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/**
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* Copyright (C) 2009 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.v24_30;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.List;
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import java.util.UUID;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.database.update.CaseType;
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import eu.etaxonomy.cdm.database.update.ISchemaUpdaterStep;
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import eu.etaxonomy.cdm.database.update.SchemaUpdateResult;
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import eu.etaxonomy.cdm.database.update.SchemaUpdaterStepBase;
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/**
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* @author a.mueller
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* @since 16.09.2010
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*
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*/
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public class PolytomousKeyDataMover extends SchemaUpdaterStepBase implements ISchemaUpdaterStep {
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private static final Logger logger = LogManager.getLogger(PolytomousKeyDataMover.class);
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private String featureTreeTableName;
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private String featureNodeTableName;
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private String polytomousKeyTableName;
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private String polytomousKeyNodeTableName;
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private boolean includeAudTable;
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public static final PolytomousKeyDataMover NewInstance(List<ISchemaUpdaterStep> stepList, String stepName, boolean includeAudTable){
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return new PolytomousKeyDataMover(stepList, stepName, includeAudTable);
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}
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protected PolytomousKeyDataMover(List<ISchemaUpdaterStep> stepList, String stepName, boolean includeAudTable) {
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super(stepList, stepName);
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this.featureTreeTableName = "FeatureTree";
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this.featureNodeTableName = "FeatureNode";
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this.polytomousKeyTableName = "PolytomousKey";
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this.polytomousKeyNodeTableName = "PolytomousKeyNode";
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this.includeAudTable = includeAudTable;
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}
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@Override
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public void invoke(ICdmDataSource datasource, IProgressMonitor monitor,
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CaseType caseType, SchemaUpdateResult result) throws SQLException {
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try {
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movePolytomousKeys(caseType.transformTo(featureTreeTableName),
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caseType.transformTo(featureNodeTableName),
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caseType.transformTo(polytomousKeyTableName),
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caseType.transformTo(polytomousKeyNodeTableName),
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datasource, monitor, false, caseType, result);
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if (includeAudTable){
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String aud = "_AUD";
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movePolytomousKeys(caseType.transformTo(featureTreeTableName + aud),
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caseType.transformTo(featureNodeTableName + aud),
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caseType.transformTo(polytomousKeyTableName + aud),
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caseType.transformTo(polytomousKeyNodeTableName + aud),
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datasource, monitor, true, caseType, result);
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}
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return;
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} catch (Exception e) {
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monitor.warning(e.getMessage(), e);
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logger.error(e.getMessage());
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result.addException(e, e.getMessage(), "PolytomousKeyDataMover.invoke");
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}
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}
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private void movePolytomousKeys(String featureTreeTableName, String featureNodeTableName, String polytomousKeyTableName,
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String polytomousKeyNodeTableName, ICdmDataSource datasource, IProgressMonitor monitor,
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boolean isAudit, CaseType caseType, SchemaUpdateResult result) throws SQLException {
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movePolytomousKey(featureTreeTableName, polytomousKeyTableName, datasource, isAudit, result);
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movePolytomousKeyMns(featureTreeTableName, polytomousKeyTableName, datasource, isAudit, caseType, result);
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movePolytomousKeyNodes(featureTreeTableName, featureNodeTableName, polytomousKeyNodeTableName, datasource, isAudit, result);
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moveQuestions(featureNodeTableName, polytomousKeyNodeTableName, datasource, isAudit, caseType, result);
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deleteOldData(datasource, isAudit, caseType, result);
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return;
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}
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private void moveQuestions(String featureNodeTableName, String polytomousKeyNodeTableName, ICdmDataSource datasource, boolean isAudit,
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CaseType caseType, SchemaUpdateResult result) throws SQLException {
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String aud = "";
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String audValue = "";
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String audParam = "";
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if (isAudit){
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aud = "_AUD";
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audValue = ",@REV, @revtype";
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audParam = ", REV, revtype";
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}
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//For each Question
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String questionSql = " SELECT * " +
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" FROM @@FeatureNode_Representation@_aud@@ mn INNER JOIN Representation@_aud r ON mn.questions_id = r.id ";
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questionSql = questionSql.replace("@_aud", aud);
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ResultSet rs = datasource.executeQuery(caseType.replaceTableNames(questionSql));
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while (rs.next()){
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//Created KeyStatement
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String updateQuery = " INSERT INTO @@KeyStatement@_aud@@ (id, uuid, created, updated, createdby_id, updatedby_id @audParam)" +
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" VALUES (@id, @uuid, @createdWhen, @updatedWhen, @createdby_id, @updatedby_id @audValue)";
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updateQuery = updateQuery.replace("@audValue", audValue);
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updateQuery = updateQuery.replace("@id", rs.getObject("FeatureNode_id").toString()); //use feature node id for key statement id
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updateQuery = updateQuery.replace("@uuid", UUID.randomUUID().toString()); //use random uuid
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updateQuery = updateQuery.replace("@createdWhen", nullSafeString(rs.getString("created")));
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updateQuery = updateQuery.replace("@updatedWhen", nullSafeString((rs.getString("updated"))));
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updateQuery = updateQuery.replace("@createdby_id", nullSafe(rs.getObject("createdby_id")));
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updateQuery = updateQuery.replace("@updatedby_id", nullSafe(rs.getObject("updatedby_id")));
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if (isAudit){
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updateQuery = updateQuery.replace("@REV", nullSafe(rs.getObject("r.REV")));
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updateQuery = updateQuery.replace("@revtype", nullSafe(rs.getObject("r.revtype")));
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}
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updateQuery = updateQuery.replace("@_aud", aud);
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updateQuery = updateQuery.replace("@audParam", audParam);
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try {
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datasource.executeUpdate(caseType.replaceTableNames(updateQuery));
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} catch (SQLException e) {
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logger.error(e);
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result.addException(e);;
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}
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//create entry in Language String
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updateQuery = " INSERT INTO @@LanguageString@_aud@@ (id, created, uuid, updated, text, createdby_id, updatedby_id, language_id @audParam) " +
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" VALUES (@id, @createdWhen, @uuid, @updatedWhen, @text, @createdby_id, @updatedby_id, @language_id @audValue)";
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updateQuery = updateQuery.replace("@audValue", audValue);
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updateQuery = updateQuery.replace("@id", rs.getObject("id").toString());
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updateQuery = updateQuery.replace("@createdWhen", nullSafeString(rs.getString("created")));
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updateQuery = updateQuery.replace("@updatedWhen", nullSafeString(rs.getString("updated")));
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updateQuery = updateQuery.replace("@createdby_id", nullSafe(rs.getObject("createdby_id")));
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updateQuery = updateQuery.replace("@updatedby_id", nullSafe(rs.getObject("updatedby_id")));
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updateQuery = updateQuery.replace("@uuid", nullSafeString(rs.getString("uuid")));
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updateQuery = updateQuery.replace("@text", nullSafeString(rs.getString("text")));
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updateQuery = updateQuery.replace("@language_id", nullSafe(rs.getObject("language_id")));
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if (isAudit){
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updateQuery = updateQuery.replace("@REV", nullSafe(rs.getObject("r.REV")));
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updateQuery = updateQuery.replace("@revtype", nullSafe(rs.getObject("r.revtype")));
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}
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updateQuery = updateQuery.replace("@_aud", aud);
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updateQuery = updateQuery.replace("@audParam", audParam);
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try {
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datasource.executeUpdate(caseType.replaceTableNames(updateQuery));
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} catch (SQLException e) {
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logger.error(e);
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result.addException(e);;
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}
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//create entry in KeyStatement_LanguageString
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updateQuery = " INSERT INTO @@KeyStatement_LanguageString@_aud@@ (KeyStatement_id, label_id, label_mapkey_id @audParam) " +
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" VALUES (@keystatement_id, @languagestring_id, @language_id @audValue) ";
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updateQuery = updateQuery.replace("@audValue", audValue);
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updateQuery = updateQuery.replace("@keystatement_id", nullSafe(rs.getObject("FeatureNode_id")));
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updateQuery = updateQuery.replace("@languagestring_id", nullSafe(rs.getObject("id")));
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updateQuery = updateQuery.replace("@language_id", nullSafe(rs.getObject("language_id")));
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if (isAudit){
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updateQuery = updateQuery.replace("@REV", nullSafe(rs.getObject("r.REV")));
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updateQuery = updateQuery.replace("@revtype", nullSafe(rs.getObject("r.revtype")));
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}
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updateQuery = updateQuery.replace("@_aud", aud);
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updateQuery = updateQuery.replace("@audParam", audParam);
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try {
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datasource.executeUpdate(caseType.replaceTableNames(updateQuery));
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} catch (SQLException e) {
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logger.error(e);
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result.addException(e);
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}
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//link polytomouskeynode statement to KeyStatement
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updateQuery = " UPDATE @@PolytomousKeyNode@_aud@@ " +
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" SET statement_id = id " +
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" WHERE id = @id ";
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updateQuery = updateQuery.replace("@id", nullSafe(rs.getObject("FeatureNode_id")));
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updateQuery = updateQuery.replace("@_aud", aud);
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try {
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datasource.executeUpdate(caseType.replaceTableNames(updateQuery));
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} catch (SQLException e) {
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logger.error(e);
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result.addException(e);
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}
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}
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return;
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// // move representations
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// String languageStringTable = "LanguageString" + (isAudit ? "_AUD" : "");
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// String representationTable = "Representation" + (isAudit ? "_AUD" : "");
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// String oldMnTable = "featuretree_representation" + (isAudit ? "_AUD" : "");
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// String newMnTable = "KeyStatement_LanguageString" + (isAudit ? "_AUD" : "");
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// String keyStatementTable = "KeyStatement" + (isAudit ? "_AUD" : "");
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// String audit = "";
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// String rAudit = "";
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// if (isAudit){
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// audit = ", REV, revtype";
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// rAudit = ", r.REV, r.revtype";
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// }
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//
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//
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// String updateQuery = "INSERT INTO @languageStringTable (id, created, uuid, updated, text, createdby_id, updatedby_id, language_id @audit) " +
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// " SELECT id, created, uuid, updated, text, createdby_id, updatedby_id, language_id @rAudit " +
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// " FROM @representationTable r INNER JOIN @oldMnTable fr ON fr.representations_id = r.id " +
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// " WHERE (1=1) ";
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// updateQuery = updateQuery.replace("@languageStringTable", languageStringTable);
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// updateQuery = updateQuery.replace("@representationTable", representationTable);
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// updateQuery = updateQuery.replace("@oldMnTable", oldMnTable);
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// updateQuery = updateQuery.replace("@audit", audit);
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// updateQuery = updateQuery.replace("@nAudit", rAudit);
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// System.out.println(updateQuery);
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// datasource.executeUpdate(updateQuery);
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//
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// //key statement
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// audit = "";
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// rAudit = "";
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// updateQuery = "INSERT INTO @keyStatementTable (id, created, uuid, updated, createdby_id, updatedby_id @audit) " +
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// " SELECT r.id, r.created, r.uuid, r.updated, r.createdby_id, r.updatedby_id @rAudit " +
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// " FROM @oldMnTable mn INNER JOIN representationTable r ";
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// updateQuery = updateQuery.replace("@keyStatementTable", keyStatementTable);
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// updateQuery = updateQuery.replace("@oldMnTable", oldMnTable);
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// updateQuery = updateQuery.replace("@audit", audit);
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// updateQuery = updateQuery.replace("@rAudit", rAudit);
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//
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// System.out.println(updateQuery);
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// datasource.executeUpdate(updateQuery);
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//
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//
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// //move relation
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// audit = "";
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// updateQuery = "INSERT INTO @newMnTable (KeyStatement_id, label_id, label_mapkey_id @audit) " +
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// " SELECT FeatureNode_id, questions_id @audit, language_id " +
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// " FROM @oldMnTable fr INNER JOIN @representationTable r " +
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// " WHERE (1=1) ";
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// updateQuery = updateQuery.replace("@audit", audit);
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// updateQuery = updateQuery.replace("@representationTable", representationTable);
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// updateQuery = updateQuery.replace("@oldMnTable", oldMnTable);
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// updateQuery = updateQuery.replace("@newMnTable", newMnTable);
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// System.out.println(updateQuery);
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// datasource.executeUpdate(updateQuery);
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//
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// //link polytoumous key node statement to keyStatement
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// updateQuery = "UPDATE @polytomousKeyNodeTable pkn" +
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// " SET statement_id = (SELECT r.id FROM @representationTable r WHERE r.id = pkn.statement_id) " +
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// " WHERE pkn.id ";
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}
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private String nullSafeString(Object object){
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if (object == null){
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return "NULL";
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}else{
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String result = object.toString().replace("'", "''");
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return "'" + result + "'";
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}
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}
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private String nullSafe(Object object) {
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if (object == null){
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return "NULL";
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}else{
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return object.toString();
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}
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}
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270
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private void deleteOldData(ICdmDataSource datasource, boolean isAudit,
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CaseType caseType, SchemaUpdateResult result) {
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String updateQuery;
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String featureNodeTable = caseType.transformTo("FeatureNode" + (isAudit ? "_AUD" : ""));
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String featureTreeTable = caseType.transformTo("FeatureTree" + (isAudit ? "_AUD" : ""));
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String representationTable = caseType.transformTo("Representation" + (isAudit ? "_AUD" : ""));
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String oldMnTable = caseType.transformTo("FeatureNode_Representation" + (isAudit ? "_AUD" : ""));
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// statements
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updateQuery = " DELETE FROM @representationTable WHERE id IN (SELECT questions_id FROM @oldMnTable)";
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updateQuery = updateQuery.replace("@representationTable", representationTable);
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updateQuery = updateQuery.replace("@oldMnTable", oldMnTable);
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logger.debug(updateQuery);
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try {
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datasource.executeUpdate(updateQuery);
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} catch (SQLException e) {
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logger.error(e);
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result.addException(e);
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}
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// feature nodes
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updateQuery = " DELETE FROM @featureNodeTable WHERE featuretree_id IN (SELECT t.id FROM @featureTreeTable t WHERE t.DTYPE = 'PolytomousKey' )";
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updateQuery = updateQuery.replace("@featureNodeTable", featureNodeTable);
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updateQuery = updateQuery.replace("@featureTreeTable", featureTreeTable);
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logger.debug(updateQuery);
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try {
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datasource.executeUpdate(updateQuery);
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} catch (SQLException e) {
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logger.error(e);
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result.addException(e);
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}
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//trees
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updateQuery = " DELETE FROM @featureTreeTable WHERE DTYPE = 'PolytomousKey' " ;
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updateQuery = updateQuery.replace("@featureTreeTable", featureTreeTable);
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logger.debug(updateQuery);
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try {
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datasource.executeUpdate(updateQuery);
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309
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} catch (SQLException e) {
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310
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logger.error(e);
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result.addException(e);
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312
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}
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return;
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314
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315
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316
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}
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317
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318
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private void movePolytomousKeyNodes(String featureTreeTableName, String featureNodeTableName,
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319
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String polytomousKeyNodeTableName, ICdmDataSource datasource, boolean isAudit,
|
|
320
|
SchemaUpdateResult result) {
|
|
321
|
String updateQuery;
|
|
322
|
|
|
323
|
//PolytomousKey node
|
|
324
|
updateQuery = " INSERT INTO @polytomousKeyNodeTableName(id, created, uuid, updated, sortindex, createdby_id, updatedby_id, feature_id, parent_id, taxon_id, key_id @audit) " +
|
|
325
|
" SELECT n.id, n.created, n.uuid, n.updated, n.sortindex, n.createdby_id, n.updatedby_id, n.feature_id, n.parent_fk, n.taxon_id, n.featuretree_id @nAudit" +
|
|
326
|
" FROM @featureNodeTableName n INNER JOIN @featureTreeTableName t ON n.featuretree_id = t.id" +
|
|
327
|
" WHERE t.DTYPE = 'PolytomousKey'";
|
|
328
|
updateQuery = updateQuery.replace("@polytomousKeyNodeTableName", polytomousKeyNodeTableName);
|
|
329
|
updateQuery = updateQuery.replace("@featureNodeTableName", featureNodeTableName);
|
|
330
|
updateQuery = updateQuery.replace("@featureTreeTableName", featureTreeTableName);
|
|
331
|
|
|
332
|
String audit = "";
|
|
333
|
String nAudit = "";
|
|
334
|
if (isAudit){
|
|
335
|
audit = ", REV, revtype";
|
|
336
|
nAudit = ", n.REV, n.revtype";
|
|
337
|
}
|
|
338
|
updateQuery = updateQuery.replace("@audit", audit);
|
|
339
|
updateQuery = updateQuery.replace("@nAudit", nAudit);
|
|
340
|
logger.debug(updateQuery);
|
|
341
|
try {
|
|
342
|
datasource.executeUpdate(updateQuery);
|
|
343
|
} catch (SQLException e) {
|
|
344
|
logger.error(e);
|
|
345
|
result.addException(e);
|
|
346
|
}
|
|
347
|
return;
|
|
348
|
}
|
|
349
|
|
|
350
|
private void movePolytomousKeyMns(String featureTreeTableName, String polytomousKeyTableName,
|
|
351
|
ICdmDataSource datasource, boolean isAudit, CaseType caseType, SchemaUpdateResult result) {
|
|
352
|
//PolytomousKey MN update
|
|
353
|
updateMnTables(featureTreeTableName, polytomousKeyTableName, "Annotation", null, datasource, isAudit, false, caseType, result);
|
|
354
|
updateMnTables(featureTreeTableName, polytomousKeyTableName, "Credit", null, datasource, isAudit, true, caseType, result);
|
|
355
|
updateMnTables(featureTreeTableName, polytomousKeyTableName, "Extension", null, datasource, isAudit, false, caseType, result);
|
|
356
|
updateMnTables(featureTreeTableName, polytomousKeyTableName, "Marker", null, datasource, isAudit, false, caseType, result);
|
|
357
|
updateMnTables(featureTreeTableName, polytomousKeyTableName, "OriginalSourceBase", "Sources", datasource, isAudit, false, caseType, result);
|
|
358
|
updateMnTables(featureTreeTableName, polytomousKeyTableName, "Rights", "Rights", datasource, isAudit, false, caseType, result);
|
|
359
|
return;
|
|
360
|
}
|
|
361
|
|
|
362
|
private void movePolytomousKey(String featureTreeTableName, String polytomousKeyTableName,
|
|
363
|
ICdmDataSource datasource, boolean isAudit, SchemaUpdateResult result) {
|
|
364
|
//PolytomousKey
|
|
365
|
//TODO monitor polytomous keys with uri for data loss
|
|
366
|
|
|
367
|
String updateQuery = " INSERT INTO @polytomousKeyTableName(id, created, uuid, updated, lsid_authority, lsid_lsid, lsid_namespace, lsid_object, lsid_revision, protectedtitlecache, titleCache, createdby_id, updatedby_id, root_id @audit) " +
|
|
368
|
" SELECT id, created, uuid, updated, lsid_authority, lsid_lsid, lsid_namespace, lsid_object, lsid_revision, protectedtitlecache, titleCache, createdby_id, updatedby_id, root_id @audit" +
|
|
369
|
" FROM @featureTreeTableName WHERE DTYPE = 'PolytomousKey'";
|
|
370
|
updateQuery = updateQuery.replace("@polytomousKeyTableName", polytomousKeyTableName);
|
|
371
|
updateQuery = updateQuery.replace("@featureTreeTableName", featureTreeTableName);
|
|
372
|
String audit = "";
|
|
373
|
if (isAudit){
|
|
374
|
audit = ", REV, revtype";
|
|
375
|
}
|
|
376
|
updateQuery = updateQuery.replace("@audit", audit);
|
|
377
|
try {
|
|
378
|
datasource.executeUpdate(updateQuery);
|
|
379
|
} catch (SQLException e) {
|
|
380
|
logger.error(e);
|
|
381
|
result.addException(e, e.getMessage(), "PolytomousKeyDataMover.movePolytomousKey");
|
|
382
|
|
|
383
|
}
|
|
384
|
return;
|
|
385
|
}
|
|
386
|
|
|
387
|
private void updateMnTables(String featureTreeTableName, String polytomousKeyTableName,
|
|
388
|
String attributeName, String attributePluralString, ICdmDataSource datasource,
|
|
389
|
boolean isAudit, boolean hasSortIndex, CaseType caseType, SchemaUpdateResult result) {
|
|
390
|
|
|
391
|
String updateQuery;
|
|
392
|
String audit;
|
|
393
|
if (isAudit){
|
|
394
|
featureTreeTableName = featureTreeTableName.replace(caseType.transformTo("_AUD"), "");
|
|
395
|
polytomousKeyTableName = polytomousKeyTableName.replace(caseType.transformTo("_AUD"), "");
|
|
396
|
}
|
|
397
|
String newMnTable = caseType.transformTo(polytomousKeyTableName + "_" + attributeName + (isAudit? "_AUD" : ""));
|
|
398
|
String oldMnTable = caseType.transformTo(featureTreeTableName + "_" + attributeName + (isAudit? "_AUD" : ""));
|
|
399
|
String pluralIdAttribute = ((attributePluralString == null) ? attributeName + "s" : attributePluralString) + "_id";
|
|
400
|
String sortIndex = (hasSortIndex ? ", sortIndex" : "");
|
|
401
|
updateQuery = " INSERT INTO @newMnTable(PolytomousKey_id, @pluralIdAttribute @sortIndex @audit) " +
|
|
402
|
" SELECT FeatureTree_id, @pluralIdAttribute @sortIndex @audit" +
|
|
403
|
" FROM @oldMnTable mn INNER JOIN @featureTreeTableName pk ON mn.FeatureTree_id = pk.id " +
|
|
404
|
" WHERE pk.DTYPE = 'PolytomousKey'";
|
|
405
|
updateQuery = updateQuery.replace("@polytomousKeyTableName", polytomousKeyTableName);
|
|
406
|
updateQuery = updateQuery.replace("@featureTreeTableName", featureTreeTableName);
|
|
407
|
updateQuery = updateQuery.replace("@newMnTable", newMnTable);
|
|
408
|
updateQuery = updateQuery.replace("@oldMnTable", oldMnTable);
|
|
409
|
updateQuery = updateQuery.replace("@pluralIdAttribute", pluralIdAttribute);
|
|
410
|
updateQuery = updateQuery.replace("@sortIndex", sortIndex);
|
|
411
|
audit = "";
|
|
412
|
if (isAudit){
|
|
413
|
audit = ", REV, revtype";
|
|
414
|
}
|
|
415
|
updateQuery = updateQuery.replace("@audit", audit);
|
|
416
|
logger.debug(updateQuery);
|
|
417
|
try {
|
|
418
|
datasource.executeUpdate(updateQuery);
|
|
419
|
} catch (SQLException e) {
|
|
420
|
logger.error(e);
|
|
421
|
result.addException(e);
|
|
422
|
}
|
|
423
|
return;
|
|
424
|
}
|
|
425
|
}
|