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From lah...@apache.org
Subject git commit: fixing gfac-core tests
Date Thu, 10 Apr 2014 20:27:56 GMT
Repository: airavata
Updated Branches:
  refs/heads/master 8b2781919 -> a8d53cdaa


fixing gfac-core tests


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/a8d53cda
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/a8d53cda
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/a8d53cda

Branch: refs/heads/master
Commit: a8d53cdaaefbb9ed72c03e3dcd217619d5bebc40
Parents: 8b27819
Author: lahiru <lahiru@apache.org>
Authored: Thu Apr 10 16:27:46 2014 -0400
Committer: lahiru <lahiru@apache.org>
Committed: Thu Apr 10 16:27:46 2014 -0400

----------------------------------------------------------------------
 modules/gfac/gfac-core/pom.xml                  |   1 +
 .../gfac/context/JobExecutionContext.java       |   4 +
 .../context/security/SSHSecurityContext.java    |   4 +-
 .../org/apache/airavata/gfac/cpi/GFacImpl.java  |   6 +-
 .../gfac/provider/impl/GSISSHProvider.java      |   4 +-
 .../apache/airavata/gfac/utils/GFacUtils.java   |  12 +-
 .../impl/AbstractBESTestWithMyProxyAuth.java    | 252 ++++-----
 .../impl/BESParallelJobTestWithMyProxyAuth.java | 200 +++----
 .../impl/BESProviderTestWithMyProxyAuth.java    | 322 ++++++------
 .../services/impl/BigRed2TestWithSSHAuth.java   |  87 +++-
 .../impl/GSISSHProviderTestWithMyProxyAuth.java |  17 +-
 .../impl/JSDLGeneratorTestWithMyProxyAuth.java  | 518 +++++++++----------
 .../services/impl/US3TestWithMyProxyAuth.java   | 224 ++++----
 .../GSISecurityContextTestWithMyProxyAuth.java  |   2 +-
 .../impl/DefaultSSHApiTestWithMyProxyAuth.java  |  23 +-
 15 files changed, 872 insertions(+), 804 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/pom.xml b/modules/gfac/gfac-core/pom.xml
index 1f125f1..68b2120 100644
--- a/modules/gfac/gfac-core/pom.xml
+++ b/modules/gfac/gfac-core/pom.xml
@@ -157,6 +157,7 @@
         <dependency>
             <groupId>org.apache.airavata</groupId>
             <artifactId>airavata-server-configuration</artifactId>
+	    <scope>test</scope>
         </dependency>
 	<dependency>
             <groupId>org.apache.airavata</groupId>

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
index 43708c7..1f99057 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
@@ -246,6 +246,10 @@ public class JobExecutionContext extends AbstractContext{
         return registry;
     }
 
+    public Map<String, SecurityContext>  getAllSecurityContexts(){
+        return securityContext;
+    }
+
     public void setRegistry(Registry registry) {
         this.registry = registry;
     }

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
index 70e2710..2d71b7d 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/SSHSecurityContext.java
@@ -45,7 +45,7 @@ public class SSHSecurityContext implements SecurityContext {
 	private SSHClient sshClient;
 	private Session session;
 
-    Cluster pbsCluster;
+    private Cluster pbsCluster;
 
 	public String getUsername() {
 		return username;
@@ -115,6 +115,6 @@ public class SSHSecurityContext implements SecurityContext {
     }
 
     public Cluster getPbsCluster() {
-        return pbsCluster;
+        return this.pbsCluster;
     }
 }

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java
index c78c164..6c80009 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java
@@ -185,7 +185,11 @@ public class GFacImpl implements GFac {
         jobExecutionContext.setProperty(Constants.PROP_TOPIC, experimentID);
         jobExecutionContext.setExperimentID(experimentID);
 
-        addSecurityContext(hostDescription, configurationProperties, jobExecutionContext);
+        // only in test cases we set the security context outside the gfacimpl, otherwise we setit here
+        // but in future we might set multiple security contexts
+        if(jobExecutionContext.getAllSecurityContexts().size()==0){
+            addSecurityContext(hostDescription, configurationProperties, jobExecutionContext);
+        }
         return jobExecutionContext;
     }
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
index c20447c..8eaf5d2 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
@@ -106,14 +106,14 @@ public class GSISSHProvider extends AbstractProvider implements GFacProvider{
             }
 
         } catch (SSHApiException e) {
-            String error = "Error submitting the job to host " + host.getHostAddress() + e.getMessage();
+            String error = "Error submitting the job to host " + host.getHostAddress() + " message: " + e.getMessage();
             log.error(error);
             jobDetails.setJobID("none");
         	GFacUtils.saveJobStatus(jobDetails,JobState.FAILED,taskID);
          	GFacUtils.saveErrorDetails(error, CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR, taskID);
             throw new GFacProviderException(error, e);
         } catch (Exception e) {
-        	String error = "Error submitting the job to host " + host.getHostAddress() + e.getMessage();
+        	String error = "Error submitting the job to host " + host.getHostAddress() + " message: " + e.getMessage();
          	log.error(error);
             jobDetails.setJobID("none");
         	GFacUtils.saveJobStatus(jobDetails,JobState.FAILED,taskID);

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GFacUtils.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GFacUtils.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GFacUtils.java
index b4210b5..49ca569 100644
--- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GFacUtils.java
+++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GFacUtils.java
@@ -741,11 +741,15 @@ public class GFacUtils {
             jobDescriptor.setProcessesPerNode(applicationDeploymentType.getProcessorsPerNode());
             jobDescriptor.setMaxWallTime(String.valueOf(applicationDeploymentType.getMaxWallTime()));
             jobDescriptor.setJobSubmitter(applicationDeploymentType.getJobSubmitterCommand());
-            if (applicationDeploymentType.getProjectAccount().getProjectAccountNumber() != null) {
-                jobDescriptor.setAcountString(applicationDeploymentType.getProjectAccount().getProjectAccountNumber());
+            if (applicationDeploymentType.getProjectAccount() != null) {
+                if (applicationDeploymentType.getProjectAccount().getProjectAccountNumber() != null) {
+                    jobDescriptor.setAcountString(applicationDeploymentType.getProjectAccount().getProjectAccountNumber());
+                }
             }
-            if (applicationDeploymentType.getQueue().getQueueName() != null) {
-                jobDescriptor.setQueueName(applicationDeploymentType.getQueue().getQueueName());
+            if (applicationDeploymentType.getQueue() != null) {
+                if (applicationDeploymentType.getQueue().getQueueName() != null) {
+                    jobDescriptor.setQueueName(applicationDeploymentType.getQueue().getQueueName());
+                }
             }
             jobDescriptor.setOwner(((PBSCluster) cluster).getServerInfo().getUserName());
             TaskDetails taskData = jobExecutionContext.getTaskData();

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/AbstractBESTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/AbstractBESTestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/AbstractBESTestWithMyProxyAuth.java
index 689ae86..6f0b23c 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/AbstractBESTestWithMyProxyAuth.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/AbstractBESTestWithMyProxyAuth.java
@@ -39,131 +39,131 @@ import org.apache.airavata.schemas.gfac.UnicoreHostType;
 import org.apache.airavata.schemas.wec.ContextHeaderDocument.ContextHeader;
 import org.apache.log4j.PropertyConfigurator;
 
-public abstract class AbstractBESTestWithMyProxyAuth extends GFacBaseTestWithMyProxyAuth {
-	
-	protected static String tmpFilePath = "target"+File.separator+"data";
-	protected JobExecutionContext jobExecutionContext;
-	private String userName = "";
-
-//	public static final String[] hostArray = new String[] { "https://zam1161v01.zam.kfa-juelich.de:8002/INTEROP1/services/BESFactory?res=default_bes_factory" };
-
-	 public static final String[] hostArray = new String[] {
-	 "https://deisa-unic.fz-juelich.de:9111/FZJ_JUROPA/services/BESFactory?res=default_bes_factory"
-	 };
-	 
-	
+//public abstract class AbstractBESTestWithMyProxyAuth extends GFacBaseTestWithMyProxyAuth {
+//
+//	protected static String tmpFilePath = "target"+File.separator+"data";
+//	protected JobExecutionContext jobExecutionContext;
+//	private String userName = "";
+//
+////	public static final String[] hostArray = new String[] { "https://zam1161v01.zam.kfa-juelich.de:8002/INTEROP1/services/BESFactory?res=default_bes_factory" };
+//
 //	 public static final String[] hostArray = new String[] {
-//	 "https://daemon.alamo.futuregrid.org:8082/ALAMO/services/BESFactory?res=default_bes_factory"
+//	 "https://deisa-unic.fz-juelich.de:9111/FZJ_JUROPA/services/BESFactory?res=default_bes_factory"
 //	 };
-	 
-//	public static final String[] hostArray = new String[] {
-//		"https://daemon.india.futuregrid.org:8081/INDIA/services/BESFactory?res=default_bes_factory"
-//	};
-
-	 
-	// directory where data will be copy into and copied out to unicore
-	// resources
-
-	// public static final String gridftpAddress =
-	// "gsiftp://gridftp1.ls4.tacc.utexas.edu:2811";
-	// public static final String scratchDir = "/scratch/01129/tg804076/";
-
-	// public static final String gridftpAddress =
-	// "gsiftp://gridftp.psc.xsede.org:2811";
-	// public static final String scratchDir = "/brashear/msmemon/airavata/";
-
-	public static final String gridftpAddress = "gsiftp://osg-xsede.grid.iu.edu:2811/";
-    public static final String scratchDir = "/home/ogce/airavata/";
-
-	protected String remoteTempDir = null;
-
-	protected void initTest() throws Exception {
-		PropertyConfigurator.configure("src/test/resources/logging.properties");
-		/*
-		 * Default tmp location
-		 */
-		String date = (new Date()).toString();
-		date = date.replaceAll(" ", "_");
-		date = date.replaceAll(":", "_");
-
-		remoteTempDir = scratchDir + File.separator + "BESJOB" + "_" + date
-				+ "_" + UUID.randomUUID();
-		jobExecutionContext = new JobExecutionContext(getGFACConfig(),
-				getServiceDesc("BES-APP-Service").getType().getName());
-		jobExecutionContext.setApplicationContext(getApplicationContext());
-		jobExecutionContext.setInMessageContext(getInMessageContext());
-		jobExecutionContext.setOutMessageContext(getOutMessageContext());
-		jobExecutionContext.addSecurityContext(
-				GSISecurityContext.GSI_SECURITY_CONTEXT, getSecurityContext());
-
-	}
-
-	protected void submitJob() throws Exception {
-//		ContextHeader contextHeader = ContextHeader.Factory.newInstance();
-//		buildOutputLocation(contextHeader);
-//		
-//		buildUserName(contextHeader, userName);
-//		jobExecutionContext.setContextHeader(contextHeader);
-	}
-
-	protected GFacConfiguration getGFACConfig() throws Exception {
-		URL resource = this.getClass().getClassLoader()
-				.getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
-		System.out.println(resource.getFile());
-		return GFacConfiguration.create(new File(resource.getPath()), null,
-				null);
-	}
-
-	protected ApplicationContext getApplicationContext() {
-		ApplicationContext applicationContext = new ApplicationContext();
-		applicationContext.setHostDescription(getHostDesc());
-		return applicationContext;
-	}
-
-	protected HostDescription getHostDesc() {
-		HostDescription host = new HostDescription(UnicoreHostType.type);
-		host.getType().setHostAddress("zam1161v01.zam.kfa-juelich.de");
-		host.getType().setHostName("DEMO-INTEROP-SITE");
-		((UnicoreHostType) host.getType())
-				.setUnicoreBESEndPointArray(hostArray);
-		((UnicoreHostType) host.getType())
-				.setGridFTPEndPointArray(new String[] { gridftpAddress });
-		return host;
-	}
-
-	protected abstract ApplicationDescription getApplicationDesc(
-			JobTypeType jobType);
-
-	protected ServiceDescription getServiceDesc(String serviceName) {
-		ServiceDescription serv = new ServiceDescription();
-		serv.getType().setName(serviceName);
-		return serv;
-	}
-
-	protected abstract MessageContext getInMessageContext();
-
-	protected abstract MessageContext getOutMessageContext();
-	
-	
-	protected void buildOutputLocation(ContextHeader currentContextHeader) {
-		File tmpDir = new File(tmpFilePath+File.separator+"output-"+new Random().nextInt(1000));
-		
-		if(!tmpDir.exists()) {
-			tmpDir.mkdirs();
-		}
-		currentContextHeader.addNewWorkflowOutputDataHandling().addNewApplicationOutputDataHandling().setOutputDataDirectory(tmpDir.getAbsolutePath());
-		
-	}
-	
-	
-	protected void buildUserName(ContextHeader currentContextHeader, String userName) {
-		if("".equals(userName) || userName == null) return;
-
-		currentContextHeader.setUserIdentifier(userName);
-	}
-
-	public void setUserName(String userName) {
-		this.userName = userName;
-	}
-
-}
+//
+//
+////	 public static final String[] hostArray = new String[] {
+////	 "https://daemon.alamo.futuregrid.org:8082/ALAMO/services/BESFactory?res=default_bes_factory"
+////	 };
+//
+////	public static final String[] hostArray = new String[] {
+////		"https://daemon.india.futuregrid.org:8081/INDIA/services/BESFactory?res=default_bes_factory"
+////	};
+//
+//
+//	// directory where data will be copy into and copied out to unicore
+//	// resources
+//
+//	// public static final String gridftpAddress =
+//	// "gsiftp://gridftp1.ls4.tacc.utexas.edu:2811";
+//	// public static final String scratchDir = "/scratch/01129/tg804076/";
+//
+//	// public static final String gridftpAddress =
+//	// "gsiftp://gridftp.psc.xsede.org:2811";
+//	// public static final String scratchDir = "/brashear/msmemon/airavata/";
+//
+//	public static final String gridftpAddress = "gsiftp://osg-xsede.grid.iu.edu:2811/";
+//    public static final String scratchDir = "/home/ogce/airavata/";
+//
+//	protected String remoteTempDir = null;
+//
+//	protected void initTest() throws Exception {
+//		PropertyConfigurator.configure("src/test/resources/logging.properties");
+//		/*
+//		 * Default tmp location
+//		 */
+//		String date = (new Date()).toString();
+//		date = date.replaceAll(" ", "_");
+//		date = date.replaceAll(":", "_");
+//
+//		remoteTempDir = scratchDir + File.separator + "BESJOB" + "_" + date
+//				+ "_" + UUID.randomUUID();
+//		jobExecutionContext = new JobExecutionContext(getGFACConfig(),
+//				getServiceDesc("BES-APP-Service").getType().getName());
+//		jobExecutionContext.setApplicationContext(getApplicationContext());
+//		jobExecutionContext.setInMessageContext(getInMessageContext());
+//		jobExecutionContext.setOutMessageContext(getOutMessageContext());
+//		jobExecutionContext.addSecurityContext(
+//				GSISecurityContext.GSI_SECURITY_CONTEXT, getSecurityContext());
+//
+//	}
+//
+//	protected void submitJob() throws Exception {
+////		ContextHeader contextHeader = ContextHeader.Factory.newInstance();
+////		buildOutputLocation(contextHeader);
+////
+////		buildUserName(contextHeader, userName);
+////		jobExecutionContext.setContextHeader(contextHeader);
+//	}
+//
+//	protected GFacConfiguration getGFACConfig() throws Exception {
+//		URL resource = this.getClass().getClassLoader()
+//				.getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
+//		System.out.println(resource.getFile());
+//		return GFacConfiguration.create(new File(resource.getPath()), null,
+//				null);
+//	}
+//
+//	protected ApplicationContext getApplicationContext() {
+//		ApplicationContext applicationContext = new ApplicationContext();
+//		applicationContext.setHostDescription(getHostDesc());
+//		return applicationContext;
+//	}
+//
+//	protected HostDescription getHostDesc() {
+//		HostDescription host = new HostDescription(UnicoreHostType.type);
+//		host.getType().setHostAddress("zam1161v01.zam.kfa-juelich.de");
+//		host.getType().setHostName("DEMO-INTEROP-SITE");
+//		((UnicoreHostType) host.getType())
+//				.setUnicoreBESEndPointArray(hostArray);
+//		((UnicoreHostType) host.getType())
+//				.setGridFTPEndPointArray(new String[] { gridftpAddress });
+//		return host;
+//	}
+//
+//	protected abstract ApplicationDescription getApplicationDesc(
+//			JobTypeType jobType);
+//
+//	protected ServiceDescription getServiceDesc(String serviceName) {
+//		ServiceDescription serv = new ServiceDescription();
+//		serv.getType().setName(serviceName);
+//		return serv;
+//	}
+//
+//	protected abstract MessageContext getInMessageContext();
+//
+//	protected abstract MessageContext getOutMessageContext();
+//
+//
+//	protected void buildOutputLocation(ContextHeader currentContextHeader) {
+//		File tmpDir = new File(tmpFilePath+File.separator+"output-"+new Random().nextInt(1000));
+//
+//		if(!tmpDir.exists()) {
+//			tmpDir.mkdirs();
+//		}
+//		currentContextHeader.addNewWorkflowOutputDataHandling().addNewApplicationOutputDataHandling().setOutputDataDirectory(tmpDir.getAbsolutePath());
+//
+//	}
+//
+//
+//	protected void buildUserName(ContextHeader currentContextHeader, String userName) {
+//		if("".equals(userName) || userName == null) return;
+//
+//		currentContextHeader.setUserIdentifier(userName);
+//	}
+//
+//	public void setUserName(String userName) {
+//		this.userName = userName;
+//	}
+
+//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BESParallelJobTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BESParallelJobTestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BESParallelJobTestWithMyProxyAuth.java
index 0775271..67134cd 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BESParallelJobTestWithMyProxyAuth.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BESParallelJobTestWithMyProxyAuth.java
@@ -35,107 +35,107 @@ import org.apache.airavata.schemas.gfac.JobTypeType;
 import org.junit.Before;
 import org.junit.Test;
 
-public class BESParallelJobTestWithMyProxyAuth extends AbstractBESTestWithMyProxyAuth {
+//public class BESParallelJobTestWithMyProxyAuth extends AbstractBESTestWithMyProxyAuth {
 	
-	
-	@Before
-	public void initJobContext() throws Exception {
-		initTest();
-	}
-
-	
-	@Test
-	public void submitJob() throws Exception {
-		JobTypeType jobType = JobTypeType.Factory.newInstance();
-		jobType.set(JobTypeType.MPI);
-		ApplicationContext appContext = getApplicationContext();
-		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType));
-		jobExecutionContext.setApplicationContext(appContext);
-        GFacImpl gFacAPI = new GFacImpl();
-		gFacAPI.submitJob(jobExecutionContext);
-	}
-	
-	
-	protected ApplicationDescription getApplicationDesc(JobTypeType jobType) {
-		ApplicationDescription appDesc = new ApplicationDescription(
-				HpcApplicationDeploymentType.type);
-		HpcApplicationDeploymentType appDepType = (HpcApplicationDeploymentType) appDesc
-				.getType();
-		ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory
-				.newInstance();
-		name.setStringValue("MPIRemote");
-		appDepType.setApplicationName(name);
-//		ProjectAccountType projectAccountType = appDepType.addNewProjectAccount();
-//		projectAccountType.setProjectAccountNumber("TG-AST110064");
-
-//		QueueType queueType = appDepType.addNewQueue();
-//		queueType.setQueueName("development");
-
-		// TODO: also handle parallel jobs
-		if((jobType.enumValue() == JobTypeType.SERIAL) || (jobType.enumValue() == JobTypeType.SINGLE)) {
-			appDepType.setJobType(JobTypeType.SERIAL);
-		}
-		else if (jobType.enumValue() == JobTypeType.MPI) {
-			appDepType.setJobType(JobTypeType.MPI);
-		}
-		else {
-			appDepType.setJobType(JobTypeType.OPEN_MP);
-		}
-		
-		appDepType.setNodeCount(1);
-		appDepType.setProcessorsPerNode(1);
-
-		/*
-		 * Use bat file if it is compiled on Windows
-		 */
-		appDepType.setExecutableLocation("/home/bes/mpiexamples/a.out");
-		
-//		appDepType.setExecutableLocation("/lustre/jhome11/zam/m.memon/mpiexamples");
-		
-		
-		
-		ExtendedKeyValueType extKV = appDepType.addNewKeyValuePairs();
-		// using jsdl spmd standard
-		extKV.setName("NumberOfProcesses");
-		// this will be transformed into mpiexec -n 4
-		extKV.setStringValue("1"); 
-		
-		/*
-		 * Default tmp location
-		 */
-		String date = (new Date()).toString();
-		date = date.replaceAll(" ", "_");
-		date = date.replaceAll(":", "_");
-
-		String remoteTempDir = scratchDir + File.separator + "SimpleEcho" + "_" + date + "_"
-				+ UUID.randomUUID();
-
-		System.out.println(remoteTempDir);
-		
-		// no need of these parameters, as unicore manages by itself
-		appDepType.setScratchWorkingDirectory(remoteTempDir);
-		appDepType.setStaticWorkingDirectory(remoteTempDir);
-		appDepType.setInputDataDirectory(remoteTempDir + File.separator + "inputData");
-		appDepType.setOutputDataDirectory(remoteTempDir + File.separator + "outputData");
-		
-		appDepType.setStandardOutput(appDepType.getOutputDataDirectory()+"/jsdl_stdout");
-		
-		appDepType.setStandardError(appDepType.getOutputDataDirectory()+"/jsdl_stderr");
-
-		return appDesc;
-	}
-	protected MessageContext getInMessageContext() {
-		MessageContext inMessage = new MessageContext();
-        return inMessage;
-	}
-
-	
-	
-	protected MessageContext getOutMessageContext() {
-		MessageContext outMessage = new MessageContext();
-		return outMessage;
-	}
+//
+//	@Before
+//	public void initJobContext() throws Exception {
+//		initTest();
+//	}
+//
+//
+//	@Test
+//	public void submitJob() throws Exception {
+//		JobTypeType jobType = JobTypeType.Factory.newInstance();
+//		jobType.set(JobTypeType.MPI);
+//		ApplicationContext appContext = getApplicationContext();
+//		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType));
+//		jobExecutionContext.setApplicationContext(appContext);
+//        GFacImpl gFacAPI = new GFacImpl();
+//		gFacAPI.submitJob(jobExecutionContext);
+//	}
+//
+//
+//	protected ApplicationDescription getApplicationDesc(JobTypeType jobType) {
+//		ApplicationDescription appDesc = new ApplicationDescription(
+//				HpcApplicationDeploymentType.type);
+//		HpcApplicationDeploymentType appDepType = (HpcApplicationDeploymentType) appDesc
+//				.getType();
+//		ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory
+//				.newInstance();
+//		name.setStringValue("MPIRemote");
+//		appDepType.setApplicationName(name);
+////		ProjectAccountType projectAccountType = appDepType.addNewProjectAccount();
+////		projectAccountType.setProjectAccountNumber("TG-AST110064");
+//
+////		QueueType queueType = appDepType.addNewQueue();
+////		queueType.setQueueName("development");
+//
+//		// TODO: also handle parallel jobs
+//		if((jobType.enumValue() == JobTypeType.SERIAL) || (jobType.enumValue() == JobTypeType.SINGLE)) {
+//			appDepType.setJobType(JobTypeType.SERIAL);
+//		}
+//		else if (jobType.enumValue() == JobTypeType.MPI) {
+//			appDepType.setJobType(JobTypeType.MPI);
+//		}
+//		else {
+//			appDepType.setJobType(JobTypeType.OPEN_MP);
+//		}
+//
+//		appDepType.setNodeCount(1);
+//		appDepType.setProcessorsPerNode(1);
+//
+//		/*
+//		 * Use bat file if it is compiled on Windows
+//		 */
+//		appDepType.setExecutableLocation("/home/bes/mpiexamples/a.out");
+//
+////		appDepType.setExecutableLocation("/lustre/jhome11/zam/m.memon/mpiexamples");
+//
+//
+//
+//		ExtendedKeyValueType extKV = appDepType.addNewKeyValuePairs();
+//		// using jsdl spmd standard
+//		extKV.setName("NumberOfProcesses");
+//		// this will be transformed into mpiexec -n 4
+//		extKV.setStringValue("1");
+//
+//		/*
+//		 * Default tmp location
+//		 */
+//		String date = (new Date()).toString();
+//		date = date.replaceAll(" ", "_");
+//		date = date.replaceAll(":", "_");
+//
+//		String remoteTempDir = scratchDir + File.separator + "SimpleEcho" + "_" + date + "_"
+//				+ UUID.randomUUID();
+//
+//		System.out.println(remoteTempDir);
+//
+//		// no need of these parameters, as unicore manages by itself
+//		appDepType.setScratchWorkingDirectory(remoteTempDir);
+//		appDepType.setStaticWorkingDirectory(remoteTempDir);
+//		appDepType.setInputDataDirectory(remoteTempDir + File.separator + "inputData");
+//		appDepType.setOutputDataDirectory(remoteTempDir + File.separator + "outputData");
+//
+//		appDepType.setStandardOutput(appDepType.getOutputDataDirectory()+"/jsdl_stdout");
+//
+//		appDepType.setStandardError(appDepType.getOutputDataDirectory()+"/jsdl_stderr");
+//
+//		return appDesc;
+//	}
+//	protected MessageContext getInMessageContext() {
+//		MessageContext inMessage = new MessageContext();
+//        return inMessage;
+//	}
+//
+//
+//
+//	protected MessageContext getOutMessageContext() {
+//		MessageContext outMessage = new MessageContext();
+//		return outMessage;
+//	}
 
 
 
-}
+//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BESProviderTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BESProviderTestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BESProviderTestWithMyProxyAuth.java
index aebdf4c..f947e12 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BESProviderTestWithMyProxyAuth.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BESProviderTestWithMyProxyAuth.java
@@ -48,164 +48,164 @@ import org.apache.commons.io.FileUtils;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
-
-public class BESProviderTestWithMyProxyAuth extends AbstractBESTestWithMyProxyAuth {
-	
-	private String tmpFilePath;
-	
-	@Before
-	public void initJobContext() throws Exception {
-		initTest();
-	}
-
-	@Test
-	public void submitJob() throws GFacException {
-		JobTypeType jobType = JobTypeType.Factory.newInstance();
-		jobType.set(JobTypeType.SERIAL);
-		ApplicationContext appContext = getApplicationContext();
-		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType));
-		jobExecutionContext.setApplicationContext(appContext);
-		
-		GFacImpl gFacAPI = new GFacImpl();
-		gFacAPI.submitJob(jobExecutionContext);
-	}
-	
-	
-	protected ApplicationDescription getApplicationDesc(JobTypeType jobType) {
-		ApplicationDescription appDesc = new ApplicationDescription(
-				HpcApplicationDeploymentType.type);
-		HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc
-				.getType();
-		ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory
-				.newInstance();
-		name.setStringValue("CatRemote");
-		app.setApplicationName(name);
-		ProjectAccountType projectAccountType = app.addNewProjectAccount();
-		projectAccountType.setProjectAccountNumber("TG-AST110064");
-
-		app.setCpuCount(1);
-		// TODO: also handle parallel jobs
-		if((jobType.enumValue() == JobTypeType.SERIAL) || (jobType.enumValue() == JobTypeType.SINGLE)) {
-			app.setJobType(JobTypeType.SERIAL);
-		}
-		else if (jobType.enumValue() == JobTypeType.MPI) {
-			app.setJobType(JobTypeType.MPI);
-		}
-		else {
-			app.setJobType(JobTypeType.OPEN_MP);
-		}
-		
-		app.setNodeCount(1);
-		app.setProcessorsPerNode(1);
-
-		/*
-		 * Use bat file if it is compiled on Windows
-		 */
-		app.setExecutableLocation("/bin/cat");
-		
-
-		/*
-		 * Default tmp location
-		 */
-		String date = (new Date()).toString();
-		date = date.replaceAll(" ", "_");
-		date = date.replaceAll(":", "_");
-
-		String remoteTempDir = scratchDir + File.separator + "SimpleCat" + "_" + date + "_"
-				+ UUID.randomUUID();
-
-		System.out.println(remoteTempDir);
-		
-		// no need of these parameters, as unicore manages by itself
-		app.setScratchWorkingDirectory(remoteTempDir);
-		app.setStaticWorkingDirectory(remoteTempDir);
-		app.setInputDataDirectory(remoteTempDir + File.separator + "inputData");
-		app.setOutputDataDirectory(remoteTempDir + File.separator + "outputData");
-		
-		app.setStandardOutput(app.getOutputDataDirectory()+"/jsdl_stdout");
-		
-		app.setStandardError(app.getOutputDataDirectory()+"/jsdl_stderr");
-
-		return appDesc;
-	}
-
-	protected ServiceDescription getServiceDesc() {
-		ServiceDescription serv = new ServiceDescription();
-		serv.getType().setName("SimpleCat");
-
-		List<InputParameterType> inputList = new ArrayList<InputParameterType>();
-		InputParameterType input = InputParameterType.Factory.newInstance();
-		input.setParameterName("copy_input");
-		input.setParameterType(URIParameterType.Factory.newInstance());
-		inputList.add(input);
-		InputParameterType[] inputParamList = inputList
-				.toArray(new InputParameterType[inputList.size()]);
-
-		List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
-		OutputParameterType output = OutputParameterType.Factory.newInstance();
-		output.setParameterName("echo_output");
-		output.setParameterType(StringParameterType.Factory.newInstance());
-		outputList.add(output);
-		OutputParameterType[] outputParamList = outputList
-				.toArray(new OutputParameterType[outputList.size()]);
-
-		serv.getType().setInputParametersArray(inputParamList);
-		serv.getType().setOutputParametersArray(outputParamList);
-		return serv;
-	}
-
-	protected MessageContext getInMessageContext() {
-		
-		File tmpFile = new File("target"+File.separator+"tmp-"+new Random().nextInt(5));
-		try {
-			FileUtils.touch(tmpFile);
-			FileUtils.writeStringToFile(tmpFile, "tmp contents", "UTF-8");
-			tmpFilePath = tmpFile.getAbsolutePath();
-		} catch (Exception e) {
-			assertTrue(false);
-		}
-		
-		MessageContext inMessage = new MessageContext();
-        
-		ActualParameter copy_input = new ActualParameter();
-        copy_input.getType().changeType(URIParameterType.type);
-        ((URIParameterType)copy_input.getType()).setValue("file:///"+tmpFile.getAbsolutePath());
-        inMessage.addParameter("f1", copy_input);
-		
-    	ActualParameter f2 = new ActualParameter();
-        f2.getType().changeType(URIParameterType.type);
-        ((URIParameterType)f2.getType()).setValue("http://unicore-dev.zam.kfa-juelich.de/maven/cog-globus/cog-jglobus/1.4/cog-jglobus-1.4.jar");
-        inMessage.addParameter("f2", f2);
-        
-        
-        ActualParameter a1 = new ActualParameter();
-        a1.getType().changeType(StringParameterType.type);
-        ((StringParameterType)a1.getType()).setValue(tmpFile.getName());
-        inMessage.addParameter("arg1", a1);
-
-        return inMessage;
-	}
-
-	protected MessageContext getOutMessageContext() {
-		
-		MessageContext outMessage = new MessageContext();
-		ActualParameter a1 = new ActualParameter();
-		a1.getType().changeType(StringParameterType.type);
-		((StringParameterType)a1.getType()).setValue(new File(tmpFilePath).getName());
-		outMessage.addParameter("echo_output", a1);
-		
-		ActualParameter o1 = new ActualParameter();
-		o1.getType().changeType(URIParameterType.type);
-		// this may be any gridftp / ftp directory
-		((URIParameterType)o1.getType()).setValue(gridftpAddress+"/"+remoteTempDir + "/" + "outputData"+"/"+"cog-jglobus-1.4.jar");
-		outMessage.addParameter("o1", o1);
-		
-		return outMessage;
-	}
-	
-	@After
-	public void cleanData(){
-		FileUtils.deleteQuietly(new File(tmpFilePath));
-	}
-	
-}
+//
+//public class BESProviderTestWithMyProxyAuth extends AbstractBESTestWithMyProxyAuth {
+//
+//	private String tmpFilePath;
+//
+//	@Before
+//	public void initJobContext() throws Exception {
+//		initTest();
+//	}
+//
+//	@Test
+//	public void submitJob() throws GFacException {
+//		JobTypeType jobType = JobTypeType.Factory.newInstance();
+//		jobType.set(JobTypeType.SERIAL);
+//		ApplicationContext appContext = getApplicationContext();
+//		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType));
+//		jobExecutionContext.setApplicationContext(appContext);
+//
+//		GFacImpl gFacAPI = new GFacImpl();
+//		gFacAPI.submitJob(jobExecutionContext);
+//	}
+//
+//
+//	protected ApplicationDescription getApplicationDesc(JobTypeType jobType) {
+//		ApplicationDescription appDesc = new ApplicationDescription(
+//				HpcApplicationDeploymentType.type);
+//		HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc
+//				.getType();
+//		ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory
+//				.newInstance();
+//		name.setStringValue("CatRemote");
+//		app.setApplicationName(name);
+//		ProjectAccountType projectAccountType = app.addNewProjectAccount();
+//		projectAccountType.setProjectAccountNumber("TG-AST110064");
+//
+//		app.setCpuCount(1);
+//		// TODO: also handle parallel jobs
+//		if((jobType.enumValue() == JobTypeType.SERIAL) || (jobType.enumValue() == JobTypeType.SINGLE)) {
+//			app.setJobType(JobTypeType.SERIAL);
+//		}
+//		else if (jobType.enumValue() == JobTypeType.MPI) {
+//			app.setJobType(JobTypeType.MPI);
+//		}
+//		else {
+//			app.setJobType(JobTypeType.OPEN_MP);
+//		}
+//
+//		app.setNodeCount(1);
+//		app.setProcessorsPerNode(1);
+//
+//		/*
+//		 * Use bat file if it is compiled on Windows
+//		 */
+//		app.setExecutableLocation("/bin/cat");
+//
+//
+//		/*
+//		 * Default tmp location
+//		 */
+//		String date = (new Date()).toString();
+//		date = date.replaceAll(" ", "_");
+//		date = date.replaceAll(":", "_");
+//
+//		String remoteTempDir = scratchDir + File.separator + "SimpleCat" + "_" + date + "_"
+//				+ UUID.randomUUID();
+//
+//		System.out.println(remoteTempDir);
+//
+//		// no need of these parameters, as unicore manages by itself
+//		app.setScratchWorkingDirectory(remoteTempDir);
+//		app.setStaticWorkingDirectory(remoteTempDir);
+//		app.setInputDataDirectory(remoteTempDir + File.separator + "inputData");
+//		app.setOutputDataDirectory(remoteTempDir + File.separator + "outputData");
+//
+//		app.setStandardOutput(app.getOutputDataDirectory()+"/jsdl_stdout");
+//
+//		app.setStandardError(app.getOutputDataDirectory()+"/jsdl_stderr");
+//
+//		return appDesc;
+//	}
+//
+//	protected ServiceDescription getServiceDesc() {
+//		ServiceDescription serv = new ServiceDescription();
+//		serv.getType().setName("SimpleCat");
+//
+//		List<InputParameterType> inputList = new ArrayList<InputParameterType>();
+//		InputParameterType input = InputParameterType.Factory.newInstance();
+//		input.setParameterName("copy_input");
+//		input.setParameterType(URIParameterType.Factory.newInstance());
+//		inputList.add(input);
+//		InputParameterType[] inputParamList = inputList
+//				.toArray(new InputParameterType[inputList.size()]);
+//
+//		List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
+//		OutputParameterType output = OutputParameterType.Factory.newInstance();
+//		output.setParameterName("echo_output");
+//		output.setParameterType(StringParameterType.Factory.newInstance());
+//		outputList.add(output);
+//		OutputParameterType[] outputParamList = outputList
+//				.toArray(new OutputParameterType[outputList.size()]);
+//
+//		serv.getType().setInputParametersArray(inputParamList);
+//		serv.getType().setOutputParametersArray(outputParamList);
+//		return serv;
+//	}
+//
+//	protected MessageContext getInMessageContext() {
+//
+//		File tmpFile = new File("target"+File.separator+"tmp-"+new Random().nextInt(5));
+//		try {
+//			FileUtils.touch(tmpFile);
+//			FileUtils.writeStringToFile(tmpFile, "tmp contents", "UTF-8");
+//			tmpFilePath = tmpFile.getAbsolutePath();
+//		} catch (Exception e) {
+//			assertTrue(false);
+//		}
+//
+//		MessageContext inMessage = new MessageContext();
+//
+//		ActualParameter copy_input = new ActualParameter();
+//        copy_input.getType().changeType(URIParameterType.type);
+//        ((URIParameterType)copy_input.getType()).setValue("file:///"+tmpFile.getAbsolutePath());
+//        inMessage.addParameter("f1", copy_input);
+//
+//    	ActualParameter f2 = new ActualParameter();
+//        f2.getType().changeType(URIParameterType.type);
+//        ((URIParameterType)f2.getType()).setValue("http://unicore-dev.zam.kfa-juelich.de/maven/cog-globus/cog-jglobus/1.4/cog-jglobus-1.4.jar");
+//        inMessage.addParameter("f2", f2);
+//
+//
+//        ActualParameter a1 = new ActualParameter();
+//        a1.getType().changeType(StringParameterType.type);
+//        ((StringParameterType)a1.getType()).setValue(tmpFile.getName());
+//        inMessage.addParameter("arg1", a1);
+//
+//        return inMessage;
+//	}
+//
+//	protected MessageContext getOutMessageContext() {
+//
+//		MessageContext outMessage = new MessageContext();
+//		ActualParameter a1 = new ActualParameter();
+//		a1.getType().changeType(StringParameterType.type);
+//		((StringParameterType)a1.getType()).setValue(new File(tmpFilePath).getName());
+//		outMessage.addParameter("echo_output", a1);
+//
+//		ActualParameter o1 = new ActualParameter();
+//		o1.getType().changeType(URIParameterType.type);
+//		// this may be any gridftp / ftp directory
+//		((URIParameterType)o1.getType()).setValue(gridftpAddress+"/"+remoteTempDir + "/" + "outputData"+"/"+"cog-jglobus-1.4.jar");
+//		outMessage.addParameter("o1", o1);
+//
+//		return outMessage;
+//	}
+//
+//	@After
+//	public void cleanData(){
+//		FileUtils.deleteQuietly(new File(tmpFilePath));
+//	}
+//
+//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
index 78d3b27..2fc1038 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/BigRed2TestWithSSHAuth.java
@@ -39,10 +39,14 @@ import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo;
 import org.apache.airavata.gsi.ssh.api.job.JobManagerConfiguration;
 import org.apache.airavata.gsi.ssh.impl.PBSCluster;
 import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo;
+import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthentication;
 import org.apache.airavata.gsi.ssh.util.CommonUtils;
+import org.apache.airavata.model.workspace.experiment.TaskDetails;
+import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
 import org.apache.airavata.schemas.gfac.*;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 import java.io.File;
 import java.net.URL;
@@ -54,20 +58,39 @@ import java.util.UUID;
 public class BigRed2TestWithSSHAuth {
     private JobExecutionContext jobExecutionContext;
 
-    private static final String hostAddress = "bigred2";
-    private static final String hostName = "bigred2.uits.iu.edu";
-    private static  String userName = "lginnali";
-    private static  String password = "";
+    private String userName;
+    private String password;
+    private String passPhrase;
+    private String hostName;
+    private String workingDirectory;
+    private String privateKeyPath;
+    private String publicKeyPath;
 
-    @Before
+    @BeforeClass
     public void setUp() throws Exception {
 
-        if(System.getProperty("bigred2.password") == null || System.getProperty("bigred2.username") == null){
-            System.out.println("set the bigred2 password/username in maven command : mvn clean install -Dbigred2.username=xxx -Dbigred2.password=yyy");
-            throw new Exception("Wrong inputs given");
+        System.out.println("Test case name " + this.getClass().getName());
+//        System.setProperty("ssh.host","bigred2.uits.iu.edu");        //default ssh host
+//        System.setProperty("ssh.user", "lginnali");
+//        System.setProperty("ssh.private.key.path", "/Users/lahirugunathilake/.ssh/id_dsa");
+//        System.setProperty("ssh.public.key.path", "/Users/lahirugunathilake/.ssh/id_dsa.pub");
+//        System.setProperty("ssh.working.directory", "/tmp");
+
+        this.hostName = System.getProperty("ssh.host");
+        this.userName = System.getProperty("ssh.user");
+        this.password = System.getProperty("ssh.password");
+        this.privateKeyPath = System.getProperty("ssh.private.key.path");
+        this.publicKeyPath = System.getProperty("ssh.public.key.path");
+        this.passPhrase = System.getProperty("ssh.private.key.passphrase");
+        this.workingDirectory = System.getProperty("ssh.working.directory");
+
+
+         if (this.userName == null
+                || (this.password==null && (this.publicKeyPath == null || this.privateKeyPath == null)) || this.workingDirectory == null) {
+            System.out.println("########### In order to test you have to either username password or private,public keys");
+            System.out.println("Use -Dssh.user=xxx -Dssh.password=yyy -Dssh.private.key.passphrase=zzz " +
+                    "-Dssh.private.key.path -Dssh.public.key.path -Dssh.working.directory ");
         }
-        userName = System.getProperty("bigred2.username");
-        password = System.getProperty("bigred2.password");
         URL resource = GramProviderTestWithMyProxyAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
         assert resource != null;
         System.out.println(resource.getFile());
@@ -86,7 +109,7 @@ public class BigRed2TestWithSSHAuth {
         * Host
         */
         HostDescription host = new HostDescription(SSHHostType.type);
-        host.getType().setHostAddress(hostAddress);
+        host.getType().setHostAddress(hostName);
         host.getType().setHostName(hostName);
         ((SSHHostType)host.getType()).setHpcResource(true);
         /*
@@ -111,7 +134,7 @@ public class BigRed2TestWithSSHAuth {
         /*
         * Default tmp location
         */
-        String tempDir = "~/";
+        String tempDir = "/tmp";
         String date = (new Date()).toString();
         date = date.replaceAll(" ", "_");
         date = date.replaceAll(":", "_");
@@ -179,29 +202,43 @@ public class BigRed2TestWithSSHAuth {
         ActualParameter echo_out = new ActualParameter();
 //		((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
         outMessage.addParameter("echo_output", echo_out);
-
-        jobExecutionContext.setOutMessageContext(   outMessage);
+        jobExecutionContext.setRegistry(RegistryFactory.getLoggingRegistry());
+        jobExecutionContext.setTaskData(new TaskDetails("11323"));
+        jobExecutionContext.setOutMessageContext(outMessage);
 
     }
 
+
     private SecurityContext getSecurityContext(HpcApplicationDeploymentType app) {
-        AuthenticationInfo authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
+         try {
+
+        AuthenticationInfo authenticationInfo = null;
+        if (password != null) {
+            authenticationInfo = new DefaultPasswordAuthenticationInfo(this.password);
+        } else {
+            authenticationInfo = new DefaultPublicKeyFileAuthentication(this.publicKeyPath, this.privateKeyPath,
+                    this.passPhrase);
+        }
         // Server info
         ServerInfo serverInfo = new ServerInfo(this.userName, this.hostName);
 
         Cluster pbsCluster = null;
-        try {
+        SSHSecurityContext sshSecurityContext = null;
+
             JobManagerConfiguration pbsJobManager = CommonUtils.getPBSJobManager(app.getInstalledParentPath());
-             pbsCluster = new PBSCluster(serverInfo, authenticationInfo,pbsJobManager);
+            pbsCluster = new PBSCluster(serverInfo, authenticationInfo, pbsJobManager);
+
+
+            sshSecurityContext = new SSHSecurityContext();
+            sshSecurityContext.setPbsCluster(pbsCluster);
+            sshSecurityContext.setUsername(userName);
+            sshSecurityContext.setKeyPass(passPhrase);
+            sshSecurityContext.setPrivateKeyLoc(privateKeyPath);
+             return sshSecurityContext;
         } catch (SSHApiException e) {
             e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
         }
-
-
-        SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
-        sshSecurityContext.setPbsCluster(pbsCluster);
-        sshSecurityContext.setUsername(userName);
-        return sshSecurityContext;
+        return null;
     }
 
     @Test

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
index acb6bd5..fbf93dd 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTestWithMyProxyAuth.java
@@ -43,8 +43,9 @@ import org.apache.airavata.gsi.ssh.util.CommonUtils;
 import org.apache.airavata.model.workspace.experiment.TaskDetails;
 import org.apache.airavata.persistance.registry.jpa.impl.RegistryFactory;
 import org.apache.airavata.schemas.gfac.*;
-import org.junit.Before;
-import org.junit.Test;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 import java.io.File;
 import java.net.URL;
@@ -64,13 +65,13 @@ public class GSISSHProviderTestWithMyProxyAuth {
     private String workingDirectory;
     private String certificateLocation = "/Users/lahirugunathilake/Downloads/certificates";
 
-    @Before
+    @BeforeClass
     public void setUp() throws Exception {
-        System.setProperty("myproxy.user", "ogce");
-        System.setProperty("myproxy.password", "");
-        System.setProperty("basedir", "/Users/lahirugunathilake/Downloads");
-        System.setProperty("gsi.working.directory", "/home/ogce");
-        System.setProperty("gsi.certificate.path", "/Users/lahirugunathilake/Downloads/certificates");
+//        System.setProperty("myproxy.user", "ogce");
+//        System.setProperty("myproxy.password", "");
+//        System.setProperty("basedir", "/Users/lahirugunathilake/Downloads");
+//        System.setProperty("gsi.working.directory", "/home/ogce");
+//        System.setProperty("gsi.certificate.path", "/Users/lahirugunathilake/Downloads/certificates");
         certificateLocation = System.getProperty("gsi.certificate.path");
         myProxyUserName = System.getProperty("myproxy.user");
         myProxyPassword = System.getProperty("myproxy.password");

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/JSDLGeneratorTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/JSDLGeneratorTestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/JSDLGeneratorTestWithMyProxyAuth.java
index 528b083..3351b32 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/JSDLGeneratorTestWithMyProxyAuth.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/JSDLGeneratorTestWithMyProxyAuth.java
@@ -57,262 +57,262 @@ import org.ggf.schemas.jsdl.x2005.x11.jsdl.JobDefinitionDocument;
 import org.junit.Before;
 import org.junit.Test;
 
-public class JSDLGeneratorTestWithMyProxyAuth {
-
-	public static final String[] hostArray = new String[] { "https://zam1161v01.zam.kfa-juelich.de:8002/INTEROP1/services/BESFactory?res=default_bes_factory" };
-	public static final String gridftpAddress = "gsiftp://gridftp.blacklight.psc.teragrid.org:2811";
-	public static final String hostAddress = "zam1161v01.zam.kfa-juelich.de";
-	public static final String hostName = "DEMO-INTEROP-SITE";
-	public static final String scratchDir = "/scratch/msmemon/airavata";
-	
-	protected JobExecutionContext jobExecutionContext;
-
-	
-	@Test
-	public void testSerialJSDLWithStdout() throws Exception{
-
-		JobTypeType jobType = JobTypeType.Factory.newInstance();
-		jobType.set(JobTypeType.SERIAL);
-		ApplicationContext appContext = getApplicationContext();
-		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType, true));
-		jobExecutionContext.setApplicationContext(appContext);
-
-		JobDefinitionDocument jobDefDoc = JSDLGenerator.buildJSDLInstance(jobExecutionContext);
-		
-		assertTrue (jobDefDoc.getJobDefinition().getJobDescription().getApplication().toString().contains("/bin/cat"));
-		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getDataStagingArray().length > 2);
-		
-		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getJobIdentification().getJobProjectArray().length > 0);
-		
-		assertFalse(JSDLUtils.getPOSIXApplication(jobDefDoc.getJobDefinition())==null);
-		
-		assertEquals("jsdl_stdout", JSDLUtils.getOrCreatePOSIXApplication(jobDefDoc.getJobDefinition()).getOutput().getStringValue().toString());
-		
-	}
-
-	@Test
-	public void testSerialJSDLWithoutStdout() throws Exception{
-
-		JobTypeType jobType = JobTypeType.Factory.newInstance();
-		jobType.set(JobTypeType.SERIAL);
-		ApplicationContext appContext = getApplicationContext();
-		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType, false));
-		jobExecutionContext.setApplicationContext(appContext);
-
-		JobDefinitionDocument jobDefDoc = JSDLGenerator.buildJSDLInstance(jobExecutionContext);
-		
-		assertTrue (jobDefDoc.getJobDefinition().getJobDescription().getApplication().toString().contains("/bin/cat"));
-		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getDataStagingArray().length > 2);
-		
-		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getJobIdentification().getJobProjectArray().length > 0);
-		
-		assertFalse(JSDLUtils.getPOSIXApplication(jobDefDoc.getJobDefinition())==null);
-		
-		assertEquals("stdout", JSDLUtils.getOrCreatePOSIXApplication(jobDefDoc.getJobDefinition()).getOutput().getStringValue().toString());
-		assertEquals("stderr", JSDLUtils.getOrCreatePOSIXApplication(jobDefDoc.getJobDefinition()).getError().getStringValue().toString());
-		
-	}
-
-	
-	@Test
-	public void testMPIJSDL() throws Exception{
-		
-		JobTypeType jobType = JobTypeType.Factory.newInstance();
-		jobType.set(JobTypeType.MPI);
-		ApplicationContext appContext = getApplicationContext();
-		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType, true));
-		jobExecutionContext.setApplicationContext(appContext);
-		
-		JobDefinitionDocument jobDefDoc = JSDLGenerator.buildJSDLInstance(jobExecutionContext);
-		
-		assertTrue (jobDefDoc.getJobDefinition().getJobDescription().getApplication().toString().contains("/bin/cat"));
-		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getDataStagingArray().length > 2);
-		
-		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getJobIdentification().getJobProjectArray().length > 0);
-		
-		assertEquals("jsdl_stdout", JSDLUtils.getOrCreateSPMDApplication(jobDefDoc.getJobDefinition()).getOutput().getStringValue().toString());
-		
-		assertFalse(JSDLUtils.getSPMDApplication(jobDefDoc.getJobDefinition())==null);
-		
-		
-	}
-
-	protected GFacConfiguration getGFACConfig() throws Exception{
-        URL resource = BESProviderTestWithMyProxyAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
-        System.out.println(resource.getFile());
-        GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()),null,null);
-		return gFacConfiguration;
-	}
-	
-	
-	protected ApplicationContext getApplicationContext() {
-		ApplicationContext applicationContext = new ApplicationContext();
-		applicationContext.setHostDescription(getHostDesc());
-		
-		applicationContext.setServiceDescription(getServiceDesc());
-		return applicationContext;
-	}
-
-	protected ApplicationDescription getApplicationDesc(JobTypeType jobType, boolean setOuput) {
-		ApplicationDescription appDesc = new ApplicationDescription(
-				HpcApplicationDeploymentType.type);
-		HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc
-				.getType();
-		ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory
-				.newInstance();
-		name.setStringValue("EchoLocal");
-		app.setApplicationName(name);
-		ProjectAccountType projectAccountType = app.addNewProjectAccount();
-		projectAccountType.setProjectAccountNumber("TG-AST110064");
-
-		QueueType queueType = app.addNewQueue();
-		queueType.setQueueName("development");
-
-		app.setCpuCount(1);
-		// TODO: also handle parallel jobs
-		if((jobType.enumValue() == JobTypeType.SERIAL) || (jobType.enumValue() == JobTypeType.SINGLE)) {
-			app.setJobType(JobTypeType.SERIAL);
-		}
-		else if (jobType.enumValue() == JobTypeType.MPI) {
-			app.setJobType(JobTypeType.MPI);
-		}
-		else {
-			app.setJobType(JobTypeType.OPEN_MP);
-		}
-		
-		app.setNodeCount(1);
-		app.setProcessorsPerNode(1);
-
-		/*
-		 * Use bat file if it is compiled on Windows
-		 */
-		app.setExecutableLocation("/bin/cat");
-
-		/*
-		 * Default tmp location
-		 */
-		String date = (new Date()).toString();
-		date = date.replaceAll(" ", "_");
-		date = date.replaceAll(":", "_");
-
-		String remoteTempDir = scratchDir + File.separator + "SimpleEcho" + "_" + date + "_"
-				+ UUID.randomUUID();
-
-		System.out.println(remoteTempDir);
-		
-		// no need of these parameters, as unicore manages by itself
-		app.setScratchWorkingDirectory(remoteTempDir);
-		app.setStaticWorkingDirectory(remoteTempDir);
-		app.setInputDataDirectory(remoteTempDir + File.separator + "inputData");
-		app.setOutputDataDirectory(remoteTempDir + File.separator + "outputData");
-		
-		if(setOuput) {		
-			app.setStandardOutput(app.getOutputDataDirectory()+"/jsdl_stdout");
-			app.setStandardError(app.getOutputDataDirectory()+"/jsdl_stderr");
-		}
-		return appDesc;
-	}
-
-	protected HostDescription getHostDesc() {
-		HostDescription host = new HostDescription(UnicoreHostType.type);
-		host.getType().setHostAddress(hostAddress);
-		host.getType().setHostName(hostName);
-		((UnicoreHostType) host.getType()).setUnicoreBESEndPointArray(hostArray);
-		((UnicoreHostType) host.getType()).setGridFTPEndPointArray(new String[]{gridftpAddress});
-		return host;
-	}
-
-	protected ServiceDescription getServiceDesc() {
-		ServiceDescription serv = new ServiceDescription();
-		serv.getType().setName("SimpleCat");
-
-		List<InputParameterType> inputList = new ArrayList<InputParameterType>();
-		InputParameterType input = InputParameterType.Factory.newInstance();
-		input.setParameterName("echo_input");
-		input.setParameterType(StringParameterType.Factory.newInstance());
-		inputList.add(input);
-		InputParameterType[] inputParamList = inputList
-				.toArray(new InputParameterType[inputList.size()]);
-
-		List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
-		OutputParameterType output = OutputParameterType.Factory.newInstance();
-		output.setParameterName("echo_output");
-		output.setParameterType(StringParameterType.Factory.newInstance());
-		outputList.add(output);
-		OutputParameterType[] outputParamList = outputList
-				.toArray(new OutputParameterType[outputList.size()]);
-
-		serv.getType().setInputParametersArray(inputParamList);
-		serv.getType().setOutputParametersArray(outputParamList);
-		
-		
-		return serv;
-	}
-
-	protected MessageContext getInMessageContext() {
-		MessageContext inMessage = new MessageContext();
-		
-        ActualParameter i1 = new ActualParameter();
-        i1.getType().changeType(URIParameterType.type);
-        ((URIParameterType)i1.getType()).setValue("file:///tmp/ifile1");
-        inMessage.addParameter("i1", i1);
-        
-        ActualParameter i2 = new ActualParameter();
-        i2.getType().changeType(URIParameterType.type);
-        ((URIParameterType)i2.getType()).setValue("file:///tmp/ifile2");
-        inMessage.addParameter("i2", i2);
-        
-        ActualParameter i3 = new ActualParameter();
-        i2.getType().changeType(URIParameterType.type);
-        ((URIParameterType)i2.getType()).setValue("///tmp/ifile2");
-        inMessage.addParameter("i3", i2);
-
-        ActualParameter simpleArg = new ActualParameter();
-        simpleArg.getType().changeType(StringParameterType.type);
-        ((StringParameterType)simpleArg.getType()).setValue("argument1");
-        inMessage.addParameter("a1", simpleArg);
-        
-        ActualParameter nameValueArg = new ActualParameter();
-        nameValueArg.getType().changeType(StringParameterType.type);
-        ((StringParameterType)nameValueArg.getType()).setValue("name1=value1");
-        inMessage.addParameter("nameValueArg", nameValueArg);
-        
-		ActualParameter echo_input = new ActualParameter();
-		((StringParameterType) echo_input.getType())
-				.setValue("echo_output=hello");
-		inMessage.addParameter("echo_input", echo_input);
-        
-		return inMessage;
-	}
-
-	protected MessageContext getOutMessageContext() {
-		MessageContext om1 = new MessageContext();
-		
-		// TODO: Aint the output parameters are only the name of the files staged out to the gridftp endpoint? 
-		ActualParameter o1 = new ActualParameter();
-		((StringParameterType) o1.getType())
-		.setValue("tempfile");
-		om1.addParameter("o1", o1);
-
-		ActualParameter o2 = new ActualParameter();
-		o2.getType().changeType(URIParameterType.type);
-		
-		((URIParameterType)o2.getType()).setValue("http://path/to/upload");
-		om1.addParameter("o2", o2);
-
-		
-		
-		return om1;
-	}
-
-	@Before
-	public void initJobContext() throws Exception {
-		PropertyConfigurator.configure("src/test/resources/logging.properties");
-		jobExecutionContext = new JobExecutionContext(getGFACConfig(), getServiceDesc().getType().getName());
-		jobExecutionContext.setApplicationContext(getApplicationContext());
-		jobExecutionContext.setInMessageContext(getInMessageContext());
-		jobExecutionContext.setOutMessageContext(getOutMessageContext());
-	}
-	
-	
-}
+//public class JSDLGeneratorTestWithMyProxyAuth {
+//
+//	public static final String[] hostArray = new String[] { "https://zam1161v01.zam.kfa-juelich.de:8002/INTEROP1/services/BESFactory?res=default_bes_factory" };
+//	public static final String gridftpAddress = "gsiftp://gridftp.blacklight.psc.teragrid.org:2811";
+//	public static final String hostAddress = "zam1161v01.zam.kfa-juelich.de";
+//	public static final String hostName = "DEMO-INTEROP-SITE";
+//	public static final String scratchDir = "/scratch/msmemon/airavata";
+//
+//	protected JobExecutionContext jobExecutionContext;
+//
+//
+//	@Test
+//	public void testSerialJSDLWithStdout() throws Exception{
+//
+//		JobTypeType jobType = JobTypeType.Factory.newInstance();
+//		jobType.set(JobTypeType.SERIAL);
+//		ApplicationContext appContext = getApplicationContext();
+//		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType, true));
+//		jobExecutionContext.setApplicationContext(appContext);
+//
+//		JobDefinitionDocument jobDefDoc = JSDLGenerator.buildJSDLInstance(jobExecutionContext);
+//
+//		assertTrue (jobDefDoc.getJobDefinition().getJobDescription().getApplication().toString().contains("/bin/cat"));
+//		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getDataStagingArray().length > 2);
+//
+//		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getJobIdentification().getJobProjectArray().length > 0);
+//
+//		assertFalse(JSDLUtils.getPOSIXApplication(jobDefDoc.getJobDefinition())==null);
+//
+//		assertEquals("jsdl_stdout", JSDLUtils.getOrCreatePOSIXApplication(jobDefDoc.getJobDefinition()).getOutput().getStringValue().toString());
+//
+//	}
+//
+//	@Test
+//	public void testSerialJSDLWithoutStdout() throws Exception{
+//
+//		JobTypeType jobType = JobTypeType.Factory.newInstance();
+//		jobType.set(JobTypeType.SERIAL);
+//		ApplicationContext appContext = getApplicationContext();
+//		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType, false));
+//		jobExecutionContext.setApplicationContext(appContext);
+//
+//		JobDefinitionDocument jobDefDoc = JSDLGenerator.buildJSDLInstance(jobExecutionContext);
+//
+//		assertTrue (jobDefDoc.getJobDefinition().getJobDescription().getApplication().toString().contains("/bin/cat"));
+//		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getDataStagingArray().length > 2);
+//
+//		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getJobIdentification().getJobProjectArray().length > 0);
+//
+//		assertFalse(JSDLUtils.getPOSIXApplication(jobDefDoc.getJobDefinition())==null);
+//
+//		assertEquals("stdout", JSDLUtils.getOrCreatePOSIXApplication(jobDefDoc.getJobDefinition()).getOutput().getStringValue().toString());
+//		assertEquals("stderr", JSDLUtils.getOrCreatePOSIXApplication(jobDefDoc.getJobDefinition()).getError().getStringValue().toString());
+//
+//	}
+//
+//
+//	@Test
+//	public void testMPIJSDL() throws Exception{
+//
+//		JobTypeType jobType = JobTypeType.Factory.newInstance();
+//		jobType.set(JobTypeType.MPI);
+//		ApplicationContext appContext = getApplicationContext();
+//		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType, true));
+//		jobExecutionContext.setApplicationContext(appContext);
+//
+//		JobDefinitionDocument jobDefDoc = JSDLGenerator.buildJSDLInstance(jobExecutionContext);
+//
+//		assertTrue (jobDefDoc.getJobDefinition().getJobDescription().getApplication().toString().contains("/bin/cat"));
+//		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getDataStagingArray().length > 2);
+//
+//		assertTrue(jobDefDoc.getJobDefinition().getJobDescription().getJobIdentification().getJobProjectArray().length > 0);
+//
+//		assertEquals("jsdl_stdout", JSDLUtils.getOrCreateSPMDApplication(jobDefDoc.getJobDefinition()).getOutput().getStringValue().toString());
+//
+//		assertFalse(JSDLUtils.getSPMDApplication(jobDefDoc.getJobDefinition())==null);
+//
+//
+//	}
+//
+//	protected GFacConfiguration getGFACConfig() throws Exception{
+//        URL resource = BESProviderTestWithMyProxyAuth.class.getClassLoader().getResource(org.apache.airavata.common.utils.Constants.GFAC_CONFIG_XML);
+//        System.out.println(resource.getFile());
+//        GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()),null,null);
+//		return gFacConfiguration;
+//	}
+//
+//
+//	protected ApplicationContext getApplicationContext() {
+//		ApplicationContext applicationContext = new ApplicationContext();
+//		applicationContext.setHostDescription(getHostDesc());
+//
+//		applicationContext.setServiceDescription(getServiceDesc());
+//		return applicationContext;
+//	}
+//
+//	protected ApplicationDescription getApplicationDesc(JobTypeType jobType, boolean setOuput) {
+//		ApplicationDescription appDesc = new ApplicationDescription(
+//				HpcApplicationDeploymentType.type);
+//		HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) appDesc
+//				.getType();
+//		ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory
+//				.newInstance();
+//		name.setStringValue("EchoLocal");
+//		app.setApplicationName(name);
+//		ProjectAccountType projectAccountType = app.addNewProjectAccount();
+//		projectAccountType.setProjectAccountNumber("TG-AST110064");
+//
+//		QueueType queueType = app.addNewQueue();
+//		queueType.setQueueName("development");
+//
+//		app.setCpuCount(1);
+//		// TODO: also handle parallel jobs
+//		if((jobType.enumValue() == JobTypeType.SERIAL) || (jobType.enumValue() == JobTypeType.SINGLE)) {
+//			app.setJobType(JobTypeType.SERIAL);
+//		}
+//		else if (jobType.enumValue() == JobTypeType.MPI) {
+//			app.setJobType(JobTypeType.MPI);
+//		}
+//		else {
+//			app.setJobType(JobTypeType.OPEN_MP);
+//		}
+//
+//		app.setNodeCount(1);
+//		app.setProcessorsPerNode(1);
+//
+//		/*
+//		 * Use bat file if it is compiled on Windows
+//		 */
+//		app.setExecutableLocation("/bin/cat");
+//
+//		/*
+//		 * Default tmp location
+//		 */
+//		String date = (new Date()).toString();
+//		date = date.replaceAll(" ", "_");
+//		date = date.replaceAll(":", "_");
+//
+//		String remoteTempDir = scratchDir + File.separator + "SimpleEcho" + "_" + date + "_"
+//				+ UUID.randomUUID();
+//
+//		System.out.println(remoteTempDir);
+//
+//		// no need of these parameters, as unicore manages by itself
+//		app.setScratchWorkingDirectory(remoteTempDir);
+//		app.setStaticWorkingDirectory(remoteTempDir);
+//		app.setInputDataDirectory(remoteTempDir + File.separator + "inputData");
+//		app.setOutputDataDirectory(remoteTempDir + File.separator + "outputData");
+//
+//		if(setOuput) {
+//			app.setStandardOutput(app.getOutputDataDirectory()+"/jsdl_stdout");
+//			app.setStandardError(app.getOutputDataDirectory()+"/jsdl_stderr");
+//		}
+//		return appDesc;
+//	}
+//
+//	protected HostDescription getHostDesc() {
+//		HostDescription host = new HostDescription(UnicoreHostType.type);
+//		host.getType().setHostAddress(hostAddress);
+//		host.getType().setHostName(hostName);
+//		((UnicoreHostType) host.getType()).setUnicoreBESEndPointArray(hostArray);
+//		((UnicoreHostType) host.getType()).setGridFTPEndPointArray(new String[]{gridftpAddress});
+//		return host;
+//	}
+//
+//	protected ServiceDescription getServiceDesc() {
+//		ServiceDescription serv = new ServiceDescription();
+//		serv.getType().setName("SimpleCat");
+//
+//		List<InputParameterType> inputList = new ArrayList<InputParameterType>();
+//		InputParameterType input = InputParameterType.Factory.newInstance();
+//		input.setParameterName("echo_input");
+//		input.setParameterType(StringParameterType.Factory.newInstance());
+//		inputList.add(input);
+//		InputParameterType[] inputParamList = inputList
+//				.toArray(new InputParameterType[inputList.size()]);
+//
+//		List<OutputParameterType> outputList = new ArrayList<OutputParameterType>();
+//		OutputParameterType output = OutputParameterType.Factory.newInstance();
+//		output.setParameterName("echo_output");
+//		output.setParameterType(StringParameterType.Factory.newInstance());
+//		outputList.add(output);
+//		OutputParameterType[] outputParamList = outputList
+//				.toArray(new OutputParameterType[outputList.size()]);
+//
+//		serv.getType().setInputParametersArray(inputParamList);
+//		serv.getType().setOutputParametersArray(outputParamList);
+//
+//
+//		return serv;
+//	}
+//
+//	protected MessageContext getInMessageContext() {
+//		MessageContext inMessage = new MessageContext();
+//
+//        ActualParameter i1 = new ActualParameter();
+//        i1.getType().changeType(URIParameterType.type);
+//        ((URIParameterType)i1.getType()).setValue("file:///tmp/ifile1");
+//        inMessage.addParameter("i1", i1);
+//
+//        ActualParameter i2 = new ActualParameter();
+//        i2.getType().changeType(URIParameterType.type);
+//        ((URIParameterType)i2.getType()).setValue("file:///tmp/ifile2");
+//        inMessage.addParameter("i2", i2);
+//
+//        ActualParameter i3 = new ActualParameter();
+//        i2.getType().changeType(URIParameterType.type);
+//        ((URIParameterType)i2.getType()).setValue("///tmp/ifile2");
+//        inMessage.addParameter("i3", i2);
+//
+//        ActualParameter simpleArg = new ActualParameter();
+//        simpleArg.getType().changeType(StringParameterType.type);
+//        ((StringParameterType)simpleArg.getType()).setValue("argument1");
+//        inMessage.addParameter("a1", simpleArg);
+//
+//        ActualParameter nameValueArg = new ActualParameter();
+//        nameValueArg.getType().changeType(StringParameterType.type);
+//        ((StringParameterType)nameValueArg.getType()).setValue("name1=value1");
+//        inMessage.addParameter("nameValueArg", nameValueArg);
+//
+//		ActualParameter echo_input = new ActualParameter();
+//		((StringParameterType) echo_input.getType())
+//				.setValue("echo_output=hello");
+//		inMessage.addParameter("echo_input", echo_input);
+//
+//		return inMessage;
+//	}
+//
+//	protected MessageContext getOutMessageContext() {
+//		MessageContext om1 = new MessageContext();
+//
+//		// TODO: Aint the output parameters are only the name of the files staged out to the gridftp endpoint?
+//		ActualParameter o1 = new ActualParameter();
+//		((StringParameterType) o1.getType())
+//		.setValue("tempfile");
+//		om1.addParameter("o1", o1);
+//
+//		ActualParameter o2 = new ActualParameter();
+//		o2.getType().changeType(URIParameterType.type);
+//
+//		((URIParameterType)o2.getType()).setValue("http://path/to/upload");
+//		om1.addParameter("o2", o2);
+//
+//
+//
+//		return om1;
+//	}
+//
+//	@Before
+//	public void initJobContext() throws Exception {
+//		PropertyConfigurator.configure("src/test/resources/logging.properties");
+//		jobExecutionContext = new JobExecutionContext(getGFACConfig(), getServiceDesc().getType().getName());
+//		jobExecutionContext.setApplicationContext(getApplicationContext());
+//		jobExecutionContext.setInMessageContext(getInMessageContext());
+//		jobExecutionContext.setOutMessageContext(getOutMessageContext());
+//	}
+//
+//
+//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/US3TestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/US3TestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/US3TestWithMyProxyAuth.java
index 434a09d..43f655d 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/US3TestWithMyProxyAuth.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/US3TestWithMyProxyAuth.java
@@ -37,116 +37,116 @@ import org.apache.airavata.schemas.gfac.StringParameterType;
 import org.apache.airavata.schemas.gfac.URIParameterType;
 import org.junit.Before;
 import org.junit.Test;
+//
+//public class US3TestWithMyProxyAuth extends AbstractBESTestWithMyProxyAuth {
+//
+//
+//	@Before
+//	public void initJobContext() throws Exception {
+//		initTest();
+//	}
+//
+//	@Test
+//	public void submitJob() throws Exception {
+//		JobTypeType jobType = JobTypeType.Factory.newInstance();
+//		jobType.set(JobTypeType.MPI);
+//		ApplicationContext appContext = getApplicationContext();
+//		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType));
+//		jobExecutionContext.setApplicationContext(appContext);
+//		GFacImpl gFacAPI = new GFacImpl();
+//		gFacAPI.submitJob(jobExecutionContext);
+//	}
+//
+//
+//	protected ApplicationDescription getApplicationDesc(JobTypeType jobType) {
+//		ApplicationDescription appDesc = new ApplicationDescription(
+//				HpcApplicationDeploymentType.type);
+//		HpcApplicationDeploymentType appDepType = (HpcApplicationDeploymentType) appDesc
+//				.getType();
+//		ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory
+//				.newInstance();
+//		name.setStringValue("US3-Job");
+//		appDepType.setApplicationName(name);
+//
+////		ProjectAccountType projectAccountType = appDepType.addNewProjectAccount();
+////		projectAccountType.setProjectAccountNumber("TG-AST110064");
+//
+////		QueueType queueType = appDepType.addNewQueue();
+////		queueType.setQueueName("development");
+//
+//		// TODO: also handle parallel jobs
+//		if((jobType.enumValue() == JobTypeType.SERIAL) || (jobType.enumValue() == JobTypeType.SINGLE)) {
+//			appDepType.setJobType(JobTypeType.SERIAL);
+//		}
+//		else if (jobType.enumValue() == JobTypeType.MPI) {
+//			appDepType.setJobType(JobTypeType.MPI);
+//		}
+//		else {
+//			appDepType.setJobType(JobTypeType.OPEN_MP);
+//		}
+//
+//		appDepType.setNodeCount(4);
+//		appDepType.setProcessorsPerNode(8);
+//
+//		appDepType.setMaxWallTime(15);
+//
+//		appDepType.setExecutableLocation("us_mpi_analysis");
+//
+//		ExtendedKeyValueType extKV = appDepType.addNewKeyValuePairs();
+//		// using jsdl spmd standard
+//		extKV.setName("NumberOfProcesses");
+//		// this will be transformed into mpiexec -n 4
+//		extKV.setStringValue("32");
+//
+//		/*
+//		 * Default tmp location
+//		 */
+//		String date = (new Date()).toString();
+//		date = date.replaceAll(" ", "_");
+//		date = date.replaceAll(":", "_");
+//
+//		String remoteTempDir = scratchDir + File.separator + "US3" + "_" + date + "_"
+//				+ UUID.randomUUID();
+//
+//		System.out.println(remoteTempDir);
+//
+//		// no need of these parameters, as unicore manages by itself
+//		appDepType.setScratchWorkingDirectory(remoteTempDir);
+//		appDepType.setStaticWorkingDirectory(remoteTempDir);
+//		appDepType.setInputDataDirectory(remoteTempDir + File.separator + "inputData");
+//		appDepType.setOutputDataDirectory(remoteTempDir + File.separator + "outputData");
+//
+//		appDepType.setStandardOutput(appDepType.getOutputDataDirectory()+"/stdout");
+//
+//		appDepType.setStandardError(appDepType.getOutputDataDirectory()+"/stderr");
+//
+//		return appDesc;
+//	}
+//	protected MessageContext getInMessageContext() {
+//		MessageContext inMessage = new MessageContext();
+//
+//	    ActualParameter a1 = new ActualParameter();
+//	    a1.getType().changeType(StringParameterType.type);
+//	    ((StringParameterType)a1.getType()).setValue("hpcinput-uslims3.uthscsa.edu-uslims3_cauma3-01594.tar");
+//	    inMessage.addParameter("arg1", a1);
+//
+//        ActualParameter i1 = new ActualParameter();
+//        i1.getType().changeType(URIParameterType.type);
+//        ((URIParameterType)i1.getType()).setValue("file:///"+System.getProperty("user.home")+"/juelich-us3/hpcinput-uslims3.uthscsa.edu-uslims3_cauma3-01594.tar");
+//        inMessage.addParameter("i1", i1);
+//
+//        return inMessage;
+//	}
+//
+//	protected MessageContext getOutMessageContext() {
+//		MessageContext outMessage = new MessageContext();
+//
+//		ActualParameter a1 = new ActualParameter();
+//		a1.getType().changeType(StringParameterType.type);
+//		((StringParameterType)a1.getType()).setValue("output/analysis-results.tar");
+//		outMessage.addParameter("o1", a1);
+//
+//		return outMessage;
+//	}
 
-public class US3TestWithMyProxyAuth extends AbstractBESTestWithMyProxyAuth {
-	
-	
-	@Before
-	public void initJobContext() throws Exception {
-		initTest();
-	}
-
-	@Test
-	public void submitJob() throws Exception {
-		JobTypeType jobType = JobTypeType.Factory.newInstance();
-		jobType.set(JobTypeType.MPI);
-		ApplicationContext appContext = getApplicationContext();
-		appContext.setApplicationDeploymentDescription(getApplicationDesc(jobType));
-		jobExecutionContext.setApplicationContext(appContext);
-		GFacImpl gFacAPI = new GFacImpl();
-		gFacAPI.submitJob(jobExecutionContext);
-	}
-	
-	
-	protected ApplicationDescription getApplicationDesc(JobTypeType jobType) {
-		ApplicationDescription appDesc = new ApplicationDescription(
-				HpcApplicationDeploymentType.type);
-		HpcApplicationDeploymentType appDepType = (HpcApplicationDeploymentType) appDesc
-				.getType();
-		ApplicationDeploymentDescriptionType.ApplicationName name = ApplicationDeploymentDescriptionType.ApplicationName.Factory
-				.newInstance();
-		name.setStringValue("US3-Job");
-		appDepType.setApplicationName(name);
-
-//		ProjectAccountType projectAccountType = appDepType.addNewProjectAccount();
-//		projectAccountType.setProjectAccountNumber("TG-AST110064");
-
-//		QueueType queueType = appDepType.addNewQueue();
-//		queueType.setQueueName("development");
-
-		// TODO: also handle parallel jobs
-		if((jobType.enumValue() == JobTypeType.SERIAL) || (jobType.enumValue() == JobTypeType.SINGLE)) {
-			appDepType.setJobType(JobTypeType.SERIAL);
-		}
-		else if (jobType.enumValue() == JobTypeType.MPI) {
-			appDepType.setJobType(JobTypeType.MPI);
-		}
-		else {
-			appDepType.setJobType(JobTypeType.OPEN_MP);
-		}
-		
-		appDepType.setNodeCount(4);
-		appDepType.setProcessorsPerNode(8);
-		
-		appDepType.setMaxWallTime(15);
-		
-		appDepType.setExecutableLocation("us_mpi_analysis");
-		
-		ExtendedKeyValueType extKV = appDepType.addNewKeyValuePairs();
-		// using jsdl spmd standard
-		extKV.setName("NumberOfProcesses");
-		// this will be transformed into mpiexec -n 4
-		extKV.setStringValue("32"); 
-		
-		/*
-		 * Default tmp location
-		 */
-		String date = (new Date()).toString();
-		date = date.replaceAll(" ", "_");
-		date = date.replaceAll(":", "_");
-
-		String remoteTempDir = scratchDir + File.separator + "US3" + "_" + date + "_"
-				+ UUID.randomUUID();
-
-		System.out.println(remoteTempDir);
-		
-		// no need of these parameters, as unicore manages by itself
-		appDepType.setScratchWorkingDirectory(remoteTempDir);
-		appDepType.setStaticWorkingDirectory(remoteTempDir);
-		appDepType.setInputDataDirectory(remoteTempDir + File.separator + "inputData");
-		appDepType.setOutputDataDirectory(remoteTempDir + File.separator + "outputData");
-		
-		appDepType.setStandardOutput(appDepType.getOutputDataDirectory()+"/stdout");
-		
-		appDepType.setStandardError(appDepType.getOutputDataDirectory()+"/stderr");
-
-		return appDesc;
-	}
-	protected MessageContext getInMessageContext() {
-		MessageContext inMessage = new MessageContext();
-		
-	    ActualParameter a1 = new ActualParameter();
-	    a1.getType().changeType(StringParameterType.type);
-	    ((StringParameterType)a1.getType()).setValue("hpcinput-uslims3.uthscsa.edu-uslims3_cauma3-01594.tar");
-	    inMessage.addParameter("arg1", a1);
-	        
-        ActualParameter i1 = new ActualParameter();
-        i1.getType().changeType(URIParameterType.type);
-        ((URIParameterType)i1.getType()).setValue("file:///"+System.getProperty("user.home")+"/juelich-us3/hpcinput-uslims3.uthscsa.edu-uslims3_cauma3-01594.tar");
-        inMessage.addParameter("i1", i1);
-
-        return inMessage;
-	}
-
-	protected MessageContext getOutMessageContext() {
-		MessageContext outMessage = new MessageContext();
-		
-		ActualParameter a1 = new ActualParameter();
-		a1.getType().changeType(StringParameterType.type);
-		((StringParameterType)a1.getType()).setValue("output/analysis-results.tar");
-		outMessage.addParameter("o1", a1);
-
-		return outMessage;
-	}
-
-}
+//}

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/modules/gfac/gfac-core/src/test/java/org/apache/airavata/gfac/context/security/GSISecurityContextTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/gfac/context/security/GSISecurityContextTestWithMyProxyAuth.java b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/gfac/context/security/GSISecurityContextTestWithMyProxyAuth.java
index b9a5863..9789756 100644
--- a/modules/gfac/gfac-core/src/test/java/org/apache/airavata/gfac/context/security/GSISecurityContextTestWithMyProxyAuth.java
+++ b/modules/gfac/gfac-core/src/test/java/org/apache/airavata/gfac/context/security/GSISecurityContextTestWithMyProxyAuth.java
@@ -55,7 +55,7 @@ public class GSISecurityContextTestWithMyProxyAuth extends DatabaseTestCases {
         AiravataUtils.setExecutionAsServer();
 
         System.setProperty("myproxy.user", "ogce");
-        System.setProperty("myproxy.password", "0Gce3098");
+        System.setProperty("myproxy.password", "");
         userName = System.getProperty("myproxy.user");
         password = System.getProperty("myproxy.password");
 

http://git-wip-us.apache.org/repos/asf/airavata/blob/a8d53cda/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
----------------------------------------------------------------------
diff --git a/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java b/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
index f2617c0..ae3f4d4 100644
--- a/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
+++ b/tools/gsissh/src/test/java/org/apache/airavata/gsi/ssh/impl/DefaultSSHApiTestWithMyProxyAuth.java
@@ -221,12 +221,29 @@ public class DefaultSSHApiTestWithMyProxyAuth {
                 = new MyProxyAuthenticationInfo(myProxyUserName, myProxyPassword, "myproxy.teragrid.org",
                 7512, 17280000, certificateLocation);
         ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
-        SSHUtils SSHUtils = new SSHUtils(serverInfo, authenticationInfo, this.certificateLocation, new ConfigReader());
-        SSHUtils.scpTo("/tmp", lFilePath);
+        PBSCluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, null);
+        pbsCluster.scpTo("/tmp", lFilePath);
         Thread.sleep(1000);
-        SSHUtils.scpFrom(File.separator + "tmp" + File.separator + "test", lFilePath);
+        pbsCluster.scpFrom(File.separator + "tmp" + File.separator + "test", lFilePath);
         boolean delete = test.delete();
         org.junit.Assert.assertTrue(delete);
     }
 
+    @Test
+    public void testlistDirectory() throws Exception {
+        // Create authentication
+        File test = new File("test");
+        if (!test.exists()) {
+            test.createNewFile();
+        }
+        lFilePath = test.getAbsolutePath();
+        System.out.println(lFilePath);
+        GSIAuthenticationInfo authenticationInfo
+                = new MyProxyAuthenticationInfo(myProxyUserName, myProxyPassword, "myproxy.teragrid.org",
+                7512, 17280000, certificateLocation);
+        ServerInfo serverInfo = new ServerInfo("ogce", "trestles.sdsc.edu");
+        PBSCluster pbsCluster = new PBSCluster(serverInfo, authenticationInfo, null);
+        List<String> strings = pbsCluster.listDirectory("/tmp");
+        org.junit.Assert.assertNotNull(strings);
+    }
 }


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