EDIT

/**

 * 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.v41_47;

import java.util.ArrayList;

import java.util.List;

import org.apache.log4j.Logger;

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

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

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

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

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

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

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.UniqueIndexDropper;

import eu.etaxonomy.cdm.database.update.v40_41.SchemaUpdater_40_41;

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

/**

 * @author a.mueller

 * @since 09.05.2017

 *

 */

public class SchemaUpdater_41_47 extends SchemaUpdaterBase {

	@SuppressWarnings("unused")

	private static final Logger logger = Logger.getLogger(SchemaUpdater_41_47.class);

	private static final String startSchemaVersion = "4.1.0.0.201607300000";

	private static final String endSchemaVersion = "4.7.0.0.201710040000";

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

	public static SchemaUpdater_41_47 NewInstance() {

		return new SchemaUpdater_41_47();

	}

	/**

	 * @param startSchemaVersion

	 * @param endSchemaVersion

	 */

	protected SchemaUpdater_41_47() {

		super(startSchemaVersion, endSchemaVersion);

	}

	@Override

	protected List<ISchemaUpdaterStep> getUpdaterList() {

		String stepName;

		String tableName;

		ISchemaUpdaterStep step;

		String newColumnName;

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

	    //#6600 remove unique indexes from Rights MN tables

        removeUniqueIndexForRights(stepList);

        //#5149 remove unique index on Sequence_Reference.citations_id

        tableName = "Sequence_Reference";

        String columnName = "citations_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        //#6340 nom status invalid updater

        step = NomStatusInvalidUpdater.NewInstance();

        stepList.add(step);

		//#6529

		//Extend WorkingSet to allow a more fine grained definiton of taxon set

		//min rank

        stepName = "Add minRank column";

        tableName = "WorkingSet";

        newColumnName = "minRank_id";

        String referencedTable = "DefinedTermBase";

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

        stepList.add(step);

        //max rank

        stepName = "Add maxRank column";

        tableName = "WorkingSet";

        newColumnName = "maxRank_id";

        referencedTable = "DefinedTermBase";

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

        stepList.add(step);

        //subtree filter

        stepName= "Add geo filter MN table to WorkingSet";

        String firstTableName = "WorkingSet";

        String secondTableAlias = "NamedArea";

        String secondTableName = "DefinedTermBase";

        String attributeName = "geoFilter";

        boolean isList = ! IS_LIST;

        step = MnTableCreator.NewMnInstance(stepName, firstTableName, null, secondTableName, secondTableAlias, attributeName, INCLUDE_AUDIT, isList, IS_M_TO_M);

        stepList.add(step);

        //subtree filter

        stepName= "Add subtree filter MN table to WorkingSet";

        firstTableName = "WorkingSet";

        secondTableName = "TaxonNode";

        secondTableAlias = null;

        attributeName = "taxonSubtreeFilter";

        isList = ! IS_LIST;

        step = MnTableCreator.NewMnInstance(stepName, firstTableName, null, secondTableName, secondTableAlias, attributeName, INCLUDE_AUDIT, isList, IS_M_TO_M);

        stepList.add(step);

        //#6258

        stepName = "Add Registration table";

        tableName = "Registration";

        String[] columnNames = new String[]{"identifier","specificIdentifier","registrationDate","status",

                "institution_id","name_id","submitter_id"};

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

                "AgentBase","TaxonNameBase","UserAccount"};

        String[] columnTypes = new String[]{"string_255","string_255","datetime","string_10","int","int","int"};

        step = TableCreator.NewAnnotatableInstance(stepName, tableName,

                columnNames, columnTypes, referencedTables, INCLUDE_AUDIT);

        stepList.add(step);

        //add blockedBy_id

        stepName= "Add blockedBy_id to Registration";

        firstTableName = "Registration";

        secondTableName = "Registration";

        attributeName = "blockedBy";

        isList = ! IS_LIST;

        step = MnTableCreator.NewMnInstance(stepName, firstTableName, null, secondTableName, null, attributeName, INCLUDE_AUDIT, isList, IS_M_TO_M);

        stepList.add(step);

        //add type designations

        stepName= "Add type designations to Registration";

        firstTableName = "Registration";

        String firstColumnName = "registrations";

        secondTableName = "TypeDesignationBase";

        attributeName = "typeDesignations";

        isList = false;

        step = MnTableCreator.NewMnInstance(stepName, firstTableName, null, firstColumnName, secondTableName, null, attributeName, INCLUDE_AUDIT, isList, IS_M_TO_M);

        stepList.add(step);

        //#5258

        //Add "accessed" to Reference

        stepName = "Add 'accessed' to Reference";

        tableName = "Reference";

        newColumnName = "accessed";

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

        stepList.add(step);

        //#6618 Add structure column to DefinedTermBase (Character)

        stepName = "Add structure column to DefinedTermBase (Character)";

        tableName = "DefinedTermBase";

        newColumnName = "structure_id";

        referencedTable = "FeatureNode";

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

        stepList.add(step);

        //#6618 Add property column to DefinedTermBase (Character)

        stepName = "Add property column to DefinedTermBase (Character)";

        tableName = "DefinedTermBase";

        newColumnName = "property_id";

        referencedTable = "FeatureNode";

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

        stepList.add(step);

        //#6361 and children

        mergeTaxonName(stepList);

        //#6535 update termtype for CdmMetaData (int => string)

        updateTermTypeForCdmMetaDataPropertyName(stepList);

        //##6661 Add initials to agent base

        stepName = "Add initials to AgentBase";

        tableName = "AgentBase";

        newColumnName = "initials";

        int length = 80;

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

        stepList.add(step);

        stepName = "Update initials and firstname";

        step = InitialsUpdater.NewInstance();

        stepList.add(step);

        //#6663

        //Add "lastRetrieved" to Reference

        stepName = "Add 'lastRetrieved' to Reference";

        tableName = "Reference";

        newColumnName = "lastRetrieved";

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

        stepList.add(step);

        stepName = "Add externalId to Reference";

        tableName = "Reference";

        newColumnName = "externalId";

        length = 255;

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

        stepList.add(step);

        stepName = "Add externalLink to Reference";

        tableName = "Reference";

        newColumnName = "externalLink";

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

        stepList.add(step);

        stepName = "Add authorityType to Reference";

        tableName = "Reference";

        newColumnName = "authorityType";

        length = 10;

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

        stepList.add(step);

        //#6472 add key to IntextReference

        stepName = "Add key to IntextReference";

        tableName = "IntextReference";

        newColumnName = "key_id";

        referencedTable = "PolytomousKey";

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

        stepList.add(step);

        //#5817 rename relationshipTermBase_inverseRepresentation

        stepName = "Rename relationshipTermBase_inverseRepresentation";

        String oldName = "RelationshipTermBase_inverseRepresentation";

        String newName = "TermBase_inverseRepresentation";

        step = TableNameChanger.NewInstance(stepName, oldName, newName, INCLUDE_AUDIT);

        stepList.add(step);

        //#5817 rename TermBase_inverseRepresentation.relationshipTermBase_id

        stepName = "Rename relationshipTermBase_inverseRepresentation.relationshipTermBase_id";

        tableName = newName;

        String oldColumnName = "relationshipTermBase_id";

        newColumnName = "term_id";

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

        stepList.add(step);

        //#6226 remove orphaned PolytomousKeyNodes

        stepName = "remove orphaned PolytomousKeyNodes";

        String query = " DELETE FROM @@PolytomousKeyNode@@ WHERE key_id NOT IN (SELECT id FROM @@PolytomousKey@@)";

        String aud_query = " DELETE FROM @@PolytomousKeyNode_AUD@@ WHERE key_id NOT IN (SELECT id FROM @@PolytomousKey_AUD@@)";

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

        stepList.add(step);

        //#6226 remove orphaned key statements

        step = OrphanedKeyStatementRemover.NewInstance();

        stepList.add(step);

        return stepList;

    }

    /**

     * @param stepList

     */

	//#6600 remove Unique indexes from Rights MN tables

    private void removeUniqueIndexForRights(List<ISchemaUpdaterStep> stepList) {

        String tableName;

        ISchemaUpdaterStep step;

        tableName = "AgentBase_RightsInfo";

        String columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "Classification_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "Collection_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "DefinedTermBase_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "DescriptionBase_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "FeatureTree_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "Media_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "PolytomousKey_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "Reference_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "SpecimenOrObservationBase_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "TaxonBase_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "TaxonNameBase_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

        tableName = "TermVocabulary_RightsInfo";

        columnName = "rights_id";

        step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);

        stepList.add(step);

    }

    /**

     * #6535 update termtype for CdmMetaData (int => string)

     */

    private void updateTermTypeForCdmMetaDataPropertyName(List<ISchemaUpdaterStep> stepList) {

        String stepName = "Rename CdmMetaData.propertyName column";

        String tableName = "CdmMetaData";

        String oldColumnName = "propertyName";

        String newColumnName = "propertyNameOld";

        ISchemaUpdaterStep step = ColumnNameChanger.NewIntegerInstance(stepName, tableName, oldColumnName, newColumnName, ! INCLUDE_AUDIT);

        stepList.add(step);

        //... create new column

        stepName = "Create new CdmMetaData.propertyName column";

        tableName = "CdmMetaData";

        newColumnName = "propertyName";

        step = ColumnAdder.NewStringInstance(stepName, tableName, newColumnName, 20, ! INCLUDE_AUDIT);

        stepList.add(step);

        updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "SCHEMA_VERSION", 0);

        updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "TERM_VERSION", 1 );

        updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "CREATED", 2 );

        updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "CREATE_NOTE", 3 );

        updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "INST_NAME", 4 );

        updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "INST_ID", 5 );

        //... create new column

        stepName = "Remove column CdmMetaData.propertyNameOld";

        tableName = "CdmMetaData";

        oldColumnName = "propertyNameOld";

        step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, ! INCLUDE_AUDIT);

        stepList.add(step);

    }

    /**

     * @param stepList

     * @param name

     * @param index

     */

    private void updateSingleTermTypeForCdmMetaDataPropertyName(List<ISchemaUpdaterStep> stepList,

            String name, int index) {

        String stepName = "Update value for " + name;

        String query = "UPDATE @@CdmMetaData@@ SET propertyName = '"+name+"' WHERE propertyNameOld = "+index;

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

        stepList.add(step);

    }

    /**

     * #6361 and children

     */

    private void mergeTaxonName(List<ISchemaUpdaterStep> stepList) {

        //#6367 Add nameType column to TaxonNameBase

        String stepName = "Add nameType column to TaxonNameBase";

        String tableName = "TaxonNameBase";

        String newColumnName = "nameType";

        int length = 15;

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

        stepList.add(step);

        //#6367 #6368

        updateNameTypes(stepList);

        // update anamorphic

        stepName = "Update anamorphic ";

        String query = "UPDATE @@TaxonNameBase@@ tnb "

                + " SET anamorphic = @FALSE@ "

                + " WHERE anamorphic IS NULL " ;

        SimpleSchemaUpdaterStep simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "TaxonNameBase", -99);

        stepList.add(simpleStep);

        //#6368 Remove DTYPE

        stepName = "Remove DTYPE from TaxonNameBase";

        tableName = "TaxonNameBase";

        String oldColumnName = "DTYPE";

        step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, INCLUDE_AUDIT);

        stepList.add(step);

        //#6368

        changeTaxonNameTableName(stepList);

        //#6717 update index names

        step = IndexRenamer.NewStringInstance("TaxonName",

                "taxonNameBaseNameCacheIndex", "taxonNameNameCacheIndex", "nameCache", 255);

        stepList.add(step);

        step = IndexRenamer.NewStringInstance("TaxonName",

                "taxonNameBaseTitleCacheIndex", "taxonNameTitleCacheIndex", "titleCache", 333);

        stepList.add(step);

    }

    /**

     * #6368

     */

    private void changeTaxonNameTableName(List<ISchemaUpdaterStep> stepList) {

        //Update

        String oldName = "TaxonNameBase";

        changeSingleTaxonNameTableName(stepList, oldName);

        oldName = "TaxonNameBase_Annotation";

        changeSingleTaxonNameTableName(stepList, oldName);

        oldName = "TaxonNameBase_Credit";

        changeSingleTaxonNameTableName(stepList, oldName);

        oldName = "TaxonNameBase_Extension";

        changeSingleTaxonNameTableName(stepList, oldName);

        oldName = "TaxonNameBase_Identifier";

        changeSingleTaxonNameTableName(stepList, oldName);

        oldName = "TaxonNameBase_Marker";

        changeSingleTaxonNameTableName(stepList, oldName);

        oldName = "TaxonNameBase_NomenclaturalStatus";

        changeSingleTaxonNameTableName(stepList, oldName);

        oldName = "TaxonNameBase_OriginalSourceBase";

        changeSingleTaxonNameTableName(stepList, oldName);

        oldName = "TaxonNameBase_RightsInfo";

        changeSingleTaxonNameTableName(stepList, oldName);

        oldName = "TaxonNameBase_TypeDesignationBase";

        changeSingleTaxonNameTableName(stepList, oldName);

        //hibernate sequence

        String stepName = "Update hibernate sequence entry name for TaxonNameBase";

        String query = "UPDATE hibernate_sequences SET sequence_name = 'TaxonName' WHERE sequence_name = 'TaxonNameBase'";

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

        stepList.add(step);

        //grantedauthority for taxonnamebase

        stepName = "Update GrantedAuthorityImpl for TaxonNameBase";

        query = "UPDATE GrantedAuthorityImpl " +

                " SET authority = Replace (authority, 'TAXONNAMEBASE','TAXONNAME') " +

                " WHERE authority like '%TAXONNAMEBASE%' ";

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

        stepList.add(step);

        //LSIDAuthority_namespaces for taxonnamebase

        stepName = "Upate LSIDAuthority_namespaces for TaxonNameBase";

        query = "UPDATE LSIDAuthority_namespaces " +

                " SET namespaces_element = Replace (namespaces_element, 'TaxonNameBase','TaxonName') " +

                " WHERE namespaces_element like '%TaxonNameBase%' ";

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

        stepList.add(step);

    }

    /**

     * @param #6368

     */

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

        String stepName = "Rename " +  oldTableName;

        String newTableName = oldTableName.replace("TaxonNameBase", "TaxonName");

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

        stepList.add(step);

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

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

            String oldColumnName = "TaxonNameBase_id";

            String newColumnName = "TaxonName_id";

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

            stepList.add(step);

        }

    }

    /**

     * #6367

     */

    private void updateNameTypes(List<ISchemaUpdaterStep> stepList) {

        updateSingleNameType(stepList, "ViralName", "ICVCN");

        updateSingleNameType(stepList, "NonViralName", "NonViral");

        updateSingleNameType(stepList, "BotanicalName", "ICNAFP");

        updateSingleNameType(stepList, "ZoologicalName", "ICZN");

        updateSingleNameType(stepList, "CultivarPlantName", "ICNCP");

        updateSingleNameType(stepList, "BacterialName", "ICNB");

    }

    /**

     * @param uuid the uuid

     * @param oldSymbol

     * @param newSybol

     */

    private void updateSingleNameType(List<ISchemaUpdaterStep> stepList,

            String dtype, String nameType) {

        String stepName = "Update nameType for " + dtype;

        String query = "UPDATE @@TaxonNameBase@@ tnb "

                + " SET nameType = '" + nameType + "'"

                + " WHERE dtype = '" + dtype + "'" ;

        SimpleSchemaUpdaterStep simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "TaxonNameBase", -99);

        stepList.add(simpleStep);

    }

    @Override

	public ISchemaUpdater getNextUpdater() {

		return SchemaUpdater_47_49.NewInstance() ;

	}

	@Override

	public ISchemaUpdater getPreviousUpdater() {

		return SchemaUpdater_40_41.NewInstance();

	}

}