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.mexico;

import java.util.Arrays;

import java.util.HashMap;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.commons.lang3.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

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

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.Annotation;

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

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

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

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

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

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

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

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

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.TaxonNameBase;

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.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.TaxonRelationship;

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

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

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

/**

 * @author a.mueller

 * @date 16.06.2016

 *

 */

@Component

public class MexicoConabioTaxonImport<CONFIG extends MexicoConabioImportConfigurator>

        extends SimpleExcelTaxonImport<CONFIG>{

    private static final long serialVersionUID = 3691221053127007258L;

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

    public static final String TAXON_NAMESPACE = "Taxonomia";

    @Override

    protected String getWorksheetName() {

        return "Taxonomia";

    }

    //dirty I know, but who cares, needed by distribution and commmon name import

    protected static final Map<String, TaxonBase<?>> taxonIdMap = new HashMap<>();

    private Classification classification;

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

            "IdCAT","IdCATRel","IdCAT_AscendenteInmediato"

            ,"IdCAT_AscendenteObligatorio","CategoriaTaxonomica","Nombre",

            "EstatusNombre","AutorNombre","AutorSinAnio","Anio",

            "ReferenciaNombre",

            "Division","AutorDivision","ReferenciaClasificacionDivision",

            "Clase","AutorClase","ReferenciaClasificacionClase",

            "Subclase","AutorSubclase","ReferenciaClasificacionSubclase",

            "Superorden","AutorSuperorden","ReferenciaClasificacionSuperorden",

            "Orden","AutorOrden","ReferenciaClasificacionOrden",

            "Familia",     "EstatusFamilia","AutorFamilia","ReferenciaClasificacionFamilia",

            "Tribu",  "EstatusTribu","AutorTribu","ReferenciaNombreTribu",

            "Genero","EstatusGenero","AutorGenero","","ReferenciaNombreGenero",

            "Epiteto_especifico","EstatusEspecie","AutorEpiteto_especifico","ReferenciaNombreEspecie",

            "CategoriaInfraespecifica","NombreInfraespecifico","EstatusInfraespecie","AutorInfraespecie","ReferenciaNombreInfraespecifico",

            "CitaNomenclatural","Anotacion al Taxon","Fuente_BDs",

            "FamAceptada","GenAceptado","CategoriaTaxAceptada","NombreAceptado","AutorNombreAceptado","AutorSinAnioAceptado","AnioAceptado",

            "TipoRelacion","ReferenciaSinonimia","ComentariosRevisor",

            "CompareID","IdCAT_OLD","Nombre_OLD","AutorSinAnio_OLD",

            "CitaNomenclatural_OLD","ReferenceType","IsUpdated"

        });

    @Override

    protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {

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

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

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

        checkAllKeysExist(line, keys, expectedKeys);

        if (getValue(record, "Nombre") == null ){

            logger.warn("No FullnameNoAuthors given: " + line);

            return;

        }

        //Name

        BotanicalName speciesName = makeName(line, record, state);

        //sec

        String secRefStr = getValueNd(record, "ReferenciaNombre");

        Reference sec = getSecRef(state, secRefStr, line);

        //status

        String statusStr = getValue(record, "EstatusNombre");

        TaxonBase<?> taxonBase;

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

            taxonBase = Taxon.NewInstance(speciesName, sec);

        }else if (statusStr.startsWith("sin")){

            taxonBase = Synonym.NewInstance(speciesName, sec);

        }else{

            throw new RuntimeException(line + " Status not recognized: " + statusStr);

        }

        //annotation

        String annotation = getValue(record, "Anotacion al Taxon");

        if (annotation != null && (!annotation.equals("nom. illeg.") || !annotation.equals("nom. cons."))){

            taxonBase.addAnnotation(Annotation.NewInstance(annotation, AnnotationType.EDITORIAL(), Language.SPANISH_CASTILIAN()));

        }

        //id

        String idCat = getValue(record, "IdCAT");

        this.addOriginalSource(taxonBase, idCat, TAXON_NAMESPACE, state.getConfig().getSourceReference());

        //save

        getTaxonService().save(taxonBase);

        taxonIdMap.put(idCat, taxonBase);

    }

    /**

     * @param state

     * @param secRefStr

     * @return

     */

    private Reference getSecRef(SimpleExcelTaxonImportState<CONFIG> state, String secRefStr, String line) {

        Reference result = state.getReference(secRefStr);

        if (result == null && secRefStr != null){

            result = ReferenceFactory.newBook();

            TimePeriod tp = TimePeriodParser.parseString(secRefStr.substring(secRefStr.length()-4));

            String authorStrPart = secRefStr.substring(0, secRefStr.length()-6);

            if (! (authorStrPart + ", " + tp.getYear()).equals(secRefStr)){

                logger.warn(line + "Sec ref could not be parsed: " + secRefStr);

            }else{

                result.setDatePublished(tp);

            }

            TeamOrPersonBase<?> author = state.getAgentBase(authorStrPart);

            if (author == null){

                if (authorStrPart.contains("&")){

                    Team team = Team.NewInstance();

                    String[] authorSplit = authorStrPart.split("&");

                    String[] firstAuthorSplit = authorSplit[0].trim().split(",");

                    for (String authorStr : firstAuthorSplit){

                        addTeamMember(team, authorStr);

                    }

                    addTeamMember(team, authorSplit[1]);

                    result.setAuthorship(team);

                    state.putAgentBase(team.getTitleCache(), team);

                }else if (authorStrPart.equalsIgnoreCase("Tropicos") || authorStrPart.equalsIgnoreCase("The Plant List")

                        || authorStrPart.equalsIgnoreCase("APG IV")){

                    result.setTitle(authorStrPart);

                }else{

                    Person person = Person.NewInstance();

                    person.setLastname(authorStrPart);

                    result.setAuthorship(person);

                    state.putAgentBase(person.getTitleCache(), person);

                }

            }else{

                result.setAuthorship(author);

            }

            state.putReference(secRefStr, result);

        }else if(secRefStr == null){

            return state.getConfig().getSecReference();

        }

        return result;

    }

    /**

     * @param team

     * @param author

     */

    private void addTeamMember(Team team, String author) {

        if (StringUtils.isNotBlank(author)){

            Person person = Person.NewInstance();

            person.setLastname(author.trim());

            team.addTeamMember(person);

        }

    }

    /**

     * @param record

     * @param state

     * @return

     */

    private BotanicalName makeName(String line, HashMap<String, String> record, SimpleExcelTaxonImportState<CONFIG> state) {

        String authorStr = getValueNd(record, "AutorSinAnio");

        String nameStr = getValue(record, "Nombre");

        String nomRefStr = getValue(record, "CitaNomenclatural");

        String refType = getValue(record, "ReferenceType");

        String idCat = getValue(record, "IdCAT");

        String rankStr = getValue(record, "CategoriaTaxonomica");

        String annotation = getValue(record, "Anotacion al Taxon");

        //rank

        Rank rank = null;

        try {

            rank = state.getTransformer().getRankByKey(rankStr);

            if (Rank.SUBSPECIES().equals(rank) || Rank.VARIETY().equals(rank)){

                int i = nameStr.lastIndexOf(" ");

                nameStr = nameStr.substring(0, i) + " " + rank.getAbbreviation() + nameStr.substring(i);

            }

        } catch (UndefinedTransformerMethodException e) {

            logger.warn(line + "Rank not recognized: " + rankStr);

        }

        //name + author

        String fullNameStr = nameStr + (authorStr != null ? " " + authorStr : "");

        BotanicalName fullName = (BotanicalName)nameParser.parseFullName(fullNameStr, NomenclaturalCode.ICNAFP, rank);

        if (fullName.isProtectedTitleCache()){

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

        }else{

            replaceAuthorNamesAndNomRef(state, fullName);

        }

        BotanicalName existingName = getExistingName(state, fullName);

        //reference

        String refNameStr = getRefNameStr(nomRefStr, refType, fullNameStr);

        BotanicalName referencedName = (BotanicalName)nameParser.parseReferencedName(refNameStr, NomenclaturalCode.ICNAFP, rank);

        if (referencedName.isProtectedFullTitleCache() || referencedName.isProtectedTitleCache()){

            logger.warn(line + "Referenced name could not be parsed: " + refNameStr );

        }else{

            addSourcesToReferences(referencedName, state);

            replaceAuthorNamesAndNomRef(state, referencedName);

        }

        adaptRefTypeForGeneric(referencedName, refType);

        //compare nom. ref. with Borhidi

        BotanicalName result= referencedName;

        Boolean equal = null;

        if (existingName != null){

            String existingRefTitle = existingName.getFullTitleCache();

            String conabioRefTitle = referencedName.getFullTitleCache();

            if (!existingRefTitle.equals(conabioRefTitle)){

                existingName.setNomenclaturalMicroReference(referencedName.getNomenclaturalMicroReference());

                existingName.setNomenclaturalReference(referencedName.getNomenclaturalReference());

                equal = false;

            }else{

                equal = true;

            }

            result = existingName;

        }

        addNomRefExtension(state, result, equal);

        //status

        if (annotation != null && (annotation.equals("nom. illeg.") || annotation.equals("nom. cons."))){

            try {

                NomenclaturalStatusType nomStatusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(annotation, result);

                result.addStatus(NomenclaturalStatus.NewInstance(nomStatusType));

            } catch (UnknownCdmTypeException e) {

                logger.warn(line + "nomStatusType not recognized: " + annotation);

            }

        }

        this.addOriginalSource(result, idCat, TAXON_NAMESPACE + "_Name", state.getConfig().getSourceReference());

        return result;

    }

    /**

     * @param name

     * @param state

     */

    private void addSourcesToReferences(IBotanicalName name, SimpleExcelTaxonImportState<CONFIG> state) {

        Reference nomRef = (Reference)name.getNomenclaturalReference();

        if (nomRef != null){

            nomRef.addSource(makeOriginalSource(state));

            if (nomRef.getInReference() != null){

                nomRef.getInReference().addSource(makeOriginalSource(state));

            }

        }

    }

    /**

     * @param referencedName

     * @param refType

     */

    private void adaptRefTypeForGeneric(IBotanicalName referencedName, String refTypeStr) {

        INomenclaturalReference ref = referencedName.getNomenclaturalReference();

        if (ref == null){

            return;

        }

        ReferenceType refType = refTypeByRefTypeStr(refTypeStr);

        if (ref.getType() != refType && refType == ReferenceType.Book){

            ref.setType(refType);

        }

    }

    private ReferenceType refTypeByRefTypeStr(String refType){

        if ("A".equals(refType)){  //Article

            return ReferenceType.Article;

        }else if ("B".equals(refType)){   //Book

            return ReferenceType.Book;

        }else if (refType == null){   //Book

            return null;

        }else{

            throw new IllegalArgumentException("RefType not supported " + refType);

        }

    }

    /**

     * @param nomRefStr

     * @param refType

     * @param fullNameStr

     * @return

     */

    private String getRefNameStr(String nomRefStr, String refTypeStr, String fullNameStr) {

        String refNameStr = fullNameStr;

        ReferenceType refType = refTypeByRefTypeStr(refTypeStr);

        if (refType == ReferenceType.Article){

            refNameStr = fullNameStr + " in " + nomRefStr;

        }else if (refType == ReferenceType.Book){

            refNameStr = fullNameStr + ", " + nomRefStr;

        }else if (refType == null && nomRefStr != null){

            logger.warn("RefType is null but nomRefStr exists");

        }

        return refNameStr;

    }

    /**

     * @param state

     * @param equal

     * @param referencedName

     */

    private void addNomRefExtension(SimpleExcelTaxonImportState<CONFIG> state, BotanicalName name, Boolean equal) {

        String equalStr = equal == null ? "" : equal == true ? "EQUAL\n" : "NOT EQUAL\n";

        name.setFullTitleCache(null, false);

        String newExtensionStr = name.getFullTitleCache() + " - CONABIO";

        UUID uuidNomRefExtension = MexicoConabioTransformer.uuidNomRefExtension;

        for (Extension extension : name.getExtensions()){

            if (extension.getType().getUuid().equals(uuidNomRefExtension)){

                extension.setValue(equalStr + extension.getValue() + "\n" + newExtensionStr);

                return;

            }

        }

        String label = "Nomenclatural reference in Sources";

        String abbrev = "Nom. ref. src.";

        ExtensionType extensionType = getExtensionType(state, uuidNomRefExtension, label, label, abbrev);

        Extension.NewInstance(name, newExtensionStr, extensionType);

    }

    boolean nameMapIsInitialized = false;

    /**

     * @param state

     * @param fullName

     * @return

     */

    private BotanicalName getExistingName(SimpleExcelTaxonImportState<CONFIG> state, BotanicalName fullName) {

        initExistinNames(state);

        return (BotanicalName)state.getName(fullName.getTitleCache());

    }

    /**

     * @param state

     */

    @SuppressWarnings("rawtypes")

    private void initExistinNames(SimpleExcelTaxonImportState<CONFIG> state) {

        if (!nameMapIsInitialized){

            List<String> propertyPaths = Arrays.asList("");

            List<TaxonNameBase> existingNames = this.getNameService().list(null, null, null, null, propertyPaths);

            for (TaxonNameBase tnb : existingNames){

                state.putName(tnb.getTitleCache(), tnb);

            }

            nameMapIsInitialized = true;

        }

    }

    /**

     * @param record

     * @param string

     * @return

     */

    private String getValueNd(HashMap<String, String> record, String string) {

        String value = getValue(record, string);

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

            return null;

        }else{

            return value;

        }

    }

    @Override

    protected void secondPass(SimpleExcelTaxonImportState<CONFIG> state) {

//        IdCAT_AscendenteInmediato, IdCATRel, TipoRelacion

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

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

        String parentStr = getValue(record, "IdCAT_AscendenteInmediato");

        String relStr = getValue(record, "IdCATRel");

        String statusStr = getValue(record, "EstatusNombre");

        Classification classification = getClassification(state);

        String idCat = getValue(record, "IdCAT");

        TaxonBase<?> taxonBase = taxonIdMap.get(idCat);

        Taxon parent;

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

            parent = (Taxon)taxonIdMap.get(parentStr);

            if (parent == null){

                logger.warn(line + "Parent is missing: "+ parentStr);

            }else{

                Taxon taxon = (Taxon)taxonBase;

                Reference relRef = null;  //TODO

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

                makeConceptRelation(line, taxon.getName());

            }

        }else if (statusStr.startsWith("sin")){

            parent = (Taxon)taxonIdMap.get(relStr);

            if (parent == null){

                logger.warn(line + "Accepted taxon is missing: "+ relStr);

            }else{

                Synonym synonym = (Synonym)taxonBase;

                parent.addSynonym(synonym, SynonymType.SYNONYM_OF());

                makeConceptRelation(line, synonym.getName());

            }

        }

    }

     /**

     * @param line

     * @param name

     */

    private void makeConceptRelation(String line, TaxonNameBase<?,?> name) {

        if (name.getTaxonBases().size()==2){

            Iterator<TaxonBase> it = name.getTaxonBases().iterator();

            Taxon taxon1 = getAccepted(it.next());

            Taxon taxon2 = getAccepted(it.next());

            Reference citation = null;

            TaxonRelationship rel;

            if (taxon1.getSec().getUuid().equals(MexicoConabioTransformer.uuidReferenceBorhidi)){

                rel = taxon1.addTaxonRelation(taxon2, TaxonRelationshipType.CONGRUENT_TO(),

                        citation, null);

            }else{

                rel = taxon2.addTaxonRelation(taxon1, TaxonRelationshipType.CONGRUENT_TO(),

                        citation, null);

            }

            rel.setDoubtful(true);

        }else if (name.getTaxonBases().size()>2){

            logger.warn(line + "Names with more than 2 taxa not yet handled");

        }

    }

    /**

     * @param next

     * @return

     */

    private Taxon getAccepted(TaxonBase<?> taxonBase) {

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

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

        }else{

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

            return syn.getAcceptedTaxon();

        }

    }

    /**

     * @return

     */

    private Classification getClassification(SimpleExcelTaxonImportState<CONFIG> state) {

        if (classification == null){

            MexicoConabioImportConfigurator config = state.getConfig();

            classification = Classification.NewInstance(config.getClassificationName());

            classification.setUuid(config.getClassificationUuid());

            classification.setReference(config.getSecReference());

            getClassificationService().save(classification);

        }

        return classification;

    }

    @Override

    protected boolean isIgnore(SimpleExcelTaxonImportState<CONFIG> state) {

        return ! state.getConfig().isDoTaxa();

    }

}