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.caryo;

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 java.util.regex.Matcher;

import java.util.regex.Pattern;

import org.apache.commons.lang3.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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.IdentifiableSource;

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

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.Rank;

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * Kew excel taxon import for Caryophyllaceae.

 *

 * @author a.mueller

 * @since 05.01.2022

 */

@Component

public class KewExcelTaxonImport<CONFIG extends KewExcelTaxonImportConfigurator>

            extends SimpleExcelTaxonImport<CONFIG>{

    private static final long serialVersionUID = 1081966876789613803L;

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

    private static final String NO_SIMPLE_DIFF = "xxxxx";

    private static final String KEW_UNPLACED_NODE = "82a9e3a1-2519-402a-b3c9-ec4c1fddf4d0";

    private static final String KEW_ACCEPTED_NODE = "b44da8af-6ad8-4b41-98cd-8f4c1a1bd00c";

    private static final String KEW_ORPHANED_PLACEHOLDER_TAXON = "dccac79b-a967-49ed-b153-5faa83194060";

    private static final String CDM_Name_UUID = "CDM-Name_UUID";

    private static final String Kew_Name_ID = "Kew-Name-ID";

    private static final String Kew_Name_Citation = "Kew-Name-Citation";

    private static final String Kew_Taxonomic_Status = "Kew-Taxonomic-Status";

    private static final String Kew_Nomencl_Status = "Kew-Nomencl-Status";

    private static final String Kew_Rel_Acc_Name_ID = "Kew-Rel-Acc-Name-ID";

    private static final String Kew_Rel_Basionym_Name_ID = "Kew-Rel-Basionym-Name-ID";

    private static final String GENUS_HYBRID = "genus_hybrid";

    private static final String GENUS = "genus";

    private static final String SPECIES_HYBRID = "species_hybrid";

    private static final String SPECIES = "species";

    private static final String infraspecific_rank = "infraspecific_rank";

    private static final String infraspecies = "infraspecies";

    private static final String parenthetical_author = "parenthetical_author";

    private static final String primary_author = "primary_author";

    private static final String publication_author = "publication_author";

    private static final String place_of_publication = "place_of_publication";

    private static final String volume_and_page = "volume_and_page";

    private static final String KewYear4CDM = "KewYear4CDM";

    private static final String PubTypeABSG = "PubTypeABSG";

    private static final String Sec_Ref_CDM_UUID = "Sec-Ref-CDM-UUID";

    private static final Map<String, UUID> nameMap = new HashMap<>();

    private static final Map<String, UUID> taxonMap = new HashMap<>();

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

            CDM_Name_UUID, Kew_Name_ID, Kew_Name_Citation, Kew_Taxonomic_Status,

            Kew_Nomencl_Status, Kew_Rel_Acc_Name_ID, Kew_Rel_Basionym_Name_ID, GENUS_HYBRID, GENUS,

            SPECIES_HYBRID, SPECIES, infraspecific_rank, infraspecies,

            parenthetical_author, primary_author, publication_author, place_of_publication,

            volume_and_page, KewYear4CDM, PubTypeABSG, Sec_Ref_CDM_UUID

    });

    private Reference sourceReference;

    private Reference secReference;

    private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();

//    @Override

//    protected String getWorksheetName(CONFIG config) {

//        return "valid taxa names";

//    }

    @Override

    protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {

        String line = getLine(state, 50);

        System.out.println(line);

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

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

        for (String key: keys) {

            if (! expectedKeys.contains(key)){

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

            }

        }

        makeTaxon(state, line, record);

    }

    private void makeTaxon(SimpleExcelTaxonImportState<CONFIG> state, String line, Map<String, String> record) {

//        state.getTransactionStatus().flush();

        Reference sec = getSecReference(state, record);

        //name

        TaxonName existingName = getExistingName(state, line);

        if (existingName != null){

            verifyName(state, existingName, record, line, false);

        }else{

            existingName = createName(state, line);

        }

        //taxon

        TaxonBase<?> taxonBase = makeTaxonBase(state, line, record, existingName, sec);

        if (taxonBase != null){

            getTaxonService().saveOrUpdate(taxonBase);

        }

        return;

    }

    private TaxonName createName(SimpleExcelTaxonImportState<CONFIG> state, String line) {

        //parse

        String fullTitle = getValue(state, Kew_Name_Citation);

        String kewNameId = getValue(state, Kew_Name_ID);

        fullTitle = replaceBookSectionAuthor(state, fullTitle);

        TaxonName newName = parser.parseReferencedName(fullTitle, NomenclaturalCode.ICNAFP, Rank.SPECIES());

        handleBookSectionAuthor(newName, state, line);

        putName(kewNameId, newName.getUuid(), line);

        //name status

        makeNameStatus(line, state.getOriginalRecord(), newName);

        verifyName(state, newName, state.getOriginalRecord(), line, true);

        //deduplication

        replaceNameAuthorsAndReferences(state, newName);

        newName.addSource(makeOriginalSource(state));

        getNameService().saveOrUpdate(newName);

        //Kew-Nomencl-Status

        return newName;

    }

    private void handleBookSectionAuthor(TaxonName newName, SimpleExcelTaxonImportState<CONFIG> state, String line) {

        String type = getValue(state, PubTypeABSG);

        if ("BS".equals(type)){

            Reference book = newName.getNomenclaturalReference();

            String pubAuthor = getValue(state, publication_author);

            if (book != null && StringUtils.isNotEmpty(pubAuthor)){

                TeamOrPersonBase<?> bookAuthor = parseBookSectionAuthor(pubAuthor, line);

                Reference bookSection = ReferenceFactory.newBookSection();

                bookSection.setAuthorship(book.getAuthorship());

                book.setAuthorship(bookAuthor);

                bookSection.setInReference(book);

                bookSection.setDatePublished(book.getDatePublished());

                newName.setNomenclaturalReference(bookSection);

            }else{

                logger.warn(line + "unexpected booksection author handling");

            }

        }

    }

    private TeamOrPersonBase<?> parseBookSectionAuthor(String pubAuthor, String line) {

        TeamOrPersonBase<?> result;

        String ed = "";

        if (pubAuthor.endsWith(" (ed.)")){

            ed = " (ed.)";

        }else if (pubAuthor.endsWith(" (eds.)")){

            ed = " (eds.)";

        }

        pubAuthor = pubAuthor.substring(0, pubAuthor.length() - ed.length());

        String[] splits = pubAuthor.split("(, | & )");

        if (splits.length > 1){

            Team team = Team.NewInstance();

            result = team;

            for (String split : splits){

                if ("al.".equals(split.trim())){

                    team.setHasMoreMembers(true);

                }else{

                    team.addTeamMember(getPerson(split, line));

                }

            }

        }else{

            result = getPerson(splits[0], line);

        }

        if (ed.length() > 0){

            result.setTitleCache(result.getTitleCache() + ed, true);

        }

        return result;

    }

    private Person getPerson(String personStr, String line) {

        Person result = Person.NewInstance();

        String regEx = "([A-ZÉ]\\.\\-?)+((de|von)\\s)?(?<famname>[A-Z][a-zèéöü]+((\\-|\\s(i|de)?\\s*)[A-Z][a-zèéü]+)?)";

//        regEx = "([A-ZÉ]\\.\\-?)+((de|von)\\s)?Boissier";

        Matcher matcher = Pattern.compile(regEx).matcher(personStr);

        if (matcher.matches()){

            String famName = matcher.group("famname");

            result.setFamilyName(famName);

            String initials = personStr.replace(famName,"").trim();

            result.setInitials(initials);

        }else{

            result.setTitleCache(personStr, true);

            logger.warn(line + "BookSection author could not be parsed: " +  personStr);

        }

        return result;

    }

    private String replaceBookSectionAuthor(SimpleExcelTaxonImportState<CONFIG> state, String fullTitle) {

        String type = getValue(state, PubTypeABSG);

        if ("BS".equals(type)){

            String pubAuthor = getValue(state, publication_author);

            int inIndex = fullTitle.indexOf(" in ");

            int commaIndex = fullTitle.indexOf(", ");

        }

        return fullTitle;

    }

    private void verifyName(SimpleExcelTaxonImportState<CONFIG> state, TaxonName taxonName,

            Map<String, String> record, String line, boolean isNew) {

        if (isNew){

            boolean parsed = checkParsed(taxonName, getValue(state, Kew_Name_Citation), null, line);

            if (!parsed){

                return;

            }

        }

        String fullDiff = verifyField(replaceStatus(taxonName.getFullTitleCache()), record, Kew_Name_Citation, line, null, isNew);

        verifyField(taxonName.getGenusOrUninomial(), record, GENUS, line, null, isNew);

        verifyField(taxonName.getSpecificEpithet(), record, SPECIES, line, null, isNew);

        verifyField(taxonName.getInfraSpecificEpithet(), record, infraspecies, line, null, isNew);

        String existingBasionymAuthor = authorAndExAuthor(taxonName.getBasionymAuthorship(), taxonName.getExBasionymAuthorship());

        verifyField(existingBasionymAuthor, record, parenthetical_author, line, null, isNew);

        String existingCombinationAuthor = authorAndExAuthor(taxonName.getCombinationAuthorship(), taxonName.getExCombinationAuthorship());

        verifyField(existingCombinationAuthor, record, primary_author, line, null, isNew);

        //reference

        Reference nomRef = taxonName.getNomenclaturalReference();

        if (nomRef == null){

            logger.warn(line + "no nom.ref. exists in existing name");

        }else{

            //place of publication

            boolean hasInRef = nomRef.getInReference() != null;

            String existingAbbrevTitle = hasInRef && (nomRef.getType() == ReferenceType.BookSection || nomRef.getType() == ReferenceType.Article) ?

                    nomRef.getInReference().getAbbrevTitle() :

                    nomRef.getAbbrevTitle();

            String diffPlacePub = verifyField(existingAbbrevTitle, record, place_of_publication, line, fullDiff, isNew);

            //author

            String inRefAuthor = (!hasInRef || nomRef.getInReference().getAuthorship() == null) ? null : nomRef.getInReference().getAuthorship().getTitleCache();

            verifyField(inRefAuthor, record, publication_author, line, fullDiff, isNew);

            //vol and page

            String existingVolume = getVolume(nomRef);

            String existingVolAndPage = CdmUtils.Nz(existingVolume) + ": " + CdmUtils.Nz(taxonName.getNomenclaturalSource().getCitationMicroReference());

            verifyField(existingVolAndPage, record, volume_and_page, line, fullDiff, diffPlacePub, isNew);

            //year

            verifyField(nomRef.getYear(), record, KewYear4CDM, line, fullDiff, isNew);

            //pub type

            verifyField(abbrefRefType(nomRef.getType()), record, PubTypeABSG, line, null, isNew);

        }

    }

    private String getVolume(Reference nomRef) {

        Reference ref = nomRef.isBookSection()? nomRef.getInReference(): nomRef;

        String vol = ref.getVolume();

        String edition = ref.getEdition();

        if (StringUtils.isNotBlank(edition)){

            edition = ", " + (isNumber(edition)? "ed. ":"") + edition + ",";

        }

        String series = ref.getSeriesPart();

        if (StringUtils.isNotBlank(series)){

            series = ", " + (isNumber(series)? "ser. ":"") + series + ",";

        }

        return vol;

    }

    private boolean isNumber(String edition) {

        try {

            Integer.valueOf(edition);

        } catch (NumberFormatException e) {

            return false;

        }

        return true;

    }

    private String authorAndExAuthor(TeamOrPersonBase<?> author,

            TeamOrPersonBase<?> exAuthor) {

        return author == null? null : (exAuthor != null ? (exAuthor.getNomenclaturalTitleCache() + " ex "): "")

                + author.getNomenclaturalTitleCache();

    }

    private String replaceStatus(String fullTitleCache) {

        return fullTitleCache.replaceAll(", nom\\. inval\\.$", "").replaceAll(", nom\\. illeg\\.$", "");

    }

    private String abbrefRefType(ReferenceType type) {

        return type == ReferenceType.Article ? "A" :

            type == ReferenceType.Book ? "B" :

            type == ReferenceType.BookSection ? "BS" :

            type == ReferenceType.Generic ? "GEN" :

            type.getLabel() ;

    }

    private String verifyField(String expectedValue, Map<String, String> record, String fieldName, String line, String noLogIf, boolean isNew) {

        return verifyField(expectedValue, record, fieldName, line, noLogIf, null, isNew);

    }

    private String verifyField(String expectedValue, Map<String, String> record, String fieldName, String line,

            String noLogIf, String noLogIf2, boolean isNew) {

        String value = getValue(record, fieldName);

        if (!CdmUtils.nullSafeEqual(expectedValue, value)){

            String diff = singleDiff(expectedValue, value);

            String label = isNew ? "New     " : "Existing";

            if (!diff.equals(noLogIf) && !diff.equals(noLogIf2) || diff.equals(NO_SIMPLE_DIFF)){

                System.out.println("   " + line + fieldName + "\n        "+label+": " + expectedValue + "\n        Kew     : " + value);

            }

            return diff;

        }else{

            return "";

        }

    }

    private String singleDiff(String expectedValue, String value) {

        if (expectedValue == null){

            return CdmUtils.Nz(value);

        }else if (value == null){

            return CdmUtils.Nz(expectedValue);

        }

        expectedValue = expectedValue.trim();

        value = value.trim();

        String diff_ab = StringUtils.difference(expectedValue, value);

        String diff_ba = StringUtils.difference(value, expectedValue);

        if (diff_ab.endsWith(diff_ba)){

            return "+" + diff_ab.substring(0, diff_ab.length() - diff_ba.length());

        }else if (diff_ba.endsWith(diff_ab)){

            return "-" + diff_ba.substring(0, diff_ba.length() - diff_ab.length());

        }else{

            return NO_SIMPLE_DIFF;

        }

    }

    private TaxonName getExistingName(SimpleExcelTaxonImportState<CONFIG> state, String line) {

        String cdmNameUuid = getValue(state, CDM_Name_UUID);

        String kewNameId = getValue(state, Kew_Name_ID);

        if (cdmNameUuid == null){

            return null;

        }

        TaxonName existingName = getNameService().load(UUID.fromString(cdmNameUuid));

        if (existingName != null){

            putName(kewNameId, existingName.getUuid(), line);

            return CdmBase.deproxy(existingName);

        }else{

            return null;

        }

    }

    private void putName(String kewNameId, UUID uuid, String line) {

        UUID existingUuid = nameMap.put(kewNameId, uuid);

        if (existingUuid != null){

            logger.warn(line + "Kew-Name-id already exists: " + kewNameId);

        }

    }

    private void makeNameStatus(String line, Map<String, String> record,

            TaxonName taxonName) {

        String nameStatus = getValue(record, Kew_Nomencl_Status);

        NomenclaturalStatusType status;

        if (isBlank(nameStatus)){

            status = null;

        }else if ("Illegitimate".equals(nameStatus)){

            status = NomenclaturalStatusType.ILLEGITIMATE();

        }else if ("Invalid".equals(nameStatus)){

            status = NomenclaturalStatusType.INVALID();

        }else{

            logger.warn(line + "Nom. status not recognized: " + nameStatus);

            status = null;

        }

        if (status != null){

            taxonName.addStatus(NomenclaturalStatus.NewInstance(status));

        }

    }

    private TaxonBase<?> makeTaxonBase(SimpleExcelTaxonImportState<CONFIG> state, String line,

            Map<String, String> record, TaxonName taxonName, Reference sec) {

        TaxonBase<?> taxonBase;

        boolean isUnplaced = false;

        String taxStatusStr = getValue(record, Kew_Taxonomic_Status);

        if ("Accepted".equals(taxStatusStr)){

            taxonBase = Taxon.NewInstance(taxonName, sec);

        }else if ("Synonym".equals(taxStatusStr)){

            taxonBase = Synonym.NewInstance(taxonName, sec);

        }else if ("Artificial Hybrid".equals(taxStatusStr)){

            taxonBase = Synonym.NewInstance(taxonName, sec);

        }else if ("Unplaced".equals(taxStatusStr)){

            taxonBase = Taxon.NewInstance(taxonName, sec);

        }else{

            logger.warn(line + "Status not handled: " + taxStatusStr);

            return null;

        }

        taxonBase.addSource(makeOriginalSource(state));

        taxonMap.put(getValue(record, Kew_Name_ID), taxonBase.getUuid());

        if (taxonBase instanceof Taxon){

            UUID existing = taxonMap.get(taxonBase.getName().getNameCache());

            if (existing == null || !isUnplaced){

                taxonMap.put(taxonBase.getName().getNameCache(), taxonBase.getUuid());

            }else if (!isUnplaced){

                taxonMap.put(taxonBase.getName().getNameCache(), taxonBase.getUuid());

                System.out.println("  " + line + "There is more than 1 taxon with name: " + taxonBase.getName().getNameCache());

            }

        }

        return taxonBase;

    }

    int c2 = 0;

    @Override

    protected void secondPass(SimpleExcelTaxonImportState<CONFIG> state) {

        String kewId = getValue(state, Kew_Name_ID) + ": ";

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

//        System.out.println(line);

        if (c2++ % 100 == 0){

            this.commitTransaction(state.getTransactionStatus());

            this.classification = null;

            this.secReference = null;

            this.sourceReference = null;

            this.orphanedSynonymTaxon = null;

            TransactionStatus tx = this.startTransaction();

            state.setTransactionStatus(tx);

            logger.info(line + "New transaction started.");

        }

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

        Classification classification = getClassification(state);

        TaxonBase<?> taxonBase = getTaxon(record);

        TaxonName taxonName = taxonBase.getName();

        if (taxonBase.isInstanceOf(Taxon.class)){

            Taxon parent = getParent(record, taxonName, line, kewId);

            if (parent != null){

                classification.addParentChild(parent, CdmBase.deproxy(taxonBase, Taxon.class), null, null);

            }

        }else if (taxonBase.isInstanceOf(Synonym.class)){

            Taxon taxon = getAcceptedTaxon(record, line, kewId);

            if (taxon == null){

                taxon = getOrphanedSynonymTaxon(state);

                logger.warn(kewId + "Accepted taxon not found. Added synonym to 'orphaned synonym taxon': " + getValue(record, Kew_Rel_Acc_Name_ID) + line);

            }

            taxon.addSynonym(CdmBase.deproxy(taxonBase, Synonym.class), SynonymType.SYNONYM_OF());

        }else{

            logger.warn("Unhandled");

        }

        String basionymId = getValue(record, Kew_Rel_Basionym_Name_ID);

        if (basionymId != null){

            UUID basionymUuid = nameMap.get(basionymId);

            TaxonName basionym = getNameService().find(basionymUuid);

            if(basionym == null){

                logger.warn(kewId + "Basionym does not exist: " + basionymId + line);

            }else{

                taxonName.addBasionym(basionym);

                taxonName.mergeHomotypicGroups(basionym);  //just in case this is not automatically done

                //TODO

                //          adjustSynonymType(taxonBase, basionymTaxon, line);

            }

        }

    }

    Taxon orphanedSynonymTaxon;

    private Taxon getOrphanedSynonymTaxon(SimpleExcelTaxonImportState<CONFIG> state) {

        if (orphanedSynonymTaxon != null) {

            return orphanedSynonymTaxon;

        }

        UUID orphanedTaxonUuid = UUID.fromString(KEW_ORPHANED_PLACEHOLDER_TAXON);

        orphanedSynonymTaxon = CdmBase.deproxy(getTaxonService().find(orphanedTaxonUuid), Taxon.class);

        if (orphanedSynonymTaxon == null){

            TaxonName placeholderName = TaxonNameFactory.NewBacterialInstance(Rank.SUBFAMILY());

            placeholderName.setTitleCache("Orphaned_Synonyms_KEW", true);

            orphanedSynonymTaxon = Taxon.NewInstance(placeholderName, getSecReference(state, state.getOriginalRecord()));

            orphanedSynonymTaxon.setUuid(orphanedTaxonUuid);

            Taxon unplacedTaxon = CdmBase.deproxy(getTaxonService().find(UUID.fromString(KEW_UNPLACED_NODE)), Taxon.class);

            TaxonNode orphandNode = getClassification(state).addParentChild(unplacedTaxon, orphanedSynonymTaxon, null, null);

            getTaxonNodeService().save(orphandNode);

        }

        return orphanedSynonymTaxon;

    }

    private Classification classification;

    private Classification getClassification(SimpleExcelTaxonImportState<CONFIG> state) {

        if (classification == null){

            classification = getClassificationService().find(state.getConfig().getClassificationUuid());

        }

        return classification;

    }

    private Taxon getAcceptedTaxon(Map<String, String> record, String line, String kewId) {

        String statusStr = getValue(record, Kew_Taxonomic_Status);

        if ("Synonym".equals(statusStr) || "Artificial Hybrid".equals(statusStr) ){

            String accKewId = getValue(record, Kew_Rel_Acc_Name_ID);

            UUID accUuid = taxonMap.get(accKewId);

            TaxonBase<?> accBase = getTaxonService().find(accUuid);

            if (accBase == null){

                logger.warn(kewId + "Accepted Taxon does not exist: " + accKewId + line);

                return null;

            }else if (accBase.isInstanceOf(Synonym.class)){

                logger.warn(kewId + "Accepted Taxon is synonym: " + accKewId + line);

                return null;

            }else{

                return CdmBase.deproxy(accBase, Taxon.class);

            }

        }else{

            logger.warn(kewId + "Parent not retrieved" +  line);

            return null;

        }

    }

    private Taxon getParent(Map<String, String> record, TaxonName taxonName, String line, String kewId) {

        String statusStr = getValue(record, Kew_Taxonomic_Status);

        if ("Unplaced".equals(statusStr)){

            return CdmBase.deproxy(getTaxonService().find(UUID.fromString(KEW_UNPLACED_NODE)), Taxon.class);

        }else if ("Artificial Hybrid".equals(statusStr)){

            return null ; //getTaxonNodeService().find(UUID.fromString(KEW_HYBRIDS_NODE)); hybrids are handled as synonyms now

        }else if ("Accepted".equals(statusStr)){

            String higherName = getHigherRankName(taxonName);

            UUID parentTaxonUuid = higherName == null ? null : taxonMap.get(higherName);

            if (parentTaxonUuid != null){

                TaxonBase<?> parentBase = getTaxonService().find(parentTaxonUuid);

                if (parentBase == null){

                    return null;

                } else if (parentBase.isInstanceOf(Taxon.class)){

                    Taxon parentTaxon = CdmBase.deproxy(parentBase, Taxon.class);

                    return parentTaxon;

                } else {

                    logger.warn(kewId + "Parent is synonym " + line);

                    return null;

                }

            }else{

                return CdmBase.deproxy(getTaxonService().find(UUID.fromString(KEW_ACCEPTED_NODE)), Taxon.class);

            }

        }else if ("Synonym".equals(statusStr)){

            //not relevant

            return null;

        }else{

            logger.warn(kewId + "Parent not retrieved" + line);

            return null;

        }

    }

    private String getHigherRankName(TaxonName taxonName) {

        if (Rank.SPECIES().equals(taxonName.getRank())){

            return taxonName.getGenusOrUninomial();

        }else if (taxonName.isInfraSpecific()){

            return taxonName.getGenusOrUninomial() + " " + taxonName.getSpecificEpithet();

        }

        return null;

    }

    private void adjustSynonymType(TaxonBase<?> taxonBase, TaxonBase<?> homotypicTaxon, String line) {

        adjustSynonymTypeOrdered(taxonBase, homotypicTaxon, line);

        adjustSynonymTypeOrdered(homotypicTaxon, taxonBase, line);

    }

    private void adjustSynonymTypeOrdered(TaxonBase<?> firstTaxon, TaxonBase<?> secondTaxon, String line) {

        if (firstTaxon == null){

            logger.warn(line + "first taxon is null for adjust synonym type");

        }else if (secondTaxon == null){

            logger.warn(line + "second taxon is null for adjust synonym type");

        }else if (secondTaxon.isInstanceOf(Synonym.class)){

            Synonym syn = CdmBase.deproxy(secondTaxon, Synonym.class);

            if (firstTaxon.equals(syn.getAcceptedTaxon())){

                syn.setType(SynonymType.HOMOTYPIC_SYNONYM_OF());

            }

        }

    }

    protected TaxonBase<?> getTaxon(Map<String, String> record) {

        String kew_name_id = getValue(record, Kew_Name_ID);

        UUID taxonUuid = taxonMap.get(kew_name_id);

        TaxonBase<?> taxon = getTaxonService().find(taxonUuid);

        return taxon;

    }

	private boolean checkParsed(TaxonName name, String fullName, String nameStr, String line) {

		boolean result = true;

	    if (name.isProtectedTitleCache() || name.isProtectedFullTitleCache() || name.isProtectedNameCache()) {

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

			result = false;

		}

		Reference nomRef = name.getNomenclaturalReference();

		if (nomRef != null && (nomRef.isProtectedTitleCache()

		        || nomRef.getInReference() != null && nomRef.getInReference().isProtectedTitleCache())){

		    logger.warn(line + "Nom ref could not be parsed: " + fullName);

            result = false;

		}

		if (nameStr != null && !name.getTitleCache().equals(nameStr)){

            logger.warn(line + "Name part not parsed correctly: " + name.getTitleCache() + "<-> expected: " + nameStr);

            result = false;

        }

		return result;

	}

    private Reference getSecReference(SimpleExcelTaxonImportState<CONFIG> state, Map<String, String> record) {

        if (this.secReference == null){

            logger.warn("Load sec ref");

            String secUuid = record.get(Sec_Ref_CDM_UUID);

            secReference = getReferenceService().load(UUID.fromString(secUuid));

            if (this.secReference == null){

                logger.warn("Sec ref is null");

            }

        }

        return this.secReference;

    }

    private Reference getSourceCitation(SimpleExcelTaxonImportState<CONFIG> state) {

        if (this.sourceReference == null){

            this.sourceReference = getPersistentReference(state.getConfig().getSourceReference());

        }

        return this.sourceReference;

    }

    private Reference getPersistentReference(Reference reference) {

        Reference result = getReferenceService().find(reference.getUuid());

        logger.warn("Loaded persistent reference: "+ reference.getUuid());

        if (result == null){

            logger.warn("Persistent reference is null: " + reference.getUuid());

            result = reference;

            getReferenceService().saveOrUpdate(result);

        }

        return result;

    }

    private void replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, INonViralName name) {

        state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(name);

    }

    @Override

    protected IdentifiableSource makeOriginalSource(SimpleExcelTaxonImportState<CONFIG> state) {

    	String noStr = getValue(state.getOriginalRecord(), Kew_Name_ID);

        return IdentifiableSource.NewDataImportInstance(noStr, Kew_Name_ID, getSourceCitation(state));

    }

}