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.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.Source;

//import eu.etaxonomy.cdm.io.profiler.ProfilerController;

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

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

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;

//import com.yourkit.api.Controller;

/**

 * @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.IoStateBase)

	 */

	@Override

	protected void doInvoke(FaunaEuropaeaImportState state) {	

		/*

		logger.warn("Start distribution doInvoke");

		ProfilerController.memorySnapshot();

		*/

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

		UUID noDataUuid;

		/* 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;

		TransactionStatus txStatus = null;

		//txStatus = startTransaction();

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

		//commitTransaction(txStatus);	

		FaunaEuropaeaTransformer.setUUIDs(noDataUuid);

		txStatus = null;

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		Source source = fauEuConfig.getSource();

        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 orderBy = " ORDER BY distribution.dis_tax_id";

		String countQuery = 

			selectCount + fromClause;

		String selectQuery = 

			selectColumns + fromClause + orderBy;

		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);

			}

			//int taxonId;

			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"); 

					}

				}

				//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.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);

					fauEuDistributionTaxon = null;

				} 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 {

						commitTaxaAndDistribution(state, noDataUuid, taxonUuids, fauEuTaxonMap, txStatus);

						taxonUuids = null;

						taxonList = null;

						fauEuTaxonMap = null;

					} catch (Exception e) {

						logger.error("Commit of taxa and distributions failed" + e.getMessage());

						e.printStackTrace();

					}

					if(logger.isInfoEnabled()) { logger.info("i = " + i + " - Transaction committed");}

				}

			}	

			if (taxonUuids != null){

				try {

					commitTaxaAndDistribution(state, noDataUuid, taxonUuids, fauEuTaxonMap, txStatus);

					taxonUuids = null;

					taxonList = null;

					fauEuTaxonMap = null;

				} catch (Exception e) {

					logger.error("Commit of taxa and distributions failed");

					logger.error(e.getMessage());

					e.printStackTrace();

				}

			}

		} catch (SQLException e) {

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

			state.setUnsuccessfull();

		}

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

		return;

	}

	private void commitTaxaAndDistribution(

			FaunaEuropaeaImportState state, UUID noDataUuid,

			Set<UUID> taxonUuids,

			Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap,

			TransactionStatus txStatus) throws Exception {

		 List<TaxonBase> taxonList = prepareTaxaAndDistribution(getTaxonService().find(taxonUuids), fauEuTaxonMap, noDataUuid, state);

		getTaxonService().save(taxonList);

		commitTransaction(txStatus);

	}

	private List<TaxonBase> prepareTaxaAndDistribution(List<TaxonBase> taxonList, Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap, UUID noData, FaunaEuropaeaImportState state) throws Exception{

		Distribution newDistribution = null;

		NamedArea namedArea;

		PresenceAbsenceTermBase<?> presenceAbsenceStatus;

		FaunaEuropaeaDistributionTaxon fauEuHelperTaxon;

		UUID taxonUuid;

		TaxonDescription taxonDescription;

		Taxon taxon;

		for (TaxonBase<?> taxonBase : taxonList) {

			if (taxonBase != null) {

				if (taxonBase instanceof Taxon) {

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

				} else {

					logger.warn("TaxonBase (" + taxonBase.getId() + " is not of type Taxon but: " 

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

					continue;

				}

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

				if (descriptionSet.size() > 0) {

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

				} else {

					taxonDescription = TaxonDescription.NewInstance();

					taxon.addDescription(taxonDescription);

				}

				taxonUuid = taxonBase.getUuid();

				fauEuHelperTaxon= fauEuTaxonMap.get(taxonUuid);

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

					namedArea = null;

					newDistribution = null;

					presenceAbsenceStatus = null;

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

						presenceAbsenceStatus = (PresenceAbsenceTermBase<?>)getTermService().find(noData);

					}else{

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

					}

					namedArea = FaunaEuropaeaTransformer.areaId2TdwgArea(fauEuHelperDistribution);

					if (namedArea == null){

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

						if (areaUuid == null){

							logger.warn("Area " + fauEuHelperDistribution.getAreaCode() + "not found in FE transformer");

						}

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

					}

					newDistribution = Distribution.NewInstance(namedArea, presenceAbsenceStatus);

					newDistribution.setCreated(null);

					taxonDescription.addElement(newDistribution);

				}

			}

		}

		return taxonList;

	}

	/* (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();

	}

}