EDIT

// $Id$

/**

* Copyright (C) 2017 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.redlist.gefaesspflanzen.excel;

import java.util.Map;

import java.util.UUID;

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.common.utils.ImportDeduplicationHelper;

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

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

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

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

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

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.taxon.Classification;

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

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

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

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

import eu.etaxonomy.cdm.strategy.homotypicgroup.BasionymRelationCreator;

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

/**

 * Import for German red list checklist for plantae.

 * @author a.mueller

 * @since 13.06.2019

 */

@Component

public class RedListGefaesspflanzenTaxonExcelImport<CONFIG extends RedListGefaesspflanzenExcelImportConfigurator>

        extends SimpleExcelTaxonImport<CONFIG> {

    private static final long serialVersionUID = -884838817884874228L;

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

    private static final String ID_COL = "SORT_ID";

    private static final String UUID_COL = "TAXON_UUID";

    private static final String SYN_FLAG_COL = "SYN_FLAG";

    private static final String VOLLNAME_COL = "VOLLNAME";

    private static final String WISS_NAME_COL = "WISS_NAME";

    private static final String AUTHOR_COL = "AUTOR";

    private static final String RANK_COL = "RANG";

    private static final String ZUSATZ_COL = "ZUSATZ";

    private static UUID rootUuid = UUID.fromString("235ae474-227f-438a-b132-4508053fcb1c");

    private static UUID plantaeUuid = UUID.fromString("31bd1b7c-245a-416d-b076-aa090c7469ce");

    @SuppressWarnings("unchecked")

    private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> deduplicationHelper

           = (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewStandaloneInstance();

    private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();

    private BasionymRelationCreator basionymCreator = new BasionymRelationCreator();

    @Override

    protected String getWorksheetName(CONFIG config) {

        return "Florenliste";

    }

    private boolean isFirst = true;

    private TransactionStatus tx = null;

    /**

     * {@inheritDoc}

     */

    @Override

    protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {

        if (isFirst){

            tx = this.startTransaction();

            isFirst = false;

        }

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

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

        String noStr = getValue(record, ID_COL);

        //species

        TaxonBase<?> taxon = makeTaxon(state, line, record, noStr);

        getTaxonService().save(taxon);

        saveNameRelations(taxon.getName());

    }

    @Override

    protected void secondPass(SimpleExcelTaxonImportState<CONFIG> state) {

        if (tx != null){

            this.commitTransaction(tx);

            tx = null;

        }

    }

    /**

     * @param col

     * @return

     */

    private String getNamespace(CONFIG config) {

        return getWorksheetName(config)+"."+ ID_COL;

    }

    /**

     * @param state

     * @param line

     * @param record

     * @param noStr

     * @return

     */

    private TaxonBase<?> makeTaxon(SimpleExcelTaxonImportState<CONFIG> state, String line, Map<String, String> record,

            String noStr) {

//        TaxonNode familyTaxon = getFamilyTaxon(record, state);

//        if (familyTaxon == null){

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

//        }

        String nameStr = getValue(record, WISS_NAME_COL);

        String authorStr = getValue(record, AUTHOR_COL);

        String synFlag = getValue(record, SYN_FLAG_COL);

        String uuidTaxon = getValue(record, UUID_COL);

        String vollName = getValue(record, VOLLNAME_COL);

        String zusatz = getValue(record, ZUSATZ_COL);

        String sensuStr;

        if (StringUtils.isNotEmpty(zusatz) && zusatz.startsWith("s. ")){

            sensuStr = zusatz.split(",")[0].trim();

        }else {

           sensuStr = null;

        }

        String nomStatusStr;

        if (StringUtils.isNotEmpty(zusatz) && !zusatz.trim().equals(sensuStr)){

            nomStatusStr = sensuStr == null? zusatz.trim():zusatz.split(",")[1].trim();

        }else{

            nomStatusStr = null;

        }

        nameStr = CdmUtils.concat(" ", nameStr, authorStr);

        boolean isAuct = nameStr.endsWith("auct.");

        nameStr = normalizeNameStr(nameStr);

        Rank rank = Rank.SPECIES();

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

        name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);

        name = deduplicationHelper.getExistingName(state, name);

        if (name.isProtectedTitleCache()){

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

        }

        deduplicationHelper.replaceAuthorNamesAndNomRef(state, name);

        TaxonBase<?> taxon;

        if ("1".equals(synFlag) || isAuct){

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

        }else if ("b".equals(synFlag)||"x".equals(synFlag)){

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

        }else{

            logger.warn("Unknown synFlag: " + synFlag);

            return null;

        }

        taxon.setUuid(UUID.fromString(uuidTaxon));

        if (isAuct){

            taxon.setAppendedPhrase("auct.");  //TODO

        }

        if (sensuStr != null){

            taxon.setAppendedPhrase(sensuStr);

        }

        taxon.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);

        checkVollname(state, taxon, vollName, sensuStr, isAuct);

        return taxon;

    }

    /**

     * @param state

     * @param taxon

     * @param sensuStr

     * @param isAuct

     * @param vollName

     */

    private void checkVollname(SimpleExcelTaxonImportState<CONFIG> state, TaxonBase<?> taxon, String vollName, String sensuStr, boolean isAuct) {

        TaxonName name = taxon.getName();

        String titleCache = (sensuStr == null && !isAuct) ? name.getTitleCache() : taxon.getTitleCache();

        vollName = vollName.replace(" agg.", " aggr.").replace(" (E)", "");

        if (!titleCache.equals(vollName)){

            logger.warn("Vollname weicht ab: " + vollName +" <-> " +  titleCache);

        }

    }

    /**

     * @param nameStr

     */

    private String normalizeNameStr(String nameStr) {

        String result = nameStr.replace(" agg.", " aggr.").replaceAll(" auct.$", "")

                .replaceAll(" grex ", " subsp. ").replaceAll(" sublusus ", " subsp. ");

        return result;

    }

    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);

            IBotanicalName 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;

    }

//    protected IBotanicalName makeFamilyName(SimpleExcelTaxonImportState<CONFIG> state, String famStr) {

//        IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());

//        famStr = decapitalize(famStr);

//        name.setGenusOrUninomial(famStr);

//        name.addSource(makeOriginalSource(state));

//        return name;

//    }

    /**

     * @param state

     * @return

     */

    @Override

    protected IdentifiableSource makeOriginalSource(SimpleExcelTaxonImportState<CONFIG> state) {

        return IdentifiableSource.NewDataImportInstance(getValue(state.getOriginalRecord(),ID_COL),

                getNamespace(state.getConfig()), state.getConfig().getSourceReference());

    }

    protected Reference getSecReference(SimpleExcelTaxonImportState<CONFIG> state) {

        return state.getConfig().getSecReference();

    }

    /**

     * @param state

     * @return

     */

    protected Reference getSourceCitation(SimpleExcelTaxonImportState<CONFIG> state) {

        return state.getConfig().getSourceReference();

    }

    /**

     * @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();

    }

}