VIVO-801 Added some flexibility to the RDB migration.

The tool now detects if you have additional RDB models, and offers the option of skipping them.
Also, the tool runs with 2G of memory.

utilities/rdbmigration/build.xml

@@ -125,6 +125,8 @@
 			<arg value="${VitroConnection.DataSource.url}" />
 			<arg value="${VitroConnection.DataSource.username}" />
 			<arg value="${VitroConnection.DataSource.password}" />
+			<jvmarg value="-Xms512m"/>
+			<jvmarg value="-Xmx2048m"/>
 			<classpath refid="migrate.run.classpath" />
 		</java>
 	</target>

utilities/rdbmigration/src/edu/cornell/mannlib/vivo/utilities/rdbmigration/RdbMigrator.java

@@ -14,23 +14,34 @@ import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.Statement;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
 import java.util.Properties;
 
+import org.apache.commons.lang.StringUtils;
+
 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
+ * A free-standing application that walks the user through the process of
+ * copying VIVO configuration data from RDB to TDB.
  */
 public class RdbMigrator {
 	private static final String TABLE_RDB = "jena_graph";
 	private static final String TABLE_MIGRATED = "vivo_rdb_migrated";
+	private static final List<String> EXPECTED_MODELS = Arrays
+			.asList(new String[] {
+					"http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadata",
+					"http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadata-displayModel",
+					"http://vitro.mannlib.cornell.edu/default/vitro-kb-displayMetadataTBOX",
+					"http://vitro.mannlib.cornell.edu/default/vitro-kb-userAccounts" });
+
 	private final String vivoHomeDir;
 	private final String jdbcUrl;
 	private final String username;
@@ -38,29 +49,67 @@ public class RdbMigrator {
 
 	private File targetDir;
 	private boolean alreadyMigrated;
+	private List<String> modelsToCopy;
 
+	/**
+	 * Confirm all of the parameters. Ask the user for approval. Do the
+	 * migration.
+	 * 
+	 * @throws UserDeclinedException
+	 *             If the user decides not to continue.
+	 */
 	public RdbMigrator(String vivoHomeDir, String jdbcUrl, String username,
-			String password) throws UserDeclinedException, IOException, SQLException {
+			String password) throws UserDeclinedException, IOException,
+			SQLException {
 		this.vivoHomeDir = vivoHomeDir;
 		this.jdbcUrl = jdbcUrl;
 		this.username = username;
 		this.password = password;
 
+		testDbConnection();
+
+		checkThatRdbExists();
+
 		confirmTargetDirectory();
 
 		if (doesTdbExist()) {
 			askContinueOverTdb();
 		}
 
-		testDbConnection();
-
-		checkThatRdbExists();
-
 		if (isAlreadyMigrated()) {
 			askMigrateAgain();
 		}
 
+		getListOfRdbModels();
+
+		if (isUnexpectedModels()) {
+			askMigrateAllModels();
+		}
+
 		askApprovalForMigrationPlan();
+
+		migrate();
+	}
+
+	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 void confirmTargetDirectory() {
@@ -100,27 +149,6 @@ public class RdbMigrator {
 				+ "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();
@@ -159,28 +187,46 @@ public class RdbMigrator {
 		ask("Migrate again? (y/n)");
 	}
 
+	private void getListOfRdbModels() throws SQLException {
+		try (Connection conn = getSqlConnection();
+				ClosingDBConnection rdb = new ClosingDBConnection(conn)) {
+			modelsToCopy = rdb.getAllModelNames().toList();
+		}
+	}
+
+	private boolean isUnexpectedModels() {
+		List<String> unexpectedModels = new ArrayList<>(modelsToCopy);
+		unexpectedModels.removeAll(EXPECTED_MODELS);
+		if (unexpectedModels.isEmpty()) {
+			return false;
+		}
+
+		System.out
+				.println("VIVO requires only these models from RDB:\n   "
+						+ StringUtils.join(EXPECTED_MODELS, "\n   ")
+						+ "\nYour RDB triple-store contains these additional models:\n   "
+						+ StringUtils.join(unexpectedModels, "\n   "));
+		return true;
+	}
+
+	private void askMigrateAllModels() throws IOException {
+		try {
+			ask("Migrate all models? (y/n)");
+		} catch (UserDeclinedException e) {
+			modelsToCopy = EXPECTED_MODELS;
+		}
+	}
+
 	private void askApprovalForMigrationPlan() throws SQLException,
 			UserDeclinedException, IOException {
 		int modelCount = 0;
 		int tripleCount = 0;
-		try (Connection conn = getSqlConnection()) {
+		try (Connection conn = getSqlConnection();
-			IDBConnection rdb = null;
+				ClosingDBConnection rdb = new ClosingDBConnection(conn)) {
-			try {
+			for (String modelName : modelsToCopy) {
-				rdb = getRdbConnection(conn);
+				modelCount++;
-				for (String modelName : rdb.getAllModelNames().toList()) {
+				try (ClosingGraphRDB graph = new ClosingGraphRDB(rdb, modelName)) {
-					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();
 				}
 			}
 		}
@@ -192,49 +238,56 @@ public class RdbMigrator {
 		ask(question);
 	}
 
+	private void quit(String message) {
+		throw new IllegalArgumentException(
+				"--------------------------------------------------------------\n"
+						+ message
+						+ "\n--------------------------------------------------------------");
+	}
+
+	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);
+		}
+	}
+
 	public void migrate() throws SQLException {
 		copyData();
-		writeMigratedRecord();
+		writeMigrationRecord();
 	}
 
 	private void copyData() throws SQLException {
-		try (Connection conn = getSqlConnection()) {
+		try (Connection conn = getSqlConnection();
-			IDBConnection rdbConnection = null;
+				ClosingDBConnection rdb = new ClosingDBConnection(conn)) {
-			try {
+			Dataset tdbDataset = TDBFactory.createDataset(targetDir
-				rdbConnection = getRdbConnection(conn);
+					.getAbsolutePath());
-				Dataset tdbDataset = TDBFactory.createDataset(targetDir
+			copyGraphs(rdb, tdbDataset);
-						.getAbsolutePath());
-				copyGraphs(rdbConnection, tdbDataset);
-			} finally {
-				if (rdbConnection != null) {
-					rdbConnection.close();
-				}
-			}
 		}
 	}
 
 	@SuppressWarnings("deprecation")
-	private void copyGraphs(IDBConnection rdbConnection, Dataset tdbDataset) {
+	private void copyGraphs(ClosingDBConnection rdb, Dataset tdbDataset) {
 		DatasetGraph tdbDsGraph = tdbDataset.asDatasetGraph();
-		for (String modelName : rdbConnection.getAllModelNames().toList()) {
+		for (String modelName : modelsToCopy) {
-			Graph graph = null;
+			try (ClosingGraphRDB graph = new ClosingGraphRDB(rdb, modelName)) {
-			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 {
+	private void writeMigrationRecord() throws SQLException {
 		String createTable = String.format("CREATE TABLE %s (date DATE)",
 				TABLE_MIGRATED);
 		String deleteOldDates = String.format("DELETE FROM %s", TABLE_MIGRATED);
@@ -253,25 +306,6 @@ public class RdbMigrator {
 		}
 	}
 
-	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();
@@ -280,19 +314,34 @@ public class RdbMigrator {
 		return DriverManager.getConnection(jdbcUrl, connectionProps);
 	}
 
-	private IDBConnection getRdbConnection(Connection sqlConnection) {
+	private static class ClosingDBConnection extends DBConnection implements
-		return new DBConnection(sqlConnection, "MySQL");
+			AutoCloseable {
+		ClosingDBConnection(Connection sqlConnection) {
+			super(sqlConnection, "MySQL");
+		}
+
 	}
 
-	public static void main(String[] args) throws SQLException {
+	private static class ClosingGraphRDB extends GraphRDB implements
+			AutoCloseable {
+		ClosingGraphRDB(DBConnection rdb, String modelName) {
+			super(rdb, modelName, null,
+					GraphRDB.OPTIMIZE_ALL_REIFICATIONS_AND_HIDE_NOTHING, false);
+		}
+	}
+
+	// ----------------------------------------------------------------------
+	// Main routine
+	// ----------------------------------------------------------------------
+
+	public static void main(String[] args) {
 		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]);
+			new RdbMigrator(args[0], args[1], args[2], args[3]);
-			rdbm.migrate();
 		} catch (IllegalArgumentException | UserDeclinedException e) {
 			System.out.println(e.getMessage());
 		} catch (Exception e) {