EDIT

     private static final String dbSchemaVersion = "4.9.0.0.20170710";

import eu.etaxonomy.cdm.database.update.v47_49.SchemaUpdater_47_49;

        return SchemaUpdater_47_49.NewInstance();

import eu.etaxonomy.cdm.database.update.v47_49.SchemaUpdater_47_49;

		return SchemaUpdater_47_49.NewInstance() ;

/**

 * 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.database.update.v47_49;

import java.util.ArrayList;

import java.util.List;

import java.util.UUID;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.database.update.ClassBaseTypeUpdater;

import eu.etaxonomy.cdm.database.update.ColumnAdder;

import eu.etaxonomy.cdm.database.update.ColumnNameChanger;

import eu.etaxonomy.cdm.database.update.ColumnTypeChanger;

import eu.etaxonomy.cdm.database.update.ISchemaUpdater;

import eu.etaxonomy.cdm.database.update.ISchemaUpdaterStep;

import eu.etaxonomy.cdm.database.update.MnTableCreator;

import eu.etaxonomy.cdm.database.update.SchemaUpdaterBase;

import eu.etaxonomy.cdm.database.update.SimpleSchemaUpdaterStep;

import eu.etaxonomy.cdm.database.update.TableCreator;

import eu.etaxonomy.cdm.database.update.TableNameChanger;

import eu.etaxonomy.cdm.database.update.TermRepresentationUpdater;

import eu.etaxonomy.cdm.database.update.v41_47.SchemaUpdater_41_47;

/**

/**

 * @author a.mueller

 * @date 09.06.2017

 *

 */

public class SchemaUpdater_47_49 extends SchemaUpdaterBase {

	@SuppressWarnings("unused")

	private static final Logger logger = Logger.getLogger(SchemaUpdater_47_49.class);

	private static final String endSchemaVersion = "4.9.0.0.20170710";

	private static final String startSchemaVersion = "4.7.0.0.201710040000";

	// ********************** FACTORY METHOD *************************************

	public static SchemaUpdater_47_49 NewInstance() {

		return new SchemaUpdater_47_49();

	}

	/**

	 * @param startSchemaVersion

	 * @param endSchemaVersion

	 */

	protected SchemaUpdater_47_49() {

		super(startSchemaVersion, endSchemaVersion);

	}

	@Override

	protected List<ISchemaUpdaterStep> getUpdaterList() {

		String stepName;

		String tableName;

		ISchemaUpdaterStep step;

		String newColumnName;

		String query;

		List<ISchemaUpdaterStep> stepList = new ArrayList<>();

        //#6581 make nomenclatural reference and OriginalSource

        stepName = "Make nomenclatural reference and OriginalSource";

        tableName = "TaxonName";

        newColumnName = "nomenclaturalSource_id";

        String referencedTable = "OriginalSourceBase";

        step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);

        stepList.add(step);

		//#7109 nom. valid => nom. val.

		stepName = "nom valid => nom. val. (abbrevLabel)";

		UUID uuidTerm = UUID.fromString("bd036217-5499-4ccd-8f4c-72e06158db93");

		UUID uuidLanguage = UUID.fromString("160a5b6c-87f5-4422-9bda-78cd404c179e");

		step = TermRepresentationUpdater.NewInstance(stepName, uuidTerm,

		        null, null, "nom. val.", uuidLanguage);

		stepList.add(step);

		//... idInVoc

		stepName = "nom valid => nom. val. (idInVocabulary)";

        query = "UPDATE @@DefinedTermBase@@ "

                + " SET idInVocabulary = 'nom. val.' "

                + " WHERE uuid = '" + uuidTerm + "'";

		tableName = "DefinedTermBase";

		step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, tableName, -99);

		stepList.add(step);

		//#6752 add Reference.datePublished_verbatimDate

	    stepName = "Add Reference.datePublished_verbatimDate";

	    tableName = "Reference";

	    newColumnName = "datePublished_verbatimDate";

	    step = ColumnAdder.NewStringInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT);

	    stepList.add(step);

		//#7096 Add second symbol attribute to DefinedTermBase

		stepName = "Add second symbol to DefinedTermBase";

		tableName = "DefinedTermBase";

		newColumnName = "symbol2";

		int length = 30;

		step = ColumnAdder.NewStringInstance(stepName, tableName, newColumnName, length, INCLUDE_AUDIT);

		stepList.add(step);

		//#6879 Update uuid and name for admin user group

	    stepName = "Update uuid and name for admin user group";

        query = "UPDATE @@PermissionGroup@@ "

                + " SET uuid='1739df71-bf73-4dc6-8320-aaaf72cb555f', name='Admin' "

                + " WHERE  name='admin' or name='Admin'";

        step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query, -99);

        stepList.add(step);

        //#7405 Rename WorkingSet to DescriptiveDataSet

        String oldTableName = "WorkingSet";

        changeSingleWorkingSetTableName(stepList, oldTableName);

        oldTableName = "WorkingSet_Annotation";

        changeSingleWorkingSetTableName(stepList, oldTableName);

        oldTableName = "WorkingSet_DescriptionBase";

        changeSingleWorkingSetTableName(stepList, oldTableName);

        oldTableName = "WorkingSet_Marker";

        changeSingleWorkingSetTableName(stepList, oldTableName);

        oldTableName = "WorkingSet_NamedArea";

        changeSingleWorkingSetTableName(stepList, oldTableName);

        oldTableName = "WorkingSet_Representation";

        changeSingleWorkingSetTableName(stepList, oldTableName);

        oldTableName = "WorkingSet_TaxonNode";

        changeSingleWorkingSetTableName(stepList, oldTableName);

        //#2335 Make DescriptiveDataSet IdentifiableEntity

        stepName = "Make DescriptiveDataSet IdentifiableEntity";

        tableName = "DescriptiveDataSet";

        step = ClassBaseTypeUpdater.NewAnnotatableToIdentifiableInstance(stepName, tableName, INCLUDE_AUDIT);

        stepList.add(step);

        //TODO add titleCache updater, but maybe not necessary as real data does not really exist

        //except for Campanula test data, and it is easy to update via TaxEditor cache updater

        //#7374 Set titleCache of feature trees to protected

        stepName = "Set titleCache of feature trees to protected";

        query = "UPDATE @@FeatureTree@@ "

                + " SET protectedTitleCache = @TRUE@ ";

        tableName = "FeatureTree";

        step = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, tableName, -99);

        stepList.add(step);

        //#7238 rename lastName and firstName

        stepName = "rename lastName";

        tableName = "AgentBase";

        String oldColumnName = "lastname";

        newColumnName = "familyName";

        int size = 255;

        step = ColumnNameChanger.NewVarCharInstance(stepName, tableName, oldColumnName, newColumnName, size, INCLUDE_AUDIT);

        stepList.add(step);

        //... firstName

        stepName = "rename firstName";

        tableName = "AgentBase";

        oldColumnName = "firstname";

        newColumnName = "givenName";

        size = 255;

        step = ColumnNameChanger.NewVarCharInstance(stepName, tableName, oldColumnName, newColumnName, size, INCLUDE_AUDIT);

        stepList.add(step);

        //#7210 Add salt field for User

        stepName = "Add salt field for User";

        tableName = "UserAccount";

        newColumnName = "salt";

        step = ColumnAdder.NewStringInstance(stepName, tableName, newColumnName, length, INCLUDE_AUDIT);

        stepList.add(step);

        //#6943 Add combination 'in'-author

        stepName = "Add combination 'in'-author";

        tableName = "TaxonName";

        newColumnName = "inCombinationAuthorship_id";

        referencedTable = "AgentBase";

        step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);

        stepList.add(step);

        //#6943 Add basionym 'in'-author

        stepName = "Add basionym 'in'-author";

        tableName = "TaxonName";

        newColumnName = "inBasionymAuthorship_id";

        referencedTable = "AgentBase";

        step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);

        stepList.add(step);

        //#6916 Link IntextReference to OriginalSource

        stepName = "Link IntextReference to OriginalSource";

        tableName = "IntextReference";

        newColumnName = "source_id";

        referencedTable = "OriginalSourceBase";

        step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);

        stepList.add(step);

        //#6720 Make individual count a string

        stepName = "Make individual count a string";

        tableName = "SpecimenOrObservationBase";

        String columnName = "individualCount";

        size = 255;

        step = ColumnTypeChanger.NewInt2StringInstance(stepName, tableName, columnName, size, INCLUDE_AUDIT, null, !NOT_NULL);

        stepList.add(step);

        updateSpecimenTypeDesignationStatusOrder(stepList);

        //#7144 Set Country area level

        stepName = "Set Country area level";

        query = " UPDATE @@DefinedTermBase@@ " +

                " SET level_id = ( SELECT id FROM (SELECT id FROM DefinedTermBase WHERE uuid = '79db63a4-1563-461e-8e41-48f5722feca4') as drv) " +

                " WHERE DTYPE = 'Country' ";

        step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query, -99);

        stepList.add(step);

        //#6588

        stepName = "Add ExternalLink table";

        tableName = "ExternalLink";

        String[] columnNames = new String[]{"linkType","uri","size"};

        String[] referencedTables = new String[]{null, null, null};

        String[] columnTypes = new String[]{"string_10","clob","int"};

        step = TableCreator.NewVersionableInstance(stepName, tableName,

                columnNames, columnTypes, referencedTables, INCLUDE_AUDIT);

        stepList.add(step);

        //add i18n description

        stepName= "Add i18n description to ExternalLink";

        String firstTableName = "ExternalLink";

        String attributeName = "description";

        step = MnTableCreator.NewDescriptionInstance(stepName, firstTableName, null, attributeName, INCLUDE_AUDIT);

        stepList.add(step);

//        //7276  Make User.emailAddress a unique field

//        //TODO H2 / PostGreSQL / SQL Server

//        //User.email unique

//        stepName = "Update User.emailAdress unique index";

//        tableName = "UserAccount";

//        columnName = "emailAddress";

//        step = UsernameConstraintUpdater.NewInstance(stepName, tableName, columnName);

//        stepList.add(step);

        return stepList;

    }

    /**

     * @param stepList

     */

    private void updateSpecimenTypeDesignationStatusOrder(List<ISchemaUpdaterStep> stepList) {

        VocabularyOrderUpdater updater = VocabularyOrderUpdater.NewInstance(stepList);

        updater.add("a407dbc7-e60c-46ff-be11-eddf4c5a970d", 1);

        updater.add("05002d46-083e-4b27-8731-2e7c28a8825c", 2);

        updater.add("93ef8257-0a08-47bb-9b36-542417ae7560", 3);

        updater.add("7a1a8a53-78f4-4fc0-89f7-782e94992d08", 4);

        updater.add("f3b60bdb-4638-4ca9-a0c7-36e77d8459bb", 5);

        updater.add("052a5ff0-8e9a-4355-b24f-5e4bb6071f44", 6);

        updater.add("26e13359-8f77-4e40-a85a-56c01782fce0", 7);

        updater.add("7afc2f4f-f70a-4aa5-80a5-87764f746bde", 8);

        updater.add("989a2715-71d5-4fbe-aa9a-db9168353744", 9);

        updater.add("95b90696-e103-4bc0-b60b-c594983fb566", 10);

        updater.add("eb7df2e5-d9a7-479d-970c-c6f2b0a761d7", 11);

        updater.add("497137f3-b614-4183-8a22-97fcd6e2bdd8", 12);

        updater.add("7244bc51-14d8-41a6-9524-7dc5303bba29", 13);

        updater.add("0c39e2a5-2fe0-4d4f-819a-f609b5340339", 14);

        updater.add("01d91053-7004-4984-aa0d-9f4de59d6205", 15);

        updater.add("8d2fed1f-242e-4bcf-bbd7-e85133e479dc", 16);

        updater.add("49c96cae-6be6-401e-9b36-1bc12d9dc8f9", 17);

        updater.add("643513d0-32f5-46ba-840b-d9b9caf8160f", 18);

        updater.add("b7807acc-f559-474e-ad4a-e7a41e085e34", 19);

        updater.add("230fd762-b143-49de-ac2e-744bcc48a63b", 20);

        updater.add("7194020b-a326-4b47-9bfe-9f31a30aba7f", 21);

    }

    /**

     * @param #6368

     */

    private void changeSingleWorkingSetTableName(List<ISchemaUpdaterStep> stepList, String oldTableName) {

        String stepName = "Rename " +  oldTableName;

        String newTableName = oldTableName.replace("WorkingSet", "DescriptiveDataSet");

        ISchemaUpdaterStep step = TableNameChanger.NewInstance(stepName, oldTableName, newTableName, INCLUDE_AUDIT);

        stepList.add(step);

        if (oldTableName.contains("_")){

            stepName = "Rename " +  oldTableName + ".workingSet_id";

            String oldColumnName = "WorkingSet_id";

            String newColumnName = "DescriptiveDataSet_id";

            if ("WorkingSet_DescriptionBase".equals(oldTableName)){

                oldColumnName = "WorkingSets_id";

                newColumnName = "DescriptiveDataSets_id";

            }

            step = ColumnNameChanger.NewIntegerInstance(stepName, newTableName, oldColumnName, newColumnName, INCLUDE_AUDIT);

            stepList.add(step);

        }

    }

    @Override

	public ISchemaUpdater getNextUpdater() {

		return null;

	}

	@Override

	public ISchemaUpdater getPreviousUpdater() {

		return SchemaUpdater_41_47.NewInstance();

	}

}

/**

* Copyright (C) 2009 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.database.update.v47_49;

import java.sql.SQLException;

import java.util.ArrayList;

import java.util.List;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.database.update.CaseType;

import eu.etaxonomy.cdm.database.update.ISchemaUpdaterStep;

import eu.etaxonomy.cdm.database.update.SchemaUpdateResult;

import eu.etaxonomy.cdm.database.update.SchemaUpdaterStepBase;

/**

 * Updates the CdmPreference NomenclaturalCode  #3658

 *

 * @author a.mueller

 * @since 13.10.2016

 */

public class VocabularyOrderUpdater extends SchemaUpdaterStepBase {

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

	private static final String stepName = "Update vocabulary order";

	private List<String[]> data = new ArrayList<>();

// **************************** STATIC METHODS ********************************/

	public static final VocabularyOrderUpdater NewInstance(List<ISchemaUpdaterStep> stepList){

		VocabularyOrderUpdater result = new VocabularyOrderUpdater();

		stepList.add(result);

		return result;

	}

	private VocabularyOrderUpdater() {

		super(stepName);

	}

	public void add(String uuid, Integer id){

	    data.add(new String[]{uuid, String.valueOf(id)});

	}

    @Override

    public void invoke(ICdmDataSource datasource, IProgressMonitor monitor,

            CaseType caseType, SchemaUpdateResult result) throws SQLException {

        try{

            for (String[] dat : data){

                invokeSingle(datasource, monitor, caseType, result, dat);

            }

        } catch (Exception e) {

            String message = e.getMessage();

            monitor.warning(message, e);

            result.addException(e, message, this, "invoke");

        }

	    return;

	}

    /**

     * @param datasource

     * @param monitor

     * @param caseType

     * @param result

     * @param dat

     * @throws SQLException

     */

    private void invokeSingle(ICdmDataSource datasource, IProgressMonitor monitor, CaseType caseType,

            SchemaUpdateResult result, String[] dat) throws SQLException {

        String query = "UPDATE DefinedTermBase "

                + " SET orderIndex = " + dat[1] + " "

                + " WHERE uuid = '" + dat[0] + "'";

        datasource.executeUpdate(query);

    }

}