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.caryo;

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.io.common.DbImportBase;

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

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

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

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

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

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

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

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.NomenclaturalStatus;

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

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

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

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

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

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

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

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.SynonymRelationshipType;

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

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

import eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy;

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

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

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

/**

 * @author a.mueller

 * @created 20.02.2010

 * @version 1.0

 */

@Component

public class CaryoTaxonImport  extends DbImportBase<CaryoImportState, CaryoImportConfigurator> {

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

	private int modCount = 10000;

	private static final String pluralString = "taxa";

	private static final String dbTableName = "CARYOPHYLLALES";

	private Map<String, Taxon> familyMap = new HashMap<String, Taxon>();

	private Map<String, Person> personMap = new HashMap<String, Person>();

	private Map<String, Team> teamMap = new HashMap<String, Team>();

	private Map<String, TeamOrPersonBase> inAuthorMap = new HashMap<String, TeamOrPersonBase>();

	private Map<String, IJournal> journalMap = new HashMap<String, IJournal>();

	private Map<String, IBook> bookMap = new HashMap<String, IBook>();

	private Classification classification;

	public CaryoTaxonImport(){

		super(dbTableName, pluralString);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.DbImportBase#getIdQuery(eu.etaxonomy.cdm.io.common.DbImportStateBase)

	 */

	@Override

	protected String getIdQuery(CaryoImportState state) {

		String strRecordQuery = 

			" SELECT ID " + 

			" FROM " + dbTableName +

			" ORDER BY id "; 

		return strRecordQuery;	

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.DbImportBase#getRecordQuery(eu.etaxonomy.cdm.io.common.DbImportConfiguratorBase)

	 */

	@Override

	protected String getRecordQuery(CaryoImportConfigurator config) {

		String strRecordQuery = 

			" SELECT t.* " + 

			" FROM " + getTableName() + " t " +

			" WHERE ( t.ID IN (" + ID_LIST_TOKEN + ") )";

		return strRecordQuery;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doPartition(eu.etaxonomy.cdm.io.common.ResultSetPartitioner, eu.etaxonomy.cdm.io.globis.GlobisImportState)

	 */

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, CaryoImportState state) {

		boolean success = true;

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

//		Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE);

		classification = getClassification(state);

		try {

			doFamilies(state);

			doAuthors(state);

			doInAuthors(state);

			doJournals(state);

			doBooks(state);

			ResultSet rs = partitioner.getResultSet();

			int i = 0;

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

			//for each reference

            while (rs.next()){

        		if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}

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

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

        		String genus = rs.getString("Genus");

        		String family = rs.getString("Family");

				String pages = rs.getString("Pages");

				String autoren = rs.getString("Autoren");

				String typeStr = rs.getString("Type");

				String nomStatusStr = rs.getString("NomenclaturalStatus");

				String basioStr = rs.getString("Basionym");

//        	      ,[EtInCitation]

//        	      ,[Gender]

//        	      ,[Basionym]

//        	      ,[OriginalCitation]

				BotanicalName name = BotanicalName.NewInstance(Rank.GENUS());

				name.setGenusOrUninomial(genus);

				makeAuthors(name, autoren, id);

				INomenclaturalReference nomRef = makeNomRef(state, rs, id);

        		name.setNomenclaturalReference(nomRef);

				name.setNomenclaturalMicroReference(pages);

				makeStatus(name, nomStatusStr, id);

				Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());

				handleTypes(state, rs, taxon, typeStr, id);

				handleBasionym(state, rs, taxon, basioStr, id);

				Taxon parent = familyMap.get(family);

				classification.addParentChild(parent, taxon, sec, null);

				taxon.addSource(String.valueOf(taxonId), "NCUGenID", sec, null);

				objectsToSave.add(taxon);

            }

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

			getTaxonService().save(objectsToSave);	

			return success;

		} catch (SQLException e) {

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

			return false;

		}

	}

	private INonViralNameParser parser = NonViralNameParserImpl.NewInstance();

	private void handleBasionym(CaryoImportState state, ResultSet rs, Taxon taxon, String basioStr, Integer id) {

		if (StringUtils.isNotBlank(basioStr)){

			BotanicalName name = (BotanicalName) taxon.getName();

			BotanicalName basionym = BotanicalName.PARSED_NAME(basioStr);

			name.addBasionym(basionym);

			Synonym syn = Synonym.NewInstance(basionym, state.getTransactionalSourceReference());

			taxon.addSynonym(syn, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());

			getTaxonService().save(syn);

		}

	}

	private void handleTypes(CaryoImportState state, ResultSet rs, Taxon taxon, String origType, Integer id) {

		NameTypeDesignation desig = NameTypeDesignation.NewInstance();

		String type = origType;

		if (StringUtils.isBlank(type) ){

			return;

		}else{

			BotanicalName name = (BotanicalName)taxon.getName();

			BotanicalName typeName = BotanicalName.NewInstance(Rank.SPECIES());

			if ("not designated".equalsIgnoreCase(type)){

				desig.setNotDesignated(true);

			}else{

				String genus = name.getGenusOrUninomial();

				typeName.setGenusOrUninomial(genus);

				if (! type.startsWith(genus.substring(0,1) + ". " )){

					int i = type.indexOf(" ");

					String genusOrig = type.substring(0, i);

					logger.warn("First genus letter not recognized: " + genusOrig + "-" + genus + ":"+  id);

					typeName.setGenusOrUninomial(genusOrig);

					type = type.substring(i + 1).trim();

				}else{

					type = type.substring(3);

				}

				int i = type.indexOf(" ");

				if (i <= 0){

					logger.warn("No space: " + type +"; " + id);

				}else{

					String species = type.substring(0, i);

					typeName.setSpecificEpithet(species);

					type = type.substring(i + 1).trim();

					int posBracket = type.indexOf("(", 2);

					if (posBracket > 0){

						String bracket = type.substring(posBracket);

						//TODO

//						logger.warn("Type has bracket("+id+"): " + bracket);

						//TODO Annotation

						type = type.substring(0, posBracket).trim();

					}

					type = makeTypeNomStatus(typeName, type);

					makeAuthors(typeName, type, id);

				}

				desig.setTypeName(typeName);

			}

			name.addTypeDesignation(desig, true);

		}

	}

	private String makeTypeNomStatus(BotanicalName typeName, String type) {

		if (type.endsWith(", nom. illeg.")){

			type = type.replaceAll(", nom. illeg.", "");

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

		}

		return type;

	}

	private void makeStatus(BotanicalName name, String nomStatusStr, Integer id) throws SQLException {

//	      ,[NomenclaturalStatus]

		if (StringUtils.isNotBlank(nomStatusStr)){

			NomenclaturalStatusType nomStatusType;

			try {

				nomStatusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(nomStatusStr);

			} catch (UnknownCdmTypeException e) {

				if (nomStatusStr.startsWith("nom. rej. prop.")){

					nomStatusType = NomenclaturalStatusType.REJECTED_PROP();

					logger.warn("in favour not supported ("+id+"): " + nomStatusStr);

				}else if (nomStatusStr.startsWith("nom. rej. in favour")){

					nomStatusType = NomenclaturalStatusType.REJECTED();

					logger.warn("in favour not supported ("+id+"): " + nomStatusStr);

				}else if (nomStatusStr.startsWith("nom. cons. against")){

					nomStatusType = NomenclaturalStatusType.CONSERVED();

					logger.warn("against not supported ("+id+"): " + nomStatusStr);

				}else if (nomStatusStr.startsWith("nom. cons. prop. against")){

					nomStatusType = NomenclaturalStatusType.CONSERVED_PROP();

					logger.warn("against not supported ("+id+"): " + nomStatusStr);

				}else{

					logger.warn("Unknown status type ("+id+"): " + nomStatusStr);

					nomStatusType = NomenclaturalStatusType.DOUBTFUL();

				}

			}

			NomenclaturalStatus status = NomenclaturalStatus.NewInstance(nomStatusType);

			name.addStatus(status);

		}

	}

	private INomenclaturalReference makeNomRef(CaryoImportState state, ResultSet rs, Integer id) throws SQLException {

		INomenclaturalReference result;

		String periodicalTitle = rs.getString("PeriodicalTitle");

		String volume = rs.getString("PeriodicalVolume");

		String bookTitle = rs.getString("BookTitle");

		String inAutorStr = rs.getString("InAutor");

		String autorenStr = rs.getString("Autoren");

		TeamOrPersonBase<?> author = getNomRefAuthor(autorenStr, id);

		if (StringUtils.isNotBlank(periodicalTitle)){

			IJournal journal = journalMap.get(periodicalTitle);

			if (journal == null){

				logger.warn("Journal not found: " + periodicalTitle + ";" + id);

			}

			IArticle article = ReferenceFactory.newArticle();

			article.setInJournal(journal);

			article.setVolume(volume);

			result = article;

		}else if (StringUtils.isNotBlank(bookTitle)){

			IBook book = bookMap.get(bookTitle);

			if (inAutorStr != null){

				IBookSection section = ReferenceFactory.newBookSection();

				section.setInBook(book);

				TeamOrPersonBase<?> inAuthor = getInAuthor(inAutorStr);

				book.setAuthorTeam(inAuthor);

				result = section;

			}else{

				result = book;

			}

		}else{

			logger.warn("No nomRef found: " +  id);

			result = null;

		}

		if (result != null){

			result.setAuthorTeam(author);

			makeDate(state, rs, result, id);

		}

		return result;

	}

	private void makeDate(CaryoImportState state, ResultSet rs, INomenclaturalReference ref, Integer id) throws SQLException {

		TimePeriod tp = TimePeriod.NewInstance();

		String pre1 = rs.getString("DatePre1");

		String pre2 = rs.getString("DatePre2");

		Float year1 = nullSafeFloat(rs, "DateYear1");

		Float year2 = nullSafeFloat(rs, "DateYear2");

		if (year2 == 0.0 ){

			year2 = null;

		}

		String modi1 = rs.getString("DateModi1");

		String modi2 = rs.getString("DateModi2");

		String date = rs.getString("Date");

		tp.setStartYear(year1.intValue());

		Integer[] preDate1 = getDay(pre1,id);

		tp.setStartMonth(preDate1[1]);

		tp.setStartDay(preDate1[0]);

		if (year2 != null){

			tp.setEndYear(year2.intValue());

		}

		Integer[] preDate2 = getDay(pre2, id);

		tp.setEndMonth(preDate2[1]);

		tp.setEndDay(preDate2[0]);

		if (StringUtils.isNotBlank(modi1) || StringUtils.isNotBlank(modi2)){

			tp.setFreeText(date);

		}

		ref.setDatePublished(tp);

	}

	private Integer[] getDay(String pre, Integer id) {

		Integer[] result = new Integer[2];

		if (! StringUtils.isBlank(pre)){

			try {

				String[] split = pre.split("\\s");

				String monthStr;

				if (split.length > 2){

					logger.warn("L > 2: " + pre);

					monthStr = "";

				}else if(split.length == 2){

					result[0] = Integer.valueOf(split[0]);

					monthStr = split[1];

				}else{

					monthStr = split[0];

				}

				Integer month;

				if ("Jan".equalsIgnoreCase(monthStr)){

					month = 1;

				}else if ("Feb".equalsIgnoreCase(monthStr)){

					month = 2;

				}else if ("Mar".equalsIgnoreCase(monthStr)){

					month = 3;

				}else if ("Apr".equalsIgnoreCase(monthStr)){

					month = 4;

				}else if ("Mai".equalsIgnoreCase(monthStr)){

					month = 5;

				}else if ("Jun".equalsIgnoreCase(monthStr)){

					month = 6;

				}else if ("Jul".equalsIgnoreCase(monthStr)){

					month = 7;

				}else if ("Aug".equalsIgnoreCase(monthStr)){

					month = 8;

				}else if ("Sep".equalsIgnoreCase(monthStr)){

					month = 9;

				}else if ("Oct".equalsIgnoreCase(monthStr)){

					month = 10;

				}else if ("Nov".equalsIgnoreCase(monthStr)){

					month = 11;

				}else if ("Dec".equalsIgnoreCase(monthStr)){

					month = 12;

				}else{

					logger.warn("Unknown month ("+id+"): " + monthStr );

					month = null;

				}

				result[1]= month;

			} catch (Exception e) {

				e.printStackTrace();

			}

		}

		return result;

	}

	private TeamOrPersonBase<?> getInAuthor(String inAutorStr) {

		if (StringUtils.isBlank(inAutorStr)){

			return null;

		}

		TeamOrPersonBase<?> inAuthor = inAuthorMap.get(inAutorStr);

		if (inAuthor == null){

			logger.warn("Inauthor not found: " +  inAutorStr);

		}

		return inAuthor;

	}

	private void makeAuthors(BotanicalName name, String autoren, Integer id) {

		String[] parsedAuthorTeams = getParsedAuthors(autoren);

		name.setBasionymAuthorTeam(getTeam(parsedAuthorTeams[0], id));

		name.setExBasionymAuthorTeam(getTeam(parsedAuthorTeams[1], id));

		name.setCombinationAuthorTeam(getTeam(parsedAuthorTeams[2], id));

		name.setExCombinationAuthorTeam(getTeam(parsedAuthorTeams[3], id));

	}

	private TeamOrPersonBase<?> getNomRefAuthor(String authorStr, Integer id) {

		String[] parsedAuthorTeams = getParsedAuthors(authorStr);

		TeamOrPersonBase<?> team = getTeam(parsedAuthorTeams[2], id);

		return team;

	}

	private TeamOrPersonBase<?> getTeam(String author, Integer id) {

		if (StringUtils.isBlank(author)){

			return null;

		}

		TeamOrPersonBase<?> result;

		if (personMap.get(author) != null){

			result = personMap.get(author);

		}else{

			result = teamMap.get(author);

		}

		if (result == null){

			logger.warn("Team not found ("+id+"): " + author);

		}

		return result;

	}

	private void doInAuthors(CaryoImportState state) throws SQLException {

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

		String sql = "SELECT DISTINCT inAutor FROM " + getTableName() + " WHERE inAutor IS NOT NULL AND inAutor <> '' ";

		ResultSet rs = source.getResultSet(sql);

		while (rs.next()){

			String inAutorStr = rs.getString("inAutor");

			if (inAuthorMap.get(inAutorStr) == null){

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

				inAuthorMap.put(inAutorStr, team);

				getAgentService().save(team);

			}

		}

	}

	private void doAuthors(CaryoImportState state) throws SQLException {

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

		String sql = "SELECT DISTINCT Autoren FROM " + getTableName() + " WHERE Autoren IS NOT NULL AND Autoren <> '' ";

		ResultSet rs = source.getResultSet(sql);

		doTypeAuthors(state);

		while (rs.next()){

			String autorenStr = rs.getString("Autoren");

			String[] parsedAuthorTeams = getParsedAuthors(autorenStr);

			for (String teamStr : parsedAuthorTeams){

				doTeam(teamStr);

			}

		}

	}

	private void doTypeAuthors(CaryoImportState state) {

		doTeam("Dinter & Derenb.");

		doTeam("Marloth");

		doTeam("Engl.");

		doTeam("Kensit");

		doTeam("Sond.");

		doTeam("L. f.");

		doTeam("Dinter & A. Berger");

		doTeam("Schltr.");

		doTeam("Dinter & Berger");

		doTeam("Poir.");

		doTeam("J. C. Wendl.");

		doTeam("Baker & Clarke");

		doTeam("Vahl");

		doTeam("Nicolai");

		doTeam("Gürke");

		doTeam("Cels");

		doTeam("Dams");

		doTeam("Coult.");

		doTeam("A. Weber");

		doTeam("Vaupel");

		doTeam("Gay");

		doTeam("Pall.");

		doTeam("Moq. & Coss.");

		doTeam("Durieu & Moq.");

		doTeam("Lag. & Rodrigues");

		doTeam("M. Martens & Galeotti");

		doTeam("Steud.");

		doTeam("Aitch. & Hemsl.");

		doTeam("Ikonn.-Gal.");

		doTeam("Freitag");

		doTeam("Regel");

		doTeam("Ledeb.");

		doTeam("Schur");

		doTeam("Asch.");

		doTeam("G. Forst.");

		doTeam("Gray");

		doTeam("Curran");

		doTeam("Donn. Sm.");

		doTeam("Diels");

		doTeam("Colla");

		doTeam("Miers");

		doTeam("Gillis");

		doTeam("Royle");

		doTeam("Monv.");

		doTeam("Werderm. & Backeb.");

		doTeam("Wright");

		doTeam("Meyen");

		doTeam("Runge");

		doTeam("Böd.");

		doTeam("Rol.-Goss.");

		doTeam("Poselg.");

		doTeam("Andreae & Backeberg");

		doTeam("Miq.");

		doTeam("Rol.");

		doTeam("Backeb. & Voll");

		doTeam("Engelm. & Bigelow");

		doTeam("Pfeiffer & Otto");

		doTeam("Humb. & Bonpl.");

		doTeam("Schmalh.");

		doTeam("Preobr.");

		doTeam("Labill.");

		doTeam("Barkoudah");

		doTeam("Regel & Schmalh.");

		doTeam("Cambess.");

		doTeam("Pax & K. Hoff.");

		doTeam("Bergeret");

		doTeam("Walp.");

		doTeam("Huds.");

		doTeam("Kit.");

		doTeam("Schott, Nymann & Kotschy");

		doTeam("Boiss. & Buhse");

		doTeam("Medik.");

		doTeam("Coss. & Germ.");

		doTeam("Moss");

		doTeam("Pax & Hoffm.");

		doTeam("Schischk.");

		doTeam("Lipsch.");

		doTeam("Maerkl.");

		doTeam("Vierh.");

		doTeam("Exell");

	}

	/**

	 * @param teamStr

	 * @return

	 */

	protected void doTeam(String teamStr) {

		if (StringUtils.isBlank(teamStr)){

			return;

		}

		String[] parsedTeam = parseTeam(teamStr);

		if (parsedTeam.length == 1){

			savePerson(parsedTeam[0]);

		}else{

			Team team = teamMap.get(teamStr);

			if (team == null){

				team = Team.NewInstance();

				for (String member : parsedTeam){

					Person person = savePerson(member);

					team.addTeamMember(person);

				}

				teamMap.put(teamStr, team);

				getAgentService().saveOrUpdate(team);

			}

		}

		return;

	}

	private String[] parseTeam(String teamStr) {

		String[] split = teamStr.split("[&,]");

		for (int i = 0; i < split.length; i++){

			split[i] = split[i].trim();

		}

		return split;

	}

	private Person savePerson(String personStr) {

		Person result = personMap.get(personStr);

		if (result == null ){

			Person person = Person.NewTitledInstance(personStr);

			personMap.put(personStr, person);

			getAgentService().save(person);

			result = person;

		}

		return result;

	}

	private String[] getParsedAuthors(String autorenStr) {

		String[] result = new String[4]; 

		String basioFull = null;

		String origFull;

			String[]  split = autorenStr.split("\\)");

		if (split.length > 1){

			basioFull = split[0].replace("(", "").trim();

			origFull = split[1].trim();

		}else{

			origFull = split[0].trim();

		}

		String[] splitBasio = splitExAuthors(basioFull);

		String[] splitOrig = splitExAuthors(origFull);

		result[0] = splitBasio[0];

		result[1] = splitBasio[1];

		result[2] = splitOrig[0];

		result[3] = splitOrig[1];

		return result;

	}

	private String[] splitExAuthors(String author) {

		String[] result = new String[2]; 

		if (author != null){

			String[]  split = author.split("\\sex\\s");

			if (split.length > 1){

				//TODO richtige Reihenfolge ?

				result[0] = split[1].trim();

				result[1] = split[0].trim();

			}else{

				result[0] = split[0].trim();

			}

		}

		return result;

	}

	private void doBooks(CaryoImportState state) throws SQLException {

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

		String sql = "SELECT DISTINCT BookTitle FROM " + getTableName() + " WHERE BookTitle IS NOT NULL AND BookTitle <> '' ";

		ResultSet rs = source.getResultSet(sql);

		while (rs.next()){

			String bookStr = rs.getString("BookTitle");

			if (bookMap.get(bookStr) == null ){

				IBook book = ReferenceFactory.newBook(); 

				book.setTitle(bookStr);

				bookMap.put(bookStr, book);

				getReferenceService().save((Reference<?>)book);

			}

		}

	}

	private void doJournals(CaryoImportState state) throws SQLException {

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

		String sqlPeriodical = "SELECT DISTINCT PeriodicalTitle FROM " + getTableName() + " WHERE PeriodicalTitle IS NOT NULL AND PeriodicalTitle <> '' ";

		ResultSet rs = source.getResultSet(sqlPeriodical);

		while (rs.next()){

			String periodical = rs.getString("PeriodicalTitle");

			if (journalMap.get(periodical) == null ){

				Reference<?> journal = ReferenceFactory.newJournal(); 

				journal.setTitle(periodical);

				journalMap.put(periodical, journal);

				getReferenceService().save(journal);

			}

		}

	}

	private void doFamilies(CaryoImportState state) throws SQLException {

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

		String sqlFamily = "SELECT DISTINCT Family FROM " + getTableName() + " WHERE Family IS NOT NULL";

		ResultSet rs = source.getResultSet(sqlFamily);

		while (rs.next()){

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

			if (familyMap.get(family) == null ){

				BotanicalName name = BotanicalName.NewInstance(Rank.FAMILY());

				name.setGenusOrUninomial(family);

				Taxon taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());

				classification.addChildTaxon(taxon, null, null, null);

	//			taxon.addSource(id, idNamespace, citation, null);

				familyMap.put(family, taxon);

				getTaxonService().save(taxon);

			}

		}

	}

	private Classification getClassification(CaryoImportState state) {

		if (this.classification == null){

			String name = state.getConfig().getClassificationName();

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

			this.classification = Classification.NewInstance(name, reference, Language.DEFAULT());

			if (state.getConfig().getClassificationUuid() != null){

				classification.setUuid(state.getConfig().getClassificationUuid());

			}

			getClassificationService().save(classification);

		}

		return this.classification;

	}

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

//			

//			while (rs.next()){

////				handleForeignKey(rs, taxonIdSet, "taxonId");

//			}

//			

//			//taxon map

//			nameSpace = TAXON_NAMESPACE;

//			cdmClass = Taxon.class;

//			idSet = taxonIdSet;

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

//			result.put(nameSpace, objectMap);

//

//			

//		} catch (SQLException e) {

//			throw new RuntimeException(e);

//		}

		return result;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean doCheck(CaryoImportState state){

		return true;

	}