EDIT

/**

* 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.euromed;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.Set;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.service.pager.Pager;

import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.term.TermVocabulary;

/**

 * This import adds the distribution source to data imported via E+M IPNI new names import.

 *

 * @author a.mueller

 * @since 10.07.2020

 */

@Component

public class IpniSourcesImport<CONFIG extends IpniSourcesImportConfigurator>

        extends SimpleExcelTaxonImport<CONFIG> {

    private static final long serialVersionUID = -6723116237971852295L;

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

    private static final String NAMECACHE = "full_name_without_family_and_authors";

    private static final String GENUS = "genus";

    private static final String SPECIES = "species";

    private static final String INFRA_SPECIES = "infraspecies";

    private static final String RANK = "rank";

    private static final String AUTHORS = "EMauthors";

    private static final String EM_GEO = "EM-geo";

    private Map<String,NamedArea> areaMap;

    @Override

    protected String getWorksheetName(CONFIG config) {

        return "_11_IPNI_name_w_EM_genus_tax_m2";

    }

    private boolean isFirst = true;

    private TransactionStatus tx = null;

    @Override

    protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {

        if (isFirst){

            tx = this.startTransaction();

            isFirst = false;

        }

        getAreaMap();

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

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

        String uninomial = getValue(record, GENUS);

        String specificEpithet = getValue(record, SPECIES);

        String infraspecificEpithet = getValue(record, INFRA_SPECIES);

        String nameCache = getValue(record, NAMECACHE);

        List<String> propertyPaths = null;

        String authorshipCache = "*";

        Rank rank = getRank(state);

        Pager<Taxon> taxonPager = getTaxonService().findTaxaByName(Taxon.class, uninomial, "*", specificEpithet,

                infraspecificEpithet, authorshipCache, rank, null, null, propertyPaths);

        List<Taxon> taxa = getPublishedTaxa(taxonPager, line);

        if (taxa.size() == 1){

            Taxon taxon = taxa.get(0);

            makeDistributionSource(state, line, taxon);

        }else{

            logger.warn(line + "Could not find unique taxon. Count: " + taxa.size() +"; "  + nameCache);

        }

    }

    private List<Taxon> getPublishedTaxa(Pager<Taxon> taxonPager, String line) {

        List<Taxon> result = new ArrayList<>();

        for (Taxon taxon : taxonPager.getRecords()){

            if (!taxon.isPublish()){

                logger.warn(line + "Unpublished taxon exists: " +  taxon.getTitleCache());

            }else{

                result.add(taxon);

            }

        }

        return result;

    }

    private void makeDistributionSource(SimpleExcelTaxonImportState<CONFIG> state, String line, Taxon taxon) {

        Set<Distribution> distributions = taxon.getDescriptionItems(Feature.DISTRIBUTION(), Distribution.class);

        //single areas

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

        String allAreaStr = getValue(record, EM_GEO);

        if(isBlank(allAreaStr)){

            logger.warn(line + "No distribution data exists in IPNI file: " + taxon.getName().getTitleCache());

        }else{

            NamedArea emArea = getAreaMap().get("EM");

            handleArea(line, taxon, distributions, emArea);

            String[] areaSplit = allAreaStr.split(",");

            for (String areaStr: areaSplit){

                NamedArea area = getAreaMap().get(areaStr.trim());

                handleArea(line, taxon, distributions, area);

            }

        }

    }

    /**

     * @param line

     * @param taxon

     * @param distributions

     * @param area

     */

    private void handleArea(String line, Taxon taxon, Set<Distribution> distributions, NamedArea area) {

        Distribution distribution = findDistribution(distributions, area);

        if (distribution == null){

            logger.warn("line + Distribution not found: " + taxon.getName().getTitleCache() + ":" + area.getTitleCache());

        }else{

            if (distribution.getSources().isEmpty()){

                addNomenclaturalSource(taxon, distribution, line);

            }else{

                logger.warn(line + "Distribution has source already: " + taxon.getName().getTitleCache() + ": " + area.getTitleCache() + "; Source(s): " + getSourceString(distribution.getSources()));

            }

        }

    }

    private String getSourceString(Set<DescriptionElementSource> sources) {

        String result = "";

        for (DescriptionElementSource source : sources){

            if (source.getCitation() != null){

                result += source.getCitation().getTitleCache();

            }else{

                result += "--source has no citation --";

            }

        }

        return result;

    }

    private void addNomenclaturalSource(Taxon taxon, Distribution distribution, String line) {

        distribution.addSource(OriginalSourceType.PrimaryTaxonomicSource,

                null, null, taxon.getName().getNomenclaturalReference(),

                taxon.getName().getNomenclaturalMicroReference(),

                taxon.getName(), null);

        if(taxon.getName().getNomenclaturalReference() == null){

            logger.warn(line + "No nomenclatural source available" + taxon.getName().getTitleCache());

        }

    }

    private Distribution findDistribution(Set<Distribution> distributions, NamedArea area) {

        Distribution result = null;

        for (Distribution distribution : distributions){

            if (area.equals(distribution.getArea())){

                result = distribution;

            }

        }

        return result;

    }

    private Map<String, NamedArea> getAreaMap() {

        if (areaMap == null){

            makeAreaMap();

        }

        return areaMap;

    }

    private void makeAreaMap() {

        areaMap = new HashMap<>();

        @SuppressWarnings("unchecked")

        TermVocabulary<NamedArea> emAreaVoc = getVocabularyService().find(BerlinModelTransformer.uuidVocEuroMedAreas);

        for (NamedArea area: emAreaVoc.getTerms()){

            areaMap.put(area.getIdInVocabulary(), area);

        }

    }

    private Rank getRank(SimpleExcelTaxonImportState<CONFIG> state) {

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

        String rankStr = getValue(record, RANK);

        if ("spec.".equals(rankStr)){

            return Rank.SPECIES();

        }else if ("subsp.".equals(rankStr)){

            return Rank.SUBSPECIES();

        }else{

            logger.warn("Unknown rank: " + rankStr);

            return null;

        }

    }

    @Override

    protected void secondPass(SimpleExcelTaxonImportState<CONFIG> state) {

        if (tx != null){

            this.commitTransaction(tx);

            tx = null;

        }

    }

}