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.old;

import java.sql.Connection;

import java.sql.PreparedStatement;

import java.sql.SQLException;

import java.util.HashMap;

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.common.Source;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;

/**

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

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

 * @author e.-m.lee

 * @since 02.03.2010

 *

 */

@Component

public class PesiOccurrenceExport extends PesiExportBase {

    private static final long serialVersionUID = 1444152605658503549L;

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

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

	private static int modCount = 1000;

	private static final String dbTableName = "Occurrence";

	private static final String pluralString = "Occurrences";

	private static final String parentPluralString = "Taxa";

	private static Taxon taxon = null;

	private static Map<Integer, Integer> sourceId2OccurenceIdMap = new HashMap<Integer, Integer>();

	private static NamedArea namedArea = null;

	private static Distribution distribution = null;

	public PesiOccurrenceExport() {

		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.error("*** Started Making " + pluralString + " ...");

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

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

			// Stores whether this invoke was successful or not.

			boolean success = true;

			// PESI: Clear the database table Occurrence.

//			doDelete(state);

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

			PesiExportMapping mapping = getMapping();

			// Initialize the db mapper

			mapping.initialize(state);

			// PESI: Create the Occurrences

			int count = 0;

			int taxonCount = 0;

			int pastCount = 0;

			TransactionStatus txStatus = null;

			List<TaxonBase> list = null;

			// Start transaction

			txStatus = startTransaction(true);

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

			while ((list = getTaxonService().list(null, limit, taxonCount, null, null)).size() > 0) {

				taxonCount += list.size();

				logger.error("Fetched " + list.size() + " " + parentPluralString + ".");

				for (TaxonBase taxonBase : list) {

					if (taxonBase.isInstanceOf(Taxon.class)) {

						// Set the current Taxon

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

						// Determine the TaxonDescriptions

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

						// Determine the DescriptionElements (Citations) for the current Taxon

						for (TaxonDescription taxonDescription : taxonDescriptions) {

							Set<DescriptionElementBase> descriptionElements = taxonDescription.getElements();

							for (DescriptionElementBase descriptionElement : descriptionElements) {

								Set<DescriptionElementSource> elementSources = descriptionElement.getSources();

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

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

									setNamedArea(distribution.getArea());

									setDistribution(distribution);

									// Differentiate between descriptionElements with and without sources.

									if (elementSources.size() == 0 && state.getDbId(descriptionElement) != null) {

										if (neededValuesNotNull(descriptionElement, state)) {

											doCount(count++, modCount, pluralString);

											success &= mapping.invoke(descriptionElement);

										}

									} else {

										for (DescriptionElementSource elementSource : elementSources) {

											Reference reference = elementSource.getCitation();

											// Citations can be empty (null): Is it wrong data or just a normal case?

											if (reference != null && state.getDbId(reference) != null) {

												if (neededValuesNotNull(reference, state)) {

													doCount(count++, modCount, pluralString);

													success &= mapping.invoke(reference);

												}

											}

										}

									}

									setDistribution(null);

								}

							}

						}

					}

				}

				// Commit transaction

				commitTransaction(txStatus);

				logger.error("Committed transaction.");

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

				pastCount = count;

				// Start transaction

				txStatus = startTransaction(true);

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

			}

			if (list.size() == 0) {

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

			}

			list = null;

			// Commit transaction

			commitTransaction(txStatus);

			logger.error("Committed transaction.");

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

			if (!success){

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

			}

			return;

		} catch (SQLException e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.getResult().addException(e);

			return;

		}

	}

	/**

	 * Checks whether needed values for an entity are NULL.

	 * @return

	 */

	private boolean neededValuesNotNull(AnnotatableEntity entity, PesiExportState state) {

		boolean result = true;

		if (getTaxonFk(entity, state) == null) {

			logger.error("TaxonFk is NULL, but is not allowed to be. Therefore no record was written to export database for this entity: " + entity.getUuid());

			result = false;

		}

		if (getAreaFk(entity) == null) {

			logger.error("AreaFk is NULL, but is not allowed to be. Therefore no record was written to export database for this entity: " + entity.getUuid());

			result = false;

		}

		if (getOccurrenceStatusFk(entity) == null) {

			logger.error("OccurrenceStatusFk is NULL, but is not allowed to be. Therefore no record was written to export database for this entity: " + entity.getUuid());

			result = false;

		}

		return result;

	}

	/**

	 * Creates the entries for the database table 'OccurrenceSource'.

	 * @param entity

	 * @param state

	 * @return

	 */

	protected boolean invokeOccurrenceSource(AnnotatableEntity entity, PesiExportState state) {

		if (entity == null) {

			return true;

		} else {

			// Create OccurrenceSource database table entry

			String lastStoredRecordSql = "Insert Into OccurrenceSource (OccurrenceFk, SourceFk, SourceNameCache, OldTaxonName) " +

					"values(?, ?, ?, ?)";

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

			try {

				PreparedStatement stmt = con.prepareStatement(lastStoredRecordSql);

				Integer sourceFk = getSourceFk(entity, state);

				stmt.setInt(1, sourceId2OccurenceIdMap.get(sourceFk));

				stmt.setInt(2, sourceFk);

				stmt.setString(3, getSourceCache(entity));

				stmt.setString(4, null); // Which taxon are we talking about?

				stmt.executeUpdate();

				return true;

			} catch (SQLException e) {

				logger.error("SQLException during getOccurrenceId invoke...");

				e.printStackTrace();

				return false;

			}

		}

	}

	/**

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

	 * @param state The {@link PesiExportState PesiExportState}.

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

	 */

	protected boolean doDelete(PesiExportState state) {

		PesiExportConfigurator pesiConfig = state.getConfig();

		String sql;

		Source destination =  pesiConfig.getDestination();

		// Clear Occurrence

		sql = "DELETE FROM " + dbTableName;

		destination.setQuery(sql);

		destination.update(sql);

		return true;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean isIgnore(PesiExportState state) {

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

	}

	/**

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

	 * @param entity An {@link AnnotatableEntity AnnotatableEntity}.

	 * @param state The {@link PesiExportState PesiExportState}.

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

	 * @see MethodMapper

	 */

	private static Integer getTaxonFk(AnnotatableEntity entity, PesiExportState state) {

		// AnnotatableEntity parameter isn't needed, but the DbSingleAttributeExportMapperBase throws a type mismatch exception otherwise

		// since it awaits two parameters if one of them is of instance DbExportStateBase.

		Integer result = null;

		if (state != null && taxon != null) {

			result = state.getDbId(taxon.getName());

		}

		return result;

	}

	/**

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

	 * @param entity An {@link AnnotatableEntity AnnotatableEntity}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getTaxonFullNameCache(AnnotatableEntity entity) {

		String result = null;

		result = taxon.getName().getTitleCache();

		return result;

	}

	/**

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

	 * @param entity An {@link AnnotatableEntity AnnotatableEntity}.

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

	 * @see MethodMapper

	 */

	private static Integer getAreaFk(AnnotatableEntity entity) {

		Integer result = null;

		if (getNamedArea() != null) {

			//TODO not working any more after transformer refactoring

			try {

				result = (Integer)new PesiTransformer(null).getKeyByNamedArea(namedArea);

			} catch (UndefinedTransformerMethodException e) {

				e.printStackTrace();

			}

		} else {

			logger.warn("This should never happen, but a NamedArea could not be found for entity: " + entity.getUuid());

		}

		return result;

	}

	/**

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

	 * @param entity An {@link AnnotatableEntity AnnotatableEntity}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getAreaNameCache(AnnotatableEntity entity) {

		String result = null;

		if (getNamedArea() != null) {

			//TODO not working any more after transformer refactoring

			try {

				result = new PesiTransformer(null).getCacheByNamedArea(namedArea);

			} catch (UndefinedTransformerMethodException e) {

				e.printStackTrace();

			}

		} else {

			logger.warn("This should never happen, but a NamedArea could not be found for entity: " + entity.getUuid());

		}

		return result;

	}

	/**

	 * @return the distribution

	 */

	public static Distribution getDistribution() {

		return distribution;

	}

	/**

	 * @param distribution the distribution to set

	 */

	public static void setDistribution(Distribution distribution) {

		PesiOccurrenceExport.distribution = distribution;

	}

	/**

	 * @return the namedArea

	 */

	public static NamedArea getNamedArea() {

		return namedArea;

	}

	/**

	 * @param namedArea the namedArea to set

	 */

	public static void setNamedArea(NamedArea namedArea) {

		PesiOccurrenceExport.namedArea = namedArea;

	}

	/**

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

	 * @param entity An {@link AnnotatableEntity AnnotatableEntity}.

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

	 * @throws UnknownCdmTypeException

	 * @see MethodMapper

	 */

	private static Integer getOccurrenceStatusFk(AnnotatableEntity entity) {

		Integer result = null;

		if (getDistribution() != null) {

			result = PesiTransformer.presenceAbsenceTerm2OccurrenceStatusId(getDistribution().getStatus());

		}

		return result;

	}

	/**

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

	 * @param entity An {@link AnnotatableEntity AnnotatableEntity}.

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

	 * @throws UndefinedTransformerMethodException

	 * @throws UnknownCdmTypeException

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getOccurrenceStatusCache(AnnotatableEntity entity, PesiExportState state) throws UndefinedTransformerMethodException {

		String result = null;

		if (getDistribution() != null) {

			result = state.getTransformer().getCacheByPresenceAbsenceTerm(getDistribution().getStatus());

		}

		return result;

	}

	/**

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

	 * @param entity An {@link AnnotatableEntity AnnotatableEntity}.

	 * @param state The {@link PesiExportState PesiExportState}.

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

	 * @see MethodMapper

	 */

	private static Integer getSourceFk(AnnotatableEntity entity, PesiExportState state) {

		Integer result = null;

		if (state != null && entity != null && entity.isInstanceOf(Distribution.class)) {

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

			Set<DescriptionElementSource> sources = distribution.getSources();

			if (sources.size() == 1) {

				DescriptionElementSource source = sources.iterator().next();

				result = state.getDbId(source.getCitation());

			} else if (sources.size() > 1) {

				logger.warn("Found Distribution with " + sources.size() + " sources.");

			}

		}

		return result;

	}

	/**

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

	 * @param entity An {@link AnnotatableEntity AnnotatableEntity}.

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

	 * @see MethodMapper

	 */

	private static String getSourceCache(AnnotatableEntity entity) {

		String result = null;

		Reference reference;

		if (entity != null && entity.isInstanceOf(Distribution.class)) {

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

			Set<DescriptionElementSource> sources = distribution.getSources();

			if (sources.size() == 1) {

				DescriptionElementSource source = sources.iterator().next();

				reference = source.getCitation();

				if (reference != null) {

					result = reference.getTitle();

				}

			} else if (sources.size() > 1) {

				logger.warn("Found Distribution with " + sources.size() + " sources.");

			}

		}

		return result;

	}

	/**

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

	 * @param entity An {@link AnnotatableEntity AnnotatableEntity}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getNotes(AnnotatableEntity entity) {

		// TODO

		return null;

	}

	/**

	 * Returns the CDM to PESI specific export mappings.

	 * @return The {@link PesiExportMapping PesiExportMapping}.

	 */

	private PesiExportMapping getMapping() {

		PesiExportMapping mapping = new PesiExportMapping(dbTableName);

		mapping.addMapper(MethodMapper.NewInstance("TaxonFk", this.getClass(), "getTaxonFk", standardMethodParameter, PesiExportState.class));

		mapping.addMapper(MethodMapper.NewInstance("AreaFk", this));

		mapping.addMapper(MethodMapper.NewInstance("TaxonFullNameCache", this));

		mapping.addMapper(MethodMapper.NewInstance("AreaNameCache", this));

		mapping.addMapper(MethodMapper.NewInstance("OccurrenceStatusFk", this));

		mapping.addMapper(MethodMapper.NewInstance("OccurrenceStatusCache", this, AnnotatableEntity.class, PesiExportState.class));

		mapping.addMapper(MethodMapper.NewInstance("SourceFk", this.getClass(), "getSourceFk", standardMethodParameter, PesiExportState.class));

		mapping.addMapper(MethodMapper.NewInstance("SourceCache", this));

		mapping.addMapper(MethodMapper.NewInstance("Notes", this));

		return mapping;

	}

}