EDIT

	private boolean includeFlatClassifications = true;

//	static final boolean doRelTaxa = true;

		config.setIncludeFlatClassifications(includeFlatClassifications);

	private boolean specimenVocabulariesCreated = false;

	public boolean isSpecimenVocabulariesCreated() {

		return specimenVocabulariesCreated;

	}

	public void setSpecimenVocabulariesCreated(boolean specimenVocabulariesCreated) {

		this.specimenVocabulariesCreated = specimenVocabulariesCreated;

	}

import java.net.URI;

import java.sql.Date;

import java.util.UUID;

import org.springframework.transaction.TransactionStatus;

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

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.location.NamedArea;

import eu.etaxonomy.cdm.model.location.TdwgArea;

import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;

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

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

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

	public static final String FIELD_OBSERVATION_NAMESPACE = "FieldObservation";

	public static final String TERMS_NAMESPACE = "ALGA_TERRA_TERMS";

	//move to transformrer

	final static UUID uuidMarkerAlkalinity = UUID.fromString("e52d0ea2-0c1f-4d95-ae6d-e21ab317c594");  

	final static UUID uuidRefSystemGps = UUID.fromString("c23e4928-c137-4e4a-b6ab-b430da3d0b94");  

	final static UUID uuidFeatureSpecimenCommunity = UUID.fromString("3ff5b1ab-3999-4b5a-b8f7-01fd2f6c12c7");

	final static UUID uuidFeatureAdditionalData = UUID.fromString("0ac82ab8-2c2b-4953-98eb-a9f718eb9c57");

	final static UUID uuidVocAlgaTerraClimate = UUID.fromString("b0a677c6-8bb6-43f4-b1b8-fc377a10feb5");

	final static UUID uuidVocAlgaTerraHabitat = UUID.fromString("06f30114-e19c-4e7d-a8e5-5488c41fcbc5");

	final static UUID uuidVocAlgaTerraLifeForm = UUID.fromString("3c0b194e-809c-4b42-9498-6ff034066ed7");

	final static UUID uuidFeatureAlgaTerraClimate = UUID.fromString("8754674c-9ab9-4f28-95f1-91eeee2314ee");

	final static UUID uuidFeatureAlgaTerraHabitat = UUID.fromString("7def3fc2-cdc5-4739-8e13-62edbd053415");

	final static UUID uuidFeatureAlgaTerraLifeForm = UUID.fromString("9b657901-1b0d-4a2a-8d21-dd8c1413e2e6");

				" FROM Fact " +

					" INNER JOIN EcoFact ON Fact.ExtensionFk = EcoFact.EcoFactId " +

					"INNER JOIN PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk "

				+ " ORDER BY EcoFact.EcoFactId, PTaxon.RIdentifier, Fact.FactId ";

            " SELECT PTaxon.RIdentifier as taxonId, Fact.FactId, Fact.RecordBasis, EcoFact.*, " + 

               " tg.ID AS GazetteerId, tg.L2Code, tg.L3Code, tg.L4Code, tg.Country, tg.ISOCountry, " +

               " ec.UUID as climateUuid, eh.UUID as habitatUuid, elf.UUID as lifeFormUuid" +

                 " LEFT OUTER JOIN TDWGGazetteer tg ON EcoFact.TDWGGazetteerFk = tg.ID " +

                 " LEFT OUTER JOIN EcoClimate  ec  ON EcoFact.ClimateFk  = ec.ClimateId " +

                 " LEFT OUTER JOIN EcoHabitat  eh  ON EcoFact.HabitatFk  = eh.HabitatId " +

                 " LEFT OUTER JOIN EcoLifeForm elf ON EcoFact.LifeFormFk = elf.LifeFormId " +

              " WHERE Fact.FactCategoryFk = 202 AND (Fact.FactId IN (" + ID_LIST_TOKEN + ")  )"  

            + " ORDER BY EcoFact.EcoFactId, PTaxon.RIdentifier, Fact.FactId "

	public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {

		AlgaTerraImportState state = (AlgaTerraImportState)bmState;

		try {

			makeVocabulariesAndFeatures(state);

		} catch (SQLException e1) {

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

			e1.printStackTrace();

		}

		Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>) partitioner.getObjectMap(FIELD_OBSERVATION_NAMESPACE);

				int ecoFactId = rs.getInt("EcoFactId");

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

					//source ref

					//facade

					FieldObservation fieldObservation = getFieldObservation(ecoFactId, fieldObservationMap);

					DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(type, fieldObservation);

					//field observation

					handleSingleSpecimen(rs, facade, state);

					//description element

					TaxonDescription taxonDescription = getTaxonDescription(state, newTaxonId, taxonMap, factId, sourceRef);

					taxaToSave.add(taxonDescription.getTaxon()); 

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

	/**

	 * Creates the vocabularies and the features for Climate, Habitat and Lifeform

	 * @param state

	 * @throws SQLException

	 */

	private void makeVocabulariesAndFeatures(AlgaTerraImportState state) throws SQLException {

		String abbrevLabel = null;

		URI uri = null;

		if (! state.isSpecimenVocabulariesCreated()){

			TransactionStatus txStatus = this.startTransaction();

			boolean isOrdered = true;

			OrderedTermVocabulary<State> climateVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraClimate, "Climate", "Climate", abbrevLabel, uri, isOrdered, null);

			OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraHabitat, "Habitat", "Habitat", abbrevLabel, uri, isOrdered, null);

			OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraLifeForm, "Lifeform", "Lifeform", abbrevLabel, uri, isOrdered, null);

			Feature feature = getFeature(state, uuidFeatureAlgaTerraClimate, "Climate","Climate", null, null);

			feature.setSupportsCategoricalData(true);

			feature = getFeature(state, uuidFeatureAlgaTerraLifeForm, "LifeForm","LifeForm", null, null);

			feature.setSupportsCategoricalData(true);

			feature = Feature.HABITAT();

			feature.setSupportsCategoricalData(true);

			getTermService().saveOrUpdate(feature);

			Source source = state.getAlgaTerraConfigurator().getSource();

			String climateSql = "SELECT * FROM EcoClimate";

			ResultSet rs = source.getResultSet(climateSql);

			while (rs.next()){

				String climate = rs.getString("Climate");

				String description = rs.getString("Description");

				Integer id = rs.getInt("ClimateId");

				UUID uuid = UUID.fromString(rs.getString("UUID"));

				State stateTerm = getStateTerm(state, uuid, climate, description, null, climateVoc);

				addOriginalSource(stateTerm, id.toString(), "EcoClimate", state.getConfig().getSourceReference());

				getTermService().saveOrUpdate(stateTerm);

			}

			String habitatSql = "SELECT * FROM EcoHabitat";

			rs = source.getResultSet(habitatSql);

			while (rs.next()){

				String habitat = rs.getString("Habitat");

				String description = rs.getString("Description");

				Integer id = rs.getInt("HabitatId");

				UUID uuid = UUID.fromString(rs.getString("UUID"));

				State stateTerm = getStateTerm(state, uuid, habitat, description, null, habitatVoc);

				addOriginalSource(stateTerm, id.toString(), "EcoHabitat", state.getConfig().getSourceReference());

				getTermService().saveOrUpdate(stateTerm);

			}

			String lifeformSql = "SELECT * FROM EcoLifeForm";

			rs = source.getResultSet(lifeformSql);

			while (rs.next()){

				String lifeform = rs.getString("LifeForm");

				String description = rs.getString("Description");

				Integer id = rs.getInt("LifeFormId");

				UUID uuid = UUID.fromString(rs.getString("UUID"));

				State stateTerm = getStateTerm(state, uuid, lifeform, description, null, lifeformVoc);

				addOriginalSource(stateTerm, id.toString(), "EcoLifeForm", state.getConfig().getSourceReference());

				getTermService().saveOrUpdate(stateTerm);

			}

			this.commitTransaction(txStatus);

			state.setSpecimenVocabulariesCreated(true);

		}

	}

	private void handleSingleSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {

       	//CollectionFk, Collector, AltitudeMethod, 

    	//ISOCountrySub, CreatedWhen/Who/Updated/who

    	//P1-10Value/Unit/Parameter/Method

		try {

			Object alkalinityFlag = rs.getBoolean("AlkalinityFlag");

			String locality = rs.getString("Locality");

			Double latitude = nullSafeDouble(rs, "Latitude");

			Double longitude = nullSafeDouble(rs, "Longitude");

			Integer errorRadius = nullSafeInt(rs,"Prec");

			String geoCodeMethod = rs.getString("GeoCodeMethod");

			Integer altitude = nullSafeInt(rs, "Altitude");

			Integer lowerAltitude = nullSafeInt(rs,"AltitudeLowerValue");

			String altitudeUnit = rs.getString("AltitudeUnit");

			Double depth = nullSafeDouble(rs, "Depth");

			Double depthLow = nullSafeDouble(rs, "DepthLow");

			String collectorsNumber = rs.getString("CollectorsNumber");

			Date collectionDateStart = rs.getDate("CollectionDate");

			Date collectionDateEnd = rs.getDate("CollectionDateEnd");

			String climateUuid = rs.getString("climateUuid");

			String habitatUuid = rs.getString("habitatUuid");

			String lifeFormUuid = rs.getString("lifeFormUuid");

			String habitat = rs.getString("HabitatExplanation");

			String community = rs.getString("Comunity");

			String additionalData = rs.getString("AdditionalData");

			FieldObservation fieldObservation = facade.innerFieldObservation();

			//alkalinity marker

			if (alkalinityFlag != null){

				MarkerType alkalinityMarkerType = getMarkerType(state, uuidMarkerAlkalinity, "Alkalinity", "Alkalinity", null);

				boolean alkFlag = Boolean.valueOf(alkalinityFlag.toString());

				Marker alkalinityMarker = Marker.NewInstance(alkalinityMarkerType, alkFlag);

				fieldObservation.addMarker(alkalinityMarker);

			}

			//location

			facade.setLocality(locality);

			//exact location

			ReferenceSystem referenceSystem = makeRefrenceSystem(geoCodeMethod, state);

			Point exactLocation = Point.NewInstance(longitude, latitude, referenceSystem, errorRadius);

			facade.setExactLocation(exactLocation);

			//altitude, depth

			if (StringUtils.isNotBlank(altitudeUnit) && ! altitudeUnit.trim().equalsIgnoreCase("m")){

				logger.warn("Altitude unit is not [m] but: " +  altitudeUnit);

			}

			if ( altitude != null){

				if (lowerAltitude == null){

					facade.setAbsoluteElevation(altitude);

				}else{

			   		if (! facade.isEvenDistance(lowerAltitude, altitude)){

			   			//FIXME there is a ticket for this

			   			altitude = altitude + 1;

			   			logger.warn("Current implementation of altitude does not allow uneven distances");

			   		}

					facade.setAbsoluteElevationRange(lowerAltitude,altitude);

			   	}

			}

			if ( depth != null){

				//FIXME needs model change to accept double #3072

				Integer intDepth = depth.intValue();

				if (depthLow == null){

					facade.setDistanceToWaterSurface(intDepth);

				}else{

					//FIXME range not yet in model #3074

			   		facade.setDistanceToWaterSurface(intDepth);

			   	}

			}

			//habitat, ecology, community, etc.

			DescriptionBase<?> fieldDescription = getFieldObservationDescription(facade);

			addCategoricalValue(state, fieldDescription, climateUuid, uuidFeatureAlgaTerraClimate);

			addCategoricalValue(state, fieldDescription, habitatUuid, Feature.HABITAT().getUuid());

			addCategoricalValue(state, fieldDescription, lifeFormUuid, uuidFeatureAlgaTerraLifeForm);

			if (isNotBlank(habitat)){

				//FIXME

				facade.setEcology(habitat);  //or use an own feature ??

			}

			if (isNotBlank(community)){

				Feature communityFeature = getFeature(state, uuidFeatureSpecimenCommunity, "Community", "The community of a specimen (e.g. other algae in the same sample)", null, null);

				TextData textData = TextData.NewInstance(communityFeature);

				textData.putText(Language.DEFAULT(), community);

				getFieldObservationDescription(facade).addElement(textData);

			}

			if (isNotBlank(additionalData)){  //or handle it as Annotation ??

				Feature additionalDataFeature = getFeature(state, uuidFeatureAdditionalData, "Additional Data", "Additional Data", null, null);

				TextData textData = TextData.NewInstance(additionalDataFeature);

				textData.putText(Language.DEFAULT(), additionalData);

				getFieldObservationDescription(facade).addElement(textData);

			}

			//field

			facade.setFieldNumber(collectorsNumber);

			TimePeriod gatheringPeriod = TimePeriod.NewInstance(collectionDateStart, collectionDateEnd);

			facade.setGatheringPeriod(gatheringPeriod);

			handleCollectorTeam(state, facade, rs);

			//areas

			makeAreas(state, rs, facade);

			//parameters

			//TODO

			//notes

			//TODO is this an annotation on field observation or on the derived unit?

			//TODO id, created for fact +  ecoFact

			//    	this.doIdCreatedUpdatedNotes(state, descriptionElement, rs, id, namespace);

		} catch (IllegalArgumentException e) {

			throw e;

		}

	}

	private void addCategoricalValue(AlgaTerraImportState importState, DescriptionBase description, String uuidTerm, UUID featureUuid) {

		if (uuidTerm != null){

			State state = this.getStateTerm(importState, UUID.fromString(uuidTerm));

			Feature feature = getFeature(importState, featureUuid);

			CategoricalData categoricalData = CategoricalData.NewInstance(state, feature);

			description.addElement(categoricalData);

		}

	}

	private void handleCollectorTeam(AlgaTerraImportState state, DerivedUnitFacade facade, ResultSet rs) throws SQLException {

		// FIXME parsen

		String collector = rs.getString("Collector");

		Team team = Team.NewTitledInstance(collector, collector);

		facade.setCollector(team);

	}

	private void makeAreas(AlgaTerraImportState state, ResultSet rs, DerivedUnitFacade facade) throws SQLException {

	   	Object gazetteerId = rs.getObject("GazetteerId");

	   	if (gazetteerId != null){

	   		//TDWG

	   		NamedArea tdwgArea;

	   		String tdwg4 = rs.getString("L4Code");

	   		if (isNotBlank(tdwg4)){

	   			tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg4);

	   		}else{

	   			String tdwg3 = rs.getString("L3Code");

	   			if (isNotBlank(tdwg3)){

	   				tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg3);

	   			}else{

	   				Integer tdwg2 = rs.getInt("L2Code");   				

	   				tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(String.valueOf(tdwg2));

		   		}

	   		}

	   		if (tdwgArea == null){

	   			logger.warn("TDWG area could not be defined for gazetterId: " + gazetteerId);

	   		}else{

	   			facade.addCollectingArea(tdwgArea);

	   		}

	   		//Countries

	   		WaterbodyOrCountry country = null;

	   		String isoCountry = rs.getString("ISOCountry");

	   		String countryStr = rs.getString("Country");

	   		if (isNotBlank(isoCountry)){

		   		country = WaterbodyOrCountry.getWaterbodyOrCountryByIso3166A2(isoCountry);

	   		}else if (isNotBlank(countryStr)){

	   			logger.warn("Country exists but no ISO code");

	   		}

	   		if (country == null){

	   			logger.warn("Country does not exist for GazetteerID " + gazetteerId);

	   		}else{

	   			facade.setCountry(country);

	   		}

	   	}

	   	//Waterbody

	   	WaterbodyOrCountry waterbody = null;

	   	String waterbodyStr = rs.getString("WaterBody");

	   	if (isNotBlank(waterbodyStr)){

	   		if (waterbodyStr.equals("Atlantic Ocean")){

	   			waterbody = WaterbodyOrCountry.ATLANTICOCEAN();

	   		}else{

	   			logger.warn("Waterbody not recognized: " + waterbody);

	   		}

	   		if (waterbody != null){

	   			facade.addCollectingArea(waterbody);

	   		}

	   	}

	   	//countries sub

	   	//TODO

	}

	private DescriptionBase getFieldObservationDescription(DerivedUnitFacade facade) {

		Set<DescriptionBase> descriptions = facade.innerFieldObservation().getDescriptions();

		for (DescriptionBase desc : descriptions){

			if (desc.isImageGallery() == false){

				return desc;

			}

		}

		SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldObservation());

		descriptions.add(specDesc);

		return specDesc;

	}

	private ReferenceSystem makeRefrenceSystem(String geoCodeMethod, AlgaTerraImportState state) {

		if (StringUtils.isBlank(geoCodeMethod)){

			return null;

		}else if(geoCodeMethod.startsWith("GPS")){

			getReferenceSystem(state, uuidRefSystemGps, "GPS", "GPS", "GPS", ReferenceSystem.GOOGLE_EARTH().getVocabulary());

			return ReferenceSystem.WGS84(); 

		}else if(geoCodeMethod.startsWith("Google")){

			return ReferenceSystem.GOOGLE_EARTH();

		}else if(geoCodeMethod.startsWith("Map")){

			logger.warn("Reference system " +  geoCodeMethod +  " not yet supported.");

			return null;

		}else if(geoCodeMethod.startsWith("WikiProjekt Georeferenzierung") || geoCodeMethod.startsWith("http://toolserver.org/~geohack/geohack.php") ){

			return ReferenceSystem.WGS84();

		}else {

			logger.warn("Reference system " +  geoCodeMethod +  " not yet supported.");

			return null;

		}

	}

	private FieldObservation getFieldObservation(int ecoFactId, Map<String, FieldObservation> fieldObservationMap) {

		String key = String.valueOf(ecoFactId);

		FieldObservation fieldObservation = fieldObservationMap.get(key);

		if (fieldObservation == null){

			fieldObservation = FieldObservation.NewInstance();

			fieldObservationMap.put(key, fieldObservation);

		}

		return fieldObservation;

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

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

				handleForeignKey(rs, fieldObservationIdSet, "ecoFactId");

				handleForeignKey(rs, termsIdSet, "ClimateFk");

				handleForeignKey(rs, termsIdSet, "HabitatFk");

				handleForeignKey(rs, termsIdSet, "LifeFormFk");

			//field observation map map

			nameSpace = AlgaTerraSpecimenImport.FIELD_OBSERVATION_NAMESPACE;

			cdmClass = FieldObservation.class;

			idSet = taxonIdSet;

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

			result.put(nameSpace, fieldObservationMap);

			//terms

			nameSpace = AlgaTerraSpecimenImport.TERMS_NAMESPACE;

			cdmClass = FieldObservation.class;

			idSet = taxonIdSet;

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

			result.put(nameSpace, termMap);

	 * @param state 

	private TaxonDescription getTaxonDescription(AlgaTerraImportState state, int newTaxonId, Map<String, TaxonBase> taxonMap, int factId, Reference<?> sourceSec){

		TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(newTaxonId));

		//TODO for testing

		if (taxonBase == null && ! state.getConfig().isDoTaxa()){

			taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null);

		}

		Taxon taxon;

		if ( taxonBase instanceof Taxon ) {

			taxon = (Taxon) taxonBase;

		} else if (taxonBase != null) {

			logger.warn("TaxonBase for Fact(Specimen) with factId" + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());

			return null;

		} else {

			logger.warn("TaxonBase for Fact(Specimen) " + factId + " is null.");

			return null;

		}		

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

		if (descriptionSet.size() > 0) {

			result = descriptionSet.iterator().next(); 

			result = TaxonDescription.NewInstance();

			result.setTitleCache(sourceSec.getTitleCache(), true);

			taxon.addDescription(result);