EDIT

/**

* Copyright (C) 2007 EDIT

* 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.

*/

public class AlgaTerraFactEcologyImport  extends AlgaTerraSpecimenImportBase {

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

	private static int modCount = 5000;

	private static final String pluralString = "determinations";

	public AlgaTerraFactEcologyImport(){

		super(dbTableName, pluralString);

	}

	@Override

	protected String getIdQuery(BerlinModelImportState state) {

				+ " WHERE f.FactCategoryFk = 202 "

				+ " ORDER BY pt.RIdentifier, f.FactId ";

		return result;

	@Override

	protected String getRecordQuery(BerlinModelImportConfigurator config) {

                 " LEFT JOIN PTaxon pt ON f.PTNameFk =pt.PTNameFk AND f.PTRefFk = pt.PTRefFk " +

            + " ORDER BY pt.RIdentifier, f.FactId "

            ;

		return strQuery;

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {

		boolean success = true;

		AlgaTerraImportState state = (AlgaTerraImportState)bmState;

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

		ResultSet rs = partitioner.getResultSet();

		try {

			int i = 0;

			//for each reference

            while (rs.next()){

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

				Integer taxonId = nullSafeInt(rs, "taxonId");

				int factId = rs.getInt("FactId");

				Integer ecoFactId = nullSafeInt(rs, "ExtensionFk");

				String recordBasis = rs.getString("RecordBasis");

				try {

					//source ref

					DerivedUnit ecoFact = ecoFactDerivedUnitMap.get(String.valueOf(ecoFactId));

					if (ecoFact == null){

						logger.warn("EcoFact is null for EcoFact: " + CdmUtils.Nz(ecoFactId) + ", taxonId: " + CdmUtils.Nz(taxonId));

					}

					//description element

					if (taxonId != null){

						if(taxon != null){

							DerivedUnit identifiedSpecimen = makeIdentifiedSpecimen(ecoFact, recordBasis, taxonId, ecoFactId);

							makeDetermination(state, rs, taxon, identifiedSpecimen, factId, partitioner);

							makeIndividualsAssociation(state, taxon, sourceRef, identifiedSpecimen);

							this.doIdCreatedUpdatedNotes(state, identifiedSpecimen, rs, factId, getDerivedUnitNameSpace());

							identifiedSpecimen.setCacheStrategy(new DerivedUnitFacadeCacheStrategy());

					}else{

						logger.warn("No taxon defined for ecology fact: " +  factId);

					}

				} catch (Exception e) {

					logger.warn("Exception in FactEcology: FactId " + factId + ". " + e.getMessage());

					e.printStackTrace();

            }

//            logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );

			logger.warn("Taxa to save: " + taxaToSave.size());

			return success;

		} catch (SQLException e) {

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

			return false;

		}

	}

		TaxonDescription taxonDescription = getTaxonDescription(state, taxon, sourceRef);

		IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();

		Feature feature = makeFeature(identifiedSpecimen.getRecordBasis(), state);

		indAssociation.setAssociatedSpecimenOrObservation(identifiedSpecimen);

		indAssociation.setFeature(feature);

	}

	private void makeDetermination(AlgaTerraImportState state, ResultSet rs, Taxon taxon, DerivedUnit identifiedSpecimen, int factId, ResultSetPartitioner partitioner) throws SQLException {

		Date identifiedWhen = rs.getDate("IdentifiedWhen");

		Date identifiedWhenEnd = rs.getDate("IdentiedWhenEnd");

		String identifiedBy = rs.getString("IdentifiedBy");

		String identificationReference = rs.getString("IdentificationReference");

		Integer refFk = nullSafeInt(rs, "IdentifidationRefFk");

		DeterminationEvent determination = DeterminationEvent.NewInstance(taxon, identifiedSpecimen);

		TimePeriod determinationPeriod = TimePeriod.NewInstance(identifiedWhen, identifiedWhenEnd);

		determination.setTimeperiod(determinationPeriod);

		determination.setPreferredFlag(! restrictedFlag);

		TeamOrPersonBase<?> author = getAuthor(identifiedBy);

		determination.setDeterminer(author);

		if (refFk != null){

			if (ref != null){

				determination.addReference(ref);

			}else{

				logger.warn("IdentificationReference exists without IdentificationRefFk. FactId: "+  factId);

			}

		}

		//TODO

	}

	private DerivedUnit makeIdentifiedSpecimen(DerivedUnit ecoFact, String recordBasis, Integer taxonId, Integer ecoFactId) {

		//TODO event type

		DerivationEvent event = DerivationEvent.NewInstance();

			logger.warn(String.format(message, recordBasis, taxonId));

			derivedUnitType = SpecimenOrObservationType.PreservedSpecimen;

		}

		DerivedUnit result = DerivedUnit.NewInstance(derivedUnitType);

		result.setDerivedFrom(event);

		if (ecoFact == null){

		return FACT_ECOLOGY_NAMESPACE;

	}

		return null;

	}

	 * @param state

	 * @param ecoFactId

	 * @param derivedUnitMap

	 * @return

	 */

	private DerivedUnitFacade getDerivedUnit(AlgaTerraImportState state, int ecoFactId, Map<String, DerivedUnit> derivedUnitMap, SpecimenOrObservationType type) {

				facade = DerivedUnitFacade.NewInstance(type);

			}

		}

		return facade;

	}

		Class<?> cdmClass;

		Set<String> idSet;

		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();

		try{

			Set<String> taxonIdSet = new HashSet<String>();

			Set<String> extensionFkSet = new HashSet<String>();

			Set<String> referenceIdSet = new HashSet<String>();

			while (rs.next()){

				handleForeignKey(rs, taxonIdSet, "taxonId");

				handleForeignKey(rs, extensionFkSet, "extensionFk");

				handleForeignKey(rs, referenceIdSet, "IdentifidationRefFk");

			}

			//taxon map

			nameSpace = BerlinModelTaxonImport.NAMESPACE;

			cdmClass = TaxonBase.class;

			Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, referenceMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

	protected boolean isIgnore(BerlinModelImportState state){

		return ! ((AlgaTerraImportState)state).getAlgaTerraConfigurator().isDoFactEcology();

	}

}