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.faunaEuropaea;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

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.io.common.CdmImportBase;

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.babadshanjan

 * @created 12.05.2009

 * @version 1.0

 */

@Component

public class FaunaEuropaeaDistributionImport extends FaunaEuropaeaImportBase {

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

	/* (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 Distributions not yet fully implemented");

		result &= checkReferenceStatus(fauEuConfig);

		return result;

	}

	private boolean checkReferenceStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {

		boolean result = true;

//		try {

			Source source = fauEuConfig.getSource();

			String sqlStr = "";

	//		ResultSet rs = source.getResultSet(sqlStr);

			return result;

//		} catch (SQLException e) {

//			e.printStackTrace();

//			return false;

//		}

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)

	 */

	@Override

	protected boolean doInvoke(FaunaEuropaeaImportState state) {	

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

		UUID noData;

		UUID doubtfullPresent;

		/* Taxon store for retrieving taxa from and saving taxa to CDM */

		List<TaxonBase> taxonList = null;

		/* UUID store as input for retrieving taxa from CDM */

		Set<UUID> taxonUuids = null;

		/* Store to hold helper objects */

		Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap = null;

//		Map<UUID, TaxonBase<?>> taxonMap = null;

//		Set<TaxonBase<?>> taxonSet = null;

		TransactionStatus txStatus = null;

		txStatus = startTransaction();

			noData = getTermService().save(PresenceTerm.NewInstance("no data", "no data", "nod"));

			//doubtfullPresent = getTermService().save(PresenceTerm.NewInstance("doubtfull present", "doubtfull present", "dp"));

			HashMap<String, UUID> uuids = new HashMap<String, UUID>();

			uuids.put("noData", noData);

			logger.debug("uuid no Data: " + noData.toString() );

			//uuids.put("doubtfullPresent", doubtfullPresent);

			FaunaEuropaeaTransformer.setUUIDs(uuids);

		commitTransaction(txStatus);

		txStatus = null;

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		Source source = fauEuConfig.getSource();

		String namespace = "Distribution";

		boolean success = true;

        int i = 0;

		String selectCount = 

			" SELECT count(*) ";

		String selectColumns = 

			" SELECT distribution.*, Area.*, Taxon.UUID ";

		String fromClause = 

			" FROM distribution INNER JOIN " +

            " Area ON distribution.dis_ara_id = Area.ara_id INNER JOIN " +

            " Taxon ON distribution.dis_tax_id = Taxon.TAX_ID ";

		String countQuery = 

			selectCount + fromClause;

		String selectQuery = 

			selectColumns + fromClause;

//		String strQuery = 

//		" SELECT distribution.*, Area.*, Taxon.UUID " + 

//		" FROM distribution INNER JOIN " +

//        " Area ON distribution.dis_ara_id = Area.ara_id INNER JOIN " +

//        " Taxon ON distribution.dis_tax_id = Taxon.TAX_ID ";

		if(logger.isInfoEnabled()) { logger.info("Start making distributions..."); }

		try {

			ResultSet rs = source.getResultSet(countQuery);

			rs.next();

			int count = rs.getInt(1);

			rs = source.getResultSet(selectQuery);

			if (logger.isInfoEnabled()) {

				logger.info("Number of rows: " + count);

				logger.info("Count Query: " + countQuery);

				logger.info("Select Query: " + selectQuery);

			}

			while (rs.next()) {

				if ((i++ % limit) == 0) {

					txStatus = startTransaction();

					taxonUuids = new HashSet<UUID>(limit);

					fauEuTaxonMap = new HashMap<UUID, FaunaEuropaeaDistributionTaxon>(limit);

					if(logger.isInfoEnabled()) {

						logger.info("i = " + i + " - Distribution import transaction started"); 

					}

				}

				int taxonId = rs.getInt("dis_tax_id");

				int disId = rs.getInt("dis_id");

				int occStatusId = rs.getInt("dis_present");

				int areaId = rs.getInt("ara_id");

				String areaName = rs.getString("ara_name");

				String areaCode = rs.getString("ara_code");

				int extraLimital = rs.getInt("ara_extralimital");

				UUID currentTaxonUuid = null;

				if (resultSetHasColumn(rs,"UUID")){

					currentTaxonUuid = UUID.fromString(rs.getString("UUID"));

				} else {

					currentTaxonUuid = UUID.randomUUID();

				}

				FaunaEuropaeaDistribution fauEuDistribution = new FaunaEuropaeaDistribution();

//				fauEuDistribution.setTaxonUuid(currentTaxonUuid);

//				fauEuDistribution.setTaxonId(taxonId);

				fauEuDistribution.setDistributionId(disId);

				fauEuDistribution.setOccurrenceStatusId(occStatusId);

				fauEuDistribution.setAreaId(areaId);

				fauEuDistribution.setAreaName(areaName);

				fauEuDistribution.setAreaCode(areaCode);

				fauEuDistribution.setExtraLimital(extraLimital);

				if (!taxonUuids.contains(currentTaxonUuid)) {

					taxonUuids.add(currentTaxonUuid);

					FaunaEuropaeaDistributionTaxon fauEuDistributionTaxon = 

						new FaunaEuropaeaDistributionTaxon(currentTaxonUuid);

					fauEuTaxonMap.put(currentTaxonUuid, fauEuDistributionTaxon);

				} else {

					if (logger.isTraceEnabled()) { 

						logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");

						continue;

					}

				}

				fauEuTaxonMap.get(currentTaxonUuid).addDistribution(fauEuDistribution);

				if (((i % limit) == 0 && i != 1 ) || i == count) { 

					try {

						taxonList = getTaxonService().find(taxonUuids);

						for (TaxonBase taxonBase : taxonList) {

							if (taxonBase != null) {

								Taxon taxon;

								if (taxonBase instanceof Taxon) {

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

								} else {

									logger.warn("TaxonBase (" + taxonId + " is not of type Taxon but: " 

											+ taxonBase.getClass().getSimpleName());

									continue;

								}

								TaxonDescription taxonDescription;

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

								if (descriptionSet.size() > 0) {

									taxonDescription = descriptionSet.iterator().next(); 

								} else {

									taxonDescription = TaxonDescription.NewInstance();

									taxon.addDescription(taxonDescription);

								}

								UUID taxonUuid = taxonBase.getUuid();

								FaunaEuropaeaDistributionTaxon fauEuHelperTaxon = fauEuTaxonMap.get(taxonUuid);

								for (FaunaEuropaeaDistribution fauEuHelperDistribution : fauEuHelperTaxon.getDistributions()) {

									PresenceAbsenceTermBase<?> presenceAbsenceStatus;

									if (fauEuHelperDistribution.getOccurrenceStatusId() != 0 && fauEuHelperDistribution.getOccurrenceStatusId() != 2 && fauEuHelperDistribution.getOccurrenceStatusId() != 1){

										presenceAbsenceStatus = (PresenceAbsenceTermBase)getTermService().find(noData);

									}else{

										presenceAbsenceStatus 

										= FaunaEuropaeaTransformer.occStatus2PresenceAbsence(fauEuHelperDistribution.getOccurrenceStatusId());

									}

									NamedArea namedArea = 

										FaunaEuropaeaTransformer.areaId2TdwgArea(fauEuHelperDistribution);

									if (namedArea == null){

										UUID areaUuid= FaunaEuropaeaTransformer.getUUIDByAreaAbbr(fauEuHelperDistribution.getAreaCode());

										namedArea = getNamedArea(state, areaUuid, fauEuHelperDistribution.getAreaName(), fauEuHelperDistribution.getAreaName(), fauEuHelperDistribution.getAreaCode(), null, null);

									}

									Distribution newDistribution = Distribution.NewInstance(namedArea, presenceAbsenceStatus);

									newDistribution.setType(Feature.DISTRIBUTION());

									taxonDescription.addElement(newDistribution);

								}

							}

						}

						getTaxonService().save(taxonList);

						taxonUuids = null;

						taxonList = null;

						fauEuTaxonMap = null;

						commitTransaction(txStatus);

						if(logger.isInfoEnabled()) { 

							logger.info("i = " + i + " - Transaction committed"); 

						}

					} catch (Exception e) {

						logger.warn("An exception occurred when creating distribution with id " + disId);

						e.printStackTrace();

					}

				}

			}		

		} catch (SQLException e) {

			logger.error("SQLException:" +  e);

			return false;

		}

		if(logger.isInfoEnabled()) { logger.info("End making distributions..."); }

		return success;

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(FaunaEuropaeaImportState state){

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

	}

}