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From lah...@apache.org
Subject svn commit: r1532904 - in /airavata/trunk: ./ modules/distribution/airavata-server/src/main/resources/conf/ modules/gfac-core/src/main/java/org/apache/airavata/gfac/ modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/ modules/gfac-core/sr...
Date Wed, 16 Oct 2013 20:50:11 GMT
Author: lahiru
Date: Wed Oct 16 20:50:11 2013
New Revision: 1532904

URL: http://svn.apache.org/r1532904
Log:
fixiing bigred 2 issues.

Modified:
    airavata/trunk/modules/distribution/airavata-server/src/main/resources/conf/airavata-server.properties
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/AbstractSecurityContext.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/GFacException.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GFacHandlerException.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/GFacProviderException.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/SSHProvider.java
    airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTest.java
    airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
    airavata/trunk/pom.xml

Modified: airavata/trunk/modules/distribution/airavata-server/src/main/resources/conf/airavata-server.properties
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/distribution/airavata-server/src/main/resources/conf/airavata-server.properties?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/distribution/airavata-server/src/main/resources/conf/airavata-server.properties
(original)
+++ airavata/trunk/modules/distribution/airavata-server/src/main/resources/conf/airavata-server.properties
Wed Oct 16 20:50:11 2013
@@ -103,6 +103,7 @@ myproxy.life=3600
 trusted.cert.location=/path/to/trusted/certificates
 
 # SSH PKI key pair or ssh password can be used SSH based authentication is used.
+# if user specify both password authentication gets the higher preference
 
 ################# ---------- For ssh key pair authentication ------------------- ################
 #public.ssh.key=/path to public key for ssh

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/AbstractSecurityContext.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/AbstractSecurityContext.java?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/AbstractSecurityContext.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/AbstractSecurityContext.java
Wed Oct 16 20:50:11 2013
@@ -43,6 +43,9 @@ public abstract class AbstractSecurityCo
         this.credentialReader = credentialReader;
         this.requestData = requestData;
     }
+    public AbstractSecurityContext() {
+
+    }
 
     public CredentialReader getCredentialReader() {
         return credentialReader;

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/GFacException.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/GFacException.java?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/GFacException.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/GFacException.java
Wed Oct 16 20:50:11 2013
@@ -21,7 +21,12 @@
 
 package org.apache.airavata.gfac;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 public class GFacException extends Exception {
+    private static final Logger log = LoggerFactory.getLogger(GFacException.class);
+
     /**
 	 *
 	 */
@@ -33,9 +38,11 @@ public class GFacException extends Excep
 
     public GFacException(Exception e) {
         super(e);
+        log.error(e.getMessage(),e);
     }
 
 	public GFacException(String s, Throwable throwable) {
         super(s, throwable);
+        log.error(s,throwable);
     }
 }

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/JobExecutionContext.java
Wed Oct 16 20:50:11 2013
@@ -181,9 +181,6 @@ public class JobExecutionContext extends
 
 	public SecurityContext getSecurityContext(String name) throws GFacException{
 		SecurityContext secContext = securityContext.get(name);
-		if(secContext == null){
-			throw new GFacException( name + " not set in security context");
-		}
 		return secContext;
 	}
 

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/security/GSISecurityContext.java
Wed Oct 16 20:50:11 2013
@@ -104,6 +104,11 @@ public class GSISecurityContext extends 
         super(credentialReader, requestData);
     }
 
+
+    public GSISecurityContext(Cluster pbsCluster) {
+        this.setPbsCluster(pbsCluster);
+    }
+
     /**
      * Gets GSSCredentials. The process is as follows;
      * If credentials were queried for the first time create credentials.

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GFacHandlerException.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GFacHandlerException.java?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GFacHandlerException.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GFacHandlerException.java
Wed Oct 16 20:50:11 2013
@@ -38,13 +38,13 @@ public class GFacHandlerException extend
     public GFacHandlerException(String s, Throwable throwable) {
         super(s, throwable);
         sendFaultNotification(s, new Exception(throwable));
-        log.error(s);
+        log.error(s,throwable);
     }
 
     public GFacHandlerException(String message, Exception e, String... additionExceptiondata)
{
         super(message, e);
         sendFaultNotification(message, e, additionExceptiondata);
-        log.error(message);
+        log.error(message,e);
     }
 
     private void sendFaultNotification(String message,

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/GFacProviderException.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/GFacProviderException.java?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/GFacProviderException.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/GFacProviderException.java
Wed Oct 16 20:50:11 2013
@@ -40,7 +40,7 @@ public class GFacProviderException exten
     public GFacProviderException(String message, Throwable cause) {
         super(message, cause);
         sendFaultNotification(message, new Exception(cause));
-        log.error(message);
+        log.error(message,cause);
     }
 
 
@@ -48,7 +48,7 @@ public class GFacProviderException exten
         super(message);
         this.aditionalInfo = additionExceptiondata;
         sendFaultNotification(message, e, additionExceptiondata);
-        log.error(message);
+        log.error(message,e);
     }
 
     private void sendFaultNotification(String message,

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java
Wed Oct 16 20:50:11 2013
@@ -68,12 +68,12 @@ public class GSISSHProvider implements G
             Cluster cluster = null;
             if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)
!= null) {
                 cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
-            }else{
+            } else {
                 cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
             }
-            if(cluster == null){
+            if (cluster == null) {
                 throw new GFacProviderException("Security context is not set properly");
-            }else{
+            } else {
                 log.info("Successfully retrieved the Security Context");
             }
             // This installed path is a mandetory field, because this could change based
on the computing resource
@@ -82,7 +82,7 @@ public class GSISSHProvider implements G
             jobDescriptor.setShellName("/bin/bash");
             Random random = new Random();
             int i = random.nextInt();
-            jobDescriptor.setJobName(app.getApplicationName() + String.valueOf(i));
+            jobDescriptor.setJobName(app.getApplicationName().getStringValue() + String.valueOf(i));
             jobDescriptor.setExecutablePath(app.getExecutableLocation());
             jobDescriptor.setAllEnvExport(true);
             jobDescriptor.setMailOptions("n");
@@ -125,12 +125,13 @@ public class GSISSHProvider implements G
             jobDescriptor.setInputValues(inputValues);
 
             log.info(jobDescriptor.toXML());
-            String jobID = cluster.submitBatchJob(jobDescriptor);
+            final String jobID = cluster.submitBatchJob(jobDescriptor);
             log.info("Job Submitted successfully and returned Job ID: " + jobID);
             jobExecutionContext.getNotifier().publish(new JobIDEvent(jobID));
 
-            JobSubmissionListener listener = new GSISSHJobSubmissionListener(jobExecutionContext);
-            try {
+            final JobSubmissionListener listener = new GSISSHJobSubmissionListener(jobExecutionContext);
+            final Cluster finalCluster = cluster;
+//            try {
 //            // Wait 5 seconds to start the first poll, this is hard coded, user doesn't
have
 //            // to configure this.
 //            Thread.sleep(5000);
@@ -139,41 +140,40 @@ public class GSISSHProvider implements G
 //            throw new SSHApiException("Error during job status monitoring", e);
 //        }
 //        // Get the job status first
-//        try {
-////
-////            Thread t = new Thread() {
-////                @Override
-////                public void run() {
-////                    try {
-                // p
-                JobStatus jobStatus = cluster.getJobStatus(jobID);
-                listener.statusChanged(jobStatus);
-                while (true) {
-                    while (!jobStatus.equals(JobStatus.C)) {
-                        if (!jobStatus.equals(listener.getJobStatus().toString())) {
-                            listener.setJobStatus(jobStatus);
+            try {
+//
+                Thread t = new Thread() {
+                    @Override
+                    public void run() {
+                        try {
+                            JobStatus jobStatus = finalCluster.getJobStatus(jobID);
                             listener.statusChanged(jobStatus);
-                        }
-                        Thread.sleep(60000);
+                            while (true) {
+                                while (!jobStatus.equals(JobStatus.C)) {
+                                    if (!jobStatus.equals(listener.getJobStatus().toString()))
{
+                                        listener.setJobStatus(jobStatus);
+                                        listener.statusChanged(jobStatus);
+                                    }
+                                    Thread.sleep(60000);
 
-                        jobStatus = cluster.getJobStatus(jobID);
+                                    jobStatus = finalCluster.getJobStatus(jobID);
+                                }
+                                //Set the job status to Complete
+                                listener.setJobStatus(JobStatus.C);
+                                listener.statusChanged(jobStatus);
+                                break;
+                            }
+                        } catch (InterruptedException e) {
+                            log.error("Error listening to the submitted job", e);
+                        } catch (SSHApiException e) {
+                            log.error("Error listening to the submitted job", e);
+                        }
                     }
-                    //Set the job status to Complete
-                    listener.setJobStatus(JobStatus.C);
-                    listener.statusChanged(jobStatus);
-                    break;
-                }
-//                    } catch (InterruptedException e) {
-//                        log.error("Error listening to the submitted job", e);
-//                    } catch (SSHApiException e) {
-//                        log.error("Error listening to the submitted job", e);
-//                    }
-//                }
-//            };
+                };
                 //  This thread runs until the program termination, so that use can provide
 //            // any action in onChange method of the listener, without worrying for waiting
in the caller thread.
-                //t.setDaemon(true);
-//            t.start();
+                t.setDaemon(false);
+                t.start();
             } catch (Exception e) {
                 String error = "Error during job status monitoring";
                 log.error(error);

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/SSHProvider.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/SSHProvider.java?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/SSHProvider.java
(original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/SSHProvider.java
Wed Oct 16 20:50:11 2013
@@ -135,6 +135,8 @@ public class SSHProvider implements GFac
                 throw new GFacProviderException(e.getMessage(), e);
             } catch (IOException e) {
                 throw new GFacProviderException(e.getMessage(), e);
+            }catch (Exception e) {
+                throw new GFacProviderException(e.getMessage(), e);
             } finally {
                 if (securityContext != null) {
                     securityContext.closeSession(session);

Modified: airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTest.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTest.java?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTest.java
(original)
+++ airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GSISSHProviderTest.java
Wed Oct 16 20:50:11 2013
@@ -31,6 +31,7 @@ import org.apache.airavata.gfac.Security
 import org.apache.airavata.gfac.context.ApplicationContext;
 import org.apache.airavata.gfac.context.JobExecutionContext;
 import org.apache.airavata.gfac.context.MessageContext;
+import org.apache.airavata.gfac.context.security.GSISecurityContext;
 import org.apache.airavata.gfac.context.security.SSHSecurityContext;
 import org.apache.airavata.gsi.ssh.api.Cluster;
 import org.apache.airavata.gsi.ssh.api.SSHApiException;
@@ -194,9 +195,7 @@ public class GSISSHProviderTest {
         } 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(myProxyUserName);
+        GSISecurityContext sshSecurityContext = new GSISecurityContext(pbsCluster);
         return sshSecurityContext;
     }
     @Test

Modified: airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
(original)
+++ airavata/trunk/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/invoker/EmbeddedGFacInvoker.java
Wed Oct 16 20:50:11 2013
@@ -442,10 +442,7 @@ public class EmbeddedGFacInvoker impleme
                     e.printStackTrace();  //To change body of catch statement use File |
Settings | File Templates.
                 }
 
-
-                SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
-                sshSecurityContext.setPbsCluster(pbsCluster);
-                sshSecurityContext.setUsername(requestData.getMyProxyUserName());
+                context.setPbsCluster(pbsCluster);
                 jobExecutionContext.addSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT,
context);
             }
         } else if (registeredHost.getType() instanceof Ec2HostType) {
@@ -462,10 +459,11 @@ public class EmbeddedGFacInvoker impleme
             SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
             if (((SSHHostType) registeredHost.getType()).getHpcResource()) {
                 AuthenticationInfo authenticationInfo = null;
-                if(sshPassword != null){
+                // we give higher preference to the password over keypair ssh authentication
+                if (sshPassword != null) {
                     authenticationInfo = new DefaultPasswordAuthenticationInfo(sshPassword);
-                }else{
-                    authenticationInfo = new DefaultPublicKeyFileAuthentication(sshPublicKey,
sshPrivateKey,sshPrivateKeyPass);
+                } else {
+                    authenticationInfo = new DefaultPublicKeyFileAuthentication(sshPublicKey,
sshPrivateKey, sshPrivateKeyPass);
                 }
                 ServerInfo serverInfo = new ServerInfo(sshUserName, registeredHost.getType().getHostAddress());
 
@@ -479,13 +477,12 @@ public class EmbeddedGFacInvoker impleme
                 sshSecurityContext.setPbsCluster(pbsCluster);
                 sshSecurityContext.setUsername(sshUserName);
             } else {
-                 sshSecurityContext = new SSHSecurityContext();
+                sshSecurityContext = new SSHSecurityContext();
                 sshSecurityContext.setUsername(sshUserName);
                 sshSecurityContext.setPrivateKeyLoc(sshPrivateKey);
                 sshSecurityContext.setKeyPass(sshPrivateKeyPass);
             }
             jobExecutionContext.addSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT,
sshSecurityContext);
-
         }
     }
 

Modified: airavata/trunk/pom.xml
URL: http://svn.apache.org/viewvc/airavata/trunk/pom.xml?rev=1532904&r1=1532903&r2=1532904&view=diff
==============================================================================
--- airavata/trunk/pom.xml (original)
+++ airavata/trunk/pom.xml Wed Oct 16 20:50:11 2013
@@ -342,6 +342,11 @@
     </dependencyManagement>
 
     <repositories>
+	<repository>
+           <name>ogce.m2.all</name>
+            <id>ogce.m2.all</id>
+            <url>http://community.ucs.indiana.edu:9090/archiva/repository/ogce.m2.all</url>
+        </repository>
         <repository>
             <id>central</id>
             <name>Maven Central</name>



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