EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

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

import static eu.etaxonomy.cdm.io.pesi.faunaEuropaea.FaunaEuropaeaTransformer.P_PARENTHESIS;

import static eu.etaxonomy.cdm.io.pesi.faunaEuropaea.FaunaEuropaeaTransformer.R_GENUS;

import static eu.etaxonomy.cdm.io.pesi.faunaEuropaea.FaunaEuropaeaTransformer.R_SPECIES;

import static eu.etaxonomy.cdm.io.pesi.faunaEuropaea.FaunaEuropaeaTransformer.R_SUBGENUS;

import static eu.etaxonomy.cdm.io.pesi.faunaEuropaea.FaunaEuropaeaTransformer.R_SUBSPECIES;

import static eu.etaxonomy.cdm.io.pesi.faunaEuropaea.FaunaEuropaeaTransformer.T_STATUS_ACCEPTED;

import static eu.etaxonomy.cdm.io.pesi.faunaEuropaea.FaunaEuropaeaTransformer.T_STATUS_NOT_ACCEPTED;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.sql.Timestamp;

import java.util.Collection;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.joda.time.DateTime;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

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

import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;

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

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

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

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

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

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

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

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

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

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

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.strategy.exceptions.UnknownCdmTypeException;

/**

 * @author a.babadshanjan

 * @created 12.05.2009

 * @version 1.0

 */

@Component

public class FaunaEuropaeaTaxonNameImport extends FaunaEuropaeaImportBase  {

	public static final String OS_NAMESPACE_TAXON = "Taxon";

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

	/* Max number of taxa to retrieve (for test purposes) */

	private final int maxTaxa = 0;

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)

	 */

	@Override

	protected boolean doCheck(FaunaEuropaeaImportState state) {

		boolean result = true;

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		logger.warn("Checking for Taxa not yet fully implemented");

//		result &= checkTaxonStatus(fauEuConfig);

		return result;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)

	 */

	@Override

    protected boolean isIgnore(FaunaEuropaeaImportState state) {

		return ! state.getConfig().isDoTaxa();

	}

	/**

	 * Import taxa from FauEU DB

	 */

	@Override

    protected void doInvoke(FaunaEuropaeaImportState state) {

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

		if (!state.getConfig().isDoTaxa()){

			return;

		}

		processTaxa(state);

		logger.info("End making taxa...");

		return;

	}

	/**

	 * Returns an empty string in case of a null string.

	 * This avoids having the string "null" when using StringBuilder.append(null);

	 * @param string

	 * @return

	 */

	private String NullToEmpty(String string) {

		if (string == null) {

			return "";

		} else {

			return string;

		}

	}

	/** Retrieve taxa from FauEu DB, process in blocks */

	private void processTaxa(FaunaEuropaeaImportState state) {

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

		TransactionStatus txStatus = null;

		Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();

		MapWrapper<TeamOrPersonBase> authorStore = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.TEAM_STORE);

		Map<Integer, TaxonBase<?>> taxonMap = null;

		Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap = null;

		/* Store for heterotypic synonyms to be save separately */

		Set<Synonym> synonymSet = null;

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		Reference sourceRef = fauEuConfig.getSourceReference();

		Source source = fauEuConfig.getSource();

		int i = 0;

		String selectCount =

			" SELECT count(*) ";

		String selectColumns =

			" SELECT Parent.TAX_NAME AS P2Name, Parent.TAX_RNK_ID AS P2RankId, " +

			" GrandParent.TAX_ID AS GP3Id, GrandParent.TAX_NAME AS GP3Name, GrandParent.TAX_RNK_ID AS GP3RankId, " +

			" GreatGrandParent.TAX_ID AS GGP4Id, GreatGrandParent.TAX_NAME AS GGP4Name, GreatGrandParent.TAX_RNK_ID AS GGP4RankId, " +

			" GreatGreatGrandParent.TAX_ID AS GGGP5Id, GreatGreatGrandParent.TAX_NAME AS GGGP5Name, GreatGreatGrandParent.TAX_RNK_ID AS GGGP5RankId, " +

			" OriginalGenusTaxon.TAX_NAME AS OGenusName, " +

			" GreatGreatGreatGrandParent.TAX_ID AS GGGGP6Id, GreatGreatGreatGrandParent.TAX_NAME AS GGGGP6Name, GreatGreatGreatGrandParent.TAX_RNK_ID AS GGGGP6RankId," +

			" expertUsers.usr_id AS expertUserId, expertUsers.usr_title AS ExpertUsrTitle, expertUsers.usr_firstname AS ExpertUsrFirstname, expertUsers.usr_lastname AS ExpertUsrLastname," +

			" speciesExpertUsers.usr_id AS speciesExpertUserId, speciesExpertUsers.usr_title AS SpeciesUsrTitle, speciesExpertUsers.usr_firstname AS SpeciesUsrFirstname, speciesExpertUsers.usr_lastname AS SpeciesUsrLastname," +

			" Taxon.*, rank.*, author.* ";

		String fromClause =

			" FROM Taxon LEFT OUTER JOIN " +

			" Taxon AS Parent ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID LEFT OUTER JOIN " +

			" Taxon AS GrandParent ON Parent.TAX_TAX_IDPARENT = GrandParent.TAX_ID LEFT OUTER JOIN " +

			" Taxon AS GreatGrandParent ON GrandParent.TAX_TAX_IDPARENT = GreatGrandParent.TAX_ID LEFT OUTER JOIN " +

			" Taxon AS GreatGreatGrandParent ON GreatGrandParent.TAX_TAX_IDPARENT = GreatGreatGrandParent.TAX_ID LEFT OUTER JOIN " +

			" Taxon AS GreatGreatGreatGrandParent ON GreatGreatGrandParent.TAX_TAX_IDPARENT = GreatGreatGreatGrandParent.TAX_ID LEFT OUTER JOIN " +

			" Taxon AS OriginalGenusTaxon ON Taxon.TAX_TAX_IDGENUS = OriginalGenusTaxon.TAX_ID LEFT OUTER JOIN " +

			" author ON Taxon.TAX_AUT_ID = author.aut_id LEFT OUTER JOIN " +

			" users AS expertUsers ON Taxon.TAX_USR_IDGC = expertUsers.usr_id LEFT OUTER JOIN " +

			" users AS speciesExpertUsers ON Taxon.TAX_USR_IDSP = speciesExpertUsers.usr_id LEFT OUTER JOIN " +

			" rank ON Taxon.TAX_RNK_ID = rank.rnk_id ";

		String countQuery =

			selectCount + fromClause;

		String selectQuery =

			selectColumns + fromClause;

        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);

			}

			while (rs.next()) {

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

					txStatus = startTransaction();

					taxonMap = new HashMap<Integer, TaxonBase<?>>(limit);

					fauEuTaxonMap = new HashMap<Integer, FaunaEuropaeaTaxon>(limit);

					synonymSet = new HashSet<Synonym>();

					if(logger.isInfoEnabled()) {

						logger.info("i = " + i + " - Transaction started");

					}

				}

				String localName = rs.getString("TAX_NAME");

				String parentName = rs.getString("P2Name");

				int grandParentId = rs.getInt("GP3Id");

				String grandParentName = rs.getString("GP3Name");

				int greatGrandParentId = rs.getInt("GGP4Id");

				String greatGrandParentName = rs.getString("GGP4Name");

				int greatGreatGrandParentId = rs.getInt("GGGP5Id");

				String greatGreatGrandParentName = rs.getString("GGGP5Name");

				String greatGreatGreatGrandParentName = rs.getString("GGGGP6Name");

				String originalGenusName = rs.getString("OGenusName");

				String autName = rs.getString("aut_name");

				int taxonId = rs.getInt("TAX_ID");

				int rankId = rs.getInt("TAX_RNK_ID");

				int parentId = rs.getInt("TAX_TAX_IDPARENT");

				int parentRankId = rs.getInt("P2RankId");

				int grandParentRankId = rs.getInt("GP3RankId");

				int greatGrandParentRankId = rs.getInt("GGP4RankId");

				int greatGreatGrandParentRankId = rs.getInt("GGGP5RankId");

				int greatGreatGreatGrandParentRankId = rs.getInt("GGGGP6RankId");

				int originalGenusId = rs.getInt("TAX_TAX_IDGENUS");

				int autId = rs.getInt("TAX_AUT_ID");

				int status = rs.getInt("TAX_VALID");

				// user related

				String expertUsrTitle = rs.getString("ExpertUsrTitle");

				String expertUsrFirstname = rs.getString("ExpertUsrFirstname");

				String expertUsrLastname = rs.getString("ExpertUsrLastname");

				String speciesUsrTitle = rs.getString("SpeciesUsrTitle");

				String speciesUsrFirstname = rs.getString("SpeciesUsrFirstname");

				String speciesUsrLastname = rs.getString("SpeciesUsrLastname");

				String expertUserId = "" + rs.getInt("expertUserId");

				String speciesExpertUserId = "" + rs.getInt("speciesExpertUserId");

				String expertName = "";

				if (expertUsrTitle != null) {

					expertName = expertUsrTitle;

					if (! expertUsrTitle.endsWith(".")) {

						expertName += ".";

					}

				}

				expertName += expertUsrTitle == null ? NullToEmpty(expertUsrFirstname) : " " + NullToEmpty(expertUsrFirstname);

				if ((expertUsrTitle != null || expertUsrFirstname != null) && expertUsrLastname != null) {

					expertName += " " + expertUsrLastname;

				}

				String speciesExpertName = speciesUsrTitle == null ? "" : speciesUsrTitle + ".";

				if (speciesUsrTitle != null) {

					speciesExpertName = speciesUsrTitle;

					if (! speciesUsrTitle.endsWith(".")) {

						speciesExpertName += ".";

					}

				}

				speciesExpertName += speciesUsrTitle == null ? NullToEmpty(speciesUsrFirstname) : " " + NullToEmpty(speciesUsrFirstname);

				if ((speciesUsrTitle != null || speciesUsrFirstname != null) && speciesUsrLastname != null) {

					speciesExpertName += " " + speciesUsrLastname;

				}

				// date related

				Timestamp createdTimeStamp = rs.getTimestamp("TAX_CREATEDAT");

				Timestamp modifiedTimeStamp = rs.getTimestamp("TAX_MODIFIEDAT");

				boolean isCreated = createdTimeStamp.equals(modifiedTimeStamp);

				String lastAction = isCreated ? "created" : "modified";

				DateTime created = new DateTime(createdTimeStamp);

				DateTime modified = isCreated ? null : new DateTime(modifiedTimeStamp);

				DateTime lastActionDate = isCreated ?  created : modified;

				String lastActionDateStr = isCreated ? createdTimeStamp.toString() : modifiedTimeStamp.toString();

				// note related

				String taxComment = rs.getString("TAX_TAXCOMMENT");

				String fauComment = rs.getString("TAX_FAUCOMMENT");

				String fauExtraCodes = rs.getString("TAX_FAUEXTRACODES");

				// Avoid publication year 0 for NULL values in database.

				Integer year = rs.getInt("TAX_YEAR");

				if (year != null && year.intValue() == 0) {

					year = null;

				}

				//int familyId = rs.getInt("TAX_TAX_IDFAMILY");

				Rank rank = null;

				int parenthesis = rs.getInt("TAX_PARENTHESIS");

				UUID taxonBaseUuid = null;

				if (resultSetHasColumn(rs,"UUID")){

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

					taxonBaseUuid = UUID.fromString(uuid);

				} else {

					taxonBaseUuid = UUID.randomUUID();

				}

				FaunaEuropaeaTaxon fauEuTaxon = new FaunaEuropaeaTaxon();

				fauEuTaxon.setUuid(taxonBaseUuid);

				fauEuTaxon.setId(taxonId);

				fauEuTaxon.setRankId(rankId);

				fauEuTaxon.setLocalName(localName);

				fauEuTaxon.setParentId(parentId);

				fauEuTaxon.setParentRankId(parentRankId);

				fauEuTaxon.setParentName(parentName);

				fauEuTaxon.setGrandParentId(grandParentId);

				fauEuTaxon.setGrandParentRankId(grandParentRankId);

				fauEuTaxon.setGrandParentName(grandParentName);

				fauEuTaxon.setGreatGrandParentId(greatGrandParentId);

				fauEuTaxon.setGreatGrandParentRankId(greatGrandParentRankId);

				fauEuTaxon.setGreatGrandParentName(greatGrandParentName);

				fauEuTaxon.setGreatGreatGrandParentId(greatGreatGrandParentId);

				fauEuTaxon.setGreatGreatGrandParentRankId(greatGreatGrandParentRankId);

				fauEuTaxon.setGreatGreatGrandParentName(greatGreatGrandParentName);

				fauEuTaxon.setGreatGreatGreatGrandParentRankId(greatGreatGreatGrandParentRankId);

				fauEuTaxon.setGreatGreatGreatGrandParentName(greatGreatGreatGrandParentName);

				fauEuTaxon.setOriginalGenusId(originalGenusId);

				fauEuTaxon.setYear(year);

				fauEuTaxon.setOriginalGenusName(originalGenusName);

				fauEuTaxon.setAuthorName(autName);

				if (parenthesis == P_PARENTHESIS) {

					fauEuTaxon.setParenthesis(true);

				} else {

					fauEuTaxon.setParenthesis(false);

				}

				if (status == T_STATUS_ACCEPTED) {

					fauEuTaxon.setValid(true);

				} else {

					fauEuTaxon.setValid(false);

				}

//				fauEuTaxon.setAuthorId(autId);

				try {

					rank = FaunaEuropaeaTransformer.rankId2Rank(rs, false);

				} catch (UnknownCdmTypeException e) {

					logger.warn("Taxon (" + taxonId + ") has unknown rank (" + rankId + ") and could not be saved.");

					continue;

				} catch (NullPointerException e) {

					logger.warn("Taxon (" + taxonId + ") has rank null and can not be saved.");

					continue;

				}

				Reference sourceReference = fauEuConfig.getSourceReference();

				Reference auctReference = fauEuConfig.getAuctReference();

				TaxonName zooName = TaxonNameFactory.NewZoologicalInstance(rank);

				TeamOrPersonBase<?> author = authorStore.get(autId);

				zooName.setCombinationAuthorship(author);

				zooName.setPublicationYear(year);

				// Add Date extensions to this zooName

				Extension.NewInstance(zooName, lastAction, getExtensionType(state, PesiTransformer.lastActionUuid, "LastAction", "LastAction", "LA"));

//				Extension.NewInstance(zooName, lastActionDateStr, getExtensionType(state, PesiTransformer.lastActionDateUuid, "LastActionDate", "LastActionDate", "LAD"));

				zooName.setCreated(created);

				zooName.setUpdated(modified);

				/* Add Note extensions to this zooName

				Extension.NewInstance(zooName, taxComment, getExtensionType(PesiTransformer.taxCommentUuid, "TaxComment", "TaxComment", "TC"));

				Extension.NewInstance(zooName, fauComment, getExtensionType(PesiTransformer.fauCommentUuid, "FauComment", "FauComment", "FC"));

				Extension.NewInstance(zooName, fauExtraCodes, getExtensionType(PesiTransformer.fauExtraCodesUuid, "FauExtraCodes", "FauExtraCodes", "FEC"));

				*/

				TaxonBase<?> taxonBase;

				Synonym synonym = null;

				Taxon taxon;

				try {

					// check for occurrence of the auct string in auctName

					String auctRegEx = "\\bauct\\b\\.?"; // The word "auct" with or without "."

					String auctWithNecRegEx = "\\bauct\\b\\.?.*\\bnec\\b\\.?.*";

					String necAuctRegEx = ".*\\bnec\\b\\.?.*\\bauct\\b\\.?";

					boolean auctNecFound = expressionMatches(auctWithNecRegEx, autName);

					boolean necAuctFound = expressionMatches(necAuctRegEx, autName);

					boolean auctWordFound = expressionMatches(auctRegEx, autName);

					if (status == T_STATUS_ACCEPTED ) {

							taxon = Taxon.NewInstance(zooName, sourceReference);

							if (logger.isDebugEnabled()) {

								logger.debug("Taxon created (" + taxonId + ")");

							}

						taxonBase = taxon;

					} else if ((status == T_STATUS_NOT_ACCEPTED) && ! auctWordFound) { // synonym

						synonym = Synonym.NewInstance(zooName, sourceReference);

						//logger.info("Synonym created: " + synonym.getTitleCache() + " taxonName: " + zooName.getTitleCache());

						if (logger.isDebugEnabled()) {

							logger.debug("Synonym created (" + taxonId + ")");

						}

						taxonBase = synonym;

					} else if (status == T_STATUS_NOT_ACCEPTED && (necAuctFound || auctNecFound)){

						synonym = Synonym.NewInstance(zooName, sourceReference);

						NomenclaturalStatus tempNameNomStatus = NomenclaturalStatus.NewInstance(FaunaEuropaeaTransformer.getNomStatusTempNamed(getTermService()));

						zooName.addStatus(tempNameNomStatus);

						taxonBase = synonym;

						logger.info("temporary named name created ("+ taxonId + ") " + zooName.getTitleCache()+ zooName.getStatus().toString());

					}else if (status == T_STATUS_NOT_ACCEPTED && auctWordFound){

							// misapplied name

								zooName.setCombinationAuthorship(null);

								zooName.setPublicationYear(null);

								// now we do it with appended phrase and without auct reference

								taxon = Taxon.NewInstance(zooName, null);

								taxonBase = taxon;

								//logger.info("Misapplied name created ("+ taxonId + ") " + autName);

								if (logger.isDebugEnabled()) {

									logger.debug("Misapplied name created (" + taxonId + ")");

									}

					}else{

						logger.warn("Unknown taxon status " + status + ". Taxon (" + taxonId + ") ignored.");

						continue;

					}

					taxonBase.setUuid(taxonBaseUuid);

					taxonBase.setLsid(new LSID( "urn:lsid:faunaeur.org:taxname:"+taxonId));

					taxonBase.setCreated(created);

					taxonBase.setUpdated(modified);

					// Add Note extensions to this taxon

					if (!StringUtils.isBlank(taxComment)){

						Extension.NewInstance(taxonBase, taxComment, getExtensionType(state, PesiTransformer.taxCommentUuid, "TaxComment", "TaxComment", "TC"));

					}

					if (!StringUtils.isBlank(fauComment)){

						Extension.NewInstance(taxonBase, fauComment, getExtensionType(state, PesiTransformer.fauCommentUuid, "FauComment", "FauComment", "FC"));

					}

					if (!StringUtils.isBlank(fauExtraCodes)){

						Extension.NewInstance(taxonBase, fauExtraCodes, getExtensionType(state, PesiTransformer.fauExtraCodesUuid, "FauExtraCodes", "FauExtraCodes", "FEC"));

					}

					// Add UserId extensions to this zooName

					//Extension.NewInstance(zooName, expertUserId, getExtensionType(state, PesiTransformer.expertUserIdUuid, "expertUserId", "expertUserId", "EUID"));

					//Extension.NewInstance(zooName, speciesExpertUserId, getExtensionType(state, PesiTransformer.speciesExpertUserIdUuid, "speciesExpertUserId", "speciesExpertUserId", "SEUID"));

					// Add Expert extensions to this zooName

					Extension.NewInstance(taxonBase, expertName, getExtensionType(state, PesiTransformer.expertNameUuid, "ExpertName", "ExpertName", "EN"));

					Extension.NewInstance(taxonBase, speciesExpertName, getExtensionType(state, PesiTransformer.speciesExpertNameUuid, "SpeciesExpertName", "SpeciesExpertName", "SEN"));

					ImportHelper.setOriginalSource(taxonBase, fauEuConfig.getSourceReference(), taxonId, OS_NAMESPACE_TAXON);

					ImportHelper.setOriginalSource(zooName, fauEuConfig.getSourceReference(), taxonId, "TaxonName");

					if (!taxonMap.containsKey(taxonId)) {

						taxonMap.put(taxonId, taxonBase);

						fauEuTaxonMap.put(taxonId, fauEuTaxon);

					} else {

						logger.warn("Not imported taxon base with duplicated TAX_ID (" + taxonId +

								") " + localName);

					}

				} catch (Exception e) {

					logger.warn("An exception occurred when creating taxon base with id " + taxonId +

					". Taxon base could not be saved.");

					e.printStackTrace();

				}

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

					commitTaxa(state, txStatus, taxonMap, fauEuTaxonMap,

							synonymSet);

					taxonMap = null;

					synonymSet = null;

					fauEuTaxonMap = null;

					if(logger.isInfoEnabled()) {

						logger.info("i = " + i + " - Transaction committed");

					}

				}

			}

			rs = null;

			if (taxonMap != null){

				commitTaxa(state, txStatus, taxonMap, fauEuTaxonMap,

						synonymSet);

				taxonMap = null;

				synonymSet = null;

				fauEuTaxonMap = null;

			}

		} catch (SQLException e) {

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

			state.setUnsuccessfull();

		}

        taxonMap = null;

		synonymSet = null;

		fauEuTaxonMap = null;

		return;

	}

	private void commitTaxa(FaunaEuropaeaImportState state,

			TransactionStatus txStatus, Map<Integer, TaxonBase<?>> taxonMap,

			Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap,

			Set<Synonym> synonymSet) {

		processTaxaSecondPass(state, taxonMap, fauEuTaxonMap, synonymSet);

		if(logger.isDebugEnabled()) { logger.debug("Saving taxa ... " + taxonMap.size()); }

		getTaxonService().save((Collection)taxonMap.values());

		commitTransaction(txStatus);

	}

	/**

	 * Processes taxa from complete taxon store

	 */

	private void processTaxaSecondPass(FaunaEuropaeaImportState state, Map<Integer, TaxonBase<?>> taxonMap,

			Map<Integer, FaunaEuropaeaTaxon> fauEuTaxonMap, Set<Synonym> synonymSet) {

		if(logger.isDebugEnabled()) { logger.debug("Processing taxa second pass..."); }

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		for (int id : taxonMap.keySet())

		{

			if (logger.isDebugEnabled()) { logger.debug("Taxon # " + id); }

			TaxonBase<?> taxonBase = taxonMap.get(id);

			TaxonName taxonName = CdmBase.deproxy(taxonBase.getName());

			FaunaEuropaeaTaxon fauEuTaxon = fauEuTaxonMap.get(id);

			boolean useOriginalGenus = false;

			//if (taxonBase instanceof Synonym){

			if (!fauEuTaxon.isValid() ){

				useOriginalGenus = true;

			}

			String nameString =

				buildTaxonName(fauEuTaxon, taxonBase, taxonName, useOriginalGenus, fauEuConfig);

			if (taxonBase instanceof Synonym){

				logger.debug("Name of Synonym: " + nameString);

			}

			if (fauEuConfig.isDoBasionyms()

					&& fauEuTaxon.getRankId() > R_SUBGENUS

					&& (fauEuTaxon.getOriginalGenusId() != 0)) {

				Integer originalGenusId = fauEuTaxon.getOriginalGenusId();

				Integer actualGenusId = getActualGenusId(fauEuTaxon);

				if (logger.isDebugEnabled()) {

					logger.debug("actual genus id = " + actualGenusId + ", original genus id = " + originalGenusId);

				}

				if (actualGenusId.intValue() != originalGenusId.intValue() && taxonBase.isInstanceOf(Taxon.class)) {

					createBasionym(fauEuTaxon, taxonBase, taxonName, fauEuConfig, synonymSet, state);

				} else if (fauEuTaxon.isParenthesis()) {

					//the authorteam should be set in parenthesis because there should be a basionym, but we do not know it?

					taxonName.setBasionymAuthorship(taxonName.getCombinationAuthorship());

					taxonName.setCombinationAuthorship(null);

					taxonName.setOriginalPublicationYear(taxonName.getPublicationYear());

					taxonName.setPublicationYear(null);

				}

			}

		}

		return;

	}

	private void createBasionym(FaunaEuropaeaTaxon fauEuTaxon, TaxonBase<?> taxonBase,

	        TaxonName taxonName, FaunaEuropaeaImportConfigurator fauEuConfig,

			Set<Synonym> synonymSet, FaunaEuropaeaImportState state) {

		try {

//			fIZoologicalName zooName = CdmBase.deproxy(taxonName);

			// create basionym

			TaxonName basionym =TaxonNameFactory.NewZoologicalInstance(taxonName.getRank());

			basionym.setCombinationAuthorship(taxonName.getCombinationAuthorship());

			basionym.setPublicationYear(taxonName.getPublicationYear());

			taxonName.addBasionym(basionym, fauEuConfig.getSourceReference(), null, null);

			//TODO:this is a workaround for fauna europaea, this should be fixed in cdm model. this should be not a basionym but an orthographic variant (original spelling)

			if (fauEuTaxon.isParenthesis()){

				taxonName.setOriginalPublicationYear(taxonName.getPublicationYear());

				taxonName.setBasionymAuthorship(taxonName.getCombinationAuthorship());

				taxonName.setCombinationAuthorship(null);

			} else{

			    taxonName.setBasionymAuthorship(null);

			    taxonName.setAuthorshipCache(taxonName.getAuthorshipCache(), true);

			    taxonName.setCombinationAuthorship(null);

			}

			taxonName.setPublicationYear(null);

			taxonName.setTitleCache(null); // This should (re)generate the titleCache automatically

			if (logger.isDebugEnabled()) {

				logger.debug("Basionym created (" + fauEuTaxon.getId() + ")");

			}

			// create synonym

			Synonym synonym = Synonym.NewInstance(basionym, fauEuConfig.getSourceReference());

			MarkerType markerType =getMarkerType(state, PesiTransformer.uuidMarkerGuidIsMissing, "Uuid is missing", "Uuid is missing", null);

			synonym.addMarker(Marker.NewInstance(markerType, true));

			if (fauEuTaxon.isValid()) { // Taxon

				// homotypic synonym

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

				taxon.addHomotypicSynonym(synonym);

				if (logger.isDebugEnabled()) {

					logger.debug("Homotypic synonym created (" + fauEuTaxon.getId() + ")");

				}

			} else { // Synonym

				// heterotypic synonym

				// synonym relationship to the accepted taxon is created later

				synonymSet.add(synonym);

				if (logger.isDebugEnabled()) {

					logger.debug("Heterotypic synonym stored (" + fauEuTaxon.getId() + ")");

				}

			}

			buildTaxonName(fauEuTaxon, synonym, basionym, true, fauEuConfig);

			//originalSources zufügen

			ImportHelper.setOriginalSource(synonym, fauEuConfig.getSourceReference(), fauEuTaxon.getId(), PesiTransformer.STR_NAMESPACE_NOMINAL_TAXON);

			ImportHelper.setOriginalSource(synonym.getName(), fauEuConfig.getSourceReference(), fauEuTaxon.getId(), PesiTransformer.STR_NAMESPACE_NOMINAL_TAXON);

			// add originalGenusId as source

//			String originalGenusIdString = String.valueOf(fauEuTaxon.getId());

//			IdentifiableSource basionymSource = IdentifiableSource.NewInstance(originalGenusIdString, "originalGenusId");

//			basionym.addSource(basionymSource);

//

//			// add original database reference

//			ImportHelper.setOriginalSource(basionym, fauEuConfig.getSourceReference(), fauEuTaxon.getId(), "TaxonName");

		} catch (Exception e) {

			logger.warn("Exception occurred when creating basionym for " + fauEuTaxon.getId());

			e.printStackTrace();

		}

		return;

	}

	/* Build name title cache */

	private String buildNameTitleCache(String nameString, boolean useOriginalGenus, FaunaEuropaeaTaxon fauEuTaxon) {

		StringBuilder titleCacheStringBuilder = new StringBuilder(nameString);

		Integer year = fauEuTaxon.getYear();

		if (year != null) { // TODO: Ignore authors like xp, xf, etc?

			titleCacheStringBuilder.append(" ");

			if ((fauEuTaxon.isParenthesis() == true) && !useOriginalGenus) {

				titleCacheStringBuilder.append("(");

			}

			titleCacheStringBuilder.append(fauEuTaxon.getAuthor());

			titleCacheStringBuilder.append(" ");

			titleCacheStringBuilder.append(year);

			if ((fauEuTaxon.isParenthesis() == true) && !useOriginalGenus) {

				titleCacheStringBuilder.append(")");

			}

		}

		return titleCacheStringBuilder.toString();

	}

	/* Build taxon title cache */

	private String buildTaxonTitleCache(String nameCache, Reference reference) {

		StringBuilder titleCacheStringBuilder = new StringBuilder(nameCache);

		titleCacheStringBuilder.append(" sec. ");

		titleCacheStringBuilder.append(reference.getTitleCache());

		return titleCacheStringBuilder.toString();

	}

	/* Build name full title cache */

	private String buildNameFullTitleCache(String titleCache, FaunaEuropaeaImportConfigurator fauEuConfig) {

		StringBuilder fullTitleCacheStringBuilder = new StringBuilder(titleCache);

		fullTitleCacheStringBuilder.append(" ");

		fullTitleCacheStringBuilder.append(fauEuConfig.getSourceReferenceTitle());

		return fullTitleCacheStringBuilder.toString();

	}

	private String genusPart(StringBuilder originalGenusName, boolean useOriginalGenus,

			StringBuilder genusOrUninomial) {

		StringBuilder stringBuilder = new StringBuilder();

		if(useOriginalGenus) {

			stringBuilder.append(originalGenusName);

			genusOrUninomial.delete(0, genusOrUninomial.length());

			genusOrUninomial.append(originalGenusName);

		} else {

			stringBuilder.append(genusOrUninomial);

		}

		stringBuilder.append(" ");

		return stringBuilder.toString();

	}

	private String genusSubGenusPart(StringBuilder originalGenusName, boolean useOriginalGenus,

			StringBuilder genusOrUninomial,

			StringBuilder infraGenericEpithet,

			FaunaEuropaeaTaxon fauEuTaxon) {

		StringBuilder stringBuilder = new StringBuilder();

		stringBuilder.append(genusPart(originalGenusName, useOriginalGenus, genusOrUninomial));

		// The infraGenericEpithet is set to empty only if the original genus should be used and

		// the actualGenusId is not the originalGenusId.

		// This differentiation is relevant for synonyms and for basionyms.

		// InfraGenericEpithets of accepted taxa are not touched at all.

		Integer originalGenusId = fauEuTaxon.getOriginalGenusId();

		Integer actualGenusId = getActualGenusId(fauEuTaxon);

		if (useOriginalGenus &&

				originalGenusId.intValue() != actualGenusId.intValue() &&

				originalGenusId.intValue() > 0 &&

				actualGenusId.intValue() > 0) {

			infraGenericEpithet.delete(0, infraGenericEpithet.length());

			stringBuilder.append(" ");

			return stringBuilder.toString();

		}

		stringBuilder.append("(");

		stringBuilder.append(infraGenericEpithet);

		stringBuilder.append(")");

		stringBuilder.append(" ");

		return stringBuilder.toString();

	}

	/** Get actual genus id **/

	private Integer getActualGenusId(FaunaEuropaeaTaxon fauEuTaxon) {

		Integer actualGenusId = null;

		HashMap<Integer, Integer> ranks = new HashMap<Integer, Integer>();

		ranks.put(fauEuTaxon.getParentRankId(), fauEuTaxon.getParentId());

		ranks.put(fauEuTaxon.getGrandParentRankId(), fauEuTaxon.getGrandParentId());

		ranks.put(fauEuTaxon.getGreatGrandParentRankId(), fauEuTaxon.getGreatGrandParentId());

		ranks.put(fauEuTaxon.getGreatGreatGrandParentRankId(), fauEuTaxon.getGreatGreatGrandParentId());

		ranks.put(fauEuTaxon.getGreatGreatGreatGrandParentRankId(), fauEuTaxon.getGreatGreatGreatGrandParentId());

		actualGenusId = ranks.get(R_GENUS);

		return actualGenusId;

	}

	/** Build species and subspecies names */

	private String buildLowerTaxonName(StringBuilder originalGenus, boolean useOriginalGenus,

			StringBuilder genusOrUninomial, StringBuilder infraGenericEpithet,

			StringBuilder specificEpithet, StringBuilder infraSpecificEpithet,

			FaunaEuropaeaTaxon fauEuTaxon) {

		// species or subspecies name

		String localName = fauEuTaxon.getLocalName();

		int taxonId = fauEuTaxon.getId();

		int parentId = fauEuTaxon.getParentId();

		StringBuilder nameCacheStringBuilder = new StringBuilder();

//		FaunaEuropaeaTaxon parent = fauEuTaxonMap.get(parentId);

		if (parentId == 0) {

			nameCacheStringBuilder.append(localName);

			if (logger.isInfoEnabled()) {

				logger.info("Parent of (" + taxonId + ") is null");

			}

			return nameCacheStringBuilder.toString();

		}

		String parentName = fauEuTaxon.getParentName();

		String grandParentName = fauEuTaxon.getGrandParentName();

		String greatGrandParentName = fauEuTaxon.getGreatGrandParentName();

		int rank = fauEuTaxon.getRankId();

		int parentRankId = fauEuTaxon.getParentRankId();

		int grandParentRankId = fauEuTaxon.getGrandParentRankId();

		int greatGrandParentRankId = fauEuTaxon.getGreatGrandParentRankId();

//		int grandParentId = fauEuTaxon.getGrandParentId();

//		int greatGrandParentId = grandParent.getParentId();

		if (fauEuTaxon.isValid()) { // Taxon

			if (rank == R_SPECIES) {

				if(parentRankId == R_SUBGENUS) {

					//differ between isParanthesis= true and false

					String genusSubGenusPart = genusSubGenusPart(originalGenus, useOriginalGenus,

							genusOrUninomial.append(grandParentName),

							infraGenericEpithet.append(parentName),

							fauEuTaxon);

						nameCacheStringBuilder.append(genusSubGenusPart);

				} else if(parentRankId == R_GENUS) {

					String genusPart = genusPart(originalGenus, useOriginalGenus,

							genusOrUninomial.append(parentName));

					nameCacheStringBuilder.append(genusPart);