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.SQLException;

import java.sql.Types;

import java.util.Arrays;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.Language;

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

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.media.Media;

import eu.etaxonomy.cdm.model.media.MediaRepresentation;

import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;

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

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

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

import eu.etaxonomy.cdm.profiler.ProfilerController;

/**

 * The export class for {@link eu.etaxonomy.cdm.model.description.DescriptionElementBase DescriptionElements}.<p>

 * Inserts into DataWarehouse database table <code>Note</code>.<p>

 * It is divided into two phases:<ul>

 * <li>Phase 1:	Export of DescriptionElements as Notes.

 * <li>Phase 2:	Export of TaxonName extensions <code>taxComment</code>, <code>fauComment</code> and <code>fauExtraCodes</code> as Notes.</ul>

 * @author e.-m.lee

 * @since 23.02.2010

 * @author a.mueller

 */

@Component

public class PesiDescriptionExport extends PesiExportBase {

    private static final long serialVersionUID = -1486235807814098217L;

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

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

	private static int modCount = 1000;

	private static final String dbNoteTableName = "Note";

	private static final String dbOccurrenceTableName = "Occurrence";

	private static final String dbVernacularTableName = "CommonName";

	private static final String dbImageTableName = "Image";

	private static final String dbAdditionalSourceTableName = "AdditionalTaxonSource";

	private static final String pluralString = "descriptions";

	private static final String parentPluralString = "Taxa";

	//decide where to handle them best (configurator, transformer, single method, ...)

	private static Set<Integer> excludedNoteCategories = new HashSet<>(Arrays.asList(new Integer[]{250,251,252,253,10,11,13}));

	//debugging

	private static int countDescriptions;

	private static int countTaxa;

	private static int countDistribution;

	private static int countAdditionalSources;

	private static int countImages;

	private static int countNotes;

	private static int countCommonName;

	private static int countOccurrence;

	private static int countOthers;

	public PesiDescriptionExport() {

		super();

	}

	@Override

	public Class<? extends CdmBase> getStandardMethodParameter() {

		return standardMethodParameter;

	}

	@Override

	protected void doInvoke(PesiExportState state) {

		try {

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

			// Stores whether this invoke was successful or not.

			boolean success = true;

			success &= doDelete(state);

			// Get specific mappings: (CDM) DescriptionElement -> (PESI) Note

			PesiExportMapping notesMapping = getNotesMapping();

			notesMapping.initialize(state);

			// Get specific mappings: (CDM) DescriptionElement -> (PESI) Occurrence

			PesiExportMapping occurrenceMapping = getOccurrenceMapping();

			occurrenceMapping.initialize(state);

			// Get specific mappings: (CDM) DescriptionElement -> (PESI) Additional taxon source

			PesiExportMapping addSourceSourceMapping = getAddTaxonSourceSourceMapping();

			addSourceSourceMapping.initialize(state);

			PesiExportMapping additionalSourceMapping = getAdditionalTaxonSourceMapping();

			additionalSourceMapping.initialize(state);

			// Get specific mappings: (CDM) DescriptionElement -> (PESI) Common name

			PesiExportMapping vernacularMapping = getCommonNamesMapping();

			vernacularMapping.initialize(state);

			// Get specific mappings: (CDM) DescriptionElement -> (PESI) Image

			PesiExportMapping imageMapping = getImageMapping();

			imageMapping.initialize(state);

			// Taxon Descriptions

			success &= doPhase01(state, notesMapping, occurrenceMapping, addSourceSourceMapping, additionalSourceMapping, vernacularMapping, imageMapping);

			// Name Descriptions

			success &= doPhase01b(state, notesMapping, occurrenceMapping, addSourceSourceMapping, additionalSourceMapping, vernacularMapping, imageMapping);

			logger.info("PHASE 2...");

			success &= doPhase02(state);

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

			if (!success){

				state.getResult().addError("An unknown problem occurred");

			}

			return;

		} catch (SQLException e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.getResult().addException(e, e.getMessage());

		}

	}

	//PHASE 01: Description Elements

	private boolean doPhase01(PesiExportState state, PesiExportMapping notesMapping, PesiExportMapping occurrenceMapping, PesiExportMapping addSourceSourceMapping,

			PesiExportMapping additionalSourceMapping, PesiExportMapping vernacularMapping, PesiExportMapping imageMapping) throws SQLException {

//	    System.out.println("PHASE 1 of description import");

	    logger.info("PHASE 1...");

		int count = 0;

		int pastCount = 0;

		boolean success = true;

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

		int limit = 1000;

		List<Taxon> taxonList = null;

		TransactionStatus txStatus = startTransaction(true);

		if (logger.isDebugEnabled()){

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

		    logger.debug("Start snapshot, before starting loop");

		    ProfilerController.memorySnapshot();

		}

		List<String> propPath = Arrays.asList(new String[]{"descriptions.elements.*"});

		int partitionCount = 0;

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

			if (logger.isDebugEnabled()) {

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

            }

			for (Taxon taxon : taxonList) {

				countTaxa++;

				doCount(count++, modCount, parentPluralString);

				state.setCurrentTaxon(taxon);

				if (!taxon.getDescriptions().isEmpty()){

					success &= handleSingleTaxon(taxon, state, notesMapping, occurrenceMapping, addSourceSourceMapping,

						additionalSourceMapping, vernacularMapping, imageMapping);

				}

			}

			taxonList = null;

			state.setCurrentTaxon(null);

			// Commit transaction

			commitTransaction(txStatus);

			logger.info("Exported " + (count - pastCount) + " " + parentPluralString + ". Total: " + count + " (Phase 01)");

			pastCount = count;

			ProfilerController.memorySnapshot();

			// Start transaction

			txStatus = startTransaction(true);

			if(logger.isDebugEnabled()) {

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

            }

		}

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

		logger.info("Partition: " + partitionCount);

		logger.info("Taxa: " + countTaxa);

		logger.info("Desc: " + countDescriptions);

		logger.info("Distr: " + countDistribution);

		logger.info("Occur: " + countOccurrence);

		logger.info("Commons: " + countCommonName);

		logger.info("AddSrc: " + countAdditionalSources);

		logger.info("Images: " + countImages);

		logger.info("Notes: " + countNotes);

		logger.info("Others: " + countOthers);

		// Commit transaction

		commitTransaction(txStatus);

		logger.debug("Committed transaction.");

		return success;

	}

	//PHASE 01b: Name Descriptions

	private boolean doPhase01b(PesiExportState state, PesiExportMapping notesMapping, PesiExportMapping occurrenceMapping, PesiExportMapping addSourceSourceMapping,

			PesiExportMapping additionalSourceMapping, PesiExportMapping vernacularMapping, PesiExportMapping imageMapping) throws SQLException {

		logger.info("PHASE 1b...");

		int count = 0;

		int pastCount = 0;

		boolean success = true;

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

		int limit = 2000;

		List<TaxonNameDescription> nameDescList = null;

		TransactionStatus txStatus = startTransaction(true);

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

		List<String> propPath = Arrays.asList(new String[]{"descriptions.elements.*"});

		//name descriptions

		int partitionCount = 0;

		while ((nameDescList = getNextNameDescriptionPartition( limit, partitionCount++, propPath )) != null   ) {

			logger.info("Fetched " + nameDescList.size() + " name descriptions. Exporting...");

			for (TaxonNameDescription desc : nameDescList) {

				countTaxa++;

				doCount(count++, modCount, "name descriptions");

				boolean isImageGallery = desc.isImageGallery();

				TaxonName name = desc.getTaxonName();

				for (DescriptionElementBase element : desc.getElements()){

					if (isPurePesiName(name)){

						success &= handleDescriptionElement(state, notesMapping, occurrenceMapping, vernacularMapping, imageMapping,

								addSourceSourceMapping, additionalSourceMapping, isImageGallery, element);

					}else{

						for (TaxonBase<?> taxonBase : name.getTaxonBases()){

							if (isPesiTaxon(taxonBase)){

								state.setCurrentTaxon(taxonBase);

								success &= handleDescriptionElement(state, notesMapping, occurrenceMapping, vernacularMapping, imageMapping,

										addSourceSourceMapping, additionalSourceMapping, isImageGallery, element);

								state.setSourceForAdditionalSourceCreated(true);

							}

						}

						state.setSourceForAdditionalSourceCreated(false);

					}

				}

			}

			nameDescList = null;

			state.setCurrentTaxon(null);

			// Commit transaction

			commitTransaction(txStatus);

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

			pastCount = count;

			// Start transaction

			txStatus = startTransaction(true);

			logger.info("Started new transaction. Fetching some name descriptions (max: " + limit + ") for description import ...");

		}

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

		logger.info("Partition: " + partitionCount);

		logger.info("Taxa: " + countTaxa);

		logger.info("Desc: " + countDescriptions);

		logger.info("Distr: " + countDistribution);

		logger.info("Occur: " + countOccurrence);

		logger.info("Commons: " + countCommonName);

		logger.info("AddSrc: " + countAdditionalSources);

		logger.info("Images: " + countImages);

		logger.info("Notes: " + countNotes);

        logger.info("Others: " + countOthers);

		// Commit transaction

		commitTransaction(txStatus);

		logger.debug("Committed transaction.");

		return success;

	}

	private boolean handleSingleTaxon(Taxon taxon, PesiExportState state, PesiExportMapping notesMapping, PesiExportMapping occurrenceMapping,

			PesiExportMapping addSourceSourceMapping, PesiExportMapping additionalSourceMapping,

			PesiExportMapping vernacularMapping, PesiExportMapping imageMapping) throws SQLException {

	    boolean success = true;

		Set<DescriptionBase<?>> descriptions = new HashSet<>();

		descriptions.addAll(taxon.getDescriptions());

		for (DescriptionBase<?> desc : descriptions){

			boolean isImageGallery = desc.isImageGallery();

			for (DescriptionElementBase element : desc.getElements()){

				success &= handleDescriptionElement(state, notesMapping, occurrenceMapping, vernacularMapping, imageMapping,

						addSourceSourceMapping, additionalSourceMapping, isImageGallery, element);

				countDescriptions++;

			}

		}

		if (logger.isDebugEnabled()) {

            logger.info("number of handled decriptionelements " + countDescriptions);

        }

		descriptions = null;

		return success;

	}

	private boolean handleDescriptionElement(PesiExportState state, PesiExportMapping notesMapping,

			PesiExportMapping occurrenceMapping, PesiExportMapping vernacularMapping, PesiExportMapping imageMapping,

			PesiExportMapping addSourceSourceMapping, PesiExportMapping additionalSourceMapping, boolean isImageGallery, DescriptionElementBase element) throws SQLException {

	    try {

			boolean success = true;

			if (isImageGallery){

				for (Media media : element.getMedia()){

				    countImages++;

				    success &= imageMapping.invoke(media);

				}

			}else if (isCommonName(element)){

				countCommonName++;

				if (element.isInstanceOf(TextData.class)){

					//we do not import text data common names

				}else{

					success &= vernacularMapping.invoke(element);

				}

			}else if (isOccurrence(element)){

				countOccurrence++;

				Distribution distribution = CdmBase.deproxy(element, Distribution.class);

				MarkerType markerType = getUuidMarkerType(PesiTransformer.uuidMarkerTypeHasNoLastAction, state);

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

				if (!isPesiDistribution(state, distribution)){

				    logger.debug("Distribution is not PESI distribution: " + distribution.toString());

				}else{

					countDistribution++;

					try{

					    success &=occurrenceMapping.invoke(distribution);

					}catch(Exception e){

					    System.err.println(distribution.getInDescription().getTitleCache());

					    e.printStackTrace();

					}

				}

			}else if (isAdditionalTaxonSource(element)){

				countAdditionalSources++;

				if (! state.isSourceForAdditionalSourceCreated()){

					success &= addSourceSourceMapping.invoke(element);

				}

				success &= additionalSourceMapping.invoke(element);

			}else if (isExcludedNote(element)){

				//do nothing

			}else if (isPesiNote(element)){

				countNotes++;

				success &= notesMapping.invoke(element);

            }else{

				countOthers++;

				String featureTitle = element.getFeature() == null ? "no feature" :element.getFeature().getTitleCache();

				logger.warn("Description element type not yet handled by PESI export: " + element.getUuid() + ", " +  element.getClass() + ", " +  featureTitle);

			}

			return success;

		} catch (Exception e) {

			logger.warn("Exception appeared in description element handling: " + e);

			e.printStackTrace();

			return false;

		}

	}

    private boolean isExcludedNote(DescriptionElementBase element) {

		Integer categoryFk = PesiTransformer.feature2NoteCategoryFk(element.getFeature());

		//TODO decide where to handle them best (configurator, transformer, single method, ...)

		return (excludedNoteCategories.contains(categoryFk));

	}

    boolean isFirstUndefinedStatusWarnung = true;

	private boolean isPesiDistribution(PesiExportState state, Distribution distribution) {

		//currently we use the E+M summary status to decide if a distribution should be exported

		if (distribution.getStatus() == null){

			return false;

		}else if (distribution.getStatus().getUuid().equals(BerlinModelTransformer.uuidStatusUndefined)){

		    if (isFirstUndefinedStatusWarnung){

                logger.warn("Status 'undefined' is not mapped to any status for now. Needs further checking. (E+M specific)");

                isFirstUndefinedStatusWarnung = false;

            }

            return false;

		}

		//...this may change in future so we keep the following code

		//area filter

		NamedArea area = distribution.getArea();

		if (area == null){

			logger.warn("Area is null for distribution " +  distribution.getUuid());

			return false;

		}else if (area.getUuid().equals(BerlinModelTransformer.euroMedUuid)){

			//E+M area only holds endemic status information and therefore is not exported to PESI

			return false;

//		}else if (area.equals(TdwgAreaProvider.getAreaByTdwgAbbreviation("1"))){

//			//Europe area never holds status information (may probably be deleted in E+M)

//			return false;

//		}else if (area.equals(TdwgArea.getAreaByTdwgAbbreviation("21"))){

//			//Macaronesia records should not be exported to PESI

//			return false;

//		//TODO exclude Russion areas Rs*, and maybe others

		} else {

            try {

				if (state.getTransformer().getKeyByNamedArea(area) == null){

					String warning = "Area (%s,%s) not available in PESI transformer for taxon %s: ";

					TaxonBase<?> taxon =  state.getCurrentTaxon();

					warning = String.format(warning, area.getTitleCache(), area.getRepresentation(Language.ENGLISH()).getAbbreviatedLabel(),taxon ==null? "-" : taxon.getTitleCache());

					logger.warn(warning);

					return false;

				}

			} catch (UndefinedTransformerMethodException e1) {

				logger.warn("Area not available in PESI transformer " +  area.getTitleCache());

				return false;

			}

        }

		return true;

	}

	private boolean isPesiNote(DescriptionElementBase element) {

		return (getNoteCategoryFk(element) != null);

	}

	private boolean isAdditionalTaxonSource(DescriptionElementBase element) {

		Feature feature = element.getFeature();

		if (feature == null){

			return false;

		}

		return (feature.equals(Feature.CITATION()) || feature.equals(Feature.ADDITIONAL_PUBLICATION()));

	}

	private boolean isOccurrence(DescriptionElementBase element) {

		Feature feature = element.getFeature();

		if (element.isInstanceOf(Distribution.class)){

		    if (!Feature.DISTRIBUTION().equals(feature)){

		        logger.warn("Description element has class 'Distribution' but has no feature 'Distribution'");

		    }

		    return true;

		}else if (Feature.DISTRIBUTION().equals(feature)){

		    logger.debug("Description element has feature Distribtuion but is not of class 'Distribution'");

            return false;

		}else{

			return false;

		}

	}

	private boolean isCommonName(DescriptionElementBase element) {

		Feature feature = element.getFeature();

		if (feature == null){

			return false;

		}

		return (feature.equals(Feature.COMMON_NAME()));

	}

	//PHASE 02: Name extensions

	private boolean doPhase02(PesiExportState state) {

		TransactionStatus txStatus;

		boolean success =  true;

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

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

		int limit = 2000;

		txStatus = startTransaction(true);

		ExtensionType taxCommentExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtTaxComment);

		ExtensionType fauCommentExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtFauComment);

		ExtensionType fauExtraCodesExtensionType = (ExtensionType)getTermService().find(PesiTransformer.uuidExtFauExtraCodes);

		List<TaxonName> taxonNameList;

		int count = 0;

		int pastCount = 0;

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

		if (logger.isDebugEnabled()) {

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

        }

		logger.warn("TODO handle extensions on taxon level, not name level (");

		while ((taxonNameList = getNameService().list(null, limit, count, null, null)).size() > 0) {

			if(logger.isDebugEnabled()) {

                logger.info("Fetched " + taxonNameList.size() + " names. Exporting...");

            }

			for (TaxonName taxonName : taxonNameList) {

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

				for (Extension extension : extensions) {

					if (extension.getType().equals(taxCommentExtensionType)) {

						String taxComment = extension.getValue();

						invokeNotes(taxComment,

								PesiTransformer.getNoteCategoryFk(PesiTransformer.uuidExtTaxComment),

								PesiTransformer.getNoteCategoryCache(PesiTransformer.uuidExtTaxComment),

								null, null, getTaxonKey(taxonName, state),connection);

					} else if (extension.getType().equals(fauCommentExtensionType)) {

						String fauComment = extension.getValue();

						invokeNotes(fauComment,

								PesiTransformer.getNoteCategoryFk(PesiTransformer.uuidExtFauComment),

								PesiTransformer.getNoteCategoryCache(PesiTransformer.uuidExtFauComment),

								null, null, getTaxonKey(taxonName, state),connection);

					} else if (extension.getType().equals(fauExtraCodesExtensionType)) {

						String fauExtraCodes = extension.getValue();

						invokeNotes(fauExtraCodes,

								PesiTransformer.getNoteCategoryFk(PesiTransformer.uuidExtFauExtraCodes),

								PesiTransformer.getNoteCategoryCache(PesiTransformer.uuidExtFauExtraCodes),

								null, null, getTaxonKey(taxonName, state),connection);

					}

				}

				doCount(count++, modCount, parentPluralString);

			}

			// Commit transaction

			commitTransaction(txStatus);

			logger.debug("Committed transaction.");

			logger.info("Exported " + (count - pastCount) + " names. Total: " + count + " (Phase 02)");

			pastCount = count;

			// Start transaction

			txStatus = startTransaction(true);

			if (logger.isDebugEnabled()) {

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

            }

		}

		// Commit transaction

		commitTransaction(txStatus);

		logger.debug("Committed transaction.");

		return success;

	}

	private void invokeNotes(String note, Integer noteCategoryFk,

			String noteCategoryCache, Integer languageFk, String languageCache,

			Integer taxonFk, Connection connection) {

	    String notesSql = "UPDATE Note SET Note_1 = ?, NoteCategoryFk = ?, NoteCategoryCache = ?, LanguageFk = ?, LanguageCache = ? WHERE TaxonFk = ?";

		try {

			PreparedStatement notesStmt = connection.prepareStatement(notesSql);

			if (note != null) {

				notesStmt.setString(1, note);

			} else {

				notesStmt.setObject(1, null);

			}

			if (noteCategoryFk != null) {

				notesStmt.setInt(2, noteCategoryFk);

			} else {

				notesStmt.setObject(2, null);

			}

			if (noteCategoryCache != null) {

				notesStmt.setString(3, noteCategoryCache);

			} else {

				notesStmt.setObject(3, null);

			}

			if (languageFk != null) {

				notesStmt.setInt(4, languageFk);

			} else {

				notesStmt.setObject(4, null);

			}

			if (languageCache != null) {

				notesStmt.setString(5, languageCache);

			} else {

				notesStmt.setObject(5, null);

			}

			if (taxonFk != null) {

				notesStmt.setInt(6, taxonFk);

			} else {

				notesStmt.setObject(6, null);

			}

			notesStmt.executeUpdate();

		} catch (SQLException e) {

			logger.error("Note could not be created: " + note);

			e.printStackTrace();

		}

	}

	/**

	 * Deletes all entries of database tables related to <code>Note</code>.

	 * @param state The PesiExportState

	 * @return Whether the delete operation was successful or not.

	 */

	protected boolean doDelete(PesiExportState state) {

	    Source destination = state.getConfig().getDestination();

		// Clear NoteSource

		String sql = "DELETE FROM NoteSource";

		destination.update(sql);

		// Clear Note

		sql = "DELETE FROM Note "; // + dbNoteTableName;

		destination.update(sql);

	    // Clear OccurrenceSource

        sql = "DELETE FROM OccurrenceSource ";

        destination.update(sql);

        // Clear Occurrence

        sql = "DELETE FROM Occurrence ";

        destination.update(sql);

        // Clear Image

        sql = "DELETE FROM Image ";

        destination.update(sql);

        // Clear CommonName

        sql = "DELETE FROM CommonNameSource ";

        destination.update(sql);

        sql = "DELETE FROM CommonName ";

        destination.update(sql);

        // Clear AdditionalTaxonSource

        sql = "DELETE FROM AdditionalTaxonSource WHERE SourceFk >= 2000000 ";

        destination.update(sql);

        // Clear Sources for AdditionalTaxonSource

        sql = "DELETE FROM Source WHERE SourceId >= 2000000 ";

        destination.update(sql);

		return true;

	}

	/**

	 * Returns the <code>Note_2</code> attribute.

	 * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.

	 * @return The <code>Note_2</code> attribute.

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused") //used for mapper

	private static String getNote_2(DescriptionElementBase element) {

		//E+M map links -> medium

		if (element.getFeature() != null && element.getFeature().getUuid().equals(BerlinModelTransformer.uuidFeatureMaps)){

			String text = CdmBase.deproxy(element, TextData.class).getText(Language.ENGLISH());

			if (text.contains("medium")){

				return "medium";

			}

		}

		return null;

	}

	/**

	 * Returns the <code>NoteCategoryFk</code> attribute.

	 * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.

	 * @return The <code>NoteCategoryFk</code> attribute.

	 * @see MethodMapper

	 */

	private static Integer getNoteCategoryFk(DescriptionElementBase descriptionElement) {

		Integer result = null;

		result = PesiTransformer.feature2NoteCategoryFk(descriptionElement.getFeature());

		//TODO decide where to handle them best (configurator, transformer, single method, ...)

		if (excludedNoteCategories.contains(result)){

			result = null;

		}

		return result;

	}

	/**

	 * Returns the <code>NoteCategoryCache</code> attribute.

	 * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.

	 * @return The <code>NoteCategoryCache</code> attribute.

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getNoteCategoryCache(DescriptionElementBase descriptionElement, PesiExportState state) {

		return state.getTransformer().getCacheByFeature(descriptionElement.getFeature());

	}

	/**

	 * Returns the <code>LanguageFk</code> attribute.

	 * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.

	 * @return The <code>LanguageFk</code> attribute.

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static Integer getLanguageFk(DescriptionElementBase descriptionElement) {

		Language language = getLanguage(descriptionElement);

		return PesiTransformer.language2LanguageId(language);

	}

	/**

	 * Returns the <code>LanguageCache</code> attribute.

	 * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.

	 * @return The <code>LanguageCache</code> attribute.

	 * @throws UndefinedTransformerMethodException

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getLanguageCache(DescriptionElementBase descriptionElement, PesiExportState state) throws UndefinedTransformerMethodException {

		Language language = getLanguage(descriptionElement);

		return state.getTransformer().getCacheByLanguage(language);

	}

	private static Language getLanguage(DescriptionElementBase descriptionElement) {

		Language language = null;

		Map<Language, LanguageString> multilanguageText = null;

		if (descriptionElement.isInstanceOf(CommonTaxonName.class)) {

			CommonTaxonName commonTaxonName = CdmBase.deproxy(descriptionElement, CommonTaxonName.class);

			language = commonTaxonName.getLanguage();

		} else if (descriptionElement.isInstanceOf(TextData.class)) {

			TextData textData = CdmBase.deproxy(descriptionElement, TextData.class);

			multilanguageText = textData.getMultilanguageText();

		} else if (descriptionElement.isInstanceOf(IndividualsAssociation.class)) {

			IndividualsAssociation individualsAssociation = CdmBase.deproxy(descriptionElement, IndividualsAssociation.class);

			multilanguageText = individualsAssociation.getDescription();

		} else if (descriptionElement.isInstanceOf(TaxonInteraction.class)) {

			TaxonInteraction taxonInteraction = CdmBase.deproxy(descriptionElement, TaxonInteraction.class);

			multilanguageText = taxonInteraction.getDescription();

		} else {

			logger.debug("Given descriptionElement does not support languages. Hence LanguageCache could not be determined: " + descriptionElement.getUuid());

		}

		if (multilanguageText != null) {

			Set<Language> languages = multilanguageText.keySet();

			// TODO: Think of something more sophisticated than this

			if (languages.size() > 0) {

				language = languages.iterator().next();

			}

			if (languages.size() > 1){

				logger.warn("There is more than 1 language for a given description (" + descriptionElement.getClass().getSimpleName() + "):" + descriptionElement.getUuid());

			}

		}

		return language;

	}

//	/**

//	 * Returns the <code>Region</code> attribute.

//	 * @param descriptionElement The {@link DescriptionElementBase DescriptionElement}.

//	 * @return The <code>Region</code> attribute.

//	 * @see MethodMapper

//	 */

//	@SuppressWarnings("unused")

//	private static String getRegion(DescriptionElementBase descriptionElement) {

//		String result = null;

//		DescriptionBase<?> inDescription = descriptionElement.getInDescription();

//

//		// Area information are associated to TaxonDescriptions and Distributions.

//		if (descriptionElement.isInstanceOf(Distribution.class)) {

//			Distribution distribution = CdmBase.deproxy(descriptionElement, Distribution.class);

//			result = PesiTransformer.area2AreaCache(distribution.getArea());

//		} else if (inDescription != null && inDescription.isInstanceOf(TaxonDescription.class)) {

//			TaxonDescription taxonDescription = CdmBase.deproxy(inDescription, TaxonDescription.class);

//			Set<NamedArea> namedAreas = taxonDescription.getGeoScopes();

//			if (namedAreas.size() == 1) {

//				result = PesiTransformer.area2AreaCache(namedAreas.iterator().next());

//			} else if (namedAreas.size() > 1) {

//				logger.warn("This TaxonDescription contains more than one NamedArea: " + taxonDescription.getTitleCache());

//			}

//		}

//		return result;

//	}

	/**

	 * @param state The {@link DbExportStateBase DbExportState}.

	 * @return

	 */

	@SuppressWarnings("unused")  //used by mapper

	private static Integer getTaxonFk(DescriptionElementBase deb, PesiExportState state) {

		TaxonBase<?> entity = state.getCurrentTaxon();

		return state.getDbId(entity);

	}

	/**

	 * Returns the TaxonFk for a given TaxonName.

	 * @param taxonName The {@link TaxonNameBase TaxonName}.

	 * @param state The {@link DbExportStateBase DbExportState}.

	 * @return

	 */

	private static Integer getTaxonKey(TaxonName taxonName, DbExportStateBase<?, PesiTransformer> state) {

		return state.getDbId(taxonName);

	}

	/**

	 * Returns the <code>FullName</code> attribute.

	 * @param taxonName The {@link NonViralName NonViralName}.

	 * @return The <code>FullName</code> attribute.

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getTaxonFullNameCache(DescriptionElementBase deb, PesiExportState state) {

		TaxonBase<?> taxon =  state.getCurrentTaxon();

		TaxonName taxonName = taxon.getName();

		TaxonName nvn = CdmBase.deproxy(taxonName);

		String result = getCacheStrategy(nvn).getTitleCache(nvn);

		return result;

	}

    @SuppressWarnings("unused")  //used by mapper

    private static Integer getCurrentTaxonFk(Media media, PesiExportState state) {