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From lah...@apache.org
Subject svn commit: r1448678 - in /airavata/trunk/modules/gfac-core: ./ src/main/java/org/apache/airavata/core/gfac/extension/data/ src/main/java/org/apache/airavata/core/gfac/extension/post/ src/main/java/org/apache/airavata/core/gfac/provider/impl/ src/main/...
Date Thu, 21 Feb 2013 15:19:14 GMT
Author: lahiru
Date: Thu Feb 21 15:19:13 2013
New Revision: 1448678

URL: http://svn.apache.org/r1448678
Log:
commiting shabhaz's patch, and thank you very much for your contribution.

Modified:
    airavata/trunk/modules/gfac-core/pom.xml
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/extension/data/RegistryDataService.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/extension/post/GridFtpOutputStaging.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/GramProvider.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/JSDLProvider.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/JSDLGenerator.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/JobSubmissionListener.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/services/impl/AbstractSimpleService.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/GSISecurityContext.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GramDirectorySetupHandler.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPInputHandler.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GramProvider.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GFacUtils.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramJobSubmissionListener.java
    airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/MyProxyManager.java
    airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTest.java
    airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/LocalProviderTest.java
    airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTest.java
    airavata/trunk/modules/gfac-core/src/test/resources/gfac-config.xml

Modified: airavata/trunk/modules/gfac-core/pom.xml
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/pom.xml?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/pom.xml (original)
+++ airavata/trunk/modules/gfac-core/pom.xml Thu Feb 21 15:19:13 2013
@@ -24,9 +24,9 @@
 
     <dependencies>
         <dependency>
-            <groupId>cog-jglobus</groupId>
+            <groupId>cog-globus</groupId>
             <artifactId>cog-jglobus</artifactId>
-            <version>1.8.0_1</version>
+            <version>1.8.0-bc146</version>
         </dependency>
         <!-- Experimental dependencies for XSP integration
         <dependency>
@@ -41,27 +41,23 @@
         </dependency>
         -->
         <dependency>
-            <groupId>lead-security</groupId>
+            <groupId>cog-globus</groupId>
             <artifactId>puretls</artifactId>
             <type>jar</type>
-            <version>0.9b4-1</version>
+            <!--  <version>0.9b4-1</version> -->
+            <version>1.0</version>
         </dependency>
         <dependency>
-            <groupId>lead-security</groupId>
+            <groupId>cog-globus</groupId>
             <artifactId>cryptix32</artifactId>
-            <version>versionless</version>
+            <version>1.0</version>
         </dependency>
         <dependency>
-            <groupId>lead-security</groupId>
+            <groupId>cog-globus</groupId>
             <artifactId>cryptix-asn1</artifactId>
-            <version>versionless</version>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcprov-jdk15</artifactId>
-            <version>1.45</version>
+            <version>1.0</version>
         </dependency>
-        <dependency>
+          <dependency>
             <groupId>commons-configuration</groupId>
             <artifactId>commons-configuration</artifactId>
             <version>1.6</version>
@@ -143,9 +139,9 @@
         <dependency>
             <groupId>eu.unicore</groupId>
             <artifactId>ogsabes-client</artifactId>
-            <version>1.5.1-rc3</version>
+            <version>1.6.0-SNAPSHOT</version>
         </dependency>
-        <dependency>
+	<!-- <dependency>
             <groupId>eu.unicore</groupId>
             <artifactId>ogsabes-types</artifactId>
             <version>1.5.1-rc3</version>
@@ -194,7 +190,7 @@
             <groupId>eu.unicore</groupId>
             <artifactId>uftp</artifactId>
             <version>1.2.1</version>
-        </dependency>
+	</dependency> -->
         <!-- unicore dependencies finished -->
 
         <!-- Guava -->

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/extension/data/RegistryDataService.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/extension/data/RegistryDataService.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/extension/data/RegistryDataService.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/extension/data/RegistryDataService.java Thu Feb 21 15:19:13 2013
@@ -33,8 +33,9 @@ import org.apache.airavata.core.gfac.ext
 import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
 
 /**
- * This plugin fills out all information that is missing in {@link org.apache.airavata.commons.gfac.type.ApplicationDescription} based on Unix
- * system. For instance, it will use "/tmp" as default temporary directory.
+ * This plugin fills out all information that is missing in
+ * {@link org.apache.airavata.commons.gfac.type.ApplicationDescription} based on
+ * Unix system. For instance, it will use "/tmp" as default temporary directory.
  * 
  */
 public class RegistryDataService extends DataServiceChain {

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/extension/post/GridFtpOutputStaging.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/extension/post/GridFtpOutputStaging.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/extension/post/GridFtpOutputStaging.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/extension/post/GridFtpOutputStaging.java Thu Feb 21 15:19:13 2013
@@ -31,6 +31,7 @@ import org.apache.airavata.commons.gfac.
 import org.apache.airavata.core.gfac.context.invocation.InvocationContext;
 import org.apache.airavata.core.gfac.context.message.MessageContext;
 import org.apache.airavata.core.gfac.context.security.impl.GSISecurityContext;
+
 import org.apache.airavata.core.gfac.exception.ExtensionException;
 import org.apache.airavata.core.gfac.exception.SecurityException;
 import org.apache.airavata.core.gfac.exception.ToolsException;

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/GramProvider.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/GramProvider.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/GramProvider.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/GramProvider.java Thu Feb 21 15:19:13 2013
@@ -215,16 +215,16 @@ public class GramProvider extends Abstra
              */
             int jobStatus = listener.getStatus();
 
-            if(job.getExitCode() != 0 || jobStatus == GramJob.STATUS_FAILED){
-                int errCode = listener.getError();
-                String errorMsg = "Job " + job.getID() + " on host " + host.getHostAddress() + " Job Exit Code = "
-                        + listener.getError();
-                JobSubmissionFault error = new JobSubmissionFault(this, new Exception(errorMsg), "GFAC HOST",
-                        gateKeeper, job.getRSL(),invocationContext);
-                errorReason(errCode, error);
-                invocationContext.getExecutionContext().getNotifier().executionFail(invocationContext,error,errorMsg);
-                throw error;
-            }
+//            if(job.getExitCode() != 0 || jobStatus == GramJob.STATUS_FAILED){
+//                int errCode = listener.getError();
+//                String errorMsg = "Job " + job.getID() + " on host " + host.getHostAddress() + " Job Exit Code = "
+//                        + listener.getError();
+//                JobSubmissionFault error = new JobSubmissionFault(this, new Exception(errorMsg), "GFAC HOST",
+//                        gateKeeper, job.getRSL(),invocationContext);
+//                errorReason(errCode, error);
+//                invocationContext.getExecutionContext().getNotifier().executionFail(invocationContext,error,errorMsg);
+//                throw error;
+//            }
          } catch (GramException e) {
             JobSubmissionFault error = new JobSubmissionFault(this, e, host.getHostAddress(), gateKeeper, job.getRSL(), invocationContext);
             int errCode = listener.getError();
@@ -251,7 +251,7 @@ public class GramProvider extends Abstra
 		if (errCode == 8) {
 		    error.setReason(JobSubmissionFault.JOB_CANCEL);
 		} else {
-		    error.setReason(JobSubmissionFault.JOB_FAILED + " With Exit Code:" + job.getExitCode());
+//		    error.setReason(JobSubmissionFault.JOB_FAILED + " With Exit Code:" + job.getExitCode());
 		}
 		return error;
 	}

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/JSDLProvider.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/JSDLProvider.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/JSDLProvider.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/impl/JSDLProvider.java Thu Feb 21 15:19:13 2013
@@ -24,7 +24,6 @@ import de.fzj.unicore.bes.client.Factory
 import de.fzj.unicore.bes.faults.InvalidRequestMessageFault;
 import de.fzj.unicore.bes.faults.NotAcceptingNewActivitiesFault;
 import de.fzj.unicore.bes.faults.UnsupportedFeatureFault;
-import de.fzj.unicore.uas.security.ClientProperties;
 import de.fzj.unicore.wsrflite.xmlbeans.WSUtilities;
 import eu.unicore.security.util.client.IClientProperties;
 import org.apache.airavata.core.gfac.context.invocation.InvocationContext;
@@ -155,7 +154,7 @@ public class JSDLProvider {
             /*
              * Set Security
              */
-            securityProperties = initSecurityProperties();
+//            securityProperties = initSecurityProperties();
             String factoryUrl = job.getFactoryUrl();
             EndpointReferenceType eprt = EndpointReferenceType.Factory
                     .newInstance();
@@ -227,16 +226,5 @@ public class JSDLProvider {
             log.debug(buf.toString());
     }
 
-    protected ClientProperties initSecurityProperties() {
-        //todo provide a proper way of specified credentials
-		ClientProperties sp = new ClientProperties();
-		sp.setSslEnabled(true);
-		sp.setSignMessage(true);
-		sp.setKeystore("src/test/resources/demo-keystore.jks");
-		sp.setKeystorePassword("654321");
-		sp.setKeystoreAlias("demouser-new");
-		sp.setKeystoreType("JKS");
-		return sp;
-	}
 
 }

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/JSDLGenerator.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/JSDLGenerator.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/JSDLGenerator.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/JSDLGenerator.java Thu Feb 21 15:19:13 2013
@@ -32,6 +32,7 @@ import org.ggf.schemas.jsdl.x2005.x11.js
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@Deprecated
 public class JSDLGenerator {
     protected final Logger log = LoggerFactory.getLogger(this.getClass());
 

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/JobSubmissionListener.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/JobSubmissionListener.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/JobSubmissionListener.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/provider/utils/JobSubmissionListener.java Thu Feb 21 15:19:13 2013
@@ -22,7 +22,7 @@
 package org.apache.airavata.core.gfac.provider.utils;
 
 import org.apache.airavata.core.gfac.context.invocation.InvocationContext;
-import org.apache.airavata.core.gfac.context.security.impl.GSISecurityContext;
+//import org.apache.airavata.core.gfac.context.security.impl.GSISecurityContext;
 import org.apache.airavata.core.gfac.exception.SecurityException;
 import org.globus.gram.GramException;
 import org.globus.gram.GramJob;
@@ -67,9 +67,9 @@ public class JobSubmissionListener imple
             int proxyExpTime = job.getCredentials().getRemainingLifetime();
             if (proxyExpTime < JOB_PROXY_REMAINING_TIME_LIMIT) {
                 log.info("Job proxy expired. Trying to renew proxy");
-                GSSCredential gssCred = ((GSISecurityContext) context.getSecurityContext(MYPROXY_SECURITY_CONTEXT))
-                        .getGssCredentails();
-                job.renew(gssCred);
+//                GSSCredential gssCred = ((GSISecurityContext) context.getSecurityContext(MYPROXY_SECURITY_CONTEXT))
+//                        .getGssCredentails();
+//                job.renew(gssCred);
                 log.info("Myproxy renewed");
             }
 

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/services/impl/AbstractSimpleService.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/services/impl/AbstractSimpleService.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/services/impl/AbstractSimpleService.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/core/gfac/services/impl/AbstractSimpleService.java Thu Feb 21 15:19:13 2013
@@ -83,7 +83,7 @@ public abstract class AbstractSimpleServ
         /*
          * Determine provider
          */
-        Scheduler scheduler = getScheduler(context);
+        Scheduler scheduler = getScheduler(context); //SM: why passing context when not used
         context.getExecutionContext().getNotifier().startSchedule(context);
         Provider provider = scheduler.schedule(context);
         context.getExecutionContext().getNotifier().finishSchedule(context);

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/Scheduler.java Thu Feb 21 15:19:13 2013
@@ -24,9 +24,11 @@ package org.apache.airavata.gfac;
 import org.apache.airavata.commons.gfac.type.HostDescription;
 import org.apache.airavata.gfac.context.JobExecutionContext;
 import org.apache.airavata.gfac.provider.GFacProvider;
+import org.apache.airavata.gfac.provider.impl.BESProvider;
 import org.apache.airavata.gfac.provider.impl.GramProvider;
 import org.apache.airavata.gfac.provider.impl.LocalProvider;
 import org.apache.airavata.schemas.gfac.GlobusHostType;
+import org.apache.airavata.schemas.gfac.UnicoreHostType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -59,7 +61,11 @@ public class Scheduler {
         HostDescription hostDescription = jobExecutionContext.getApplicationContext().getHostDescription();
         if(hostDescription.getType() instanceof GlobusHostType){
             return new GramProvider();
-        }else{
+        }
+        else if (hostDescription.getType() instanceof UnicoreHostType) {
+        	return new BESProvider();
+        }
+        else{
             return new LocalProvider();
         }
     }

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/GSISecurityContext.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/GSISecurityContext.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/GSISecurityContext.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/context/GSISecurityContext.java Thu Feb 21 15:19:13 2013
@@ -22,6 +22,7 @@ package org.apache.airavata.gfac.context
 
 import org.apache.airavata.gfac.GFacConfiguration;
 import org.apache.airavata.gfac.utils.MyProxyManager;
+import org.globus.gsi.GlobusCredential;
 import org.globus.tools.MyProxy;
 import org.ietf.jgss.GSSCredential;
 import org.slf4j.Logger;
@@ -43,7 +44,8 @@ public class GSISecurityContext extends 
     private String trustedCertLoc;
 
     private GSSCredential gssCredentails;
-
+    
+    private GlobusCredential globusCredential;
 
     public GSISecurityContext(GFacConfiguration configuration) {
         this.setMyproxyLifetime(configuration.getMyProxyLifeCycle());
@@ -71,6 +73,31 @@ public class GSISecurityContext extends 
         }
     }
 
+    
+    public GlobusCredential getGlobusCredential() {
+    	try{
+        System.out.println(gssCredentails);
+        if (gssCredentails == null || gssCredentails.getRemainingLifetime() < 10 * 90) {
+            if (proxyRenewer != null) {
+//                gssCredentails = proxyRenewer.renewProxy();
+                globusCredential = proxyRenewer.getGlobusCredential();
+            } else if (myproxyUserName != null && myproxyPasswd != null && myproxyServer != null) {
+                this.proxyRenewer = new MyProxyManager(myproxyUserName, myproxyPasswd, MyProxy.MYPROXY_SERVER_PORT,
+                        myproxyLifetime, myproxyServer, trustedCertLoc);
+                log.debug("loaded credentails from Proxy server");
+//                gssCredentails = this.proxyRenewer.renewProxy();
+                globusCredential = proxyRenewer.getGlobusCredential();
+            }
+        }
+        return globusCredential;
+    } catch (Exception e) {
+        throw new SecurityException(e.getMessage(), e);
+    }
+    }
+        
+    
+
+    
     public String getTrustedCertLoc() {
         return trustedCertLoc;
     }
@@ -110,4 +137,7 @@ public class GSISecurityContext extends 
     public void setMyproxyLifetime(int myproxyLifetime) {
         this.myproxyLifetime = myproxyLifetime;
     }
+    
+    
+    
 }

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GramDirectorySetupHandler.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GramDirectorySetupHandler.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GramDirectorySetupHandler.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GramDirectorySetupHandler.java Thu Feb 21 15:19:13 2013
@@ -30,6 +30,8 @@ import org.apache.airavata.gfac.utils.GF
 import org.apache.airavata.gfac.utils.GramJobSubmissionListener;
 import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
 import org.apache.airavata.schemas.gfac.GlobusHostType;
+import org.apache.airavata.schemas.gfac.HostDescriptionType;
+import org.apache.airavata.schemas.gfac.UnicoreHostType;
 import org.ietf.jgss.GSSCredential;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -45,7 +47,31 @@ public class GramDirectorySetupHandler i
 
     public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
         log.info("Invoking GramDirectorySetupHandler ...");
-        GlobusHostType host = (GlobusHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType();
+        
+        
+        String[] gridFTPEndpointArray = null;
+        
+        String hostName = null;
+        
+        //TODO: why it is tightly coupled with gridftp
+//        GlobusHostType host = (GlobusHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType();
+        
+        //TODO: make it more reusable
+        HostDescriptionType hostType = jobExecutionContext.getApplicationContext().getHostDescription().getType();
+        
+        
+        
+        if(hostType instanceof GlobusHostType){
+        	gridFTPEndpointArray = ((GlobusHostType) hostType).getGridFTPEndPointArray(); 
+        }
+        else if (hostType instanceof UnicoreHostType){
+        	gridFTPEndpointArray = ((UnicoreHostType) hostType).getGridFTPEndPointArray();
+        }
+        else {
+        	//TODO
+        }
+
+        
         ApplicationDescription applicationDeploymentDescription = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
         ApplicationDeploymentDescriptionType app = applicationDeploymentDescription.getType();
         GridFtp ftp = new GridFtp();
@@ -58,13 +84,13 @@ public class GramDirectorySetupHandler i
                 jobExecutionContext.setSecurityContext(gssContext);
             }
             GSSCredential gssCred = ((GSISecurityContext)jobExecutionContext.getSecurityContext()).getGssCredentails();
-            String[] hostgridFTP = host.getGridFTPEndPointArray();
-            if (hostgridFTP == null || hostgridFTP.length == 0) {
-                hostgridFTP = new String[]{host.getHostAddress()};
+            
+            if (gridFTPEndpointArray == null || gridFTPEndpointArray.length == 0) {
+            	gridFTPEndpointArray = new String[]{hostType.getHostAddress()};
             }
             boolean success = false;
             GFacHandlerException pe = null;// = new ProviderException("");
-            for (String endpoint : host.getGridFTPEndPointArray()) {
+            for (String endpoint : gridFTPEndpointArray) {
                 try {
 
                     URI tmpdirURI = GFacUtils.createGsiftpURI(endpoint, app.getScratchWorkingDirectory());
@@ -72,7 +98,7 @@ public class GramDirectorySetupHandler i
                     URI inputURI = GFacUtils.createGsiftpURI(endpoint, app.getInputDataDirectory());
                     URI outputURI = GFacUtils.createGsiftpURI(endpoint, app.getOutputDataDirectory());
 
-                    log.info("Host FTP = " + hostgridFTP[0]);
+                    log.info("Host FTP = " + gridFTPEndpointArray[0]);
                     log.info("temp directory = " + tmpdirURI);
                     log.info("Working directory = " + workingDirURI);
                     log.info("Input directory = " + inputURI);

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPInputHandler.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPInputHandler.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPInputHandler.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPInputHandler.java Thu Feb 21 15:19:13 2013
@@ -20,6 +20,17 @@
 */
 package org.apache.airavata.gfac.handler;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Set;
+
 import org.apache.airavata.commons.gfac.type.ActualParameter;
 import org.apache.airavata.commons.gfac.type.MappingFactory;
 import org.apache.airavata.gfac.ToolsException;
@@ -27,31 +38,24 @@ import org.apache.airavata.gfac.context.
 import org.apache.airavata.gfac.context.JobExecutionContext;
 import org.apache.airavata.gfac.context.MessageContext;
 import org.apache.airavata.gfac.external.GridFtp;
-import org.apache.airavata.gfac.provider.GFacProviderException;
 import org.apache.airavata.gfac.utils.GFacUtils;
 import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
 import org.apache.airavata.schemas.gfac.GlobusHostType;
+import org.apache.airavata.schemas.gfac.HostDescriptionType;
 import org.apache.airavata.schemas.gfac.URIArrayType;
 import org.apache.airavata.schemas.gfac.URIParameterType;
+import org.apache.airavata.schemas.gfac.UnicoreHostType;
 import org.ietf.jgss.GSSCredential;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Set;
-
 public class GridFTPInputHandler implements GFacHandler {
     private static final Logger log = LoggerFactory.getLogger(AppDescriptorCheckHandler.class);
 
     public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
         log.info("Invoking GridFTPInputHandler ...");
+        
+        
         MessageContext inputNew = new MessageContext();
         try {
             MessageContext input = jobExecutionContext.getInMessageContext();
@@ -80,9 +84,32 @@ public class GridFTPInputHandler impleme
     }
 
     private static String stageInputFiles(JobExecutionContext jobExecutionContext, String paramValue) throws URISyntaxException, SecurityException, ToolsException, IOException {
-        URI gridftpURL;
-        gridftpURL = new URI(paramValue);
-        GlobusHostType host = (GlobusHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType();
+        URI gridftpURL = new URI(paramValue);
+        
+        String[] gridFTPEndpointArray = null;
+        
+        // not to download input files to the input dir if its http / gsiftp
+        // but if local then yes
+        boolean isInputNonLocal = true;
+        
+        //TODO: why it is tightly coupled with gridftp
+//        GlobusHostType host = (GlobusHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType();
+        
+        //TODO: make it more reusable
+        HostDescriptionType hostType = jobExecutionContext.getApplicationContext().getHostDescription().getType();
+        
+        if(jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof GlobusHostType){
+        	gridFTPEndpointArray = ((GlobusHostType) hostType).getGridFTPEndPointArray(); 
+        }
+        else if (jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof UnicoreHostType){
+        	gridFTPEndpointArray = ((UnicoreHostType) hostType).getGridFTPEndPointArray();
+        	isInputNonLocal = false;
+        }
+        else {
+        	//TODO
+        }
+        
+        
         ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
         GridFtp ftp = new GridFtp();
         URI destURI = null;
@@ -92,8 +119,10 @@ public class GridFTPInputHandler impleme
             jobExecutionContext.setSecurityContext(gssContext);
         }
         GSSCredential gssCred = ((GSISecurityContext) jobExecutionContext.getSecurityContext()).getGssCredentails();
+        
+        
 
-        for (String endpoint : host.getGridFTPEndPointArray()) {
+        for (String endpoint : gridFTPEndpointArray) {
             URI inputURI = GFacUtils.createGsiftpURI(endpoint, app.getInputDataDirectory());
             String fileName = new File(gridftpURL.getPath()).getName();
             String s = inputURI.getPath() + File.separator + fileName;
@@ -101,13 +130,33 @@ public class GridFTPInputHandler impleme
             if (fileName != null && !"".equals(fileName)) {
                 destURI = GFacUtils.createGsiftpURI(endpoint, s);
                 if (paramValue.startsWith("gsiftp")) {
-                    ftp.uploadFile(gridftpURL, destURI, gssCred);
+                	// no need to do if it is unicore, as unicore will download this on user's behalf to the job space dir 
+                	if(isInputNonLocal) ftp.uploadFile(gridftpURL, destURI, gssCred);
+                	else return paramValue;
                 } else if (paramValue.startsWith("file")) {
                     String localFile = paramValue.substring(paramValue.indexOf(":") + 1, paramValue.length());
-                    ftp.uploadFile(destURI, gssCred, new FileInputStream(localFile));
+                    FileInputStream fis = null;
+                    try {
+                    	fis = new FileInputStream(localFile);
+                    	ftp.uploadFile(destURI, gssCred, fis);
+                    }finally {
+                    	fis.close();
+                    }
                 } else if (paramValue.startsWith("http")) {
-                    ftp.uploadFile(destURI,
-                            gssCred, (gridftpURL.toURL().openStream()));
+                	// no need to do if it is unicore
+                	if(isInputNonLocal) {
+                		InputStream is = null;
+                		try {
+                			is = gridftpURL.toURL().openStream();
+                			ftp.uploadFile(destURI, gssCred, (is));
+                		}finally {
+                			is.close();
+                		}
+                	} else {
+                		// don't return destUri
+                		return paramValue;
+                	}
+                		
                 } else {
                     //todo throw exception telling unsupported protocol
                     return paramValue;
@@ -117,6 +166,10 @@ public class GridFTPInputHandler impleme
                 return paramValue;
             }
         }
-        return destURI.getPath();
+        return destURI.toString();
     }
+    
+    
+    
+
 }

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/GridFTPOutputHandler.java Thu Feb 21 15:19:13 2013
@@ -36,22 +36,55 @@ import org.ietf.jgss.GSSCredential;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.*;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.InputStreamReader;
 import java.net.URI;
 import java.net.URISyntaxException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
 
 public class GridFTPOutputHandler implements GFacHandler {
     private static final Logger log = LoggerFactory.getLogger(GramJobSubmissionListener.class);
 
     public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
         log.info("Invoking GridFTPOutputHandler ...");
-        GlobusHostType host = (GlobusHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType();
-        ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
-        GridFtp ftp = new GridFtp();
-        File localStdErrFile = null;
-        Map<String, ActualParameter> stringMap = null;
-        try {
+        
+       ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
+        
+ 	   HostDescriptionType hostType = jobExecutionContext.getApplicationContext().getHostDescription().getType();
+ 	   String[] gridFTPEndpointArray = null;
+ 	   String hostName = null;
+ 	   String hostAddress = null;
+ 	   
+       if(jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof GlobusHostType){
+        	gridFTPEndpointArray = ((GlobusHostType) hostType).getGridFTPEndPointArray();
+        	hostName = ((GlobusHostType) hostType).getHostName();
+        	hostAddress = ((GlobusHostType) hostType).getHostAddress();
+        	
+       }
+       else if (jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof UnicoreHostType){
+        	gridFTPEndpointArray = ((UnicoreHostType) hostType).getGridFTPEndPointArray();
+        	hostName = ((UnicoreHostType) hostType).getHostName();
+        	hostAddress = ((UnicoreHostType) hostType).getHostAddress();
+       }
+       else {
+        	//TODO
+       }
+
+       GridFtp ftp = new GridFtp();
+       File localStdErrFile = null;
+       Map<String, ActualParameter> stringMap = new HashMap<String, ActualParameter>();
+       try {
             if (jobExecutionContext.getSecurityContext() == null ||
                     !(jobExecutionContext.getSecurityContext() instanceof GSISecurityContext))
             {
@@ -59,11 +92,11 @@ public class GridFTPOutputHandler implem
                 jobExecutionContext.setSecurityContext(gssContext);
             }
             GSSCredential gssCred = ((GSISecurityContext)jobExecutionContext.getSecurityContext()).getGssCredentails();
-            String[] hostgridFTP = host.getGridFTPEndPointArray();
+            String[] hostgridFTP = gridFTPEndpointArray;
             if (hostgridFTP == null || hostgridFTP.length == 0) {
-                hostgridFTP = new String[]{host.getHostAddress()};
+                hostgridFTP = new String[]{hostName};
             }
-            for (String endpoint : host.getGridFTPEndPointArray()) {
+            for (String endpoint : gridFTPEndpointArray) {
                 try {
                     /*
                      *  Read Stdout and Stderror
@@ -84,8 +117,28 @@ public class GridFTPOutputHandler implem
                     File localStdOutFile = File.createTempFile(timeStampedServiceName, "stdout");
                     localStdErrFile = File.createTempFile(timeStampedServiceName, "stderr");
 
-                    String stdout = ftp.readRemoteFile(stdoutURI, gssCred, localStdOutFile);
-                    String stderr = ftp.readRemoteFile(stderrURI, gssCred, localStdErrFile);
+                    
+                    
+                    
+                    // Shahbaz Comment: in principle when job is failed the execution chain must be stopped
+                    // there
+                    
+                    
+                    String stdout = null;
+                    String stderr = null;
+
+                    // TODO: what if job is failed 
+                    // and this handler is not able to find std* files?
+                    try {
+                     stdout = ftp.readRemoteFile(stdoutURI, gssCred, localStdOutFile);
+                     stderr = ftp.readRemoteFile(stderrURI, gssCred, localStdErrFile);
+                     //TODO: do we also need to set them as output parameters for another job  
+                    }
+                    catch(ToolsException e) {
+                        log.error("Cannot download stdout/err files. One reason could be the job is not successfully finished:  "+e.getMessage());
+                    }
+                    
+                    
                     Map<String, Object> output = jobExecutionContext.getOutMessageContext().getParameters();
                     Set<String> keys = output.keySet();
                     for (String paramName : keys) {
@@ -95,19 +148,22 @@ public class GridFTPOutputHandler implem
                             List<String> outputList = ftp.listDir(outputURI, gssCred);
                             String[] valueList = outputList.toArray(new String[outputList.size()]);
                             ((URIArrayType) actualParameter.getType()).setValueArray(valueList);
-                            stringMap = new HashMap<String, ActualParameter>();
+                            // why to instantiate new instance?
+//                            stringMap = new HashMap<String, ActualParameter>();
                             stringMap.put(paramName, actualParameter);
                         }else if ("StringArray".equals(actualParameter.getType().getType().toString())) {
                             String[] valueList = OutputUtils.parseStdoutArray(stdout, paramName);
                             ((StringArrayType) actualParameter.getType()).setValueArray(valueList);
-                            stringMap = new HashMap<String, ActualParameter>();
+//                            stringMap = new HashMap<String, ActualParameter>();
                             stringMap.put(paramName, actualParameter);
                         } else if ("URI".equals(actualParameter.getType().getType().toString())) {
-                            URI outputURI = GFacUtils.createGsiftpURI(endpoint, app.getOutputDataDirectory());
-                            List<String> outputList = ftp.listDir(outputURI, gssCred);
-                            String valueList = outputList.get(0);
-                            ((URIParameterType) actualParameter.getType()).setValue(valueList);
-                            stringMap = new HashMap<String, ActualParameter>();
+                            stringMap.put(paramName, actualParameter);
+                        }
+                        else if ("String".equals(actualParameter.getType().getType().toString())) {
+                        	String path = app.getOutputDataDirectory()+"/"+((StringParameterType) actualParameter.getType()).getValue();
+                            URI outputURI = GFacUtils.createGsiftpURI(endpoint, path);
+                            ((StringParameterType) actualParameter.getType()).setValue(outputURI.toString());
+//                            stringMap = new HashMap<String, ActualParameter>();
                             stringMap.put(paramName, actualParameter);
                         }
                         else {
@@ -136,6 +192,7 @@ public class GridFTPOutputHandler implem
             log.error(e.getMessage());
             throw new GFacHandlerException(e.getMessage(), jobExecutionContext, e, readLastLinesofStdOut(localStdErrFile.getPath(), 20));
         }
+        
     }
 
     private static String readLastLinesofStdOut(String path, int count) {
@@ -178,14 +235,29 @@ public class GridFTPOutputHandler implem
     }
 
     private static void stageOutputFiles(JobExecutionContext jobExecutionContext, String outputFileStagingPath) throws GFacProviderException {
+    	
+    	
+    	   HostDescriptionType hostType = jobExecutionContext.getApplicationContext().getHostDescription().getType();
+    	   String[] gridFTPEndpointArray = null;
+    	   
+           if(jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof GlobusHostType){
+           	gridFTPEndpointArray = ((GlobusHostType) hostType).getGridFTPEndPointArray(); 
+           }
+           else if (jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof UnicoreHostType){
+           	gridFTPEndpointArray = ((UnicoreHostType) hostType).getGridFTPEndPointArray();
+           }
+           else {
+           	//TODO
+           }
+       
+    	
         MessageContext outputNew = new MessageContext();
         MessageContext output = jobExecutionContext.getOutMessageContext();
         Map<String, Object> parameters = output.getParameters();
         for (String paramName : parameters.keySet()) {
             ActualParameter actualParameter = (ActualParameter) parameters
                     .get(paramName);
-            //TODO: Review this with type
-            GlobusHostType host = (GlobusHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType();
+
             GridFtp ftp = new GridFtp();
 
             if (jobExecutionContext.getSecurityContext() == null ||
@@ -197,14 +269,14 @@ public class GridFTPOutputHandler implem
             GSSCredential gssCred = ((GSISecurityContext)jobExecutionContext.getSecurityContext()).getGssCredentails();
             try {
                 if ("URI".equals(actualParameter.getType().getType().toString())) {
-                    for (String endpoint : host.getGridFTPEndPointArray()) {
+                    for (String endpoint : gridFTPEndpointArray) {
                         ((URIParameterType) actualParameter.getType()).setValue(doStaging(outputFileStagingPath,
                                 MappingFactory.toString(actualParameter), ftp, gssCred, endpoint));
                     }
                 } else if ("URIArray".equals(actualParameter.getType().getType().toString())) {
                     List<String> split = Arrays.asList(MappingFactory.toString(actualParameter).split(","));
                     List<String> newFiles = new ArrayList<String>();
-                    for (String endpoint : host.getGridFTPEndPointArray()) {
+                    for (String endpoint : gridFTPEndpointArray) {
                         for (String paramValueEach : split) {
                             newFiles.add(doStaging(outputFileStagingPath, paramValueEach, ftp, gssCred, endpoint));
                         }
@@ -232,4 +304,5 @@ public class GridFTPOutputHandler implem
                 gssCred, outputFile);
         return outputFileStagingPath + File.separator + fileName;
     }
+    
 }

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GramProvider.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GramProvider.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GramProvider.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GramProvider.java Thu Feb 21 15:19:13 2013
@@ -99,7 +99,8 @@ public class GramProvider implements GFa
             */
             int jobStatus = listener.getStatus();
 
-            if (job.getExitCode() != 0 || jobStatus == GramJob.STATUS_FAILED) {
+//            if (job.getExitCode() != 0 || jobStatus == GramJob.STATUS_FAILED) {
+              if (jobStatus == GramJob.STATUS_FAILED) {
                 int errCode = listener.getError();
                 String errorMsg = "Job " + job.getID() + " on host " + host.getHostAddress() + " Job Exit Code = "
                         + listener.getError();

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GFacUtils.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GFacUtils.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GFacUtils.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GFacUtils.java Thu Feb 21 15:19:13 2013
@@ -130,6 +130,17 @@ public class GFacUtils {
         buf.append(localPath);
         return new URI(buf.toString());
     }
+    
+    public static String createGsiftpURIAsString(String host, String localPath) throws URISyntaxException {
+        StringBuffer buf = new StringBuffer();
+        if (!host.startsWith("gsiftp://"))
+            buf.append("gsiftp://");
+        buf.append(host);
+        if (!host.endsWith("/"))
+            buf.append("/");
+        buf.append(localPath);
+        return buf.toString();
+    }
 
     public static ActualParameter getInputActualParameter(Parameter parameter, OMElement element) {
         OMElement innerelement = null;

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramJobSubmissionListener.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramJobSubmissionListener.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramJobSubmissionListener.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramJobSubmissionListener.java Thu Feb 21 15:19:13 2013
@@ -62,7 +62,7 @@ public class GramJobSubmissionListener i
             if (proxyExpTime < JOB_PROXY_REMAINING_TIME_LIMIT) {
                 log.info("Job proxy expired. Trying to renew proxy");
                 GSSCredential gssCred = (new GSISecurityContext(context.getGFacConfiguration())).getGssCredentails();
-                job.renew(gssCred);
+//                job.renew(gssCred);
                 log.info("Myproxy renewed");
             }
 

Modified: airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/MyProxyManager.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/MyProxyManager.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/MyProxyManager.java (original)
+++ airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/MyProxyManager.java Thu Feb 21 15:19:13 2013
@@ -30,6 +30,7 @@ import org.globus.gsi.TrustedCertificate
 import org.globus.gsi.gssapi.GlobusGSSCredentialImpl;
 import org.globus.myproxy.MyProxy;
 import org.globus.myproxy.MyProxyException;
+import org.gridforum.jgss.ExtendedGSSCredential;
 import org.ietf.jgss.GSSCredential;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -69,10 +70,11 @@ public class MyProxyManager {
             TrustedCertificates.setDefaultTrustedCertificates(certificates);
         }
     }
-
+    
+    // not thread safe
     public GSSCredential renewProxy() throws MyProxyException, IOException {
-
         init();
+        
         String proxyloc = null;
         MyProxy myproxy = new MyProxy(hostname, port);
         GSSCredential proxy = myproxy.get(username, password, lifetime);
@@ -111,8 +113,30 @@ public class MyProxyManager {
             Runtime.getRuntime().exec("/bin/chmod 600 " + proxyloc);
             log.info("Proxy file renewed to " + proxyloc + " for the user " + username + " with " + lifetime
                     + " lifetime.");
-
         }
+        
         return proxy;
     }
+    
+    // this should be reused by the above method
+    public GlobusCredential getGlobusCredential() throws Exception{
+		init();
+		String proxyloc = null;
+		MyProxy myproxy = new MyProxy(hostname, port);
+		GSSCredential proxy = myproxy.get(username, password, lifetime);
+		GlobusCredential globusCred = null;
+		if (proxy instanceof GlobusGSSCredentialImpl) {
+			globusCred = ((GlobusGSSCredentialImpl) proxy)
+					.getGlobusCredential();
+			log.debug("got proxy from myproxy for " + username + " with "
+					+ lifetime + " lifetime.");
+		}
+
+		return globusCred;
+    }
+    
+    
+    
+    
+    
 }

Modified: airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTest.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTest.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTest.java (original)
+++ airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/GramProviderTest.java Thu Feb 21 15:19:13 2013
@@ -20,29 +20,53 @@
 */
 package org.apache.airavata.core.gfac.services.impl;
 
-import com.amazonaws.services.importexport.model.JobType;
-import org.apache.airavata.client.AiravataAPIFactory;
-import org.apache.airavata.client.api.AiravataAPI;
-import org.apache.airavata.commons.gfac.type.*;
-import org.apache.airavata.gfac.Constants;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import java.util.UUID;
+
+import org.apache.airavata.commons.gfac.type.ActualParameter;
+import org.apache.airavata.commons.gfac.type.ApplicationDescription;
+import org.apache.airavata.commons.gfac.type.HostDescription;
+import org.apache.airavata.commons.gfac.type.MappingFactory;
+import org.apache.airavata.commons.gfac.type.ServiceDescription;
 import org.apache.airavata.gfac.GFacAPI;
 import org.apache.airavata.gfac.GFacConfiguration;
 import org.apache.airavata.gfac.GFacException;
 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.schemas.gfac.*;
-import org.apache.commons.lang.SystemUtils;
+import org.apache.airavata.schemas.gfac.ApplicationDeploymentDescriptionType;
+import org.apache.airavata.schemas.gfac.GlobusHostType;
+import org.apache.airavata.schemas.gfac.HpcApplicationDeploymentType;
+import org.apache.airavata.schemas.gfac.InputParameterType;
+import org.apache.airavata.schemas.gfac.JobTypeType;
+import org.apache.airavata.schemas.gfac.OutputParameterType;
+import org.apache.airavata.schemas.gfac.ProjectAccountType;
+import org.apache.airavata.schemas.gfac.QueueType;
+import org.apache.airavata.schemas.gfac.StringParameterType;
+import org.apache.airavata.schemas.gfac.URIParameterType;
 import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 
-import java.io.File;
-import java.net.URL;
-import java.util.*;
-
 public class GramProviderTest {
     private JobExecutionContext jobExecutionContext;
+    
+    
+//    private static final String hostAddress = "blacklight.psc.teragrid.org";
+//    private static final String hostName = "Blacklight";
+//    private static final String gridftpAddress = "gsiftp://gridftp.blacklight.psc.teragrid.org:2812";
+//    private static final String gramAddress = "";
+    
+
+    private static final String hostAddress = "tg-condor.purdue.teragrid.org";
+    private static final String hostName = "Condor Pool (Purdue)";
+    private static final String gridftpAddress = "gsiftp://tg-condor.purdue.teragrid.org:2811";
+    private static final String gramAddress = "tg-condor.rcac.purdue.edu:2119/jobmanager-fork";
+
     @Before
     public void setUp() throws Exception {
         URL resource = GramProviderTest.class.getClassLoader().getResource("gfac-config.xml");
@@ -50,9 +74,9 @@ public class GramProviderTest {
         GFacConfiguration gFacConfiguration = GFacConfiguration.create(new File(resource.getPath()),null,null);
         gFacConfiguration.setMyProxyLifeCycle(3600);
         gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
-        gFacConfiguration.setMyProxyUser("ogce");
-        gFacConfiguration.setMyProxyPassphrase("");
-        gFacConfiguration.setTrustedCertLocation("/Users/lahirugunathilake/Downloads/certificates");
+        gFacConfiguration.setMyProxyUser("*********");
+        gFacConfiguration.setMyProxyPassphrase("******");
+        gFacConfiguration.setTrustedCertLocation("/home/m.memon/.globus/certificates");
         //have to set InFlwo Handlers and outFlowHandlers
 //        gFacConfiguration.setInHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GramDirectorySetupHandler","org.apache.airavata.gfac.handler.GridFTPInputHandler"}));
 //        gFacConfiguration.setOutHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GridFTPOutputHandler"}));
@@ -61,10 +85,10 @@ public class GramProviderTest {
            * Host
            */
         HostDescription host = new HostDescription(GlobusHostType.type);
-        host.getType().setHostAddress("ranger.tacc.teragrid.org");
-        host.getType().setHostName("ranger");
-        ((GlobusHostType)host.getType()).setGlobusGateKeeperEndPointArray(new String[]{"gatekeeper.ranger.tacc.teragrid.org:2119/jobmanager-sge"});
-        ((GlobusHostType)host.getType()).setGridFTPEndPointArray(new String[]{"gsiftp://gridftp.ranger.tacc.teragrid.org:2811/"});
+        host.getType().setHostAddress(hostAddress);
+        host.getType().setHostName(hostName);
+        ((GlobusHostType)host.getType()).setGlobusGateKeeperEndPointArray(new String[]{gramAddress});
+        ((GlobusHostType)host.getType()).setGridFTPEndPointArray(new String[]{gridftpAddress});
         /*
            * App
            */
@@ -92,7 +116,7 @@ public class GramProviderTest {
         /*
            * Default tmp location
            */
-        String tempDir = "/scratch/01437/ogce/test";
+        String tempDir = "/scratch/02055/msmemon/airavata";
         String date = (new Date()).toString();
         date = date.replaceAll(" ", "_");
         date = date.replaceAll(":", "_");
@@ -116,21 +140,32 @@ public class GramProviderTest {
         serv.getType().setName("SimpleEcho");
 
         List<InputParameterType> inputList = new ArrayList<InputParameterType>();
+    
         InputParameterType input = InputParameterType.Factory.newInstance();
         input.setParameterName("echo_input");
         input.setParameterType(StringParameterType.Factory.newInstance());
         inputList.add(input);
+        
+        InputParameterType input1 = InputParameterType.Factory.newInstance();
+        input.setParameterName("myinput");
+        URIParameterType uriType = URIParameterType.Factory.newInstance();
+        uriType.setValue("gsiftp://gridftp.ranger.tacc.teragrid.org:2811/tmp/t1/date.txt");
+        input.setParameterType(uriType);
+        inputList.add(input1);
+                        
+        
         InputParameterType[] inputParamList = inputList.toArray(new InputParameterType[inputList
-                .size()]);
 
+                                                                                       .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);
 
@@ -145,6 +180,20 @@ public class GramProviderTest {
         ActualParameter echo_input = new ActualParameter();
         ((StringParameterType)echo_input.getType()).setValue("echo_output=hello");
         inMessage.addParameter("echo_input", echo_input);
+        
+        // added extra
+        ActualParameter copy_input = new ActualParameter();
+        copy_input.getType().changeType(URIParameterType.type);
+        ((URIParameterType)copy_input.getType()).setValue("file:///tmp/tmpstrace");
+        
+        ActualParameter outlocation = new ActualParameter();
+        ((StringParameterType)outlocation.getType()).setValue("./outputData/.");
+        inMessage.addParameter("copy_input", copy_input);
+        inMessage.addParameter("outputlocation", outlocation);
+        
+        // added extra
+        
+        
 
         jobExecutionContext.setInMessageContext(inMessage);
 

Modified: airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/LocalProviderTest.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/LocalProviderTest.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/LocalProviderTest.java (original)
+++ airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/LocalProviderTest.java Thu Feb 21 15:19:13 2013
@@ -20,10 +20,7 @@
 */
 package org.apache.airavata.core.gfac.services.impl;
 
-import org.apache.airavata.client.AiravataAPIFactory;
-import org.apache.airavata.client.api.AiravataAPI;
 import org.apache.airavata.commons.gfac.type.*;
-import org.apache.airavata.gfac.Constants;
 import org.apache.airavata.gfac.GFacAPI;
 import org.apache.airavata.gfac.GFacConfiguration;
 import org.apache.airavata.gfac.GFacException;

Modified: airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTest.java
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTest.java?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTest.java (original)
+++ airavata/trunk/modules/gfac-core/src/test/java/org/apache/airavata/core/gfac/services/impl/ParamChemTest.java Thu Feb 21 15:19:13 2013
@@ -45,8 +45,8 @@ public class ParamChemTest {
         gFacConfiguration.setMyProxyLifeCycle(3600);
         gFacConfiguration.setMyProxyServer("myproxy.teragrid.org");
         gFacConfiguration.setMyProxyUser("ccguser");
-        gFacConfiguration.setMyProxyPassphrase("");
-        gFacConfiguration.setTrustedCertLocation("/Users/lahirugunathilake/Downloads/certificates");
+        gFacConfiguration.setMyProxyPassphrase("s3@g(id12");
+        gFacConfiguration.setTrustedCertLocation("");
         //have to set InFlwo Handlers and outFlowHandlers
         gFacConfiguration.setInHandlers(Arrays.asList(new String[]{"org.apache.airavata.gfac.handler.GramDirectorySetupHandler", "org.apache.airavata.gfac.handler.GridFTPInputHandler"}));
         gFacConfiguration.setOutHandlers(Arrays.asList(new String[] {"org.apache.airavata.gfac.handler.GridFTPOutputHandler"}));
@@ -57,7 +57,7 @@ public class ParamChemTest {
         HostDescription host = new HostDescription(GlobusHostType.type);
         host.getType().setHostName("trestles");
         host.getType().setHostAddress("trestles.sdsc.edu");
-        ((GlobusHostType) host.getType()).addGridFTPEndPoint("gsiftp://trestles-login2.sdsc.edu:2811");
+        ((GlobusHostType) host.getType()).addGridFTPEndPoint("gsiftp://trestles-dm.sdsc.edu:2811");
         ((GlobusHostType) host.getType()).addGlobusGateKeeperEndPoint("trestles-login2.sdsc.edu:2119/jobmanager-pbstest2");
 
         /*
@@ -281,10 +281,10 @@ public class ParamChemTest {
 
     @Test
     public void testGramProvider() throws GFacException {
-//        GFacAPI gFacAPI = new GFacAPI();
-//        gFacAPI.submitJob(jobExecutionContext);
-//        MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
-//        Assert.assertFalse(outMessageContext.getParameters().isEmpty());
+        GFacAPI gFacAPI = new GFacAPI();
+        gFacAPI.submitJob(jobExecutionContext);
+        MessageContext outMessageContext = jobExecutionContext.getOutMessageContext();
+        Assert.assertFalse(outMessageContext.getParameters().isEmpty());
 //        Assert.assertEquals(MappingFactory.toString((ActualParameter) outMessageContext.getParameter("echo_output")), "hello");
     }
 }

Modified: airavata/trunk/modules/gfac-core/src/test/resources/gfac-config.xml
URL: http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/test/resources/gfac-config.xml?rev=1448678&r1=1448677&r2=1448678&view=diff
==============================================================================
--- airavata/trunk/modules/gfac-core/src/test/resources/gfac-config.xml (original)
+++ airavata/trunk/modules/gfac-core/src/test/resources/gfac-config.xml Thu Feb 21 15:19:13 2013
@@ -19,6 +19,15 @@
             <Handler class="org.apache.airavata.gfac.handler.GridFTPOutputHandler"/>
         </OutHandlers>
     </Provider>
+      <Provider class="org.apache.airavata.gfac.provider.BESProvider">
+        <InHandlers>
+        	<Handler class="org.apache.airavata.gfac.handler.GramDirectorySetupHandler"/>
+            <Handler class="org.apache.airavata.gfac.handler.GridFTPInputHandler"/>
+        </InHandlers>
+        <OutHandlers>
+            <Handler class="org.apache.airavata.gfac.handler.GridFTPOutputHandler"/>
+        </OutHandlers>
+    </Provider>
     <Application name="UltraScan">
         <InHandlers>
             <Handler class="org.apache.airavata.handlers.GramDirectorySetupHandler"/>



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