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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.v518_522;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.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.ColumnValueUpdater;
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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.SchemaUpdaterBase;
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import eu.etaxonomy.cdm.database.update.SimpleSchemaUpdaterStep;
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import eu.etaxonomy.cdm.database.update.v512_515.Reference2SourceMover;
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import eu.etaxonomy.cdm.database.update.v515_518.SchemaUpdater_5185_5186;
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import eu.etaxonomy.cdm.model.metadata.CdmMetaData.CdmVersion;
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/**
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* @author a.mueller
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* @date 15.02.2021
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*/
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public class SchemaUpdater_5186_5220 extends SchemaUpdaterBase {
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(SchemaUpdater_5186_5220.class);
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private static final CdmVersion startSchemaVersion = CdmVersion.V_05_18_06;
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private static final CdmVersion endSchemaVersion = CdmVersion.V_05_22_00;
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// ********************** FACTORY METHOD *************************************
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public static SchemaUpdater_5186_5220 NewInstance() {
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return new SchemaUpdater_5186_5220();
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}
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protected SchemaUpdater_5186_5220() {
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super(startSchemaVersion.versionString(), endSchemaVersion.versionString());
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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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String newColumnName;
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String referencedTable;
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List<ISchemaUpdaterStep> stepList = new ArrayList<>();
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//#9315
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removeOldSingleSourceCitations(stepList);
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//9507
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stepName = "Add ratioToStructure column to DefinedTermBase (Character)";
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tableName = "DefinedTermBase";
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newColumnName = "ratioToStructure_id";
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referencedTable = "DefinedTermBase";
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ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
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//9331
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//set DTYPE for NamedSource-s
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stepName = "Set DTYPE for NamedSources";
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String query = " UPDATE @@OriginalSourceBase@@ "
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+ " SET DTYPE = 'NamedSource' "
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+ " WHERE id IN (SELECT source_id FROM @@HybridRelationship@@) "
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+ " OR id IN (SELECT source_id FROM @@NameRelationship@@) "
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+ " OR id IN (SELECT source_id FROM @@TaxonRelationship@@) "
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+ " OR id IN (SELECT source_id FROM @@TaxonNode@@) "
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+ " OR id IN (SELECT source_id FROM @@NomenclaturalStatus@@) "
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+ " OR id IN (SELECT source_id FROM @@TypeDesignationBase@@) ";
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String auditQuery = " UPDATE @@OriginalSourceBase_AUD@@ "
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+ " SET DTYPE = 'NamedSource' "
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+ " WHERE id IN (SELECT source_id FROM @@HybridRelationship_AUD@@) "
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+ " OR id IN (SELECT source_id FROM @@NameRelationship_AUD@@) "
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+ " OR id IN (SELECT source_id FROM @@TaxonRelationship_AUD@@) "
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+ " OR id IN (SELECT source_id FROM @@TaxonNode@@) "
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+ " OR id IN (SELECT source_id FROM @@NomenclaturalStatus_AUD@@) "
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+ " OR id IN (SELECT source_id FROM @@TypeDesignationBase_AUD@@) ";
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SimpleSchemaUpdaterStep.NewExplicitAuditedInstance(stepList, stepName, query, auditQuery, -99);
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//#9327
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//add sourcedElement column
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stepName = "Add sourcedElement_id column to DescriptionElementSource";
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tableName = "OriginalSourceBase";
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newColumnName = "sourcedElement_id";
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referencedTable = "DescriptionElementBase";
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ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
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//#9327
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//update sourcedElement column
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stepName = "UPdate sourcedElement column";
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String sql = " UPDATE @@OriginalSourceBase@@ "
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+ " SET sourcedElement_id = (SELECT MN.descriptionElementBase_id "
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+ " FROM @@DescriptionElementBase_OriginalSourceBase@@ MN "
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+ " WHERE MN.sources_id = @@OriginalSourceBase@@.id) "
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+ " WHERE EXISTS ( "
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+ " SELECT * "
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+ " FROM @@DescriptionElementBase_OriginalSourceBase@@ MN "
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+ " WHERE MN.sources_id = @@OriginalSourceBase@@.id)";
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String sql_aud = " UPDATE @@OriginalSourceBase_AUD@@ "
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+ " SET sourcedElement_id = (SELECT MN.id "
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+ " FROM @@DescriptionElementBase_OriginalSourceBase_AUD@@ tn "
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+ " WHERE MN.sources_id = @@OriginalSourceBase_AUD@@.id) "
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+ " WHERE EXISTS ( "
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+ " SELECT * "
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+ " FROM @@DescriptionElementBase_OriginalSourceBase_AUD@@ MN "
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+ " WHERE MN.sources_id = @@OriginalSourceBase_AUD@@.id)";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, sql, sql_aud, -99);
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//#9327
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//add sourcedTaxon column
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stepName = "Add sourcedTaxon column to SecundumSource";
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tableName = "OriginalSourceBase";
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newColumnName = "sourcedTaxon_id";
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referencedTable = "TaxonBase";
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ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
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//#9327
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//move secundum reference to nomenclatural source
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stepName = "move secundum reference to secundum source";
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tableName = "TaxonBase";
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String referenceColumnName = "sec_id";
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String microReferenceColumnName = "secMicroReference";
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String sourceColumnName = "sourcedTaxon_id";
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String sourceType = "PTS";
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String dtype = "SecundumSource";
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SecReference2SourceMover.NewInstance(stepList, stepName, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName, dtype, sourceType);
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//#9330
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//remove source type 'NOR'
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stepName = "Remove source type 'nomenclatural reference'";
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tableName = "OriginalSourceBase";
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String columnName = "sourceType";
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String newValue = "PTS";
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String where = columnName + "='NOR'";
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ColumnValueUpdater.NewStringInstance(stepList, stepName, tableName,
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columnName, newValue, where, INCLUDE_AUDIT);
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//#9332
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stepName = "Rename TypeDesignationBase.soure to designationSource";
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tableName = "TypeDesignationBase";
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String oldColumnName = "source_id";
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newColumnName = "designationSource_id";
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ColumnNameChanger.NewIntegerInstance(stepList, stepName, tableName, oldColumnName, newColumnName, INCLUDE_AUDIT);
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//#8761
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//add name column to nomenclatural status
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stepName = "add name_id column to nomenclatural status";
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tableName = "NomenclaturalStatus";
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newColumnName = "name_id";
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referencedTable = "TaxonName";
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ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, !NOT_NULL, referencedTable);
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//#8761
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//update nomenclatural status' name column
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stepName = "Update nomenclatural status' name column";
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sql = " UPDATE @@NomenclaturalStatus@@ "
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+ " SET name_id = (SELECT MN.TaxonName_id "
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+ " FROM @@TaxonName_NomenclaturalStatus@@ MN "
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+ " WHERE MN.status_id = @@NomenclaturalStatus@@.id) "
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+ " WHERE EXISTS ( "
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+ " SELECT * "
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+ " FROM @@TaxonName_NomenclaturalStatus@@ MN "
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+ " WHERE MN.status_id = @@NomenclaturalStatus@@.id)";
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sql_aud = " UPDATE @@NomenclaturalStatus_AUD@@ "
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+ " SET name_id = (SELECT MN.id "
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+ " FROM @@TaxonName_NomenclaturalStatuse_AUD@@ tn "
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+ " WHERE MN.status_id = @@NomenclaturalStatus_AUD@@.id) "
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+ " WHERE EXISTS ( "
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+ " SELECT * "
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+ " FROM @@TaxonName_NomenclaturalStatus_AUD@@ MN "
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+ " WHERE MN.status_id = @@NomenclaturalStatus_AUD@@.id)";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, sql, sql_aud, -99);
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//9211
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//move classification reference to classification source
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stepName = "move classification reference to classification source";
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tableName = "Classification";
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referenceColumnName = "reference_id";
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microReferenceColumnName = "microReference";
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sourceColumnName = "source_id";
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sourceType = "PTS";
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dtype = "NamedSource";
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Reference2SourceMover.NewInstance(stepList, stepName, tableName, referenceColumnName, microReferenceColumnName, sourceColumnName, dtype, sourceType);
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return stepList;
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}
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//#9315 remove
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private void removeOldSingleSourceCitations(List<ISchemaUpdaterStep> stepList) {
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//TaxonName.nomenclaturalSource_id
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String stepName = "Remove TaxonName.nomenclaturalSource_id";
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String tableName = "TaxonName";
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String oldColumnName = "nomenclaturalSource_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//TaxonName.nomenclaturalMicroReference
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stepName = "Remove TaxonName.nomenclaturalMicroReference";
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tableName = "TaxonName";
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oldColumnName = "nomenclaturalMicroReference";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//TaxonName.nomenclaturalReference_id
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stepName = "Remove TaxonName.nomenclaturalReference_id";
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tableName = "TaxonName";
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oldColumnName = "nomenclaturalReference_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//TaxonNode.microReferenceForParentChildRelation
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stepName = "Remove TaxonNode.microReferenceForParentChildRelation";
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tableName = "TaxonNode";
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oldColumnName = "microReferenceForParentChildRelation";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//TaxonNode.referenceForParentChildRelation_id
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stepName = "Remove TaxonNode.referenceForParentChildRelation_id";
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tableName = "TaxonNode";
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oldColumnName = "referenceForParentChildRelation_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//NomenclaturalStatus.citationMicroReference
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stepName = "Remove NomenclaturalStatus.citationMicroReference";
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tableName = "NomenclaturalStatus";
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oldColumnName = "citationMicroReference";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//NomenclaturalStatus.citation_id
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stepName = "Remove NomenclaturalStatus.citation_id";
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tableName = "NomenclaturalStatus";
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oldColumnName = "citation_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//TypeDesignationBase.citationMicroReference
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stepName = "Remove TypeDesignationBase.citationMicroReference";
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tableName = "TypeDesignationBase";
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oldColumnName = "citationMicroReference";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//TypeDesignationBase.citation_id
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stepName = "Remove TypeDesignationBase.citation_id";
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tableName = "TypeDesignationBase";
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oldColumnName = "citation_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//TaxonRelationship.citationMicroReference
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stepName = "Remove TaxonRelationship.citationMicroReference";
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tableName = "TaxonRelationship";
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oldColumnName = "citationMicroReference";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//TaxonRelationship.citation_id
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stepName = "Remove TaxonRelationship.citation_id";
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tableName = "TaxonRelationship";
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oldColumnName = "citation_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//NameRelationship.citationMicroReference
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stepName = "Remove NameRelationship.citationMicroReference";
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tableName = "NameRelationship";
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oldColumnName = "citationMicroReference";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//NameRelationship.citation_id
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stepName = "Remove NameRelationship.citation_id";
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tableName = "NameRelationship";
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oldColumnName = "citation_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//HybridRelationship.citationMicroReference
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stepName = "Remove HybridRelationship.citationMicroReference";
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tableName = "HybridRelationship";
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oldColumnName = "citationMicroReference";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//HybridRelationship.citation_id
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stepName = "Remove HybridRelationship.citation_id";
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tableName = "HybridRelationship";
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oldColumnName = "citation_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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}
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@Override
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public ISchemaUpdater getPreviousUpdater() {
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return SchemaUpdater_5185_5186.NewInstance();
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}
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}
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