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.eflora.centralAfrica.ferns;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import java.util.regex.Matcher;

import java.util.regex.Pattern;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

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

import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;

import eu.etaxonomy.cdm.common.CdmUtils;

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

import eu.etaxonomy.cdm.io.common.mapping.DbImportAnnotationMapper;

import eu.etaxonomy.cdm.io.common.mapping.DbImportExtensionMapper;

import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;

import eu.etaxonomy.cdm.io.common.mapping.DbImportMethodMapper;

import eu.etaxonomy.cdm.io.common.mapping.DbImportObjectCreationMapper;

import eu.etaxonomy.cdm.io.common.mapping.DbNotYetImplementedMapper;

import eu.etaxonomy.cdm.io.common.mapping.IMappingImport;

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

import eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.validation.CentralAfricaFernsTaxonImportValidator;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.parser.NonViralNameParserImpl;

/**

 * @author a.mueller

 * @created 20.02.2010

 * @version 1.0

 */

@Component

public class CentralAfricaFernsTaxonImport  extends CentralAfricaFernsImportBase<TaxonBase> implements IMappingImport<TaxonBase, CentralAfricaFernsImportState>{

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

	public static final UUID TNS_EXT_UUID = UUID.fromString("41cb0450-ac84-4d73-905e-9c7773c23b05");

	private DbImportMapping mapping;

	//second path is not used anymore, there is now an ErmsTaxonRelationImport class instead

	private boolean isSecondPath = false;

	private static final String pluralString = "taxa";

	private static final String dbTableName = "[African pteridophytes]";

	private static final Class cdmTargetClass = TaxonBase.class;

	public CentralAfricaFernsTaxonImport(){

		super(pluralString, dbTableName, cdmTargetClass);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportBase#getIdQuery()

	 */

	@Override

	protected String getIdQuery() {

		String strQuery = " SELECT [Taxon number] FROM " + dbTableName ;

		return strQuery;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.eflora.centralAfrica.ferns.CentralAfricaFernsImportBase#getMapping()

	 */

	protected DbImportMapping getMapping() {

		if (mapping == null){

			mapping = new DbImportMapping();

			mapping.addMapper(DbImportObjectCreationMapper.NewInstance(this, "Taxon number", TAXON_NAMESPACE)); //id + tu_status

			mapping.addMapper(DbImportMethodMapper.NewInstance(this, "mapTypes", ResultSet.class, CentralAfricaFernsImportState.class));

			mapping.addMapper(DbImportAnnotationMapper.NewInstance("Notes", AnnotationType.EDITORIAL()));

			mapping.addMapper(DbImportMethodMapper.NewInstance(this, "mapReferences", ResultSet.class, CentralAfricaFernsImportState.class));

			mapping.addMapper(DbImportMethodMapper.NewInstance(this, "mapNomRemarks", ResultSet.class, CentralAfricaFernsImportState.class));

			mapping.addMapper(DbImportExtensionMapper.NewInstance("Illustrations - non-original", CentralAfricaFernsTransformer.uuidIllustrationsNonOriginal, "Illustrations - non-original", "Illustrations - non-original", null));

//			mapping.addMapper(DbImportTextDataCreationMapper.NewInstance("Illustrations - non-original", objectToCreateNamespace, dbTaxonFkAttribute, this.TAXON_NAMESPACE, "Illustrations - non-original", Language.ENGLISH(), Feature, null);

//			mapping.addMapper(DbImportTextDataCreationMapper.NewInstance(dbIdAttribute, objectToCreateNamespace, dbTaxonFkAttribute, taxonNamespace, dbTextAttribute, Language.ENGLISH(), Feature.ECOLOGY(), null));

			//not yet implemented or ignore

			mapping.addMapper(DbNotYetImplementedMapper.NewInstance("Types XXX", "Method Mapper does not work yet. Needs implementation for all 5 types. FIXMEs in implementation"));

			mapping.addMapper(DbNotYetImplementedMapper.NewInstance("Basionym of", "Needs better understanding"));

			mapping.addMapper(DbNotYetImplementedMapper.NewInstance("Synonym of", "Needs better understanding. Strange values like "));

			mapping.addMapper(DbNotYetImplementedMapper.NewInstance("Chromosome number" , "Wrong data. Seems to be 'reference full'"));

			mapping.addMapper(DbNotYetImplementedMapper.NewInstance("Book Publisher & Place" , "How to access the reference via String mapper?"));

			mapping.addMapper(DbNotYetImplementedMapper.NewInstance("Reprint no" , "What's this?"));

			mapping.addMapper(DbNotYetImplementedMapper.NewInstance("Date verified" , "Needed?"));

//			

//			UUID credibilityUuid = ErmsTransformer.uuidCredibility;

//			mapping.addMapper(DbImportExtensionMapper.NewInstance("tu_credibility", credibilityUuid, "credibility", "credibility", "credibility")); //Werte: null, unknown, marked for deletion

//			

			//ignore

//			mapping.addMapper(DbIgnoreMapper.NewInstance("cache_citation", "citation cache not needed in PESI"));

			//not yet implemented or ignore

//			mapping.addMapper(DbNotYetImplementedMapper.NewInstance("tu_hidden", "Needs DbImportMarkerMapper implemented"));

		}

		return mapping;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected String getRecordQuery(CentralAfricaFernsImportConfigurator config) {

		String strSelect = " SELECT * ";

		String strFrom = " FROM [African pteridophytes] as ap";

		String strWhere = " WHERE ( ap.[taxon number] IN (" + ID_LIST_TOKEN + ") )";

		String strOrderBy = " ORDER BY [Taxon number]";

		String strRecordQuery = strSelect + strFrom + strWhere + strOrderBy;

		return strRecordQuery;

	}

	/* (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> nameIdSet = new HashSet<String>();

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

				while (rs.next()){

	//				handleForeignKey(rs, nameIdSet, "PTNameFk");

	//				handleForeignKey(rs, referenceIdSet, "PTRefFk");

				}

			//reference map

//			nameSpace = "Reference";

//			cdmClass = Reference.class;

//			Map<String, Person> referenceMap = (Map<String, Person>)getCommonService().getSourcedObjectsByIdInSource(Person.class, teamIdSet, nameSpace);

//			result.put(Reference.class, referenceMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	private TaxonBase mapTypes(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException{

		TaxonBase<?> taxonBase = state.getRelatedObject(state.CURRENT_OBJECT_NAMESPACE, state.CURRENT_OBJECT_ID, TaxonBase.class);

		TaxonNameBase name = taxonBase.getName();

		for (int i = 1; i <= 5; i++){

			String[] typeInfo = new String[3];

			typeInfo = getTypeInfo(rs, i);

			if (StringUtils.isBlank(typeInfo[0]) && StringUtils.isBlank(typeInfo[1]) && StringUtils.isBlank(typeInfo[2])){

				continue;

			}

			makeSingleType(state, name, typeInfo[0], typeInfo[1], typeInfo[2]);

		}

		return taxonBase;

	}

	private String[] getTypeInfo(ResultSet rs, int i) throws SQLException {

		String[] typeInfo = new String[3];

		String number;

		if (i == 1){

			number = "";

		}else{

			number = String.valueOf(i);

		}

		typeInfo[0] = rs.getString("Type" + number);

		typeInfo[1] = rs.getString("Type collector and number" + number);

		typeInfo[2] = rs.getString("Type location" + number);

		return typeInfo;

	}

	private void makeSingleType(CentralAfricaFernsImportState state, TaxonNameBase name, String typeString, String typeCollectorString, String typeLocationString) {

		if (name.getRank().isHigher(Rank.SPECIES())){

			//TODO move to TaxonRelationImport

			handleNameType(state, name, typeString, typeCollectorString, typeLocationString);

		}else{

			handleSpecimenType(state, name, typeString, typeCollectorString, typeLocationString);

		}

	}

	private void handleSpecimenType(CentralAfricaFernsImportState state, TaxonNameBase name, String typeString, String typeCollectorString, String typeLocationString) {

		List<SpecimenTypeDesignation> designations = new ArrayList<SpecimenTypeDesignation>();

		typeLocationString = CdmUtils.Nz(typeLocationString);

		if (typeLocationString.equalsIgnoreCase("not located")){

		}else{

			String[] splits = typeLocationString.split(";");

			for (String split : splits){

				List<SpecimenTypeDesignation> splitDesignations = handleTypeLocationPart(state, typeString, typeCollectorString, split);

				designations.addAll(splitDesignations);

			}

		}

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

			logger.error(state.getTaxonNumber() + " - No designations defined. TypeString: " + CdmUtils.Nz(typeString) + ", CollectorString: " + typeCollectorString);

		}

		//type and collector

		DerivedUnitFacade lastFacade = null;

		for (SpecimenTypeDesignation designation: designations){

			name.addTypeDesignation(designation, false);

			if (typeString != null && (typeString.contains("Not designated.")|| typeString.contains("No type designated."))){

				designation.setNotDesignated(true);

			}

			DerivedUnitBase specimen = designation.getTypeSpecimen();

			if (lastFacade != null){

				lastFacade.addDuplicate(specimen);

			}else{

				try {

					lastFacade = DerivedUnitFacade.NewInstance(specimen);

				} catch (DerivedUnitFacadeNotSupportedException e) {

					throw new RuntimeException(e);

				}

				//TODO not so nice

				lastFacade.setLocality(typeString);

				makeTypeCollectorInfo(lastFacade, typeCollectorString);

			}

		}

	}

	private List<SpecimenTypeDesignation> handleTypeLocationPart(CentralAfricaFernsImportState state, 

				String typeString, String typeCollectorString, String typeLocationPart) {

		List<SpecimenTypeDesignation> result = new ArrayList<SpecimenTypeDesignation>();

		String[] splits = typeLocationPart.split(","); 

		//see also SpecimenTypeParser

		String typeTypePattern = "(holo.|lecto.|iso.|isolecto.|syn.|isosyn.|neo.|isoneo.)";

		String collectionPattern = "^[A-Z]+(\\-[A-Z]+)?";

		String numberPattern = "([0-9]+([\\-\\s\\.\\/][0-9]+)?)?";

		String addInfoPattern = "[!\\+\\?]?";

		String typeCollectionPattern = collectionPattern + "\\s?" + numberPattern + addInfoPattern;

		SpecimenTypeDesignation lastDesignation = null;

		for (String split: splits){

			split = split.trim();

			if (StringUtils.isBlank(split)){

				continue;

			}else if(split.trim().startsWith("designated by")){

				split = handleDesignatedBy(lastDesignation, split);

			}else if (split.trim().matches(typeTypePattern)){

				makeSpecimentTypeStatus(lastDesignation, split);

			}else if(split.matches(typeCollectionPattern)){

				lastDesignation = makeSpecimenTypeCollection(lastDesignation, split, collectionPattern, numberPattern, addInfoPattern);

			}else if(split.equalsIgnoreCase("not located")){

				lastDesignation = makeCachedSpecimenDesignation(split);

			}else{

				logger.error(state.getTaxonNumber() + " - Unknown type location part: " +  split);

				if (lastDesignation == null){

					lastDesignation = makeCachedSpecimenDesignation(split);

				}

			}

			if (lastDesignation != null && ! result.contains(lastDesignation)){

				result.add(lastDesignation);

			}else if (lastDesignation == null){

				logger.warn("Last Designation is null");

			}

		}

		return result;

	}

	/**

	 * @param split

	 * @return

	 */

	private SpecimenTypeDesignation makeCachedSpecimenDesignation(String split) {

		SpecimenTypeDesignation lastDesignation;

		lastDesignation = SpecimenTypeDesignation.NewInstance();

		Specimen specimen = Specimen.NewInstance();

		specimen.setTitleCache(split, true);

		lastDesignation.setTypeSpecimen(specimen);

		return lastDesignation;

	}

	private SpecimenTypeDesignation makeSpecimenTypeCollection(SpecimenTypeDesignation designation, String collectionString, String strCollectionPattern, String strNumberPattern, String strAddInfoPattern) {

		SpecimenTypeDesignation result = SpecimenTypeDesignation.NewInstance();

		Specimen specimen = Specimen.NewInstance();

		result.setTypeSpecimen(specimen);

		//collection

		Pattern collectionPattern = Pattern.compile(strCollectionPattern);

		Matcher matcher = collectionPattern.matcher(collectionString);

		if (! matcher.find()){

			throw new RuntimeException("collectionString doesn't match: " + collectionString);

		}

		String strCollection = matcher.group();

		Collection collection = getCollection(strCollection);

		specimen.setCollection(collection);

		collectionString = collectionString.substring(strCollection.length()).trim();

		//collection number

		Pattern numberPattern = Pattern.compile(strNumberPattern);

		matcher = numberPattern.matcher(collectionString);

		if (matcher.find()){

			String strNumber = matcher.group();

			collectionString = collectionString.substring(strNumber.length()).trim();

			if (StringUtils.isNotBlank(strNumber)){

				specimen.setCatalogNumber(strNumber);

			}

		}else{

			//throw new RuntimeException("numberString doesn't match: " + collectionString);

		}

		//additional info

		Pattern addInfoPattern = Pattern.compile(strAddInfoPattern);

		matcher = addInfoPattern.matcher(collectionString);

		if (matcher.find()){

			String strAddInfo = matcher.group();

			collectionString = collectionString.substring(strAddInfo.length()).trim();

			if (StringUtils.isBlank(strAddInfo)){

				//do nothing

			}else if (strAddInfo.equals("!")){

				//TODO add seen by author

			}else if (strAddInfo.equals("?")){

				//TODO add doubtful

			}else if (strAddInfo.equals("+")){

				//TODO add +

			}

		}else{

			//throw new RuntimeException("addInfoString doesn't match: " + collectionString);

		}

		if (StringUtils.isNotBlank(collectionString)){

			logger.error("Collection string is not empty: " + collectionString );

		}

		return result;

	}

	private Collection getCollection(String strCollection) {

		//TODO use BCI and deduplication

		Collection result = Collection.NewInstance();

		return result;

	}

	private void makeSpecimentTypeStatus(SpecimenTypeDesignation designation, String type) {

		SpecimenTypeDesignationStatus status; 

		if (type.equalsIgnoreCase("iso.")){

			status = SpecimenTypeDesignationStatus.ISOTYPE();

		}else if (type.equalsIgnoreCase("isolecto.")){

			status = SpecimenTypeDesignationStatus.ISOLECTOTYPE();

		}else if (type.equalsIgnoreCase("syn.")){

			status = SpecimenTypeDesignationStatus.SYNTYPE();

		}else if (type.equalsIgnoreCase("holo.")){

			status = SpecimenTypeDesignationStatus.HOLOTYPE();

		}else if (type.equalsIgnoreCase("lecto.")){

			status = SpecimenTypeDesignationStatus.LECTOTYPE();

		}else if (type.equalsIgnoreCase("isosyn.")){

			status = SpecimenTypeDesignationStatus.ISOSYNTYPE();

		}else if (type.equalsIgnoreCase("neo.")){

			status = SpecimenTypeDesignationStatus.NEOTYPE();

		}else if (type.equalsIgnoreCase("isoneo.")){

			status = SpecimenTypeDesignationStatus.ISONEOTYPE();

		}else{

			logger.error("Type Status not supported: " + type);

			throw new RuntimeException("Type Status not supported: " + type);

		}

		if (designation == null){

			logger.error("Designation is null");

		}else{

			designation.setTypeStatus(status);

		}

	}

	private void handleNameType(CentralAfricaFernsImportState state, TaxonNameBase name, String typeString, String typeCollectorString, String typeLocation) {

		String originalString = typeString; //just for testing

		if (StringUtils.isNotBlank(typeCollectorString)){

			logger.error(state.getTaxonNumber() + " - Type collector string for name type is not empty: " + typeCollectorString);

		}

		if (StringUtils.isNotBlank(typeLocation)){

			logger.error(state.getTaxonNumber() + " - Type location string for name type is not empty: " + typeLocation);

		}

		NameTypeDesignation nameTypeDesignation = NameTypeDesignation.NewInstance();

		NameTypeDesignationStatus status = null;

		if (StringUtils.isBlank(typeString)){

			logger.warn(state.getTaxonNumber() + " - TypeString is empty");

		}

		if (typeString.startsWith("None designated.")){

			nameTypeDesignation.setNotDesignated(true);

			typeString = typeString.replaceFirst("None designated\\.", "").trim();

		}

		if (typeString.contains("Lectotype: ")|| typeString.contains(", lecto." )){

			status = NameTypeDesignationStatus.LECTOTYPE();

			typeString = typeString.replace("Lectotype: ", "");

			typeString = typeString.replace(", lecto.", "");

			typeString = handleDesignatedBy(nameTypeDesignation, typeString);

		}else{

			typeString = handleDesignatedBy(nameTypeDesignation, typeString);

		}

//		String strSecondNamePattern = "([^\\(]*|\\(.*\\))+;.+"; //never ending story

		String strSecondNamePattern = ".+;.+";

		String firstName;

		String secondName = null;

		if (typeString.matches(strSecondNamePattern)){

			String[] split = typeString.split(";");

			firstName = split[0].trim();

			secondName = split[1].trim();

			if (split.length > 2){

				logger.warn(state.getTaxonNumber() + " - There are more than 2 name types: " + typeString);

			}

		}else{

			firstName = typeString;

		}

		if (StringUtils.isNotBlank(firstName)){

			BotanicalName[] nameTypeNames = getNameTypeName(firstName);

			BotanicalName nameTypeName = nameTypeNames[0];

			BotanicalName nameTypeAcceptedName = nameTypeNames[1];

			nameTypeDesignation.setTypeName(nameTypeName);

			if (nameTypeName.isProtectedTitleCache()){

				logger.error(state.getTaxonNumber() + " - Name type could not be parsed: " + nameTypeName.getTitleCache());

			}

			if (! nameTypeName.getRank().equals(Rank.SPECIES())){

				logger.warn(state.getTaxonNumber() + " - Name type is not of rank species: " + nameTypeName.getTitleCache());

			}

		}

		if (StringUtils.isNotBlank(secondName)){

			TaxonNameBase secondNameType = handleSecondNameTypeName(secondName);

			if (secondNameType.isProtectedTitleCache()){

				logger.error(state.getTaxonNumber() + " - Second name type could not be parsed: " + secondNameType.getTitleCache());

			}

			if (! secondNameType.getRank().equals(Rank.SPECIES())){

				logger.error(state.getTaxonNumber() + " - Second name type is not of rank species: " + secondNameType.getTitleCache());

			}

		}

		nameTypeDesignation.setTypeStatus(status);

		name.addTypeDesignation(nameTypeDesignation, false);

	}

	private TaxonNameBase handleSecondNameTypeName(String strName) {

		//TODO needs feedbacke from Thomas

		logger.info("Not yet implemented");

		if (strName.endsWith(",")){

			strName = strName.substring(0, strName.length() -1);

		}

		BotanicalName result = (BotanicalName)NonViralNameParserImpl.NewInstance().parseFullName(strName, NomenclaturalCode.ICBN, Rank.SPECIES());

		return result;

	}

	private BotanicalName[] getNameTypeName(String strName) {

		//TODO implement get existing names 

		logger.info("Not yet fully implemented");

		BotanicalName[] result = new BotanicalName[2];

		if (strName.endsWith(",")){

			strName = strName.substring(0, strName.length() -1);

		}

		String acceptedName;

		String acceptedNamePattern = "\\(.*\\)\\.?$";

		if (strName.matches(".*" + acceptedNamePattern)){

			int accStart = strName.lastIndexOf("(");

			String notAcceptedName = strName.substring(0, accStart -1 );

			acceptedName = strName.substring(accStart + 1, strName.length() - 1);

			if (acceptedName.endsWith(")")){

				acceptedName = acceptedName.substring(0, acceptedName.length()-1);

			}

			acceptedName = acceptedName.replaceFirst("=", "").trim();

			result[1] = (BotanicalName)NonViralNameParserImpl.NewInstance().parseFullName(acceptedName, NomenclaturalCode.ICBN, null);

			strName = notAcceptedName;

		}

		result[0] = (BotanicalName)NonViralNameParserImpl.NewInstance().parseFullName(strName, NomenclaturalCode.ICBN, Rank.SPECIES());

		return result;

	}

	private String handleDesignatedBy(TypeDesignationBase typeDesignation, String typeString) {

		String[] splitDesignated = typeString.split(", designated by ");

		if (splitDesignated.length > 1){

			Reference designationCitation = getDesignationCitation(typeDesignation, splitDesignated[1]);

			typeDesignation.setCitation(designationCitation);

			if (splitDesignated.length > 2){

				throw new IllegalStateException("More than one designation is not expected");

			}

		}

		return splitDesignated[0].trim();

	}

	private Reference getDesignationCitation(TypeDesignationBase typeDesignation, String citationString) {

		// TODO try to find an existing Reference

		Reference result = ReferenceFactory.newGeneric();

		String strBracketPattern = "\\((10 Oct. )?\\d{4}:\\s?(\\d{1,3}(--\\d{1,3})?|[XLVI]{1,7}|\\.{1,8})\\)\\.?";

		String strStandardPattern = ".*" + strBracketPattern;

//		strStandardPattern = ".*";

		if (Pattern.matches(strStandardPattern, citationString)){

			parseStandardPattern(typeDesignation, result, citationString, strBracketPattern);

		}else{

			logger.error("Can't parse designation citation: " + citationString);

			result.setTitleCache(citationString);

		}

		return result;

	}

	private void parseStandardPattern(TypeDesignationBase typeDesignation, Reference result, String citationString, String bracketPattern) {

		String authorPart = citationString.split(bracketPattern)[0];

		String bracket = citationString.substring(authorPart.length()+1, citationString.length()-1).trim();

		authorPart = authorPart.trim();

		if (bracket.endsWith(")")){

			bracket = bracket.substring(0, bracket.length()-1);

		}

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

		result.setAuthorTeam(team);

		String[] bracketSplit = bracket.split(":");

		TimePeriod datePublished = TimePeriod.parseString(bracketSplit[0].trim());

		result.setDatePublished(datePublished);

		String citationMicroReference = bracketSplit[1].trim();

		citationMicroReference = citationMicroReference.replace("--", "-");

		typeDesignation.setCitationMicroReference(citationMicroReference);

	}

	private void makeTypeCollectorInfo(DerivedUnitFacade specimen, String collectorAndNumberString) {

		if (StringUtils.isBlank(collectorAndNumberString)){

			return;

		}

		String reNumber = "(s\\.n\\.|\\d.*)";

		Pattern reNumberPattern = Pattern.compile(reNumber);

		Matcher matcher = reNumberPattern.matcher(collectorAndNumberString);

		if ( matcher.find()){

			int numberStart = matcher.start();

			String number = collectorAndNumberString.substring(numberStart).trim();

			if (numberStart > 0){

				numberStart = numberStart -1;

			}

			String collectorString = collectorAndNumberString.substring(0, numberStart).trim();

			specimen.setFieldNumber(number);

			TeamOrPersonBase team = getTeam(collectorString);

			specimen.setCollector(team);

		}else{

			logger.warn("collector string did not match number pattern: " + collectorAndNumberString);

		}

	}

	private TeamOrPersonBase getTeam(String teamString) {

		//TODO check existing team

		TeamOrPersonBase result = Team.NewTitledInstance(teamString, teamString);

		return result;

	}

	/**

	 * for internal use only, used by MethodMapper

	 */

	private TaxonBase mapReferences(ResultSet rs, CentralAfricaFernsImportState state) throws SQLException{

		String taxonNumber = state.getTaxonNumber();

		String referenceFullString = rs.getString("Reference full");

		String referenceAbbreviatedString = rs.getString("Reference - abbreviated");

		String volume = rs.getString("Book / Journal volume");

		String pages = rs.getString("Book / Journal pages");

		String illustrations = rs.getString("Illustration/s");

		String fascicle = rs.getString("Book / Journal fascicle");

		String part = rs.getString("Book / Journal part");

		String paperTitle = rs.getString("Book / Paper title");

		String datePublishedString = rs.getString("Date published");

		String referenceString = referenceFullString;

		if (StringUtils.isBlank(referenceString)){

			referenceString = referenceAbbreviatedString;

		}

		TaxonBase<?> taxonBase = state.getRelatedObject(state.CURRENT_OBJECT_NAMESPACE, state.CURRENT_OBJECT_ID, TaxonBase.class);

		if (StringUtils.isNotBlank(referenceString) || StringUtils.isNotBlank(volume) || 

					StringUtils.isNotBlank(pages) || StringUtils.isNotBlank(illustrations) || 

					StringUtils.isNotBlank(datePublishedString) || StringUtils.isNotBlank(paperTitle)){

			NonViralName name = CdmBase.deproxy(taxonBase.getName(), NonViralName.class);

			Reference reference = ReferenceFactory.newGeneric();

			reference.setAuthorTeam((TeamOrPersonBase)name.getCombinationAuthorTeam());

			reference.setTitle(referenceString);

			reference.setVolume(volume);

			reference.setEdition(part);

			Reference inrefernce = null;

			//TODO parser

			TimePeriod datePublished = TimePeriod.parseString(datePublishedString);

			reference.setDatePublished(datePublished);

			if (StringUtils.isNotBlank(paperTitle)){

				Reference innerReference = ReferenceFactory.newGeneric();

				innerReference.setDatePublished(datePublished);

				name.setNomenclaturalReference(innerReference);

				innerReference.setInReference(reference);

				reference = innerReference;

			}else{

				name.setNomenclaturalReference(reference);

			}

			//details

			String details = CdmUtils.concat(", ", pages, illustrations);

			details = StringUtils.isBlank(details) ? null : details.trim();

			name.setNomenclaturalMicroReference(details);

			try {

				UUID uuidFascicle = state.getTransformer().getExtensionTypeUuid("fascicle");

				ExtensionType extensionType = getExtensionType(state, uuidFascicle, "Fascicle", "Fascicle", null);

				reference.addExtension(fascicle, extensionType);

			} catch (UndefinedTransformerMethodException e) {

				e.printStackTrace();

			}

		}else{

			logger.warn(taxonNumber + " - Taxon has no reference");

		}

		return taxonBase;

	}

	/**

	 * for internal use only, used by MethodMapper

	 * @throws Exception 

	 */

	private TaxonBase mapNomRemarks(ResultSet rs, CentralAfricaFernsImportState state) throws Exception{

		try {

			String taxonNumber = state.getTaxonNumber();

			String nomRemarksString = rs.getString("Nom  remarks");

			String taxonStatus = rs.getString("Current/Synonym");

			TaxonBase<?> taxonBase = state.getRelatedObject(state.CURRENT_OBJECT_NAMESPACE, state.CURRENT_OBJECT_ID, TaxonBase.class);

			if (StringUtils.isNotBlank(nomRemarksString)){

				NonViralName name = CdmBase.deproxy(taxonBase.getName(), NonViralName.class);

				parseNomRemark(state, name, nomRemarksString.trim(),taxonStatus, taxonNumber);

			}

			return taxonBase;

		} catch (Exception e) {

			throw e;

		}

	}

	private void parseNomRemark(CentralAfricaFernsImportState state, NonViralName name, String nomRemarksString, String taxonStatus, String taxonNumber) {

		if (nomRemarksString.equalsIgnoreCase("comb. illeg.")){

			name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.COMBINATION_ILLEGITIMATE()));

			return;

//		}else if (nomRemarksString.startsWith("comb. inval.")){

//			//TODO

//			nomRemarksString = nomRemarksString.replace("comb. inval.", "");

//		}else if (nomRemarksString.equals("comb. nov.")){

//			name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.COMBINATION_NOVUM);

		}else if (nomRemarksString.equals("nom. ambig.")){

			name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.AMBIGUOUS()));

			return;

		}else if (nomRemarksString.matches("nom\\. cons(erv)?\\.")){

			name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.CONSERVED()));

			return;

		}else if (nomRemarksString.matches("nom\\. illeg(it)?\\.")){

			name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.ILLEGITIMATE()));

			return;

		}else if (nomRemarksString.matches("nom\\. inval(id)?\\.")){

			name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.INVALID()));

			return;

		}else if (nomRemarksString.matches("nom\\. nov\\.")){

			name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.NOVUM()));

			return;

		}else if (nomRemarksString.matches("nom\\. nud\\.")){

			name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.NUDUM()));

			return;

		}else if (nomRemarksString.matches("nom\\. superfl\\.")){

			name.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.SUPERFLUOUS()));

			return;

		}else if (nomRemarksString.matches("p(\\.|ro\\s)?p(\\.|arte)")){

			//pro parte is handled in taxon relationship import

			if (! taxonStatus.equals("s")){

				logger.warn(" - " +  taxonNumber + " Pro parte synonym is not of type synonym");

			}

			return;

		}else if (nomRemarksString.matches("as '.*'")){

			String nameAsString = nomRemarksString.substring(4, nomRemarksString.length()-1);

			//TODO discuss make it a name relationship

			UUID uuidPublishedAs = CentralAfricaFernsTransformer.uuidNamePublishedAs;

			ExtensionType extensionType = getExtensionType(state, uuidPublishedAs, "Name published as", "Name published as", "as");

			name.addExtension(nameAsString, extensionType);

			return;

		}

		if (StringUtils.isNotBlank(nomRemarksString)){

			ExtensionType extensionType = getExtensionType(state, CentralAfricaFernsTransformer.uuidNomenclaturalRemarks, "Nomenclatural remarks", "Nomenclatural remarks", null);

			name.addExtension(nomRemarksString, extensionType);

		}

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet)

	 */