Author: lahiru
Date: Mon Oct 14 19:50:20 2013
New Revision: 1532043
URL: http://svn.apache.org/r1532043
Log:
fixing gsi ssh integration and refactoring.
Modified:
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/JobSubmissionFault.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/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/handler/LocalDirectorySetupHandler.java
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.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/EC2Provider.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/LocalProvider.java
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/SSHProvider.java
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramProviderUtils.java
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/LocalProviderUtil.java
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=1532043&r1=1532042&r2=1532043&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
Mon Oct 14 19:50:20 2013
@@ -29,6 +29,7 @@ package org.apache.airavata.gfac;
import org.apache.airavata.credential.store.store.CredentialReader;
import org.apache.airavata.gfac.SecurityContext;
+import org.apache.commons.math.stat.clustering.Cluster;
/**
* Abstract implementation of the security context.
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/JobSubmissionFault.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/JobSubmissionFault.java?rev=1532043&r1=1532042&r2=1532043&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/JobSubmissionFault.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/JobSubmissionFault.java
Mon Oct 14 19:50:20 2013
@@ -41,7 +41,7 @@ public class JobSubmissionFault extends
public JobSubmissionFault(Throwable cause, String submitHost, String
contact, String rsl,
JobExecutionContext jobExecutionContext, String
reason, int errorCode) {
- super(cause.getMessage(), cause,jobExecutionContext);
+ super(cause.getMessage(), cause);
this.host = submitHost;
this.contact = contact;
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=1532043&r1=1532042&r2=1532043&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
Mon Oct 14 19:50:20 2013
@@ -33,6 +33,7 @@ import org.apache.airavata.gfac.Abstract
import org.apache.airavata.gfac.Constants;
import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.RequestData;
+import org.apache.airavata.gsi.ssh.api.Cluster;
import org.globus.gsi.X509Credential;
import org.globus.gsi.gssapi.GlobusGSSCredentialImpl;
import org.globus.gsi.provider.GlobusProvider;
@@ -60,6 +61,8 @@ public class GSISecurityContext extends
private GSSCredential gssCredentials = null;
+ private Cluster pbsCluster = null;
+
// Set trusted cert path and add provider
static {
Security.addProvider(new GlobusProvider());
@@ -263,4 +266,12 @@ public class GSISecurityContext extends
throw new GFacException("An error occurred while renewing security
credentials.", e);
}
}
+
+ public Cluster getPbsCluster() {
+ return pbsCluster;
+ }
+
+ public void setPbsCluster(Cluster pbsCluster) {
+ this.pbsCluster = pbsCluster;
+ }
}
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=1532043&r1=1532042&r2=1532043&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
Mon Oct 14 19:50:20 2013
@@ -23,35 +23,35 @@ package org.apache.airavata.gfac.handler
import org.apache.airavata.gfac.GFacException;
import org.apache.airavata.gfac.context.JobExecutionContext;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
-public class GFacHandlerException extends GFacException{
- public GFacHandlerException(String s) {
- super(s,new Throwable(s));
+public class GFacHandlerException extends GFacException {
+ private static final Logger log =
LoggerFactory.getLogger(GFacHandlerException.class);
+
+ public GFacHandlerException(String message) {
+ super(message, new Throwable(message));
+ sendFaultNotification(message, new Exception(message));
+ log.error(message);
}
public GFacHandlerException(String s, Throwable throwable) {
super(s, throwable);
- }
- public GFacHandlerException(String message, Throwable
cause,JobExecutionContext context) {
- super(message, cause);
- sendFaultNotification(message,context,new Exception(cause));
+ sendFaultNotification(s, new Exception(throwable));
+ log.error(s);
}
- public GFacHandlerException(String message, JobExecutionContext context) {
- super(message,new Throwable(message));
- sendFaultNotification(message,context,new Exception(message));
- }
-
- public GFacHandlerException(String message, JobExecutionContext
context,Exception e,String... additionExceptiondata) {
- super(message,e);
- sendFaultNotification(message,context,e, additionExceptiondata);
+ public GFacHandlerException(String message, Exception e, String...
additionExceptiondata) {
+ super(message, e);
+ sendFaultNotification(message, e, additionExceptiondata);
+ log.error(message);
}
private void sendFaultNotification(String message,
- JobExecutionContext executionContext, Exception e,
- String... additionalExceptiondata) {
- if (additionalExceptiondata==null ||
additionalExceptiondata.length==0){
- additionalExceptiondata=new
String[]{message,e.getLocalizedMessage()};
+ Exception e,
+ String... additionalExceptiondata) {
+ if (additionalExceptiondata == null || additionalExceptiondata.length
== 0) {
+ additionalExceptiondata = new String[]{message,
e.getLocalizedMessage()};
}
- }
+ }
}
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=1532043&r1=1532042&r2=1532043&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
Mon Oct 14 19:50:20 2013
@@ -107,17 +107,17 @@ public class GramDirectorySetupHandler i
success = true;
break;
} catch (URISyntaxException e) {
- pe = new GFacHandlerException("URI is malformatted:" +
e.getMessage(), e, jobExecutionContext);
+ pe = new GFacHandlerException("URI is malformatted:" +
e.getMessage(), e);
} catch (ToolsException e) {
- pe = new GFacHandlerException(e.getMessage(), e,
jobExecutionContext);
+ pe = new GFacHandlerException(e.getMessage(), e);
}
}
if (success == false) {
throw pe;
}
} catch (SecurityException e) {
- throw new GFacHandlerException(e.getMessage(), e,
jobExecutionContext);
+ throw new GFacHandlerException(e.getMessage(), e);
}
}
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=1532043&r1=1532042&r2=1532043&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
Mon Oct 14 19:50:20 2013
@@ -75,7 +75,7 @@ public class GridFTPInputHandler impleme
}
} catch (Exception e) {
log.error(e.getMessage());
- throw new GFacHandlerException("Error while input File Staging",
jobExecutionContext, e, e.getLocalizedMessage());
+ throw new GFacHandlerException("Error while input File Staging",
e, e.getLocalizedMessage());
}
jobExecutionContext.setInMessageContext(inputNew);
}
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=1532043&r1=1532042&r2=1532043&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
Mon Oct 14 19:50:20 2013
@@ -190,15 +190,15 @@ public class GridFTPOutputHandler implem
}
} catch (ToolsException e) {
log.error(e.getMessage());
- throw new GFacHandlerException(e.getMessage(),
jobExecutionContext, e, readLastLinesofStdOut(localStdErrFile.getPath(), 20));
+ throw new GFacHandlerException(e.getMessage(), e,
readLastLinesofStdOut(localStdErrFile.getPath(), 20));
} catch (URISyntaxException e) {
log.error(e.getMessage());
- throw new GFacHandlerException("URI is malformatted:" +
e.getMessage(), jobExecutionContext, e,
readLastLinesofStdOut(localStdErrFile.getPath(), 20));
+ throw new GFacHandlerException("URI is malformatted:" +
e.getMessage(), e, readLastLinesofStdOut(localStdErrFile.getPath(), 20));
}
}
} catch (Exception e) {
log.error(e.getMessage());
- throw new GFacHandlerException(e.getMessage(),
jobExecutionContext, e, readLastLinesofStdOut(localStdErrFile.getPath(), 20));
+ throw new GFacHandlerException(e.getMessage(), e,
readLastLinesofStdOut(localStdErrFile.getPath(), 20));
}
}
@@ -287,10 +287,10 @@ public class GridFTPOutputHandler implem
}
} catch (URISyntaxException e) {
log.error(e.getMessage());
- throw new GFacProviderException(e.getMessage(), e,
jobExecutionContext);
+ throw new GFacProviderException(e.getMessage(), e);
} catch (ToolsException e) {
log.error(e.getMessage());
- throw new GFacProviderException(e.getMessage(), e,
jobExecutionContext);
+ throw new GFacProviderException(e.getMessage(), e);
}
outputNew.getParameters().put(paramName, actualParameter);
}
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/LocalDirectorySetupHandler.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/LocalDirectorySetupHandler.java?rev=1532043&r1=1532042&r2=1532043&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/LocalDirectorySetupHandler.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/LocalDirectorySetupHandler.java
Mon Oct 14 19:50:20 2013
@@ -52,7 +52,7 @@ public class LocalDirectorySetupHandler
if (f.isDirectory() && f.exists()) {
return;
} else if (!new File(dir).mkdir()) {
- throw new GFacHandlerException("Cannot make directory "+dir,
jobExecutionContext);
+ throw new GFacHandlerException("Cannot make directory "+dir);
}
}
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java?rev=1532043&r1=1532042&r2=1532043&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/handler/SCPInputHandler.java
Mon Oct 14 19:50:20 2013
@@ -74,7 +74,7 @@ public class SCPInputHandler implements
}
} catch (Exception e) {
log.error(e.getMessage());
- throw new GFacHandlerException("Error while input File
Staging", jobExecutionContext, e, e.getLocalizedMessage());
+ throw new GFacHandlerException("Error while input File
Staging", e, e.getLocalizedMessage());
}
jobExecutionContext.setInMessageContext(inputNew);
}
@@ -90,7 +90,7 @@ public class SCPInputHandler implements
pbsCluster.scpTo(targetFile, paramValue);
return targetFile;
} catch (SSHApiException e) {
- throw new GFacHandlerException("Error while input File Staging",
context, e, e.getLocalizedMessage());
+ throw new GFacHandlerException("Error while input File Staging",
e, e.getLocalizedMessage());
}
}
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=1532043&r1=1532042&r2=1532043&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
Mon Oct 14 19:50:20 2013
@@ -32,35 +32,27 @@ public class GFacProviderException exten
public GFacProviderException(String message) {
super(message);
+ sendFaultNotification(message, new Exception(message));
log.error(message);
}
- public GFacProviderException(String message, Throwable cause) {
- super(message, cause);
- log.error(message);
- }
- public GFacProviderException(String message, Throwable cause,
JobExecutionContext context) {
+ public GFacProviderException(String message, Throwable cause) {
super(message, cause);
- sendFaultNotification(message, context, new Exception(cause));
+ sendFaultNotification(message, new Exception(cause));
log.error(message);
}
- public GFacProviderException(String message, JobExecutionContext context) {
- super(message);
- sendFaultNotification(message, context, new Exception(message));
- log.error(message);
- }
- public GFacProviderException(String message, JobExecutionContext context,
Exception e, String... additionExceptiondata) {
+ public GFacProviderException(String message, Exception e, String...
additionExceptiondata) {
super(message);
this.aditionalInfo = additionExceptiondata;
- sendFaultNotification(message, context, e, additionExceptiondata);
+ sendFaultNotification(message, e, additionExceptiondata);
log.error(message);
}
private void sendFaultNotification(String message,
- JobExecutionContext executionContext,
Exception e,
+ Exception e,
String... additionalExceptiondata) {
if (additionalExceptiondata == null || additionalExceptiondata.length
== 0) {
additionalExceptiondata = new String[]{message,
e.getLocalizedMessage()};
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/EC2Provider.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/EC2Provider.java?rev=1532043&r1=1532042&r2=1532043&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/EC2Provider.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/EC2Provider.java
Mon Oct 14 19:50:20 2013
@@ -111,15 +111,15 @@ public class EC2Provider implements GFac
// job
/* Validation */
if (amazonSecurityContext.getAccessKey() == null ||
amazonSecurityContext.getAccessKey().isEmpty())
- throw new GFacProviderException("EC2 Access Key is empty",
jobExecutionContext);
+ throw new GFacProviderException("EC2 Access Key is empty");
if (amazonSecurityContext.getSecretKey() == null ||
amazonSecurityContext.getSecretKey().isEmpty())
- throw new GFacProviderException("EC2 Secret Key is empty",
jobExecutionContext);
+ throw new GFacProviderException("EC2 Secret Key is empty");
if ((amazonSecurityContext.getAmiId() == null &&
amazonSecurityContext.getInstanceId() == null) ||
(amazonSecurityContext.getAmiId() != null &&
amazonSecurityContext.getAmiId().isEmpty()) ||
(amazonSecurityContext.getInstanceId() != null &&
amazonSecurityContext.getInstanceId().isEmpty()))
- throw new GFacProviderException("EC2 AMI or Instance ID is empty",
jobExecutionContext);
+ throw new GFacProviderException("EC2 AMI or Instance ID is empty");
if (amazonSecurityContext.getUserName() == null ||
amazonSecurityContext.getUserName().isEmpty())
- throw new GFacProviderException("EC2 Username is empty",
jobExecutionContext);
+ throw new GFacProviderException("EC2 Username is empty");
/* Need to start EC2 instance before running it */
AWSCredentials credential =
@@ -166,7 +166,7 @@ public class EC2Provider implements GFac
outParamName = outputParametersArray[0].getParameterName();
} else {
throw new GFacProviderException("Output parameter name is not
set. Therefore, not being able " +
- "to filter the job result from standard out ",
jobExecutionContext);
+ "to filter the job result from standard out ");
}
sshClient.connect(properties, new HostKeyVerification() {
@@ -187,10 +187,10 @@ public class EC2Provider implements GFac
// Authenticate
int result = sshClient.authenticate(publicKeyAuth);
if(result== AuthenticationProtocolState.FAILED) {
- throw new GFacProviderException("The authentication failed",
jobExecutionContext);
+ throw new GFacProviderException("The authentication failed");
} else if(result==AuthenticationProtocolState.PARTIAL) {
throw new GFacProviderException("The authentication succeeded
but another"
- + "authentication is required", jobExecutionContext);
+ + "authentication is required");
} else if(result==AuthenticationProtocolState.COMPLETE) {
log.info("ssh client authentication is complete...");
}
@@ -246,7 +246,6 @@ public class EC2Provider implements GFac
// Do nothing
}
- @Override
public void cancelJob(String jobId, JobExecutionContext
jobExecutionContext) throws GFacException {
throw new NotImplementedException();
}
@@ -368,7 +367,7 @@ public class EC2Provider implements GFac
this.instance.getInstanceId() + " is running with public
name " + this.instance.getPublicDnsName()));
} catch (Exception e) {
- throw new GFacProviderException("Invalid
Request",e,jobExecutionContext);
+ throw new GFacProviderException("Invalid Request",e);
}
}
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=1532043&r1=1532042&r2=1532043&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
Mon Oct 14 19:50:20 2013
@@ -26,6 +26,7 @@ import org.apache.airavata.commons.gfac.
import org.apache.airavata.gfac.GFacException;
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.gfac.notification.events.JobIDEvent;
import org.apache.airavata.gfac.notification.events.StartExecutionEvent;
@@ -64,8 +65,17 @@ public class GSISSHProvider implements G
HpcApplicationDeploymentType app = (HpcApplicationDeploymentType)
jobExecutionContext.getApplicationContext().
getApplicationDeploymentDescription().getType();
try {
- SSHSecurityContext securityContext = (SSHSecurityContext)
jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT);
- Cluster cluster = securityContext.getPbsCluster();
+ Cluster cluster = null;
+ if
(jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)
!= null) {
+ cluster = ((GSISecurityContext)
jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
+ }else{
+ cluster = ((SSHSecurityContext)
jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
+ }
+ if(cluster == null){
+ throw new GFacProviderException("Security context is not set
properly");
+ }else{
+ log.info("Successfully retrieved the Security Context");
+ }
// This installed path is a mandetory field, because this could
change based on the computing resource
JobDescriptor jobDescriptor = new JobDescriptor();
jobDescriptor.setWorkingDirectory(app.getScratchWorkingDirectory());
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/LocalProvider.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/LocalProvider.java?rev=1532043&r1=1532042&r2=1532043&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/LocalProvider.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/LocalProvider.java
Mon Oct 14 19:50:20 2013
@@ -170,9 +170,9 @@ public class LocalProvider implements GF
log.info(buf.toString());
} catch (IOException io) {
- throw new GFacProviderException(io.getMessage(),
io,jobExecutionContext);
+ throw new GFacProviderException(io.getMessage(), io);
} catch (InterruptedException e) {
- throw new GFacProviderException(e.getMessage(), e,
jobExecutionContext);
+ throw new GFacProviderException(e.getMessage(), e);
}
}
@@ -206,11 +206,11 @@ public class LocalProvider implements GF
Map<String, Object> output =
jobExecutionContext.getOutMessageContext().getParameters();
OutputUtils.fillOutputFromStdout(output, stdOutStr, stdErrStr);
} catch (XmlException e) {
- throw new GFacProviderException("Cannot read output:" +
e.getMessage(), e, jobExecutionContext);
+ throw new GFacProviderException("Cannot read output:" +
e.getMessage(), e);
} catch (IOException io) {
- throw new GFacProviderException(io.getMessage(), io,
jobExecutionContext);
+ throw new GFacProviderException(io.getMessage(), io);
} catch (Exception e){
- throw new GFacProviderException("Error in retrieving
results",e,jobExecutionContext);
+ throw new GFacProviderException("Error in retrieving
results",e);
}
}
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=1532043&r1=1532042&r2=1532043&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
Mon Oct 14 19:50:20 2013
@@ -66,6 +66,8 @@ public class SSHProvider implements GFac
private static final Logger log =
LoggerFactory.getLogger(SSHProvider.class);
private SSHSecurityContext securityContext;
private String jobID = null;
+ // we keep gsisshprovider to support qsub submission incase of hpc
scenario with ssh
+ private GSISSHProvider gsiSshProvider = null;
public void initialize(JobExecutionContext jobExecutionContext) throws
GFacProviderException, GFacException {
if (!((SSHHostType)
jobExecutionContext.getApplicationContext().getHostDescription().getType()).getHpcResource())
{
@@ -84,6 +86,8 @@ public class SSHProvider implements GFac
} catch (IOException e) {
throw new GFacProviderException(e.getLocalizedMessage(), e);
}
+ }else{
+ gsiSshProvider = new GSISSHProvider();
}
}
@@ -98,7 +102,7 @@ public class SSHProvider implements GFac
}
public void execute(JobExecutionContext jobExecutionContext) throws
GFacProviderException {
- if (!((SSHHostType)
jobExecutionContext.getApplicationContext().getHostDescription().getType()).getHpcResource())
{
+ if (gsiSshProvider == null) {
ApplicationDeploymentDescriptionType app =
jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
Session session = null;
try {
@@ -137,9 +141,8 @@ public class SSHProvider implements GFac
}
}
} else {
- GSISSHProvider gsisshProvider = new GSISSHProvider();
try {
- gsisshProvider.execute(jobExecutionContext);
+ gsiSshProvider.execute(jobExecutionContext);
} catch (GFacException e) {
throw new GFacProviderException(e.getMessage(), e);
}
@@ -148,9 +151,16 @@ public class SSHProvider implements GFac
}
public void dispose(JobExecutionContext jobExecutionContext) throws
GFacProviderException {
+ if (gsiSshProvider != null){
+ try {
+ gsiSshProvider.dispose(jobExecutionContext);
+ } catch (GFacException e) {
+ throw new GFacProviderException(e.getMessage(),e);
+ }
+ }
}
- @Override
+
public void cancelJob(String jobId, JobExecutionContext
jobExecutionContext) throws GFacException {
throw new NotImplementedException();
}
@@ -233,7 +243,13 @@ public class SSHProvider implements GFac
}
public void initProperties(Map<String, String> properties) throws
GFacProviderException, GFacException {
-
+ if (gsiSshProvider != null){
+ try {
+ initProperties(properties);
+ } catch (GFacException e) {
+ throw new GFacProviderException(e.getMessage(),e);
+ }
+ }
}
}
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramProviderUtils.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramProviderUtils.java?rev=1532043&r1=1532042&r2=1532043&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramProviderUtils.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/GramProviderUtils.java
Mon Oct 14 19:50:20 2013
@@ -45,7 +45,7 @@ public class GramProviderUtils {
GramJob job = new GramJob(rsl);
return job;
} catch (ToolsException te) {
- throw new GFacProviderException(te.getMessage(), te,
jobExecutionContext);
+ throw new GFacProviderException(te.getMessage(), te);
}
}
Modified:
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/LocalProviderUtil.java
URL:
http://svn.apache.org/viewvc/airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/LocalProviderUtil.java?rev=1532043&r1=1532042&r2=1532043&view=diff
==============================================================================
---
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/LocalProviderUtil.java
(original)
+++
airavata/trunk/modules/gfac-core/src/main/java/org/apache/airavata/gfac/utils/LocalProviderUtil.java
Mon Oct 14 19:50:20 2013
@@ -31,12 +31,12 @@ import java.io.File;
public class LocalProviderUtil {
private static final Logger log =
LoggerFactory.getLogger(LocalProviderUtil.class);
- private void makeFileSystemDir(String dir, JobExecutionContext
jobExecutionContext) throws GFacProviderException {
+ private void makeFileSystemDir(String dir) throws GFacProviderException {
File f = new File(dir);
if (f.isDirectory() && f.exists()) {
return;
} else if (!new File(dir).mkdir()) {
- throw new GFacProviderException("Cannot make directory " + dir,
jobExecutionContext);
+ throw new GFacProviderException("Cannot make directory " + dir);
}
}
@@ -45,10 +45,10 @@ public class LocalProviderUtil {
getApplicationContext().getApplicationDeploymentDescription().getType();
log.info("working diectroy = " + app.getStaticWorkingDirectory());
log.info("temp directory = " + app.getScratchWorkingDirectory());
- makeFileSystemDir(app.getStaticWorkingDirectory(),
jobExecutionContext);
- makeFileSystemDir(app.getScratchWorkingDirectory(),
jobExecutionContext);
- makeFileSystemDir(app.getInputDataDirectory(), jobExecutionContext);
- makeFileSystemDir(app.getOutputDataDirectory(), jobExecutionContext);
+ makeFileSystemDir(app.getStaticWorkingDirectory());
+ makeFileSystemDir(app.getScratchWorkingDirectory());
+ makeFileSystemDir(app.getInputDataDirectory());
+ makeFileSystemDir(app.getOutputDataDirectory());
}
}
