EDIT

package eu.etaxonomy.cdm.app.pesi.merging;

import java.io.FileWriter;

import java.io.IOException;

import java.util.ArrayList;

import java.util.Iterator;

import java.util.List;

import java.util.Set;

import eu.etaxonomy.cdm.api.application.CdmApplicationController;

import eu.etaxonomy.cdm.app.common.CdmDestinations;

import eu.etaxonomy.cdm.app.common.TestDatabase;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

import eu.etaxonomy.cdm.io.pesi.merging.FaunaEuErmsMerging;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.common.IdentifiableSource;

import eu.etaxonomy.cdm.model.name.IZoologicalName;

import eu.etaxonomy.cdm.model.name.Rank;

import eu.etaxonomy.cdm.model.name.TaxonName;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonNode;

public class FaunaEuErmsFindIdenticalNamesActivator {

	static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.localH2();

	//static final ICdmDataSource ermsSource = CdmDestinations.cdm_test_andreasM();

	//TODO hole aus beiden DB alle TaxonNameBases

	private CdmApplicationController initDb(ICdmDataSource db) {

		// Init source DB

		CdmApplicationController appCtrInit = null;

		appCtrInit = TestDatabase.initDb(db, DbSchemaValidation.VALIDATE, false);

		return appCtrInit;

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		FaunaEuErmsFindIdenticalNamesActivator sc = new FaunaEuErmsFindIdenticalNamesActivator();

		CdmApplicationController appCtrFaunaEu = sc.initDb(faunaEuropaeaSource);

		String sFileName = "c:\\test";

		//CdmApplicationController appCtrErms = sc.initDb(ermsSource);

		List<String> propertyPaths = new ArrayList<>();

		propertyPaths.add("sources.*");

		propertyPaths.add("sources.idInSource");

		propertyPaths.add("sources.idNamespace");

		propertyPaths.add("taxonBases.*");

		propertyPaths.add("taxonBases.relationsFromThisTaxon");

		propertyPaths.add("taxonBases.taxonNodes.*");

		propertyPaths.add("taxonBases.taxonNodes.parent.*");

		propertyPaths.add("taxonBases.taxonNodes.parent.taxon.name.*");

		System.err.println("Start getIdenticalNames...");

		List<TaxonName> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(propertyPaths);

		//List<UUID> namesOfIdenticalTaxa = appCtrFaunaEu.getTaxonService().findIdenticalTaxonNameIds(propertyPaths);

		System.err.println("first name: " + namesOfIdenticalTaxa.get(0) + " " + namesOfIdenticalTaxa.size());

		TaxonName zooName = namesOfIdenticalTaxa.get(0);

		System.err.println(zooName + " nr of taxa " + namesOfIdenticalTaxa.size());

		//TaxonNameComparator taxComp = new TaxonNameComparator();

		//Collections.sort(namesOfIdenticalTaxa,taxComp);

		System.err.println(namesOfIdenticalTaxa.get(0) + " - " + namesOfIdenticalTaxa.get(1) + " - " + namesOfIdenticalTaxa.get(2));

		List<FaunaEuErmsMerging> mergingObjects = new ArrayList<>();

		FaunaEuErmsMerging mergeObject;

		TaxonName faunaEuTaxName;

		TaxonName ermsTaxName;

		mergingObjects= sc.createMergeObjects(namesOfIdenticalTaxa, appCtrFaunaEu);

		sc.writeSameNamesdifferentAuthorToCsv(mergingObjects, sFileName + "_authors.csv");

		sc.writeSameNamesdifferentStatusToCsv(mergingObjects, sFileName + "_status.csv");

		sc.writeSameNamesToCsVFile(mergingObjects, sFileName + "_names.csv");

		sc.writeSameNamesdifferentPhylumToCsv(mergingObjects, sFileName + "_phylum.csv");

		System.out.println("End merging Fauna Europaea and Erms");

	}

	private boolean writeSameNamesToCsVFile(

			List<FaunaEuErmsMerging> mergingObjects, String string) {

	    try{

    		FileWriter writer = new FileWriter(string);

    	    //create Header

    	    String firstLine = "same names";

    	    createHeader(writer, firstLine);

    		for (FaunaEuErmsMerging merging : mergingObjects){

    	    	writeCsvLine(writer, merging) ;

    		}

    		writer.flush();

    		writer.close();

    	}catch(IOException e){

    	    return false;

    	}

    	return true;

	}

	private boolean writeSameNamesdifferentPhylumToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){

		try

		{

		    FileWriter writer = new FileWriter(sfileName);

		    //create Header

		   String firstLine = "same names but different phylum";

		   createHeader(writer, firstLine);

			//write data

			for (FaunaEuErmsMerging merging : mergingObjects){

		    	//TODO

				if ((merging.getPhylumInErms()== null )^ (merging.getPhylumInFaunaEu()== null)){

					writeCsvLine(writer, merging) ;

				}else if(!((merging.getPhylumInErms()==null) && (merging.getPhylumInFaunaEu()==null))){

					if(!merging.getPhylumInErms().equals(merging.getPhylumInFaunaEu())){

						writeCsvLine(writer, merging) ;

					}

				}

			}

			writer.flush();

			writer.close();

		}

		catch(IOException e)

		{

		 return false;

		}

		return true;

	}

	private boolean writeSameNamesdifferentRankToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){

		try

		{

		    FileWriter writer = new FileWriter(sfileName);

		    String firstLine = "same names but different rank";

		    //create Header

		    createHeader(writer, firstLine);

			//write data

			for (FaunaEuErmsMerging merging : mergingObjects){

				if (!merging.getRankInErms().equals(merging.getRankInFaunaEu())){

					writeCsvLine(writer, merging);

				}

			}

			writer.flush();

			writer.close();

		}

		catch(IOException e)

		{

		 return false;

		}

		return true;

	}

	private void createHeader(FileWriter writer, String firstLine) throws IOException{

		 	writer.append(firstLine);

		    writer.append('\n');

		    writer.append("uuid in Fauna Europaea");

			writer.append(';');

			writer.append("id in Fauna Europaea");

			writer.append(';');

			writer.append("name");

			writer.append(';');

			writer.append("author");

			writer.append(';');

			writer.append("rank");

			writer.append(';');

			writer.append("state");

			writer.append(';');

			writer.append("phylum");

			writer.append(';');

			writer.append("parent");

			writer.append(';');

			writer.append("parent rank");

			writer.append(';');

			writer.append("uuid in Erms");

			writer.append(';');

			writer.append("id in Erms");

			writer.append(';');

			writer.append("name");

			writer.append(';');

			writer.append("author");

			writer.append(';');

			writer.append("rank");

			writer.append(';');

			writer.append("state");

			writer.append(';');

			writer.append("phylum");

			writer.append(';');

			writer.append("parent");

			writer.append(';');

			writer.append("parent rank");

			writer.append('\n');

	}

	private boolean writeSameNamesdifferentStatusToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){

		try

		{

		    FileWriter writer = new FileWriter(sfileName);

		    //create Header

		    String firstLine = "same names but different status";

		    createHeader(writer, firstLine);

			//write data

			for (FaunaEuErmsMerging merging : mergingObjects){

				if (merging.isStatInErms()^merging.isStatInFaunaEu()){

					 writeCsvLine(writer, merging);

				}

			}

			writer.flush();

			writer.close();

		}

		catch(IOException e)

		{

		 return false;

		}

		return true;

	}

	private boolean writeSameNamesdifferentAuthorToCsv(List<FaunaEuErmsMerging> mergingObjects, String sfileName){

		try

		{

		    FileWriter writer = new FileWriter(sfileName);

		    //create Header

		   String firstLine = "same names but different authors";

		   createHeader(writer, firstLine);

			//write data

			for (FaunaEuErmsMerging merging : mergingObjects){

				if (!merging.getAuthorInErms().equals(merging.getAuthorInFaunaEu())){

					 writeCsvLine(writer, merging);

				}

			}

			writer.flush();

			writer.close();

		}

		catch(IOException e)

		{

		 return false;

		}

		return true;

	}

	private void writeCsvLine(FileWriter writer, FaunaEuErmsMerging merging) throws IOException{

		writer.append(merging.getUuidFaunaEu());

		writer.append(';');

		writer.append(merging.getIdInFaunaEu());

		writer.append(';');

		writer.append(merging.getNameCacheInFaunaEu());

		writer.append(';');

		writer.append(merging.getAuthorInFaunaEu());

		writer.append(';');

		writer.append(merging.getRankInFaunaEu());

		writer.append(';');

		if (merging.isStatInFaunaEu()){

			writer.append("accepted");

		}else{

			writer.append("synonym");

		}

		writer.append(';');

		writer.append(merging.getPhylumInFaunaEu());

		writer.append(';');

		writer.append(merging.getParentStringInFaunaEu());

		writer.append(';');

		writer.append(merging.getParentRankStringInFaunaEu());

		writer.append(';');

		writer.append(merging.getUuidErms());

		writer.append(';');

		writer.append(merging.getIdInErms());

		writer.append(';');

		writer.append(merging.getNameCacheInErms());

		writer.append(';');

		writer.append(merging.getAuthorInErms());

		writer.append(';');

		writer.append(merging.getRankInErms());

		writer.append(';');

		if (merging.isStatInErms()){

			writer.append("accepted");

		}else{

			writer.append("synonym");

		}

		writer.append(';');

		writer.append(merging.getPhylumInErms());

		writer.append(';');

		writer.append(merging.getParentStringInErms());

		writer.append(';');

		writer.append(merging.getParentRankStringInErms());

		writer.append('\n');

	}

	private List<FaunaEuErmsMerging> createMergeObjects(List<TaxonName> names, CdmApplicationController appCtr){

		List<FaunaEuErmsMerging> merge = new ArrayList<>();

		TaxonName zooName, zooName2;

		FaunaEuErmsMerging mergeObject;

		String idInSource1;

		for (int i = 0; i<names.size()-1; i=i+2){

			zooName = names.get(i);

			zooName2 = names.get(i+1);

			mergeObject = new FaunaEuErmsMerging();

			//TODO:überprüfen, ob die beiden Namen identisch sind und aus unterschiedlichen DB kommen

			//getPhylum

			String phylum1 = null;

			if (!zooName.getRank().isHigher(Rank.PHYLUM())){

				phylum1 =appCtr.getTaxonService().getPhylumName(zooName);

			}

			String phylum2 = null;

			if (!zooName2.getRank().isHigher(Rank.PHYLUM())){

				phylum2 = appCtr.getTaxonService().getPhylumName(zooName2);

			}

			mergeObject.setPhylumInErms(phylum1);

			mergeObject.setPhylumInFaunaEu(phylum2);

			//getUuids

			mergeObject.setUuidErms(zooName.getUuid().toString());

			mergeObject.setUuidFaunaEu(zooName.getUuid().toString());

			Iterator<IdentifiableSource> sources = zooName.getSources().iterator();

			if (sources.hasNext()){

				IdentifiableSource source = sources.next();

				idInSource1 = source.getIdInSource();

				mergeObject.setIdInErms(idInSource1);

			}

			sources = zooName2.getSources().iterator();

			if (sources.hasNext()){

				IdentifiableSource source = sources.next();

				idInSource1 = source.getIdInSource();

				mergeObject.setIdInFaunaEu(idInSource1);

			}

			mergeObject.setNameCacheInErms(zooName.getNameCache());

			mergeObject.setNameCacheInFaunaEu(zooName2.getNameCache());

			mergeObject.setAuthorInErms(zooName.getAuthorshipCache());

			mergeObject.setAuthorInFaunaEu(zooName2.getAuthorshipCache());

			Set<Taxon> taxa = zooName.getTaxa();

			if (!taxa.isEmpty()){

				mergeObject.setStatInErms(true);

				Iterator<Taxon> taxaIterator = taxa.iterator();

				Taxon taxon = null;

				while (taxaIterator.hasNext()){

					taxon = taxaIterator.next();

					if (!taxon.isMisapplication()){

						break;

					}

				}

				Set<TaxonNode> nodes = taxon.getTaxonNodes();

				Iterator<TaxonNode> taxonNodeIterator = nodes.iterator();

				TaxonNode node, parentNode = null;

				while (taxonNodeIterator.hasNext()){

					node = taxonNodeIterator.next();

					if (!node.isTopmostNode()){

						parentNode = node.getParent();

					}

				}

				//TODO: ändern mit erweitertem Initializer..

				if (parentNode != null){

				    TaxonName parentName = HibernateProxyHelper.deproxy(parentNode.getTaxon().getName());

					String parentNameCache = parentName.getNameCache();

					mergeObject.setParentStringInErms(parentNameCache);

					mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());

					//System.err.println("parentName: " + parentNameCache);

				}

			}else{

				mergeObject.setStatInErms(false);

			}

			taxa = zooName2.getTaxa();

			if (!taxa.isEmpty()){

				mergeObject.setStatInFaunaEu(true);

				Iterator<Taxon> taxaIterator = taxa.iterator();

				Taxon taxon = null;

				while (taxaIterator.hasNext()){

					taxon = taxaIterator.next();

					if (!taxon.isMisapplication()){

						break;

					}

				}

				Set<TaxonNode> nodes = taxon.getTaxonNodes();

				Iterator<TaxonNode> taxonNodeIterator = nodes.iterator();

				TaxonNode node, parentNode = null;

				while (taxonNodeIterator.hasNext()){

					node = taxonNodeIterator.next();

					if (!node.isTopmostNode()){

						parentNode = node.getParent();

					}

				}

				//TODO: ändern mit erweitertem Initializer..

				if (parentNode != null){

					if (parentNode.getTaxon().getName().isZoological()){

    					IZoologicalName parentName = CdmBase.deproxy(parentNode.getTaxon().getName());

    					String parentNameCache = parentName.getNameCache();

    					mergeObject.setParentStringInFaunaEu(parentNameCache);

    					mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());

    					System.err.println("parentName: " + parentNameCache);

					}else{

						System.err.println("no zoologicalName: " + parentNode.getTaxon().getName().getTitleCache() +" . "+parentNode.getTaxon().getName().getUuid());

					}

				}

			}else{

				mergeObject.setStatInErms(false);

			}

			taxa = zooName2.getTaxa();

			if (!taxa.isEmpty()){

				mergeObject.setStatInFaunaEu(true);

			}else{

				mergeObject.setStatInFaunaEu(false);

			}

			mergeObject.setRankInErms(zooName.getRank().getLabel());

			mergeObject.setRankInFaunaEu(zooName2.getRank().getLabel());

			//set parent informations

			/*

			Set<HybridRelationship> parentRelations = zooName.getParentRelationships();

			Iterator parentIterator = parentRelations.iterator();

			HybridRelationship parentRel;

			ZoologicalName parentName;

			while (parentIterator.hasNext()){

				parentRel = (HybridRelationship)parentIterator.next();

				parentName = (ZoologicalName)parentRel.getParentName();

				mergeObject.setParentRankStringInErms(parentName.getRank().getLabel());

				mergeObject.setParentStringInErms(parentName.getNameCache());

			}

			parentRelations = zooName2.getParentRelationships();

			parentIterator = parentRelations.iterator();

			while (parentIterator.hasNext()){

				parentRel = (HybridRelationship)parentIterator.next();

				parentName = (ZoologicalName)parentRel.getParentName();

				mergeObject.setParentRankStringInFaunaEu(parentName.getRank().getLabel());

				mergeObject.setParentStringInFaunaEu(parentName.getNameCache());

			}*/

			merge.add(mergeObject);

		}

		return merge;

	}

}