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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.v30_40;
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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.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.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.TableDropper;
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/**
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* @author a.mueller
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* @since Jan 14, 2014
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*/
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public class SchemaUpdater_34_341 extends SchemaUpdaterBase {
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(SchemaUpdater_34_341.class);
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private static final String endSchemaVersion = "3.4.1.0.201411210000";
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private static final String startSchemaVersion = "3.4.0.0.201407010000";
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// ********************** FACTORY METHOD *************************************
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public static SchemaUpdater_34_341 NewInstance() {
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return new SchemaUpdater_34_341();
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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_34_341() {
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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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// String columnName;
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String newColumnName;
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String oldColumnName;
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String query;
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List<ISchemaUpdaterStep> stepList = new ArrayList<>();
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//DnaMarker in Primer
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//TODO H2 / PostGreSQL / SQL Server
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stepName = "Add foreign key for Primer.dnaMarker";
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tableName = "Primer";
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newColumnName = "dnaMarker_id";
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boolean notNull = false;
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String referencedTable = "DefinedTermBase";
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ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, notNull, referencedTable);
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//Institution for DerivationEvent
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stepName = "Add foreign key for DerivationEvent.institution";
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tableName = "DerivationEvent";
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newColumnName = "institution_id";
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referencedTable = "AgentBase";
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ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, notNull, referencedTable);
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//Institution for Amplication
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stepName = "Add foreign key for Amplification.institution";
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tableName = "Amplification";
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newColumnName = "institution_id";
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referencedTable = "AgentBase";
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ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, notNull, referencedTable);
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//TaxonName for DeterminationEvent
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stepName = "Add foreign key for DeterminationEvent.taxonName";
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tableName = "DeterminationEvent";
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newColumnName = "taxonname_id";
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referencedTable = "TaxonNameBase";
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ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, notNull, referencedTable);
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//TaxonName for DeterminationEvent #3448, #4203, #4518
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stepName = "Add foreign key for DeterminationEvent.taxonName";
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tableName = "DnaQuality";
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newColumnName = "typedPurificationMethod_id";
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referencedTable = "MaterialOrMethodEvent";
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ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, notNull, referencedTable);
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//update DerivationEvent.taxonname_id #3448, #4203, #4518
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stepName = "Update taxon name in derivation event";
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query = "UPDATE DeterminationEvent " +
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" SET taxonname_id = (SELECT name_id FROM TaxonBase tb WHERE tb.id = taxon_id) " +
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" WHERE taxon_id IS NOT NULL ";
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tableName = "DeterminationEvent";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, query, "", -99);
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mergePresenceAbsenceVocs(stepList);
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//SingleReadAlignment #4529
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stepName = "Remove Sequence_SingleRead"; //we assume that this field is not yet used
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tableName = "Sequence_SingleRead";
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TableDropper.NewInstance(stepList, stepName, tableName, INCLUDE_AUDIT, true);
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//Add SingleReadAlignment #4529
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stepName = "Add SingleReadAlignment";
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tableName = "SingleReadAlignment";
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String[] columnNames = new String[]{"shifts","editedsequence","reversecomplement",
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"consensusalignment_id","singleread_id"};
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String[] columnTypes = new String[]{"clob","clob","bit","int","int"};
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String[] referencedTables = new String[]{null, null,null,"Sequence","SingleRead"};
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TableCreator.NewInstance(stepList, stepName, tableName, columnNames, columnTypes,
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referencedTables, INCLUDE_AUDIT, true);
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//Add labelCache to amplification #4542
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stepName = "Add column 'labelCache'";
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tableName = "Amplification";
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newColumnName = "labelcache";
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ColumnAdder.NewStringInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT);
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//SPLIT Amplification and Amplification result
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// Amplification #4541
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stepName = "Create table 'AmplificationResult'";
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tableName = "AmplificationResult";
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TableCreator.NewAnnotatableInstance(stepList, stepName, tableName,
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new String[] { "successful", "successText", "dnaSample_id", "amplification_id",
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"cloning_id", "gelPhoto_id",
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}, // colNames
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new String[] {"bit", "string_255", "int", "int", "int", "int"}, // columnTypes
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new String[] { null, null, "SpecimenOrObservationBase", "Amplification", "MaterialOrMethodEvent",
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"DefinedTermBase", "Media" }, // referencedTables
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INCLUDE_AUDIT);
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// // amplification result - single reads #4541
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// stepName = "Add single reads to amplification result";
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// String firstTable = "AmplificationResult";
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// String secondTable = "SingleRead";
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// MnTableCreator
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// .NewMnInstance(stepList, stepName, firstTable, null, secondTable, null,
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// SchemaUpdaterBase.INCLUDE_AUDIT, false, true);
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//Institution for Amplication
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stepName = "Add foreign key for SingleRead.amplificationresult";
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tableName = "SingleRead";
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newColumnName = "amplificationresult_id";
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referencedTable = "AmplificationResult";
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ColumnAdder.NewIntegerInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, notNull, referencedTable);
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//drop Amplification_SingleRead #4541
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stepName = "Drop Amplification_SingleRead";
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tableName = "Amplification_SingleRead";
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TableDropper.NewInstance(stepList, stepName, tableName, INCLUDE_AUDIT, true);
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//remove successful, successText, ...
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stepName = "Remove successful ... from Amplification";
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tableName = "Amplification";
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oldColumnName = "successful";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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oldColumnName = "successText";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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oldColumnName = "dnaSample_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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oldColumnName = "cloning_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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oldColumnName = "gelPhoto_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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stepName = "Remove amplification_id from SingleRead";
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tableName = "SingleRead";
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oldColumnName = "amplification_id";
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ColumnRemover.NewInstance(stepList, stepName, tableName, oldColumnName, INCLUDE_AUDIT);
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//SpecimenOrObservationBase_Sequence (was incorrect mapping before)
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stepName = "Remove SpecimenOrObservationBase_Sequence";
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tableName = "SpecimenOrObservationBase_Sequence";
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TableDropper.NewInstance(stepList, stepName, tableName, true, true);
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return stepList;
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}
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private void mergePresenceAbsenceVocs(List<ISchemaUpdaterStep> stepList) {
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String stepName;
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String tableName;
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String newColumnName;
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String query;
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//PAT
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//ad absence term
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stepName = "Create absenceterm column";
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tableName = "DefinedTermBase";
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newColumnName = "absenceterm";
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ColumnAdder.NewBooleanInstance(stepList, stepName, tableName, newColumnName, INCLUDE_AUDIT, null);
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//set default value
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stepName ="Update AbsenceTerm vocabulary";
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tableName = "DefinedTermBase";
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query = " UPDATE @@DefinedTermBase@@ " +
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" SET absenceterm = @@FALSE@@ " +
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" WHERE termType = 'PAT' ";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, query, tableName, 99);
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//vocabulary for absence terms
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stepName ="Update AbsenceTerm vocabulary";
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tableName = "DefinedTermBase";
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query = " UPDATE @@DefinedTermBase@@ " +
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" SET absenceterm = @TRUE@, "
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+ " vocabulary_id = "
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+ "(SELECT id FROM @@TermVocabulary@@ "
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+ " WHERE uuid = 'adbbbe15-c4d3-47b7-80a8-c7d104e53a05'),"
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+ " orderindex = orderindex + "
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+ " (SELECT max(orderindex) FROM "
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+ " (SELECT * FROM DefinedTermBase dtb2 "
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+ " WHERE dtb2.termtype = 'PAT' AND dtb2.absenceterm = 0 "
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+ ") as tmp )" +
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" WHERE DTYPE = 'AbsenceTerm' ";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, query, tableName, 99);
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//PAT - DTYPE
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stepName ="Update PresenceAbsenceTerms DTYPE";
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tableName = "DefinedTermBase";
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query = " UPDATE @@DefinedTermBase@@ " +
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" SET DTYPE = 'PresenceAbsenceTerm' " +
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" WHERE termType = 'PAT' ";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, query, tableName, 99);
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//PAT - remove absence vocabulary
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stepName ="Remove Absence Vocabulary I";
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tableName = "TermVocabulary_Representation";
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query = " DELETE FROM TermVocabulary_Representation " +
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" WHERE TermVocabulary_id in (SELECT id FROM TermVocabulary WHERE uuid = '5cd438c8-a8a1-4958-842e-169e83e2ceee') ";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, query, tableName, 99);
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//PAT - remove absence vocabulary
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stepName ="Remove Absence Vocabulary II";
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tableName = "TermVocabulary_Representation";
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query = " DELETE FROM TermVocabulary"
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+ " WHERE uuid = '5cd438c8-a8a1-4958-842e-169e83e2ceee' ";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, query, tableName, 99);
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//PAT - remove absence vocabulary
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stepName ="Remove Absence Vocabulary III";
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tableName = "Representation";
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query = " DELETE FROM Representation "
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+ " WHERE text = 'AbsenceTerm' AND label = 'AbsenceTerm' ";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, query, tableName, 99);
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//PAT - update representation
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stepName ="Update Presence Absence vocabulary representation";
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tableName = "Representation";
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query = " UPDATE Representation "
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+ " SET text = 'Presence Absence Term', label = 'Presence Absence Term' "
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+ " WHERE text = 'Presence Term' AND label = 'Presence Term' ";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, query, tableName, 99);
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//PAT - update titlecache
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stepName ="Update Presence Absence vocabulary titlecache";
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tableName = "TermVocabulary";
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query = " UPDATE TermVocabulary "
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+ " SET titleCache = 'Presence Absence Term' "
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+ " WHERE uuid = 'adbbbe15-c4d3-47b7-80a8-c7d104e53a05' ";
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SimpleSchemaUpdaterStep.NewAuditedInstance(stepList, stepName, query, tableName, 99);
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}
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@Override
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public ISchemaUpdater getPreviousUpdater() {
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return SchemaUpdater_331_34.NewInstance();
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}
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}
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