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 AlgaTerraDnaImport  extends AlgaTerraSpecimenImportBase {

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

	private static int modCount = 5000;

	private static final String pluralString = "dna facts";

	public AlgaTerraDnaImport(){

		super(dbTableName, pluralString);

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected String getIdQuery(BerlinModelImportState bmState) {

		AlgaTerraImportState state = (AlgaTerraImportState)bmState;

				" FROM DNAFact df " +

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

					" WHERE f.FactCategoryFk = 203 ";

	 */

	@Override

	protected String getRecordQuery(BerlinModelImportConfigurator config) {

	            " SELECT df.*, pt.RIdentifier as taxonId, f.FactId, f.restrictedFlag, ecoFact.ecoFactId as ecoFactId " +

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

	            	" LEFT OUTER JOIN EcoFact ecoFact ON ecoFact.CultureStrain = df.CultureStrainNo " +

	            + " ORDER BY DNAFactID "

            ;

		return strQuery;

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {

		boolean success = true;

		AlgaTerraImportState state = (AlgaTerraImportState)bmState;

		try {

//			makeVocabulariesAndFeatures(state);

		}

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

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

		ResultSet rs = partitioner.getResultSet();

		Map<String, Reference> referenceMap = new HashMap<String, Reference>();

		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");

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

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

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

				try {

					//source ref

					//import date

					DateTime importDateTime = makeImportDateTime(rs);

					//DNA Sample

					DnaSample dnaSample = DnaSample.NewInstance();

					dnaSample.setCreated(importDateTime);

					//ecoFactFk

					makeDerivationFromEcoFact(state, rs, dnaSample, samplesToSave, dnaFactId);

					//sequence

					Sequence sequence = makeSequence(rs, dnaSample, dnaFactId, importDateTime);

					//locus

					//FIXME Deduplicate DnaMarker

					DefinedTerm locus = DefinedTerm.NewDnaMarkerInstance(definitionStr, keywordsStr, null);

					locus.setCreated(importDateTime);

					this.getTermService().save(locus);

					sequence.setDnaMarker(locus);

					//GenBank Accession

					makeGenBankAccession(rs, sequence, importDateTime, dnaFactId);

					//Comment

					String commentStr = rs.getString("Comment");

					if (isNotBlank(commentStr)){

						annotation.setCreated(importDateTime);

						sequence.addAnnotation(annotation);

					}

					//Indiv.Assoc.

					makeIndividualsAssociation(partitioner, rs, state, taxaToSave, dnaSample);

					//TODO titleCache

					//prelim implementation:

					String cultStrain = rs.getString("CultureStrainNo");

					//TODO preliminary implementation

					String referenceStr = rs.getString("FactReference");

					if (isNotBlank(referenceStr)){

						if (ref == null){

							ref = ReferenceFactory.newGeneric();

							ref.setTitleCache(referenceStr, true);

						}

						sequence.addCitation(ref);

					}

					//save

				} catch (Exception e) {

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

					e.printStackTrace();

            }

			logger.warn("DNASample or EcoFacts to save: " + samplesToSave.size());

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

			getTaxonService().saveOrUpdate(taxaToSave);

			return success;

		} catch (SQLException e) {

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

	private void makeDerivationFromEcoFact(AlgaTerraImportState state, ResultSet rs, DnaSample dnaSample, Set<SpecimenOrObservationBase> samplesToSave, Integer dnaFactId) throws SQLException {

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

		if (ecoFactFk != null){

			DerivedUnit ecoFact = (DerivedUnit)state.getRelatedObject(ECO_FACT_DERIVED_UNIT_NAMESPACE, ecoFactFk.toString());

			if (ecoFact == null){

				logger.warn("EcoFact is null for ecoFactFk: " + ecoFactFk + ", DnaFactId: " + dnaFactId);

				DerivationEvent.NewSimpleInstance(ecoFact, dnaSample, DerivationEventType.DNA_EXTRACTION());

				samplesToSave.add(ecoFact);

			}

	}

	private void makeIndividualsAssociation(ResultSetPartitioner partitioner, ResultSet rs, AlgaTerraImportState state, Set<TaxonBase> taxaToSave, DnaSample dnaSample) throws SQLException{

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

		Integer factId = rs.getInt("factId");

		Taxon taxon = getTaxon(state, taxonId, taxonMap, factId);

		desc.addElement(assoc);

		taxaToSave.add(taxon);

	}

	/**

	 * @param rs

//								append;

			DateTimeParser p = new DateTimeParser(dayFormatter);

			importDateTime = p.parse(importDateTimeStr, Locale.GERMANY);

		}

		return importDateTime;

	}

				logger.warn("SeqLen (" + seqLen+ ") and OriginalLen ("+sequenceStr.length()+") differ for dnaFact: "  + dnaFactId);

			}

		}

		Sequence sequence = Sequence.NewInstance(sequenceStr, seqLen);

		sequence.setCreated(importDateTime);

		dnaSample.addSequence(sequence);

	/**

	 * @param accessionStr

	 * @param notesStr

	 * @param sequence

	 * @return

	 */

	private void makeGenBankAccession(ResultSet rs, Sequence sequence, DateTime importDateTime, Integer dnaFactId) throws SQLException {

		String accessionStr = rs.getString("Accession");

		String notesStr = rs.getString("Notes");

		String versionStr = rs.getString("Version");

		URI genBankUri = null;

		if (StringUtils.isNotBlank(notesStr)){

			if (notesStr.startsWith("http")){

				logger.warn("Notes do not start with URI: " +  notesStr);

			}

		}

		if (isNotBlank(accessionStr) || genBankUri != null){

			if (accessionStr != null && accessionStr.trim().equals("")){

				accessionStr = null;

			}

		}

	}

	private boolean isGenBankAccessionNumber(String accessionStr, String versionStr, URI genBankUri, Integer dnaFactId) {

		boolean isGenBankAccessionNumber = accessionStr.matches("[A-Z]{2}\\d{6}");

		boolean versionHasGenBankPart = versionStr.matches(".*GI:.*");

			return true;

		}else {

			if (genBankUri != null){

			}

			if(isGenBankAccessionNumber || versionHasGenBankPart){

			}

			return false;

		}

		return ECO_FACT_DERIVED_UNIT_NAMESPACE;

	}

		return ECO_FACT_FIELD_OBSERVATION_NAMESPACE;

	}

		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> ecoFactFkSet = new HashSet<String>();

			while (rs.next()){

				handleForeignKey(rs, taxonIdSet, "taxonId");

				handleForeignKey(rs, ecoFactFkSet, "ecoFactId");

			}

			//taxon map

			nameSpace = BerlinModelTaxonImport.NAMESPACE;

			cdmClass = TaxonBase.class;

			idSet = taxonIdSet;

			Map<String, TaxonBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, objectMap);

			//eco fact derived unit map

			nameSpace = AlgaTerraFactEcologyImport.ECO_FACT_DERIVED_UNIT_NAMESPACE;

			idSet = ecoFactFkSet;

			Map<String, DerivedUnit> derivedUnitMap = (Map<String, DerivedUnit>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, derivedUnitMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

	protected boolean isIgnore(BerlinModelImportState state){

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

	}

}