EDIT

package eu.etaxonomy.cdm.io.pesi.faunaEuropaea;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.ArrayList;

import java.util.Collection;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import java.util.Map.Entry;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.io.common.Source;

import eu.etaxonomy.cdm.jaxb.TDWGNamespacePrefixMapper;

import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.location.NamedArea;

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

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

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

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

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

@Component

public class FaunaEuropaeaVernacularNamesImport extends FaunaEuropaeaImportBase {

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

	private HashMap<String, Reference> sourceMap = new HashMap<String, Reference>();

	@Override

	protected void doInvoke(FaunaEuropaeaImportState state) {

		int limit = state.getConfig().getLimitSave();

		if (state.getConfig().isDoVernacularNames()){

			/* Taxon store for retrieving taxa from and saving taxa to CDM */

			List<TaxonBase> taxonList = null;

			/* UUID store as input for retrieving taxa from CDM */

			Set<UUID> taxonUuids = null;

			/* Store to hold helper objects */

			Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuVernacularNamesMap = null;

			TransactionStatus txStatus = null;

			createSourceMap(state);

			FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

			Source source = fauEuConfig.getSource();

	        int i = 0;

			String selectCount =

				" SELECT count(*) ";

			String selectColumns =

				" SELECT vernacularNames.*, Taxon.UUID ";

			String fromClause =

				" FROM vernacularNames INNER JOIN " +

	            " Taxon ON vernacularnames.UUID = Taxon.UUID ";

			String orderBy = " ORDER BY vernacularNames.UUID";

			String countQuery =

				selectCount + fromClause;

			String selectQuery =

				selectColumns + fromClause + orderBy;

			if(logger.isInfoEnabled()) { logger.info("Start making vernacular names..."); }

			try {

				ResultSet rs = source.getResultSet(countQuery);

				rs.next();

				int count = rs.getInt(1);

				rs = source.getResultSet(selectQuery);

				if (logger.isInfoEnabled()) {

					logger.info("Number of rows: " + count);

					logger.info("Count Query: " + countQuery);

					logger.info("Select Query: " + selectQuery);

				}

				//int taxonId;

				while (rs.next()) {

					if ((i++ % limit) == 0) {

						txStatus = startTransaction();

						taxonUuids = new HashSet<UUID>(limit);

						fauEuVernacularNamesMap = new HashMap<UUID, FaunaEuropaeaVernacularNamesTaxon>(limit);

						if(logger.isInfoEnabled()) {

							logger.info("i = " + i + " - vernacular names import transaction started");

						}

					}

					//taxonId = rs.getInt("dis_tax_id");

					String vernameGUID = rs.getString("GUID");

					String vernacularNameString = rs.getString("verName");

					//int taxonFk = rs.getInt("taxonFK");

					int languageFK= rs.getInt("languageFK");

					String languageCache = rs.getString("languageCache");

					String taxonUUID= rs.getString("UUID");

					String verSource = rs.getString("VerSource");

					UUID currentTaxonUuid = null;

					FaunaEuropaeaVernacularName fauEuVernacularName = new FaunaEuropaeaVernacularName();

					fauEuVernacularName.setGuid(vernameGUID);

					fauEuVernacularName.setLanguageCache(languageCache);

					fauEuVernacularName.setLanguageFk(languageFK);

					fauEuVernacularName.setVernacularName(vernacularNameString);

					fauEuVernacularName.setSource(verSource);

					fauEuVernacularName.setTaxonUuid(UUID.fromString(taxonUUID));

					currentTaxonUuid =UUID.fromString(taxonUUID);

					if (!taxonUuids.contains(currentTaxonUuid)) {

						taxonUuids.add(currentTaxonUuid);

						FaunaEuropaeaVernacularNamesTaxon fauEuVernacularNameTaxon =

							new FaunaEuropaeaVernacularNamesTaxon(currentTaxonUuid);

						fauEuVernacularNamesMap.put(currentTaxonUuid, fauEuVernacularNameTaxon);

						fauEuVernacularNameTaxon = null;

					} else {

						if (logger.isTraceEnabled()) {

							logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");

							continue;

						}

					}

					fauEuVernacularNamesMap.get(currentTaxonUuid).addVernacularName(fauEuVernacularName);

					if (((i % limit) == 0 && i != 1 ) || i == count ) {

						try {

							commitTaxaAndVernacularNames(state,  taxonUuids, fauEuVernacularNamesMap, txStatus);

							taxonUuids = null;

							taxonList = null;

							fauEuVernacularNamesMap = null;

						} catch (Exception e) {

							logger.error("Commit of taxa and distributions failed" + e.getMessage());

							e.printStackTrace();

						}

						if(logger.isInfoEnabled()) { logger.info("i = " + i + " - Transaction committed");}

					}

				}

				if (taxonUuids != null){

					try {

						commitTaxaAndVernacularNames(state, taxonUuids, fauEuVernacularNamesMap, txStatus);

						taxonUuids = null;

						taxonList = null;

						fauEuVernacularNamesMap = null;

					} catch (Exception e) {

						logger.error("Commit of taxa and vernacular names failed");

						logger.error(e.getMessage());

						e.printStackTrace();

					}

				}

				rs = null;

			} catch (SQLException e) {

				logger.error("SQLException:" +  e);

				state.setUnsuccessfull();

			}

			if(logger.isInfoEnabled()) { logger.info("End making vernacular names..."); }

			return;

		}

	}

	@Override

	protected boolean doCheck(FaunaEuropaeaImportState state) {

		// TODO Auto-generated method stub

		return false;

	}

	@Override

	protected boolean isIgnore(FaunaEuropaeaImportState state) {

		// TODO Auto-generated method stub

		return false;

	}

	private void commitTaxaAndVernacularNames(

			FaunaEuropaeaImportState state, 

			Set<UUID> taxonUuids,

			Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuTaxonMap,

			TransactionStatus txStatus) throws Exception {

		List<TaxonBase> taxonList = prepareTaxaAndVernacularNames(getTaxonService().find(taxonUuids), fauEuTaxonMap, state);

		getTaxonService().saveOrUpdate(taxonList);

		taxonList = null;

		taxonUuids = null;

		fauEuTaxonMap = null;

		commitTransaction(txStatus);

	}

	private List<TaxonBase> prepareTaxaAndVernacularNames(List<TaxonBase> taxonList, Map<UUID, FaunaEuropaeaVernacularNamesTaxon> fauEuTaxonMap,  FaunaEuropaeaImportState state) throws Exception{

		CommonTaxonName verName = null;

		FaunaEuropaeaVernacularNamesTaxon fauEuHelperTaxon;

		UUID taxonUuid;

		TaxonDescription taxonDescription;

		Taxon taxon;

		for (TaxonBase<?> taxonBase : taxonList) {

			if (taxonBase != null) {

				if (taxonBase instanceof Taxon) {

					taxon = CdmBase.deproxy(taxonBase, Taxon.class);

				} else {

					Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);

					if (syn.getAcceptedTaxa().size()>0){

						taxon = syn.getAcceptedTaxa().iterator().next();

					}

					logger.warn("TaxonBase (" + taxonBase.getId() + " is not of type Taxon but: "

							+ taxonBase.getClass().getSimpleName() + " using accepted Taxon for vernacular name");

					continue;

				}

				Set<TaxonDescription> descriptionSet = taxon.getDescriptions();

				taxonDescription = TaxonDescription.NewInstance();

				taxon.addDescription(taxonDescription);

				taxonUuid = taxonBase.getUuid();

				fauEuHelperTaxon= fauEuTaxonMap.get(taxonUuid);

				for (FaunaEuropaeaVernacularName fauEuHelperVernacularName: fauEuHelperTaxon.getVernacularNames()) {

					verName = null;

					/*

					 * UUID uuid = state.getTransformer().getLanguageUuid(languageKey);

					result = (Language)getTermService().find(uuid);

				}

				if (result == null){

					result = state.getTransformer().getLanguageByKey(languageKey);

					if (result == null){

						UUID uuidLanguage;

						uuidLanguage = state.getTransformer().getLanguageUuid(languageKey);

						if (uuidLanguage == null){

							logger.warn("Language not defined: " + languageKey)  ;

						}

						result = getLanguage(state, uuidLanguage, languageKey, languageKey, null);

						if (result == null){

							logger.warn("Language not defined: " + languageKey)  ;

						}

					}else if (result.getId() == 0){

//						UUID uuidLanguageVoc = UUID.fromString("45ac7043-7f5e-4f37-92f2-3874aaaef2de"); 

						UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084"); 

						TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, result);

//						TermVocabulary<Language> voc = getVocabularyService().find(uuidLanguageVoc);

						voc.addTerm(result);

						getTermService().saveOrUpdate(result);

						state.putLanguage(result);

					}

					 * 

					 */

					Language lang = FaunaEuropaeaTransformer.langFK2Language(fauEuHelperVernacularName.getLanguageFk());

					if (lang == null && fauEuHelperVernacularName.getLanguageFk() == 83){

						lang = Language.ENGLISH();

						fauEuHelperVernacularName.setArea("USA");

					} 

					if (lang == null){

						UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084"); 

						logger.info("languageFk = " + fauEuHelperVernacularName.getLanguageFk());

						TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, lang);

						lang = Language.NewInstance("Dummy", "", "");

						voc.addTerm(lang);

						lang =(Language)getTermService().save(lang);

						FaunaEuropaeaTransformer.languageFK2Language.put(fauEuHelperVernacularName.getLanguageFk(), lang);

					}

//					if (lang.getId() == 0){

//						UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084"); 

//						TermVocabulary<Language> voc = getVocabulary(TermType.Language, uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, lang);

//						voc.addTerm(lang);

//						lang =(Language)getTermService().save(lang);

//						//FaunaEuropaeaTransformer.languageFK2Language.put(fauEuHelperVernacularName.getLanguageFk(), lang);

//					}

					verName = CommonTaxonName.NewInstance(fauEuHelperVernacularName.getVernacularName(), lang);

					if (fauEuHelperVernacularName.getArea()!= null && fauEuHelperVernacularName.getArea().equals("USA")){

						verName.setArea(NamedArea.NORTH_AMERICA());

					}

					verName.setCreated(null);

					addOriginalSource(verName, null, null, sourceMap.get(fauEuHelperVernacularName.getSource()));

					taxonDescription.addElement(verName);

				}

			}

		}

		return taxonList;

	}

	private void createSourceMap(FaunaEuropaeaImportState state){

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		Source source = fauEuConfig.getSource();

		TransactionStatus txStatus = null;

		String sourceSelect = "SELECT DISTINCT vernacularNames.VerSource FROM vernacularNames group by vernacularNames.VerSource";

		try {

			txStatus =startTransaction();

			ResultSet rs = source.getResultSet(sourceSelect);

			Reference sourceRef;

			String title ;

			Set<Reference> referncesToSave = new HashSet<Reference>();

			while (rs.next()) {

				sourceRef = ReferenceFactory.newGeneric();

				title = rs.getString("VerSource");

				sourceRef.setTitle(title);

				referncesToSave.add(sourceRef);

			}

			commitReferences(referncesToSave, txStatus);

		}catch (SQLException e) {

			logger.error("SQLException:" +  e);

			state.setUnsuccessfull();

		}

	}	

	private void commitReferences(Collection<Reference> references,  TransactionStatus txStatus) {

		Map <UUID, Reference> referenceMap =getReferenceService().save(references);

		Iterator<Entry<UUID, Reference>> it = referenceMap.entrySet().iterator();

		while (it.hasNext()){

			Reference<?> ref = it.next().getValue();

			String refID = ref.getTitle();

			sourceMap.put(refID, ref);

		}

		commitTransaction(txStatus);

	}

}