EDIT

/**

* Copyright (C) 2016 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.greece;

import java.net.URI;

import java.util.Arrays;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.service.ITermService;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.ext.geo.GeoServiceArea;

import eu.etaxonomy.cdm.ext.geo.GeoServiceAreaAnnotatedMapping;

import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @date 14.12.2016

 *

 */

@Component

public class FloraHellenicaTaxonImport<CONFIG extends FloraHellenicaImportConfigurator>

            extends FloraHellenicaImportBase<CONFIG>{

    private static final long serialVersionUID = -6291948918967763381L;

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

    private static final String LIFE_FORM = "Life-form";

    private static final String STATUS = "Status";

    private static final String CHOROLOGICAL_CATEGOGY = "Chorological categogy";

    private static UUID rootUuid = UUID.fromString("aa667b0b-b417-470e-a9b0-ef9409a3431e");

    private static UUID plantaeUuid = UUID.fromString("4f151932-ab97-4d81-b88e-46fe82cd3e88");

    private OrderedTermVocabulary<NamedArea> areasVoc;

    private NamedArea greece;

    private OrderedTermVocabulary<State> lifeformVoc;

    private OrderedTermVocabulary<State> habitatVoc;

    private Map<String, State> lifeformMap = new HashMap<>();

    private OrderedTermVocabulary<PresenceAbsenceTerm> statusVoc;

    private PresenceAbsenceTerm rangeRestricted;

    private PresenceAbsenceTerm doubtfullyRangeRestricted;

    private OrderedTermVocabulary<State> chorologicalVoc;

    private Map<String, State> chorologyMap = new HashMap<>();

   private  static List<String> expectedKeys= Arrays.asList(new String[]{

            "Unique ID","uuid","Group","Family","Genus","Species","Species Author","Subspecies","Subspecies Author",

            "IoI","NPi","SPi","Pe","StE","EC","NC","NE","NAe","WAe","Kik","KK","EAe",

            STATUS,CHOROLOGICAL_CATEGOGY,LIFE_FORM,"A","C","G","H","M","P","R","W", "Taxon"

    });

    private String lastGenus;

    private String lastSpecies;

    private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();

    @Override

    protected String getWorksheetName() {

        return "valid taxa names";

    }

    private boolean isFirst = true;

    private TransactionStatus tx = null;

    /**

     * {@inheritDoc}

     */

    @Override

    protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {

        if (isFirst){

            tx = this.startTransaction();

            isFirst = false;

        }

        initAreaVocabulary(state);

        initLifeformVocabulary(state);

        initHabitatVocabulary(state);

        initChorologicalVocabulary(state);

        initStatusVocabulary(state);

        makeFeatureTree(state);

        String line = state.getCurrentLine() + ": ";

        HashMap<String, String> record = state.getOriginalRecord();

        Set<String> keys = record.keySet();

        for (String key: keys) {

            if (! expectedKeys.contains(key)){

                logger.warn(line + "Unexpected Key: " + key);

            }

        }

        String noStr = getValue(record, "Unique ID");

        Taxon taxon = makeTaxon(state, line, record, noStr);

        //Distribution

        TaxonDescription desc = getTaxonDescription(taxon);

        makeDistribution(state, line, noStr, desc);

        makeChorologicalCategory(state, line, noStr, desc);

        //lifeform

        makeLifeform(state, line, noStr, desc);

        //habitat

        makeHabitat(state, line, noStr, desc);

        state.putTaxon(noStr, taxon);

    }

    @Override

    protected void secondPass(SimpleExcelTaxonImportState<CONFIG> state) {

        if (tx != null){

            this.commitTransaction(tx);

            tx = null;

        }

    }

    boolean hasFeatureTree = false;

    /**

     * @param state

     */

    private void makeFeatureTree(SimpleExcelTaxonImportState<CONFIG> state) {

        if (hasFeatureTree  ){

            return;

        }

        if (getFeatureTreeService().find(state.getConfig().getUuidFeatureTree()) != null){

            hasFeatureTree = true;

            return;

        }

        FeatureTree result = FeatureTree.NewInstance(state.getConfig().getUuidFeatureTree());

        result.setTitleCache(state.getConfig().getFeatureTreeTitle(), true);

        FeatureNode root = result.getRoot();

        FeatureNode newNode;

        ITermService service = getTermService();

        Feature newFeature = (Feature)service.find(Feature.DISTRIBUTION().getUuid());

        newNode = FeatureNode.NewInstance(newFeature);

        root.addChild(newNode);

        newFeature = (Feature)service.find(FloraHellenicaTransformer.uuidFloraHellenicaChorologyFeature);

        newNode = FeatureNode.NewInstance(newFeature);

        root.addChild(newNode);

        newFeature = (Feature)service.find(Feature.LIFEFORM().getUuid());

        newNode = FeatureNode.NewInstance(newFeature);

        root.addChild(newNode);

        newFeature = (Feature)service.find(Feature.HABITAT().getUuid());

        newNode = FeatureNode.NewInstance(newFeature);

        root.addChild(newNode);

        newFeature = (Feature)service.find(Feature.NOTES().getUuid());

        newNode = FeatureNode.NewInstance(newFeature);

        root.addChild(newNode);

        getFeatureTreeService().saveOrUpdate(result);

        hasFeatureTree = true;

    }

    /**

     * @param state

     * @param line

     * @param noStr

     * @param desc

     */

    private void makeChorologicalCategory(SimpleExcelTaxonImportState<CONFIG> state, String line, String noStr,

            TaxonDescription desc) {

        HashMap<String, String> record = state.getOriginalRecord();

        String valueStr = getValue(record, CHOROLOGICAL_CATEGOGY);

        String value = valueStr;

        if (value == null){

            return;

        }

        Feature choroFeature = getFeature(state, FloraHellenicaTransformer.uuidFloraHellenicaChorologyFeature,

                "Chorology", "The Chorological Category", "Choro", null);

        CategoricalData catData = CategoricalData.NewInstance(choroFeature);

        catData.setOrderRelevant(true);

        String[] splits = value.split(" & ");

        replaceDirection(splits, line);

        for (String split: splits){

            String[] splitsA = split.split("/");

            for (String splitA : splitsA){

                String[] splitsB = splitA.split(", ");

                for (String splitB : splitsB){

                    splitB = normalizeChorology(splitB);

                    State choroTerm = chorologyMap.get(splitB);

                    if (choroTerm == null){

                        logger.warn(line + "Some chorology could not be recognized in: " + value + "; Term was: " +splitB);

                    }else{

                        catData.addStateData(choroTerm);

                    }

                }

            }

        }

        if (catData.getStateData().size() > 1){

            catData.setOrderRelevant(true);

        }

        desc.addElement(catData);

    }

    /**

     * @param splitB

     * @return

     */

    private String normalizeChorology(String choroStr) {

        choroStr = choroStr.trim()

                .replace("BK", "Bk")

                .replace("Austral.", "Austr.")

                .replace("trop.As.", "trop. As.");

        if (choroStr.startsWith("[") && !choroStr.endsWith("]")){

            choroStr += "]";

        }else if (!choroStr.startsWith("[") && choroStr.endsWith("]")){

            choroStr = "[" + choroStr;

        }

        return choroStr;

    }

    /**

     * @param splits

     * @param line

     */

    private void replaceDirection(String[] splits, String line) {

        if (splits.length > 1){

            String[] divs = splits[1].split("-");

            if (divs.length == 2){

                splits[0] = splits[0] + "-" + divs[1];

            }else{

                logger.warn(line + "Splits[1] has not expected format: " + splits[1]);

            }

        }

    }

    /**

     * @param state

     * @param line

     * @param noStr

     * @param desc

     */

    private void makeLifeform(SimpleExcelTaxonImportState<CONFIG> state, String line, String noStr,

            TaxonDescription desc) {

        HashMap<String, String> record = state.getOriginalRecord();

        String value = getValue(record, LIFE_FORM);

        String[] splits = value.split("\\s+");

        if (splits.length > 2){

            logger.warn("Unexpected length of lifeform: " + value + " line: "  + line );

        }

        CategoricalData catData = CategoricalData.NewInstance(Feature.LIFEFORM());

        for (String split : splits){

            State lifeform = lifeformMap.get(split);

            if (lifeform == null){

                logger.warn(line + "Unexpected lifeform: " + value);

            }else{

                catData.addStateData(lifeform);

            }

        }

        desc.addElement(catData);

    }

    /**

     * @param state

     * @param line

     * @param noStr

     * @param desc

     */

    private void makeHabitat(SimpleExcelTaxonImportState<CONFIG> state, String line, String noStr,

            TaxonDescription desc) {

        CategoricalData catData = CategoricalData.NewInstance(Feature.HABITAT());

        handleHabitat(state, catData, "A", FloraHellenicaTransformer.uuidHabitatA, line, noStr);

        handleHabitat(state, catData, "C", FloraHellenicaTransformer.uuidHabitatC, line, noStr);

        handleHabitat(state, catData, "G", FloraHellenicaTransformer.uuidHabitatG, line, noStr);

        handleHabitat(state, catData, "H", FloraHellenicaTransformer.uuidHabitatH, line, noStr);

        handleHabitat(state, catData, "M", FloraHellenicaTransformer.uuidHabitatM, line, noStr);

        handleHabitat(state, catData, "P", FloraHellenicaTransformer.uuidHabitatP, line, noStr);

        handleHabitat(state, catData, "R", FloraHellenicaTransformer.uuidHabitatR, line, noStr);

        handleHabitat(state, catData, "W", FloraHellenicaTransformer.uuidHabitatW, line, noStr);

        desc.addElement(catData);

    }

    /**

     * @param state

     * @param catData

     * @param string

     * @param uuidhabitata

     * @param line

     * @param noStr

     */

    private void handleHabitat(SimpleExcelTaxonImportState<CONFIG> state, CategoricalData catData, String label,

            UUID uuidHabitat, String line, String noStr) {

        HashMap<String, String> record = state.getOriginalRecord();

        String value = getValue(record, "" + label);

        if (value == null){

            //do nothing

        }else if (value.matches("[ACGHMPRW]")){

            State habitatState = this.getStateTerm(state, uuidHabitat, null, null, null, habitatVoc);

            catData.addStateData(habitatState);

        }else{

            logger.warn(line + "Unrecognized habitat state '" + value + "' for " + label);

        }

    }

    /**

     * @param state

     * @param line

     * @param noStr

     * @param desc

     */

    private void makeDistribution(SimpleExcelTaxonImportState<CONFIG> state, String line, String noStr,

            TaxonDescription desc) {

        //TODO status Greece

        handleStatus(state, desc, STATUS, FloraHellenicaTransformer.uuidAreaGreece, line, noStr);

        handleDistribution(state, desc, "IoI", FloraHellenicaTransformer.uuidAreaIoI, line, noStr);

        handleDistribution(state, desc, "NPi", FloraHellenicaTransformer.uuidAreaNPi, line, noStr);

        handleDistribution(state, desc, "SPi", FloraHellenicaTransformer.uuidAreaSPi, line, noStr);

        handleDistribution(state, desc, "Pe", FloraHellenicaTransformer.uuidAreaPe, line, noStr);

        handleDistribution(state, desc, "StE", FloraHellenicaTransformer.uuidAreaStE, line, noStr);

        handleDistribution(state, desc, "EC", FloraHellenicaTransformer.uuidAreaEC, line, noStr);

        handleDistribution(state, desc, "NC", FloraHellenicaTransformer.uuidAreaNC, line, noStr);

        handleDistribution(state, desc, "NE", FloraHellenicaTransformer.uuidAreaNE, line, noStr);

        handleDistribution(state, desc, "NAe", FloraHellenicaTransformer.uuidAreaNAe, line, noStr);

        handleDistribution(state, desc, "WAe", FloraHellenicaTransformer.uuidAreaWAe, line, noStr);

        handleDistribution(state, desc, "Kik", FloraHellenicaTransformer.uuidAreaKik, line, noStr);

        handleDistribution(state, desc, "KK", FloraHellenicaTransformer.uuidAreaKK, line, noStr);

        handleDistribution(state, desc, "EAe", FloraHellenicaTransformer.uuidAreaEAe, line, noStr);

    }

    /**

     * @param state

     * @param line

     * @param record

     * @param noStr

     * @return

     */

    private Taxon makeTaxon(SimpleExcelTaxonImportState<CONFIG> state, String line, HashMap<String, String> record,

            String noStr) {

        TaxonNode familyTaxon = getFamilyTaxon(record, state);

        if (familyTaxon == null){

            logger.warn(line + "Family not created: " + record.get("Family"));

        }

        String genusStr = getValue(record, "Genus");

        String speciesStr = getValue(record, "Species");

        String speciesAuthorStr = getValue(record, "Species Author");

        String subSpeciesStr = getValue(record, "Subspecies");

        String subSpeciesAuthorStr = getValue(record, "Subspecies Author");

        String uuidStr = getValue(record, "uuid");

        UUID uuid = UUID.fromString(uuidStr);

        boolean isSubSpecies = isNotBlank(subSpeciesStr);

        boolean isAutonym = isSubSpecies && speciesStr.equals(subSpeciesStr);

        if (isSubSpecies && ! isAutonym && isBlank(subSpeciesAuthorStr)){

            logger.warn(line + "Non-Autonym subspecies has no auhtor");

        }else if (isSubSpecies && isAutonym && isNotBlank(subSpeciesAuthorStr)){

            logger.warn(line + "Autonym subspecies has subspecies auhtor");

        }

        String[] nameParts;

        if (!isSubSpecies){

            nameParts = new String[]{genusStr, speciesStr, speciesAuthorStr};

        }else if (!isAutonym){

            nameParts = new String[]{genusStr, speciesStr, "subsp. " + subSpeciesStr, subSpeciesAuthorStr};

        }else{

            nameParts = new String[]{genusStr, speciesStr, speciesAuthorStr, "subsp. " + subSpeciesStr};

        }

        String nameStr = CdmUtils.concat(" ", nameParts);

        Rank rank = isSubSpecies ? Rank.SUBSPECIES() : Rank.SPECIES();

        BotanicalName name = (BotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);

        if (name.isProtectedTitleCache()){

            logger.warn(line + "Name could not be parsed: " + nameStr);

        }

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

        taxon.addImportSource(noStr, getWorksheetName(), getSourceCitation(state), null);

//        String parentStr = isSubSpecies ? makeSpeciesKey(genusStr, speciesStr, speciesAuthorStr) : genusStr;

        taxon.setUuid(uuid);

        String parentStr = genusStr;

        boolean genusAsBefore = genusStr.equals(lastGenus);

        boolean speciesAsBefore = speciesStr.equals(lastSpecies);

        TaxonNode parent = getParent(state, parentStr);

        if (parent != null){

//            if (!isSubSpecies && genusAsBefore || isSubSpecies && speciesAsBefore){

            if (genusAsBefore ){

                        //everything as expected

                TaxonNode newNode = parent.addChildTaxon(taxon, getSecReference(state), null);

                getTaxonNodeService().save(newNode);

            }else{

                logger.warn(line + "Unexpected non-missing parent");

            }

        }else{

//            if (isSubSpecies){

//                logger.warn(line + "Subspecies should always have an existing parent");

//            }else

            if (genusAsBefore){

                logger.warn(line + "Unexpected missing genus parent");

            }else{

                parent = makeGenusNode(state, record, genusStr);

                TaxonNode newNode = parent.addChildTaxon(taxon, getSecReference(state), null);

                getTaxonNodeService().save(newNode);

            }

        }

        if (!isSubSpecies){

            state.putHigherTaxon(makeSpeciesKey(genusStr, speciesStr, speciesAuthorStr), taxon);

        }

//        this.lastFamily = familyStr

        this.lastGenus = genusStr;

        this.lastSpecies = speciesStr;

        return taxon;

    }

    /**

     * @param genusStr

     * @param speciesStr

     * @param speciesAuthorStr

     * @return

     */

    private String makeSpeciesKey(String genusStr, String speciesStr, String speciesAuthorStr) {

        return CdmUtils.concat(" ", new String[]{genusStr, speciesStr, speciesAuthorStr});

    }

    /**

     * @param state

     * @param record

     * @param genusStr

     * @return

     */

    private TaxonNode makeGenusNode(SimpleExcelTaxonImportState<CONFIG> state,

            HashMap<String, String> record, String genusStr) {

        BotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());

        name.setGenusOrUninomial(genusStr);

        Taxon genus = Taxon.NewInstance(name, getSecReference(state));

        TaxonNode family = getFamilyTaxon(record, state);

        TaxonNode genusNode = family.addChildTaxon(genus, getSecReference(state), null);

        state.putHigherTaxon(genusStr, genus);

        genus.addSource(makeOriginalSource(state));

        getTaxonNodeService().save(genusNode);

        return genusNode;

    }

    /**

     * @param state

     * @param parentStr

     * @return

     */

    private TaxonNode getParent(SimpleExcelTaxonImportState<CONFIG> state, String parentStr) {

        Taxon taxon = state.getHigherTaxon(parentStr);

        return taxon == null ? null : taxon.getTaxonNodes().iterator().next();

    }

    /**

     * @param record

     * @param state

     * @return

     */

    private TaxonNode getFamilyTaxon(HashMap<String, String> record, SimpleExcelTaxonImportState<CONFIG> state) {

        String familyStr = getValue(record, "Family");

        if (familyStr == null){

            return null;

        }

        familyStr = familyStr.trim();

        Taxon family = state.getHigherTaxon(familyStr);

        TaxonNode familyNode;

        if (family != null){

            familyNode = family.getTaxonNodes().iterator().next();

        }else{

            BotanicalName name = makeFamilyName(state, familyStr);

            Reference sec = getSecReference(state);

            family = Taxon.NewInstance(name, sec);

            ITaxonTreeNode groupNode = getGroupTaxon(record, state);

            familyNode = groupNode.addChildTaxon(family, sec, null);

            state.putHigherTaxon(familyStr, family);

            getTaxonNodeService().save(familyNode);

        }

        return familyNode;

    }

    /**

     * @param record

     * @param state

     * @return

     */

    private TaxonNode getGroupTaxon(HashMap<String, String> record, SimpleExcelTaxonImportState<CONFIG> state) {

        String groupStr = getValue(record, "Group");

        if (groupStr == null){

            return null;

        }

        groupStr = groupStr.trim();

        Taxon group = state.getHigherTaxon(groupStr);

        TaxonNode groupNode;

        if (group != null){

            groupNode = group.getTaxonNodes().iterator().next();

        }else{

            BotanicalName name = makeFamilyName(state, groupStr);

            Reference sec = getSecReference(state);

            group = Taxon.NewInstance(name, sec);

            ITaxonTreeNode rootNode = getClassification(state);

            groupNode = rootNode.addChildTaxon(group, sec, null);

            state.putHigherTaxon(groupStr, group);

            getTaxonNodeService().save(groupNode);

        }

        return groupNode;

    }

    private TaxonNode rootNode;

    private TaxonNode getClassification(SimpleExcelTaxonImportState<CONFIG> state) {

        if (rootNode == null){

            Reference sec = getSecReference(state);

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

            Language language = Language.DEFAULT();

            Classification classification = Classification.NewInstance(classificationName, sec, language);

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

            classification.getRootNode().setUuid(rootUuid);

            BotanicalName plantaeName = TaxonNameFactory.NewBotanicalInstance(Rank.KINGDOM());

            plantaeName.setGenusOrUninomial("Plantae");

            Taxon plantae = Taxon.NewInstance(plantaeName, sec);

            TaxonNode plantaeNode = classification.addChildTaxon(plantae, null, null);

            plantaeNode.setUuid(plantaeUuid);

            getClassificationService().save(classification);

            rootNode = plantaeNode;

        }

        return rootNode;

    }

    /**

     * @param desc

     * @param string

     * @param uuidUserDefinedAnnotationTypeVocabulary

     */

    private void handleDistribution(SimpleExcelTaxonImportState<CONFIG> state,

                TaxonDescription desc, String key, UUID uuid, String line, String id) {

        HashMap<String, String> record = state.getOriginalRecord();

        String value = getValue(record, key);

        if (value == null || value.matches("[x\\.\\?]")){

            NamedArea area = getNamedArea(state, uuid, null, null, null, null, null);

            Distribution dist;

            if (".".equals(value)){

                logger.warn(line + "'.' Should not exist anmore as a distribution status: '" + value + "' for " + key);

                dist = Distribution.NewInstance(area, PresenceAbsenceTerm.ABSENT());

            }else if (value == null){

                //TODO is absent wanted

                dist = Distribution.NewInstance(area, PresenceAbsenceTerm.ABSENT());

            }else if ("x".equals(value)){

                dist = Distribution.NewInstance(area, PresenceAbsenceTerm.PRESENT());

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

                dist = Distribution.NewInstance(area, PresenceAbsenceTerm.PRESENT_DOUBTFULLY());

            }else {

                logger.warn(line + "Not matching status. THis should not happpen '" + value + "' for " + key);

                return;

            }

            desc.addElement(dist);

            dist.addImportSource(id, getWorksheetName(), getSourceCitation(state), line);

        }else {

            logger.warn(line + "Unrecognized distribution status '" + value + "' for " + key);

        }

    }

    private void handleStatus(SimpleExcelTaxonImportState<CONFIG> state,

            TaxonDescription desc, String key, UUID uuid, String line, String id) {

        HashMap<String, String> record = state.getOriginalRecord();

        String value = getValue(record, key);

        NamedArea area = getNamedArea(state, uuid, null, null, null, null, null);

        Distribution dist;

        if (value == null || ".".equals(value) ){

            dist = Distribution.NewInstance(area, PresenceAbsenceTerm.NATIVE());

            if (".".equals(value)){

                logger.warn(line + "'.' Should not exist anmore as a distribution status: '" + value + "' for " + key);

            }

        }else if ("Range-restricted".equals(value)){

            dist = Distribution.NewInstance(area, rangeRestricted);

        }else if ("?Range-restricted".equals(value)){

            dist = Distribution.NewInstance(area, doubtfullyRangeRestricted);

        }else if ("Xenophyte".equals(value)){

            dist = Distribution.NewInstance(area, PresenceAbsenceTerm.INTRODUCED());

        }else if ("?Xenophyte".equals(value)){

            dist = Distribution.NewInstance(area, PresenceAbsenceTerm.INTRODUCED_DOUBTFULLY_INTRODUCED());

        }else {

            logger.warn(line + "Not matching status. This should not happpen '" + value + "' for " + key);

            return;

        }

        desc.addElement(dist);

        dist.addImportSource(id, getWorksheetName(), getSourceCitation(state), line);

    }

    @SuppressWarnings("unchecked")

    private void initAreaVocabulary(SimpleExcelTaxonImportState<CONFIG> state) {

        if (areasVoc == null){

            areasVoc = (OrderedTermVocabulary<NamedArea>)this.getVocabularyService().find(FloraHellenicaTransformer.uuidFloraHellenicaAreasVoc);

            if (areasVoc == null){

                createAreasVoc(state);

            }

        }

    }

    /**

     * @param state

     */

    private void initChorologicalVocabulary(SimpleExcelTaxonImportState<CONFIG> state) {

        if (chorologicalVoc == null){

            UUID uuid = FloraHellenicaTransformer.uuidFloraHellenicaChorologicalVoc;

            chorologicalVoc = (OrderedTermVocabulary<State>)this.getVocabularyService().find(uuid);

            if (chorologicalVoc == null){

                createChorologicalVoc(state, uuid);

            }

        }

    }

    @SuppressWarnings("unchecked")

    private void initLifeformVocabulary(SimpleExcelTaxonImportState<CONFIG> state) {

        if (lifeformVoc == null){

            UUID uuid = FloraHellenicaTransformer.uuidFloraHellenicaLifeformVoc;

            lifeformVoc = (OrderedTermVocabulary<State>)this.getVocabularyService().find(uuid);

            if (lifeformVoc == null){

                createLifeformVoc(state, uuid);

            }

        }

    }

    /**

     * @param state

     * @param vocUuid

     */

    private void createLifeformVoc(SimpleExcelTaxonImportState<CONFIG> state, UUID vocUuid) {

        //voc

        URI termSourceUri = null;

        String label = "Checklist of Greece Lifeforms";

        String description = "Lifeforms as used in the Checklist of Greece";

        lifeformVoc = OrderedTermVocabulary.NewInstance(TermType.State,

                description, label, null, termSourceUri);

        lifeformVoc.setUuid(vocUuid);

        addLifeform(state, "A", "Aquatic", FloraHellenicaTransformer.uuidLifeformA);

        addLifeform(state, "C", "Chamaephyte", FloraHellenicaTransformer.uuidLifeformC);

        addLifeform(state, "G", "Geophyte (Cryptophyte)", FloraHellenicaTransformer.uuidLifeformG);

        addLifeform(state, "H", "Hemicryptophyte", FloraHellenicaTransformer.uuidLifeformH);

        addLifeform(state, "P", "Phanerophyte", FloraHellenicaTransformer.uuidLifeformP);

        addLifeform(state, "T", "Therophyte", FloraHellenicaTransformer.uuidLifeformT);

        this.getVocabularyService().save(lifeformVoc);

        return;

    }

    /**

     * @param state

     * @param uuid

     */

    private void createChorologicalVoc(SimpleExcelTaxonImportState<CONFIG> state, UUID vocUuid) {

        //voc

        URI termSourceUri = null;

        String label = "Checklist of Greece Chorological Categories";

        String description = "Chorological Categories as used in the Checklist of Greece";

        chorologicalVoc = OrderedTermVocabulary.NewInstance(TermType.State,

                description, label, null, termSourceUri);

        chorologicalVoc.setUuid(vocUuid);

        addChorological(state, "*", "Greek endemic", "Greek endemics (incl. single-island and single-mountain endemics)", FloraHellenicaTransformer.uuidChorologicalStar);

        addChorological(state, "Bk", "Balkan", "Taxa restricted to Balkan countries, occasionally extending to adjacent parts of SE Europe", FloraHellenicaTransformer.uuidChorologicalBk);

        addChorological(state, "BI", "Balkan-Italy", "Taxa restricted to Balkan countries and Italy (amphi-Adreatic)", FloraHellenicaTransformer.uuidChorologicalBI);

        addChorological(state, "BA", "Balkan-Anatolia", "Taxa restricted to Balkan countries and to Asia minor (Anatolia), occasionally extending to S Ukraine (Crimea), adjacent Caucasian countries (Georgia, Armenia) or N Iraq", FloraHellenicaTransformer.uuidChorologicalBA);

        addChorological(state, "BC", "Balkan-Central Europe", "Taxa distributed in the Balkans, Carpathians, Alps and adjacent areas (mainly in the mountains)", FloraHellenicaTransformer.uuidChorologicalBC);

        addChorological(state, "EM", "East Mediterranean", "Taxa restricted to the E Mediterranean, occasionally extending to S Italy or adjacent Caucasian countries", FloraHellenicaTransformer.uuidChorologicalEM);

        addChorological(state, "Me", "Mediterranean", "Taxa with a circum-Mediterranean distribution including Portugal, occasionally extending to the Caucasus area and N Iran", FloraHellenicaTransformer.uuidChorologicalMe);

        addChorological(state, "MA", "Mediterranean-Atlantic", "Taxa restricted to maritime W Europe and the Mediterranean", FloraHellenicaTransformer.uuidChorologicalMA);

        addChorological(state, "ME", "Mediterranean-European", "Taxa restricted to the Mediterranean and temperate Europe, occasionally extending to NW Africa and the Caucasus area", FloraHellenicaTransformer.uuidChorologicalME);

        addChorological(state, "MS", "Mediterranean-SW Asian", "Taxa distributed in one or more Mediterranean countries and extending to SW and C Asia", FloraHellenicaTransformer.uuidChorologicalMS);

        addChorological(state, "EA", "European-SW Asian", "Eruopean taxa (occasionally reachin N Africa) with a distribution extending to SW Asia, occasionally reaching C Asia", FloraHellenicaTransformer.uuidChorologicalEA);

        addChorological(state, "ES", "Euro-Siberian", "Taxa with main distribution in temperate Eurasia (occasionally reaching the Caucasus area)", FloraHellenicaTransformer.uuidChorologicalES);

        addChorological(state, "Eu", "European", "Taxa with a distribution all over Europe. In S European countries this category in fact represents the C European element", FloraHellenicaTransformer.uuidChorologicalEu);

        addChorological(state, "Pt", "Paleotemperate", "Taxa of extratropical Eurasia including the Himalaya and E Asia, not (or at most marginally) extending to North America", FloraHellenicaTransformer.uuidChorologicalPt);

        addChorological(state, "Ct", "Circumtemperate", "Taxa of both extratropical Eurasia and North America", FloraHellenicaTransformer.uuidChorologicalCt);

        addChorological(state, "IT", "Irano-Turanian", "Taxa with main distribution in arid SW and C Asia, extrazonally extending to the Mediterranean", FloraHellenicaTransformer.uuidChorologicalIT);

        addChorological(state, "SS", "Saharo-Sindian", "Taxa with main distribution in arid N Africa and SQ Asia, extrazonally extending to the Mediterranean", FloraHellenicaTransformer.uuidChorologicalSS);

        addChorological(state, "ST", "Subtropical-tropical", "Taxa widespread in the warmer regions of both hemispheres", FloraHellenicaTransformer.uuidChorologicalST);

        addChorological(state, "Bo", "(Circum-)Boreal", "Taxa with main distribution in N and high-montane Eurasia (occasionally extending to North America)", FloraHellenicaTransformer.uuidChorologicalBo);

        addChorological(state, "AA", "Arctic-Alpine", "Taxa with main distribution beyound the N and aove the high-montane timerlines o fEurasia (occasionally extending to North America)", FloraHellenicaTransformer.uuidChorologicalAA);

        addChorological(state, "Co", "Cosmopolitan", "Taxa distributed in all continents, i.e. beyond the N hemisphere. This category may be given in brackets after the known or supposed native distribution in cases of taxa that have been spread worldwide by humans", FloraHellenicaTransformer.uuidChorologicalCo);

        addChorological(state, "[trop.]", "[tropical]", "", FloraHellenicaTransformer.uuidChorologicaltrop);