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From shame...@apache.org
Subject [07/39] airavata git commit: Refactored gfac sub modules, merged gfac-ssh, gfac-gsissh, gfac-local, gfac-monitor and gsissh modules and create gface-impl, removed implementation from gfac-core to gfac-impl
Date Wed, 03 Jun 2015 18:14:24 GMT
http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACPassiveJobSubmitter.java
----------------------------------------------------------------------
diff --git a/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACPassiveJobSubmitter.java b/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACPassiveJobSubmitter.java
index 36282a0..21df198 100644
--- a/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACPassiveJobSubmitter.java
+++ b/modules/orchestrator/orchestrator-core/src/main/java/org/apache/airavata/orchestrator/core/impl/GFACPassiveJobSubmitter.java
@@ -25,7 +25,7 @@ import org.apache.airavata.common.utils.AiravataUtils;
 import org.apache.airavata.common.utils.ServerSettings;
 import org.apache.airavata.credential.store.store.CredentialReader;
 import org.apache.airavata.gfac.client.GFACInstance;
-import org.apache.airavata.gfac.core.utils.GFacUtils;
+import org.apache.airavata.gfac.core.GFacUtils;
 import org.apache.airavata.messaging.core.MessageContext;
 import org.apache.airavata.messaging.core.Publisher;
 import org.apache.airavata.messaging.core.PublisherFactory;

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java
----------------------------------------------------------------------
diff --git a/modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java b/modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java
index 4ef9dbc..389913b 100644
--- a/modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java
+++ b/modules/orchestrator/orchestrator-service/src/main/java/org/apache/airavata/orchestrator/server/OrchestratorServerHandler.java
@@ -36,7 +36,7 @@ import org.apache.airavata.common.utils.Constants;
 import org.apache.airavata.common.utils.ServerSettings;
 import org.apache.airavata.credential.store.store.CredentialReader;
 import org.apache.airavata.gfac.core.scheduler.HostScheduler;
-import org.apache.airavata.gfac.core.utils.GFacUtils;
+import org.apache.airavata.gfac.core.GFacUtils;
 import org.apache.airavata.messaging.core.MessageContext;
 import org.apache.airavata.messaging.core.MessageHandler;
 import org.apache.airavata.messaging.core.MessagingConstants;

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
index 2234b67..23f5f16 100644
--- a/pom.xml
+++ b/pom.xml
@@ -556,7 +556,6 @@
 				<module>modules/security</module>
 				<module>modules/credential-store</module>
 				<module>modules/orchestrator</module>
-				<module>tools</module>
 				<module>modules/server</module>
 				<module>modules/test-suite</module>
 				<module>modules/distribution</module>

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh-cli-tools/README.txt
----------------------------------------------------------------------
diff --git a/tools/gsissh-cli-tools/README.txt b/tools/gsissh-cli-tools/README.txt
index bc352dd..11d2674 100644
--- a/tools/gsissh-cli-tools/README.txt
+++ b/tools/gsissh-cli-tools/README.txt
@@ -6,4 +6,4 @@ To run the SSHApiClientWithMyProxyAuth tool, first add all the jars in target/li
 export CP=`echo ./target/lib/*.jar | tr ' ' ':'`
 
 Then use the following command line:
-java -classpath ./target/gsissh-cli-tools-0.14-SNAPSHOT.jar:$CP -Dmyproxy.server=myproxy.teragrid.org -Dmyproxy.username=<your.username> -Dmyproxy.password=<your.password> -Dmyproxy.cert.location=<path-to>/airavata/tools/gsissh-cli-tools/target/classes/certificates/ -Dremote.host=trestles.sdsc.xsede.org -Dremote.host.port=22 -Dremote.cmd=/bin/ls org.apache.airavata.gsi.ssh.cli.SSHApiClientWithMyProxyAuth 
+java -classpath ./target/gsissh-cli-tools-0.14-SNAPSHOT.jar:$CP -Dmyproxy.server=myproxy.teragrid.org -Dmyproxy.username=<your.username> -Dmyproxy.password=<your.password> -Dmyproxy.cert.location=<path-to>/airavata/tools/gsissh-cli-tools/target/classes/certificates/ -Dremote.host=trestles.sdsc.xsede.org -Dremote.host.port=22 -Dremote.cmd=/bin/ls org.apache.airavata.gfac.ssh.cli.SSHApiClientWithMyProxyAuth

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh-cli-tools/src/main/java/org/apache/airavata/gsi/ssh/cli/SSHApiClientWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/tools/gsissh-cli-tools/src/main/java/org/apache/airavata/gsi/ssh/cli/SSHApiClientWithMyProxyAuth.java b/tools/gsissh-cli-tools/src/main/java/org/apache/airavata/gsi/ssh/cli/SSHApiClientWithMyProxyAuth.java
index 9179f08..b22dc61 100644
--- a/tools/gsissh-cli-tools/src/main/java/org/apache/airavata/gsi/ssh/cli/SSHApiClientWithMyProxyAuth.java
+++ b/tools/gsissh-cli-tools/src/main/java/org/apache/airavata/gsi/ssh/cli/SSHApiClientWithMyProxyAuth.java
@@ -19,25 +19,20 @@
  *
  */
 
-package org.apache.airavata.gsi.ssh.cli;
+package org.apache.airavata.gfac.ssh.cli;
 
-import org.apache.airavata.gsi.ssh.api.*;
-import org.apache.airavata.gsi.ssh.api.authentication.GSIAuthenticationInfo;
-import org.apache.airavata.gsi.ssh.api.job.JobDescriptor;
-import org.apache.airavata.gsi.ssh.config.ConfigReader;
-import org.apache.airavata.gsi.ssh.impl.PBSCluster;
-import org.apache.airavata.gsi.ssh.impl.RawCommandInfo;
-import org.apache.airavata.gsi.ssh.impl.SystemCommandOutput;
-import org.apache.airavata.gsi.ssh.impl.authentication.MyProxyAuthenticationInfo;
-import org.apache.airavata.gsi.ssh.util.CommonUtils;
+import org.apache.airavata.gfac.ssh.api.*;
+import org.apache.airavata.gfac.ssh.api.authentication.GSIAuthenticationInfo;
+import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gfac.ssh.config.ConfigReader;
+import org.apache.airavata.gfac.ssh.impl.PBSCluster;
+import org.apache.airavata.gfac.ssh.impl.RawCommandInfo;
+import org.apache.airavata.gfac.ssh.impl.SystemCommandOutput;
+import org.apache.airavata.gfac.ssh.impl.authentication.MyProxyAuthenticationInfo;
+import org.apache.airavata.gfac.ssh.util.CommonUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
 public class SSHApiClientWithMyProxyAuth {
 
     public static void main(String[]ars){

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/SSHDemo.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/SSHDemo.java b/tools/gsissh/src/main/java/SSHDemo.java
index c5e410c..ea73e3c 100644
--- a/tools/gsissh/src/main/java/SSHDemo.java
+++ b/tools/gsissh/src/main/java/SSHDemo.java
@@ -39,7 +39,7 @@
  */
 
 import com.jcraft.jsch.*;
-import org.apache.airavata.gsi.ssh.jsch.ExtendedJSch;
+import org.apache.airavata.gfac.ssh.jsch.ExtendedJSch;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -54,7 +54,7 @@ public class SSHDemo {
 
     private static final Logger logger = LoggerFactory.getLogger(SSHDemo.class);
     static {
-        JSch.setConfig("gssapi-with-mic.x509", "org.apache.airavata.gsi.ssh.GSSContextX509");
+        JSch.setConfig("gssapi-with-mic.x509", "org.apache.airavata.gfac.ssh.GSSContextX509");
         JSch.setConfig("userauth.gssapi-with-mic", "com.jcraft.jsch.UserAuthGSSAPIWithMICGSSCredentials");
         System.setProperty("X509_CERT_DIR",
                 "/Users/smarru/deploy/certificates");

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/com/jcraft/jsch/ExtendedSession.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/com/jcraft/jsch/ExtendedSession.java b/tools/gsissh/src/main/java/com/jcraft/jsch/ExtendedSession.java
index f3ead64..5b7f7d7 100644
--- a/tools/gsissh/src/main/java/com/jcraft/jsch/ExtendedSession.java
+++ b/tools/gsissh/src/main/java/com/jcraft/jsch/ExtendedSession.java
@@ -21,7 +21,7 @@
 
 package com.jcraft.jsch;
 
-import org.apache.airavata.gsi.ssh.api.authentication.GSIAuthenticationInfo;
+import org.apache.airavata.gfac.ssh.api.authentication.GSIAuthenticationInfo;
 
 public class ExtendedSession extends Session {
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/com/jcraft/jsch/UserAuthGSSAPIWithMICGSSCredentials.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/com/jcraft/jsch/UserAuthGSSAPIWithMICGSSCredentials.java b/tools/gsissh/src/main/java/com/jcraft/jsch/UserAuthGSSAPIWithMICGSSCredentials.java
index 24028b6..d9fb822 100644
--- a/tools/gsissh/src/main/java/com/jcraft/jsch/UserAuthGSSAPIWithMICGSSCredentials.java
+++ b/tools/gsissh/src/main/java/com/jcraft/jsch/UserAuthGSSAPIWithMICGSSCredentials.java
@@ -25,8 +25,8 @@ import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 
-import org.apache.airavata.gsi.ssh.GSSContextX509;
-import org.apache.airavata.gsi.ssh.api.authentication.GSIAuthenticationInfo;
+import org.apache.airavata.gfac.ssh.GSSContextX509;
+import org.apache.airavata.gfac.ssh.api.authentication.GSIAuthenticationInfo;
 import org.globus.gsi.gssapi.GSSConstants;
 import org.ietf.jgss.GSSException;
 import org.ietf.jgss.Oid;

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java
new file mode 100644
index 0000000..1c07a39
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/GSSContextX509.java
@@ -0,0 +1,210 @@
+/*
+ *
+ * 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.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/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java
new file mode 100644
index 0000000..beb5b37
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Cluster.java
@@ -0,0 +1,162 @@
+/*
+ *
+ * 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.ssh.api;
+
+import java.util.List;
+import java.util.Map;
+
+import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
+import org.apache.airavata.gfac.ssh.impl.JobStatus;
+
+import com.jcraft.jsch.Session;
+
+/**
+ * This interface represents a Cluster machine
+ * End users of the API can implement this and come up with their own
+ * implementations, but mostly this interface is for internal usage.
+ */
+public interface Cluster {
+
+    /**
+     * This will submit a job to the cluster with a given pbs file and some parameters
+     *
+     * @param pbsFilePath  path of the pbs file
+     * @param workingDirectory working directory where pbs should has to copy
+     * @return jobId after successful job submission
+     * @throws SSHApiException throws exception during error
+     */
+    public String submitBatchJobWithScript(String pbsFilePath, String workingDirectory) throws SSHApiException;
+
+    /**
+     * This will submit the given job and not performing any monitoring
+     *
+     * @param jobDescriptor  job descriptor to submit to cluster, this contains all the parameter
+     * @return jobID after successful job submission.
+     * @throws SSHApiException  throws exception during error
+     */
+    public String submitBatchJob(JobDescriptor jobDescriptor) throws SSHApiException;
+
+    /**
+     * This will copy the localFile to remoteFile location in configured cluster
+     *
+     * @param remoteFile remote file location, this can be a directory too
+     * @param localFile local file path of the file which needs to copy to remote location
+     * @throws SSHApiException throws exception during error
+     */
+    public void scpTo(String remoteFile, String localFile) throws SSHApiException;
+
+    /**
+     * This will copy a remote file in path rFile to local file lFile
+     * @param remoteFile remote file path, this has to be a full qualified path
+     * @param localFile This is the local file to copy, this can be a directory too
+     * @throws SSHApiException
+     */
+    public void scpFrom(String remoteFile, String localFile) throws SSHApiException;
+
+    /**
+     * This will copy a remote file in path rFile to local file lFile
+     * @param remoteFile remote file path, this has to be a full qualified path
+     * @param localFile This is the local file to copy, this can be a directory too
+     * @throws SSHApiException
+     */
+    public void scpThirdParty(String remoteFileSorce, String remoteFileTarget) throws SSHApiException;
+    
+    /**
+     * This will create directories in computing resources
+     * @param directoryPath the full qualified path for the directory user wants to create
+     * @throws SSHApiException throws during error
+     */
+    public void makeDirectory(String directoryPath) throws SSHApiException;
+
+
+    /**
+     * This will get the job description of a job which is there in the cluster
+     * if jbo is not available with the given ID it returns
+     * @param jobID jobId has to pass
+     * @return Returns full job description of the job which submitted successfully
+     * @throws SSHApiException throws exception during error
+     */
+    public JobDescriptor getJobDescriptorById(String jobID) throws SSHApiException;
+
+    /**
+     * This will delete the given job from the queue
+     *
+     * @param jobID  jobId of the job which user wants to delete
+     * @return return the description of the deleted job
+     * @throws SSHApiException throws exception during error
+     */
+    public JobDescriptor cancelJob(String jobID) throws SSHApiException;
+
+    /**
+     * This will get the job status of the the job associated with this jobId
+     *
+     * @param jobID jobId of the job user want to get the status
+     * @return job status of the given jobID
+     * @throws SSHApiException throws exception during error
+     */
+    public JobStatus getJobStatus(String jobID) throws SSHApiException;
+    /**
+     * This will get the job status of the the job associated with this jobId
+     *
+     * @param jobName jobName of the job user want to get the status
+     * @return jobId of the given jobName
+     * @throws SSHApiException throws exception during error
+     */
+    public String getJobIdByJobName(String jobName, String userName) throws SSHApiException;
+
+    /**
+     * This method can be used to poll the jobstatuses based on the given
+     * user but we should pass the jobID list otherwise we will get unwanted
+     * job statuses which submitted by different middleware outside apache
+     * airavata with the same uername which we are not considering
+     * @param userName userName of the jobs which required to get the status
+     * @param jobIDs precises set of jobIDs
+     * @return
+     */
+    public void getJobStatuses(String userName,Map<String,JobStatus> jobIDs)throws SSHApiException;
+    /**
+     * This will list directories in computing resources
+     * @param directoryPath the full qualified path for the directory user wants to create
+     * @throws SSHApiException throws during error
+     */
+    public List<String> listDirectory(String directoryPath) throws SSHApiException;
+
+    /**
+     * This method can be used to get created ssh session
+     * to reuse the created session.
+     * @throws SSHApiException
+     */
+    public Session getSession() throws SSHApiException;
+    
+    /**
+     * This method can be used to close the connections initialized
+     * to handle graceful shutdown of the system
+     * @throws SSHApiException
+     */
+    public void disconnect() throws SSHApiException;
+
+    /**
+     * This gives the server Info
+     * @return
+     */
+    public ServerInfo getServerInfo();
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
new file mode 100644
index 0000000..024c53d
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandExecutor.java
@@ -0,0 +1,278 @@
+/*
+ *
+ * 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.ssh.api;
+
+import com.jcraft.jsch.*;
+import org.apache.airavata.gfac.ssh.api.authentication.*;
+import org.apache.airavata.gfac.ssh.config.ConfigReader;
+import org.apache.airavata.gfac.ssh.jsch.ExtendedJSch;
+import org.apache.airavata.gfac.ssh.util.SSHAPIUIKeyboardInteractive;
+import org.apache.airavata.gfac.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/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java
new file mode 100644
index 0000000..e6797ce
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandInfo.java
@@ -0,0 +1,34 @@
+package org.apache.airavata.gfac.ssh.api;/*
+ *
+ * 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.
+ *
+ */
+
+/**
+ * Encapsulates information about
+ */
+public interface CommandInfo {
+
+    /**
+     * Gets the executable command as a string.
+     * @return String encoded command. Should be able to execute
+     * directly on remote shell. Should includes appropriate parameters.
+     */
+    String getCommand();
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java
new file mode 100644
index 0000000..f275ff0
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/CommandOutput.java
@@ -0,0 +1,49 @@
+package org.apache.airavata.gfac.ssh.api;/*
+ *
+ * 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.
+ *
+ */
+
+
+import com.jcraft.jsch.Channel;
+
+import java.io.OutputStream;
+
+/**
+ * Output of a certain command. TODO rethink
+ */
+public interface CommandOutput {
+
+    /**
+     * Gets the output of the command as a stream.
+     * @param  channel Command output as a stream.
+     */
+    void onOutput(Channel channel);
+
+    /**
+     * Gets standard error as a output stream.
+     * @return Command error as a stream.
+     */
+    OutputStream getStandardError();
+
+    /**
+     * The command exit code.
+     * @param code The program exit code
+     */
+    void exitCode(int code);
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java
new file mode 100644
index 0000000..67dd043
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Core.java
@@ -0,0 +1,59 @@
+/*
+ *
+ * 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.ssh.api;
+
+import org.apache.airavata.gfac.ssh.api.job.JobDescriptor;
+
+/**
+ * This represents a CPU core of a machine in the cluster
+ */
+public class Core {
+    private JobDescriptor job;
+    private String id;
+
+    public Core(String id) {
+        this.id = id;
+        this.job = null;
+    }
+
+    /**
+     * @return core's id
+     */
+    public String getId() {
+        return id;
+    }
+
+    public void setId(String id) {
+        this.id = id;
+    }
+
+    /**
+     * @return job running on the core
+     */
+    public JobDescriptor getJob() {
+        return job;
+    }
+
+    public void setJob(JobDescriptor job) {
+        this.job = job;
+    }
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java
new file mode 100644
index 0000000..1515f39
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/Node.java
@@ -0,0 +1,104 @@
+/*
+ *
+ * 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.ssh.api;
+
+import java.util.HashMap;
+
+public class Node {
+    private String Name;
+    private Core[] Cores;
+    private String state;
+    private HashMap<String, String> status;
+    private String np;
+    private String ntype;
+
+    /**
+     * @return the machine's name
+     */
+    public String getName() {
+        return Name;
+    }
+
+    public void setName(String Name) {
+        this.Name = Name;
+    }
+
+    /**
+     * @return machine cores as an array
+     */
+    public Core[] getCores() {
+        return Cores;
+    }
+
+    public void setCores(Core[] Cores) {
+        this.Cores = Cores;
+    }
+
+
+    /**
+     * @return the machine state
+     */
+    public String getState() {
+        return state;
+    }
+
+    public void setState(String state) {
+        this.state = state;
+    }
+
+    /**
+     * @return the status
+     */
+    public HashMap<String, String> getStatus() {
+        return status;
+    }
+
+    public void setStatus(HashMap<String, String> status) {
+        this.setStatus(status);
+    }
+
+
+    /**
+     * @return the number of cores in the machine
+     */
+    public String getNp() {
+        return np;
+    }
+
+
+    public void setNp(String np) {
+        this.np = np;
+    }
+
+    /**
+     * @return the ntype of the machine
+     */
+    public String getNtype() {
+        return ntype;
+    }
+
+
+    public void setNtype(String ntype) {
+        this.ntype = ntype;
+    }
+
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java
new file mode 100644
index 0000000..f78825b
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/SSHApiException.java
@@ -0,0 +1,36 @@
+/*
+ *
+ * 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.ssh.api;
+
+/**
+ * An exception class to wrap SSH command execution related errors.
+ */
+public class SSHApiException extends Exception {
+
+    public SSHApiException(String message) {
+        super(message);
+    }
+
+    public SSHApiException(String message, Exception e) {
+        super(message, e);
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java
new file mode 100644
index 0000000..d3c2160
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/ServerInfo.java
@@ -0,0 +1,65 @@
+package org.apache.airavata.gfac.ssh.api;/*
+ *
+ * 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.
+ *
+ */
+
+/**
+ * Encapsulate server information.
+ */
+public class ServerInfo {
+
+    private String host;
+    private String userName;
+    private int port = 22;
+
+    public ServerInfo(String userName, String host) {
+        this.userName = userName;
+        this.host = host;
+    }
+
+    public ServerInfo(String userName,String host,  int port) {
+        this.host = host;
+        this.userName = userName;
+        this.port = port;
+    }
+
+    public String getHost() {
+        return host;
+    }
+
+    public void setHost(String host) {
+        this.host = host;
+    }
+
+    public String getUserName() {
+        return userName;
+    }
+
+    public void setUserName(String userName) {
+        this.userName = userName;
+    }
+
+    public int getPort() {
+        return port;
+    }
+
+    public void setPort(int port) {
+        this.port = port;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/AuthenticationInfo.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/AuthenticationInfo.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/AuthenticationInfo.java
new file mode 100644
index 0000000..6b4e913
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/AuthenticationInfo.java
@@ -0,0 +1,32 @@
+package org.apache.airavata.gfac.ssh.api.authentication;/*
+ *
+ * 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.
+ *
+ */
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 10/4/13
+ * Time: 11:25 AM
+ */
+
+/**
+ * An empty interface that represents authentication data to the API.
+ */
+public interface AuthenticationInfo {
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/GSIAuthenticationInfo.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/GSIAuthenticationInfo.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/GSIAuthenticationInfo.java
new file mode 100644
index 0000000..1f327f0
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/GSIAuthenticationInfo.java
@@ -0,0 +1,43 @@
+package org.apache.airavata.gfac.ssh.api.authentication;/*
+ *
+ * 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.
+ *
+ */
+
+import org.ietf.jgss.GSSCredential;
+
+import java.util.Properties;
+
+/**
+ * Authentication data. Could be MyProxy user name, password, could be GSSCredentials
+ * or could be SSH keys.
+ */
+public abstract class GSIAuthenticationInfo implements AuthenticationInfo {
+
+    public Properties properties = new Properties();
+
+    public abstract GSSCredential getCredentials() throws SecurityException;
+
+    public Properties getProperties() {
+        return properties;
+    }
+
+    public void setProperties(Properties properties) {
+        this.properties = properties;
+    }
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHKeyAuthentication.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHKeyAuthentication.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHKeyAuthentication.java
new file mode 100644
index 0000000..ebd79f2
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHKeyAuthentication.java
@@ -0,0 +1,46 @@
+package org.apache.airavata.gfac.ssh.api.authentication;/*
+ *
+ * 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.
+ *
+ */
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 10/4/13
+ * Time: 2:39 PM
+ */
+
+/**
+ * Abstracts out common methods for SSH key authentication.
+ */
+public interface SSHKeyAuthentication extends AuthenticationInfo {
+
+    /**
+     * This is needed only if private key and public keys are encrypted.
+     * If they are not encrypted we can just return null.
+     * @return User should return pass phrase if keys are encrypted. If not null.
+     */
+    String getPassPhrase();
+
+    /**
+     * Callback with the banner message. API user can get hold of banner message
+     * by implementing this method.
+     * @param message The banner message.
+     */
+    void bannerMessage(String message);
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPasswordAuthentication.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPasswordAuthentication.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPasswordAuthentication.java
new file mode 100644
index 0000000..fd884f8
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPasswordAuthentication.java
@@ -0,0 +1,43 @@
+/*
+ *
+ * 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.ssh.api.authentication;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 10/4/13
+ * Time: 11:22 AM
+ */
+
+/**
+ * Password authentication for vanilla SSH.
+ */
+public interface SSHPasswordAuthentication extends AuthenticationInfo {
+
+    /**
+     * Gets the password for given host name and given user name.
+     * @param userName The connecting user name name.
+     * @param hostName The connecting host.
+     * @return Password for the given user.
+     */
+    String getPassword(String userName, String hostName);
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyAuthentication.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyAuthentication.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyAuthentication.java
new file mode 100644
index 0000000..dcedfec
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyAuthentication.java
@@ -0,0 +1,54 @@
+/*
+ *
+ * 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.ssh.api.authentication;
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 10/4/13
+ * Time: 9:48 AM
+ */
+
+
+/**
+ * Public key authentication for vanilla SSH.
+ * The public key and private key are returned as byte arrays. Useful when we store private key/public key
+ * in a secure storage such as credential store. API user should implement this.
+ */
+public interface SSHPublicKeyAuthentication extends SSHKeyAuthentication {
+
+    /**
+     * Gets the public key as byte array.
+     * @param userName The user who is trying to SSH
+     * @param hostName The host which user wants to connect to.
+     * @return The public key as a byte array.
+     */
+    byte[] getPrivateKey(String userName, String hostName);
+
+    /**
+     * Gets the private key as byte array.
+     * @param userName The user who is trying to SSH
+     * @param hostName The host which user wants to connect to.
+     * @return The private key as a byte array.
+     */
+    byte[] getPublicKey(String userName, String hostName);
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyFileAuthentication.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyFileAuthentication.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyFileAuthentication.java
new file mode 100644
index 0000000..e22b9af
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/authentication/SSHPublicKeyFileAuthentication.java
@@ -0,0 +1,52 @@
+package org.apache.airavata.gfac.ssh.api.authentication;/*
+ *
+ * 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.
+ *
+ */
+
+
+/**
+ * User: AmilaJ (amilaj@apache.org)
+ * Date: 10/4/13
+ * Time: 9:52 AM
+ */
+
+/**
+ * Public key authentication for vanilla SSH.
+ * The public key and private key stored files are returned. API user should implement this.
+ */
+public interface SSHPublicKeyFileAuthentication extends SSHKeyAuthentication {
+
+    /**
+     * The file which contains the public key.
+     * @param userName The user who is trying to SSH
+     * @param hostName The host which user wants to connect to.
+     * @return The name of the file which contains the public key.
+     */
+    String getPublicKeyFile(String userName, String hostName);
+
+    /**
+     * The file which contains the public key.
+     * @param userName The user who is trying to SSH
+     * @param hostName The host which user wants to connect to.
+     * @return The name of the file which contains the private key.
+     */
+    String getPrivateKeyFile(String userName, String hostName);
+
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobDescriptor.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobDescriptor.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobDescriptor.java
new file mode 100644
index 0000000..7e936ec
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobDescriptor.java
@@ -0,0 +1,473 @@
+/*
+ *
+ * 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.ssh.api.job;
+
+import org.apache.airavata.gfac.ssh.api.CommandOutput;
+import org.apache.airavata.gfac.ssh.util.CommonUtils;
+import org.apache.airavata.gfac.ssh.x2012.x12.*;
+import org.apache.xmlbeans.XmlException;
+
+import java.util.List;
+
+/**
+ * This class define a job with required parameters, based on this configuration API is generating a Pbs script and
+ * submit the job to the computing resource
+ */
+public class JobDescriptor {
+
+    private JobDescriptorDocument jobDescriptionDocument;
+
+
+    public JobDescriptor() {
+        jobDescriptionDocument = JobDescriptorDocument.Factory.newInstance();
+        jobDescriptionDocument.addNewJobDescriptor();
+    }
+
+    public JobDescriptor(JobDescriptorDocument jobDescriptorDocument) {
+        this.jobDescriptionDocument = jobDescriptorDocument;
+    }
+
+
+    public JobDescriptor(CommandOutput commandOutput) {
+        jobDescriptionDocument = JobDescriptorDocument.Factory.newInstance();
+        jobDescriptionDocument.addNewJobDescriptor();
+    }
+
+
+    public String toXML() {
+        return jobDescriptionDocument.xmlText();
+    }
+
+    public JobDescriptorDocument getJobDescriptorDocument() {
+        return this.jobDescriptionDocument;
+    }
+
+    /**
+     * With new app catalog thrift object integration, we don't use this
+     * @param xml
+     * @return
+     * @throws XmlException
+     */
+    @Deprecated
+    public static JobDescriptor fromXML(String xml)
+            throws XmlException {
+        JobDescriptorDocument parse = JobDescriptorDocument.Factory
+                .parse(xml);
+        JobDescriptor jobDescriptor = new JobDescriptor(parse);
+        return jobDescriptor;
+    }
+
+
+    //todo write bunch of setter getters to set and get jobdescription parameters
+    public void setWorkingDirectory(String workingDirectory) {
+        this.getJobDescriptorDocument().getJobDescriptor().setWorkingDirectory(workingDirectory);
+    }
+
+    public String getWorkingDirectory() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory();
+    }
+
+    public void setShellName(String shellName) {
+        this.getJobDescriptorDocument().getJobDescriptor().setShellName(shellName);
+    }
+
+    public void setJobName(String name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setJobName(name);
+    }
+
+    public void setExecutablePath(String name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setExecutablePath(name);
+    }
+
+    public void setAllEnvExport(boolean name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setAllEnvExport(name);
+    }
+
+    public void setMailOptions(String name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setMailOptions(name);
+    }
+
+    public void setStandardOutFile(String name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setStandardOutFile(name);
+    }
+
+    public void setStandardErrorFile(String name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setStandardErrorFile(name);
+    }
+
+    public void setNodes(int name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setNodes(name);
+    }
+
+    public void setProcessesPerNode(int name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setProcessesPerNode(name);
+    }
+
+    public String getOutputDirectory() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getOutputDirectory();
+    }
+
+    public String getInputDirectory() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getInputDirectory();
+    }
+    public void setOutputDirectory(String name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setOutputDirectory(name);
+    }
+
+    public void setInputDirectory(String name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setInputDirectory(name);
+    }
+
+    /**
+     * Users can pass the minute count for maxwalltime
+     * @param minutes
+     */
+    public void setMaxWallTime(String minutes) {
+        this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(
+                CommonUtils.maxWallTimeCalculator(Integer.parseInt(minutes)));
+
+    }
+
+
+    public void setMaxWallTimeForLSF(String minutes) {
+        this.getJobDescriptorDocument().getJobDescriptor().setMaxWallTime(
+                CommonUtils.maxWallTimeCalculatorForLSF(Integer.parseInt(minutes)));
+
+    }
+    public void setAcountString(String name) {
+        this.getJobDescriptorDocument().getJobDescriptor().setAcountString(name);
+    }
+
+    public void setInputValues(List<String> inputValue) {
+        InputList inputList = this.getJobDescriptorDocument().getJobDescriptor().addNewInputs();
+        inputList.setInputArray(inputValue.toArray(new String[inputValue.size()]));
+    }
+
+    public void setJobID(String jobID) {
+        this.getJobDescriptorDocument().getJobDescriptor().setJobID(jobID);
+    }
+
+    public void setQueueName(String queueName) {
+        this.getJobDescriptorDocument().getJobDescriptor().setQueueName(queueName);
+    }
+
+    public void setStatus(String queueName) {
+        this.getJobDescriptorDocument().getJobDescriptor().setStatus(queueName);
+    }
+
+    public void setAfterAnyList(String[] afterAnyList) {
+        AfterAnyList afterAny = this.getJobDescriptorDocument().getJobDescriptor().addNewAfterAny();
+        afterAny.setAfterAnyArray(afterAnyList);
+    }
+
+    public void setAfterOKList(String[] afterOKList) {
+        AfterOKList afterAnyList = this.getJobDescriptorDocument().getJobDescriptor().addNewAfterOKList();
+        afterAnyList.setAfterOKListArray(afterOKList);
+    }
+    public void setCTime(String cTime) {
+        this.getJobDescriptorDocument().getJobDescriptor().setCTime(cTime);
+    }
+    public void setQTime(String qTime) {
+        this.getJobDescriptorDocument().getJobDescriptor().setQTime(qTime);
+    }
+    public void setMTime(String mTime) {
+        this.getJobDescriptorDocument().getJobDescriptor().setMTime(mTime);
+    }
+    public void setSTime(String sTime) {
+        this.getJobDescriptorDocument().getJobDescriptor().setSTime(sTime);
+    }
+    public void setCompTime(String compTime) {
+        this.getJobDescriptorDocument().getJobDescriptor().setCompTime(compTime);
+    }
+    public void setOwner(String owner) {
+        this.getJobDescriptorDocument().getJobDescriptor().setOwner(owner);
+    }
+    public void setExecuteNode(String executeNode) {
+        this.getJobDescriptorDocument().getJobDescriptor().setExecuteNode(executeNode);
+    }
+    public void setEllapsedTime(String ellapsedTime) {
+        this.getJobDescriptorDocument().getJobDescriptor().setEllapsedTime(ellapsedTime);
+    }
+
+    public void setUsedCPUTime(String usedCPUTime) {
+        this.getJobDescriptorDocument().getJobDescriptor().setUsedCPUTime(usedCPUTime);
+    }
+    public void setCPUCount(int usedCPUTime) {
+            this.getJobDescriptorDocument().getJobDescriptor().setCpuCount(usedCPUTime);
+        }
+    public void setUsedMemory(String usedMemory) {
+        this.getJobDescriptorDocument().getJobDescriptor().setUsedMem(usedMemory);
+    }
+    public void setVariableList(String variableList) {
+        this.getJobDescriptorDocument().getJobDescriptor().setVariableList(variableList);
+    }
+    public void setSubmitArgs(String submitArgs) {
+        this.getJobDescriptorDocument().getJobDescriptor().setSubmitArgs(submitArgs);
+    }
+
+    public void setPreJobCommands(String[] commands){
+        if(this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands() == null){
+            this.getJobDescriptorDocument().getJobDescriptor().addNewPreJobCommands();
+        }
+        this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands().setCommandArray(commands);
+    }
+
+     public void setPostJobCommands(String[] commands){
+        if(this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands() == null){
+            this.getJobDescriptorDocument().getJobDescriptor().addNewPostJobCommands();
+        }
+        this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands().setCommandArray(commands);
+    }
+
+    public void setModuleLoadCommands(String[] commands) {
+        if (this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands() == null) {
+            this.getJobDescriptorDocument().getJobDescriptor().addNewModuleLoadCommands();
+        }
+        this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands().setCommandArray(commands);
+    }
+
+    public void addModuleLoadCommands(String command) {
+        if (this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands() == null) {
+            this.getJobDescriptorDocument().getJobDescriptor().addNewModuleLoadCommands();
+        }
+        this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands().addCommand(command);
+    }
+
+    public void addPreJobCommand(String command){
+        if(this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands() == null){
+            this.getJobDescriptorDocument().getJobDescriptor().addNewPreJobCommands();
+        }
+        this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands().addCommand(command);
+    }
+
+     public void addPostJobCommand(String command){
+        if(this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands() == null){
+            this.getJobDescriptorDocument().getJobDescriptor().addNewPostJobCommands();
+        }
+        this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands().addCommand(command);
+    }
+
+    public void setPartition(String partition){
+        this.getJobDescriptorDocument().getJobDescriptor().setPartition(partition);
+    }
+
+     public void setUserName(String userName){
+        this.getJobDescriptorDocument().getJobDescriptor().setUserName(userName);
+    }
+     public void setNodeList(String nodeList){
+        this.getJobDescriptorDocument().getJobDescriptor().setNodeList(nodeList);
+    }
+    public void setJobSubmitter(String jobSubmitter){
+           this.getJobDescriptorDocument().getJobDescriptor().setJobSubmitterCommand(jobSubmitter);
+    }
+    public String getNodeList(){
+        return this.getJobDescriptorDocument().getJobDescriptor().getNodeList();
+    }
+    public String getExecutablePath() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getExecutablePath();
+    }
+
+    public boolean getAllEnvExport() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getAllEnvExport();
+    }
+
+    public String getMailOptions() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getMailOptions();
+    }
+
+    public String getStandardOutFile() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile();
+    }
+
+    public String getStandardErrorFile() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile();
+    }
+
+    public int getNodes(int name) {
+        return this.getJobDescriptorDocument().getJobDescriptor().getNodes();
+    }
+
+    public int getCPUCount(int name) {
+        return this.getJobDescriptorDocument().getJobDescriptor().getCpuCount();
+    }
+
+    public int getProcessesPerNode() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getProcessesPerNode();
+    }
+
+    public String getMaxWallTime() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getMaxWallTime();
+    }
+
+    public String getAcountString() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getAcountString();
+    }
+
+    public String[] getInputValues() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getInputs().getInputArray();
+    }
+
+    public String getJobID() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+    }
+
+    public String getQueueName() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getQueueName();
+    }
+
+    public String getStatus() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getStatus();
+    }
+
+    public String[] getAfterAnyList() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getAfterAny().getAfterAnyArray();
+    }
+
+    public String[] getAfterOKList() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getAfterOKList().getAfterOKListArray();
+    }
+    public String getCTime() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getCTime();
+    }
+    public String getQTime() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getQTime();
+    }
+    public String getMTime() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getMTime();
+    }
+    public String getSTime() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getSTime();
+    }
+    public String getCompTime() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getCompTime();
+    }
+    public String getOwner() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getOwner();
+    }
+    public String getExecuteNode() {
+         return this.getJobDescriptorDocument().getJobDescriptor().getExecuteNode();
+    }
+    public String getEllapsedTime() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getEllapsedTime();
+    }
+
+    public String getUsedCPUTime() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getUsedCPUTime();
+    }
+
+    public String getUsedMemory() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getUsedMem();
+    }
+    public void getShellName() {
+        this.getJobDescriptorDocument().getJobDescriptor().getShellName();
+    }
+
+    public String getJobName() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getJobName();
+    }
+
+    public String getJobId() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+    }
+
+
+    public String getVariableList() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+    }
+    public String getSubmitArgs() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getJobID();
+    }
+
+    public String[] getPostJobCommands(){
+        if(this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands() != null) {
+            return this.getJobDescriptorDocument().getJobDescriptor().getPostJobCommands().getCommandArray();
+        }
+        return null;
+    }
+
+    public String[] getModuleCommands() {
+        if (this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands() != null) {
+            return this.getJobDescriptorDocument().getJobDescriptor().getModuleLoadCommands().getCommandArray();
+        }
+        return null;
+    }
+
+    public String[] getPreJobCommands(){
+        if(this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands() != null) {
+            return this.getJobDescriptorDocument().getJobDescriptor().getPreJobCommands().getCommandArray();
+        }
+        return null;
+    }
+
+    public String getJobSubmitterCommand(){
+          return this.getJobDescriptorDocument().getJobDescriptor().getJobSubmitterCommand();
+    }
+
+    public String getPartition(){
+        return this.getJobDescriptorDocument().getJobDescriptor().getPartition();
+    }
+
+    public String getUserName(){
+        return this.getJobDescriptorDocument().getJobDescriptor().getUserName();
+    }
+
+    public void setCallBackIp(String ip){
+        this.jobDescriptionDocument.getJobDescriptor().setCallBackIp(ip);
+    }
+
+    public void setCallBackPort(String ip){
+        this.jobDescriptionDocument.getJobDescriptor().setCallBackPort(ip);
+    }
+
+
+    public String getCallBackIp(){
+        return this.jobDescriptionDocument.getJobDescriptor().getCallBackIp();
+    }
+    public String getCallBackPort(){
+        return this.jobDescriptionDocument.getJobDescriptor().getCallBackPort();
+    }
+
+    public void setMailType(String emailType) {
+        this.getJobDescriptorDocument().getJobDescriptor().setMailType(emailType);
+    }
+
+    public String getMailType() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getMailType();
+    }
+    public void setMailAddress(String emailAddress) {
+        this.getJobDescriptorDocument().getJobDescriptor().setMailAddress(emailAddress);
+    }
+
+    public String getMailAddress() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getMailAddress();
+    }
+
+    public String getChassisName() {
+        return this.getJobDescriptorDocument().getJobDescriptor().getChassisName();
+    }
+
+    public void setChassisName(String chassisName){
+        this.getJobDescriptorDocument().getJobDescriptor().setChassisName(chassisName);
+    }
+    
+
+}
+

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobManagerConfiguration.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobManagerConfiguration.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobManagerConfiguration.java
new file mode 100644
index 0000000..d58a994
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobManagerConfiguration.java
@@ -0,0 +1,51 @@
+/*
+ *
+ * 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.ssh.api.job;
+
+import org.apache.airavata.gfac.ssh.impl.RawCommandInfo;
+
+public interface JobManagerConfiguration {
+
+	public RawCommandInfo getCancelCommand(String jobID);
+
+	public String getJobDescriptionTemplateName();
+
+	public RawCommandInfo getMonitorCommand(String jobID);
+
+	public RawCommandInfo getUserBasedMonitorCommand(String userName);
+
+    public RawCommandInfo getJobIdMonitorCommand(String jobName , String userName);
+
+	public String getScriptExtension();
+
+	public RawCommandInfo getSubmitCommand(String workingDirectory, String pbsFilePath);
+
+	public OutputParser getParser();
+
+	public String getInstalledPath();
+
+	public String getBaseCancelCommand();
+
+	public String getBaseMonitorCommand();
+
+	public String getBaseSubmitCommand();
+
+}

http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobType.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobType.java b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobType.java
new file mode 100644
index 0000000..556f4ef
--- /dev/null
+++ b/tools/gsissh/src/main/java/org/apache/airavata/gfac/gsi/ssh/api/job/JobType.java
@@ -0,0 +1,32 @@
+/*
+ *
+ * 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.ssh.api.job;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: lahirugunathilake
+ * Date: 8/22/13
+ * Time: 7:19 AM
+ * To change this template use File | Settings | File Templates.
+ */
+public enum JobType {
+            SERIAL, SINGLE, MPI, MULTIPLE, CONDOR
+}


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