EDIT

	public static ICdmDataSource cdm_production_redlist_gefaesspflanzen(){

		DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;

		String cdmServer = "160.45.63.171";

		String cdmDB = "cdm_production_rl_plantae";

		String cdmUserName = "edit";

		return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);

	}

	public static Source ROTE_LISTE_GEFAESSPFLANZEN_DB(){

		String dbms = Source.ACCESS;

		String strServer = null;

		String strDB = "/home/pplitzner/Rote Listen 2020/Gefaesspflanzen/tax_atlas_d20_export.accdb";

		int port = -1;

		String userName = "";

		return  makeSource(dbms, strServer, strDB, port, userName, null);

	}

package eu.etaxonomy.cdm.app.redlist;

import java.util.UUID;

import org.apache.log4j.Logger;

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

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

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.Source;

import eu.etaxonomy.cdm.io.redlist.gefaesspflanzen.RedListGefaesspflanzenImportConfigurator;

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

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

public class RedListGefaesspflanzenActivator {

	@SuppressWarnings("unused")

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

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

	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final Source mySource = CdmImportSources.ROTE_LISTE_GEFAESSPFLANZEN_DB();

//	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

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

  static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();

	//feature tree uuid

	public static final UUID featureTreeUuid = UUID.fromString("75a0e0fc-838a-4c12-8fbb-90d42ba98a34");

	public static final String sourceReference = "Rote Listen - Gefäßpflanzen";

	//classification

	public static final UUID classificationUuid = UUID.fromString("c4053649-1994-4b79-b409-f3986227a4af");

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	//taxa

	static final boolean doTaxa = true;

	private void doImport(ICdmDataSource cdmDestination){

		//make Source

		Source source = mySource;

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

		config.setClassificationUuid(classificationUuid);

//		config.setDoTaxa(doTaxa);

		config.setCheck(check);

		config.setDbSchemaValidation(hbm2dll);

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

		System.out.println("Start import from ("+ source.toString() + ") ...");

		config.setSourceReference(getSourceReference(sourceReference));

		myImport.invoke(config);

		System.out.println("End import from ("+ source.toString() + ")...");

	}

	private Reference<?> getSourceReference(String string) {

		Reference<?> result = ReferenceFactory.newGeneric();

		result.setTitleCache(string, true);

		return result;

	}

	public static void main(String[] args) {

		RedListGefaesspflanzenActivator me = new RedListGefaesspflanzenActivator();

		me.doImport(cdmDestination);

	}

}

package eu.etaxonomy.cdm.io.redlist.gefaesspflanzen;

import eu.etaxonomy.cdm.database.ICdmDataSource;

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

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

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

import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;

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

@SuppressWarnings("serial")

public class RedListGefaesspflanzenImportConfigurator extends

		DbImportConfiguratorBase<RedListGefaesspflanzenImportState> implements

		IImportConfigurator {

    public static RedListGefaesspflanzenImportConfigurator NewInstance(Source source, ICdmDataSource cdmDestination) {

        return new RedListGefaesspflanzenImportConfigurator(source, cdmDestination, new RedListGefaesspflanzenTransformer());

    }

	protected RedListGefaesspflanzenImportConfigurator(Source source,

			ICdmDataSource destination, IInputTransformer defaultTransformer) {

		super(source, destination, NomenclaturalCode.ICNAFP, defaultTransformer);

	}

	@Override

	public RedListGefaesspflanzenImportState getNewState() {

		return new RedListGefaesspflanzenImportState(this);

	}

    @Override

    protected void makeIoClassList() {

        ioClassList = new Class[]{

                RedListGefaesspflanzenImportTaxa.class,

        };

    }

}

// $Id$

/**

* Copyright (C) 2007 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;

import org.apache.log4j.Logger;

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

/**

 * @author a.mueller

 * @created 11.05.2009

 */

public class RedListGefaesspflanzenImportState extends DbImportStateBase<RedListGefaesspflanzenImportConfigurator, RedListGefaesspflanzenImportState>{

	@SuppressWarnings("unused")

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

    protected RedListGefaesspflanzenImportState(RedListGefaesspflanzenImportConfigurator config) {

        super(config);

    }

}

/**

 * Copyright (C) 2007 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;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

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

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

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

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

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

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

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

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

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

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

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

/**

 * @author a.mueller

 * @created 05.01.2016

 */

@Component

@SuppressWarnings("serial")

public class RedListGefaesspflanzenImportTaxa extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {

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

    private static final String tableName = "Rote Liste Gefäßpflanzen";

    private static final String pluralString = "taxa";

    private static final String TAXON_NAMESPACE = "taxon";

    public RedListGefaesspflanzenImportTaxa() {

        super(tableName, pluralString);

    }

    @Override

    protected String getIdQuery(RedListGefaesspflanzenImportState state) {

        return "SELECT NAMNR FROM V_TAXATLAS_D20_EXPORT t "

//                + " ORDER BY NAMNR"

                ;

    }

    @Override

    protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {

        String result = " SELECT * "

                + " FROM V_TAXATLAS_D20_EXPORT t "

                + " WHERE t.NAMNR IN (@IDSET)";

        result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);

        return result;

    }

    @Override

    protected void doInvoke(RedListGefaesspflanzenImportState state) {

        super.doInvoke(state);

    }

    @Override

    public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {

        ResultSet rs = partitioner.getResultSet();

        Set<TaxonBase> taxaToSave = new HashSet<>();

        try {

            while (rs.next()){

                taxaToSave = makeSingleTaxon(state, rs);

            }

        } catch (SQLException e) {

            e.printStackTrace();

        }

        getTaxonService().saveOrUpdate(taxaToSave);

        return true;

    }

    private Set<TaxonBase> makeSingleTaxon(RedListGefaesspflanzenImportState state, ResultSet rs)

            throws SQLException {

        Set<TaxonBase> taxaToSave = new HashSet<>();

        long id = rs.getLong("NAMNR");

        String taxonNameString = rs.getString("TAXNAME");

        NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();

        NonViralName<?> name = parser.parseFullName(taxonNameString);

        TaxonBase taxon = Taxon.NewInstance(name, null);

        taxaToSave.add(taxon);

        //id

        ImportHelper.setOriginalSource(taxon, state.getTransactionalSourceReference(), id, TAXON_NAMESPACE);

        ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, TAXON_NAMESPACE);

        return taxaToSave;

    }

    private Rank makeRank(RedListGefaesspflanzenImportState state, String rankStr) {

        Rank rank = null;

        try {

            rank = state.getTransformer().getRankByKey(rankStr);

        } catch (UndefinedTransformerMethodException e) {

            e.printStackTrace();

        }

        return rank;

    }

    @Override

    public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,

            RedListGefaesspflanzenImportState state) {

        Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();

//        Map<String, TeamOrPersonBase<?>> authorMap = new HashMap<>();

//        Set<String> authorSet = new HashSet<>();

//        Set<String> referenceIdSet = new HashSet<String>();

//

//        try {

//            while (rs.next()){

//                String authorStr = rs.getString("tax_author_name");

//                authorSet.add(authorStr);

//                handleForeignKey(rs, referenceIdSet, "tax_document");

//            }

//        } catch (SQLException e) {

//            e.printStackTrace();

//        }

//

//        //Authors

//        Set<UUID> uuidSet = new HashSet<>();

//        for (String authorStr : authorSet){

//            UUID uuid = state.getAuthorUuid(authorStr);

//            uuidSet.add(uuid);

//        }

//        List<TeamOrPersonBase<?>> authors = (List)getAgentService().find(uuidSet);

//        Map<UUID, TeamOrPersonBase<?>> authorUuidMap = new HashMap<>();

//        for (TeamOrPersonBase<?> author : authors){

//            authorUuidMap.put(author.getUuid(), author);

//        }

//

//        for (String authorStr : authorSet){

//            UUID uuid = state.getAuthorUuid(authorStr);

//            TeamOrPersonBase<?> author = authorUuidMap.get(uuid);

//            authorMap.put(authorStr, author);

//        }

//        result.put(AUTHOR_NAMESPACE, authorMap);

//

//        //reference map

//        String nameSpace = REFERENCE_NAMESPACE;

//        Class<?> cdmClass = Reference.class;

//        Set<String> idSet = referenceIdSet;

//        Map<String, Reference<?>> referenceMap = (Map<String, Reference<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

//        result.put(nameSpace, referenceMap);

//

//        //secundum

//        UUID secUuid = state.getConfig().getSecUuid();

//        Reference<?> secRef = getReferenceService().find(secUuid);

//        referenceMap.put(secUuid.toString(), secRef);

        return result;

    }

    @Override

    protected boolean doCheck(RedListGefaesspflanzenImportState state) {

        return false;

    }

    @Override

    protected boolean isIgnore(RedListGefaesspflanzenImportState state) {

        return false;

    }

}

// $Id$

/**

* Copyright (C) 2007 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;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.io.common.mapping.InputTransformerBase;

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

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

/**

 * @author a.mueller

 * @created 01.03.2010

 */

@SuppressWarnings("serial")

public final class RedListGefaesspflanzenTransformer extends InputTransformerBase {

    @SuppressWarnings("unused")

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

    @Override

    public Rank getRankByKey(String key) throws UndefinedTransformerMethodException {

        if (key == null){return null;}

        if (key.equals("GAT")){return Rank.GENUS();}

        else if (key.equals("SPE")){return Rank.SPECIES();}

        return null;

    }

}