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 static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.T_STATUS_ACCEPTED;

import static eu.etaxonomy.cdm.io.faunaEuropaea.FaunaEuropaeaTransformer.T_STATUS_NOT_ACCEPTED;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

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.berlinModel.CdmOneToManyMapper;

import eu.etaxonomy.cdm.io.berlinModel.CdmStringMapper;

import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.agent.Team;

import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.babadshanjan

 * @created 12.05.2009

 * @version 1.0

 */

@Component

public class FaunaEuropaeaRefImport extends FaunaEuropaeaImportBase {

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

	/* Interval for progress info message when retrieving taxa */

	private int modCount = 10000;

	/* (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 References 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) {				

		Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();

		MapWrapper<TeamOrPersonBase> authorStore = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.TEAM_STORE);

		MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);

		MapWrapper<ReferenceBase> refStore = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);

		TransactionStatus txStatus = null;

		FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();

		Source source = fauEuConfig.getSource();

		String namespace = "Reference";

		boolean success = true;

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

		try {

			String strQuery = 

				" SELECT MAX(TAX_ID) AS TAX_ID FROM dbo.Taxon ";

			ResultSet rs = source.getResultSet(strQuery);

			while (rs.next()) {

				int maxTaxonId = rs.getInt("TAX_ID");

//				highestTaxonIndex = maxTaxonId;

			}

			strQuery = 

				" SELECT Reference.*, TaxRefs.* " + 

                " FROM Reference INNER JOIN TaxRefs ON Reference.ref_id = TaxRefs.trf_ref_id " +

                " WHERE (1=1)" + 

                " ORDER BY TaxRefs.trf_tax_id";

			rs = source.getResultSet(strQuery) ;

			int i = 0;

			while (rs.next()) {

				if ((i++ % modCount) == 0 && i!= 1 ) { 

					if(logger.isInfoEnabled()) {

						logger.info("References handled: " + (i-1)); 

					}

				}

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

				int refId = rs.getInt("ref_id");

				String refAuthor = rs.getString("ref_author");

				String year = rs.getString("ref_year");

				String title = rs.getString("ref_title");

				String refSource = rs.getString("ref_source");

				String page = rs.getString("trf_page");

				StrictReferenceBase<?> reference = null;

				TeamOrPersonBase<Team> author = null;

				try {

					reference = Generic.NewInstance();

					reference.setTitleCache(title);

					reference.setDatePublished(ImportHelper.getDatePublished(year));

					author = Team.NewInstance();

					author.setTitleCache(refAuthor);

					ImportHelper.setOriginalSource(reference, fauEuConfig.getSourceReference(), refId, namespace);

					ImportHelper.setOriginalSource(author, fauEuConfig.getSourceReference(), refId, namespace);

					// Create references

					if (!refStore.containsId(refId)) {

						if (reference == null) {

							logger.warn("Reference is null");

						}

						refStore.put(refId, reference);

						if (logger.isDebugEnabled()) { 

							logger.debug("Stored reference (" + refId + ") " + refAuthor); 

						}

					} else {

						if (logger.isDebugEnabled()) { 

							logger.debug("Not imported reference with duplicated ref_id (" + refId + 

									") " + refAuthor);

						}

						continue;

					}

					// Create authors

					if (!authorStore.containsId(refId)) { // TODO: Don't insert identical author names

						if (refAuthor == null) {

							logger.warn("Reference author is null");

						}

						authorStore.put(refId, author);

						if (logger.isDebugEnabled()) { 

							logger.debug("Stored author (" + refId + ") " + refAuthor); 

						}

					} else {

						if (logger.isDebugEnabled()) { 

							logger.debug("Not imported author with duplicated aut_id (" + refId + 

									") " + refAuthor);

						}

					}

				} catch (Exception e) {

					logger.warn("An exception occurred when creating reference with id " + refId + 

					". Reference could not be saved.");

				}

				try {

					// Create descriptions

					Taxon taxon;

					TaxonBase taxonBase = taxonStore.get(taxonId);

					if (taxonBase == null) { continue; }

					boolean isSynonym = taxonBase.isInstanceOf(Synonym.class);

					if (isSynonym){

						Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);

						taxon = syn.getAcceptedTaxa().iterator().next();

					}else{

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

					}

					TaxonDescription taxonDescription = null;

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

					if (descriptions.size() > 0) {

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

					} else {

						taxonDescription = TaxonDescription.NewInstance();

						taxon.addDescription(taxonDescription);

					}

					TextData textData = TextData.NewInstance(Feature.CITATION());

					if (isSynonym){

						Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);

						textData.setNameUsedInReference(syn.getName());

					}

					textData.setCitation(reference);

					textData.setCitationMicroReference(page);

					taxonDescription.addElement(textData);

				} catch (Exception e) {

					logger.warn("An exception occurred when creating description for reference " + refId + 

					". Taxon description could not be saved.");

					e.printStackTrace();

				}

			}

			if(logger.isInfoEnabled()) { logger.info("Saving references ..."); }

			if (state.getConfig().isUseTransactions()) {

				txStatus = startTransaction();

			}

			// save taxa, references, and authors

			success = saveTaxa(state, state.getHighestTaxonIndex(), state.getConfig().getLimitSave());

			getReferenceService().saveReferenceAll(refStore.objects());

			getAgentService().saveAgentAll(authorStore.objects());

			if (state.getConfig().isUseTransactions()) {

				commitTransaction(txStatus);

			}

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

		} catch (SQLException e) {

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

			success = false;

		}

		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().getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);

	}

}