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.faunaEuropaea;

import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.A_AUCT;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

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

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

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

import eu.etaxonomy.cdm.io.profiler.ProfilerController;

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.persistence.query.MatchMode;

/**

 * @author a.babadshanjan

 * @created 12.05.2009

 * @version 1.0

 */

@Component

public class FaunaEuropaeaRelTaxonIncludeImport extends FaunaEuropaeaImportBase  {

	public static final String OS_NAMESPACE_TAXON = "Taxon";

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

	private ReferenceBase<?> sourceRef;

	private static String ALL_SYNONYM_FROM_CLAUSE = " FROM Taxon INNER JOIN Taxon AS Parent " +

	" ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +

	" WHERE (Taxon.TAX_VALID = 0) " +

	" AND (Taxon.TAX_AUT_ID <> " + A_AUCT + " OR Taxon.TAX_AUT_ID IS NULL)";

	/* (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)

	 */

	protected boolean isIgnore(FaunaEuropaeaImportState state) {

		return ! (state.getConfig().isDoTaxonomicallyIncluded() || 

		state.getConfig().isDoMisappliedNames() || state.getConfig().isDoHeterotypicSynonyms());

	}

	private boolean checkTaxonStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {

		boolean result = true;

//		try {

			Source source = fauEuConfig.getSource();

			String sqlStr = "";

			ResultSet rs = source.getResultSet(sqlStr);

			return result;

//		} catch (SQLException e) {

//			e.printStackTrace();

//			return false;

//		}

	}

	protected boolean doInvoke(FaunaEuropaeaImportState state) {				

		boolean success = true;

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

	//	MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);

//		taxonStore.makeEmpty();

	//	taxonStore = null;

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

		authorStore.makeEmpty();

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

		TransactionStatus txStatus = startTransaction();

		TaxonBase taxon = getTaxonService().find(UUID.fromString("5932B630-5299-4A65-A4BF-BC38C6C108E2"));

		sourceRef = taxon.getSec();

		TaxonomicTree tree = getTaxonomicTreeFor(state, sourceRef);

		commitTransaction(txStatus);

		//ProfilerController.memorySnapshot();

		if (state.getConfig().isDoTaxonomicallyIncluded()) {

			success = processParentsChildren(state);

		}

		//ProfilerController.memorySnapshot();

		if (state.getConfig().isDoMisappliedNames()) {

			success = processMisappliedNames(state);

		}

		//ProfilerController.memorySnapshot();

		if (state.getConfig().isDoHeterotypicSynonyms()) {

			if(logger.isInfoEnabled()) { 

				logger.info("Start making heterotypic synonym relationships..."); 

			}

			success = processHeterotypicSynonyms(state, ALL_SYNONYM_FROM_CLAUSE);

		}

		//ProfilerController.memorySnapshot();

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

		return success;

	}

	/** Retrieve child-parent uuid map from CDM DB */

	private boolean processParentsChildren(FaunaEuropaeaImportState state) {

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

		TransactionStatus txStatus = null;

		Map<UUID, UUID> childParentMap = null;

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		Source source = fauEuConfig.getSource();

		int i = 0;

		boolean success = true;

		String selectCount = 

			" SELECT count(*) ";

		String selectColumns = " SELECT Taxon.UUID AS ChildUuid, Parent.UUID AS ParentUuid ";

		String fromClause = " FROM Taxon INNER JOIN Taxon AS Parent " +

		" ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +

		" WHERE (Taxon.TAX_VALID <> 0) AND (Taxon.TAX_AUT_ID <> " + A_AUCT + " OR Taxon.TAX_AUT_ID IS NULL )";

		String orderClause = " ORDER BY Taxon.TAX_RNK_ID ASC";

		String countQuery = 

			selectCount + fromClause;

		String selectQuery = 

			selectColumns + fromClause + orderClause;

		if(logger.isInfoEnabled()) { logger.info("Start making taxonomically included relationships..."); }

		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();

					childParentMap = new HashMap<UUID, UUID>(limit);

					if(logger.isInfoEnabled()) {

						logger.info("Taxonomically included retrieved: " + (i-1)); 

					}

				}

				String childUuidStr = rs.getString("ChildUuid");

				String parentUuidStr = rs.getString("ParentUuid");

				UUID childUuid = UUID.fromString(childUuidStr);

				UUID parentUuid = UUID.fromString(parentUuidStr);

				if (!childParentMap.containsKey(childUuid)) {

						childParentMap.put(childUuid, parentUuid);

				} else {

					if(logger.isDebugEnabled()) {

						logger.debug("Duplicated child UUID (" + childUuid + ")");

					}

				}

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

					success = createParentChildRelationships(state, childParentMap);

					childParentMap = null;

					commitTransaction(txStatus);

					if(logger.isInfoEnabled()) {

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

					}

				}

			}

		} catch (SQLException e) {

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

			success = false;

		}

		return success;		

	}

	/** Retrieve misapplied name / accepted taxon uuid map from CDM DB */

	private boolean processMisappliedNames(FaunaEuropaeaImportState state) {

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

		TransactionStatus txStatus = null;

		Map<UUID, UUID> childParentMap = null;

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		Source source = fauEuConfig.getSource();

		int i = 0;

		boolean success = true;

		String selectCount = 

			" SELECT count(*) ";

		String selectColumns = " SELECT Taxon.UUID AS MisappliedUuid, Parent.UUID AS AcceptedUuid ";

		String fromClause = " FROM Taxon INNER JOIN Taxon AS Parent " +

		" ON Taxon.TAX_TAX_IDPARENT = Parent.TAX_ID " +

		" WHERE (Taxon.TAX_VALID = 0) AND (Taxon.TAX_AUT_ID = " + A_AUCT + ")";

		String orderClause = " ORDER BY dbo.Taxon.TAX_RNK_ID ASC ";

		String countQuery = 

			selectCount + fromClause;

		String selectQuery = 

			selectColumns + fromClause + orderClause;

		if(logger.isInfoEnabled()) { logger.info("Start making misapplied name relationships..."); }

		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();

					childParentMap = new HashMap<UUID, UUID>(limit);

					if(logger.isInfoEnabled()) {

						logger.info("Misapplied names retrieved: " + (i-1) ); 

					}

				}

				String childUuidStr = rs.getString("MisappliedUuid");

				String parentUuidStr = rs.getString("AcceptedUuid");

				UUID childUuid = UUID.fromString(childUuidStr);

				UUID parentUuid = UUID.fromString(parentUuidStr);

				if (!childParentMap.containsKey(childUuid)) {

						childParentMap.put(childUuid, parentUuid);

				} else {

					if(logger.isDebugEnabled()) {

						logger.debug("Duplicated child UUID (" + childUuid + ")");

					}

				}

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

					success = createMisappliedNameRelationships(state, childParentMap);

					childParentMap = null;

					commitTransaction(txStatus);

					if(logger.isInfoEnabled()) {

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

					}

				}

			}

		} catch (SQLException e) {

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

			success = false;

		}

		return success;		

	}

	/** Retrieve synonyms from FauEuDB DB */

	private boolean processHeterotypicSynonyms(FaunaEuropaeaImportState state, String fromClause) {

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		Source source = fauEuConfig.getSource();

		boolean success = true;

		String selectCount = 

			" SELECT count(*) ";

		String selectColumns = " SELECT Taxon.UUID AS SynonymUuid, Parent.UUID AS AcceptedUuid ";

		String orderClause = " ORDER BY dbo.Taxon.TAX_RNK_ID ASC ";

		String countQuery = 

			selectCount + fromClause;

		String selectQuery = 

			selectColumns + fromClause + orderClause;

		logger.debug(selectQuery);

		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);

			}

	        success = storeSynonymRelationships(rs, count, state);

		} catch (SQLException e) {

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

			success = false;

		}

		return success;		

	}

	private boolean storeSynonymRelationships(ResultSet rs, int count, FaunaEuropaeaImportState state) 

	throws SQLException {

		TransactionStatus txStatus = null;

		Map<UUID, UUID> synonymAcceptedMap = null;

		int i = 0;

		boolean success = true;

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

		while (rs.next()) {

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

				txStatus = startTransaction();

				synonymAcceptedMap = new HashMap<UUID, UUID>(limit);

				if(logger.isInfoEnabled()) {

					logger.info("Synonyms retrieved: " + (i-1)); 

				}

			}

			String synonymUuidStr = rs.getString("SynonymUuid");

			String acceptedUuidStr = rs.getString("AcceptedUuid");

			UUID synonymUuid = UUID.fromString(synonymUuidStr);

			UUID acceptedUuid = UUID.fromString(acceptedUuidStr);

			if (!synonymAcceptedMap.containsKey(synonymUuid)) {

				synonymAcceptedMap.put(synonymUuid, acceptedUuid);

			} else {

				if(logger.isDebugEnabled()) {

					logger.debug("Duplicated synonym UUID (" + synonymUuid + ")");

				}

			}

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

				success = createHeterotypicSynonyms(state, synonymAcceptedMap);

				synonymAcceptedMap = null;

				commitTransaction(txStatus);

				if(logger.isInfoEnabled()) {

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

				}

			}

		}

		return success;

	}

	/* Creates parent-child relationships.

	 * Parent-child pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB. 

	 */

	private boolean createParentChildRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> childParentMap) {

		//gets the taxon "Hydroscaphidae"(family)

		TaxonBase taxon = getTaxonService().find(UUID.fromString("5932B630-5299-4A65-A4BF-BC38C6C108E2"));

		sourceRef = taxon.getSec();

		boolean success = true;

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

			TaxonomicTree tree = getTaxonomicTreeFor(state, sourceRef);

			Set<TaxonBase> childSet = new HashSet<TaxonBase>(limit);

			Set<UUID> childKeysSet = childParentMap.keySet();

			Set<UUID> parentValuesSet = new HashSet<UUID>(childParentMap.values());

			if (logger.isTraceEnabled()) {

				logger.trace("Start reading children and parents");

			}

			List<TaxonBase> children = getTaxonService().find(childKeysSet);

			List<TaxonBase> parents = getTaxonService().find(parentValuesSet);

			Map<UUID, TaxonBase> parentsMap = new HashMap<UUID, TaxonBase>(parents.size());

			for (TaxonBase taxonBase : parents){

				parentsMap.put(taxonBase.getUuid(), taxonBase);

			}

			if (logger.isTraceEnabled()) {

				logger.debug("End reading children and parents");

				for (UUID uuid : childKeysSet) {

					logger.trace("child uuid query: " + uuid);

				}

				for (UUID uuid : parentValuesSet) {

					logger.trace("parent uuid query: " + uuid);

				}

				for (TaxonBase tb : children) {

					logger.trace("child uuid result: " + tb.getUuid());

				}

				for (TaxonBase tb : parents) {

					logger.trace("parent uuid result: " + tb.getUuid());

				}

			}

			UUID mappedParentUuid = null;

			UUID childUuid = null;

			for (TaxonBase child : children) {

				try {

					Taxon childTaxon = child.deproxy(child, Taxon.class);

					childUuid = childTaxon.getUuid();

					mappedParentUuid = childParentMap.get(childUuid);

					TaxonBase parent = null;

					TaxonBase potentialParent = parentsMap.get(mappedParentUuid);

//					for (TaxonBase potentialParent : parents ) {

//						parentUuid = potentialParent.getUuid();

//						if(parentUuid.equals(mappedParentUuid)) {

							parent = potentialParent;

							if (logger.isDebugEnabled()) {

								logger.debug("Parent (" + mappedParentUuid + ") found for child (" + childUuid + ")");

							}

//							break;

//						}

//					}

					Taxon parentTaxon = parent.deproxy(parent, Taxon.class);

					if (childTaxon != null && parentTaxon != null) {

						tree.addParentChild(parentTaxon, childTaxon, sourceRef, null);

						if (logger.isDebugEnabled()) {

							logger.debug("Parent-child (" + mappedParentUuid + "-" + childUuid + 

							") relationship created");

						}

						if (childTaxon != null && !childSet.contains(childTaxon)) {

							childSet.add(childTaxon);

							if (logger.isTraceEnabled()) {

								logger.trace("Child taxon (" + childUuid + ") added to Set");

							}

						} else {

							if (logger.isDebugEnabled()) {

								logger.debug("Duplicated child taxon (" + childUuid + ")");

							}

						}

					} else {

						if (logger.isDebugEnabled()) {

							logger.debug("Parent(" + mappedParentUuid + ") or child (" + childUuid + " is null");

						}

					}

				} catch (Exception e) {

					logger.error("Error creating taxonomically included relationship parent-child (" + 

						mappedParentUuid + "-" + childUuid + ")", e);

				}

			}

			if (logger.isTraceEnabled()) {

				logger.trace("Start saving childSet");

			}

			getTaxonService().save(childSet);

			if (logger.isTraceEnabled()) {

				logger.trace("End saving childSet");

			}

			parentValuesSet = null;

			childSet = null;

			children = null;

			parents = null;

			tree = null;

		return success;

	}

	/* Creates misapplied name relationships.

	 * Misapplied name-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB. 

	 */

	private boolean createMisappliedNameRelationships(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {

		//gets the taxon "Hydroscaphidae" (family)

		TaxonBase taxon = getTaxonService().find(UUID.fromString("5932B630-5299-4A65-A4BF-BC38C6C108E2"));

		sourceRef = taxon.getSec();

		boolean success = true;

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

			Set<TaxonBase> misappliedNameSet = new HashSet<TaxonBase>(limit);

			Set<UUID> misappliedNamesSet = fromToMap.keySet();

			Set<UUID> acceptedTaxaSet = new HashSet<UUID>(fromToMap.values());

			if (logger.isTraceEnabled()) {

				logger.trace("Start reading misapplied names and accepted taxa");

			}

			List<TaxonBase> misappliedNames = getTaxonService().find(misappliedNamesSet);

			List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaSet);

			Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());

			for (TaxonBase taxonBase : acceptedTaxa){

				acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);

			}

			if (logger.isTraceEnabled()) {

				logger.info("End reading misapplied names and accepted taxa");

				for (UUID uuid : misappliedNamesSet) {

					logger.trace("misapplied name uuid query: " + uuid);

				}

				for (UUID uuid : acceptedTaxaSet) {

					logger.trace("accepted taxon uuid query: " + uuid);

				}

				for (TaxonBase tb : misappliedNames) {

					logger.trace("misapplied name uuid result: " + tb.getUuid());

				}

				for (TaxonBase tb : acceptedTaxa) {

					logger.trace("accepted taxon uuid result: " + tb.getUuid());

				}

			}

			UUID mappedAcceptedTaxonUuid = null;

			UUID misappliedNameUuid = null;

			Taxon misappliedNameTaxon = null;

			TaxonBase acceptedTaxonBase = null;

			Taxon acceptedTaxon = null;

			for (TaxonBase misappliedName : misappliedNames) {

				try {

					misappliedNameTaxon = misappliedName.deproxy(misappliedName, Taxon.class);

					misappliedNameUuid = misappliedNameTaxon.getUuid();

					mappedAcceptedTaxonUuid = fromToMap.get(misappliedNameUuid);

					acceptedTaxonBase = null;

					acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);

							if (logger.isDebugEnabled()) {

								logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + misappliedNameUuid + ")");

							}

							acceptedTaxon = acceptedTaxonBase.deproxy(acceptedTaxonBase, Taxon.class);

					if (misappliedNameTaxon != null && acceptedTaxon != null) {

						acceptedTaxon.addMisappliedName(misappliedNameTaxon, sourceRef, null);

						if (logger.isDebugEnabled()) {

							logger.debug("Accepted taxon / misapplied name (" + mappedAcceptedTaxonUuid + "-" + misappliedNameUuid + 

							") relationship created");

						}

						if (!misappliedNameSet.contains(misappliedNameTaxon)) {

							misappliedNameSet.add(misappliedNameTaxon);

							if (logger.isTraceEnabled()) {

								logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");

							}

						} else {

							if (logger.isDebugEnabled()) {

								logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");

							}

						}

					} else {

						if (logger.isDebugEnabled()) {

							logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + misappliedNameUuid + " is null");

						}

					}

					if (misappliedNameTaxon != null && !misappliedNameSet.contains(misappliedNameTaxon)) {

						misappliedNameSet.add(misappliedNameTaxon);

						if (logger.isTraceEnabled()) {

							logger.trace("Misapplied name taxon (" + misappliedNameUuid + ") added to Set");

						}

					} else {

						if (logger.isDebugEnabled()) {

							logger.debug("Duplicated misapplied name taxon (" + misappliedNameUuid + ")");

						}

					}

				} catch (Exception e) {

					logger.error("Error creating misapplied name relationship accepted taxon-misapplied name (" + 

						mappedAcceptedTaxonUuid + "-" + misappliedNameUuid + ")", e);

				}

			}

			if (logger.isTraceEnabled()) {

				logger.trace("Start saving misappliedNameSet");

			}

			getTaxonService().save(misappliedNameSet);

			if (logger.isTraceEnabled()) {

				logger.trace("End saving misappliedNameSet");

			}

			acceptedTaxaSet = null;

			misappliedNameSet = null;

			misappliedNames = null;

			acceptedTaxa = null;

		return success;

	}

	/* Creates heterotypic synonym relationships.

	 * Synonym-accepted taxon pairs are retrieved in blocks via findByUUID(Set<UUID>) from CDM DB. 

	 */

	private boolean createHeterotypicSynonyms(FaunaEuropaeaImportState state, Map<UUID, UUID> fromToMap) {

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

		boolean success = true;

		Set<TaxonBase> synonymSet = new HashSet<TaxonBase>(limit);

		Set<UUID> synonymUuidSet = fromToMap.keySet();

		Set<UUID> acceptedTaxaUuidSet = new HashSet<UUID>(fromToMap.values());

		if (logger.isTraceEnabled()) {

			logger.trace("Reading synonym names and accepted taxa...");

		}

		List<TaxonBase> synonyms = getTaxonService().find(synonymUuidSet);

		List<TaxonBase> acceptedTaxa = getTaxonService().find(acceptedTaxaUuidSet);

		Map<UUID, TaxonBase> acceptedTaxaMap = new HashMap<UUID, TaxonBase>(acceptedTaxa.size());

		for (TaxonBase taxonBase : acceptedTaxa){

			acceptedTaxaMap.put(taxonBase.getUuid(), taxonBase);

		}

		if (logger.isTraceEnabled()) {

			logger.trace("End reading synonyms names and accepted taxa");

			for (UUID uuid : synonymUuidSet) {

				logger.trace("synonym uuid query: " + uuid);

			}

			for (UUID uuid : acceptedTaxaUuidSet) {

				logger.trace("accepted taxon uuid query: " + uuid);

			}

			for (TaxonBase tb : synonyms) {

				logger.trace("synonym uuid result: " + tb.getUuid());

			}

			for (TaxonBase tb : acceptedTaxa) {

				logger.trace("accepted taxon uuid result: " + tb.getUuid());

			}

		}

		UUID mappedAcceptedTaxonUuid = null;

		UUID synonymUuid = null;

		Synonym synonym = null;

		TaxonBase acceptedTaxonBase = null;

		Taxon acceptedTaxon = null;

		for (TaxonBase synonymTaxonBase : synonyms) {

			try {

				synonym = synonymTaxonBase.deproxy(synonymTaxonBase, Synonym.class);

				synonymUuid = synonym.getUuid();

				mappedAcceptedTaxonUuid = fromToMap.get(synonymUuid);

				acceptedTaxonBase = null;

				acceptedTaxonBase = acceptedTaxaMap.get(mappedAcceptedTaxonUuid);

				if (logger.isDebugEnabled()) {

					logger.debug("Parent (" + mappedAcceptedTaxonUuid + ") found for child (" + synonymUuid + ")");

				}

				acceptedTaxon = acceptedTaxonBase.deproxy(acceptedTaxonBase, Taxon.class);

				if (synonym != null && acceptedTaxon != null) {

					//TODO: in case original genus exists must add synonym to original genus instead of to accepted taxon

					acceptedTaxon.addSynonym(synonym, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());

					if (logger.isDebugEnabled()) {

						logger.debug("Accepted taxon - synonym (" + mappedAcceptedTaxonUuid + " - " + synonymUuid + 

						") relationship created");

					}

					if (synonym != null && !synonymSet.contains(synonym)) {

						synonymSet.add(synonym);

						if (logger.isTraceEnabled()) {

							logger.trace("Synonym (" + synonymUuid + ") added to Set");

						}

					} else {

						if (logger.isDebugEnabled()) {

							logger.debug("Duplicated synonym (" + synonymUuid + ")");

						}

					}

				} else {

					if (logger.isDebugEnabled()) {

						logger.debug("Accepted taxon (" + mappedAcceptedTaxonUuid + ") or misapplied name (" + synonymUuid + " is null");

					}

				}

			} catch (Exception e) {

				logger.error("Error creating synonym relationship: accepted taxon-synonym (" + 

						mappedAcceptedTaxonUuid + "-" + synonymUuid + ")", e);

			}

		}

		if (logger.isTraceEnabled()) {

			logger.trace("Start saving synonymSet");

		}

		getTaxonService().save(synonymSet);

		if (logger.isTraceEnabled()) {

			logger.trace("End saving synonymSet");

		}

		acceptedTaxaUuidSet = null;

		synonymSet = null;

		synonyms = null;

		acceptedTaxa = null;

		return success;

	}

}