r/org.eclipse.statet.r.core/src/org/eclipse/statet/internal/r/core/pkgmanager/DB.java - statet/org.eclipse.statet-r - Git at Google

 /*=============================================================================#
  # Copyright (c) 2012, 2019 Stephan Wahlbrink and others.
  #
  # This program and the accompanying materials are made available under the
  # terms of the Eclipse Public License 2.0 which is available at
  # https://www.eclipse.org/legal/epl-2.0, or the Apache License, Version 2.0
  # which is available at https://www.apache.org/licenses/LICENSE-2.0.
  #
  # SPDX-License-Identifier: EPL-2.0 OR Apache-2.0
  #
  # Contributors:
  #     Stephan Wahlbrink <sw@wahlbrink.eu> - initial API and implementation
  #=============================================================================*/

 package org.eclipse.statet.internal.r.core.pkgmanager;

 import java.io.File;
 import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.Statement;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;

 import org.eclipse.core.filesystem.EFS;
 import org.eclipse.core.filesystem.IFileStore;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IStatus;
 import org.eclipse.core.runtime.Status;
 import org.eclipse.osgi.util.NLS;

 import org.apache.commons.dbcp2.ConnectionFactory;

 import org.eclipse.statet.ecommons.edb.core.EmbeddedDB;

 import org.eclipse.statet.internal.r.core.RCorePlugin;
 import org.eclipse.statet.r.core.RCore;
 import org.eclipse.statet.r.core.pkgmanager.IRPkgInfo;
 import org.eclipse.statet.r.core.pkgmanager.RPkgInfo;
 import org.eclipse.statet.rj.renv.core.BasicRPkgCompilation;
 import org.eclipse.statet.rj.renv.core.REnv;
 import org.eclipse.statet.rj.renv.core.RLibGroup;
 import org.eclipse.statet.rj.renv.core.RLibLocation;
 import org.eclipse.statet.rj.renv.core.RNumVersion;


 final class DB {

 	/** DB definitions */
 	@SuppressWarnings({ "hiding", "nls" })
 	private static final class REnvDB { // SCHMEMA

 		static final String NAME= "RENV";

 		static final class LibPaths {

 			static final String NAME= "LIBPATHS";
 			static final String QNAME= REnvDB.NAME + '.' + NAME;

 			static final String COL_ID= "LIB_ID";
 			static final String COL_LIB_PATH= "LIB_PATH";
 			static final String COL_STAMP= "STAMP";

 			static final String DEFINE_1= "create table " + QNAME + " ("
 						+ COL_ID        + " int not null "
 								+ "primary key "
 								+ "generated always as identity, "
 						+ COL_LIB_PATH      + " varchar(4096) not null unique, "
 						+ COL_STAMP         + " bigint"
 					+ ")";

 			static final String OP_insert= "insert into " + QNAME + " ("
 						+ COL_LIB_PATH + ") "
 					+ "values (?)";

 			static final String OP_delete_byPath= "delete from " + QNAME + " "
 					+ "where (" + COL_LIB_PATH + "= ?)";

 			static final String OP_getAll= "select "
 						+ COL_ID + ", "
 						+ COL_LIB_PATH + " "
 					+ "from " + QNAME;

 		}

 		static final class Pkgs {

 			static final String NAME= "PKGS";
 			static final String QNAME= REnvDB.NAME + '.' + NAME;

 			static final String COL_LIB_ID= "LIB_ID";
 			static final String COL_NAME= "NAME";
 			static final String COL_VERSION= "VERSION";
 			static final String COL_BUILT= "BUILT";
 			static final String COL_TITLE= "TITLE";
 			static final String COL_FLAGS= "FLAGS";
 			static final String COL_INST_STAMP= "INST_STAMP";
 			static final String COL_REPO_ID= "REPO_ID";

 			static final String DEFINE_1= "create table " + QNAME + " ("
 						+ COL_LIB_ID        + " int not null "
 								+ "references " + LibPaths.QNAME + " on delete cascade, "
 						+ COL_NAME          + " varchar(64) not null, "
 						+ COL_VERSION       + " varchar(64) not null, "
 						+ COL_BUILT         + " varchar(256) not null, "
 						+ COL_TITLE         + " varchar(256) not null, "
 						+ COL_FLAGS         + " int, "
 						+ COL_INST_STAMP    + " bigint, "
 						+ COL_REPO_ID       + " varchar(256), "
 						+ "primary key ("
 							+ COL_LIB_ID + ", "
 							+ COL_NAME + ")"
 					+ ")";

 			static final String OP_insert= "insert into " + QNAME + " ("
 						+ COL_LIB_ID + ", "
 						+ COL_NAME + ", "
 						+ COL_VERSION + ", "
 						+ COL_BUILT + ", "
 						+ COL_TITLE + ", "
 						+ COL_FLAGS + ", "
 						+ COL_INST_STAMP + ", "
 						+ COL_REPO_ID + ") "
 					+ "values (? , ?, ?, ?, ?, ?, ?, ?)";

 			static final String OP_update= "update " + QNAME + " set "
 						+ COL_VERSION + "= ?, "
 						+ COL_BUILT + "= ?, "
 						+ COL_TITLE + "= ?, "
 						+ COL_FLAGS + "= ?, "
 						+ COL_INST_STAMP + "= ?, "
 						+ COL_REPO_ID +"= ? "
 					+ "where (" + COL_LIB_ID + "= ? and " + COL_NAME + "= ?)";

 			static final String OP_delete= "delete from " + QNAME + " "
 					+ "where (" + COL_LIB_ID + "= ? and " + COL_NAME + "= ?)";

 			static final String OP_get_ofLib= "select "
 						+ COL_NAME + ", "
 						+ COL_VERSION + ", "
 						+ COL_BUILT + ", "
 						+ COL_TITLE + ", "
 						+ COL_FLAGS + ", "
 						+ COL_INST_STAMP + ", "
 						+ COL_REPO_ID + " "
 					+ "from " + QNAME + " "
 					+ "where (" + COL_LIB_ID + "= ?)";

 		}

 	}

 	private static RLibLocation getLibLocation(final List<? extends RLibGroup> envLibs, final String path) {
 		for (final RLibGroup group : envLibs) {
 			for (final RLibLocation location : group.getLibLocations()) {
 				if (path.equals(location.getDirectory())) {
 					return location;
 				}
 			}
 		}
 		return null;
 	}

 	static DB create(final REnv rEnv, final IFileStore parent) {
 		try {
 			final File file= parent.getChild("db").toLocalFile(EFS.NONE, null); //$NON-NLS-1$
 			final ConnectionFactory connectionFactory= EmbeddedDB.createConnectionFactory(file.getAbsolutePath());

 			return new DB(rEnv, connectionFactory);
 		}
 		catch (final CoreException e) {

 			return null;
 		}
 	}


 	private final REnv rEnv;

 	private final Map<String, Integer> libIdMap= new HashMap<>();

 	private final ConnectionFactory connectionFactory;
 	private Connection connection;

 	private PreparedStatement libAddStatement;
 	private PreparedStatement pkgDeleteStatement;
 	private PreparedStatement pkgAddStatement;
 	private PreparedStatement pkgChangeStatement;


 	private DB(final REnv rEnv, final ConnectionFactory connectionFactory) throws CoreException {
 		this.rEnv= rEnv;
 		this.connectionFactory= connectionFactory;
 	}


 	private Connection getConnection() throws SQLException {
 		if (this.connection != null) {
 			try {
 				if (!this.connection.isClosed()) {
 					return this.connection;
 				}
 			}
 			catch (final SQLException e) {}
 			closeOnError();
 		}
 		this.connection= this.connectionFactory.createConnection();
 		this.connection.setAutoCommit(false);
 		return this.connection;
 	}

 	private void closeOnError() {
 		if (this.connection != null) {
 			try {
 				this.connection.close();
 			}
 			catch (final SQLException e) {
 			}
 			this.connection= null;
 			this.libAddStatement= null;
 			this.pkgDeleteStatement= null;
 			this.pkgAddStatement= null;
 			this.pkgChangeStatement= null;
 		}
 	}

 	BasicRPkgCompilation<IRPkgInfo> loadInstalled(final List<? extends RLibGroup> envLibs) {
 		try {
 			checkDB();

 			final BasicRPkgCompilation<IRPkgInfo> newInstalled= new BasicRPkgCompilation<>(8);
 			List<String> removeLibPath= null;

 			final Connection connection= getConnection();
 			try (
 				final Statement libStatement= connection.createStatement();
 				final PreparedStatement pkgStatement= connection.prepareStatement(
 						REnvDB.Pkgs.OP_get_ofLib )
 			) {
 				final ResultSet libResult= libStatement.executeQuery(REnvDB.LibPaths.OP_getAll);

 				while (libResult.next()) {
 					final String libPath= libResult.getString(2);
 					final RLibLocation location= getLibLocation(envLibs, libPath);
 					if (location == null) {
 						if (removeLibPath == null) {
 							removeLibPath= new ArrayList<>();
 						}
 						removeLibPath.add(libPath);
 					}
 					else {
 						final int id= libResult.getInt(1);
 						this.libIdMap.put(location.getDirectory(), id);

 						final RPkgListImpl<IRPkgInfo> list= new RPkgListImpl<>(16);
 						newInstalled.add(location.getDirectory(), list);

 						pkgStatement.setInt(1, id);
 						final ResultSet pkgResult= pkgStatement.executeQuery();
 						while (pkgResult.next()) {
 							final RPkgInfo pkg= new RPkgInfo(pkgResult.getString(1),
 									RNumVersion.create(pkgResult.getString(2)),
 									pkgResult.getString(3), pkgResult.getString(4), location,
 									pkgResult.getInt(5), pkgResult.getLong(6), pkgResult.getString(7) );
 							list.add(pkg);
 						}
 					}
 				}
 			}

 			if (removeLibPath != null) {
 				clean(removeLibPath);
 			}

 			return newInstalled;
 		}
 		catch (final SQLException e) {
 			closeOnError();
 			final String name= this.rEnv.getName();
 			RCorePlugin.log(new Status(IStatus.ERROR, RCore.BUNDLE_ID,
 					NLS.bind("An error occurred when loading R package information of " +
 							"the R environment ''{0}''.", name ), e ));
 			return null;
 		}
 	}

 	private void checkDB() throws SQLException {
 		final Connection connection= getConnection();

 		final ResultSet schemas= connection.getMetaData().getSchemas(null, REnvDB.NAME);
 		while (schemas.next()) {
 			if (REnvDB.NAME.equals(schemas.getString(1))) {
 				return;
 			}
 		}

 		try (final Statement statement= connection.createStatement()) {
 			statement.execute(REnvDB.LibPaths.DEFINE_1);
 			statement.execute(REnvDB.Pkgs.DEFINE_1);

 			connection.commit();
 		}
 		catch (final SQLException e) {
 			closeOnError();
 			throw e;
 		}
 	}

 	private void clean(final List<String> removeLibPath) throws SQLException {
 		final Connection connection= getConnection();
 		try (final PreparedStatement statement= connection.prepareStatement(
 				REnvDB.LibPaths.OP_delete_byPath )) {
 			for (final String libPath : removeLibPath) {
 				statement.setString(1, libPath);
 				statement.execute();
 			}

 			connection.commit();
 		}
 		catch (final SQLException e) {
 			closeOnError();
 			throw e;
 		}
 	}

 	void updatePkgs(final Change change) {
 		try {
 			final Connection connection= getConnection();

 			final RPkgChangeSet changeSet= change.installedPkgs;
 			if (!changeSet.deleted.isEmpty()) {
 				if (this.pkgDeleteStatement == null) {
 					this.pkgDeleteStatement= connection.prepareStatement(REnvDB.Pkgs.OP_delete);
 				}
 				for (final IRPkgInfo pkg : changeSet.deleted) {
 					final Integer id= this.libIdMap.get(pkg.getLibLocation().getDirectory());
 					this.pkgDeleteStatement.setInt(1, id.intValue());
 					this.pkgDeleteStatement.setString(2, pkg.getName());

 					this.pkgDeleteStatement.execute();
 				}
 			}
 			if (!changeSet.added.isEmpty()) {
 				if (this.pkgAddStatement == null) {
 					this.pkgAddStatement= connection.prepareStatement(REnvDB.Pkgs.OP_insert);
 				}
 				for (final IRPkgInfo pkg : changeSet.added) {
 					Integer id= this.libIdMap.get(pkg.getLibLocation().getDirectory());
 					if (id == null) {
 						id= addLib(connection, pkg.getLibLocation());
 					}
 					this.pkgAddStatement.setInt(1, id.intValue());
 					this.pkgAddStatement.setString(2, pkg.getName());
 					this.pkgAddStatement.setString(3, pkg.getVersion().toString());
 					this.pkgAddStatement.setString(4, pkg.getBuilt());
 					this.pkgAddStatement.setString(5, pkg.getTitle());
 					this.pkgAddStatement.setInt(6, pkg.getFlags());
 					this.pkgAddStatement.setLong(7, pkg.getInstallStamp());
 					this.pkgAddStatement.setString(8, pkg.getRepoId());

 					this.pkgAddStatement.execute();
 				}
 			}
 			if (!changeSet.changed.isEmpty()) {
 				if (this.pkgChangeStatement == null) {
 					this.pkgChangeStatement= connection.prepareStatement(REnvDB.Pkgs.OP_update);
 				}
 				for (final IRPkgInfo pkg : changeSet.changed) {
 					final Integer id= this.libIdMap.get(pkg.getLibLocation().getDirectory());
 					this.pkgChangeStatement.setInt(7, id.intValue());
 					this.pkgChangeStatement.setString(8, pkg.getName());
 					this.pkgChangeStatement.setString(1, pkg.getVersion().toString());
 					this.pkgChangeStatement.setString(2, pkg.getBuilt());
 					this.pkgChangeStatement.setString(3, pkg.getTitle());
 					this.pkgChangeStatement.setInt(4, pkg.getFlags());
 					this.pkgChangeStatement.setLong(5, pkg.getInstallStamp());
 					this.pkgChangeStatement.setString(6, pkg.getRepoId());

 					this.pkgChangeStatement.execute();
 				}
 			}

 			connection.commit();
 		}
 		catch (final SQLException e) {
 			closeOnError();
 			final String name= this.rEnv.getName();
 			RCorePlugin.log(new Status(IStatus.ERROR, RCore.BUNDLE_ID,
 					NLS.bind("An error occurred when saving R package information of " +
 							"the R environment ''{0}''.", name ), e ));
 		}
 	}

 	private Integer addLib(final Connection connection, final RLibLocation location) throws SQLException {
 		if (this.libAddStatement == null) {
 			this.libAddStatement= connection.prepareStatement(REnvDB.LibPaths.OP_insert,
 					new String[] { REnvDB.LibPaths.COL_ID } );
 		}
 		this.libAddStatement.setString(1, location.getDirectory());
 		this.libAddStatement.execute();
 		final ResultSet result= this.libAddStatement.getGeneratedKeys();
 		if (result.next()) {
 			final Integer id= result.getInt(1);
 			this.libIdMap.put(location.getDirectory(), id);
 			return id;
 		}
 		throw new SQLException("Unexpected result");
 	}

 }
	/*=============================================================================#
	# Copyright (c) 2012, 2019 Stephan Wahlbrink and others.
	#
	# This program and the accompanying materials are made available under the
	# terms of the Eclipse Public License 2.0 which is available at
	# https://www.eclipse.org/legal/epl-2.0, or the Apache License, Version 2.0
	# which is available at https://www.apache.org/licenses/LICENSE-2.0.
	#
	# SPDX-License-Identifier: EPL-2.0 OR Apache-2.0
	#
	# Contributors:
	# Stephan Wahlbrink <sw@wahlbrink.eu> - initial API and implementation
	#=============================================================================*/

	package org.eclipse.statet.internal.r.core.pkgmanager;

	import java.io.File;
	import java.sql.Connection;
	import java.sql.PreparedStatement;
	import java.sql.ResultSet;
	import java.sql.SQLException;
	import java.sql.Statement;
	import java.util.ArrayList;
	import java.util.HashMap;
	import java.util.List;
	import java.util.Map;

	import org.eclipse.core.filesystem.EFS;
	import org.eclipse.core.filesystem.IFileStore;
	import org.eclipse.core.runtime.CoreException;
	import org.eclipse.core.runtime.IStatus;
	import org.eclipse.core.runtime.Status;
	import org.eclipse.osgi.util.NLS;

	import org.apache.commons.dbcp2.ConnectionFactory;

	import org.eclipse.statet.ecommons.edb.core.EmbeddedDB;

	import org.eclipse.statet.internal.r.core.RCorePlugin;
	import org.eclipse.statet.r.core.RCore;
	import org.eclipse.statet.r.core.pkgmanager.IRPkgInfo;
	import org.eclipse.statet.r.core.pkgmanager.RPkgInfo;
	import org.eclipse.statet.rj.renv.core.BasicRPkgCompilation;
	import org.eclipse.statet.rj.renv.core.REnv;
	import org.eclipse.statet.rj.renv.core.RLibGroup;
	import org.eclipse.statet.rj.renv.core.RLibLocation;
	import org.eclipse.statet.rj.renv.core.RNumVersion;


	final class DB {

	/** DB definitions */
	@SuppressWarnings({ "hiding", "nls" })
	private static final class REnvDB { // SCHMEMA

	static final String NAME= "RENV";

	static final class LibPaths {

	static final String NAME= "LIBPATHS";
	static final String QNAME= REnvDB.NAME + '.' + NAME;

	static final String COL_ID= "LIB_ID";
	static final String COL_LIB_PATH= "LIB_PATH";
	static final String COL_STAMP= "STAMP";

	static final String DEFINE_1= "create table " + QNAME + " ("
	+ COL_ID + " int not null "
	+ "primary key "
	+ "generated always as identity, "
	+ COL_LIB_PATH + " varchar(4096) not null unique, "
	+ COL_STAMP + " bigint"
	+ ")";

	static final String OP_insert= "insert into " + QNAME + " ("
	+ COL_LIB_PATH + ") "
	+ "values (?)";

	static final String OP_delete_byPath= "delete from " + QNAME + " "
	+ "where (" + COL_LIB_PATH + "= ?)";

	static final String OP_getAll= "select "
	+ COL_ID + ", "
	+ COL_LIB_PATH + " "
	+ "from " + QNAME;

	}

	static final class Pkgs {

	static final String NAME= "PKGS";
	static final String QNAME= REnvDB.NAME + '.' + NAME;

	static final String COL_LIB_ID= "LIB_ID";
	static final String COL_NAME= "NAME";
	static final String COL_VERSION= "VERSION";
	static final String COL_BUILT= "BUILT";
	static final String COL_TITLE= "TITLE";
	static final String COL_FLAGS= "FLAGS";
	static final String COL_INST_STAMP= "INST_STAMP";
	static final String COL_REPO_ID= "REPO_ID";

	static final String DEFINE_1= "create table " + QNAME + " ("
	+ COL_LIB_ID + " int not null "
	+ "references " + LibPaths.QNAME + " on delete cascade, "
	+ COL_NAME + " varchar(64) not null, "
	+ COL_VERSION + " varchar(64) not null, "
	+ COL_BUILT + " varchar(256) not null, "
	+ COL_TITLE + " varchar(256) not null, "
	+ COL_FLAGS + " int, "
	+ COL_INST_STAMP + " bigint, "
	+ COL_REPO_ID + " varchar(256), "
	+ "primary key ("
	+ COL_LIB_ID + ", "
	+ COL_NAME + ")"
	+ ")";

	static final String OP_insert= "insert into " + QNAME + " ("
	+ COL_LIB_ID + ", "
	+ COL_NAME + ", "
	+ COL_VERSION + ", "
	+ COL_BUILT + ", "
	+ COL_TITLE + ", "
	+ COL_FLAGS + ", "
	+ COL_INST_STAMP + ", "
	+ COL_REPO_ID + ") "
	+ "values (? , ?, ?, ?, ?, ?, ?, ?)";

	static final String OP_update= "update " + QNAME + " set "
	+ COL_VERSION + "= ?, "
	+ COL_BUILT + "= ?, "
	+ COL_TITLE + "= ?, "
	+ COL_FLAGS + "= ?, "
	+ COL_INST_STAMP + "= ?, "
	+ COL_REPO_ID +"= ? "
	+ "where (" + COL_LIB_ID + "= ? and " + COL_NAME + "= ?)";

	static final String OP_delete= "delete from " + QNAME + " "
	+ "where (" + COL_LIB_ID + "= ? and " + COL_NAME + "= ?)";

	static final String OP_get_ofLib= "select "
	+ COL_NAME + ", "
	+ COL_VERSION + ", "
	+ COL_BUILT + ", "
	+ COL_TITLE + ", "
	+ COL_FLAGS + ", "
	+ COL_INST_STAMP + ", "
	+ COL_REPO_ID + " "
	+ "from " + QNAME + " "
	+ "where (" + COL_LIB_ID + "= ?)";

	}

	}

	private static RLibLocation getLibLocation(final List<? extends RLibGroup> envLibs, final String path) {
	for (final RLibGroup group : envLibs) {
	for (final RLibLocation location : group.getLibLocations()) {
	if (path.equals(location.getDirectory())) {
	return location;
	}
	}
	}
	return null;
	}

	static DB create(final REnv rEnv, final IFileStore parent) {
	try {
	final File file= parent.getChild("db").toLocalFile(EFS.NONE, null); //$NON-NLS-1$
	final ConnectionFactory connectionFactory= EmbeddedDB.createConnectionFactory(file.getAbsolutePath());

	return new DB(rEnv, connectionFactory);
	}
	catch (final CoreException e) {

	return null;
	}
	}


	private final REnv rEnv;

	private final Map<String, Integer> libIdMap= new HashMap<>();

	private final ConnectionFactory connectionFactory;
	private Connection connection;

	private PreparedStatement libAddStatement;
	private PreparedStatement pkgDeleteStatement;
	private PreparedStatement pkgAddStatement;
	private PreparedStatement pkgChangeStatement;


	private DB(final REnv rEnv, final ConnectionFactory connectionFactory) throws CoreException {
	this.rEnv= rEnv;
	this.connectionFactory= connectionFactory;
	}


	private Connection getConnection() throws SQLException {
	if (this.connection != null) {
	try {
	if (!this.connection.isClosed()) {
	return this.connection;
	}
	}
	catch (final SQLException e) {}
	closeOnError();
	}
	this.connection= this.connectionFactory.createConnection();
	this.connection.setAutoCommit(false);
	return this.connection;
	}

	private void closeOnError() {
	if (this.connection != null) {
	try {
	this.connection.close();
	}
	catch (final SQLException e) {
	}
	this.connection= null;
	this.libAddStatement= null;
	this.pkgDeleteStatement= null;
	this.pkgAddStatement= null;
	this.pkgChangeStatement= null;
	}
	}

	BasicRPkgCompilation<IRPkgInfo> loadInstalled(final List<? extends RLibGroup> envLibs) {
	try {
	checkDB();

	final BasicRPkgCompilation<IRPkgInfo> newInstalled= new BasicRPkgCompilation<>(8);
	List<String> removeLibPath= null;

	final Connection connection= getConnection();
	try (
	final Statement libStatement= connection.createStatement();
	final PreparedStatement pkgStatement= connection.prepareStatement(
	REnvDB.Pkgs.OP_get_ofLib )
	) {
	final ResultSet libResult= libStatement.executeQuery(REnvDB.LibPaths.OP_getAll);

	while (libResult.next()) {
	final String libPath= libResult.getString(2);
	final RLibLocation location= getLibLocation(envLibs, libPath);
	if (location == null) {
	if (removeLibPath == null) {
	removeLibPath= new ArrayList<>();
	}
	removeLibPath.add(libPath);
	}
	else {
	final int id= libResult.getInt(1);
	this.libIdMap.put(location.getDirectory(), id);

	final RPkgListImpl<IRPkgInfo> list= new RPkgListImpl<>(16);
	newInstalled.add(location.getDirectory(), list);

	pkgStatement.setInt(1, id);
	final ResultSet pkgResult= pkgStatement.executeQuery();
	while (pkgResult.next()) {
	final RPkgInfo pkg= new RPkgInfo(pkgResult.getString(1),
	RNumVersion.create(pkgResult.getString(2)),
	pkgResult.getString(3), pkgResult.getString(4), location,
	pkgResult.getInt(5), pkgResult.getLong(6), pkgResult.getString(7) );
	list.add(pkg);
	}
	}
	}
	}

	if (removeLibPath != null) {
	clean(removeLibPath);
	}

	return newInstalled;
	}
	catch (final SQLException e) {
	closeOnError();
	final String name= this.rEnv.getName();
	RCorePlugin.log(new Status(IStatus.ERROR, RCore.BUNDLE_ID,
	NLS.bind("An error occurred when loading R package information of " +
	"the R environment ''{0}''.", name ), e ));
	return null;
	}
	}

	private void checkDB() throws SQLException {
	final Connection connection= getConnection();

	final ResultSet schemas= connection.getMetaData().getSchemas(null, REnvDB.NAME);
	while (schemas.next()) {
	if (REnvDB.NAME.equals(schemas.getString(1))) {
	return;
	}
	}

	try (final Statement statement= connection.createStatement()) {
	statement.execute(REnvDB.LibPaths.DEFINE_1);
	statement.execute(REnvDB.Pkgs.DEFINE_1);

	connection.commit();
	}
	catch (final SQLException e) {
	closeOnError();
	throw e;
	}
	}

	private void clean(final List<String> removeLibPath) throws SQLException {
	final Connection connection= getConnection();
	try (final PreparedStatement statement= connection.prepareStatement(
	REnvDB.LibPaths.OP_delete_byPath )) {
	for (final String libPath : removeLibPath) {
	statement.setString(1, libPath);
	statement.execute();
	}

	connection.commit();
	}
	catch (final SQLException e) {
	closeOnError();
	throw e;
	}
	}

	void updatePkgs(final Change change) {
	try {
	final Connection connection= getConnection();

	final RPkgChangeSet changeSet= change.installedPkgs;
	if (!changeSet.deleted.isEmpty()) {
	if (this.pkgDeleteStatement == null) {
	this.pkgDeleteStatement= connection.prepareStatement(REnvDB.Pkgs.OP_delete);
	}
	for (final IRPkgInfo pkg : changeSet.deleted) {
	final Integer id= this.libIdMap.get(pkg.getLibLocation().getDirectory());
	this.pkgDeleteStatement.setInt(1, id.intValue());
	this.pkgDeleteStatement.setString(2, pkg.getName());

	this.pkgDeleteStatement.execute();
	}
	}
	if (!changeSet.added.isEmpty()) {
	if (this.pkgAddStatement == null) {
	this.pkgAddStatement= connection.prepareStatement(REnvDB.Pkgs.OP_insert);
	}
	for (final IRPkgInfo pkg : changeSet.added) {
	Integer id= this.libIdMap.get(pkg.getLibLocation().getDirectory());
	if (id == null) {
	id= addLib(connection, pkg.getLibLocation());
	}
	this.pkgAddStatement.setInt(1, id.intValue());
	this.pkgAddStatement.setString(2, pkg.getName());
	this.pkgAddStatement.setString(3, pkg.getVersion().toString());
	this.pkgAddStatement.setString(4, pkg.getBuilt());
	this.pkgAddStatement.setString(5, pkg.getTitle());
	this.pkgAddStatement.setInt(6, pkg.getFlags());
	this.pkgAddStatement.setLong(7, pkg.getInstallStamp());
	this.pkgAddStatement.setString(8, pkg.getRepoId());

	this.pkgAddStatement.execute();
	}
	}
	if (!changeSet.changed.isEmpty()) {
	if (this.pkgChangeStatement == null) {
	this.pkgChangeStatement= connection.prepareStatement(REnvDB.Pkgs.OP_update);
	}
	for (final IRPkgInfo pkg : changeSet.changed) {
	final Integer id= this.libIdMap.get(pkg.getLibLocation().getDirectory());
	this.pkgChangeStatement.setInt(7, id.intValue());
	this.pkgChangeStatement.setString(8, pkg.getName());
	this.pkgChangeStatement.setString(1, pkg.getVersion().toString());
	this.pkgChangeStatement.setString(2, pkg.getBuilt());
	this.pkgChangeStatement.setString(3, pkg.getTitle());
	this.pkgChangeStatement.setInt(4, pkg.getFlags());
	this.pkgChangeStatement.setLong(5, pkg.getInstallStamp());
	this.pkgChangeStatement.setString(6, pkg.getRepoId());

	this.pkgChangeStatement.execute();
	}
	}

	connection.commit();
	}
	catch (final SQLException e) {
	closeOnError();
	final String name= this.rEnv.getName();
	RCorePlugin.log(new Status(IStatus.ERROR, RCore.BUNDLE_ID,
	NLS.bind("An error occurred when saving R package information of " +
	"the R environment ''{0}''.", name ), e ));
	}
	}

	private Integer addLib(final Connection connection, final RLibLocation location) throws SQLException {
	if (this.libAddStatement == null) {
	this.libAddStatement= connection.prepareStatement(REnvDB.LibPaths.OP_insert,
	new String[] { REnvDB.LibPaths.COL_ID } );
	}
	this.libAddStatement.setString(1, location.getDirectory());
	this.libAddStatement.execute();
	final ResultSet result= this.libAddStatement.getGeneratedKeys();
	if (result.next()) {
	final Integer id= result.getInt(1);
	this.libIdMap.put(location.getDirectory(), id);
	return id;
	}
	throw new SQLException("Unexpected result");
	}

	}