EDIT

/**

* 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.caryophyllales;

import java.io.File;

import java.io.FileReader;

import java.io.IOException;

import java.io.InputStreamReader;

import java.util.UUID;

import org.apache.logging.log4j.LogManager;

import org.apache.logging.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.identifier.IdentifierImportConfigurator;

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

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

/**

 * @author a.mueller

 */

public class DianthusIdentifierActivator {

    @SuppressWarnings("unused")

    private static final Logger logger = LogManager.getLogger();

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

    static DbSchemaValidation dbSchemaValidation = DbSchemaValidation.VALIDATE;

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

    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_caryophyllales_spp();

    static final UUID identifierUuid = IdentifierType.uuidWfoNameIdentifier;

    String filename = "Dianthus_WFO_IDs.csv";

//    String filename = "Cactaceae_SpeciesAndBelowWithoutWFO-ID.txt";

    boolean warnAndDoNotOverrideIfExists = true;

//    static final UUID identifierUuid = DefinedTerm.uuidWfoNameIdentifier;

//    String filename = "WFO2CDM_Cactaceae_WFO-ID.txt";

//    static final UUID identifierUuid = DefinedTerm.uuidIpniNameIdentifier;

//    String filename = "WFO2CDM_Cactaceae_IPNI-ID.txt";

    //check - import

    static CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

    private void doImport(ICdmDataSource cdmDestination){

        InputStreamReader source = getNepenthesIdentifier();

        IdentifierImportConfigurator config= IdentifierImportConfigurator.NewInstance(source, cdmDestination);

        config.setWarnAndDoNotOverrideIfExists(warnAndDoNotOverrideIfExists);

        config.setDbSchemaValidation(dbSchemaValidation);

        config.setIdentifierTypeUuid(identifierUuid);

        config.setCdmClass(TaxonName.class);

        config.setCheck(check);

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

        myImport.invoke(config);

    }

    private InputStreamReader getNepenthesIdentifier() {

//        URI.create("file:////BGBM-PESIHPC/FloraMalesianaXml/fmvol14_final2.xml")

        String path = "C://opt//data//Caryophyllales";

        File file = new File(path + File.separator + filename);

        if (!file.exists()){

            System.exit(-1);

            return null;

        }

        try {

            InputStreamReader input = new FileReader(file);

            return input;

        } catch (IOException e) {

            e.printStackTrace();

            System.exit(-1);

            return null;

        }

    }

    public static void main(String[] args) {

        DianthusIdentifierActivator me = new DianthusIdentifierActivator();

        me.doImport(cdmDestination);

        System.exit(0);

    }

}