
merge.add(mergeObject);
|
|
565
|
}
|
|
566
|
// }
|
|
567
|
|
|
568
|
return merge;
|
|
569
|
|
|
570
|
}
|
|
571
|
|
|
572
|
|
|
573
|
/**
|
|
574
|
* @param ermsName
|
|
575
|
* @return
|
|
576
|
*/
|
|
577
|
private TaxonNode getAcceptedNode(TaxonName ermsName) {
|
|
578
|
Set<TaxonBase> taxonBases = ermsName.getTaxonBases();
|
|
579
|
Taxon taxon = null;
|
|
580
|
if (taxonBases != null && !taxonBases.isEmpty()) {
|
|
581
|
TaxonBase taxonBase = taxonBases.iterator().next();
|
|
582
|
if (taxonBase instanceof Synonym) {
|
|
583
|
taxon = ((Synonym)taxonBase).getAcceptedTaxon();
|
|
584
|
}
|
|
585
|
}
|
|
586
|
|
|
587
|
|
|
588
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
|
589
|
|
|
590
|
TaxonNode node, parentNode = null;
|
|
591
|
if (nodes != null && !nodes.isEmpty()) {
|
|
592
|
parentNode = nodes.iterator().next();
|
|
593
|
}
|
|
594
|
return parentNode;
|
|
595
|
}
|
|
596
|
|
|
597
|
|
|
598
|
/**
|
|
599
|
* @param ermsName
|
|
600
|
* @param taxon
|
|
601
|
* @return
|
|
602
|
*/
|
|
603
|
private Taxon getAcceptedTaxon(TaxonName ermsName) {
|
|
604
|
Taxon taxon = null;
|
|
605
|
if (ermsName.getTaxa() != null && !ermsName.getTaxa().isEmpty()){
|
|
606
|
taxon = ermsName.getTaxa().iterator().next();
|
|
607
|
|
|
608
|
}else if (ermsName.getTaxonBases() != null && !ermsName.getTaxonBases().isEmpty()){
|
|
609
|
TaxonBase taxonBase = ermsName.getTaxonBases().iterator().next();
|
|
610
|
if (taxonBase instanceof Synonym) {
|
|
611
|
Synonym syn = (Synonym)taxonBase;
|
|
612
|
taxon = syn.getAcceptedTaxon();
|
|
613
|
}
|
|
614
|
}
|
|
615
|
return taxon;
|
|
616
|
}
|
|
617
|
}
|