EDIT

/**

* Copyright (C) 2020 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.casearia;

import java.util.Map;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

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.common.CdmBase;

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

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

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

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

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.term.TermVocabulary;

/**

 * @author a.mueller

 * @since 12.05.2020

 */

@Component

public class CaseariaDistributionImport extends SimpleExcelTaxonImport<CaseariaImportConfigurator>{

    private static final long serialVersionUID = -7841292708411771648L;

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

    private static final String NAME_CIT = "NameCit";

    private static final String IPNI_ID = "ipni_id";

    private static final String PLANT_NAME_ID = "plant_name_id";

    private static final String TAXON_RANK = "taxon_rank";

    private static final String CONTINENT_L1 = "continent_code_l1";

    private static final String CONTINENT_LABEL = "continent";

    private static final String REGION_L2 = "region_code_l2";

    private static final String REGION_LABEL = "region";

    private static final String AREA_L3 = "area_code_l3";

    private static final String AREA_LABEL = "area";

    private static final String INTRODUCED = "introduced";

    private static final String EXTINCT = "extinct";

    private static final String LOCATION_DOUBTFUL = "location_doubtful";

    private static final int RECORDS_PER_TRANSACTION = 500;

    private SimpleExcelTaxonImportState<CaseariaImportConfigurator> state;

    @Override

    protected String getWorksheetName(CaseariaImportConfigurator config) {

        return "OutputWDistribution";

    }

    @Override

    protected void firstPass(SimpleExcelTaxonImportState<CaseariaImportConfigurator> state) {

        this.state = state;

        int line = state.getCurrentLine();

        if ((line % RECORDS_PER_TRANSACTION) == 0){

            newTransaction(state);

            System.out.println(line);

        }

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

        String fullCitation = getValue(record, NAME_CIT);

        String ipniId = getValue(record, IPNI_ID);

        String sourceId = getValue(record, PLANT_NAME_ID);

//        String rankStr = getValue(record, TAXON_RANK);

        String continent_l1 = getValue(record, CONTINENT_L1);

        String continent_label = getValue(record, CONTINENT_LABEL);

        String region_l2 = getValue(record, REGION_L2);

        String region_label = getValue(record, REGION_LABEL);

        String area_l3 = getValue(record, AREA_L3);

        String area_label = getValue(record, AREA_LABEL);

        String introduced = getValue(record, INTRODUCED);

        String extinct = getValue(record, EXTINCT);

        String location_doubtful = getValue(record, LOCATION_DOUBTFUL);

        String fullNameStr = CdmUtils.concat(" ", "","");

        String row = String.valueOf(line) + "("+fullNameStr+"): ";

        UUID uuid = getTaxonMapping().get(sourceId);

        if (uuid == null){

            logger.warn(row + "Taxon uuid not found in taxon mapping for " + sourceId);

        }

        TaxonBase<?> taxonBase = getTaxonService().find(uuid);

        if (taxonBase == null){

            logger.warn(row + "Taxon " + sourceId + " for distribution "+area_label +" does not exist: " + fullCitation);

            return;

        }

        String taxonName = taxonBase.getName().getTitleCache();

        Taxon taxon;

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

            taxon = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon();

            if (taxon == null){

                logger.warn(row + "Taxon "+taxonName+" for distribution "+area_label +" is synonym and synonym has no accepted taxon. Distribution"+area_label+"was ignored.");

                return;

            }else{

                logger.warn(row + "Taxon "+taxonName+" for distribution " + area_label + " is synonym. Distribution was moved to accepted taxon " + taxon.getName().getTitleCache());

            }

        }else {

            taxon = CdmBase.deproxy(taxonBase, Taxon.class);

        }

        @SuppressWarnings("unchecked")

        TermVocabulary<NamedArea> voc = getVocabularyService().find(NamedArea.uuidTdwgAreaVocabulary);

        NamedArea area = voc.getTermByIdInvocabulary(area_l3);

        if (area == null){

            logger.warn(row + "TDWG area not found: " + area_l3 + "; " + area_label);

        }else{

            if (taxon.getDescriptions().isEmpty()){

                TaxonDescription.NewInstance(taxon);

            }

            TaxonDescription desc = taxon.getDescriptions().iterator().next();

            PresenceAbsenceTerm status = PresenceAbsenceTerm.PRESENT();

            if (introduced.equals("1")){

                status = PresenceAbsenceTerm.INTRODUCED();

            }else if (extinct.equals("1")){

                //TODO extinct

                logger.warn(row + "Improve status to extinct");

                status = PresenceAbsenceTerm.ABSENT();

            }else if (location_doubtful.equals("1")){

                status = PresenceAbsenceTerm.PRESENT_DOUBTFULLY();

            }

            Distribution distribution = Distribution.NewInstance(area, status);

            desc.addElement(distribution);

        }

    }

    @SuppressWarnings("unchecked")

    private Map<String, UUID> getTaxonMapping() {

        return (Map<String, UUID>)state.getStatusItem(CaseariaTaxonImport.TAXON_MAPPING);

    }

    private void newTransaction(SimpleExcelTaxonImportState<CaseariaImportConfigurator> state) {

        commitTransaction(state.getTransactionStatus());

//        secRef = null;

//        dedupHelper = null;

        state.setSourceReference(null);

        System.gc();

        state.setTransactionStatus(startTransaction());

    }

}