EDIT

/**

 * 

 */

package eu.etaxonomy.cdm.io.berlinModel;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import org.apache.log4j.Logger;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.*;

import eu.etaxonomy.cdm.api.application.CdmApplicationController;

import eu.etaxonomy.cdm.api.service.ITaxonService;

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 *

 */

public class BerlinModelOccurrenceIO  extends BerlinModelIOBase {

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

	private static int modCount = 10000;

	public BerlinModelOccurrenceIO(){

		super();

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean doCheck(IImportConfigurator config){

		boolean result = true;

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

		//result &= checkArticlesWithoutJournal(bmiConfig);

		//result &= checkPartOfJournal(bmiConfig);

		return result;

	}

	/* (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(IImportConfigurator config, CdmApplicationController cdmApp, 

			Map<String, MapWrapper<? extends CdmBase>> stores){

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

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

		BerlinModelImportConfigurator bmiConfig = (BerlinModelImportConfigurator)config;

		if (true){

			return false;

		}

		Set<TaxonBase> taxonStore = new HashSet<TaxonBase>();

		Source source = bmiConfig.getSource();

		ITaxonService taxonService = cdmApp.getTaxonService();

		String dbAttrName;

		String cdmAttrName;

		logger.info("start makeFacts ...");

		boolean delete = bmiConfig.isDeleteAll();

		try {

			//get data from database

			String strQuery = 

					" SELECT xxx.*, PTaxon.RIdentifier as taxonId " + 

					" FROM Fact INNER JOIN " +

                      	" dbo.PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk "+

                    " WHERE (1=1)";

			ResultSet rs = source.getResultSet(strQuery) ;

			int i = 0;

			//for each reference

			while (rs.next()){

				if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("Facts handled: " + (i-1));}

				int occurrenceId = rs.getInt("occId");

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

				int factRefFk = rs.getInt("factRefFk");

				int categoryFk = rs.getInt("factCategoryFk");

				TaxonBase taxonBase = taxonMap.get(taxonId);

				if (taxonBase != null){

					Taxon taxon;

					if ( taxonBase instanceof Taxon ) {

						taxon = (Taxon) taxonBase;

					}else{

						logger.warn("TaxonBase for Occurrence " + occurrenceId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());

						continue;

					}

					TaxonDescription taxonDescription = TaxonDescription.NewInstance();

					taxon.addDescription(taxonDescription);

					//commonNames

					String commonNameString;

					if (taxon.getName() != null){

						commonNameString = "Common " + taxon.getName().getTitleCache(); 

					}else{

						commonNameString = "Common (null)";

					}

					Language language = bmiConfig.getFactLanguage();

					language = null;

					CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, language);

					taxonDescription.addElement(commonName);

					//TODO

					//etc.

					taxonStore.add(taxon);

				}else{

					//TODO

					logger.warn("Taxon for Fact " + occurrenceId + " does not exist in store");

				}

				//put

			}

			logger.info("Taxa to save: " + taxonStore.size());

			taxonService.saveTaxonAll(taxonStore);	

			logger.info("end makeFacts ...");

			return true;

		} catch (SQLException e) {

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

			return false;

		}

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(IImportConfigurator config){

		return ! config.isDoOccurrence();

	}

}