diff --git a/.gitignore b/.gitignore
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/ontology/public/catalog-v0001.xml
rdf/auth/firsttime/test-user-model.owl
+utilities/rdbmigration/.work
diff --git a/build.xml b/build.xml
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diff --git a/utilities/rdbmigration/build.xml b/utilities/rdbmigration/build.xml
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+ all - Compiles and runs the RDB migration tool.
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diff --git a/utilities/rdbmigration/lib/arq-2.8.5.jar b/utilities/rdbmigration/lib/arq-2.8.5.jar
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diff --git a/utilities/rdbmigration/lib/icu4j-3.4.4.jar b/utilities/rdbmigration/lib/icu4j-3.4.4.jar
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diff --git a/utilities/rdbmigration/lib/iri-0.8.jar b/utilities/rdbmigration/lib/iri-0.8.jar
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diff --git a/utilities/rdbmigration/lib/jena-2.6.4.jar b/utilities/rdbmigration/lib/jena-2.6.4.jar
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diff --git a/utilities/rdbmigration/lib/log4j-1.2.14.jar b/utilities/rdbmigration/lib/log4j-1.2.14.jar
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diff --git a/utilities/rdbmigration/lib/mysql-connector-java-5.1.16-bin.jar b/utilities/rdbmigration/lib/mysql-connector-java-5.1.16-bin.jar
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diff --git a/utilities/rdbmigration/lib/slf4j-api-1.5.6.jar b/utilities/rdbmigration/lib/slf4j-api-1.5.6.jar
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diff --git a/utilities/rdbmigration/lib/slf4j-log4j12-1.5.6.jar b/utilities/rdbmigration/lib/slf4j-log4j12-1.5.6.jar
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diff --git a/utilities/rdbmigration/lib/tdb-0.8.7.jar b/utilities/rdbmigration/lib/tdb-0.8.7.jar
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index 00000000..5b7965d6
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diff --git a/utilities/rdbmigration/lib/xercesImpl.jar b/utilities/rdbmigration/lib/xercesImpl.jar
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diff --git a/utilities/rdbmigration/src/edu/cornell/mannlib/vivo/utilities/rdbmigration/RdbMigrator.java b/utilities/rdbmigration/src/edu/cornell/mannlib/vivo/utilities/rdbmigration/RdbMigrator.java
new file mode 100644
index 00000000..f40ccc02
--- /dev/null
+++ b/utilities/rdbmigration/src/edu/cornell/mannlib/vivo/utilities/rdbmigration/RdbMigrator.java
@@ -0,0 +1,303 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vivo.utilities.rdbmigration;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.sql.Connection;
+import java.sql.DatabaseMetaData;
+import java.sql.Date;
+import java.sql.DriverManager;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Statement;
+import java.util.Properties;
+
+import com.hp.hpl.jena.db.DBConnection;
+import com.hp.hpl.jena.db.GraphRDB;
+import com.hp.hpl.jena.db.IDBConnection;
+import com.hp.hpl.jena.graph.Graph;
+import com.hp.hpl.jena.graph.Node;
+import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.sparql.core.DatasetGraph;
+import com.hp.hpl.jena.tdb.TDBFactory;
+
+/**
+ * TODO
+ */
+public class RdbMigrator {
+ private static final String TABLE_RDB = "jena_graph";
+ private static final String TABLE_MIGRATED = "vivo_rdb_migrated";
+ private final String vivoHomeDir;
+ private final String jdbcUrl;
+ private final String username;
+ private final String password;
+
+ private File targetDir;
+ private boolean alreadyMigrated;
+
+ public RdbMigrator(String vivoHomeDir, String jdbcUrl, String username,
+ String password) throws UserDeclinedException, IOException, SQLException {
+ this.vivoHomeDir = vivoHomeDir;
+ this.jdbcUrl = jdbcUrl;
+ this.username = username;
+ this.password = password;
+
+ confirmTargetDirectory();
+
+ if (doesTdbExist()) {
+ askContinueOverTdb();
+ }
+
+ testDbConnection();
+
+ checkThatRdbExists();
+
+ if (isAlreadyMigrated()) {
+ askMigrateAgain();
+ }
+
+ askApprovalForMigrationPlan();
+ }
+
+ private void confirmTargetDirectory() {
+ File vivoHome = new File(vivoHomeDir);
+ if (!vivoHome.isDirectory()) {
+ quit("'" + vivoHome + "' is not a directory.");
+ }
+ if (!vivoHome.canWrite()) {
+ quit("Can't write to '" + vivoHome + "'.");
+ }
+ targetDir = new File(vivoHome, "tdbmodels");
+ }
+
+ private boolean doesTdbExist() {
+ if (!targetDir.exists()) {
+ return false;
+ }
+
+ if (!targetDir.isDirectory()) {
+ quit("'" + targetDir + "' is not a directory.");
+ }
+ if (!targetDir.canWrite()) {
+ quit("Can't write to '" + targetDir + "'.");
+ }
+
+ String[] filenames = targetDir.list();
+ if (filenames == null || filenames.length == 0) {
+ return false;
+ }
+
+ return true;
+ }
+
+ private void askContinueOverTdb() throws UserDeclinedException, IOException {
+ ask("A directory of TDB files exists at '" + targetDir + "'.\n"
+ + " Migration will replace the existing triples.\n"
+ + "Continue? (y/n)");
+ }
+
+ private void testDbConnection() {
+ try (Connection conn = getSqlConnection()) {
+ // Just open and close it.
+ } catch (SQLException e) {
+ quit("Can't log in to database: '" + jdbcUrl + "', '" + username
+ + "', '" + password + "'\n" + e.getMessage());
+ }
+ }
+
+ private void checkThatRdbExists() throws SQLException {
+ try (Connection conn = getSqlConnection()) {
+ DatabaseMetaData md = conn.getMetaData();
+ try (ResultSet rs = md.getTables(null, null, TABLE_RDB, null);) {
+ if (!rs.next()) {
+ quit("The database at '" + jdbcUrl
+ + "' contains no RDB tables.");
+ }
+ }
+ }
+ }
+
+ private boolean isAlreadyMigrated() throws SQLException {
+ try (Connection conn = getSqlConnection()) {
+ DatabaseMetaData md = conn.getMetaData();
+ try (ResultSet rs = md.getTables(null, null, TABLE_MIGRATED, null);) {
+ if (rs.next()) {
+ alreadyMigrated = true;
+ announceMigrationDate(conn);
+ return true;
+ } else {
+ return false;
+ }
+ }
+ }
+ }
+
+ private void announceMigrationDate(Connection conn) {
+ String migrationDate = "UNKNOWN DATE";
+ String query = String.format("SELECT date FROM %s LIMIT 1",
+ TABLE_MIGRATED);
+
+ try (Statement stmt = conn.createStatement();
+ java.sql.ResultSet rs = stmt.executeQuery(query)) {
+ if (rs.next()) {
+ migrationDate = rs.getString("DATE");
+ }
+ } catch (SQLException e) {
+ // go with default answer.
+ }
+
+ System.out.println("It looks like this RDB data has already been "
+ + "migrated to TDB, on " + migrationDate
+ + "\n (found a table named '" + TABLE_MIGRATED + "')");
+ }
+
+ private void askMigrateAgain() throws UserDeclinedException, IOException {
+ ask("Migrate again? (y/n)");
+ }
+
+ private void askApprovalForMigrationPlan() throws SQLException,
+ UserDeclinedException, IOException {
+ int modelCount = 0;
+ int tripleCount = 0;
+ try (Connection conn = getSqlConnection()) {
+ IDBConnection rdb = null;
+ try {
+ rdb = getRdbConnection(conn);
+ for (String modelName : rdb.getAllModelNames().toList()) {
+ modelCount++;
+ Graph graph = new GraphRDB(
+ rdb,
+ modelName,
+ null,
+ GraphRDB.OPTIMIZE_ALL_REIFICATIONS_AND_HIDE_NOTHING,
+ false);
+ tripleCount += graph.size();
+ graph.close();
+ }
+ } finally {
+ if (rdb != null) {
+ rdb.close();
+ }
+ }
+ }
+ String warning = alreadyMigrated ? " Existing triples will be over-written.\n"
+ : "";
+ String question = String.format("Migrating %d triples in %d models "
+ + "to TDB files in '%s'\n%sContinue? (y/n)", tripleCount,
+ modelCount, targetDir, warning);
+ ask(question);
+ }
+
+ public void migrate() throws SQLException {
+ copyData();
+ writeMigratedRecord();
+ }
+
+ private void copyData() throws SQLException {
+ try (Connection conn = getSqlConnection()) {
+ IDBConnection rdbConnection = null;
+ try {
+ rdbConnection = getRdbConnection(conn);
+ Dataset tdbDataset = TDBFactory.createDataset(targetDir
+ .getAbsolutePath());
+ copyGraphs(rdbConnection, tdbDataset);
+ } finally {
+ if (rdbConnection != null) {
+ rdbConnection.close();
+ }
+ }
+ }
+ }
+
+ @SuppressWarnings("deprecation")
+ private void copyGraphs(IDBConnection rdbConnection, Dataset tdbDataset) {
+ DatasetGraph tdbDsGraph = tdbDataset.asDatasetGraph();
+ for (String modelName : rdbConnection.getAllModelNames().toList()) {
+ Graph graph = null;
+ try {
+ graph = new GraphRDB(rdbConnection, modelName, null,
+ GraphRDB.OPTIMIZE_ALL_REIFICATIONS_AND_HIDE_NOTHING,
+ false);
+ tdbDsGraph.addGraph(Node.createURI(modelName), graph);
+ System.out
+ .println(String.format(" copied %4d triples from %s",
+ graph.size(), modelName));
+ } finally {
+ if (graph != null) {
+ graph.close();
+ }
+ }
+ }
+ }
+
+ private void writeMigratedRecord() throws SQLException {
+ String createTable = String.format("CREATE TABLE %s (date DATE)",
+ TABLE_MIGRATED);
+ String deleteOldDates = String.format("DELETE FROM %s", TABLE_MIGRATED);
+ String insertDate = String.format("INSERT INTO %s (date) VALUES (?)",
+ TABLE_MIGRATED);
+ try (Connection conn = getSqlConnection();
+ Statement stmt = conn.createStatement();
+ PreparedStatement pstmt = conn.prepareStatement(insertDate)) {
+ if (alreadyMigrated) {
+ stmt.executeUpdate(deleteOldDates);
+ } else {
+ stmt.executeUpdate(createTable);
+ }
+ pstmt.setDate(1, new Date(System.currentTimeMillis()));
+ pstmt.executeUpdate();
+ }
+ }
+
+ private void quit(String message) {
+ throw new IllegalArgumentException(message);
+ }
+
+ private void ask(String string) throws UserDeclinedException, IOException {
+ System.out.println(string);
+ BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
+ String s = br.readLine();
+ if ((s == null) || (!s.trim().toLowerCase().equals("y"))) {
+ throw new UserDeclinedException("OK.");
+ }
+ }
+
+ private static class UserDeclinedException extends Exception {
+ public UserDeclinedException(String message) {
+ super(message);
+ }
+ }
+
+ private Connection getSqlConnection() throws SQLException {
+ Properties connectionProps;
+ connectionProps = new Properties();
+ connectionProps.put("user", username);
+ connectionProps.put("password", password);
+ return DriverManager.getConnection(jdbcUrl, connectionProps);
+ }
+
+ private IDBConnection getRdbConnection(Connection sqlConnection) {
+ return new DBConnection(sqlConnection, "MySQL");
+ }
+
+ public static void main(String[] args) throws SQLException {
+ if (args.length != 4) {
+ System.out.println("Usage: RdbMigrator vivoHomeDir, jdbcUrl, "
+ + "username, password");
+ }
+
+ try {
+ RdbMigrator rdbm = new RdbMigrator(args[0], args[1], args[2], args[3]);
+ rdbm.migrate();
+ } catch (IllegalArgumentException | UserDeclinedException e) {
+ System.out.println(e.getMessage());
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+}