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Posted to commits@airavata.apache.org by la...@apache.org on 2016/09/29 12:45:13 UTC
[36/50] [abbrv] airavata git commit: fixing credential store not
initializing issue
fixing credential store not initializing issue
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/a5156a92
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/a5156a92
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/a5156a92
Branch: refs/heads/lahiru/AIRAVATA-2065
Commit: a5156a9207f65c21d069b21fe7147eabc4f2dea1
Parents: 4d908fb
Author: scnakandala <su...@gmail.com>
Authored: Fri Sep 16 10:45:06 2016 -0400
Committer: scnakandala <su...@gmail.com>
Committed: Fri Sep 16 10:45:06 2016 -0400
----------------------------------------------------------------------
.../credential-store-service/pom.xml | 10 +-
.../store/server/CredentialStoreServer.java | 4 -
.../server/CredentialStoreServerHandler.java | 8 +-
.../store/store/impl/util/ConnectionPool.java | 382 +++++++++++++++++++
.../impl/util/CredentialStoreInitUtil.java | 155 ++++++++
.../store/store/impl/util/DatabaseCreator.java | 353 +++++++++++++++++
.../store/store/impl/util/JdbcStorage.java | 175 +++++++++
.../credential/catalog/model/CommunityUser.java | 72 ----
.../catalog/model/CommunityUser_Pk.java | 63 ---
.../credential/catalog/model/Configuration.java | 54 ---
.../catalog/model/Configuration_PK.java | 60 ---
.../credential/catalog/model/Credential.java | 83 ----
.../credential/catalog/model/Credential_PK.java | 55 ---
.../catalog/util/CredentialCatalogJPAUtils.java | 82 ----
.../src/main/resources/META-INF/persistence.xml | 7 -
.../src/main/resources/credstore-derby.sql | 60 +--
.../src/main/resources/credstore-mysql.sql | 60 +--
17 files changed, 1113 insertions(+), 570 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/credential-store/credential-store-service/pom.xml
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/pom.xml b/modules/credential-store/credential-store-service/pom.xml
index 7c03c4f..8b736af 100644
--- a/modules/credential-store/credential-store-service/pom.xml
+++ b/modules/credential-store/credential-store-service/pom.xml
@@ -79,11 +79,6 @@
<scope>test</scope>
</dependency>
<dependency>
- <groupId>org.apache.airavata</groupId>
- <artifactId>airavata-registry-core</artifactId>
- <version>${project.version}</version>
- </dependency>
- <dependency>
<groupId>org.apache.derby</groupId>
<artifactId>derby</artifactId>
<version>${derby.version}</version>
@@ -144,6 +139,11 @@
<artifactId>commons-io</artifactId>
<version>1.3.2</version>
</dependency>
+ <dependency>
+ <groupId>org.apache.derby</groupId>
+ <artifactId>derbynet</artifactId>
+ <version>10.11.1.1</version>
+ </dependency>
</dependencies>
<build>
<plugins>
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServer.java
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServer.java b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServer.java
index 0829fda..5ccec02 100644
--- a/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServer.java
+++ b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServer.java
@@ -24,7 +24,6 @@ package org.apache.airavata.credential.store.server;
import org.apache.airavata.common.utils.IServer;
import org.apache.airavata.common.utils.ServerSettings;
import org.apache.airavata.credential.store.cpi.CredentialStoreService;
-import org.apache.airavata.registry.core.credential.catalog.util.CredentialCatalogJPAUtils;
import org.apache.thrift.server.TServer;
import org.apache.thrift.server.TThreadPoolServer;
import org.apache.thrift.transport.TServerSocket;
@@ -108,9 +107,6 @@ public class CredentialStoreServer implements IServer {
public static void main(String[] args) {
try {
- //Initializing the database;
- CredentialCatalogJPAUtils.getEntityManager();
-
new CredentialStoreServer().start();
} catch (Exception e) {
logger.error(e.getMessage(), e);
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServerHandler.java
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServerHandler.java b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServerHandler.java
index 095958d..0f1ac93 100644
--- a/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServerHandler.java
+++ b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/server/CredentialStoreServerHandler.java
@@ -34,6 +34,7 @@ import org.apache.airavata.credential.store.store.CredentialStoreException;
import org.apache.airavata.credential.store.store.impl.CertificateCredentialWriter;
import org.apache.airavata.credential.store.store.impl.CredentialReaderImpl;
import org.apache.airavata.credential.store.store.impl.SSHCredentialWriter;
+import org.apache.airavata.credential.store.store.impl.util.CredentialStoreInitUtil;
import org.apache.airavata.credential.store.util.TokenGenerator;
import org.apache.airavata.credential.store.util.Utility;
import org.apache.commons.codec.binary.Base64;
@@ -43,8 +44,10 @@ import org.slf4j.LoggerFactory;
import sun.security.provider.X509Factory;
import java.io.ByteArrayInputStream;
+import java.io.IOException;
import java.security.cert.CertificateFactory;
import java.security.cert.X509Certificate;
+import java.sql.SQLException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -57,13 +60,16 @@ public class CredentialStoreServerHandler implements CredentialStoreService.Ifac
private CertificateCredentialWriter certificateCredentialWriter;
private CredentialReaderImpl credentialReader;
- public CredentialStoreServerHandler() throws ApplicationSettingsException, IllegalAccessException, ClassNotFoundException, InstantiationException {
+ public CredentialStoreServerHandler() throws ApplicationSettingsException, IllegalAccessException,
+ ClassNotFoundException, InstantiationException, SQLException, IOException {
String jdbcUrl = ServerSettings.getCredentialStoreDBURL();
String userName = ServerSettings.getCredentialStoreDBUser();
String password = ServerSettings.getCredentialStoreDBPassword();
String driverName = ServerSettings.getCredentialStoreDBDriver();
log.debug("Starting credential store, connecting to database - " + jdbcUrl + " DB user - " + userName + " driver name - " + driverName);
+ CredentialStoreInitUtil.initializeDB();
+
dbUtil = new DBUtil(jdbcUrl, userName, password, driverName);
sshCredentialWriter = new SSHCredentialWriter(dbUtil);
certificateCredentialWriter = new CertificateCredentialWriter(dbUtil);
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/ConnectionPool.java
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/ConnectionPool.java b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/ConnectionPool.java
new file mode 100644
index 0000000..b832604
--- /dev/null
+++ b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/ConnectionPool.java
@@ -0,0 +1,382 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.credential.store.store.impl.util;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.sql.DataSource;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Stack;
+import java.util.concurrent.Semaphore;
+
+
+/**
+ * A class for preallocating, recycling, and managing JDBC connections.
+ */
+public class ConnectionPool {
+ private static final Logger logger = LoggerFactory.getLogger(ConnectionPool.class);
+
+ private long MAX_IDLE_TIME = 5 * 60 * 1000; // 5 minutes
+
+ private String driver;
+ private String url;
+ private String username;
+ private String password;
+ private String jdbcUrl;
+
+ private int maxConnections;
+
+ private boolean autoCommit = true;
+ private boolean waitIfBusy;
+
+ private Semaphore needConnection = new Semaphore(0);
+ private boolean stop;
+
+ private Stack<Connection> availableConnections;
+ private Stack<Connection> busyConnections;
+
+ private HashMap<Connection, Long> lastAccessTimeRecord = new HashMap<Connection, Long>();
+
+ private String urlType = "";
+
+ private DataSource datasource;
+
+ private int transactionIsolation = Connection.TRANSACTION_NONE;
+
+ private Thread clenupThread;
+ private Thread producerThread;
+
+ public ConnectionPool(String driver, String url, String username, String password, int initialConnections,
+ int maxConnections, boolean waitIfBusy) throws SQLException {
+ this.driver = driver;
+ this.url = url;
+ this.username = username;
+ this.password = password;
+ this.urlType = "speratedURL";
+ initialize(initialConnections, maxConnections, waitIfBusy);
+ }
+
+ public ConnectionPool(String driver, String jdbcUrl, int initialConnections, int maxConnections,
+ boolean waitIfBusy, boolean autoCommit, int transactionIsolation) throws SQLException {
+ this.driver = driver;
+ this.jdbcUrl = jdbcUrl;
+ this.urlType = "simpleURL";
+ this.autoCommit = autoCommit;
+ this.transactionIsolation = transactionIsolation;
+ initialize(initialConnections, maxConnections, waitIfBusy);
+ }
+
+ public ConnectionPool(String driver, String jdbcUrl, int initialConnections, int maxConnections, boolean waitIfBusy)
+ throws SQLException {
+ this.driver = driver;
+ this.jdbcUrl = jdbcUrl;
+ this.urlType = "simpleURL";
+ initialize(initialConnections, maxConnections, waitIfBusy);
+ }
+
+ public ConnectionPool(DataSource dataSource, int initialConnections, int maxConnections, boolean waitIfBusy)
+ throws SQLException {
+ this.urlType = "dataSource";
+ this.datasource = dataSource;
+ initialize(initialConnections, maxConnections, waitIfBusy);
+ }
+
+ /**
+ * Check if this connection pool is auto commit or not
+ *
+ * @return
+ */
+ public boolean isAutoCommit() {
+ return this.autoCommit;
+ }
+
+ private void initialize(int initialConnections, int maxConnections, boolean waitIfBusy) throws SQLException {
+ this.maxConnections = maxConnections;
+ this.waitIfBusy = waitIfBusy;
+
+ int sizeOfConnections = (initialConnections > maxConnections) ? maxConnections : initialConnections;
+
+ availableConnections = new Stack<Connection>();
+ busyConnections = new Stack<Connection>();
+
+ for (int i = 0; i < sizeOfConnections; i++) {
+ Connection con = makeNewConnection();
+ setTimeStamp(con);
+ availableConnections.push(con);
+
+ }
+
+ producerThread = new Thread(new FillUpThread());
+ producerThread.start();
+
+ clenupThread = new Thread(new CleanUpThread());
+ clenupThread.start();
+ }
+
+ public synchronized Connection getConnection() throws SQLException {
+ if (!availableConnections.isEmpty()) {
+ Connection existingConnection = availableConnections.pop();
+
+ // If connection on available list is closed (e.g.,
+ // it timed out), then remove it from available list
+ // and race for a connection again.
+ if (existingConnection.isClosed()) {
+ lastAccessTimeRecord.remove(existingConnection);
+ // notifyAll for fairness
+ notifyAll();
+ } else {
+ busyConnections.push(existingConnection);
+ setTimeStamp(existingConnection);
+ return existingConnection;
+ }
+ } else if (!waitIfBusy && busyConnections.size() >= maxConnections) {
+ // You reached maxConnections limit and waitIfBusy flag is false.
+ // Throw SQLException in such a case.
+ throw new SQLException("Connection limit reached");
+ } else {
+
+ if (busyConnections.size() < maxConnections) {
+ // available connection is empty, but total number of connection
+ // doesn't reach maxConnection. Request for more connection
+ needConnection.release();
+ }
+
+ try {
+ // wait for free connection
+ wait();
+ } catch (InterruptedException ie) {
+ }
+ }
+ // always race for connection forever
+ return getConnection();
+ }
+
+ // This explicitly makes a new connection. Called in
+ // the foreground when initializing the ConnectionPool,
+ // and called in the background when running.
+ private Connection makeNewConnection() throws SQLException {
+ try {
+ // Load database driver if not already loaded
+ Class.forName(driver);
+ Connection connection;
+ // Establish network connection to database
+ if (urlType.equals("speratedURL")) {
+ connection = DriverManager.getConnection(url, username, password);
+ } else if (urlType.equals("simpleURL")) {
+ connection = DriverManager.getConnection(jdbcUrl);
+ } else { // if(urlType.equals("dataSource")){
+ connection = datasource.getConnection();
+ }
+ connection.setTransactionIsolation(this.transactionIsolation);
+ connection.setAutoCommit(this.autoCommit);
+ return connection;
+ } catch (ClassNotFoundException cnfe) {
+ // Simplify try/catch blocks of people using this by
+ // throwing only one exception type.
+ throw new SQLException("Can't find class for driver: " + driver);
+ }
+ }
+
+ private synchronized void fillUpConnection(Connection conn) {
+ setTimeStamp(conn);
+ availableConnections.push(conn);
+
+ // notify all since new connection is created
+ notifyAll();
+ }
+
+ private void setTimeStamp(Connection connection) {
+ lastAccessTimeRecord.put(connection, System.currentTimeMillis());
+ }
+
+ // The database connection cannot be left idle for too long, otherwise TCP
+ // connection will be broken.
+ /**
+ * From http://forums.mysql.com/read.php?39,28450,57460#msg-57460 Okay, then it looks like wait_timeout on the
+ * server is killing your connection (it is set to 8 hours of idle time by default). Either set that value higher on
+ * your server, or configure your connection pool to not hold connections idle that long (I prefer the latter). Most
+ * folks I know that run MySQL with a connection pool in high-load production environments only let connections sit
+ * idle for a matter of minutes, since it only takes a few milliseconds to open a connection, and the longer one
+ * sits idle the more chance it will go "bad" because of a network hiccup or the MySQL server being restarted.
+ *
+ * @throws java.sql.SQLException
+ */
+ private boolean isConnectionStale(Connection connection) {
+ long currentTime = System.currentTimeMillis();
+ long lastAccess = lastAccessTimeRecord.get(connection);
+ if (currentTime - lastAccess > MAX_IDLE_TIME) {
+ return true;
+ } else
+ return false;
+ }
+
+ private synchronized void closeStaleConnections() {
+ // close idle connections
+ Iterator<Connection> iter = availableConnections.iterator();
+ while (iter.hasNext()) {
+ Connection existingConnection = iter.next();
+ if (isConnectionStale(existingConnection)) {
+ try {
+ existingConnection.close();
+ iter.remove();
+ } catch (SQLException sql) {
+ logger.error(sql.getMessage(), sql);
+ }
+ }
+ }
+ // close busy connections that have been checked out for too long.
+ // This should not happen since this means program has bug for not
+ // releasing connections .
+ iter = busyConnections.iterator();
+ while (iter.hasNext()) {
+ Connection busyConnection = iter.next();
+ if (isConnectionStale(busyConnection)) {
+ try {
+ busyConnection.close();
+ iter.remove();
+ logger.warn("****Connection has checked out too long. Forced release. Check the program for calling release connection [free(Connection) method]");
+ } catch (SQLException sql) {
+ logger.error(sql.getMessage(), sql);
+ }
+ }
+ }
+ }
+
+ public synchronized void free(Connection connection) {
+ busyConnections.removeElement(connection);
+ availableConnections.addElement(connection);
+ // Wake up threads that are waiting for a connection
+ notifyAll();
+ }
+
+ /**
+ * Close all the connections. Use with caution: be sure no connections are in use before calling. Note that you are
+ * not <I>required</I> to call this when done with a ConnectionPool, since connections are guaranteed to be closed
+ * when garbage collected. But this method gives more control regarding when the connections are closed.
+ */
+ public synchronized void dispose() {
+ logger.info("Connection Pool Shutting down");
+
+ // stop clean up thread
+ this.stop = true;
+ this.clenupThread.interrupt();
+
+ // stop producer up thread
+ this.producerThread.interrupt();
+
+ // close all connection
+ closeConnections(availableConnections);
+ availableConnections = new Stack<Connection>();
+ closeConnections(busyConnections);
+ busyConnections = new Stack<Connection>();
+ lastAccessTimeRecord.clear();
+
+ logger.info("All connection is closed");
+
+ try {
+ this.clenupThread.join();
+ this.producerThread.join();
+ } catch (Exception e) {
+ logger.error("Cannot shutdown cleanup thread", e);
+ }
+
+ logger.info("Connection Pool Shutdown");
+ }
+
+ private void closeConnections(Stack<Connection> connections) {
+ while (!connections.isEmpty()) {
+ Connection connection = connections.pop();
+ try {
+ if (!connection.isClosed()) {
+ connection.close();
+ }
+ } catch (SQLException sqle) {
+ // Ignore errors; garbage collect anyhow
+ logger.warn(sqle.getMessage());
+ }
+ }
+ }
+
+ public synchronized String toString() {
+ String info = "ConnectionPool(" + url + "," + username + ")" + ", available=" + availableConnections.size()
+ + ", busy=" + busyConnections.size() + ", max=" + maxConnections;
+ return (info);
+ }
+
+ class CleanUpThread implements Runnable {
+ public void run() {
+ while (!stop) {
+ try {
+ Thread.sleep(MAX_IDLE_TIME);
+ closeStaleConnections();
+ } catch (InterruptedException e) {
+ logger.info("Clean up thread is interrupted to close");
+ }
+ }
+ }
+ }
+
+ class FillUpThread implements Runnable {
+ public void run() {
+ while (!stop) {
+ try {
+ // block until get
+ needConnection.acquire();
+
+ Connection conn = makeNewConnection();
+ fillUpConnection(conn);
+ } catch (SQLException e) {
+ // cannot create connection (increase semaphore value back)
+ needConnection.release();
+ logger.error(e.getMessage(), e);
+ } catch (InterruptedException e) {
+ logger.info("Fill up thread is interrupted to close");
+ break;
+ }
+ }
+ }
+ }
+
+ public void shutdown() throws SQLException{
+ for (Connection c : availableConnections) {
+ try {
+ c.close();
+ } catch (SQLException e) {
+ logger.error("Error while closing the connection", e);
+ throw new SQLException("Error while closing the connection", e);
+ }
+ }
+
+ for (Connection c : busyConnections) {
+ try {
+ c.close();
+ } catch (SQLException e) {
+ logger.error("Error while closing the connection", e);
+ throw new SQLException("Error while closing the connection", e);
+ }
+ }
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/CredentialStoreInitUtil.java
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/CredentialStoreInitUtil.java b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/CredentialStoreInitUtil.java
new file mode 100644
index 0000000..8320c69
--- /dev/null
+++ b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/CredentialStoreInitUtil.java
@@ -0,0 +1,155 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.credential.store.store.impl.util;
+
+import org.apache.airavata.common.exception.ApplicationSettingsException;
+import org.apache.airavata.common.utils.ServerSettings;
+import org.apache.derby.drda.NetworkServerControl;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.net.InetAddress;
+import java.net.URI;
+import java.sql.Connection;
+import java.sql.SQLException;
+
+public class CredentialStoreInitUtil {
+ private static final Logger logger = LoggerFactory.getLogger(CredentialStoreInitUtil.class);
+ public static final String CREDENTIALS = "CREDENTIALS";
+ public static final String START_DERBY_ENABLE = "start.derby.server.mode";
+ public static final String DERBY_SERVER_MODE_SYS_PROPERTY = "derby.drda.startNetworkServer";
+ private static NetworkServerControl server;
+ private static JdbcStorage db;
+ private static String jdbcURl;
+ private static String jdbcDriver;
+ private static String jdbcUser;
+ private static String jdbcPassword;
+
+
+ public static void initializeDB() {
+// System.setProperty("appcatalog.initialize.state", "0");
+ try{
+ jdbcDriver = ServerSettings.getCredentialStoreDBDriver();
+ jdbcURl = ServerSettings.getCredentialStoreDBURL();
+ jdbcUser = ServerSettings.getCredentialStoreDBUser();
+ jdbcPassword = ServerSettings.getCredentialStoreDBPassword();
+ jdbcURl = jdbcURl + "?" + "user=" + jdbcUser + "&" + "password=" + jdbcPassword;
+ } catch (ApplicationSettingsException e) {
+ logger.error("Unable to read airavata server properties", e.getMessage());
+ }
+
+ if (getDBType(jdbcURl).equals("derby") && isDerbyStartEnabled()) {
+ startDerbyInServerMode();
+ }
+ db = new JdbcStorage(10, 50, jdbcURl, jdbcDriver, true);
+
+ Connection conn = null;
+ try {
+ conn = db.connect();
+ if (!DatabaseCreator.isDatabaseStructureCreated(CREDENTIALS, conn)) {
+ DatabaseCreator.createRegistryDatabase("database_scripts/credstore", conn);
+ logger.info("New Database created for Credential Store !!! ");
+ } else {
+ logger.info("Database already created for Credential Store !!!");
+ }
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ throw new RuntimeException("Database failure", e);
+ } finally {
+ db.closeConnection(conn);
+ try {
+ if(conn != null){
+ if (!conn.getAutoCommit()) {
+ conn.commit();
+ }
+ conn.close();
+ }
+ } catch (SQLException e) {
+ logger.error("Error while closing database connection...", e.getMessage(), e);
+ }
+ }
+// System.setProperty("appcatalog.initialize.state", "1");
+ }
+
+ public static String getDBType(String jdbcUrl){
+ try{
+ String cleanURI = jdbcUrl.substring(5);
+ URI uri = URI.create(cleanURI);
+ return uri.getScheme();
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ return null;
+ }
+ }
+
+ public static boolean isDerbyStartEnabled(){
+ try {
+ String s = ServerSettings.getSetting(START_DERBY_ENABLE);
+ if("true".equals(s)){
+ return true;
+ }
+ } catch (ApplicationSettingsException e) {
+ logger.error("Unable to read airavata server properties", e.getMessage(), e);
+ return false;
+ }
+ return false;
+ }
+
+ public static void startDerbyInServerMode() {
+ try {
+ System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "true");
+ server = new NetworkServerControl(InetAddress.getByName("0.0.0.0"),
+ getPort(jdbcURl),
+ jdbcUser, jdbcPassword);
+ java.io.PrintWriter consoleWriter = new java.io.PrintWriter(System.out, true);
+ server.start(consoleWriter);
+ } catch (IOException e) {
+ logger.error("Unable to start Apache derby in the server mode! Check whether " +
+ "specified port is available");
+ } catch (Exception e) {
+ logger.error("Unable to start Apache derby in the server mode! Check whether " +
+ "specified port is available");
+ }
+ }
+
+ public static void stopDerbyInServerMode() {
+ System.setProperty(DERBY_SERVER_MODE_SYS_PROPERTY, "false");
+ if (server!=null){
+ try {
+ server.shutdown();
+ } catch (Exception e) {
+ logger.error("Error when stopping the derby server : "+e.getLocalizedMessage());
+ }
+ }
+ }
+
+ public static int getPort(String jdbcURL){
+ try{
+ String cleanURI = jdbcURL.substring(5);
+ URI uri = URI.create(cleanURI);
+ return uri.getPort();
+ } catch (Exception e) {
+ logger.error(e.getMessage(), e);
+ return -1;
+ }
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/DatabaseCreator.java
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/DatabaseCreator.java b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/DatabaseCreator.java
new file mode 100644
index 0000000..627be0e
--- /dev/null
+++ b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/DatabaseCreator.java
@@ -0,0 +1,353 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.credential.store.store.impl.util;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.sql.*;
+import java.util.StringTokenizer;
+
+/**
+ * This class creates the database tables required for airavata with default configuration this
+ * class creates derby database in server mode. User can specify required database in appropriate
+ * properties files.
+ */
+public class DatabaseCreator {
+ private final static Logger logger = LoggerFactory.getLogger(DatabaseCreator.class);
+
+ public enum DatabaseType {
+ derby("(?i).*derby.*"), mysql("(?i).*mysql.*"), other("");
+
+ private String pattern;
+
+ private DatabaseType(String matchingPattern) {
+ this.pattern = matchingPattern;
+ }
+
+ public String getMatchingPattern() {
+ return this.pattern;
+ }
+ }
+
+ private static DatabaseType[] supportedDatabase = new DatabaseType[] { DatabaseType.derby, DatabaseType.mysql };
+
+ private static Logger log = LoggerFactory.getLogger(DatabaseCreator.class);
+ private static final String delimiter = ";";
+
+ /**
+ * Creates database
+ *
+ * @throws Exception
+ */
+ public static void createRegistryDatabase(String prefix, Connection conn) throws Exception {
+ createDatabase(prefix, conn);
+ }
+
+
+
+ /**
+ * Checks whether database tables are created by using select * on given table name
+ *
+ * @param tableName
+ * Table which should be existed
+ * @return <code>true</core> if checkSQL is success, else <code>false</code> .
+ */
+ public static boolean isDatabaseStructureCreated(String tableName, Connection conn) {
+ try {
+
+ log.debug("Running a query to test the database tables existence.");
+
+ // check whether the tables are already created with a query
+ Statement statement = null;
+ try {
+ statement = conn.createStatement();
+ ResultSet rs = statement.executeQuery("select * from " + tableName);
+ if (rs != null) {
+ rs.close();
+ }
+ } finally {
+ try {
+ if (statement != null) {
+ statement.close();
+ }
+ } catch (SQLException e) {
+ return false;
+ }
+ }
+ } catch (SQLException e) {
+ return false;
+ }
+
+ return true;
+ }
+
+ /**
+ * executes given sql
+ *
+ * @param sql
+ * @throws Exception
+ */
+ private static void executeSQL(String sql, Connection conn) throws Exception {
+ // Check and ignore empty statements
+ if ("".equals(sql.trim())) {
+ return;
+ }
+
+ Statement statement = null;
+ try {
+ log.debug("SQL : " + sql);
+
+ boolean ret;
+ int updateCount = 0, updateCountTotal = 0;
+ statement = conn.createStatement();
+ ret = statement.execute(sql);
+ updateCount = statement.getUpdateCount();
+ do {
+ if (!ret) {
+ if (updateCount != -1) {
+ updateCountTotal += updateCount;
+ }
+ }
+ ret = statement.getMoreResults();
+ if (ret) {
+ updateCount = statement.getUpdateCount();
+ }
+ } while (ret);
+
+ log.debug(sql + " : " + updateCountTotal + " rows affected");
+
+ SQLWarning warning = conn.getWarnings();
+ while (warning != null) {
+ log.info(warning + " sql warning");
+ warning = warning.getNextWarning();
+ }
+ conn.clearWarnings();
+ } catch (SQLException e) {
+ if (e.getSQLState().equals("X0Y32")) {
+ // eliminating the table already exception for the derby
+ // database
+ log.info("Table Already Exists", e);
+ } else {
+ throw new Exception("Error occurred while executing : " + sql, e);
+ }
+ } finally {
+ if (statement != null) {
+ try {
+ statement.close();
+ } catch (SQLException e) {
+ log.error("Error occurred while closing result set.", e);
+ }
+ }
+ }
+ }
+
+ /**
+ * computes relatational database type using database name
+ *
+ * @return DatabaseType
+ * @throws Exception
+ *
+ */
+ public static DatabaseType getDatabaseType(Connection conn) throws Exception {
+ try {
+ if (conn != null && (!conn.isClosed())) {
+ DatabaseMetaData metaData = conn.getMetaData();
+ String databaseProductName = metaData.getDatabaseProductName();
+ return checkType(databaseProductName);
+ }
+ } catch (SQLException e) {
+ String msg = "Failed to create Airavata database." + e.getMessage();
+ log.error(msg, e);
+ throw new Exception(msg, e);
+ }
+ return DatabaseType.other;
+ }
+
+ /**
+ * Overloaded method with String input
+ *
+ * @return DatabaseType
+ * @throws Exception
+ *
+ */
+ public static DatabaseType getDatabaseType(String dbUrl) throws Exception {
+ return checkType(dbUrl);
+ }
+
+ private static DatabaseType checkType(String text) throws Exception {
+ try {
+ if (text != null) {
+ for (DatabaseType type : supportedDatabase) {
+ if (text.matches(type.getMatchingPattern()))
+ return type;
+ }
+ }
+ String msg = "Unsupported database: " + text
+ + ". Database will not be created automatically by the Airavata. "
+ + "Please create the database using appropriate database scripts for " + "the database.";
+ throw new Exception(msg);
+
+ } catch (SQLException e) {
+ String msg = "Failed to create Airavatadatabase." + e.getMessage();
+ log.error(msg, e);
+ throw new Exception(msg, e);
+ }
+ }
+
+ /**
+ * Get scripts location which is prefix + "-" + databaseType + ".sql"
+ *
+ * @param prefix
+ * @param databaseType
+ * @return script location
+ */
+ private static String getScriptLocation(String prefix, DatabaseType databaseType) {
+ String scriptName = prefix + "-" + databaseType + ".sql";
+ log.debug("Loading database script from :" + scriptName);
+ return scriptName;
+ }
+
+ private static void createDatabase(String prefix, Connection conn) throws Exception {
+ Statement statement = null;
+ try {
+ conn.setAutoCommit(false);
+ statement = conn.createStatement();
+ executeSQLScript(getScriptLocation(prefix, DatabaseCreator.getDatabaseType(conn)), conn);
+ conn.commit();
+ log.debug("Tables are created successfully.");
+ } catch (SQLException e) {
+ String msg = "Failed to create database tables for Airavata resource store. " + e.getMessage();
+ log.error(msg, e);
+ conn.rollback();
+ throw new Exception(msg, e);
+ } finally {
+ conn.setAutoCommit(true);
+ try {
+ if (statement != null) {
+ statement.close();
+ }
+ } catch (SQLException e) {
+ log.error("Failed to close statement.", e);
+ }
+ }
+ }
+
+ private static void executeSQLScript(String dbscriptName, Connection conn) throws Exception {
+ StringBuffer sql = new StringBuffer();
+ BufferedReader reader = null;
+
+ try {
+ InputStream is = DatabaseCreator.class.getClassLoader().getResourceAsStream(dbscriptName);
+ if(is == null) {
+ logger.info("Script file not found at " + dbscriptName + ". Uses default database script file");
+ DatabaseType databaseType = DatabaseCreator.getDatabaseType(conn);
+ if(databaseType.equals(DatabaseType.derby)){
+ is = DatabaseCreator.class.getClassLoader().getResourceAsStream("experiment-derby.sql");
+ }else if(databaseType.equals(DatabaseType.mysql)){
+ is = DatabaseCreator.class.getClassLoader().getResourceAsStream("experiment-mysql.sql");
+ }
+ }
+ reader = new BufferedReader(new InputStreamReader(is));
+ String line;
+ while ((line = reader.readLine()) != null) {
+ line = line.trim();
+ if (line.startsWith("//")) {
+ continue;
+ }
+ if (line.startsWith("--")) {
+ continue;
+ }
+ StringTokenizer st = new StringTokenizer(line);
+ if (st.hasMoreTokens()) {
+ String token = st.nextToken();
+ if ("REM".equalsIgnoreCase(token)) {
+ continue;
+ }
+ }
+ sql.append(" ").append(line);
+
+ // SQL defines "--" as a comment to EOL
+ // and in Oracle it may contain a hint
+ // so we cannot just remove it, instead we must end it
+ if (line.indexOf("--") >= 0) {
+ sql.append("\n");
+ }
+ if ((checkStringBufferEndsWith(sql, delimiter))) {
+ executeSQL(sql.substring(0, sql.length() - delimiter.length()), conn);
+ sql.replace(0, sql.length(), "");
+ }
+ }
+ // Catch any statements not followed by ;
+ if (sql.length() > 0) {
+ executeSQL(sql.toString(), conn);
+ }
+ } catch (IOException e) {
+ log.error("Error occurred while executing SQL script for creating Airavata database", e);
+ throw new Exception("Error occurred while executing SQL script for creating Airavata database", e);
+
+ } finally {
+ if (reader != null) {
+ reader.close();
+ }
+ }
+ }
+
+ /**
+ * Checks that a string buffer ends up with a given string. It may sound trivial with the existing JDK API but the
+ * various implementation among JDKs can make those methods extremely resource intensive and perform poorly due to
+ * massive memory allocation and copying. See
+ *
+ * @param buffer
+ * the buffer to perform the check on
+ * @param suffix
+ * the suffix
+ * @return <code>true</code> if the character sequence represented by the argument is a suffix of the character
+ * sequence represented by the StringBuffer object; <code>false</code> otherwise. Note that the result will
+ * be <code>true</code> if the argument is the empty string.
+ */
+ public static boolean checkStringBufferEndsWith(StringBuffer buffer, String suffix) {
+ if (suffix.length() > buffer.length()) {
+ return false;
+ }
+ // this loop is done on purpose to avoid memory allocation performance
+ // problems on various JDKs
+ // StringBuffer.lastIndexOf() was introduced in jdk 1.4 and
+ // implementation is ok though does allocation/copying
+ // StringBuffer.toString().endsWith() does massive memory
+ // allocation/copying on JDK 1.5
+ // See http://issues.apache.org/bugzilla/show_bug.cgi?id=37169
+ int endIndex = suffix.length() - 1;
+ int bufferIndex = buffer.length() - 1;
+ while (endIndex >= 0) {
+ if (buffer.charAt(bufferIndex) != suffix.charAt(endIndex)) {
+ return false;
+ }
+ bufferIndex--;
+ endIndex--;
+ }
+ return true;
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/JdbcStorage.java
----------------------------------------------------------------------
diff --git a/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/JdbcStorage.java b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/JdbcStorage.java
new file mode 100644
index 0000000..18b16cb
--- /dev/null
+++ b/modules/credential-store/credential-store-service/src/main/java/org/apache/airavata/credential/store/store/impl/util/JdbcStorage.java
@@ -0,0 +1,175 @@
+/*
+ *
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing,
+ * software distributed under the License is distributed on an
+ * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ * KIND, either express or implied. See the License for the
+ * specific language governing permissions and limitations
+ * under the License.
+ *
+*/
+package org.apache.airavata.credential.store.store.impl.util;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.*;
+
+public class JdbcStorage {
+ private static Logger log = LoggerFactory.getLogger(JdbcStorage.class);
+
+ private ConnectionPool connectionPool;
+
+ public JdbcStorage(String jdbcUrl, String jdbcDriver) {
+ // default init connection and max connection
+ this(3, 50, jdbcUrl, jdbcDriver, true);
+ }
+
+ public JdbcStorage(int initCon, int maxCon, String url, String driver, boolean enableTransactions) {
+ try {
+ if (enableTransactions) {
+ connectionPool = new ConnectionPool(driver, url, initCon, maxCon, true, false,
+ Connection.TRANSACTION_SERIALIZABLE);
+ } else {
+ connectionPool = new ConnectionPool(driver, url, initCon, maxCon, true);
+ }
+ } catch (Exception e) {
+ throw new RuntimeException("Failed to create database connection pool.", e);
+ }
+ }
+
+ /**
+ * Check if this connection pool is auto commit or not
+ *
+ * @return
+ */
+ public boolean isAutoCommit() {
+ return connectionPool.isAutoCommit();
+ }
+
+ public void commit(Connection conn) {
+ try {
+ if (conn != null && !conn.getAutoCommit()) {
+ conn.commit();
+ }
+ } catch (SQLException sqle) {
+ log.error("Cannot commit data", sqle);
+ }
+ }
+
+ public void commitAndFree(Connection conn) {
+ commit(conn);
+ closeConnection(conn);
+ }
+
+ public void rollback(Connection conn) {
+ try {
+ if (conn != null && !conn.getAutoCommit()) {
+ conn.rollback();
+ }
+ } catch (SQLException sqle) {
+ log.error("Cannot Rollback data", sqle);
+ }
+ }
+
+ public void rollbackAndFree(Connection conn) {
+ rollback(conn);
+ closeConnection(conn);
+ }
+
+ public Connection connect() {
+
+ Connection conn = null;
+ try {
+ conn = connectionPool.getConnection();
+ } catch (SQLException e) {
+ log.error(e.getMessage(), e);
+ }
+ return conn;
+ }
+
+ /**
+ * This method is provided so that you can have better control over the statement. For example: You can use
+ * stmt.setString to convert quotation mark automatically in an UPDATE statement
+ *
+ * NOTE: Statement is closed after execution
+ */
+ public int executeUpdateAndClose(PreparedStatement stmt) throws SQLException {
+ int rows = 0;
+ try {
+ rows = stmt.executeUpdate();
+ if (rows == 0) {
+ log.info("Problem: 0 rows affected by insert/update/delete statement.");
+ }
+ } finally {
+ stmt.close();
+ }
+ return rows;
+ }
+
+ public int countRow(String tableName, String columnName) throws SQLException {
+ String query = new String("SELECT COUNT(" + columnName + ") FROM " + tableName);
+ int count = -1;
+ Connection conn = null;
+ PreparedStatement stmt = null;
+ try {
+ conn = connectionPool.getConnection();
+ stmt = conn.prepareStatement(query);
+ ResultSet rs = stmt.executeQuery();
+ rs.next();
+ count = rs.getInt(1);
+ commit(conn);
+ } catch (SQLException sql) {
+ rollback(conn);
+ throw sql;
+ } finally {
+ try {
+ if (stmt != null && !stmt.isClosed()) {
+ stmt.close();
+ }
+ } finally {
+ closeConnection(conn);
+ }
+ }
+ return count;
+ }
+
+ public void quietlyClose(Connection conn, Statement... stmts) {
+ if (stmts != null) {
+ for (Statement stmt : stmts) {
+ try {
+ if (stmt != null && !stmt.isClosed()) {
+ stmt.close();
+ }
+ } catch (SQLException sql) {
+ log.error(sql.getMessage(), sql);
+ }
+ }
+ }
+ closeConnection(conn);
+ }
+
+ public void closeConnection(Connection conn) {
+ if (conn != null) {
+ connectionPool.free(conn);
+ }
+ }
+
+ public void closeAllConnections() {
+ if (connectionPool != null)
+ connectionPool.dispose();
+ }
+
+ public void shutdown() throws SQLException {
+ connectionPool.shutdown();
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/CommunityUser.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/CommunityUser.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/CommunityUser.java
deleted file mode 100644
index f0cac9d..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/CommunityUser.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-package org.apache.airavata.registry.core.credential.catalog.model;
-
-import javax.persistence.*;
-
-@Entity
-@Table(name ="COMMUNITY_USER")
-@IdClass(CommunityUser_Pk.class)
-public class CommunityUser {
- private String gatewayId;
- private String communityUserName;
- private String tokenId;
- private String communityUserEmail;
-
- @Id
- @Column(name = "GATEWAY_ID")
- public String getGatewayId() {
- return gatewayId;
- }
-
- public void setGatewayId(String gatewayId) {
- this.gatewayId = gatewayId;
- }
-
- @Id
- @Column(name = "COMMUNITY_USER_NAME")
- public String getCommunityUserName() {
- return communityUserName;
- }
-
- public void setCommunityUserName(String communityUserName) {
- this.communityUserName = communityUserName;
- }
-
- @Id
- @Column(name = "TOKEN_ID")
- public String getTokenId() {
- return tokenId;
- }
-
- public void setTokenId(String tokenId) {
- this.tokenId = tokenId;
- }
-
- @Column(name = "COMMUNITY_USER_EMAIL")
- public String getCommunityUserEmail() {
- return communityUserEmail;
- }
-
- public void setCommunityUserEmail(String communityUserEmail) {
- this.communityUserEmail = communityUserEmail;
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/CommunityUser_Pk.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/CommunityUser_Pk.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/CommunityUser_Pk.java
deleted file mode 100644
index 8b10999..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/CommunityUser_Pk.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-package org.apache.airavata.registry.core.credential.catalog.model;
-
-import java.io.Serializable;
-
-public class CommunityUser_Pk implements Serializable{
- private String gatewayId;
- private String communityUserName;
- private String tokenId;
-
- @Override
- public boolean equals(Object o) {
- return false;
- }
-
- @Override
- public int hashCode() {
- return 1;
- }
-
- public String getGatewayId() {
- return gatewayId;
- }
-
- public void setGatewayId(String gatewayId) {
- this.gatewayId = gatewayId;
- }
-
- public String getCommunityUserName() {
- return communityUserName;
- }
-
- public void setCommunityUserName(String communityUserName) {
- this.communityUserName = communityUserName;
- }
-
- public String getTokenId() {
- return tokenId;
- }
-
- public void setTokenId(String tokenId) {
- this.tokenId = tokenId;
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Configuration.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Configuration.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Configuration.java
deleted file mode 100644
index 281a3a1..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Configuration.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
-*
-* Licensed to the Apache Software Foundation (ASF) under one
-* or more contributor license agreements. See the NOTICE file
-* distributed with this work for additional information
-* regarding copyright ownership. The ASF licenses this file
-* to you under the Apache License, Version 2.0 (the
-* "License"); you may not use this file except in compliance
-* with the License. You may obtain a copy of the License at
-*
-* http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing,
-* software distributed under the License is distributed on an
-* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
-* KIND, either express or implied. See the License for the
-* specific language governing permissions and limitations
-* under the License.
-*
-*/
-package org.apache.airavata.registry.core.credential.catalog.model;
-
-
-import javax.persistence.*;
-import java.io.Serializable;
-
-@Entity
-@Table(name ="CONFIGURATION")
-@IdClass(Configuration_PK.class)
-public class Configuration implements Serializable {
- @Id
- @Column(name = "CONFIG_KEY")
- private String config_key;
-
- @Id
- @Column(name = "CONFIG_VAL")
- private String config_val;
-
- public String getConfig_key() {
- return config_key;
- }
-
- public String getConfig_val() {
- return config_val;
- }
-
- public void setConfig_key(String config_key) {
- this.config_key = config_key;
- }
-
- public void setConfig_val(String config_val) {
- this.config_val = config_val;
- }
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Configuration_PK.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Configuration_PK.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Configuration_PK.java
deleted file mode 100644
index 1a18aea..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Configuration_PK.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
-package org.apache.airavata.registry.core.credential.catalog.model;
-
-import java.io.Serializable;
-
-public class Configuration_PK implements Serializable {
- private String config_key;
- private String config_val;
-
- public Configuration_PK() {
- ;
- }
-
- @Override
- public boolean equals(Object o) {
- return false;
- }
-
- @Override
- public int hashCode() {
- return 1;
- }
-
- public String getConfig_key() {
- return config_key;
- }
-
- public void setConfig_key(String config_key) {
- this.config_key = config_key;
- }
-
- public void setConfig_val(String config_val) {
- this.config_val = config_val;
- }
-
- public String getConfig_val() {
- return config_val;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Credential.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Credential.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Credential.java
deleted file mode 100644
index ed146f7..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Credential.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-package org.apache.airavata.registry.core.credential.catalog.model;
-
-import javax.persistence.*;
-import java.sql.Timestamp;
-
-@Entity
-@Table(name ="CREDENTIAL")
-@IdClass(Credential_PK.class)
-public class Credential {
- private String gatewayId;
- private String tokenId;
- private Byte[] credential;
- private String portalUserId;
- private Timestamp timePersisted;
-
- @Id
- @Column(name = "GATEWAY_ID")
- public String getGatewayId() {
- return gatewayId;
- }
-
- public void setGatewayId(String gatewayId) {
- this.gatewayId = gatewayId;
- }
-
- @Id
- @Column(name = "TOKEN_ID")
- public String getTokenId() {
- return tokenId;
- }
-
- public void setTokenId(String tokenId) {
- this.tokenId = tokenId;
- }
-
- @Lob
- @Column(name = "CREDENTIAL")
- public Byte[] getCredential() {
- return credential;
- }
-
- public void setCredential(Byte[] credential) {
- this.credential = credential;
- }
-
- @Column(name = "PORTAL_USER_ID")
- public String getPortalUserId() {
- return portalUserId;
- }
-
- public void setPortalUserId(String portalUserId) {
- this.portalUserId = portalUserId;
- }
-
- @Column(name = "TIME_PERSISTED")
- public Timestamp getTimePersisted() {
- return timePersisted;
- }
-
- public void setTimePersisted(Timestamp timePersisted) {
- this.timePersisted = timePersisted;
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Credential_PK.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Credential_PK.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Credential_PK.java
deleted file mode 100644
index a9db85f..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/model/Credential_PK.java
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
-*/
-package org.apache.airavata.registry.core.credential.catalog.model;
-
-import java.io.Serializable;
-
-public class Credential_PK implements Serializable{
- private String gatewayId;
- private String tokenId;
-
-
- @Override
- public boolean equals(Object o) {
- return false;
- }
-
- @Override
- public int hashCode() {
- return 1;
- }
-
- public String getGatewayId() {
- return gatewayId;
- }
-
- public void setGatewayId(String gatewayId) {
- this.gatewayId = gatewayId;
- }
-
- public String getTokenId() {
- return tokenId;
- }
-
- public void setTokenId(String tokenId) {
- this.tokenId = tokenId;
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/util/CredentialCatalogJPAUtils.java
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/util/CredentialCatalogJPAUtils.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/util/CredentialCatalogJPAUtils.java
deleted file mode 100644
index 5a509c7..0000000
--- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/credential/catalog/util/CredentialCatalogJPAUtils.java
+++ /dev/null
@@ -1,82 +0,0 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
-package org.apache.airavata.registry.core.credential.catalog.util;
-
-import org.apache.airavata.common.exception.ApplicationSettingsException;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import javax.persistence.*;
-import java.util.HashMap;
-import java.util.Map;
-
-public class CredentialCatalogJPAUtils {
- private final static Logger logger = LoggerFactory.getLogger(CredentialCatalogJPAUtils.class);
-
- private static final String PERSISTENCE_UNIT_NAME = "credentialcatalog_data";
- private static final String CREDCATALOG_JDBC_DRIVER = "credential.store.jdbc.driver";
- private static final String CREDCATALOG_JDBC_URL = "credential.store.jdbc.url";
- private static final String CREDCATALOG_JDBC_USER = "credential.store.jdbc.user";
- private static final String CREDCACATALOG_JDBC_PWD = "credential.store.jdbc.password";
- private static final String CREDCACATALOG_VALIDATION_QUERY = "credential.store.jdbc.validationQuery";
-
- @PersistenceUnit(unitName="credentialcatalog_data")
- protected static EntityManagerFactory factory;
-
- @PersistenceContext(unitName="credentialcatalog_data")
- private static EntityManager credCatEntityManager;
-
- public static EntityManager getEntityManager() throws ApplicationSettingsException {
- if (factory == null) {
- String connectionProperties = "DriverClassName=" + readServerProperties(CREDCATALOG_JDBC_DRIVER) + "," +
- "Url=" + readServerProperties(CREDCATALOG_JDBC_URL) + "?autoReconnect=true," +
- "Username=" + readServerProperties(CREDCATALOG_JDBC_USER) + "," +
- "Password=" + readServerProperties(CREDCACATALOG_JDBC_PWD) +
- ",validationQuery=" + readServerProperties(CREDCACATALOG_VALIDATION_QUERY);
- System.out.println(connectionProperties);
- Map<String, String> properties = new HashMap<String, String>();
- properties.put("openjpa.ConnectionDriverName", "org.apache.commons.dbcp.BasicDataSource");
- properties.put("openjpa.ConnectionProperties", connectionProperties);
- properties.put("openjpa.DynamicEnhancementAgent", "true");
- properties.put("openjpa.RuntimeUnenhancedClasses", "unsupported");
- properties.put("openjpa.RemoteCommitProvider","sjvm");
- properties.put("openjpa.Log","DefaultLevel=INFO, Runtime=INFO, Tool=INFO, SQL=INFO");
- properties.put("openjpa.jdbc.SynchronizeMappings", "buildSchema(ForeignKeys=true)");
- properties.put("openjpa.jdbc.QuerySQLCache", "false");
- properties.put("openjpa.ConnectionFactoryProperties", "PrettyPrint=true, PrettyPrintLineLength=72," +
- " PrintParameters=true, MaxActive=10, MaxIdle=5, MinIdle=2, MaxWait=31536000, autoReconnect=true");
- factory = Persistence.createEntityManagerFactory(PERSISTENCE_UNIT_NAME, properties);
- }
- credCatEntityManager = factory.createEntityManager();
- return credCatEntityManager;
- }
-
- private static String readServerProperties (String propertyName) throws ApplicationSettingsException {
- try {
- return ServerSettings.getSetting(propertyName);
- } catch (ApplicationSettingsException e) {
- logger.error("Unable to read airavata-server.properties...", e);
- throw new ApplicationSettingsException("Unable to read airavata-server.properties...");
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/registry/registry-core/src/main/resources/META-INF/persistence.xml
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/resources/META-INF/persistence.xml b/modules/registry/registry-core/src/main/resources/META-INF/persistence.xml
index af23674..4833874 100644
--- a/modules/registry/registry-core/src/main/resources/META-INF/persistence.xml
+++ b/modules/registry/registry-core/src/main/resources/META-INF/persistence.xml
@@ -115,11 +115,4 @@
<class>org.apache.airavata.registry.core.workflow.catalog.model.WorkflowStatus</class>
<exclude-unlisted-classes>true</exclude-unlisted-classes>
</persistence-unit>
- <persistence-unit name="credentialcatalog_data">
- <provider>org.apache.openjpa.persistence.PersistenceProviderImpl</provider>
- <class>org.apache.airavata.registry.core.credential.catalog.model.CommunityUser</class>
- <class>org.apache.airavata.registry.core.credential.catalog.model.Configuration</class>
- <class>org.apache.airavata.registry.core.credential.catalog.model.Credential</class>
- <exclude-unlisted-classes>true</exclude-unlisted-classes>
- </persistence-unit>
</persistence>
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/registry/registry-core/src/main/resources/credstore-derby.sql
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/resources/credstore-derby.sql b/modules/registry/registry-core/src/main/resources/credstore-derby.sql
index bdae2bd..f600f24 100644
--- a/modules/registry/registry-core/src/main/resources/credstore-derby.sql
+++ b/modules/registry/registry-core/src/main/resources/credstore-derby.sql
@@ -1,49 +1,25 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
- CREATE TABLE COMMUNITY_USER
-(
- GATEWAY_ID VARCHAR(256) NOT NULL,
- COMMUNITY_USER_NAME VARCHAR(256) NOT NULL,
- TOKEN_ID VARCHAR(256) NOT NULL,
- COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL,
- PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID)
+CREATE TABLE COMMUNITY_USER (
+ GATEWAY_ID VARCHAR(256) NOT NULL,
+ COMMUNITY_USER_NAME VARCHAR(256) NOT NULL,
+ TOKEN_ID VARCHAR(256) NOT NULL,
+ COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL,
+ PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID)
);
-CREATE TABLE CREDENTIALS
-(
- GATEWAY_ID VARCHAR(256) NOT NULL,
- TOKEN_ID VARCHAR(256) NOT NULL,
- CREDENTIAL BLOB NOT NULL,
- PORTAL_USER_ID VARCHAR(256) NOT NULL,
- TIME_PERSISTED TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
- PRIMARY KEY (GATEWAY_ID, TOKEN_ID)
+CREATE TABLE CREDENTIALS (
+ GATEWAY_ID VARCHAR(256) NOT NULL,
+ TOKEN_ID VARCHAR(256) NOT NULL,
+ CREDENTIAL BLOB NOT NULL,
+ PORTAL_USER_ID VARCHAR(256) NOT NULL,
+ TIME_PERSISTED TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+ PRIMARY KEY (GATEWAY_ID, TOKEN_ID)
);
-CREATE TABLE CONFIGURATION
-(
- CONFIG_KEY VARCHAR(255),
- CONFIG_VAL VARCHAR(255),
- PRIMARY KEY(CONFIG_KEY, CONFIG_VAL)
+CREATE TABLE CONFIGURATION (
+ CONFIG_KEY VARCHAR(255),
+ CONFIG_VAL VARCHAR(255),
+ PRIMARY KEY (CONFIG_KEY, CONFIG_VAL)
);
-INSERT INTO CONFIGURATION (CONFIG_KEY, CONFIG_VAL) VALUES('app_catalog_version', '0.16');
+INSERT INTO CONFIGURATION (CONFIG_KEY, CONFIG_VAL) VALUES ('credential_store_version', '0.16');
http://git-wip-us.apache.org/repos/asf/airavata/blob/a5156a92/modules/registry/registry-core/src/main/resources/credstore-mysql.sql
----------------------------------------------------------------------
diff --git a/modules/registry/registry-core/src/main/resources/credstore-mysql.sql b/modules/registry/registry-core/src/main/resources/credstore-mysql.sql
index 3d924ce..f600f24 100644
--- a/modules/registry/registry-core/src/main/resources/credstore-mysql.sql
+++ b/modules/registry/registry-core/src/main/resources/credstore-mysql.sql
@@ -1,49 +1,25 @@
-/*
- *
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing,
- * software distributed under the License is distributed on an
- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
- * KIND, either express or implied. See the License for the
- * specific language governing permissions and limitations
- * under the License.
- *
- */
-
- CREATE TABLE COMMUNITY_USER
-(
- GATEWAY_ID VARCHAR(256) NOT NULL,
- COMMUNITY_USER_NAME VARCHAR(256) NOT NULL,
- TOKEN_ID VARCHAR(256) NOT NULL,
- COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL,
- PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID)
+CREATE TABLE COMMUNITY_USER (
+ GATEWAY_ID VARCHAR(256) NOT NULL,
+ COMMUNITY_USER_NAME VARCHAR(256) NOT NULL,
+ TOKEN_ID VARCHAR(256) NOT NULL,
+ COMMUNITY_USER_EMAIL VARCHAR(256) NOT NULL,
+ PRIMARY KEY (GATEWAY_ID, COMMUNITY_USER_NAME, TOKEN_ID)
);
-CREATE TABLE CREDENTIALS
-(
- GATEWAY_ID VARCHAR(256) NOT NULL,
- TOKEN_ID VARCHAR(256) NOT NULL,
- CREDENTIAL BLOB NOT NULL,
- PORTAL_USER_ID VARCHAR(256) NOT NULL,
- TIME_PERSISTED TIMESTAMP DEFAULT NOW() ON UPDATE NOW(),
- PRIMARY KEY (GATEWAY_ID, TOKEN_ID)
+CREATE TABLE CREDENTIALS (
+ GATEWAY_ID VARCHAR(256) NOT NULL,
+ TOKEN_ID VARCHAR(256) NOT NULL,
+ CREDENTIAL BLOB NOT NULL,
+ PORTAL_USER_ID VARCHAR(256) NOT NULL,
+ TIME_PERSISTED TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
+ PRIMARY KEY (GATEWAY_ID, TOKEN_ID)
);
-CREATE TABLE CONFIGURATION
-(
- CONFIG_KEY VARCHAR(255),
- CONFIG_VAL VARCHAR(255),
- PRIMARY KEY(CONFIG_KEY, CONFIG_VAL)
+CREATE TABLE CONFIGURATION (
+ CONFIG_KEY VARCHAR(255),
+ CONFIG_VAL VARCHAR(255),
+ PRIMARY KEY (CONFIG_KEY, CONFIG_VAL)
);
-INSERT INTO CONFIGURATION (CONFIG_KEY, CONFIG_VAL) VALUES('app_catalog_version', '0.16');
+INSERT INTO CONFIGURATION (CONFIG_KEY, CONFIG_VAL) VALUES ('credential_store_version', '0.16');