EDIT

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

import java.io.BufferedReader;

import java.io.File;

import java.io.FileNotFoundException;

import java.io.FileReader;

import java.io.IOException;

import java.util.ArrayList;

import java.util.HashSet;

import java.util.Iterator;

import java.util.List;

import java.util.Set;

import java.util.StringTokenizer;

import java.util.UUID;

import org.apache.log4j.Logger;

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

import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;

import eu.etaxonomy.cdm.api.service.pager.Pager;

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

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

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;

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

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

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

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

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

import eu.etaxonomy.cdm.model.description.Distribution;

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.description.TaxonDescription;

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

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

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

import eu.etaxonomy.cdm.model.reference.Reference;

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

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

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

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

public class FaunaEuErmsMergeActivator {

//	static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.cdm_test_patricia();

	static final ICdmDataSource faunaEuropaeaSource = CdmDestinations.localH2();

	static final int faunaEuUuid = 0;

	static final int ermsUuid = 9;

	static final int rankFaunaEu = 4;

	static final int rankErms = 13;

	CdmApplicationController appCtrInit;

	private static final Logger logger = Logger.getLogger(FaunaEuErmsMergeActivator.class);

	//csv files starting with...

	static String sFileName = "c:\\test";

	private void initDb(ICdmDataSource db) {

		// Init source DB

		appCtrInit = CdmIoApplicationController.NewInstance(db, DbSchemaValidation.VALIDATE, false);

	}

	public static void main(String[] args) {

		FaunaEuErmsMergeActivator sc = new FaunaEuErmsMergeActivator();

		sc.initDb(faunaEuropaeaSource);

		sc.mergeAuthors();

		//set the ranks of Agnatha and Gnathostomata to 50 instead of 45

		List<TaxonBase> taxaToChangeRank = new ArrayList<>();

		Pager<TaxonBase> agnatha = sc.appCtrInit.getTaxonService().findTaxaByName(TaxonBase.class, "Agnatha", null, null, null, "*", Rank.INFRAPHYLUM(), 10, 0);

		List<TaxonBase> agnathaList = agnatha.getRecords();

		taxaToChangeRank.addAll(agnathaList);

		Pager<TaxonBase> gnathostomata = sc.appCtrInit.getTaxonService().findTaxaByName(TaxonBase.class, "Gnathostomata", null, null, null, "*", Rank.INFRAPHYLUM(), 10, 0);

		List<TaxonBase> gnathostomataList = gnathostomata.getRecords();

		taxaToChangeRank.addAll(gnathostomataList);

		sc.setSpecificRank(taxaToChangeRank, Rank.SUPERCLASS());

		//ermsTaxon is accepted, fauna eu taxon is synonym

		//ermsTaxon is synonym, faunaEu is accepted

		sc.mergeDiffStatus();

		//erms is synonym, faunaEu as well

		// erms is accepted, faunaEu as well

	}

	private static List<List<String>> readCsvFile(String fileName){

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

		File file = new File(fileName);

		BufferedReader bufRdr;

		try {

			bufRdr = new BufferedReader(new FileReader(file));

			String line = null;

			//read each line of text file

			while((line = bufRdr.readLine()) != null){

				StringTokenizer st = new StringTokenizer(line,",");

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

				while (st.hasMoreTokens()){

					//get next token and store it in the array

					rowList.add(st.nextToken());

				}

			result.add(rowList);

			}

			//close the file

			bufRdr.close();

		} catch (FileNotFoundException e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		} catch (IOException e) {

			// TODO Auto-generated catch block

			e.printStackTrace();

		}

		return result;

	}

	private void mergeAuthors(){

		List<List<String>> authors = readCsvFile(sFileName + "_authors.csv");

		//authors: get firstAuthor if isFauEu = 1 otherwise get secondAuthor

		Iterator<List<String>> authorIterator = authors.iterator();

		List<String> row;

		TaxonBase<?> taxonFaunaEu;

		TaxonBase<?> taxonErms;

		List<TaxonBase<?>> taxaToSave = new ArrayList<>();

		while (authorIterator.hasNext()){

			row = authorIterator.next();

			UUID uuidFaunaEu = UUID.fromString(row.get(faunaEuUuid));

			UUID uuidErms = UUID.fromString(row.get(ermsUuid));

			taxonFaunaEu = appCtrInit.getTaxonService().find(uuidFaunaEu);

			taxonErms = appCtrInit.getTaxonService().find(uuidErms);

			if (Integer.parseInt(row.get(18)) == 1){

				//isFaunaEu = 1 -> copy the author of Fauna Europaea to Erms

				if (((IZoologicalName)taxonFaunaEu.getName()).getBasionymAuthorship()!= null){

					((IZoologicalName)taxonErms.getName()).setBasionymAuthorship(((IZoologicalName)taxonFaunaEu.getName()).getBasionymAuthorship());

				}

				if (((IZoologicalName)taxonFaunaEu.getName()).getCombinationAuthorship()!= null){

					((IZoologicalName)taxonErms.getName()).setCombinationAuthorship(((IZoologicalName)taxonFaunaEu.getName()).getCombinationAuthorship());

				}

				((IZoologicalName)taxonErms.getName()).generateAuthorship();

				taxaToSave.add(taxonErms);

			}else{

				if (((IZoologicalName)taxonErms.getName()).getBasionymAuthorship()!= null){

					((IZoologicalName)taxonFaunaEu.getName()).setBasionymAuthorship(((IZoologicalName)taxonErms.getName()).getBasionymAuthorship());

				}

				if (((IZoologicalName)taxonErms.getName()).getCombinationAuthorship()!= null){

					((IZoologicalName)taxonFaunaEu.getName()).setCombinationAuthorship(((IZoologicalName)taxonErms.getName()).getCombinationAuthorship());

				}

				((IZoologicalName)taxonFaunaEu.getName()).generateAuthorship();

				taxaToSave.add(taxonFaunaEu);

			}

		}

	}

	private void setSpecificRank(List<TaxonBase> taxa, Rank rank){

		for (TaxonBase<?> taxon: taxa){

			taxon.getName().setRank(rank);

		}

	}

	private void mergeDiffStatus(){

		List<List<String>> diffStatus = readCsvFile(sFileName + "_status.csv");

		//find all taxa accepted in erms, but synonyms in FauEu  and the same rank

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

		for (List<String> rowList: diffStatus){

			if ((rowList.get(5).equals("synonym")) && (rowList.get(rankFaunaEu).equals(rowList.get(rankErms)))){

				//both conditions are true

				accErmsSynFaunaEu.add(rowList);

			}

		}

		mergeErmsAccFaunaEuSyn(accErmsSynFaunaEu);

		//find all taxa accepted in faunaEu, but synonyms in Erms and the same rank

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

		for (List<String> rowList: diffStatus){

			if ((rowList.get(5).equals("accepted")) && (rowList.get(rankFaunaEu).equals(rowList.get(rankErms)))){

				//both conditions are true

				synErmsAccFaunaEu.add(rowList);

			}

		}

		mergeErmsSynFaunaEuAcc(synErmsAccFaunaEu);

	}

	private void mergeSameStatus(){

		List<List<String>> sameStatus = readCsvFile(sFileName + "_names.csv");

		TaxonBase<?> taxonFaunaEu;

		TaxonBase<?> taxonErms;

		for (List<String> row: sameStatus){

			taxonFaunaEu = appCtrInit.getTaxonService().find(UUID.fromString(row.get(faunaEuUuid)));

			taxonErms = appCtrInit.getTaxonService().find(UUID.fromString(row.get(ermsUuid)));

			moveAllInformationsFromFaunaEuToErms(taxonFaunaEu, taxonErms);

			if (taxonErms instanceof Taxon){

				moveFaunaEuSynonymsToErmsTaxon((Taxon)taxonFaunaEu, (Taxon)taxonErms);

			}

		}

	}

	private void mergeErmsAccFaunaEuSyn(List<List<String>> ermsAccFaEuSyn){

		// update nameRelationships -> if the nameRelationship does not exist, then create a new one with ermsAcc as relatedTo TaxonName

		updateNameRelationships(ermsAccFaEuSyn);

		//delete all synonyms of FaunaEu Syn

		for (List<String> rowList: ermsAccFaEuSyn){

			UUID faunaUUID = UUID.fromString(rowList.get(faunaEuUuid));

			//UUID ermsUUID = UUID.fromString(rowList.get(ermsUuid));

			Synonym syn = (Synonym)appCtrInit.getTaxonService().find(faunaUUID);

			appCtrInit.getTaxonService().deleteSynonym(syn, null);

		}

		//merge the infos of

	}

	private  void mergeErmsSynFaunaEuAcc (List<List<String>> ermsAccFaEuSyn){

		//occurence: verknüpfe statt dem Fauna Europaea Taxon das akzeptierte Taxon, des Synonyms mit der Occurence (CDM -> distribution)

		//suche distribution (über das Taxon der TaxonDescription), dessen Taxon, das entsprechende Fauna Eu Taxon ist und verkn�pfe es mit dem akzeptieren Taxon des Erms Syn

		for (List<String> row: ermsAccFaEuSyn){

		    Taxon taxonFaunaEu = (Taxon)appCtrInit.getTaxonService().find(UUID.fromString(row.get(faunaEuUuid)));

			Synonym synErms = (Synonym)appCtrInit.getTaxonService().find(UUID.fromString(row.get(ermsUuid)));

			synErms = HibernateProxyHelper.deproxy(synErms, Synonym.class);

			Taxon taxonErms = synErms.getAcceptedTaxon();

			if (taxonErms == null){

				logger.debug("There is no accepted taxon for the synonym" + synErms.getTitleCache());

			}

			Set<Feature> features = new HashSet<>();

			features.add(Feature.DISTRIBUTION());

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

			propertyPaths.add("inDescription.Taxon.*");

			List<Distribution> distributions = appCtrInit.getDescriptionService().getDescriptionElementsForTaxon(taxonFaunaEu, features, Distribution.class, 10, 0, null);

			for(Distribution distribution: distributions){

				TaxonDescription description = (TaxonDescription)distribution.getInDescription();

				TaxonDescription newDescription = TaxonDescription.NewInstance(taxonErms);

				newDescription.addElement(distribution);

				try{

					appCtrInit.getDescriptionService().delete(description);

				}catch (Exception e){

					logger.debug("The description of" + description.getTaxon().getTitleCache() + description.getTitleCache() + "can't be deleted because it is referenced.");

				}

			}

			//Child-Parent Relationship aktualisieren -> dem Child des Fauna Europaea Taxons als parent das akzeptierte Taxon von synErms

			Set<TaxonNode> nodesErms = taxonErms.getTaxonNodes();

			Set<TaxonNode> nodesFaunaEu =taxonFaunaEu.getTaxonNodes();

			if (nodesFaunaEu.size()>1 || nodesFaunaEu.isEmpty()){

			}else{

				Iterator<TaxonNode> iteratorNodesErms = nodesErms.iterator();

				Iterator<TaxonNode> iteratorNodesFaunaEu = nodesFaunaEu.iterator();

				TaxonNode node = iteratorNodesFaunaEu.next();

				List<TaxonNode> children = node.getChildNodes();

				Iterator<TaxonNode> childrenIterator = children.iterator();

				TaxonNode childNode;

				if (iteratorNodesErms.hasNext()){

					TaxonNode ermsNode = iteratorNodesErms.next();

					while (childrenIterator.hasNext()){

						childNode = childrenIterator.next();

						ermsNode.addChildNode(childNode, childNode.getReference(), childNode.getMicroReference());

					}

				}

			}

			moveFaunaEuSynonymsToErmsTaxon(taxonFaunaEu, taxonErms);

			moveAllInformationsFromFaunaEuToErms(taxonFaunaEu, taxonErms);

			moveOriginalDbToErmsTaxon(taxonFaunaEu, taxonErms);

			//neue sec Referenz an das ErmsTaxon oder an das Synonym und Taxon oder nur Synonym??

			try{

				deleteFaunaEuTaxon(taxonFaunaEu);

			}catch(ReferencedObjectUndeletableException e){

				logger.debug("The taxon " + taxonFaunaEu.getTitleCache() + " can't be deleted because it is referenced.");

			}

		}

	}

	private void updateNameRelationships(List<List<String>> ermsAccFaEuSyn){

		//suche alle NameRelationships aus FaunaEu und Erms, wo (faunaEu)relatedFrom.name.titleCache = (erms)relatedFrom.name.titleCache und ersetze in der faunaEu Relationship den relatedTo.name durch den relatedTo.name der erms-relationship

		//wenn es diese relationship noch nicht gibt und der typ der gleiche ist!!

		//wenn der relatedTo Name zu einem Erms Taxon und einem FaunaEu Synonym gehört

		Synonym synFaunaEu;

		Taxon taxonErms;

		for (List<String> row: ermsAccFaEuSyn){

			synFaunaEu = (Synonym)appCtrInit.getTaxonService().find(UUID.fromString(row.get(faunaEuUuid)));

			taxonErms = (Taxon)appCtrInit.getTaxonService().find(UUID.fromString(row.get(ermsUuid)));

			List<NameRelationship> relSynFaunaEu = appCtrInit.getNameService().listToNameRelationships(synFaunaEu.getName(), null, 100, 0, null, null);

			List<NameRelationship> relTaxonErms = appCtrInit.getNameService().listToNameRelationships(taxonErms.getName(), null, 100, 0, null, null);

			List<NameRelationship> deleteRel = new ArrayList<NameRelationship>();

			for (NameRelationship relFauEu: relSynFaunaEu){

				boolean createNewRelationship = true;

				for (NameRelationship relErms: relTaxonErms){

					if ((relErms.getFromName().getTitleCache().equals(relFauEu.getFromName().getTitleCache())) && (relErms.getToName().getTitleCache().equals(relFauEu.getFromName().getTitleCache()))){

						//delete the faunaEu relationship because there exist an analogous relationship in erms

						deleteRel.add(relFauEu);

						createNewRelationship = false;

						break;

					}

				}

				if (createNewRelationship){

					//if relationship does not exist, create a new one with erms synonym

					taxonErms.getName().addRelationshipFromName(relFauEu.getFromName(), relFauEu.getType(), relFauEu.getRuleConsidered(), null);

				}

			}

		}

	}

	private void updateSynonymRelationships(List<List<String>> ermsSynFaEuAcc){

//		-- Update queries for RelTaxon (synonym relationships - move relationships to ERMS accepted taxon if not already existent or delete if already existent)

//		UPDATE RelTaxon_1 SET RelTaxon_1.TaxonFk2 = RT.TaxonFk2

//		FROM         Taxon AS ERMSSyn INNER JOIN

//		                      Taxon AS FaEuAcc ON ERMSSyn.RankFk = FaEuAcc.RankFk AND ERMSSyn.FullName = FaEuAcc.FullName AND

//		                      ERMSSyn.TaxonStatusFk <> ISNULL(FaEuAcc.TaxonStatusFk, 0) INNER JOIN

//		                      RelTaxon AS RT ON ERMSSyn.TaxonId = RT.TaxonFk1 INNER JOIN

//		                      RelTaxon AS RelTaxon_1 ON FaEuAcc.TaxonId = RelTaxon_1.TaxonFk2 INNER JOIN

//		                      Taxon AS FaEuSyn ON RelTaxon_1.TaxonFk1 = FaEuSyn.TaxonId LEFT OUTER JOIN

//		                      Taxon AS ERMSAllSyn ON RT.TaxonFk1 = ERMSAllSyn.TaxonId AND FaEuSyn.FullName <> ERMSAllSyn.FullName --(!!)

//		WHERE     (ERMSSyn.OriginalDB = N'ERMS') AND (RT.RelTaxonQualifierFk > 100) AND (ERMSSyn.TaxonStatusFk <> 1) AND (ERMSSyn.KingdomFk = 2) AND

//		                      (FaEuAcc.OriginalDB = N'FaEu') AND (RelTaxon_1.RelTaxonQualifierFk > 100)

		Taxon taxonFaunaEu;

		Synonym synErms;

		Taxon taxonErms;

		Set<Taxon> acceptedTaxa = new HashSet<Taxon>();

		for (List<String> row: ermsSynFaEuAcc){

			taxonFaunaEu = (Taxon)appCtrInit.getTaxonService().find(UUID.fromString(row.get(faunaEuUuid)));

			synErms = (Synonym)appCtrInit.getTaxonService().find(UUID.fromString(row.get(ermsUuid)));

			acceptedTaxa.clear();

			acceptedTaxa.add( synErms.getAcceptedTaxon());

			if (!acceptedTaxa.isEmpty()){

				taxonErms = acceptedTaxa.iterator().next();

				if (acceptedTaxa.size() > 1){

					logger.debug("There are more than one accepted taxon for synonym " + synErms.getTitleCache());

				}

			}else{

				taxonErms = null;

				logger.debug("There is no accepted taxon for synonym "  + synErms.getTitleCache());

			}

			if (taxonErms != null){

				Pager<Synonym> synsTaxonFaunaEuPager = appCtrInit.getTaxonService().getSynonyms(taxonFaunaEu, null, null, null, null, null);

				List<Synonym> synsTaxonFaunaEu = synsTaxonFaunaEuPager.getRecords();

				Pager<Synonym> synsTaxonErmsPager = appCtrInit.getTaxonService().getSynonyms(taxonErms, null, null, null, null, null);

				List<Synonym> synsTaxonErms = synsTaxonErmsPager.getRecords();

				List<Synonym> deleteRel = new ArrayList<>();

				for (Synonym synFauEu: synsTaxonFaunaEu){

					//TODO: wenn es noch keine SynonymRelationship gibt zu einem Synonym mit gleichem Namen,

				    //dann erzeuge die SynonymRelationship vom FaunaEuSyn (des FaunaEu Taxons, das

				    //identischen Namen hat) zum akzeptierten Taxon des Erms Syn

					boolean createNewRelationship = true;

					for (Synonym relErms: synsTaxonErms){

						if (relErms.getTitleCache().equals(synFauEu.getTitleCache())){

							//es gibt schon eine Relationship zu einem Synonym mit dem gleichen Namen wie das FaunaEu Synonym, also Relationship l�schen.

							createNewRelationship = false;

							break;

						}

					}

					if (createNewRelationship){

						taxonErms.addSynonym(synFauEu, synFauEu.getType());

					}

					deleteRel.add(synFauEu);

				}

			}

		}

	}

	private void deleteFaunaEuTaxon(Taxon taxonFaunaEu) throws ReferencedObjectUndeletableException {

		appCtrInit.getTaxonService().delete(taxonFaunaEu);

	}

	//wenn Name und Rang identisch sind und auch der Status gleich, dann alle Informationen vom Fauna Europaea Taxon/Synonym zum Erms Taxon/Synonym

	private void moveAllInformationsFromFaunaEuToErms(TaxonBase<?> faunaEu, TaxonBase<?> erms){

		Set<Annotation> annotations = faunaEu.getAnnotations();

		Set<Extension> extensions = faunaEu.getExtensions();

		Set<Marker> markers = faunaEu.getMarkers();

		List<Credit> credits = faunaEu.getCredits();

		if (faunaEu instanceof Taxon){

			Set<TaxonDescription> descriptions = ((Taxon)faunaEu).getDescriptions();

			Set<Taxon> misappliedNames = ((Taxon)faunaEu).getMisappliedNames(true);

			if (erms instanceof Taxon){

				Iterator<TaxonDescription> descriptionsIterator = descriptions.iterator();

				TaxonDescription description;

				while (descriptionsIterator.hasNext()){

					description = descriptionsIterator.next();

					((Taxon) erms).addDescription(description);

				}

				Iterator<Taxon> misappliedNamesIterator = misappliedNames.iterator();

				Taxon misappliedName;

				while (misappliedNamesIterator.hasNext()){

					misappliedName = misappliedNamesIterator.next();

					((Taxon) erms).addMisappliedName(misappliedName, null, null);

				}

			}

		}

		//move all these informations to the erms taxon

		Iterator<Annotation> annotationsIterator = annotations.iterator();

		Annotation annotation;

		while (annotationsIterator.hasNext()){

			annotation = annotationsIterator.next();

			erms.addAnnotation(annotation);

		}

		Iterator<Extension> extensionIterator = extensions.iterator();

		Extension extension;

		while (extensionIterator.hasNext()){

			extension = extensionIterator.next();

			erms.addExtension(extension);

		}

		Iterator<Marker> markerIterator = markers.iterator();

		Marker marker;

		while (markerIterator.hasNext()){

			marker = markerIterator.next();

			erms.addMarker(marker);

		}

		for (Credit credit: credits){

			erms.addCredit(credit);

		}

	}

	//if name, rank, and status (accepted) are the same, then move the synonyms of faunaEu taxon to the erms taxon

	private void moveFaunaEuSynonymsToErmsTaxon(Taxon faunaEu, Taxon erms){

		Set<Synonym> syns =faunaEu.getSynonyms();

		Iterator<Synonym> synRelIterator = syns.iterator();

		while (synRelIterator.hasNext()){

			Synonym syn = synRelIterator.next();

			faunaEu.removeSynonym(syn);

			erms.addSynonym(syn, syn.getType());

		}

	}

	//after merging faunaEu taxon and erms taxon, the originalSource of the faunaEu taxon has to be moved to the erms taxon

	private void moveOriginalDbToErmsTaxon(TaxonBase faunaEu, TaxonBase erms){

		Set<IdentifiableSource> sourcesFaunaEu = faunaEu.getSources();

		IdentifiableSource sourceFaunaEu = sourcesFaunaEu.iterator().next();

		erms.addSource(sourceFaunaEu);

	}

	//merged taxon should have a new sec reference

	private void addNewSecForMergedTaxon(Taxon taxon, Reference sec){

		taxon.setSec(sec);

		taxon.setUuid(UUID.randomUUID());

	}

	// ----------- methods for merging Erms synonyms and Fauna Europaea Taxon

}