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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.database.update.v41_47;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.database.update.ColumnAdder;
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import eu.etaxonomy.cdm.database.update.ColumnNameChanger;
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import eu.etaxonomy.cdm.database.update.ColumnRemover;
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import eu.etaxonomy.cdm.database.update.ISchemaUpdater;
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import eu.etaxonomy.cdm.database.update.ISchemaUpdaterStep;
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import eu.etaxonomy.cdm.database.update.IndexRenamer;
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import eu.etaxonomy.cdm.database.update.MnTableCreator;
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import eu.etaxonomy.cdm.database.update.SchemaUpdaterBase;
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import eu.etaxonomy.cdm.database.update.SimpleSchemaUpdaterStep;
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import eu.etaxonomy.cdm.database.update.TableCreator;
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import eu.etaxonomy.cdm.database.update.TableNameChanger;
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import eu.etaxonomy.cdm.database.update.UniqueIndexDropper;
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import eu.etaxonomy.cdm.database.update.v40_41.SchemaUpdater_40_41;
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/**
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* @author a.mueller
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* @created 16.04.2016
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*/
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/**
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* @author a.mueller
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* @date 09.05.2017
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*
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*/
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public class SchemaUpdater_41_47 extends SchemaUpdaterBase {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(SchemaUpdater_41_47.class);
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private static final String startSchemaVersion = "4.1.0.0.201607300000";
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private static final String endSchemaVersion = "4.7.0.0.201710040000";
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// ********************** FACTORY METHOD *************************************
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public static SchemaUpdater_41_47 NewInstance() {
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return new SchemaUpdater_41_47();
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}
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/**
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* @param startSchemaVersion
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* @param endSchemaVersion
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*/
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protected SchemaUpdater_41_47() {
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super(startSchemaVersion, endSchemaVersion);
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}
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@Override
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protected List<ISchemaUpdaterStep> getUpdaterList() {
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String stepName;
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String tableName;
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ISchemaUpdaterStep step;
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String newColumnName;
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List<ISchemaUpdaterStep> stepList = new ArrayList<>();
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//#6600 remove unique indexes from Rights MN tables
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removeUniqueIndexForRights(stepList);
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//#5149 remove unique index on Sequence_Reference.citations_id
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tableName = "Sequence_Reference";
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String columnName = "citations_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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//#6340 nom status invalid updater
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step = NomStatusInvalidUpdater.NewInstance();
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stepList.add(step);
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//#6529
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//Extend WorkingSet to allow a more fine grained definiton of taxon set
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//min rank
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stepName = "Add minRank column";
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tableName = "WorkingSet";
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newColumnName = "minRank_id";
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String referencedTable = "DefinedTermBase";
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step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
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stepList.add(step);
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//max rank
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stepName = "Add maxRank column";
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tableName = "WorkingSet";
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newColumnName = "maxRank_id";
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referencedTable = "DefinedTermBase";
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step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
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stepList.add(step);
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//subtree filter
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stepName= "Add geo filter MN table to WorkingSet";
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String firstTableName = "WorkingSet";
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String secondTableAlias = "NamedArea";
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String secondTableName = "DefinedTermBase";
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String attributeName = "geoFilter";
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boolean isList = ! IS_LIST;
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step = MnTableCreator.NewMnInstance(stepName, firstTableName, null, secondTableName, secondTableAlias, attributeName, INCLUDE_AUDIT, isList, IS_M_TO_M);
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stepList.add(step);
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//subtree filter
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stepName= "Add subtree filter MN table to WorkingSet";
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firstTableName = "WorkingSet";
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secondTableName = "TaxonNode";
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secondTableAlias = null;
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attributeName = "taxonSubtreeFilter";
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isList = ! IS_LIST;
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step = MnTableCreator.NewMnInstance(stepName, firstTableName, null, secondTableName, secondTableAlias, attributeName, INCLUDE_AUDIT, isList, IS_M_TO_M);
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stepList.add(step);
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//#6258
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stepName = "Add Registration table";
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tableName = "Registration";
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String[] columnNames = new String[]{"identifier","specificIdentifier","registrationDate","status",
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"institution_id","name_id","submitter_id"};
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String[] referencedTables = new String[]{null, null, null, null,
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"AgentBase","TaxonNameBase","UserAccount"};
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String[] columnTypes = new String[]{"string_255","string_255","datetime","string_10","int","int","int"};
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step = TableCreator.NewAnnotatableInstance(stepName, tableName,
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columnNames, columnTypes, referencedTables, INCLUDE_AUDIT);
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stepList.add(step);
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//add blockedBy_id
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stepName= "Add blockedBy_id to Registration";
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firstTableName = "Registration";
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secondTableName = "Registration";
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attributeName = "blockedBy";
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isList = ! IS_LIST;
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step = MnTableCreator.NewMnInstance(stepName, firstTableName, null, secondTableName, null, attributeName, INCLUDE_AUDIT, isList, IS_M_TO_M);
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stepList.add(step);
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//add type designations
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stepName= "Add type designations to Registration";
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firstTableName = "Registration";
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String firstColumnName = "registrations";
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secondTableName = "TypeDesignationBase";
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attributeName = "typeDesignations";
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isList = false;
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step = MnTableCreator.NewMnInstance(stepName, firstTableName, null, firstColumnName, secondTableName, null, attributeName, INCLUDE_AUDIT, isList, IS_M_TO_M);
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stepList.add(step);
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//#5258
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//Add "accessed" to Reference
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stepName = "Add 'accessed' to Reference";
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tableName = "Reference";
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newColumnName = "accessed";
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step = ColumnAdder.NewDateTimeInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL);
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stepList.add(step);
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//#6618 Add structure column to DefinedTermBase (Character)
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stepName = "Add structure column to DefinedTermBase (Character)";
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tableName = "DefinedTermBase";
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newColumnName = "structure_id";
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referencedTable = "FeatureNode";
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step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
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stepList.add(step);
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//#6618 Add property column to DefinedTermBase (Character)
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stepName = "Add property column to DefinedTermBase (Character)";
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tableName = "DefinedTermBase";
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newColumnName = "property_id";
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referencedTable = "FeatureNode";
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step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
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stepList.add(step);
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//#6361 and children
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mergeTaxonName(stepList);
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//#6535 update termtype for CdmMetaData (int => string)
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updateTermTypeForCdmMetaDataPropertyName(stepList);
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//##6661 Add initials to agent base
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stepName = "Add initials to AgentBase";
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tableName = "AgentBase";
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newColumnName = "initials";
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int length = 80;
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step = ColumnAdder.NewStringInstance(stepName, tableName, newColumnName, length, INCLUDE_AUDIT);
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stepList.add(step);
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stepName = "Update initials and firstname";
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step = InitialsUpdater.NewInstance();
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stepList.add(step);
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//#6663
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//Add "lastRetrieved" to Reference
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stepName = "Add 'lastRetrieved' to Reference";
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tableName = "Reference";
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newColumnName = "lastRetrieved";
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step = ColumnAdder.NewDateTimeInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL);
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stepList.add(step);
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stepName = "Add externalId to Reference";
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tableName = "Reference";
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newColumnName = "externalId";
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length = 255;
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step = ColumnAdder.NewStringInstance(stepName, tableName, newColumnName, length, INCLUDE_AUDIT);
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stepList.add(step);
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stepName = "Add externalLink to Reference";
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tableName = "Reference";
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newColumnName = "externalLink";
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step = ColumnAdder.NewClobInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT);
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stepList.add(step);
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stepName = "Add authorityType to Reference";
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tableName = "Reference";
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newColumnName = "authorityType";
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length = 10;
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step = ColumnAdder.NewStringInstance(stepName, tableName, newColumnName, length, INCLUDE_AUDIT);
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stepList.add(step);
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//#6472 add key to IntextReference
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stepName = "Add key to IntextReference";
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tableName = "IntextReference";
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newColumnName = "key_id";
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referencedTable = "PolytomousKey";
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step = ColumnAdder.NewIntegerInstance(stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
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stepList.add(step);
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//#5817 rename relationshipTermBase_inverseRepresentation
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stepName = "Rename relationshipTermBase_inverseRepresentation";
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String oldName = "RelationshipTermBase_inverseRepresentation";
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String newName = "TermBase_inverseRepresentation";
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step = TableNameChanger.NewInstance(stepName, oldName, newName, INCLUDE_AUDIT);
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stepList.add(step);
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//#5817 rename TermBase_inverseRepresentation.relationshipTermBase_id
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stepName = "Rename relationshipTermBase_inverseRepresentation.relationshipTermBase_id";
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tableName = newName;
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String oldColumnName = "relationshipTermBase_id";
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newColumnName = "term_id";
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step = ColumnNameChanger.NewIntegerInstance(stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
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stepList.add(step);
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//#6226 remove orphaned PolytomousKeyNodes
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stepName = "remove orphaned PolytomousKeyNodes";
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String query = " DELETE FROM @@PolytomousKeyNode@@ WHERE key_id NOT IN (SELECT id FROM @@PolytomousKey@@)";
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String aud_query = " DELETE FROM @@PolytomousKeyNode_AUD@@ WHERE key_id NOT IN (SELECT id FROM @@PolytomousKey_AUD@@)";
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step = SimpleSchemaUpdaterStep.NewExplicitAuditedInstance(stepName, query, aud_query, -99);
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stepList.add(step);
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//#6226 remove orphaned key statements
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step = OrphanedKeyStatementRemover.NewInstance();
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stepList.add(step);
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return stepList;
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}
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/**
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* @param stepList
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*/
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//#6600 remove Unique indexes from Rights MN tables
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private void removeUniqueIndexForRights(List<ISchemaUpdaterStep> stepList) {
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String tableName;
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ISchemaUpdaterStep step;
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tableName = "AgentBase_RightsInfo";
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String columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "Classification_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "Collection_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "DefinedTermBase_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "DescriptionBase_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "FeatureTree_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "Media_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "PolytomousKey_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "Reference_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "SpecimenOrObservationBase_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "TaxonBase_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "TaxonNameBase_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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tableName = "TermVocabulary_RightsInfo";
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columnName = "rights_id";
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step = UniqueIndexDropper.NewInstance(tableName, columnName, !INCLUDE_AUDIT);
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stepList.add(step);
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}
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/**
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* #6535 update termtype for CdmMetaData (int => string)
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*/
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private void updateTermTypeForCdmMetaDataPropertyName(List<ISchemaUpdaterStep> stepList) {
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String stepName = "Rename CdmMetaData.propertyName column";
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String tableName = "CdmMetaData";
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String oldColumnName = "propertyName";
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String newColumnName = "propertyNameOld";
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ISchemaUpdaterStep step = ColumnNameChanger.NewIntegerInstance(stepName, tableName, oldColumnName, newColumnName, ! INCLUDE_AUDIT);
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stepList.add(step);
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//... create new column
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stepName = "Create new CdmMetaData.propertyName column";
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tableName = "CdmMetaData";
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newColumnName = "propertyName";
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step = ColumnAdder.NewStringInstance(stepName, tableName, newColumnName, 20, ! INCLUDE_AUDIT);
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stepList.add(step);
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updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "SCHEMA_VERSION", 0);
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updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "TERM_VERSION", 1 );
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updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "CREATED", 2 );
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updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "CREATE_NOTE", 3 );
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updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "INST_NAME", 4 );
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updateSingleTermTypeForCdmMetaDataPropertyName(stepList, "INST_ID", 5 );
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//... create new column
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stepName = "Remove column CdmMetaData.propertyNameOld";
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tableName = "CdmMetaData";
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oldColumnName = "propertyNameOld";
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step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, ! INCLUDE_AUDIT);
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stepList.add(step);
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}
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/**
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* @param stepList
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* @param name
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* @param index
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*/
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private void updateSingleTermTypeForCdmMetaDataPropertyName(List<ISchemaUpdaterStep> stepList,
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String name, int index) {
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String stepName = "Update value for " + name;
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String query = "UPDATE @@CdmMetaData@@ SET propertyName = '"+name+"' WHERE propertyNameOld = "+index;
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ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query, -99);
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stepList.add(step);
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}
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/**
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* #6361 and children
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*/
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388
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private void mergeTaxonName(List<ISchemaUpdaterStep> stepList) {
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389
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//#6367 Add nameType column to TaxonNameBase
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String stepName = "Add nameType column to TaxonNameBase";
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String tableName = "TaxonNameBase";
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String newColumnName = "nameType";
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int length = 15;
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395
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ISchemaUpdaterStep step = ColumnAdder.NewStringInstance(stepName, tableName, newColumnName, length, INCLUDE_AUDIT);
|
396
|
stepList.add(step);
|
397
|
|
398
|
//#6367 #6368
|
399
|
updateNameTypes(stepList);
|
400
|
|
401
|
// update anamorphic
|
402
|
stepName = "Update anamorphic ";
|
403
|
String query = "UPDATE @@TaxonNameBase@@ tnb "
|
404
|
+ " SET anamorphic = @FALSE@ "
|
405
|
+ " WHERE anamorphic IS NULL " ;
|
406
|
SimpleSchemaUpdaterStep simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "TaxonNameBase", -99);
|
407
|
stepList.add(simpleStep);
|
408
|
|
409
|
//#6368 Remove DTYPE
|
410
|
stepName = "Remove DTYPE from TaxonNameBase";
|
411
|
tableName = "TaxonNameBase";
|
412
|
String oldColumnName = "DTYPE";
|
413
|
step = ColumnRemover.NewInstance(stepName, tableName, oldColumnName, INCLUDE_AUDIT);
|
414
|
stepList.add(step);
|
415
|
|
416
|
//#6368
|
417
|
changeTaxonNameTableName(stepList);
|
418
|
|
419
|
//#6717 update index names
|
420
|
step = IndexRenamer.NewStringInstance("TaxonName",
|
421
|
"taxonNameBaseNameCacheIndex", "taxonNameNameCacheIndex", "nameCache", 255);
|
422
|
stepList.add(step);
|
423
|
|
424
|
step = IndexRenamer.NewStringInstance("TaxonName",
|
425
|
"taxonNameBaseTitleCacheIndex", "taxonNameTitleCacheIndex", "titleCache", 333);
|
426
|
stepList.add(step);
|
427
|
|
428
|
}
|
429
|
|
430
|
/**
|
431
|
* #6368
|
432
|
*/
|
433
|
private void changeTaxonNameTableName(List<ISchemaUpdaterStep> stepList) {
|
434
|
|
435
|
//Update
|
436
|
String oldName = "TaxonNameBase";
|
437
|
changeSingleTaxonNameTableName(stepList, oldName);
|
438
|
|
439
|
oldName = "TaxonNameBase_Annotation";
|
440
|
changeSingleTaxonNameTableName(stepList, oldName);
|
441
|
|
442
|
oldName = "TaxonNameBase_Credit";
|
443
|
changeSingleTaxonNameTableName(stepList, oldName);
|
444
|
|
445
|
oldName = "TaxonNameBase_Extension";
|
446
|
changeSingleTaxonNameTableName(stepList, oldName);
|
447
|
|
448
|
oldName = "TaxonNameBase_Identifier";
|
449
|
changeSingleTaxonNameTableName(stepList, oldName);
|
450
|
|
451
|
oldName = "TaxonNameBase_Marker";
|
452
|
changeSingleTaxonNameTableName(stepList, oldName);
|
453
|
|
454
|
oldName = "TaxonNameBase_NomenclaturalStatus";
|
455
|
changeSingleTaxonNameTableName(stepList, oldName);
|
456
|
|
457
|
oldName = "TaxonNameBase_OriginalSourceBase";
|
458
|
changeSingleTaxonNameTableName(stepList, oldName);
|
459
|
|
460
|
oldName = "TaxonNameBase_RightsInfo";
|
461
|
changeSingleTaxonNameTableName(stepList, oldName);
|
462
|
|
463
|
oldName = "TaxonNameBase_TypeDesignationBase";
|
464
|
changeSingleTaxonNameTableName(stepList, oldName);
|
465
|
|
466
|
//hibernate sequence
|
467
|
String stepName = "Update hibernate sequence entry name for TaxonNameBase";
|
468
|
String query = "UPDATE hibernate_sequences SET sequence_name = 'TaxonName' WHERE sequence_name = 'TaxonNameBase'";
|
469
|
ISchemaUpdaterStep step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query, -99);
|
470
|
stepList.add(step);
|
471
|
|
472
|
//grantedauthority for taxonnamebase
|
473
|
stepName = "Update GrantedAuthorityImpl for TaxonNameBase";
|
474
|
query = "UPDATE GrantedAuthorityImpl " +
|
475
|
" SET authority = Replace (authority, 'TAXONNAMEBASE','TAXONNAME') " +
|
476
|
" WHERE authority like '%TAXONNAMEBASE%' ";
|
477
|
step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query, -99);
|
478
|
stepList.add(step);
|
479
|
|
480
|
|
481
|
//LSIDAuthority_namespaces for taxonnamebase
|
482
|
stepName = "Upate LSIDAuthority_namespaces for TaxonNameBase";
|
483
|
query = "UPDATE LSIDAuthority_namespaces " +
|
484
|
" SET namespaces_element = Replace (namespaces_element, 'TaxonNameBase','TaxonName') " +
|
485
|
" WHERE namespaces_element like '%TaxonNameBase%' ";
|
486
|
step = SimpleSchemaUpdaterStep.NewNonAuditedInstance(stepName, query, -99);
|
487
|
stepList.add(step);
|
488
|
}
|
489
|
|
490
|
/**
|
491
|
* @param #6368
|
492
|
*/
|
493
|
private void changeSingleTaxonNameTableName(List<ISchemaUpdaterStep> stepList, String oldTableName) {
|
494
|
String stepName = "Rename " + oldTableName;
|
495
|
String newTableName = oldTableName.replace("TaxonNameBase", "TaxonName");
|
496
|
ISchemaUpdaterStep step = TableNameChanger.NewInstance(stepName, oldTableName, newTableName, INCLUDE_AUDIT);
|
497
|
stepList.add(step);
|
498
|
|
499
|
if (oldTableName.contains("_")){
|
500
|
stepName = "Rename " + oldTableName + ".taxonNameBase_id";
|
501
|
String oldColumnName = "TaxonNameBase_id";
|
502
|
String newColumnName = "TaxonName_id";
|
503
|
step = ColumnNameChanger.NewIntegerInstance(stepName, newTableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
|
504
|
stepList.add(step);
|
505
|
}
|
506
|
|
507
|
}
|
508
|
|
509
|
/**
|
510
|
* #6367
|
511
|
*/
|
512
|
private void updateNameTypes(List<ISchemaUpdaterStep> stepList) {
|
513
|
updateSingleNameType(stepList, "ViralName", "ICVCN");
|
514
|
updateSingleNameType(stepList, "NonViralName", "NonViral");
|
515
|
updateSingleNameType(stepList, "BotanicalName", "ICNAFP");
|
516
|
updateSingleNameType(stepList, "ZoologicalName", "ICZN");
|
517
|
updateSingleNameType(stepList, "CultivarPlantName", "ICNCP");
|
518
|
updateSingleNameType(stepList, "BacterialName", "ICNB");
|
519
|
}
|
520
|
|
521
|
/**
|
522
|
* @param uuid the uuid
|
523
|
* @param oldSymbol
|
524
|
* @param newSybol
|
525
|
*/
|
526
|
private void updateSingleNameType(List<ISchemaUpdaterStep> stepList,
|
527
|
String dtype, String nameType) {
|
528
|
|
529
|
String stepName = "Update nameType for " + dtype;
|
530
|
String query = "UPDATE @@TaxonNameBase@@ tnb "
|
531
|
+ " SET nameType = '" + nameType + "'"
|
532
|
+ " WHERE dtype = '" + dtype + "'" ;
|
533
|
SimpleSchemaUpdaterStep simpleStep = SimpleSchemaUpdaterStep.NewAuditedInstance(stepName, query, "TaxonNameBase", -99);
|
534
|
stepList.add(simpleStep);
|
535
|
}
|
536
|
|
537
|
@Override
|
538
|
public ISchemaUpdater getNextUpdater() {
|
539
|
return null;
|
540
|
}
|
541
|
|
542
|
@Override
|
543
|
public ISchemaUpdater getPreviousUpdater() {
|
544
|
return SchemaUpdater_40_41.NewInstance();
|
545
|
}
|
546
|
|
547
|
}
|