EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy 

* http://www.e-taxonomy.eu

* 

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.pesi.faunaEuropaea;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.database.ICdmDataSource;

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

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

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

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

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

/**

 * @author a.babadshanjan

 * @created 21.08.2010

 * @version 1.0

 */

@Component

public class FaunaEuropaeaAdditionalTaxonDataImport extends FaunaEuropaeaImportBase  {

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

//	private static final String parentPluralString = "Synonyms";

	private static final String pluralString = "InfraGenericEpithets";

	//private static final String acceptedTaxonUUID = "A9C24E42-69F5-4681-9399-041E652CF338"; // any accepted taxon uuid, taken from original fauna europaea database

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean doCheck(FaunaEuropaeaImportState state) {

		boolean result = true;

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		logger.warn("Checking for Taxa not yet fully implemented");

//		result &= checkTaxonStatus(fauEuConfig);

		return result;

	}

	/** 

	 * Import taxa from FauEU DB

	 */

	protected void doInvoke(FaunaEuropaeaImportState state) {				

		if(logger.isInfoEnabled()) {

			logger.info("Started creating " + pluralString + "...");

		}

		processAdditionalInfraGenericEpithets(state);

		logger.info("The End is Nigh... " + pluralString + "...");

		return;

	}

	/**

	 * 

	 * @param state

	 * @return

	 */

	private void processAdditionalInfraGenericEpithets(FaunaEuropaeaImportState state) {

		int count = 0;

		int pageSize = 1000;

		Set<UUID> uuidSet = new HashSet<UUID>();

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		ICdmDataSource destination = fauEuConfig.getDestination();

		TransactionStatus txStatus = null;

		List<TaxonNameBase> taxonNames = null;

		txStatus = startTransaction(false);

		String selectQuery = "SELECT t.uuid from TaxonNameBase t INNER JOIN " +

				"TaxonNameBase t2 ON t.GenusOrUninomial = t2.GenusOrUninomial AND t.SpecificEpithet = t2.SpecificEpithet " +

				"WHERE t.InfraGenericEpithet IS NULL AND t.rank_id = 764 AND t2.rank_id = 766 AND t2.InfraGenericEpithet IS NOT NULL";

		logger.info("Retrieving TaxonNames...");

		ResultSet resultSet;

		try {

			resultSet = destination.executeQuery(selectQuery);

			// Collect UUIDs

			while (resultSet.next()) {

				uuidSet.add(UUID.fromString(resultSet.getString("UUID")));

			}

		} catch (SQLException e) {

			logger.error("An error occured: ", e);

		}

		// Fetch TaxonName objects for UUIDs

		if (!uuidSet.isEmpty()){

			taxonNames = getNameService().find(uuidSet);

			for (TaxonNameBase taxonName : taxonNames) {

				// Check whether its taxonName has an infraGenericEpithet

				if (taxonName != null && (taxonName.isInstanceOf(NonViralName.class))) {

					NonViralName targetNonViralName = CdmBase.deproxy(taxonName, NonViralName.class);

					String infraGenericEpithet = targetNonViralName.getInfraGenericEpithet();

					if (infraGenericEpithet == null) {

						String genusOrUninomial = targetNonViralName.getGenusOrUninomial();

						String specificEpithet = targetNonViralName.getSpecificEpithet();

						List<TaxonBase> foundTaxa = getTaxonService().listTaxaByName(Taxon.class, genusOrUninomial, "*", specificEpithet, 

								"*", null, pageSize, 1);

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

							// one matching Taxon found

							TaxonBase taxon = foundTaxa.iterator().next();

							if (taxon != null) {

								TaxonNameBase name = taxon.getName();

								if (name != null && name.isInstanceOf(NonViralName.class)) {

									NonViralName nonViralName = CdmBase.deproxy(name, NonViralName.class);

									infraGenericEpithet = nonViralName.getInfraGenericEpithet();

									// set infraGenericEpithet

	//									targetNonViralName.setInfraGenericEpithet(infraGenericEpithet);

									logger.debug("Added an InfraGenericEpithet to this TaxonName: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");

									count++;

								}

							}

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

							logger.warn("Multiple taxa match search criteria: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");

							for (TaxonBase foundTaxon : foundTaxa) {

								logger.warn(foundTaxon.getUuid() + ", " + foundTaxon.getTitleCache());

							}

						} else if (foundTaxa.size() == 0) {

	//							logger.error("No matches for search criteria: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");

						}

					}

				}

			}

		}else {

			logger.debug("There are no additional infrageneric epithets!");

		}

		// Commit transaction

		commitTransaction(txStatus);

		logger.info("Committed transaction.");

		return;

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(FaunaEuropaeaImportState state) {

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

	}

}