EDIT

// $Id$

/**

* 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.util.HashSet;

import java.util.List;

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.IExportConfigurator.DO_REFERENCES;

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

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

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

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

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

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

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

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

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

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

/**

 * The export class for additional information linked to {@link eu.etaxonomy.cdm.model.description.Distribution Distributions} and {@link eu.etaxonomy.cdm.model.common.DescriptionElementSource DescriptionElements}.<p>

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

 * @author e.-m.lee

 * @date 15.03.2010

 *

 */

@Component

@SuppressWarnings("unchecked")

public class PesiOccurrenceSourceExport extends PesiExportBase {

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

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

	private static int modCount = 1000;

	private static final String dbTableName = "OccurrenceSource";

	private static final String pluralString = "OccurrenceSources";

	private static final String parentPluralString = "Taxa";

	private static Taxon taxon = null;

	public PesiOccurrenceSourceExport() {

		super();

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.DbExportBase#getStandardMethodParameter()

	 */

	@Override

	public Class<? extends CdmBase> getStandardMethodParameter() {

		return standardMethodParameter;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean doCheck(PesiExportState state) {

		boolean result = true;

		return result;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected void doInvoke(PesiExportState state) {

		try {

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

			String occurrenceSql = "Insert into OccurrenceSource (OccurrenceFk, SourceFk, SourceNameCache, OldTaxonName) " +

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

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

			PreparedStatement stmt = con.prepareStatement(occurrenceSql);

			// 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 OccurrenceSource.

			doDelete(state);

			// Get specific mappings: (CDM) ? -> (PESI) OccurrenceSource

			PesiExportMapping mapping = getMapping();

			// Initialize the db mapper

			mapping.initialize(state);

			// PESI: Create the OccurrenceSource

			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) {

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

				taxonCount += list.size();

				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();

								// Focus on descriptionElements with sources.

								if (elementSources.size() > 0) {

									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) {

											// Lookup sourceFk

											Integer sourceFk = getSourceFk(reference, state);

											if (sourceFk != null && ! state.alreadyProcessedSource(sourceFk)) {

												doCount(count++, modCount, pluralString);

												// Add to processed sourceFk's since sourceFk's can be scanned more than once.

												state.addToProcessedSources(sourceFk);

												// Query the database for all entries in table 'Occurrence' with the sourceFk just determined.

												Set<Integer> occurrenceIds = getOccurrenceIds(sourceFk, state);

												// Insert as many entries in database table 'OccurrenceSource' as occurrenceId's were determined.

												insertColumns(stmt, reference, sourceFk, occurrenceIds);

											}

										}

									}

								}

							}

						}

					}

				}

				state.clearAlreadyProcessedSources();

				// 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 " + pluralString + " left to fetch.");

			}

			list = null;

			// Commit transaction

			commitTransaction(txStatus);

			logger.error("Committed transaction.");

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

			if (!success){

				state.setUnsuccessfull();

			}

			return;

		} catch (SQLException e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.setUnsuccessfull();

			return;

		}

	}

	/**

	 * Inserts columns in the database table OccurrenceSource.

	 * @param stmt The prepared statement.

	 * @param reference {@link Reference Reference}.

	 * @param sourceFk The SourceFk.

	 * @param occurrenceIds A {@link java.util.Set Set} of OccurrenceId's.

	 */

	private void insertColumns(PreparedStatement stmt, Reference reference,

			Integer sourceFk, Set<Integer> occurrenceIds) {

		for (Integer occurrenceId : occurrenceIds) {

			try {

				stmt.setInt(1, occurrenceId);

				stmt.setInt(2, sourceFk);

				stmt.setString(3, getSourceNameCache(reference));

				stmt.setString(4, null); // TODO: This is the name of the former taxon (accepted taxon as well as synonym) the source was associated to. How can we get a hand on it?

				stmt.execute();

			} catch (SQLException e) {

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

				e.printStackTrace();

			}

		}

	}

	/**

	 * Returns a Set of OccurrenceId's associated to a given SourceFk.

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

	 * @return Existing OccurrenceId's for a given SourceFk.

	 */

	private static Set<Integer> getOccurrenceIds(Integer sourceFk, PesiExportState state) {

		String occurrenceSql = "Select OccurrenceId From Occurrence where SourceFk = ?";

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

		PreparedStatement stmt = null;

		Set<Integer> occurrenceIds = new HashSet();

		try {

			stmt = con.prepareStatement(occurrenceSql);

			stmt.setInt(1, sourceFk);

			ResultSet resultSet = stmt.executeQuery();

			while (resultSet.next()) {

				occurrenceIds.add(resultSet.getInt(1));

			}

		} catch (SQLException e) {

			logger.error("SQLException during getOccurrenceId invoke. (2)");

			e.printStackTrace();

		}

		return occurrenceIds;

	}

	/**

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

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

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

	 */

	protected boolean doDelete(PesiExportState state) {

		PesiExportConfigurator pesiConfig = (PesiExportConfigurator) state.getConfig();

		String sql;

		Source destination =  pesiConfig.getDestination();

		// Clear OccurrenceSource

		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().isDoOccurrenceSource() && state.getConfig().isDoOccurrence() && state.getConfig().getDoReferences().equals(DO_REFERENCES.ALL));

	}

	/**

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

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

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

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

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

		Integer result = null;

		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(Reference.class)) {

			Reference reference = CdmBase.deproxy(entity, Reference.class);

			result = state.getDbId(reference);

		}

		return result;

	}

	/**

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

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

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

	 * @see MethodMapper

	 */

	private static String getSourceNameCache(AnnotatableEntity entity) {

		String result = null;

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

			Reference reference = CdmBase.deproxy(entity, Reference.class);

			result = reference.getTitle();

		}

		return result;

	}

	/**

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

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

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getOldTaxonName(AnnotatableEntity entity) {

		// TODO: This is the name of the former taxon (accepted taxon as well as synonym) the source was associated to.

		return null;

	}

	/**

	 * Returns the CDM to PESI specific export mappings.

	 * @return The {@link PesiExportMapping PesiExportMapping}.

	 */

	private PesiExportMapping getMapping() {

		PesiExportMapping mapping = new PesiExportMapping(dbTableName);

		// These mapping are not used.

		mapping.addMapper(MethodMapper.NewInstance("OccurrenceFk", this.getClass(), "getOccurrenceFk", standardMethodParameter, PesiExportState.class));

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

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

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

		return mapping;

	}

}