EDIT

/**

* Copyright (C) 2009 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.out;

import java.sql.Connection;

import java.sql.PreparedStatement;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.sql.Types;

import java.util.ArrayList;

import java.util.BitSet;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Iterator;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import java.util.regex.Matcher;

import java.util.regex.Pattern;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.joda.time.DateTime;

import org.joda.time.format.DateTimeFormat;

import org.joda.time.format.DateTimeFormatter;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.service.TaxonServiceImpl;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;

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

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

import eu.etaxonomy.cdm.io.common.mapping.out.DbConstantMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.DbExtensionMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.DbLastActionMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.DbObjectMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.DbStringMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.IdMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.ObjectChangeMapper;

import eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.profiler.ProfilerController;

import eu.etaxonomy.cdm.strategy.cache.HTMLTagRules;

import eu.etaxonomy.cdm.strategy.cache.TagEnum;

import eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy;

import eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy;

import eu.etaxonomy.cdm.strategy.cache.name.ZooNameNoMarkerCacheStrategy;

/**

 * The export class for {@link eu.etaxonomy.cdm.model.name.TaxonNameBase TaxonNames}.<p>

 * Inserts into DataWarehouse database table <code>Taxon</code>.

 * It is divided into four phases:<p><ul>

 * <li>Phase 1:	Export of all {@link eu.etaxonomy.cdm.model.name.TaxonNameBase TaxonNames} except some data exported in the following phases.

 * <li>Phase 2:	Export of additional data: ParenTaxonFk and TreeIndex.

 * <li>Phase 3:	Export of additional data: Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk.

 * <li>Phase 4:	Export of Inferred Synonyms.</ul>

 * @author e.-m.lee

 * @date 23.02.2010

 *

 */

@Component

public class PesiTaxonExport extends PesiExportBase {

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

	private static final Class<? extends CdmBase> standardMethodParameter = TaxonBase.class;

	private static int modCount = 1000;

	private static final String dbTableName = "Taxon";

	private static final String dbTableNameSynRel = "RelTaxon";

	private static final String dbTableAdditionalSourceRel = "AdditionalTaxonSource";

	private static final String pluralString = "Taxa";

	private static final String parentPluralString = "Taxa";

	private PreparedStatement parentTaxonFk_TreeIndex_KingdomFkStmt;

	private PreparedStatement parentTaxonFkStmt;

	private PreparedStatement rankTypeExpertsUpdateStmt;

	private PreparedStatement rankUpdateStmt;

	private NomenclaturalCode nomenclaturalCode;

	private Integer kingdomFk;

	private final HashMap<Rank, Rank> rank2endRankMap = new HashMap<Rank, Rank>();

	private final List<Rank> rankList = new ArrayList<Rank>();

	private static final UUID uuidTreeIndex = UUID.fromString("28f4e205-1d02-4d3a-8288-775ea8413009");

	private AnnotationType treeIndexAnnotationType;

	private static ExtensionType lastActionExtensionType;

	private static ExtensionType lastActionDateExtensionType;

	private static ExtensionType expertNameExtensionType;

	private static ExtensionType speciesExpertNameExtensionType;

	private static ExtensionType cacheCitationExtensionType;

	public static NonViralNameDefaultCacheStrategy<?> zooNameStrategy = ZooNameNoMarkerCacheStrategy.NewInstance();

	public static NonViralNameDefaultCacheStrategy<?> botanicalNameStrategy = BotanicNameDefaultCacheStrategy.NewInstance();

	public static NonViralNameDefaultCacheStrategy<?> nonViralNameStrategy = NonViralNameDefaultCacheStrategy.NewInstance();

	public static NonViralNameDefaultCacheStrategy<?> bacterialNameStrategy = BacterialNameDefaultCacheStrategy.NewInstance();

	private static int currentTaxonId;

	/**

	 * @return the treeIndexAnnotationType

	 */

	protected AnnotationType getTreeIndexAnnotationType() {

		return treeIndexAnnotationType;

	}

	/**

	 * @param treeIndexAnnotationType the treeIndexAnnotationType to set

	 */

	protected void setTreeIndexAnnotationType(AnnotationType treeIndexAnnotationType) {

		this.treeIndexAnnotationType = treeIndexAnnotationType;

	}

	enum NamePosition {

		beginning,

		end,

		between,

		alone,

		nowhere

	}

	public PesiTaxonExport() {

		super();

	}

	@Override

	public Class<? extends CdmBase> getStandardMethodParameter() {

		return standardMethodParameter;

	}

	@Override

	protected boolean doCheck(PesiExportState state) {

		boolean result = true;

		return result;

	}

	@Override

	protected void doInvoke(PesiExportState state) {

		try {

			logger.info("*** Started Making " + pluralString + " ...");

			initPreparedStatements(state);

			// Stores whether this invoke was successful or not.

			boolean success = true;

			// PESI: Clear the database table Taxon.

//			doDelete(state);

			// Get specific mappings: (CDM) Taxon -> (PESI) Taxon

			PesiExportMapping mapping = getMapping();

			PesiExportMapping synonymRelMapping = getSynRelMapping();

			PesiExportMapping additionalSourceMapping = getAdditionalSourceMapping(state);

			// Initialize the db mapper

			mapping.initialize(state);

			synonymRelMapping.initialize(state);

			additionalSourceMapping.initialize(state);

			// Find extensionTypes

			lastActionExtensionType = (ExtensionType)getTermService().find(PesiTransformer.lastActionUuid);

			lastActionDateExtensionType = (ExtensionType)getTermService().find(PesiTransformer.lastActionDateUuid);

			expertNameExtensionType = (ExtensionType)getTermService().find(PesiTransformer.expertNameUuid);

			speciesExpertNameExtensionType = (ExtensionType)getTermService().find(PesiTransformer.speciesExpertNameUuid);

			cacheCitationExtensionType = (ExtensionType)getTermService().find(PesiTransformer.cacheCitationUuid);

			//Export Taxa..

			success &= doPhase01(state, mapping, additionalSourceMapping);

			//"PHASE 1b: Handle names without taxa ...

			success &= doNames(state, additionalSourceMapping);

			// 2nd Round: Add ParentTaxonFk to each taxon

			success &= doPhase02(state);

			//PHASE 3: Add Rank data, KingdomFk, TypeNameFk ...

			success &= doPhase03(state);

			// 4nd Round: Add TreeIndex to each taxon

			success &= doPhase04(state);

			//"PHASE 4: Creating Inferred Synonyms...

			success &= doPhase05(state, mapping, synonymRelMapping);

			logger.info("*** Finished Making " + pluralString + " ..." + getSuccessString(success));

			if (!success){

				state.getResult().addError("An error occurred in PesiTaxonExport.doInvoke");

			}

			return;

		} catch (Exception e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.getResult().addException(e);

		}

	}

	private void initPreparedStatements(PesiExportState state) throws SQLException {

		initTreeIndexStatement(state);

		initRankExpertsUpdateStmt(state);

		initRankUpdateStatement(state);

		initParentFkStatement(state);

	}

	// Prepare TreeIndex-And-KingdomFk-Statement

	private void initTreeIndexStatement(PesiExportState state) throws SQLException {

		Connection connection = state.getConfig().getDestination().getConnection();

		String parentTaxonFk_TreeIndex_KingdomFkSql = "UPDATE Taxon SET ParentTaxonFk = ?, TreeIndex = ? WHERE TaxonId = ?";

		parentTaxonFk_TreeIndex_KingdomFkStmt = connection.prepareStatement(parentTaxonFk_TreeIndex_KingdomFkSql);

	}

	// Prepare TreeIndex-And-KingdomFk-Statement

	private void initParentFkStatement(PesiExportState state) throws SQLException {

		Connection connection = state.getConfig().getDestination().getConnection();

		String parentTaxonFkSql = "UPDATE Taxon SET ParentTaxonFk = ? WHERE TaxonId = ?";

		parentTaxonFkStmt = connection.prepareStatement(parentTaxonFkSql);

	}

	private void initRankUpdateStatement(PesiExportState state) throws SQLException {

		Connection connection = state.getConfig().getDestination().getConnection();

		String rankSql = "UPDATE Taxon SET RankFk = ?, RankCache = ?, KingdomFk = ? WHERE TaxonId = ?";

		rankUpdateStmt = connection.prepareStatement(rankSql);

	}

	private void initRankExpertsUpdateStmt(PesiExportState state) throws SQLException {

//		String sql_old = "UPDATE Taxon SET RankFk = ?, RankCache = ?, TypeNameFk = ?, KingdomFk = ?, " +

//				"ExpertFk = ?, SpeciesExpertFk = ? WHERE TaxonId = ?";

		//TODO handle experts GUIDs

		Connection connection = state.getConfig().getDestination().getConnection();

		String sql = "UPDATE Taxon SET RankFk = ?, RankCache = ?, TypeNameFk = ?, KingdomFk = ? " +

				" WHERE TaxonId = ?";

		rankTypeExpertsUpdateStmt = connection.prepareStatement(sql);

	}

	private boolean doPhase01(PesiExportState state, PesiExportMapping mapping, PesiExportMapping additionalSourceMapping) throws SQLException {

		int count = 0;

		int pastCount = 0;

		List<TaxonBase> list;

		boolean success = true;

		// Get the limit for objects to save within a single transaction.

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

		logger.info("PHASE 1: Export Taxa...limit is " + limit);

		// Start transaction

		TransactionStatus txStatus = startTransaction(true);

		logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");

		int partitionCount = 0;

		logger.info("Taking snapshot at the beginning of phase 1 of taxonExport");

		//ProfilerController.memorySnapshot();

		while ((list = getNextTaxonPartition(null, limit, partitionCount++, null)) != null   ) {

			logger.debug("Fetched " + list.size() + " " + pluralString + ". Exporting...");

			for (TaxonBase<?> taxon : list) {

				doCount(count++, modCount, pluralString);

				TaxonNameBase<?,?> taxonName = taxon.getName();

				NonViralName<?> nvn = CdmBase.deproxy(taxonName, NonViralName.class);

				System.err.println(nvn.getTitleCache());

				if (! nvn.isProtectedTitleCache()){

					nvn.setTitleCache(null, false);

				}

				if (! nvn.isProtectedNameCache()){

					nvn.setNameCache(null, false);

				}

				if (! nvn.isProtectedFullTitleCache()){

					nvn.setFullTitleCache(null, false);

				}

				if (! nvn.isProtectedAuthorshipCache()){

					nvn.setAuthorshipCache(null, false);

				}

				try{

				if (nvn.getRank().equals(Rank.KINGDOM())){

				    String treeIndex = ((Taxon)taxon).getTaxonNodes().iterator().next().treeIndex();

				    Integer kingdomId = PesiTransformer.pesiKingdomMap.get(nvn.getGenusOrUninomial());

				    state.getTreeIndexKingdomMap().put(treeIndex, kingdomId);

				}}catch(NullPointerException e){

				    logger.error(nvn.getTitleCache() + "has no Rank!");

				    System.err.println(nvn.getTitleCache() + "has no Rank!");

				}

				//core mapping

				success &= mapping.invoke(taxon);

				//additional source

				if (nvn.getNomenclaturalReference() != null || StringUtils.isNotBlank(nvn.getNomenclaturalMicroReference() )){

					additionalSourceMapping.invoke(taxon);

				}

				validatePhaseOne(taxon, nvn);

				taxon = null;

				nvn = null;

				taxonName = null;

			}

			// Commit transaction

			commitTransaction(txStatus);

			logger.debug("Committed transaction.");

			logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);

			pastCount = count;

			/*logger.warn("Taking snapshot at the end of the loop of phase 1 of taxonExport");

			//ProfilerController.memorySnapshot();

			*/

			// Start transaction

			txStatus = startTransaction(true);

			logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");

		}

		if (list == null ) {

			logger.info("No " + pluralString + " left to fetch.");

		}

		// Commit transaction

		commitTransaction(txStatus);

		txStatus = null;

		logger.debug("Committed transaction.");

		list = null;

		if (logger.isDebugEnabled()){

			logger.debug("Taking snapshot at the end of phase 1 of taxonExport");

			ProfilerController.memorySnapshot();

		}

		return success;

	}

	private void validatePhaseOne(TaxonBase<?> taxon, NonViralName taxonName) {

		// Check whether some rules are violated

		nomenclaturalCode = taxonName.getNomenclaturalCode();

		String genusOrUninomial = taxonName.getGenusOrUninomial();

		String specificEpithet = taxonName.getSpecificEpithet();

		String infraSpecificEpithet = taxonName.getInfraSpecificEpithet();

		String infraGenericEpithet = taxonName.getInfraGenericEpithet();

		Integer rank = getRankFk(taxonName, nomenclaturalCode);

		if (rank == null) {

			logger.error("Rank was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");

		} else {

			// Check whether infraGenericEpithet is set correctly

			// 1. Childs of an accepted taxon of rank subgenus that are accepted taxa of rank species have to have an infraGenericEpithet

			// 2. Grandchilds of an accepted taxon of rank subgenus that are accepted taxa of rank subspecies have to have an infraGenericEpithet

			int ancestorLevel = 0;

			if (taxonName.getRank().equals(Rank.SUBSPECIES())) {

				// The accepted taxon two rank levels above should be of rank subgenus

				ancestorLevel  = 2;

			}

			if (taxonName.getRank().equals(Rank.SPECIES())) {

				// The accepted taxon one rank level above should be of rank subgenus

				ancestorLevel = 1;

			}

			if (ancestorLevel > 0) {

				if (validateAncestorOfSpecificRank(taxon, ancestorLevel, Rank.SUBGENUS())) {

					// The child (species or subspecies) of this parent (subgenus) has to have an infraGenericEpithet

					if (infraGenericEpithet == null) {

						logger.warn("InfraGenericEpithet for (sub)species of infrageneric taxon does not exist even though it should (also valid for Botanical Names?) for: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");

						// maybe the taxon could be named here

					}

				}

			}

			if (infraGenericEpithet == null && rank.intValue() == 190) {

				logger.warn("InfraGenericEpithet was not determined although it should exist for rank 190: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");

			}

			if (specificEpithet != null && rank.intValue() < 216) {

				logger.warn("SpecificEpithet was determined for rank " + rank + " although it should only exist for ranks higher or equal to 220: TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");

			}

			if (infraSpecificEpithet != null && rank.intValue() < 225) {

				String message = "InfraSpecificEpithet '" +infraSpecificEpithet + "' was determined for rank " + rank + " although it should only exist for ranks higher or equal to 230: "  + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")";

				if (StringUtils.isNotBlank(infraSpecificEpithet)){

					logger.warn(message);

				}else{

					logger.warn(message);

				}

			}

		}

		if (infraSpecificEpithet != null && specificEpithet == null) {

			logger.warn("An infraSpecificEpithet was determined, but a specificEpithet was not determined: "  + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");

		}

		if (genusOrUninomial == null) {

			logger.warn("GenusOrUninomial was not determined: " + taxon.getUuid() + " (" + taxon.getTitleCache() + ")");

		}

	}

	/**

	 * 2nd Round: Add ParentTaxonFk to each taxon and add Biota if not exists

	 * @param state

	 * @return

	 */

	private boolean doPhase02(PesiExportState state) {

		int count = 0;

		int pastCount = 0;

		boolean success = true;

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

			logger.info ("Ignore PHASE 2: Make ParentFk and Biota...");

			return success;

		}

		List<Taxon> list;

		// Get the limit for objects to save within a single transaction.

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

		insertBiota(state);

		logger.info("PHASE 2: Make ParentFk and Biota ... limit is " + limit);

		// Start transaction

		TransactionStatus txStatus = startTransaction(true);

		int partitionCount = 0;

//		ProfilerController.memorySnapshot();

		while ((list = getNextTaxonPartition(Taxon.class, limit, partitionCount++, null)) != null   ) {

			logger.info("Fetched " + list.size() + " " + pluralString + ". Exporting...");

			for (Taxon taxon : list) {

				for (TaxonNode node : taxon.getTaxonNodes()){

					doCount(count++, modCount, pluralString);

					TaxonNode parentNode = node.getParent();

					if (parentNode != null && parentNode.getTaxon() != null){  //new root node handling requires has root taxon with taxon == null

						int childId = state.getDbId( taxon);

						int parentId = state.getDbId(parentNode.getTaxon());

						success &= invokeParentTaxonFk(parentId, childId);

					}

				}

			}

			// Commit transaction

			commitTransaction(txStatus);

			logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);

			pastCount = count;

			// Start transaction

			txStatus = startTransaction(true);

			logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");

		}

		if (list == null ) {

			logger.info("No " + pluralString + " left to fetch.");

		}

		list = null;

		// Commit transaction

		commitTransaction(txStatus);

		return success;

	}

	/**

	 * Inserts the Biota Taxon if not yet exists.

	 * @param state

	 * @throws SQLException

	 */

	private void insertBiota(PesiExportState state) {

		try {

			ResultSet rs = state.getConfig().getDestination().getResultSet("SELECT * FROM Taxon WHERE GenusOrUninomial = 'Biota' ");

			if (rs.next() == false){

				int biotaId = state.getConfig().getNameIdStart() -1 ;

				String sqlInsertBiota = "INSERT INTO Taxon (TaxonId, KingdomFk, RankFk, RankCache, GenusOrUninomial, WebSearchName, WebShowName, FullName, DisplayName, TaxonStatusFk, TaxonStatusCache) " +

									       " VALUES (" + biotaId + ",    0,    0,   'Superdomain',   'Biota',          'Biota',  '<i>Biota</i>',   'Biota', '<i>Biota</i>',  1 ,      'accepted')";

				state.getConfig().getDestination().update(sqlInsertBiota);

			}

			rs = null;

		} catch (SQLException e) {

			logger.warn ("Biota could not be requested or inserted");

		}

	}

	// 4th round: Add TreeIndex to each taxon

	private boolean doPhase04(PesiExportState state) {

		boolean success = true;

		logger.info("PHASE 4: Make TreeIndex ... ");

		//TODO test if possible to move to phase 02

		String sql = " UPDATE Taxon SET ParentTaxonFk = (Select TaxonId from Taxon where RankFk = 0) " +

				" WHERE (RankFk = 10) and TaxonStatusFk = 1 ";

		state.getConfig().getDestination().update(sql);

		state.getConfig().getDestination().update("EXEC dbo.recalculateallstoredpaths");

		return success;

	}

	// 2nd Round: Add ParentTaxonFk, TreeIndex to each Taxon

	private boolean doPhase02_OLD(PesiExportState state) {

		boolean success = true;

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

			logger.info ("Ignore PHASE 2: ParentTaxonFk and TreeIndex");

			return success;

		}

		List<Classification> classificationList = null;

		logger.info("PHASE 2: Add ParenTaxonFk and TreeIndex...");

		// Specify starting ranks for tree traversing

		rankList.add(Rank.KINGDOM());

		rankList.add(Rank.GENUS());

		// Specify where to stop traversing (value) when starting at a specific Rank (key)

		rank2endRankMap.put(Rank.GENUS(), null); // Since NULL does not match an existing Rank, traverse all the way down to the leaves

		rank2endRankMap.put(Rank.KINGDOM(), Rank.GENUS()); // excludes rank genus

		StringBuffer treeIndex = new StringBuffer();

		// Retrieve list of classifications

		TransactionStatus txStatus = startTransaction(true);

		logger.info("Started transaction for parentFk and treeIndex. Fetching all classifications...");

		classificationList = getClassificationService().listClassifications(null, 0, null, null);

		commitTransaction(txStatus);

		logger.debug("Committed transaction.");

		logger.info("Fetched " + classificationList.size() + " classification(s).");

		setTreeIndexAnnotationType(getAnnotationType(uuidTreeIndex, "TreeIndex", "TreeIndex", "TI"));

		List<TaxonNode> rankSpecificRootNodes;

		for (Classification classification : classificationList) {

			for (Rank rank : rankList) {

				txStatus = startTransaction(true);

				logger.info("Started transaction to fetch all rootNodes specific to Rank " + rank.getLabel() + " ...");

				rankSpecificRootNodes = getClassificationService().listRankSpecificRootNodes(classification, rank, null, null, null);

				logger.info("Fetched " + rankSpecificRootNodes.size() + " RootNodes for Rank " + rank.getLabel());

				commitTransaction(txStatus);

				logger.debug("Committed transaction.");

				for (TaxonNode rootNode : rankSpecificRootNodes) {

					txStatus = startTransaction(false);

					Rank endRank = rank2endRankMap.get(rank);

					if (endRank != null) {

						logger.debug("Started transaction to traverse childNodes of rootNode (" + rootNode.getUuid() + ") till Rank " + endRank.getLabel() + " ...");

					} else {

						logger.debug("Started transaction to traverse childNodes of rootNode (" + rootNode.getUuid() + ") till leaves are reached ...");

					}

					TaxonNode newNode = getTaxonNodeService().load(rootNode.getUuid());

					if (isPesiTaxon(newNode.getTaxon())){

						TaxonNode parentNode = newNode.getParent();

						if (rank.equals(Rank.KINGDOM())) {

							treeIndex = new StringBuffer();

							treeIndex.append("#");

						} else {

							// Get treeIndex from parentNode

							if (parentNode != null) {

								boolean annotationFound = false;

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

								for (Annotation annotation : annotations) {

									AnnotationType annotationType = annotation.getAnnotationType();

									if (annotationType != null && annotationType.equals(getTreeIndexAnnotationType())) {

										treeIndex = new StringBuffer(CdmUtils.Nz(annotation.getText()));

										annotationFound = true;

	//									logger.error("treeIndex: " + treeIndex);

										break;

									}

								}

								if (!annotationFound) {

									// This should not happen because it means that the treeIndex was not set correctly as an annotation to parentNode

									logger.error("TreeIndex could not be read from annotation of TaxonNode: " + parentNode.getUuid() + ", Taxon: " + parentNode.getTaxon().getUuid());

									treeIndex = new StringBuffer();

									treeIndex.append("#");

								}

							} else {

								// TreeIndex could not be determined, but it's unclear how to proceed to generate a correct treeIndex if the parentNode is NULL

								logger.error("ParentNode for RootNode is NULL. TreeIndex could not be determined: " + newNode.getUuid());

								treeIndex = new StringBuffer(); // This just prevents growing of the treeIndex in a wrong manner

								treeIndex.append("#");

							}

						}

						nomenclaturalCode = newNode.getTaxon().getName().getNomenclaturalCode();

						kingdomFk = PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode);

						traverseTree(newNode, parentNode, treeIndex, endRank, state);

						parentNode =null;

					}else{

						logger.debug("Taxon is not a PESI taxon: " + newNode.getTaxon().getUuid());

					}

					newNode = null;

					try {

						commitTransaction(txStatus);

						logger.debug("Committed transaction.");

					} catch (Exception e) {

						logger.error(e.getMessage());

						e.printStackTrace();

					}

				}

				rankSpecificRootNodes = null;

			}

		}

		logger.warn("Taking snapshot at the end of phase 2 of taxonExport");

		//ProfilerController.memorySnapshot();

		return success;

	}

	//PHASE 3: Add Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk...

	private boolean doPhase03(PesiExportState state) {

		int count = 0;

		int pastCount = 0;

		boolean success = true;

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

			logger.info ("Ignore PHASE 3: Add Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk...");

			return success;

		}

		// Get the limit for objects to save within a single transaction.

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

		List<TaxonBase> list;

		logger.info("PHASE 3: Add Rank data, KingdomFk, TypeNameFk, expertFk and speciesExpertFk...");

		// Be sure to add rank information, KingdomFk, TypeNameFk, expertFk and speciesExpertFk to every taxonName

		// Start transaction

		TransactionStatus txStatus = startTransaction(true);

		logger.info("Started new transaction for rank, kingdom, typeName, expertFk and speciesExpertFK. Fetching some " + pluralString + " (max: " + limit + ") ...");

		int partitionCount = 0;

		while ((list = getNextTaxonPartition(TaxonBase.class, limit, partitionCount++, null)) != null) {

			logger.debug("Fetched " + list.size() + " " + pluralString + ". Exporting...");

			for (TaxonBase<?> taxon : list) {

				TaxonNameBase<?,?> taxonName = taxon.getName();

				// Determine expertFk

//				Integer expertFk = makeExpertFk(state, taxonName);

//

//				// Determine speciesExpertFk

//				Integer speciesExpertFk = makeSpeciesExpertFk(state, taxonName);

				doCount(count++, modCount, pluralString);

				Integer typeNameFk = getTypeNameFk(taxonName, state);

				kingdomFk = findKingdomIdFromTreeIndex(taxon, state);

				 //       PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode);

				//TODO why are expertFks needed? (Andreas M.)

//				if (expertFk != null || speciesExpertFk != null) {

					invokeRankDataAndTypeNameFkAndKingdomFk(taxonName, nomenclaturalCode, state.getDbId(taxon),

							typeNameFk, kingdomFk, state);

//				}

					taxon = null;

					taxonName = null;

			}

			// Commit transaction

			commitTransaction(txStatus);

			logger.debug("Committed transaction.");

			logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);

			pastCount = count;

			// Start transaction

			txStatus = startTransaction(true);

			logger.info("Started new transaction for rank, kingdom, typeName, expertFk and speciesExpertFK. Fetching some " + pluralString + " (max: " + limit + ") ...");

		}

		if (list == null) {

			logger.info("No " + pluralString + " left to fetch.");

		}

		list = null;

		// Commit transaction

		commitTransaction(txStatus);

		logger.debug("Committed transaction.");

		logger.debug("Try to take snapshot at the end of phase 3 of taxonExport, number of partitions: " + partitionCount);

		//ProfilerController.memorySnapshot();

		return success;

	}

	/**

     * @param taxon

     * @return

     */

    private Integer findKingdomIdFromTreeIndex(TaxonBase<?> taxon,PesiExportState state) {

        if (taxon instanceof Taxon){

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

            if (!nodes.isEmpty()){

                String treeIndex = nodes.iterator().next().treeIndex();

                Pattern pattern = Pattern.compile("#t[0-9]+#[0-9]+#[0-9]+#");

                Matcher matcher = pattern.matcher(treeIndex);

                Integer kingdomID = null;

                if(matcher.find()) {

                    String treeIndexKingdom = matcher.group(0);

                    kingdomID = state.getTreeIndexKingdomMap().get(treeIndexKingdom);

                }

                return kingdomID;

            } else {

                logger.debug("The taxon has no nodes: " + taxon.getTitleCache() + " the kingdom is taken from the nomenclatural code: " + PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));

                return PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode);

        }} else{

           return PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode);

        }

    }

    //	"PHASE 5: Creating Inferred Synonyms..."

	private boolean doPhase05(PesiExportState state, PesiExportMapping mapping, PesiExportMapping synRelMapping) throws SQLException {

		int count;

		int pastCount;

		boolean success = true;

		// Get the limit for objects to save within a single transaction.

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

			logger.info ("Ignore PHASE 5: Creating Inferred Synonyms...");

			return success;

		}

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

		// Create inferred synonyms for accepted taxa

		logger.info("PHASE 4: Creating Inferred Synonyms...");

		// Determine the count of elements in datawarehouse database table Taxon

		currentTaxonId = determineTaxonCount(state);

		currentTaxonId++;

		count = 0;

		pastCount = 0;

		int pageSize = limit/10;

		int pageNumber = 1;

		String inferredSynonymPluralString = "Inferred Synonyms";

		// Start transaction

		TransactionStatus txStatus = startTransaction(true);

		logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");

		List<TaxonBase> taxonList = null;

		while ((taxonList  = getTaxonService().listTaxaByName(Taxon.class, "*", "*", "*", "*", "*", Rank.SPECIES(), pageSize, pageNumber)).size() > 0) {

			HashMap<Integer, TaxonNameBase<?,?>> inferredSynonymsDataToBeSaved = new HashMap<Integer, TaxonNameBase<?,?>>();

			logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");

			inferredSynonymsDataToBeSaved.putAll(createInferredSynonymsForTaxonList(state, mapping,

					synRelMapping, taxonList));

			doCount(count += taxonList.size(), modCount, inferredSynonymPluralString);

			// Commit transaction

			commitTransaction(txStatus);

			logger.debug("Committed transaction.");

			logger.info("Exported " + (taxonList.size()) + " " + inferredSynonymPluralString + ". Total: " + count);

			//pastCount = count;

			// Save Rank Data and KingdomFk for inferred synonyms

			for (Integer taxonFk : inferredSynonymsDataToBeSaved.keySet()) {

				invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), nomenclaturalCode, taxonFk, kingdomFk, state);

			}

			// Start transaction

			txStatus = startTransaction(true);

			logger.info("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");

			// Increment pageNumber

			pageNumber++;

		}

		taxonList = null;

		while ((taxonList  = getTaxonService().listTaxaByName(Taxon.class, "*", "*", "*", "*", "*", Rank.SUBSPECIES(), pageSize, pageNumber)).size() > 0) {

			HashMap<Integer, TaxonNameBase<?,?>> inferredSynonymsDataToBeSaved = new HashMap<Integer, TaxonNameBase<?,?>>();

			logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");

			inferredSynonymsDataToBeSaved.putAll(createInferredSynonymsForTaxonList(state, mapping,

					synRelMapping, taxonList));

			;

			doCount(count += taxonList.size(), modCount, inferredSynonymPluralString);

			// Commit transaction

			commitTransaction(txStatus);

			logger.debug("Committed transaction.");

			logger.info("Exported " + taxonList.size()+ " " + inferredSynonymPluralString + ". Total: " + count);

			//pastCount = count;

			// Save Rank Data and KingdomFk for inferred synonyms

			for (Integer taxonFk : inferredSynonymsDataToBeSaved.keySet()) {

				invokeRankDataAndKingdomFk(inferredSynonymsDataToBeSaved.get(taxonFk), nomenclaturalCode, taxonFk, kingdomFk, state);

			}

			// Start transaction

			txStatus = startTransaction(true);