EDIT

    public static ICdmDataSource cdm_local_euromed(){

        DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;

        String cdmServer = "127.0.0.1";

        String cdmDB = "cdm_euromed";

        String cdmUserName = "edit";

        int port = 3306;

        return CdmDestinations.makeDestination(dbType, cdmServer, cdmDB, port, cdmUserName, null);

    }

/**

* Copyright (C) 2015 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.app.euromed;

import java.net.URI;

import java.util.UUID;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.app.common.CdmDestinations;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.common.CdmDefaultImport;

import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;

import eu.etaxonomy.cdm.io.common.ImportResult;

import eu.etaxonomy.cdm.io.euromed.IpniSourcesImportConfigurator;

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

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

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

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

/**

 * @author a.mueller

 * @since 18.10.2019

 */

public class EuroMedIpniDistributionSourcesImportActivator {

    @SuppressWarnings("unused")

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

    //database validation status (create, update, validate ...)

    static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE;

    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_euromed();

//   static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_euromed();

    //check - import

    static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

    private void doImport(ICdmDataSource cdmDestination){

        URI source = getEM_IpniUri();

        IpniSourcesImportConfigurator config;

//        try {

            config = IpniSourcesImportConfigurator.NewInstance(source, cdmDestination);

            config.setDbSchemaValidation(dbSchemaValidation);

            config.setCheck(check);

            config.setNomenclaturalCode(NomenclaturalCode.ICNAFP);

            config.setSourceReference(getSourceReference());

//            config.setAddAuthorsToReference(addAuthorsToReferences);

            CdmDefaultImport<IpniSourcesImportConfigurator> myImport = new CdmDefaultImport<>();

            ImportResult result = myImport.invoke(config);

            System.out.println(result.createReport());

//        } catch (IOException e) {

//            System.out.println("URI not 'found': " + source);

//        }

    }

    private URI getEM_IpniUri(){

        String fileName = "IPNI-name-EM-import.xlsx";

        URI uri = URI.create("file:////BGBM-PESIHPC/EuroMed/" +  fileName);

        return uri;

    }

    private Reference getSourceReference(){

        Reference result = ReferenceFactory.newDatabase();

        result.setTitle("Euro+Med IPNI import");

        result.setUuid(UUID.fromString("937f3a38-dbb4-4888-9ea3-2f52d47f7953"));

        result.setDatePublished(VerbatimTimePeriod.NewVerbatimNowInstance());

        return result;

    }

    public static void main(String[] args) {

        EuroMedIpniDistributionSourcesImportActivator me = new EuroMedIpniDistributionSourcesImportActivator();

        me.doImport(cdmDestination);

        System.exit(0);

    }

}

/**

* 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;

        }

    }

}

/**

* 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.net.URI;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.common.ImportStateBase;

import eu.etaxonomy.cdm.io.excel.common.ExcelImportConfiguratorBase;

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

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

/**

 * @author a.mueller

 * @since 23.10.2019

 */

public class IpniSourcesImportConfigurator extends ExcelImportConfiguratorBase {

    private static final long serialVersionUID = 7883220110057878974L;

    public static IpniSourcesImportConfigurator NewInstance(URI uri, ICdmDataSource cdmDestination) {

        return new IpniSourcesImportConfigurator(uri, cdmDestination);

    }

    private IpniSourcesImportConfigurator(URI uri, ICdmDataSource cdmDestination) {

        super(uri, cdmDestination, null);

        this.setNomenclaturalCode(NomenclaturalCode.ICNAFP);

    }

    @SuppressWarnings("unchecked")

    @Override

    protected void makeIoClassList() {

        ioClassList = new Class[]{

                IpniSourcesImport.class

            };

    }

    @Override

    public ImportStateBase getNewState() {

        return new SimpleExcelTaxonImportState<>(this);

    }

//

//    /**

//     * If <code>true</code> the name authors will be added

//     * to the nomenclatural reference (Book or Article) though

//     * it might not be the exact same author.<BR>

//     * Default is <code>true</code>

//     */

//    public boolean isAddAuthorsToReference() {

//        return addAuthorsToReference;

//    }

//    /**

//     * @see #isAddAuthorsToReference()

//     */

//    public void setAddAuthorsToReference(boolean addAuthorsToReference) {

//        this.addAuthorsToReference = addAuthorsToReference;

//    }

}