EDIT

// $Id$

/**

* Copyright (C) 2009 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.dwca.in;

import java.net.URI;

import java.util.ArrayList;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import com.ibm.lsid.MalformedLSIDException;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.io.dwca.TermUri;

import eu.etaxonomy.cdm.io.stream.StreamImportBase;

import eu.etaxonomy.cdm.io.stream.StreamImportStateBase;

import eu.etaxonomy.cdm.io.stream.StreamItem;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.strategy.exceptions.StringNotParsableException;

import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;

import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;

/**

 * @author a.mueller

 * @date 22.11.2011

 *

 */

public class  DwcTaxonStreamItem2CdmTaxonConverter<CONFIG extends DwcaDataImportConfiguratorBase, STATE extends StreamImportStateBase<CONFIG, StreamImportBase>>  extends PartitionableConverterBase<CONFIG, STATE> implements IPartitionableConverter<StreamItem, IReader<CdmBase>, String>{

	private static final Logger logger = Logger.getLogger(DwcTaxonStreamItem2CdmTaxonConverter.class);

	private static final String ID = "id";

	// temporary key for the case that no dataset information is supplied, TODO use something better

	public static final String NO_DATASET = "no_dataset_jli773oebhjklw";

	private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();

	/**

	 * @param state

	 */

	public DwcTaxonStreamItem2CdmTaxonConverter(STATE state) {

		super(state);

	}

	public IReader<MappedCdmBase> map(StreamItem csvTaxonRecord){

		List<MappedCdmBase> resultList = new ArrayList<MappedCdmBase>(); 

		//TODO what if not transactional? 

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

		String sourceReferenceDetail = null;

		//taxon

		TaxonBase<?> taxonBase = getTaxonBase(csvTaxonRecord);

		MappedCdmBase  mcb = new MappedCdmBase(csvTaxonRecord.term, csvTaxonRecord.get(ID), taxonBase);

		resultList.add(mcb);

		//original source

		String id = csvTaxonRecord.get(ID);

		IdentifiableSource source = taxonBase.addSource(OriginalSourceType.Import, id, "Taxon", sourceReference, sourceReferenceDetail);

		MappedCdmBase mappedSource = new MappedCdmBase(csvTaxonRecord.get(ID), source);

		resultList.add(mappedSource);

		csvTaxonRecord.remove(ID);

		//rank

		NomenclaturalCode nomCode = getNomCode(csvTaxonRecord);

		Rank rank = getRank(csvTaxonRecord, nomCode);

		//name && name published in

		TaxonNameBase<?,?> name = getScientificName(csvTaxonRecord, nomCode, rank, resultList, sourceReference);

		taxonBase.setName(name);

		//nameAccordingTo

		MappedCdmBase<Reference> sec = getNameAccordingTo(csvTaxonRecord, resultList);

		if (sec == null && state.getConfig().isUseSourceReferenceAsSec()){

			sec = new MappedCdmBase<Reference>(state.getTransactionalSourceReference());

		}

		if (sec != null){

			taxonBase.setSec(sec.getCdmBase());

		}

		//classification

		handleDataset(csvTaxonRecord, taxonBase, resultList, sourceReference, sourceReferenceDetail);

		//NON core

	    //term="http://purl.org/dc/terms/identifier"

		//currently only LSIDs

		handleIdentifier(csvTaxonRecord, taxonBase); 

		//TaxonRemarks

		handleTaxonRemarks(csvTaxonRecord, taxonBase);

		//TDWG_1

		handleTdwgArea(csvTaxonRecord, taxonBase);

		//VernecularName

		handleCommonNames(csvTaxonRecord, taxonBase);

		//External Sources, ID's and References

		handleIdentifiableObjects(csvTaxonRecord, taxonBase);

		//		    <!-- Top level group; listed as kingdom but may be interpreted as domain or superkingdom

//		         The following eight groups are recognized: Animalia, Archaea, Bacteria, Chromista, 

//		         Fungi, Plantae, Protozoa, Viruses -->

//		    <field index='10' term='http://rs.tdwg.org/dwc/terms/kingdom'/>

//		    <!-- Phylum in which the taxon has been classified -->

//		    <field index='11' term='http://rs.tdwg.org/dwc/terms/phylum'/>

		//		    <!-- Class in which the taxon has been classified -->

//		    <field index='12' term='http://rs.tdwg.org/dwc/terms/class'/>

		//		    <!-- Order in which the taxon has been classified -->

//		    <field index='13' term='http://rs.tdwg.org/dwc/terms/order'/>

		//		    <!-- Family in which the taxon has been classified -->

//		    <field index='14' term='http://rs.tdwg.org/dwc/terms/family'/>

		//		    <!-- Genus in which the taxon has been classified -->

//		    <field index='15' term='http://rs.tdwg.org/dwc/terms/genus'/>

		//		    <!-- Subgenus in which the taxon has been classified -->

//		    <field index='16' term='http://rs.tdwg.org/dwc/terms/subgenus'/>

//		    <!-- Specific epithet; for hybrids, the multiplication symbol is included in the epithet -->

//		    <field index='17' term='http://rs.tdwg.org/dwc/terms/specificEpithet'/>

//		    <!-- Infraspecific epithet -->

//		    <field index='18' term='http://rs.tdwg.org/dwc/terms/infraspecificEpithet'/>

//		    <!-- Authorship -->

//		    <field index='19' term='http://rs.tdwg.org/dwc/terms/scientificNameAuthorship'/>

//		==> see scientific name

//		    

//		<!-- Acceptance status published in -->

//		    <field index='20' term='http://purl.org/dc/terms/source'/>

//		    <!-- Reference in which the scientific name was first published -->

//		    <field index='21' term='http://rs.tdwg.org/dwc/terms/namePublishedIn'/>

//		    <!-- Taxon scrutinized by -->

//		    <field index='22' term='http://rs.tdwg.org/dwc/terms/nameAccordingTo'/> 

//		    <!-- Scrutiny date -->

//		    <field index='23' term='http://purl.org/dc/terms/modified'/>

//		    <!-- Additional data for the taxon -->

//		    <field index='24' term='http://purl.org/dc/terms/description'/>

//		    </core>

		return new ListReader<MappedCdmBase>(resultList);

	}

	/**

	 * @param item

	 * @param taxonBase

	 */

	private void handleIdentifiableObjects(StreamItem item,TaxonBase<?> taxonBase) {

		String references = item.get(TermUri.DC_REFERENCES);

		if (references == null || references == "") {

			references = item.get(TermUri.DWC_NAME_PUBLISHED_IN_ID);//lorna temporary until Scratchpads move the reference to the correct place.

		}

		if (StringUtils.isNotBlank(references)){

			URI uri = makeUriIfIs(references);

			if (uri != null){

				Extension.NewInstance(taxonBase, references, ExtensionType.URL());

			}else{

				String message = "Non-URI Dublin Core References not yet handled for taxa. References is: %s";

				fireWarningEvent(String.format(message, references), item, 6);

			}

		}

		//TODO: Finish properly

		String id = item.get(TermUri.CDM_SOURCE_IDINSOURCE);

		String idNamespace = item.get(TermUri.CDM_SOURCE_IDNAMESPACE);

		String reference = item.get(TermUri.CDM_SOURCE_REFERENCE);

		if(StringUtils.isNotBlank(id) && StringUtils.isNotBlank(idNamespace) && StringUtils.isNotBlank(reference)){

			Reference<?> ref = ReferenceFactory.newGeneric();

			ref.setTitle(reference);

			Taxon taxon = (Taxon) taxonBase;

			taxon.addSource(OriginalSourceType.Import, id, idNamespace, ref, null);

		}

	}

	/**

	 * If str is an uri it returns is as an {@link URI}. If not it returns <code>null</code>. 

	 * @param str

	 * @return the URI.

	 */

	private URI makeUriIfIs(String str) {

		if (! str.startsWith("http:")){

			return null;

		}else{

			try {

				URI uri = URI.create(str);

				return uri;

			} catch (Exception e) {

				return null;

			}

		}

	}

	/**

	 * @param item

	 * @param taxonBase

	 */

	private void handleCommonNames(StreamItem item,TaxonBase<?> taxonBase) {

		//TODO: handle comma separated values

		String commonName = item.get(TermUri.DWC_VERNACULAR_NAME);

		Language language = getLanguage(item);	

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

		if(taxonBase instanceof Taxon){

			Taxon taxon = (Taxon) taxonBase;

			TaxonDescription taxonDescription = getTaxonDescription(taxon, false);

			taxonDescription.addElement(commonTaxonName);

			logger.info("Common name " + commonName + " added to " + taxon.getTitleCache());

		}

	}

	/**

	 * @param csvTaxonRecord

	 * @param taxonBase

	 */

	private void handleTdwgArea(StreamItem item, TaxonBase<?> taxonBase) {

		// TODO Auto-generated method stub

		String tdwg_area = item.get(TermUri.DWC_COUNTRY_CODE);

		if (tdwg_area != null){

		if(taxonBase instanceof Synonym){

			Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);

			Set<Taxon> acceptedTaxaList = synonym.getAcceptedTaxa();

			if(acceptedTaxaList.size()>1){

				String message = "Synonym is related to more than one accepted Taxa";

				fireWarningEvent(message, item, 4);

			}else{

				for(Taxon taxon : acceptedTaxaList){

					TaxonDescription td = getTaxonDescription(taxon, false);

					NamedArea area = NamedArea.getAreaByTdwgAbbreviation(tdwg_area);

					if (area == null){

						area = NamedArea.getAreaByTdwgLabel(tdwg_area);

					}

					if (area != null){

						Distribution distribution = Distribution.NewInstance(area, PresenceTerm.PRESENT());

						td.addElement(distribution);

					}

				}

			}

		}

		if(!(taxonBase instanceof Synonym)){

			Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);

			TaxonDescription td = getTaxonDescription(taxon, false);

			NamedArea area = NamedArea.getAreaByTdwgAbbreviation(tdwg_area);

			if (area == null){

				area = NamedArea.getAreaByTdwgLabel(tdwg_area);

			}

			if (area != null){

				Distribution distribution = Distribution.NewInstance(area, PresenceTerm.PRESENT());

				td.addElement(distribution);

			}

		}

	}

	}

	/**

	 * @param item

	 * @param taxonBase

	 */

	private void handleTaxonRemarks(StreamItem item,TaxonBase<?> taxonBase) {

		String comment = item.get(TermUri.DWC_TAXON_REMARKS);

		Language language = getLanguage(item);	

		if(StringUtils.isNotBlank(comment)){

				Annotation annotation = Annotation.NewInstance(comment, language);

				taxonBase.addAnnotation(annotation);

		}else{

			String message = "Comment is empty or some error appeared while saving: %s";

//			message = String.format(message);

			fireWarningEvent(message, item, 1);

		}

	}

	//TODO handle non LSIDs

	//TODO handle LSIDs for names

	private void handleIdentifier(StreamItem csvTaxonRecord, TaxonBase<?> taxonBase) {

		String identifier = csvTaxonRecord.get(TermUri.DC_IDENTIFIER);

		if (StringUtils.isNotBlank(identifier)){

			if (identifier.trim().startsWith("urn:lsid")){

				try {

					LSID lsid = new LSID(identifier);

					taxonBase.setLsid(lsid);

				} catch (MalformedLSIDException e) {

					String message = "LSID is malformed and can't be handled as LSID: %s";

					message = String.format(message, identifier);

					fireWarningEvent(message, csvTaxonRecord, 4);

				} 

			}else{

				String message = "Identifier type not supported: %s";

				message = String.format(message, identifier);

				fireWarningEvent(message, csvTaxonRecord, 4);

			}

		}

	}

	private void handleDataset(StreamItem item, TaxonBase<?> taxonBase, List<MappedCdmBase> resultList, Reference<?> sourceReference, String sourceReferecenDetail) {

		TermUri idTerm = TermUri.DWC_DATASET_ID;

		TermUri strTerm = TermUri.DWC_DATASET_NAME;

		if (config.isDatasetsAsClassifications()){

			String datasetId = CdmUtils.Nz(item.get(idTerm)).trim();

			String datasetName = CdmUtils.Nz(item.get(strTerm)).trim();

				if (CdmUtils.areBlank(datasetId, datasetName) ){

				datasetId = NO_DATASET;

			}

			//check id

			boolean classificationExists = state.exists(idTerm.toString() , datasetId, Classification.class);

			//check name

			if (!classificationExists){

				classificationExists = state.exists(strTerm.toString() , datasetName, Classification.class);

			}

			//if not exists, create new

			if (! classificationExists){

				String classificationName = StringUtils.isBlank(datasetName)? datasetId : datasetName;

				if (classificationName.equals(NO_DATASET)){					

					classificationName = config.getClassificationName();

					//classificationName = "Classification (no name)";  //TODO define by config or zipfile or metadata

				}

				String classificationId = StringUtils.isBlank(datasetId)? datasetName : datasetId;

				Classification classification = Classification.NewInstance(classificationName);

				//source

				IdentifiableSource source = classification.addSource(OriginalSourceType.Import, classificationId, "Dataset", sourceReference, sourceReferecenDetail);

				//add to result

				resultList.add(new MappedCdmBase(idTerm, datasetId, classification));

				resultList.add(new MappedCdmBase(strTerm, datasetName, classification));

				resultList.add(new MappedCdmBase(source));

				//TODO this is not so nice but currently necessary as classifications are requested in the same partition

				state.putMapping(idTerm.toString(), classificationId, classification);

				state.putMapping(strTerm.toString(), classificationName, classification);

			}

		}else if (config.isDatasetsAsSecundumReference() || config.isDatasetsAsOriginalSource()){

			MappedCdmBase<Reference> mappedCitation = getReference(item, resultList, idTerm, strTerm, true);

			if (mappedCitation != null){

				Reference<?> ref = mappedCitation.getCdmBase();

				if (config.isDatasetsAsSecundumReference()){

					//dataset as secundum reference

					taxonBase.setSec(ref);

				}else{

					//dataset as original source

					taxonBase.addSource(OriginalSourceType.Import, null, null, ref, null);

				}

			}

		}else{

			String message = "DatasetUse type not yet implemented. Can't import dataset information.";

			fireWarningEvent(message, item, 4);

		}

		//remove to later check if all attributes were used

		item.remove(idTerm);

		item.remove(strTerm);

	}

	@Override

	public String getSourceId(StreamItem item) {

		String id = item.get(ID);

		return id;

	}

	private MappedCdmBase<Reference> getNameAccordingTo(StreamItem item, List<MappedCdmBase> resultList) {

		if (config.isDatasetsAsSecundumReference()){

			//TODO store nameAccordingTo info some where else or let the user define where to store it.

			return null;

		}else{

			TermUri idTerm = TermUri.DWC_NAME_ACCORDING_TO_ID;

			TermUri strTerm = TermUri.DWC_NAME_ACCORDING_TO;

			MappedCdmBase<Reference> secRef = getReference(item, resultList, idTerm, strTerm, false);

			return secRef;

		}

	}

	private NomenclaturalCode getNomCode(StreamItem item) {

		String strNomCode = getValue(item, TermUri.DWC_NOMENCLATURAL_CODE);

		NomenclaturalCode nomCode = null;

		// by Nomcenclatural Code

		if (strNomCode != null){

			nomCode = NomenclaturalCode.fromString(strNomCode);

			if (nomCode == null){

				String message = "NomCode '%s' not recognized";

				message = String.format(message, strNomCode);

				fireWarningEvent(message, item, 4);

			}else{

				return nomCode;

			}

		}

		// by Kingdom

		String strKingdom = getValue(item, TermUri.DWC_KINGDOM);

		if (strKingdom != null){

			if (strKingdom.equalsIgnoreCase("Plantae")){

				nomCode = NomenclaturalCode.ICNAFP;

			}else if (strKingdom.equalsIgnoreCase("Fungi")){

				nomCode = NomenclaturalCode.ICNAFP;

			}else if (strKingdom.equalsIgnoreCase("Animalia")){

				nomCode = NomenclaturalCode.ICZN;

			}else if (strKingdom.equalsIgnoreCase("Protozoa")){

				nomCode = NomenclaturalCode.ICZN;

			}

		}

		//TODO further kingdoms

		if (nomCode == null){

			//TODO warning

			if (config.getNomenclaturalCode() != null){

				nomCode = config.getNomenclaturalCode();

			}

		}

		return nomCode;

	}

	private TaxonNameBase<?,?> getScientificName(StreamItem item, NomenclaturalCode nomCode, Rank rank, List<MappedCdmBase> resultList, Reference sourceReference) {

		TaxonNameBase<?,?> name = null;

		String strScientificName = getValue(item, TermUri.DWC_SCIENTIFIC_NAME);

		//Name

		if (strScientificName != null){

			name = parser.parseFullName(strScientificName, nomCode, rank);

			if ( rank != null && name != null && name.getRank() != null &&  ! rank.equals(name.getRank())){

				if (config.isValidateRankConsistency()){

					String message = "Parsed rank %s (%s) differs from rank %s given by fields 'taxonRank' or 'verbatimTaxonRank'";

					message = String.format(message, name.getRank().getTitleCache(), strScientificName, rank.getTitleCache());

					fireWarningEvent(message, item, 4);

				}

			}

			checkAuthorship(name, item);

			resultList.add(new MappedCdmBase(TermUri.DWC_SCIENTIFIC_NAME, strScientificName, name));

		}

		//By ID

		String strScientificNameId = getValue(item, TermUri.DWC_SCIENTIFIC_NAME_ID);

		if (strScientificNameId != null){

			if (config.isScientificNameIdAsOriginalSourceId()){

				if (name != null){

					IdentifiableSource source = IdentifiableSource.NewInstance(OriginalSourceType.Import, strScientificNameId, TermUri.DWC_SCIENTIFIC_NAME_ID.toString(), sourceReference, null);

					name.addSource(source);

				}

			}else{

				String message = "ScientificNameId not yet implemented: '%s'";

				message = String.format(message, strScientificNameId);

				fireWarningEvent(message, item, 4);

			}

		}

		//namePublishedIn

		TermUri idTerm = TermUri.DWC_NAME_PUBLISHED_IN_ID;

		TermUri strTerm = TermUri.DWC_NAME_PUBLISHED_IN;

		MappedCdmBase<Reference> nomRef = getReference(item, resultList, idTerm, strTerm, false);

		if (name != null){

			if (nomRef != null){

				name.setNomenclaturalReference(nomRef.getCdmBase());  //check if name already has a nomRef, shouldn't be the case usually

			}

		}else{

			if (nomRef != null){

				String message = "NamePublishedIn information available but no name exists";

				fireWarningEvent(message, item, 4);

			}

		}

		return name;

	}

	/**

	 * General method to handle references used for multiple attributes.

	 * @param item

	 * @param resultList

	 * @param idTerm

	 * @param strTerm

	 * @param idIsInternal

	 * @return

	 */

	private MappedCdmBase<Reference> getReference(StreamItem item, List<MappedCdmBase> resultList, TermUri idTerm, TermUri strTerm, boolean idIsInternal) {

		Reference<?> newRef = null;

		Reference<?> sourceCitation = null;

		MappedCdmBase<Reference> result = null;

		if (exists(idTerm, item) || exists(strTerm, item)){

			String refId = CdmUtils.Nz(item.get(idTerm)).trim();

			String refStr = CdmUtils.Nz(item.get(strTerm)).trim();

			if (StringUtils.isNotBlank(refId)){

				List<Reference> references = state.get(idTerm.toString(), refId, Reference.class);

				if (references.size() == 0){

					if (! idIsInternal){

						//references should already exist in store if not linking to external links like URLs

						String message = "External namePublishedInIDs are not yet supported";

						fireWarningEvent(message, item, 4);//set to DEBUG

					}else{

						newRef = ReferenceFactory.newGeneric();  //TODO handle other types if possible

						newRef.addSource(OriginalSourceType.Import, refId, idTerm.toString(), sourceCitation, null);

						MappedCdmBase<Reference> idResult = new MappedCdmBase<Reference>(idTerm, refId, newRef);

						resultList.add(idResult);

					}

				}else{

					//TODO handle list.size > 1 , do we need a list here ?

					result = new MappedCdmBase<Reference>(idTerm, refId , references.get(0));

				}

			}

			if (result == null){

				List<Reference> nomRefs = state.get(strTerm.toString(), refStr, Reference.class);

				if (nomRefs.size() > 0){

					//TODO handle list.size > 1 , do we need a list here ?

					result = new MappedCdmBase<Reference>(strTerm, refStr , nomRefs.get(0));

				}else{

					// new Reference

					if (newRef == null){

						newRef = ReferenceFactory.newGeneric();  //TODO handle other types if possible

					}

					newRef.setTitleCache(refStr, true);

					//TODO distinguish available year, authorship, etc. if

					result = new MappedCdmBase<Reference>(strTerm, refStr, newRef);

					resultList.add(result);

				}

			}

		}

		return result;

	}

	//TODO we may configure in configuration that scientific name never includes Authorship

	private void checkAuthorship(TaxonNameBase nameBase, StreamItem item) {

		if (!nameBase.isInstanceOf(NonViralName.class)){

			return;

		}

		NonViralName<?> nvName = CdmBase.deproxy(nameBase, NonViralName.class); 

		String strAuthors = getValue(item, TermUri.DWC_SCIENTIFIC_NAME_AUTHORS);

		if (! nvName.isProtectedTitleCache()){

			if (StringUtils.isBlank(nvName.getAuthorshipCache())){

				if (nvName.isInstanceOf(BotanicalName.class) || nvName.isInstanceOf(ZoologicalName.class)){

					//TODO can't we also parse NonViralNames correctly ?

					try {

						parser.parseAuthors(nvName, strAuthors);

					} catch (StringNotParsableException e) {

						nvName.setAuthorshipCache(strAuthors);

					}		

				}else{

					nvName.setAuthorshipCache(strAuthors);

				}

				//TODO throw warning (scientific name should always include authorship) by DwC definition

			}

		}

	}

	private Rank getRank(StreamItem csvTaxonRecord, NomenclaturalCode nomCode) {

		boolean USE_UNKNOWN = true;

		Rank rank = null;

		String strRank = getValue(csvTaxonRecord,TermUri.DWC_TAXON_RANK);

		String strVerbatimRank = getValue(csvTaxonRecord,TermUri.DWC_VERBATIM_TAXON_RANK);

		if (strRank != null){

			try {

				rank = Rank.getRankByEnglishName(strRank, nomCode, USE_UNKNOWN);

				if (rank.equals(Rank.UNKNOWN_RANK())){

					rank = Rank.getRankByNameOrAbbreviation(strRank, USE_UNKNOWN);

					if (rank.equals(Rank.UNKNOWN_RANK())){

						String message = "Rank can not be defined for '%s'";

						message = String.format(message, strRank);

						fireWarningEvent(message, csvTaxonRecord, 4);

					}

				}

			} catch (UnknownCdmTypeException e) {

				//should not happen as USE_UNKNOWN is used

				rank = Rank.UNKNOWN_RANK();

			}

		}

		if ( (rank == null || rank.equals(Rank.UNKNOWN_RANK())) && strVerbatimRank != null){

			try {

				rank = Rank.getRankByNameOrAbbreviation(strVerbatimRank, USE_UNKNOWN);

				if (rank.equals(Rank.UNKNOWN_RANK())){

					String message = "Rank can not be defined for '%s'";

					message = String.format(message, strVerbatimRank);

					fireWarningEvent(message, csvTaxonRecord, 4);

				}

			} catch (UnknownCdmTypeException e) {

				//should not happen as USE_UNKNOWN is used

				rank = Rank.UNKNOWN_RANK();

			}

		}

		return rank;

	}

	/**

	 * Creates an empty taxon object with a given status.

	 * @param item

	 * @return

	 */

	private TaxonBase<?> getTaxonBase(StreamItem item) {

		TaxonNameBase<?,?> name = null;

		Reference<?> sec = null;

		TaxonBase<?> result;

		String taxStatus = item.get(TermUri.DWC_TAXONOMIC_STATUS);

		String status = "";

		if (taxStatus != null){

			if (taxStatus.matches("accepted.*|valid")){

				status += "A";

			} else if (taxStatus.matches(".*synonym|invalid|not accepted")){   //not accepted comes from scratchpads

				status += "S";

			} else if (taxStatus.matches("misapplied.*")){

				status += "M";

			} else{

				status += "?";

			}

			item.remove(TermUri.DWC_TAXONOMIC_STATUS);

		}

		if (! CdmUtils.isBlank(item.get(TermUri.DWC_ACCEPTED_NAME_USAGE_ID))){

			// acceptedNameUsageId = id

			if (getSourceId(item).equals(item.get(TermUri.DWC_ACCEPTED_NAME_USAGE_ID))){

				status += "A";

			}else{

				status += "S";

			}

		}

		if (status.contains("A") || status.contains("M")){

			result = Taxon.NewInstance(name, sec);

			if (status.contains("S") && ! status.contains("M") ){

				String message = "Ambigous taxon status (%s)";

				message = String.format(message, status);

				fireWarningEvent(message, item, 6);

			}

		} else if (status.contains("S")){

			result = Synonym.NewInstance(name, sec);

		} else{

			result = Taxon.NewUnknownStatusInstance(name, sec);

		}

		return result;

	}

	/**

	 * @param item

	 * @return

	 */

	private Language getLanguage(StreamItem item) {

		String langItem = item.get(TermUri.DC_LANGUAGE);

		Language language = null;

		if(StringUtils.equalsIgnoreCase(langItem, "de")){

			language = Language.GERMAN();

		}else if(StringUtils.equalsIgnoreCase(langItem, "en")){

			language = Language.ENGLISH();

		}else{

			language = Language.DEFAULT();

		}

		return language;

	}

// ********************** PARTITIONABLE ****************************************/

	@Override

	protected void makeForeignKeysForItem(StreamItem item, Map<String, Set<String>> fkMap) {

		String value;

		String key;

		//namePublishedIn

		if ( hasValue(value = item.get(key = TermUri.DWC_NAME_PUBLISHED_IN_ID.toString()))){

			Set<String> keySet = getKeySet(key, fkMap);

			keySet.add(value);

		}

		if (config.isDeduplicateNamePublishedIn()){

			if ( hasValue(value = item.get(key = TermUri.DWC_NAME_PUBLISHED_IN.toString()))){

				Set<String> keySet = getKeySet(key, fkMap);

				keySet.add(value);

			}

		}

		//nameAccordingTo

		if (! config.isDatasetsAsSecundumReference()){

			if ( hasValue(value = item.get(key = TermUri.DWC_NAME_ACCORDING_TO_ID.toString()))){

				Set<String> keySet = getKeySet(key, fkMap);

				keySet.add(value);

			}

			if ( hasValue(value = item.get(key = TermUri.DWC_NAME_ACCORDING_TO.toString()))){

				Set<String> keySet = getKeySet(key, fkMap);

				keySet.add(value);

			}

		}

		//dataset

		if ( hasValue(value = item.get(key = TermUri.DWC_DATASET_ID.toString()))){

			Set<String> keySet = getKeySet(key, fkMap);

			keySet.add(value);

		}

		if ( hasValue(value = item.get(key = TermUri.DWC_DATASET_NAME.toString()))){

			Set<String> keySet = getKeySet(key, fkMap);

			keySet.add(value);

		}

	}

	@Override

	public Set<String> requiredSourceNamespaces() {

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

 		result.add(TermUri.DWC_NAME_PUBLISHED_IN_ID.toString());

 		result.add(TermUri.DWC_NAME_PUBLISHED_IN.toString());

 		if (!config.isDatasetsAsSecundumReference()){

	 		result.add(TermUri.DWC_NAME_ACCORDING_TO_ID.toString());

	 		result.add(TermUri.DWC_NAME_ACCORDING_TO.toString());

 		}

	 	result.add(TermUri.DWC_DATASET_ID.toString());

	 	result.add(TermUri.DWC_DATASET_NAME.toString());

	 	return result;

	}

//** ***************************** TO STRING *********************************************/

	@Override

	public String toString(){

		return this.getClass().getName();

	}

}