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From shame...@apache.org
Subject [7/7] airavata git commit: Removed gsi related code
Date Tue, 16 Jun 2015 19:37:46 GMT
Removed gsi related code


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/d9b2df03
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/d9b2df03
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/d9b2df03

Branch: refs/heads/master
Commit: d9b2df0336199e7641e1af5da5e0d2b4908bf4ac
Parents: 9226453
Author: Shameera Rathanyaka <shameerainfo@gmail.com>
Authored: Tue Jun 16 15:37:32 2015 -0400
Committer: Shameera Rathanyaka <shameerainfo@gmail.com>
Committed: Tue Jun 16 15:37:32 2015 -0400

----------------------------------------------------------------------
 .../core/monitor/GfacInternalStatusUpdator.java | 103 ---
 .../airavata/gfac/core/monitor/JobMonitor.java  |  39 +
 .../airavata/gfac/gsi/ssh/GSSContextX509.java   | 210 -----
 .../gfac/gsi/ssh/api/CommandExecutor.java       | 295 -------
 .../gsi/ssh/api/job/LSFJobConfiguration.java    | 124 ---
 .../gfac/gsi/ssh/api/job/LSFOutputParser.java   | 132 ----
 .../gsi/ssh/api/job/PBSJobConfiguration.java    | 121 ---
 .../gfac/gsi/ssh/api/job/PBSOutputParser.java   | 218 ------
 .../gsi/ssh/api/job/SlurmJobConfiguration.java  | 119 ---
 .../gfac/gsi/ssh/api/job/SlurmOutputParser.java | 192 -----
 .../gsi/ssh/api/job/UGEJobConfiguration.java    | 121 ---
 .../gfac/gsi/ssh/api/job/UGEOutputParser.java   | 190 -----
 .../gfac/gsi/ssh/config/ConfigReader.java       |  76 --
 .../ssh/impl/DefaultJobSubmissionListener.java  |  43 -
 .../gsi/ssh/impl/GSISSHAbstractCluster.java     | 777 -------------------
 .../gfac/gsi/ssh/impl/HPCRemoteCluster.java     | 333 --------
 .../airavata/gfac/gsi/ssh/impl/SSHUserInfo.java |  63 --
 .../gfac/gsi/ssh/impl/StandardOutReader.java    |  79 --
 .../gfac/gsi/ssh/impl/SystemCommandOutput.java  |  78 --
 .../DefaultPasswordAuthenticationInfo.java      |  48 --
 .../DefaultPublicKeyAuthentication.java         |  68 --
 .../DefaultPublicKeyFileAuthentication.java     |  70 --
 .../MyProxyAuthenticationInfo.java              | 108 ---
 .../gfac/gsi/ssh/jsch/ExtendedJSch.java         |  64 --
 .../gsi/ssh/listener/JobSubmissionListener.java |  81 --
 .../airavata/gfac/gsi/ssh/util/CommonUtils.java |  83 --
 .../ssh/util/SSHAPIUIKeyboardInteractive.java   |  73 --
 .../gsi/ssh/util/SSHKeyPasswordHandler.java     |  68 --
 .../airavata/gfac/gsi/ssh/util/SSHUtils.java    | 760 ------------------
 .../handler/GSISSHDirectorySetupHandler.java    | 118 ---
 .../gfac/gsissh/handler/GSISSHInputHandler.java | 213 -----
 .../gsissh/handler/GSISSHOutputHandler.java     | 323 --------
 .../gsissh/handler/NewGSISSHOutputHandler.java  |  83 --
 .../gsissh/provider/impl/GSISSHProvider.java    | 344 --------
 .../gsissh/security/GSISecurityContext.java     |  67 --
 .../security/TokenizedMyProxyAuthInfo.java      | 304 --------
 .../gfac/gsissh/util/GFACGSISSHUtils.java       | 367 ---------
 .../org/apache/airavata/gfac/impl/Factory.java  |  53 ++
 .../airavata/gfac/impl/HPCRemoteCluster.java    | 332 ++++++++
 .../org/apache/airavata/gfac/impl/SSHUtils.java |   1 -
 .../airavata/gfac/impl/StandardOutReader.java   |  79 ++
 .../gfac/impl/job/LSFJobConfiguration.java      | 123 +++
 .../airavata/gfac/impl/job/LSFOutputParser.java | 133 ++++
 .../gfac/impl/job/PBSJobConfiguration.java      | 121 +++
 .../airavata/gfac/impl/job/PBSOutputParser.java | 219 ++++++
 .../gfac/impl/job/SlurmJobConfiguration.java    | 119 +++
 .../gfac/impl/job/SlurmOutputParser.java        | 193 +++++
 .../gfac/impl/job/UGEJobConfiguration.java      | 121 +++
 .../airavata/gfac/impl/job/UGEOutputParser.java | 191 +++++
 .../airavata/gfac/monitor/HPCMonitorID.java     | 107 ---
 .../airavata/gfac/monitor/HostMonitorData.java  |  88 ---
 .../airavata/gfac/monitor/UserMonitorData.java  |  76 --
 .../command/ExperimentCancelRequest.java        |  38 -
 .../gfac/monitor/command/TaskCancelRequest.java |  52 --
 .../monitor/core/AiravataAbstractMonitor.java   |  37 -
 .../gfac/monitor/core/MessageParser.java        |  43 -
 .../airavata/gfac/monitor/core/Monitor.java     |  30 -
 .../airavata/gfac/monitor/core/PullMonitor.java |  64 --
 .../airavata/gfac/monitor/core/PushMonitor.java |  60 --
 .../gfac/monitor/email/EmailBasedMonitor.java   |  18 +-
 .../gfac/monitor/email/EmailMonitorFactory.java |  47 --
 .../handlers/GridPullMonitorHandler.java        | 139 ----
 .../handlers/GridPushMonitorHandler.java        | 107 ---
 .../monitor/impl/pull/qstat/HPCPullMonitor.java | 471 -----------
 .../impl/pull/qstat/ResourceConnection.java     | 154 ----
 .../monitor/impl/push/amqp/AMQPMonitor.java     | 280 -------
 .../monitor/impl/push/amqp/BasicConsumer.java   |  87 ---
 .../impl/push/amqp/ComputingActivity.java       |  19 -
 .../impl/push/amqp/JSONMessageParser.java       |  77 --
 .../impl/push/amqp/SimpleJobFinishConsumer.java |  86 --
 .../impl/push/amqp/UnRegisterWorker.java        |  67 --
 .../gfac/monitor/util/AMQPConnectionUtil.java   |  80 --
 .../airavata/gfac/monitor/util/CommonUtils.java | 280 -------
 .../airavata/gfac/monitor/util/X509Helper.java  | 164 ----
 .../gfac/ssh/provider/impl/SSHProvider.java     |   2 +-
 .../airavata/gfac/ssh/util/GFACSSHUtils.java    |   2 +-
 .../impl/DefaultSSHApiTestWithMyProxyAuth.java  |   2 +-
 .../gfac/ssh/impl/VanilaTestWithSSHAuth.java    |   2 +-
 .../apache/airavata/job/AMQPMonitorTest.java    |   2 +-
 79 files changed, 1744 insertions(+), 9177 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/monitor/GfacInternalStatusUpdator.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/monitor/GfacInternalStatusUpdator.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/monitor/GfacInternalStatusUpdator.java
deleted file mode 100644
index 84d72fa..0000000
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/monitor/GfacInternalStatusUpdator.java
+++ /dev/null
@@ -1,103 +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.gfac.core.monitor;
-
-import com.google.common.eventbus.Subscribe;
-import org.apache.airavata.common.utils.AiravataZKUtils;
-import org.apache.airavata.common.utils.Constants;
-import org.apache.airavata.common.utils.ServerSettings;
-import org.apache.airavata.common.utils.listener.AbstractActivityListener;
-import org.apache.airavata.gfac.core.monitor.state.GfacExperimentStateChangeRequest;
-import org.apache.airavata.gfac.core.states.GfacExperimentState;
-import org.apache.curator.framework.CuratorFramework;
-import org.apache.zookeeper.CreateMode;
-import org.apache.zookeeper.WatchedEvent;
-import org.apache.zookeeper.Watcher;
-import org.apache.zookeeper.ZooDefs;
-import org.apache.zookeeper.data.Stat;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-
-public class GfacInternalStatusUpdator implements AbstractActivityListener, Watcher {
-    private final static Logger logger = LoggerFactory.getLogger(GfacInternalStatusUpdator.class);
-
-    private CuratorFramework curatorClient;
-
-    private static Integer mutex = -1;
-
-    @Subscribe
-    public void updateZK(GfacExperimentStateChangeRequest statusChangeRequest) throws Exception {
-        logger.info("Gfac internal state changed to: " + statusChangeRequest.getState().toString());
-        MonitorID monitorID = statusChangeRequest.getMonitorID();
-        String experimentNode = ServerSettings.getSetting(Constants.ZOOKEEPER_GFAC_EXPERIMENT_NODE, "/gfac-experiments");
-        String experimentPath = experimentNode + File.separator + ServerSettings.getSetting(Constants.ZOOKEEPER_GFAC_SERVER_NAME)
-                + File.separator + statusChangeRequest.getMonitorID().getExperimentID();
-        Stat exists = null;
-        if(!(GfacExperimentState.COMPLETED.equals(statusChangeRequest.getState()) || GfacExperimentState.FAILED.equals(statusChangeRequest.getState()))) {
-            exists = curatorClient.checkExists().forPath(experimentPath);
-            if (exists == null) {
-                logger.error("ZK path: " + experimentPath + " does not exists !!");
-                return;
-            }
-            Stat state = curatorClient.checkExists().forPath(experimentPath + File.separator + AiravataZKUtils.ZK_EXPERIMENT_STATE_NODE);
-            if (state == null) {
-                // state znode has to be created
-                curatorClient.create().withMode(CreateMode.PERSISTENT).withACL(ZooDefs.Ids.OPEN_ACL_UNSAFE).
-                        forPath(experimentPath + File.separator + AiravataZKUtils.ZK_EXPERIMENT_STATE_NODE,
-                                String.valueOf(statusChangeRequest.getState().getValue()).getBytes());
-            } else {
-                curatorClient.setData().withVersion(state.getVersion()).forPath(experimentPath + File.separator + AiravataZKUtils.ZK_EXPERIMENT_STATE_NODE,
-                        String.valueOf(statusChangeRequest.getState().getValue()).getBytes());
-            }
-        }
-        switch (statusChangeRequest.getState()) {
-            case COMPLETED:
-                logger.info("Experiment Completed, So removing the ZK entry for the experiment" + monitorID.getExperimentID());
-                logger.info("Zookeeper experiment Path: " + experimentPath);
-                break;
-            case FAILED:
-                logger.info("Experiment Failed, So removing the ZK entry for the experiment" + monitorID.getExperimentID());
-                logger.info("Zookeeper experiment Path: " + experimentPath);
-                break;
-            default:
-        }
-    }
-
-    public void setup(Object... configurations) {
-        for (Object configuration : configurations) {
-            if (configuration instanceof CuratorFramework) {
-                this.curatorClient = (CuratorFramework) configuration;
-            }
-        }
-    }
-
-    public void process(WatchedEvent watchedEvent) {
-        logger.info(watchedEvent.getPath());
-        synchronized (mutex) {
-            Event.KeeperState state = watchedEvent.getState();
-            if (state == Event.KeeperState.SyncConnected) {
-                mutex.notify();
-            }
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/monitor/JobMonitor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/monitor/JobMonitor.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/monitor/JobMonitor.java
new file mode 100644
index 0000000..64a9838
--- /dev/null
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/monitor/JobMonitor.java
@@ -0,0 +1,39 @@
+/*
+ *
+ * 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.gfac.core.monitor;
+
+import org.apache.airavata.gfac.core.context.ProcessContext;
+
+public interface JobMonitor {
+
+	/**
+	 * Start monitor jobId on remote computer resource.
+	 * @param jobId
+	 * @param processContext
+	 */
+	public void monitor(String jobId, ProcessContext processContext);
+
+	/**
+	 * Stop monitoring for given jobId
+	 * @param jobId
+	 */
+	public void stopMonitor(String jobId);
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java
deleted file mode 100644
index a6eea6f..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java
+++ /dev/null
@@ -1,210 +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.gfac.gsi.ssh;
-
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.net.InetAddress;
-import java.net.UnknownHostException;
-
-import org.globus.common.CoGProperties;
-import org.globus.gsi.gssapi.auth.HostAuthorization;
-import org.gridforum.jgss.ExtendedGSSCredential;
-import org.gridforum.jgss.ExtendedGSSManager;
-import org.ietf.jgss.GSSContext;
-import org.ietf.jgss.GSSCredential;
-import org.ietf.jgss.GSSException;
-import org.ietf.jgss.GSSName;
-import org.ietf.jgss.MessageProp;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.jcraft.jsch.JSchException;
-
-/**
- * This class is based on GSSContextKrb5; it substitutes the globus
- * ExtendedGSSManager and uses the SecurityUtils method to get the credential if
- * one is not passed in from memory.
- *
- */
-public class GSSContextX509 implements com.jcraft.jsch.GSSContext {
-
-    private GSSContext context = null;
-    private GSSCredential credential;
-    private static final Logger logger = LoggerFactory.getLogger(GSSContextX509.class);
-
-    public void create(String user, String host) throws JSchException {
-        try {
-//			ExtendedGSSManager manager = (ExtendedGSSManager) ExtendedGSSManager.getInstance();
-
-            if (credential == null) {
-                try {
-                    credential = getCredential();
-                } catch (SecurityException t) {
-                    System.out.printf("Could not get proxy: %s: %s\n", t.getClass().getSimpleName(), t.getMessage());
-                    throw new JSchException(t.toString());
-                }
-            }
-
-            String cname = host;
-
-            try {
-                cname = InetAddress.getByName(cname).getCanonicalHostName();
-            } catch (UnknownHostException e) {
-            }
-
-            GSSName name = HostAuthorization.getInstance().getExpectedName(credential, cname);
-
-//			context = manager.createContext(name, null, credential, GSSContext.DEFAULT_LIFETIME);
-//
-//			// RFC4462 3.4. GSS-API Session
-//			//
-//			// When calling GSS_Init_sec_context(), the client MUST set
-//			// integ_req_flag to "true" to request that per-message integrity
-//			// protection be supported for this context. In addition,
-//			// deleg_req_flag MAY be set to "true" to request access delegation,
-//			// if
-//			// requested by the user.
-//			//
-//			// Since the user authentication process by its nature authenticates
-//			// only the client, the setting of mutual_req_flag is not needed for
-//			// this process. This flag SHOULD be set to "false".
-//
-//			// TODO: OpenSSH's sshd does accept 'false' for mutual_req_flag
-//			// context.requestMutualAuth(false);
-//			context.requestMutualAuth(true);
-//			context.requestConf(true);
-//			context.requestInteg(true); // for MIC
-//			context.requestCredDeleg(true);
-//			context.requestAnonymity(false);
-
-//            context = new BCGSSContextImpl(name, (GlobusGSSCredentialImpl) credential);
-//            context.requestLifetime(GSSCredential.DEFAULT_LIFETIME);
-//            context.requestCredDeleg(true);
-//            context.requestMutualAuth(true);
-//            context.requestReplayDet(true);
-//            context.requestSequenceDet(true);
-//            context.requestConf(false);
-//            context.requestInteg(true);
-//            ((ExtendedGSSContext)context).setOption(GSSConstants.DELEGATION_TYPE, GSIConstants.DELEGATION_TYPE_FULL);
-
-            return;
-        } catch (GSSException ex) {
-            throw new JSchException(ex.toString());
-        }
-    }
-
-    private static GSSCredential getProxy() {
-        return getProxy(null, GSSCredential.DEFAULT_LIFETIME);
-    }
-
-    /**
-     * @param x509_USER_PROXY
-     *            path to the proxy.
-     * @param credentialLifetime
-     *            in seconds.
-     * @return valid credential.
-     *             if proxy task throws exception (or if proxy cannot be found).
-     */
-    private static GSSCredential getProxy(String x509_USER_PROXY, int credentialLifetime) throws SecurityException {
-        if (x509_USER_PROXY == null)
-            x509_USER_PROXY = System.getProperty("x509.user.proxy");
-
-//		if (x509_USER_PROXY == null) {
-//			SystemUtils.envToProperties();
-//			x509_USER_PROXY = System.getProperty("x509.user.proxy");
-//		}
-
-        if (x509_USER_PROXY == null || "".equals(x509_USER_PROXY))
-            x509_USER_PROXY = CoGProperties.getDefault().getProxyFile();
-
-        if (x509_USER_PROXY == null)
-            throw new SecurityException("could not get credential; no location defined");
-
-        ExtendedGSSManager manager = (ExtendedGSSManager) ExtendedGSSManager.getInstance();
-
-        // file...load file into a buffer
-        try {
-            File f = new File(x509_USER_PROXY);
-            byte[] data = new byte[(int) f.length()];
-            FileInputStream in = new FileInputStream(f);
-            // read in the credential data
-            in.read(data);
-            in.close();
-            return manager.createCredential(data, ExtendedGSSCredential.IMPEXP_OPAQUE, credentialLifetime, null, // use
-                    // default
-                    // mechanism
-                    // -
-                    // GSI
-                    GSSCredential.INITIATE_AND_ACCEPT);
-        } catch (Throwable t) {
-            throw new SecurityException("could not get credential from " + x509_USER_PROXY, t);
-        }
-    }
-
-    public boolean isEstablished() {
-        // this must check to see if the call returned GSS_S_COMPLETE
-        if (context != null){
-            return context.isEstablished();
-        }
-        return false;
-    }
-
-    public byte[] init(byte[] token, int s, int l) throws JSchException {
-        try {
-            if (context != null){
-                return context.initSecContext(token, s, l);
-            }else {
-                throw new JSchException("Context is null..");
-            }
-        } catch (GSSException ex) {
-            throw new JSchException(ex.toString());
-        }
-    }
-
-    public byte[] getMIC(byte[] message, int s, int l) {
-        try {
-            MessageProp prop = new MessageProp(0, false);
-            return context.getMIC(message, s, l, prop);
-        } catch (GSSException ex) {
-            logger.error(ex.getMessage(), ex);
-            return null;
-        }
-    }
-
-    public void dispose() {
-        try {
-            context.dispose();
-        } catch (GSSException ex) {
-        }
-    }
-
-    public void setCredential(GSSCredential credential) {
-        this.credential = credential;
-    }
-
-    public GSSCredential getCredential() {
-        return credential;
-    }
-}
-

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
deleted file mode 100644
index bf306ef..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
+++ /dev/null
@@ -1,295 +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.gfac.gsi.ssh.api;
-
-import com.jcraft.jsch.Channel;
-import com.jcraft.jsch.ChannelExec;
-import com.jcraft.jsch.ExtendedSession;
-import com.jcraft.jsch.GSISSHIdentityFile;
-import com.jcraft.jsch.GSISSHIdentityRepository;
-import com.jcraft.jsch.Identity;
-import com.jcraft.jsch.JSch;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.Session;
-import org.apache.airavata.gfac.core.SSHApiException;
-import org.apache.airavata.gfac.core.authentication.AuthenticationInfo;
-import org.apache.airavata.gfac.core.authentication.GSIAuthenticationInfo;
-import org.apache.airavata.gfac.core.authentication.SSHKeyAuthentication;
-import org.apache.airavata.gfac.core.authentication.SSHPublicKeyAuthentication;
-import org.apache.airavata.gfac.core.authentication.SSHPublicKeyFileAuthentication;
-import org.apache.airavata.gfac.core.cluster.CommandInfo;
-import org.apache.airavata.gfac.core.cluster.CommandOutput;
-import org.apache.airavata.gfac.core.authentication.SSHPasswordAuthentication;
-import org.apache.airavata.gfac.core.cluster.ServerInfo;
-import org.apache.airavata.gfac.gsi.ssh.config.ConfigReader;
-import org.apache.airavata.gfac.gsi.ssh.jsch.ExtendedJSch;
-import org.apache.airavata.gfac.gsi.ssh.util.SSHAPIUIKeyboardInteractive;
-import org.apache.airavata.gfac.gsi.ssh.util.SSHKeyPasswordHandler;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * This is a generic class which take care of command execution
- * in a shell, this is used through out the other places of the API.
- */
-public class CommandExecutor {
-    static {
-        JSch.setConfig("gssapi-with-mic.x509", "org.apache.airavata.gfac.ssh.GSSContextX509");
-        JSch.setConfig("userauth.gssapi-with-mic", "com.jcraft.jsch.UserAuthGSSAPIWithMICGSSCredentials");
-        JSch jSch = new JSch();
-    }
-
-    private static final Logger log = LoggerFactory.getLogger(CommandExecutor.class);
-    public static final String X509_CERT_DIR = "X509_CERT_DIR";
-
-    /**
-     * This will execute the given command with given session and session is not closed at the end.
-     *
-     * @param commandInfo
-     * @param session
-     * @param commandOutput
-     * @throws SSHApiException
-     */
-    public static Session executeCommand(CommandInfo commandInfo, Session session,
-                                         CommandOutput commandOutput) throws SSHApiException {
-
-        String command = commandInfo.getCommand();
-
-        Channel channel = null;
-        try {
-            if (!session.isConnected()) {
-                session.connect();
-            }
-            channel = session.openChannel("exec");
-            ((ChannelExec) channel).setCommand(command);
-        } catch (JSchException e) {
-//            session.disconnect();
-
-            throw new SSHApiException("Unable to execute command - ", e);
-        }
-
-        channel.setInputStream(null);
-        ((ChannelExec) channel).setErrStream(commandOutput.getStandardError());
-        try {
-            channel.connect();
-        } catch (JSchException e) {
-
-            channel.disconnect();
-//            session.disconnect();
-            throw new SSHApiException("Unable to retrieve command output. Command - " + command, e);
-        }
-
-
-        commandOutput.onOutput(channel);
-        //Only disconnecting the channel, session can be reused
-        channel.disconnect();
-        return session;
-    }
-
-    /**
-     * This will not reuse any session, it will create the session and close it at the end
-     *
-     * @param commandInfo        Encapsulated information about command. E.g :- executable name
-     *                           parameters etc ...
-     * @param serverInfo         The SSHing server information.
-     * @param authenticationInfo Security data needs to be communicated with remote server.
-     * @param commandOutput      The output of the command.
-     * @param configReader       configuration required for ssh/gshissh connection
-     * @throws SSHApiException   throw exception when error occurs
-     */
-    public static void executeCommand(CommandInfo commandInfo, ServerInfo serverInfo,
-                                      AuthenticationInfo authenticationInfo,
-                                      CommandOutput commandOutput, ConfigReader configReader) throws SSHApiException {
-
-        if (authenticationInfo instanceof GSIAuthenticationInfo) {
-            System.setProperty(X509_CERT_DIR, (String) ((GSIAuthenticationInfo)authenticationInfo).getProperties().
-                    get("X509_CERT_DIR"));
-        }
-
-
-        JSch jsch = new ExtendedJSch();
-
-        log.debug("Connecting to server - " + serverInfo.getHost() + ":" + serverInfo.getPort() + " with user name - "
-                + serverInfo.getUserName());
-
-        Session session;
-
-        try {
-            session = jsch.getSession(serverInfo.getUserName(), serverInfo.getHost(), serverInfo.getPort());
-        } catch (JSchException e) {
-            throw new SSHApiException("An exception occurred while creating SSH session." +
-                    "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                    " connecting user name - "
-                    + serverInfo.getUserName(), e);
-        }
-
-        java.util.Properties config = configReader.getProperties();
-        session.setConfig(config);
-
-        //=============================================================
-        // Handling vanilla SSH pieces
-        //=============================================================
-        if (authenticationInfo instanceof SSHPasswordAuthentication) {
-            String password = ((SSHPasswordAuthentication) authenticationInfo).
-                    getPassword(serverInfo.getUserName(), serverInfo.getHost());
-
-            session.setUserInfo(new SSHAPIUIKeyboardInteractive(password));
-
-            // TODO figure out why we need to set password to session
-            session.setPassword(password);
-
-        } else if (authenticationInfo instanceof SSHPublicKeyFileAuthentication) {
-            SSHPublicKeyFileAuthentication sshPublicKeyFileAuthentication
-                    = (SSHPublicKeyFileAuthentication)authenticationInfo;
-
-            String privateKeyFile = sshPublicKeyFileAuthentication.
-                    getPrivateKeyFile(serverInfo.getUserName(), serverInfo.getHost());
-
-            logDebug("The private key file for vanilla SSH " + privateKeyFile);
-
-            String publicKeyFile = sshPublicKeyFileAuthentication.
-                    getPrivateKeyFile(serverInfo.getUserName(), serverInfo.getHost());
-
-            logDebug("The public key file for vanilla SSH " + publicKeyFile);
-
-            Identity identityFile;
-
-            try {
-                identityFile = GSISSHIdentityFile.newInstance(privateKeyFile, null, jsch);
-            } catch (JSchException e) {
-                throw new SSHApiException("An exception occurred while initializing keys using files. " +
-                        "(private key and public key)." +
-                        "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                        " connecting user name - "
-                        + serverInfo.getUserName() + " private key file - " + privateKeyFile + ", public key file - " +
-                        publicKeyFile, e);
-            }
-
-            // Add identity to identity repository
-            GSISSHIdentityRepository identityRepository = new GSISSHIdentityRepository(jsch);
-            identityRepository.add(identityFile);
-
-            // Set repository to session
-            session.setIdentityRepository(identityRepository);
-
-            // Set the user info
-            SSHKeyPasswordHandler sshKeyPasswordHandler
-                    = new SSHKeyPasswordHandler((SSHKeyAuthentication)authenticationInfo);
-
-            session.setUserInfo(sshKeyPasswordHandler);
-
-        } else if (authenticationInfo instanceof SSHPublicKeyAuthentication) {
-
-            SSHPublicKeyAuthentication sshPublicKeyAuthentication
-                    = (SSHPublicKeyAuthentication)authenticationInfo;
-
-            Identity identityFile;
-
-            try {
-                String name = serverInfo.getUserName() + "_" + serverInfo.getHost();
-                identityFile = GSISSHIdentityFile.newInstance(name,
-                        sshPublicKeyAuthentication.getPrivateKey(serverInfo.getUserName(), serverInfo.getHost()),
-                        sshPublicKeyAuthentication.getPublicKey(serverInfo.getUserName(), serverInfo.getHost()), jsch);
-            } catch (JSchException e) {
-                throw new SSHApiException("An exception occurred while initializing keys using byte arrays. " +
-                        "(private key and public key)." +
-                        "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                        " connecting user name - "
-                        + serverInfo.getUserName(), e);
-            }
-
-            // Add identity to identity repository
-            GSISSHIdentityRepository identityRepository = new GSISSHIdentityRepository(jsch);
-            identityRepository.add(identityFile);
-
-            // Set repository to session
-            session.setIdentityRepository(identityRepository);
-
-            // Set the user info
-            SSHKeyPasswordHandler sshKeyPasswordHandler
-                    = new SSHKeyPasswordHandler((SSHKeyAuthentication)authenticationInfo);
-
-            session.setUserInfo(sshKeyPasswordHandler);
-
-        }
-
-        // Not a good way, but we dont have any choice
-        if (session instanceof ExtendedSession) {
-            if (authenticationInfo instanceof GSIAuthenticationInfo) {
-                ((ExtendedSession) session).setAuthenticationInfo((GSIAuthenticationInfo)authenticationInfo);
-            }
-        }
-
-        try {
-            session.connect();
-        } catch (JSchException e) {
-            throw new SSHApiException("An exception occurred while connecting to server." +
-                    "Connecting server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                    " connecting user name - "
-                    + serverInfo.getUserName(), e);
-        }
-
-        String command = commandInfo.getCommand();
-
-        Channel channel;
-        try {
-            channel = session.openChannel("exec");
-            ((ChannelExec) channel).setCommand(command);
-        } catch (JSchException e) {
-//            session.disconnect();
-
-            throw new SSHApiException("Unable to execute command - " + command +
-                    " on server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                    " connecting user name - "
-                    + serverInfo.getUserName(), e);
-        }
-
-
-        channel.setInputStream(null);
-        ((ChannelExec) channel).setErrStream(commandOutput.getStandardError());
-
-        try {
-            channel.connect();
-        } catch (JSchException e) {
-
-            channel.disconnect();
-//            session.disconnect();
-
-            throw new SSHApiException("Unable to retrieve command output. Command - " + command +
-                    " on server - " + serverInfo.getHost() + ":" + serverInfo.getPort() +
-                    " connecting user name - "
-                    + serverInfo.getUserName(), e);
-        }
-
-        commandOutput.onOutput(channel);
-
-        channel.disconnect();
-//        session.disconnect();
-    }
-
-    private static void logDebug(String message) {
-        if (log.isDebugEnabled()) {
-            log.debug(message);
-        }
-    }
-
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFJobConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFJobConfiguration.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFJobConfiguration.java
deleted file mode 100644
index 9e2a913..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFJobConfiguration.java
+++ /dev/null
@@ -1,124 +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.gfac.gsi.ssh.api.job;
-
-import org.apache.airavata.gfac.core.AbstractJobManagerConfiguration;
-import org.apache.airavata.gfac.core.JobManagerConfiguration;
-import org.apache.airavata.gfac.core.cluster.OutputParser;
-import org.apache.airavata.gfac.core.cluster.RawCommandInfo;
-import org.apache.commons.io.FilenameUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.File;
-
-public class LSFJobConfiguration implements JobManagerConfiguration {
-    private final static Logger logger = LoggerFactory.getLogger(LSFJobConfiguration.class);
-
-    private String jobDescriptionTemplateName;
-
-    private String scriptExtension;
-
-    private String installedPath;
-
-    private OutputParser parser;
-
-    public LSFJobConfiguration(){
-        // this can be used to construct and use setter methods to set all the params in order
-    }
-    public LSFJobConfiguration(String jobDescriptionTemplateName,
-                                 String scriptExtension,String installedPath,OutputParser parser) {
-        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
-        this.scriptExtension = scriptExtension;
-        this.parser = parser;
-        if (installedPath.endsWith("/") || installedPath.isEmpty()) {
-            this.installedPath = installedPath;
-        } else {
-            this.installedPath = installedPath + "/";
-        }
-    }
-
-    @Override
-    public RawCommandInfo getCancelCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "bkill " + jobID);
-    }
-
-    @Override
-    public String getJobDescriptionTemplateName() {
-        return jobDescriptionTemplateName;
-    }
-
-    @Override
-    public RawCommandInfo getMonitorCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "bjobs " + jobID);
-    }
-
-    @Override
-    public RawCommandInfo getUserBasedMonitorCommand(String userName) {
-        return new RawCommandInfo(this.installedPath + "bjobs -u " + userName);
-    }
-
-    @Override
-    public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
-        return new RawCommandInfo(this.installedPath + "bjobs -J " + jobName);
-    }
-
-    @Override
-    public String getScriptExtension() {
-        return scriptExtension;
-    }
-
-    @Override
-    public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
-        return new RawCommandInfo(this.installedPath + "bsub < " +
-                workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
-    }
-
-    @Override
-    public OutputParser getParser() {
-        return parser;
-    }
-
-    public void setParser(OutputParser parser) {
-        this.parser = parser;
-    }
-
-    @Override
-    public String getInstalledPath() {
-        return installedPath;
-    }
-
-
-    @Override
-    public String getBaseCancelCommand() {
-        return "bkill";
-    }
-
-    @Override
-    public String getBaseMonitorCommand() {
-        return "bjobs";
-    }
-
-    @Override
-    public String getBaseSubmitCommand() {
-        return "bsub";
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFOutputParser.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFOutputParser.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFOutputParser.java
deleted file mode 100644
index 76012d6..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/LSFOutputParser.java
+++ /dev/null
@@ -1,132 +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.gfac.gsi.ssh.api.job;
-
-import org.apache.airavata.gfac.core.JobDescriptor;
-import org.apache.airavata.gfac.core.cluster.JobStatus;
-import org.apache.airavata.gfac.core.cluster.OutputParser;
-import org.apache.airavata.gfac.core.SSHApiException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class LSFOutputParser implements OutputParser {
-    private final static Logger logger = LoggerFactory.getLogger(LSFOutputParser.class);
-
-    @Override
-    public void parseSingleJob(JobDescriptor jobDescriptor, String rawOutput) throws SSHApiException {
-        logger.debug(rawOutput);
-        //todo we need to implement this but we are not using it airavata runtime
-        // if someone is using the gsissh as a tool this will be useful to get a descriptive information about a single job
-    }
-
-    @Override
-    public String parseJobSubmission(String rawOutput) throws SSHApiException {
-        logger.debug(rawOutput);
-        return rawOutput.substring(rawOutput.indexOf("<")+1,rawOutput.indexOf(">"));
-    }
-
-    @Override
-    public JobStatus parseJobStatus(String jobID, String rawOutput) throws SSHApiException {
-        boolean jobFount = false;
-        logger.debug(rawOutput);
-        //todo this is not used anymore
-        return JobStatus.C;
-    }
-
-    @Override
-    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) throws SSHApiException {
-        logger.debug(rawOutput);
-
-        String[]    info = rawOutput.split("\n");
-//        int lastStop = 0;
-        for (String jobID : statusMap.keySet()) {
-            String jobName = jobID.split(",")[1];
-            boolean found = false;
-            for (int i = 0; i < info.length; i++) {
-                if (info[i].contains(jobName.substring(0,8))) {
-                    // now starts processing this line
-                    logger.info(info[i]);
-                    String correctLine = info[i];
-                    String[] columns = correctLine.split(" ");
-                    List<String> columnList = new ArrayList<String>();
-                    for (String s : columns) {
-                        if (!"".equals(s)) {
-                            columnList.add(s);
-                        }
-                    }
-//                    lastStop = i + 1;
-                    try {
-                        statusMap.put(jobID, JobStatus.valueOf(columnList.get(2)));
-                    }catch(IndexOutOfBoundsException e){
-                        statusMap.put(jobID, JobStatus.valueOf("U"));
-                    }
-                    found = true;
-                    break;
-                }
-            }
-            if(!found)
-                logger.error("Couldn't find the status of the Job with JobName: " + jobName + "Job Id: " + jobID.split(",")[0]);
-        }
-    }
-
-    @Override
-    public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
-        String regJobId = "jobId";
-        Pattern pattern = Pattern.compile("(?=(?<" + regJobId + ">\\d+)\\s+\\w+\\s+" + jobName + ")"); // regex - look ahead and match
-        if (rawOutput != null) {
-            Matcher matcher = pattern.matcher(rawOutput);
-            if (matcher.find()) {
-                return matcher.group(regJobId);
-            } else {
-                logger.error("No match is found for JobName");
-                return null;
-            }
-        } else {
-            logger.error("Error: RawOutput shouldn't be null");
-            return null;
-        }
-    }
-
-    public static void main(String[] args) {
-        String test = "Job <2477982> is submitted to queue <short>.";
-        System.out.println(test.substring(test.indexOf("<")+1, test.indexOf(">")));
-        String test1 = "JOBID   USER    STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME\n" +
-                "2636607 lg11w   RUN   long       ghpcc06     c11b02      *069656647 Mar  7 00:58\n" +
-                "2636582 lg11w   RUN   long       ghpcc06     c02b01      2134490944 Mar  7 00:48";
-        Map<String, JobStatus> statusMap = new HashMap<String, JobStatus>();
-        statusMap.put("2477983,2134490944", JobStatus.U);
-        LSFOutputParser lsfOutputParser = new LSFOutputParser();
-        try {
-            lsfOutputParser.parseJobStatuses("cjh", statusMap, test1);
-        } catch (SSHApiException e) {
-            logger.error(e.getMessage(), e);
-        }
-        System.out.println(statusMap.get("2477983,2134490944"));
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSJobConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSJobConfiguration.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSJobConfiguration.java
deleted file mode 100644
index c5be412..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSJobConfiguration.java
+++ /dev/null
@@ -1,121 +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.gfac.gsi.ssh.api.job;
-
-import org.apache.airavata.gfac.core.JobManagerConfiguration;
-import org.apache.airavata.gfac.core.cluster.OutputParser;
-import org.apache.airavata.gfac.core.cluster.RawCommandInfo;
-import org.apache.commons.io.FilenameUtils;
-
-import java.io.File;
-
-public class PBSJobConfiguration implements JobManagerConfiguration {
-
-    private String jobDescriptionTemplateName;
-
-    private String scriptExtension;
-
-    private String installedPath;
-
-    private OutputParser parser;
-
-    public PBSJobConfiguration() {
-        // this can be used to construct and use setter methods to set all the params in order
-    }
-
-    public PBSJobConfiguration(String jobDescriptionTemplateName,
-                               String scriptExtension, String installedPath, OutputParser parser) {
-        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
-        this.scriptExtension = scriptExtension;
-        this.parser = parser;
-        if (installedPath.endsWith("/")) {
-            this.installedPath = installedPath;
-        } else {
-            this.installedPath = installedPath + "/";
-        }
-    }
-
-    public RawCommandInfo getCancelCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "qdel " + jobID);
-    }
-
-    public String getJobDescriptionTemplateName() {
-        return jobDescriptionTemplateName;
-    }
-
-    public void setJobDescriptionTemplateName(String jobDescriptionTemplateName) {
-        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
-    }
-
-    public RawCommandInfo getMonitorCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "qstat -f " + jobID);
-    }
-
-    public String getScriptExtension() {
-        return scriptExtension;
-    }
-
-    public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
-        return new RawCommandInfo(this.installedPath + "qsub " +
-                workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
-    }
-
-    public String getInstalledPath() {
-        return installedPath;
-    }
-
-    public void setInstalledPath(String installedPath) {
-        this.installedPath = installedPath;
-    }
-
-    public OutputParser getParser() {
-        return parser;
-    }
-
-    public void setParser(OutputParser parser) {
-        this.parser = parser;
-    }
-
-    public RawCommandInfo getUserBasedMonitorCommand(String userName) {
-        return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
-    }
-
-    @Override
-    public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
-        // For PBS there is no option to get jobDetails by JobName, so we search with userName
-        return new RawCommandInfo(this.installedPath + "qstat -u " + userName + " -f  | grep \"Job_Name = " + jobName + "\" -B1");
-    }
-
-    @Override
-    public String  getBaseCancelCommand() {
-        return "qdel";
-    }
-
-    @Override
-    public String  getBaseMonitorCommand() {
-        return "qstat";
-    }
-
-    @Override
-    public String getBaseSubmitCommand() {
-        return "qsub ";
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSOutputParser.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSOutputParser.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSOutputParser.java
deleted file mode 100644
index 15e2405..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/PBSOutputParser.java
+++ /dev/null
@@ -1,218 +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.gfac.gsi.ssh.api.job;
-
-import org.apache.airavata.gfac.core.JobDescriptor;
-import org.apache.airavata.gfac.core.cluster.JobStatus;
-import org.apache.airavata.gfac.core.cluster.OutputParser;
-import org.apache.airavata.gfac.core.SSHApiException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class PBSOutputParser implements OutputParser {
-    private static final Logger log = LoggerFactory.getLogger(PBSOutputParser.class);
-
-    public void parseSingleJob(JobDescriptor jobDescriptor, String rawOutput) {
-        log.debug(rawOutput);
-        String[] info = rawOutput.split("\n");
-        String[] line;
-        for (int i = 0; i < info.length; i++) {
-            if (info[i].contains("=")) {
-                line = info[i].split("=", 2);
-            } else {
-                line = info[i].split(":", 2);
-            }
-            if (line.length >= 2) {
-                String header = line[0].trim();
-                log.debug("Header = " + header);
-                String value = line[1].trim();
-                log.debug("value = " + value);
-
-                if (header.equals("Variable_List")) {
-                    while (info[i + 1].startsWith("\t")) {
-                        value += info[i + 1];
-                        i++;
-                    }
-                    value = value.replaceAll("\t", "");
-                    jobDescriptor.setVariableList(value);
-                } else if ("Job Id".equals(header)) {
-                    jobDescriptor.setJobID(value);
-                } else if ("Job_Name".equals(header)) {
-                    jobDescriptor.setJobName(value);
-                } else if ("Account_Name".equals(header)) {
-                    jobDescriptor.setAcountString(value);
-                } else if ("job_state".equals(header)) {
-                    jobDescriptor.setStatus(value);
-                } else if ("Job_Owner".equals(header)) {
-                    jobDescriptor.setOwner(value);
-                } else if ("resources_used.cput".equals(header)) {
-                    jobDescriptor.setUsedCPUTime(value);
-                } else if ("resources_used.mem".equals(header)) {
-                    jobDescriptor.setUsedMemory(value);
-                } else if ("resources_used.walltime".equals(header)) {
-                    jobDescriptor.setEllapsedTime(value);
-                } else if ("job_state".equals(header)) {
-                    jobDescriptor.setStatus(value);
-                } else if ("queue".equals(header))
-                    jobDescriptor.setQueueName(value);
-                else if ("ctime".equals(header)) {
-                    jobDescriptor.setCTime(value);
-                } else if ("qtime".equals(header)) {
-                    jobDescriptor.setQTime(value);
-                } else if ("mtime".equals(header)) {
-                    jobDescriptor.setMTime(value);
-                } else if ("start_time".equals(header)) {
-                    jobDescriptor.setSTime(value);
-                } else if ("comp_time".equals(header)) {
-                    jobDescriptor.setCompTime(value);
-                } else if ("exec_host".equals(header)) {
-                    jobDescriptor.setExecuteNode(value);
-                } else if ("Output_Path".equals(header)) {
-                    if (info[i + 1].contains("=") || info[i + 1].contains(":"))
-                        jobDescriptor.setStandardOutFile(value);
-                    else {
-                        jobDescriptor.setStandardOutFile(value + info[i + 1].trim());
-                        i++;
-                    }
-                } else if ("Error_Path".equals(header)) {
-                    if (info[i + 1].contains("=") || info[i + 1].contains(":"))
-                        jobDescriptor.setStandardErrorFile(value);
-                    else {
-                        String st = info[i + 1].trim();
-                        jobDescriptor.setStandardErrorFile(value + st);
-                        i++;
-                    }
-
-                } else if ("submit_args".equals(header)) {
-                    while (i + 1 < info.length) {
-                        if (info[i + 1].startsWith("\t")) {
-                            value += info[i + 1];
-                            i++;
-                        } else
-                            break;
-                    }
-                    value = value.replaceAll("\t", "");
-                    jobDescriptor.setSubmitArgs(value);
-                }
-            }
-        }
-    }
-
-    public String parseJobSubmission(String rawOutput) {
-        log.debug(rawOutput);
-        return rawOutput;  //In PBS stdout is going to be directly the jobID
-    }
-
-    public JobStatus parseJobStatus(String jobID, String rawOutput) {
-        boolean jobFount = false;
-        log.debug(rawOutput);
-        String[] info = rawOutput.split("\n");
-        String[] line = null;
-        int index = 0;
-        for (String anInfo : info) {
-            index++;
-            if (anInfo.contains("Job Id:")) {
-                if (anInfo.contains(jobID)) {
-                    jobFount = true;
-                    break;
-                }
-            }
-        }
-        if (jobFount) {
-            for (int i=index;i<info.length;i++) {
-                String anInfo = info[i];
-                if (anInfo.contains("=")) {
-                    line = anInfo.split("=", 2);
-                    if (line.length != 0) {
-                        if (line[0].contains("job_state")) {
-                            return JobStatus.valueOf(line[1].replaceAll(" ", ""));
-                        }
-                    }
-                }
-            }
-        }
-        return null;
-    }
-
-    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) {
-        log.debug(rawOutput);
-        String[]    info = rawOutput.split("\n");
-//        int lastStop = 0;
-        for (String jobID : statusMap.keySet()) {
-            String jobName = jobID.split(",")[1];
-            boolean found = false;
-            for (int i = 0; i < info.length; i++) {
-                if (info[i].contains(jobName.substring(0,8))) {
-                    // now starts processing this line
-                    log.info(info[i]);
-                    String correctLine = info[i];
-                    String[] columns = correctLine.split(" ");
-                    List<String> columnList = new ArrayList<String>();
-                    for (String s : columns) {
-                        if (!"".equals(s)) {
-                            columnList.add(s);
-                        }
-                    }
-//                    lastStop = i + 1;
-                    try {
-                        statusMap.put(jobID, JobStatus.valueOf(columnList.get(9)));
-                    }catch(IndexOutOfBoundsException e){
-                        statusMap.put(jobID, JobStatus.valueOf("U"));
-                    }
-                    found = true;
-                    break;
-                }
-            }
-            if(!found)
-            log.error("Couldn't find the status of the Job with JobName: " + jobName + "Job Id: " + jobID.split(",")[0]);
-        }
-    }
-
-    @Override
-    public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
-        /* output will look like
-        Job Id: 2080802.gordon-fe2.local
-            Job_Name = A312402627
-        */
-        String regJobId = "jobId";
-        Pattern pattern = Pattern.compile("(?<" + regJobId + ">[^\\s]*)\\s*.* " + jobName);
-        if (rawOutput != null) {
-            Matcher matcher = pattern.matcher(rawOutput);
-            if (matcher.find()) {
-                return matcher.group(regJobId);
-            } else {
-                log.error("No match is found for JobName");
-                return null;
-            }
-        } else {
-            log.error("Error: RawOutput shouldn't be null");
-            return null;
-        }
-    }
-
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmJobConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmJobConfiguration.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmJobConfiguration.java
deleted file mode 100644
index 48ba48e..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmJobConfiguration.java
+++ /dev/null
@@ -1,119 +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.gfac.gsi.ssh.api.job;
-
-import org.apache.airavata.gfac.core.JobManagerConfiguration;
-import org.apache.airavata.gfac.core.cluster.OutputParser;
-import org.apache.airavata.gfac.core.cluster.RawCommandInfo;
-import org.apache.commons.io.FilenameUtils;
-
-import java.io.File;
-
-public class SlurmJobConfiguration implements JobManagerConfiguration {
-
-    private String jobDescriptionTemplateName;
-
-    private String scriptExtension;
-
-    private String installedPath;
-
-    private OutputParser parser;
-
-    public SlurmJobConfiguration(){
-        // this can be used to construct and use setter methods to set all the params in order
-    }
-    public SlurmJobConfiguration(String jobDescriptionTemplateName,
-                                   String scriptExtension,String installedPath,OutputParser parser) {
-        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
-        this.scriptExtension = scriptExtension;
-        this.parser = parser;
-        if (installedPath.endsWith("/")) {
-            this.installedPath = installedPath;
-        } else {
-            this.installedPath = installedPath + "/";
-        }
-    }
-
-    public RawCommandInfo getCancelCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "scancel " + jobID);
-    }
-
-    public String getJobDescriptionTemplateName() {
-        return jobDescriptionTemplateName;
-    }
-
-    public void setJobDescriptionTemplateName(String jobDescriptionTemplateName) {
-        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
-    }
-
-    public RawCommandInfo getMonitorCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "squeue -j " + jobID);
-    }
-
-    public String getScriptExtension() {
-        return scriptExtension;
-    }
-
-    public RawCommandInfo getSubmitCommand(String workingDirectory,String pbsFilePath) {
-          return new RawCommandInfo(this.installedPath + "sbatch " +
-                workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
-    }
-
-    public String getInstalledPath() {
-        return installedPath;
-    }
-
-    public void setInstalledPath(String installedPath) {
-        this.installedPath = installedPath;
-    }
-
-    public OutputParser getParser() {
-        return parser;
-    }
-
-    public void setParser(OutputParser parser) {
-        this.parser = parser;
-    }
-
-    public RawCommandInfo getUserBasedMonitorCommand(String userName) {
-        return new RawCommandInfo(this.installedPath + "squeue -u " + userName);
-    }
-
-    @Override
-    public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
-        return new RawCommandInfo(this.installedPath + "squeue -n " + jobName + " -u " + userName);
-    }
-
-    @Override
-    public String getBaseCancelCommand() {
-        return "scancel";
-    }
-
-    @Override
-    public String getBaseMonitorCommand() {
-        return "squeue";
-    }
-
-    @Override
-    public String getBaseSubmitCommand() {
-        return "sbatch";
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmOutputParser.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmOutputParser.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmOutputParser.java
deleted file mode 100644
index 3d2dc48..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/SlurmOutputParser.java
+++ /dev/null
@@ -1,192 +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.gfac.gsi.ssh.api.job;
-
-import org.apache.airavata.gfac.core.JobDescriptor;
-import org.apache.airavata.gfac.core.cluster.JobStatus;
-import org.apache.airavata.gfac.core.cluster.OutputParser;
-import org.apache.airavata.gfac.core.SSHApiException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class SlurmOutputParser implements OutputParser {
-    private static final Logger log = LoggerFactory.getLogger(SlurmOutputParser.class);
-    public static final int JOB_NAME_OUTPUT_LENGTH = 8;
-    public static final String STATUS = "status";
-
-    public void parseSingleJob(JobDescriptor descriptor, String rawOutput) throws SSHApiException {
-        log.info(rawOutput);
-        String[] info = rawOutput.split("\n");
-        String lastString = info[info.length - 1];
-        if (lastString.contains("JOB ID")) {
-            // because there's no state
-            descriptor.setStatus("U");
-        } else {
-            int column = 0;
-            System.out.println(lastString);
-            for (String each : lastString.split(" ")) {
-                if (each.trim().isEmpty()) {
-                    continue;
-                } else {
-                    switch (column) {
-                        case 0:
-                            descriptor.setJobID(each);
-                            column++;
-                            break;
-                        case 1:
-                            descriptor.setPartition(each);
-                            column++;
-                            break;
-                        case 2:
-                            descriptor.setJobName(each);
-                            column++;
-                            break;
-                        case 3:
-                            descriptor.setUserName(each);
-                            column++;
-                            break;
-                        case 4:
-                            descriptor.setStatus(each);
-                            column++;
-                            break;
-                        case 5:
-                            descriptor.setUsedCPUTime(each);
-                            column++;
-                            break;
-                        case 6:
-                            try {
-                                int nodes = Integer.parseInt(each);
-                                descriptor.setNodes(nodes);
-                            }catch (Exception e){
-                                log.error("Node count read from command output is not an integer !!!");
-                            }
-                            column++;
-                            break;
-                        case 7:
-                            descriptor.setNodeList(each);
-                            column++;
-                            break;
-                    }
-                }
-            }
-        }
-
-    }
-
-    /**
-     * This can be used to parseSingleJob the outpu of sbatch and extrac the jobID from the content
-     *
-     * @param rawOutput
-     * @return
-     */
-    public String parseJobSubmission(String rawOutput) throws SSHApiException {
-        // FIXME : use regex to match correct jobId;
-        log.info(rawOutput);
-        String[] info = rawOutput.split("\n");
-        for (String anInfo : info) {
-            if (anInfo.contains("Submitted batch job")) {
-                String[] split = anInfo.split("Submitted batch job");
-                return split[1].trim();
-            }
-        }
-        return "";
-//        throw new SSHApiException(rawOutput);  //todo//To change body of implemented methods use File | Settings | File Templates.
-    }
-
-    public JobStatus parseJobStatus(String jobID, String rawOutput) throws SSHApiException {
-        log.info(rawOutput);
-        Pattern pattern = Pattern.compile(jobID + "(?=\\s+\\S+\\s+\\S+\\s+\\S+\\s+(?<" + STATUS + ">\\w+))");
-        Matcher matcher = pattern.matcher(rawOutput);
-        if (matcher.find()) {
-            return JobStatus.valueOf(matcher.group(STATUS));
-        }
-        return null;
-    }
-
-    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) throws SSHApiException {
-        log.debug(rawOutput);
-        String[] info = rawOutput.split("\n");
-        String lastString = info[info.length - 1];
-        if (lastString.contains("JOBID") || lastString.contains("PARTITION")) {
-            log.info("There are no jobs with this username ... ");
-            return;
-        }
-//        int lastStop = 0;
-        for (String jobID : statusMap.keySet()) {
-            String jobId = jobID.split(",")[0];
-            String jobName = jobID.split(",")[1];
-            boolean found = false;
-            for (int i = 0; i < info.length; i++) {
-                if (info[i].contains(jobName.substring(0, 8))) {
-                    // now starts processing this line
-                    log.info(info[i]);
-                    String correctLine = info[i];
-                    String[] columns = correctLine.split(" ");
-                    List<String> columnList = new ArrayList<String>();
-                    for (String s : columns) {
-                        if (!"".equals(s)) {
-                            columnList.add(s);
-                        }
-                    }
-                    try {
-                        statusMap.put(jobID, JobStatus.valueOf(columnList.get(4)));
-                    } catch (IndexOutOfBoundsException e) {
-                        statusMap.put(jobID, JobStatus.valueOf("U"));
-                    }
-                    found = true;
-                    break;
-                }
-            }
-            if (!found) {
-                log.error("Couldn't find the status of the Job with JobName: " + jobName + "Job Id: " + jobId);
-            }
-        }
-    }
-
-    @Override
-    public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
-        String regJobId = "jobId";
-        if (jobName == null) {
-            return null;
-        } else if(jobName.length() > JOB_NAME_OUTPUT_LENGTH) {
-            jobName = jobName.substring(0, JOB_NAME_OUTPUT_LENGTH);
-        }
-        Pattern pattern = Pattern.compile("(?=(?<" + regJobId + ">\\d+)\\s+\\w+\\s+" + jobName + ")"); // regex - look ahead and match
-        if (rawOutput != null) {
-            Matcher matcher = pattern.matcher(rawOutput);
-            if (matcher.find()) {
-                return matcher.group(regJobId);
-            } else {
-                log.error("No match is found for JobName");
-                return null;
-            }
-        } else {
-            log.error("Error: RawOutput shouldn't be null");
-            return null;
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEJobConfiguration.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEJobConfiguration.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEJobConfiguration.java
deleted file mode 100644
index fddf210..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEJobConfiguration.java
+++ /dev/null
@@ -1,121 +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.gfac.gsi.ssh.api.job;
-
-import org.apache.airavata.gfac.core.JobManagerConfiguration;
-import org.apache.airavata.gfac.core.cluster.OutputParser;
-import org.apache.airavata.gfac.core.cluster.RawCommandInfo;
-import org.apache.commons.io.FilenameUtils;
-
-import java.io.File;
-
-public class UGEJobConfiguration implements JobManagerConfiguration {
-
-    private String jobDescriptionTemplateName;
-
-    private String scriptExtension;
-
-    private String installedPath;
-
-    private OutputParser parser;
-
-    public UGEJobConfiguration() {
-        // this can be used to construct and use setter methods to set all the params in order
-    }
-
-    public UGEJobConfiguration(String jobDescriptionTemplateName,
-                               String scriptExtension, String installedPath, OutputParser parser) {
-        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
-        this.scriptExtension = scriptExtension;
-        this.parser = parser;
-        if (installedPath.endsWith("/")) {
-            this.installedPath = installedPath;
-        } else {
-            this.installedPath = installedPath + "/";
-        }
-    }
-
-    public RawCommandInfo getCancelCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "qdel " + jobID);
-    }
-
-    public String getJobDescriptionTemplateName() {
-        return jobDescriptionTemplateName;
-    }
-
-    public void setJobDescriptionTemplateName(String jobDescriptionTemplateName) {
-        this.jobDescriptionTemplateName = jobDescriptionTemplateName;
-    }
-
-    public RawCommandInfo getMonitorCommand(String jobID) {
-        return new RawCommandInfo(this.installedPath + "qstat -j " + jobID);
-    }
-
-    public String getScriptExtension() {
-        return scriptExtension;
-    }
-
-    public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath) {
-        return new RawCommandInfo(this.installedPath + "qsub " +
-                workingDirectory + File.separator + FilenameUtils.getName(pbsFilePath));
-    }
-
-    public String getInstalledPath() {
-        return installedPath;
-    }
-
-    public void setInstalledPath(String installedPath) {
-        this.installedPath = installedPath;
-    }
-
-    public OutputParser getParser() {
-        return parser;
-    }
-
-    public void setParser(OutputParser parser) {
-        this.parser = parser;
-    }
-
-    public RawCommandInfo getUserBasedMonitorCommand(String userName) {
-        return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
-    }
-
-    @Override
-    public RawCommandInfo getJobIdMonitorCommand(String jobName, String userName) {
-        // For PBS there is no option to get jobDetails by JobName, so we search with userName
-        return new RawCommandInfo(this.installedPath + "qstat -u " + userName);
-    }
-
-    @Override
-    public String  getBaseCancelCommand() {
-        return "qdel";
-    }
-
-    @Override
-    public String  getBaseMonitorCommand() {
-        return "qstat";
-    }
-
-    @Override
-    public String getBaseSubmitCommand() {
-        return "qsub ";
-    }
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEOutputParser.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEOutputParser.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEOutputParser.java
deleted file mode 100644
index 3419b3a..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/UGEOutputParser.java
+++ /dev/null
@@ -1,190 +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.gfac.gsi.ssh.api.job;
-
-import org.apache.airavata.gfac.core.JobDescriptor;
-import org.apache.airavata.gfac.core.cluster.JobStatus;
-import org.apache.airavata.gfac.core.cluster.OutputParser;
-import org.apache.airavata.gfac.core.SSHApiException;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-public class UGEOutputParser implements OutputParser {
-    private static final Logger log = LoggerFactory.getLogger(PBSOutputParser.class);
-    public static final String JOB_ID = "jobId";
-
-    public void parseSingleJob(JobDescriptor jobDescriptor, String rawOutput) {
-        log.debug(rawOutput);
-        String[] info = rawOutput.split("\n");
-        String[] line;
-        for (int i = 0; i < info.length; i++) {
-            if (info[i].contains("=")) {
-                line = info[i].split("=", 2);
-            } else {
-                line = info[i].split(":", 2);
-            }
-            if (line.length >= 2) {
-                String header = line[0].trim();
-                log.debug("Header = " + header);
-                String value = line[1].trim();
-                log.debug("value = " + value);
-
-                if (header.equals("Variable_List")) {
-                    while (info[i + 1].startsWith("\t")) {
-                        value += info[i + 1];
-                        i++;
-                    }
-                    value = value.replaceAll("\t", "");
-                    jobDescriptor.setVariableList(value);
-                } else if ("Job Id".equals(header)) {
-                    jobDescriptor.setJobID(value);
-                } else if ("Job_Name".equals(header)) {
-                    jobDescriptor.setJobName(value);
-                } else if ("Account_Name".equals(header)) {
-                    jobDescriptor.setAcountString(value);
-                } else if ("job_state".equals(header)) {
-                    jobDescriptor.setStatus(value);
-                } else if ("Job_Owner".equals(header)) {
-                    jobDescriptor.setOwner(value);
-                } else if ("resources_used.cput".equals(header)) {
-                    jobDescriptor.setUsedCPUTime(value);
-                } else if ("resources_used.mem".equals(header)) {
-                    jobDescriptor.setUsedMemory(value);
-                } else if ("resources_used.walltime".equals(header)) {
-                    jobDescriptor.setEllapsedTime(value);
-                } else if ("job_state".equals(header)) {
-                    jobDescriptor.setStatus(value);
-                } else if ("queue".equals(header))
-                    jobDescriptor.setQueueName(value);
-                else if ("ctime".equals(header)) {
-                    jobDescriptor.setCTime(value);
-                } else if ("qtime".equals(header)) {
-                    jobDescriptor.setQTime(value);
-                } else if ("mtime".equals(header)) {
-                    jobDescriptor.setMTime(value);
-                } else if ("start_time".equals(header)) {
-                    jobDescriptor.setSTime(value);
-                } else if ("comp_time".equals(header)) {
-                    jobDescriptor.setCompTime(value);
-                } else if ("exec_host".equals(header)) {
-                    jobDescriptor.setExecuteNode(value);
-                } else if ("Output_Path".equals(header)) {
-                    if (info[i + 1].contains("=") || info[i + 1].contains(":"))
-                        jobDescriptor.setStandardOutFile(value);
-                    else {
-                        jobDescriptor.setStandardOutFile(value + info[i + 1].trim());
-                        i++;
-                    }
-                } else if ("Error_Path".equals(header)) {
-                    if (info[i + 1].contains("=") || info[i + 1].contains(":"))
-                        jobDescriptor.setStandardErrorFile(value);
-                    else {
-                        String st = info[i + 1].trim();
-                        jobDescriptor.setStandardErrorFile(value + st);
-                        i++;
-                    }
-
-                } else if ("submit_args".equals(header)) {
-                    while (i + 1 < info.length) {
-                        if (info[i + 1].startsWith("\t")) {
-                            value += info[i + 1];
-                            i++;
-                        } else
-                            break;
-                    }
-                    value = value.replaceAll("\t", "");
-                    jobDescriptor.setSubmitArgs(value);
-                }
-            }
-        }
-    }
-
-	public String parseJobSubmission(String rawOutput) {
-		log.debug(rawOutput);
-		if (rawOutput != null && !rawOutput.isEmpty()) {
-			String[] info = rawOutput.split("\n");
-			String lastLine = info[info.length - 1];
-			return lastLine.split(" ")[2]; // In PBS stdout is going to be directly the jobID
-		} else {
-			return "";
-		}
-	}
-
-    public JobStatus parseJobStatus(String jobID, String rawOutput) {
-        Pattern pattern = Pattern.compile("job_number:[\\s]+" + jobID);
-        Matcher matcher = pattern.matcher(rawOutput);
-        if (matcher.find()) {
-            return JobStatus.Q; // fixme; return correct status.
-        }
-        return JobStatus.U;
-    }
-
-    public void parseJobStatuses(String userName, Map<String, JobStatus> statusMap, String rawOutput) {
-        log.debug(rawOutput);
-        String[] info = rawOutput.split("\n");
-        int lastStop = 0;
-        for (String jobID : statusMap.keySet()) {
-            for(int i=lastStop;i<info.length;i++){
-               if(jobID.split(",")[0].contains(info[i].split(" ")[0]) && !"".equals(info[i].split(" ")[0])){
-                   // now starts processing this line
-                   log.info(info[i]);
-                   String correctLine = info[i];
-                   String[] columns = correctLine.split(" ");
-                   List<String> columnList = new ArrayList<String>();
-                   for (String s : columns) {
-                       if (!"".equals(s)) {
-                           columnList.add(s);
-                       }
-                   }
-                   lastStop = i+1;
-                   if ("E".equals(columnList.get(4))) {
-                       // There is another status with the same letter E other than error status
-                       // to avoid that we make a small tweek to the job status
-                       columnList.set(4, "Er");
-                   }
-                   statusMap.put(jobID, JobStatus.valueOf(columnList.get(4)));
-                   break;
-               }
-            }
-        }
-    }
-
-    @Override
-    public String parseJobId(String jobName, String rawOutput) throws SSHApiException {
-        if (jobName.length() > 10) {
-            jobName = jobName.substring(0, 10);
-        }
-        Pattern pattern = Pattern.compile("(?<" + JOB_ID + ">\\S+)\\s+\\S+\\s+(" + jobName + ")");
-        Matcher matcher = pattern.matcher(rawOutput);
-        if (matcher.find()) {
-            return matcher.group(JOB_ID);
-        }
-        return null;
-    }
-
-
-}

http://git-wip-us.apache.org/repos/asf/airavata/blob/d9b2df03/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/config/ConfigReader.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/config/ConfigReader.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/config/ConfigReader.java
deleted file mode 100644
index c40059e..0000000
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/gsi/ssh/config/ConfigReader.java
+++ /dev/null
@@ -1,76 +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.gfac.gsi.ssh.config;
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Properties;
-
-/**
- * Reads basic configurations.
- */
-public class ConfigReader {
-
-    private static final String CONFIGURATION_FILE = "gsissh.properties";
-
-
-    private Properties properties;
-
-    /**
-     * Reads configurations from the class path configuration file.
-     * @throws IOException If an error occurred while reading configurations.
-     */
-    public ConfigReader() throws IOException {
-        this.properties = getPropertiesFromClasspath(CONFIGURATION_FILE);
-    }
-
-    private Properties getPropertiesFromClasspath(String propFileName) throws IOException {
-        Properties props = new Properties();
-        InputStream inputStream = this.getClass().getClassLoader()
-                .getResourceAsStream(propFileName);
-
-        if (inputStream == null) {
-            throw new FileNotFoundException("System configuration file '" + propFileName
-                    + "' not found in the classpath");
-        }
-
-        props.load(inputStream);
-
-        return props;
-    }
-
-    public String getConfiguration(String key) {
-        return this.properties.getProperty(key);
-    }
-
-
-    /**
-     * Gets all the SSH related properties used by JSch.
-     * @return All properties.
-     */
-    public Properties getProperties() {
-        return this.properties;
-    }
-
-
-}


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