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.algaterra;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType;

import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraDnaImportValidator;

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.molecular.DnaSample;

import eu.etaxonomy.cdm.model.molecular.Locus;

import eu.etaxonomy.cdm.model.molecular.Sequence;

import eu.etaxonomy.cdm.model.occurrence.Collection;

import eu.etaxonomy.cdm.model.occurrence.FieldObservation;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

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

/**

 * @author a.mueller

 * @created 01.09.2012

 */

@Component

public class AlgaTerraDnaImport  extends AlgaTerraSpecimenImportBase {

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

	private static int modCount = 5000;

	private static final String pluralString = "dna facts";

	private static final String dbTableName = "DNAFact";  //??  

	public AlgaTerraDnaImport(){

		super(dbTableName, pluralString);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()

	 */

	@Override

	protected String getIdQuery(BerlinModelImportState state) {

		String result = " SELECT df.DNAFactId " + 

				" FROM DNAFact df INNER JOIN Fact f ON  f.ExtensionFk = df.DNAFactID " +

				" ORDER BY df.DNAFactID ";

		return result;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)

	 */

	@Override

	protected String getRecordQuery(BerlinModelImportConfigurator config) {

			String strQuery =   

	            " SELECT * " +

	            " FROM DNAFact df INNER JOIN Fact f ON  f.ExtensionFk = df.DNAFactID " +

	              " WHERE (df.DNAFactId IN (" + ID_LIST_TOKEN + ")  )"  

	            + " ORDER BY DNAFactID "

            ;

		return strQuery;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)

	 */

	public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {

		boolean success = true;

		AlgaTerraImportState state = (AlgaTerraImportState)bmState;

		try {

//			makeVocabulariesAndFeatures(state);

		} catch (Exception e1) {

			logger.warn("Exception occurred when trying to create Ecofact vocabularies: " + e1.getMessage());

			e1.printStackTrace();

		}

		Set<SpecimenOrObservationBase> objectsToSave = new HashSet<SpecimenOrObservationBase>();

		//TODO do we still need this map? EcoFacts are not handled separate from Facts.

		//However, they have duplicates on derived unit level. Also check duplicateFk. 

		Map<String, FieldObservation> ecoFactFieldObservationMap = (Map<String, FieldObservation>) partitioner.getObjectMap(ECO_FACT_FIELD_OBSERVATION_NAMESPACE);

		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));}

				int dnaFactId = rs.getInt("DNAFactId");

				int ecoFactFk = nullSafeInt(rs, "EcoFactFk");

				String sequenceStr = rs.getString("PlainSequence");

				String keywordsStr = rs.getString("Keywords");

				String locusStr = rs.getString("Locus");

				String definitionStr = rs.getString("Definition");

				try {

					//source ref

					Reference<?> sourceRef = state.getTransactionalSourceReference();

					//facade

					DnaSample dnaSample = DnaSample.NewInstance();

					Sequence sequence = Sequence.NewInstance(sequenceStr);

					dnaSample.addSequences(sequence);

					Locus locus = Locus.NewInstance(locusStr, definitionStr);

					sequence.setLocus(locus);

//					handleFirstDerivedSpecimen(rs, facade, state, partitioner);

//					handleEcoFactSpecificDerivedUnit(rs,facade, state);

					objectsToSave.add(dnaSample); 

				} catch (Exception e) {

					logger.warn("Exception in ecoFact: ecoFactId " + dnaFactId + ". " + e.getMessage());

					e.printStackTrace();

				} 

            }

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

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

			getOccurrenceService().save(objectsToSave);	

			return success;

		} catch (SQLException e) {

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

			return false;

		}

	}

	protected String getDerivedUnitNameSpace(){

		return ECO_FACT_DERIVED_UNIT_NAMESPACE;

	}

	protected String getFieldObservationNameSpace(){

		return ECO_FACT_FIELD_OBSERVATION_NAMESPACE;

	}

	private DerivedUnitType makeDerivedUnitType(String recordBasis) {

		DerivedUnitType result = null;

		if (StringUtils.isBlank(recordBasis)){

			result = DerivedUnitType.DerivedUnit;

		} else if (recordBasis.equalsIgnoreCase("FossileSpecimen")){

			result = DerivedUnitType.Fossil;

		}else if (recordBasis.equalsIgnoreCase("HumanObservation")){

			result = DerivedUnitType.Observation;

		}else if (recordBasis.equalsIgnoreCase("Literature")){

			logger.warn("Literature record basis not yet supported");

			result = DerivedUnitType.DerivedUnit;

		}else if (recordBasis.equalsIgnoreCase("LivingSpecimen")){

			result = DerivedUnitType.LivingBeing;

		}else if (recordBasis.equalsIgnoreCase("MachineObservation")){

			logger.warn("MachineObservation record basis not yet supported");

			result = DerivedUnitType.Observation;

		}else if (recordBasis.equalsIgnoreCase("PreservedSpecimen")){

			result = DerivedUnitType.Specimen;

		}

		return result;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)

	 */

	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {

		String nameSpace;

		Class cdmClass;

		Set<String> idSet;

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

		try{

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

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

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

			while (rs.next()){

//				handleForeignKey(rs, fieldObservationIdSet, "DuplicateFk");

//				handleForeignKey(rs, termsIdSet, "LifeFormFk");

//				handleForeignKey(rs, collectionIdSet, "CollectionFk");

			}

			//field observation map for duplicates

			nameSpace = AlgaTerraDnaImport.ECO_FACT_FIELD_OBSERVATION_NAMESPACE;

			cdmClass = FieldObservation.class;

			idSet = fieldObservationIdSet;

			Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, fieldObservationMap);

			//collections

			nameSpace = AlgaTerraCollectionImport.NAMESPACE_COLLECTION;

			cdmClass = Collection.class;

			idSet = collectionIdSet;

			Map<String, Collection> collectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, collectionMap);

			//sub-collections

			nameSpace = AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION;

			cdmClass = Collection.class;

			idSet = collectionIdSet;

			Map<String, Collection> subCollectionMap = (Map<String, Collection>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, subCollectionMap);

			//terms

			nameSpace = AlgaTerraDnaImport.TERMS_NAMESPACE;

			cdmClass = FieldObservation.class;

			idSet = termsIdSet;

			Map<String, DefinedTermBase> termMap = (Map<String, DefinedTermBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, termMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean doCheck(BerlinModelImportState state){

		IOValidator<BerlinModelImportState> validator = new AlgaTerraDnaImportValidator();

		return validator.validate(state);

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(BerlinModelImportState state){

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

	}

}