Repository: airavata Updated Branches: refs/heads/master e8a6d419a -> 0c08b94b8
fixing issue with output data handling Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/c0f20842 Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/c0f20842 Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/c0f20842 Branch: refs/heads/master Commit: c0f20842c55c36ee56d6e9db9fa3c69dff831989 Parents: 95fb3eb Author: lahiru <[email protected]> Authored: Wed Mar 12 14:30:04 2014 -0400 Committer: lahiru <[email protected]> Committed: Wed Mar 12 14:30:04 2014 -0400 ---------------------------------------------------------------------- .../java/org/apache/airavata/gfac/cpi/GFacImpl.java | 14 ++++++++++++++ .../airavata/gfac/provider/impl/GSISSHProvider.java | 2 +- 2 files changed, 15 insertions(+), 1 deletion(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/c0f20842/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java index 47dee57..6022885 100644 --- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java +++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/cpi/GFacImpl.java @@ -48,6 +48,7 @@ import org.apache.airavata.gsi.ssh.api.SSHApiException; import org.apache.airavata.gsi.ssh.api.ServerInfo; import org.apache.airavata.gsi.ssh.api.authentication.AuthenticationInfo; import org.apache.airavata.gsi.ssh.api.authentication.GSIAuthenticationInfo; +import org.apache.airavata.gsi.ssh.api.job.JobDescriptor; import org.apache.airavata.gsi.ssh.api.job.JobManagerConfiguration; import org.apache.airavata.gsi.ssh.impl.PBSCluster; import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPasswordAuthenticationInfo; @@ -55,6 +56,7 @@ import org.apache.airavata.gsi.ssh.impl.authentication.DefaultPublicKeyFileAuthe import org.apache.airavata.gsi.ssh.impl.authentication.MyProxyAuthenticationInfo; import org.apache.airavata.gsi.ssh.util.CommonUtils; import org.apache.airavata.model.workspace.experiment.DataObjectType; +import org.apache.airavata.model.workspace.experiment.JobDetails; import org.apache.airavata.model.workspace.experiment.TaskDetails; import org.apache.airavata.registry.api.AiravataRegistry2; import org.apache.airavata.registry.cpi.DataType; @@ -288,9 +290,21 @@ public class GFacImpl implements GFac { try { jobExecutionContext = createJEC(experimentID, taskID); Scheduler.schedule(jobExecutionContext); + ApplicationDescription applicationDeploymentDescription = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription(); + TaskDetails taskData = (TaskDetails) registry.get(DataType.TASK_DETAIL, taskID); + JobDetails jobDetails = taskData.getJobDetailsList().get(0); + String jobDescription = jobDetails.getJobDescription(); + JobDescriptor jobDescriptor = JobDescriptor.fromXML(jobDescription); + applicationDeploymentDescription.getType().setScratchWorkingDirectory( + jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory()); + applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getInputDirectory()); + applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getOutputDirectory()); + applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile()); + applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile()); } catch (Exception e) { throw new GFacException(e); } + List<GFacHandlerConfig> handlers = jobExecutionContext.getGFacConfiguration().getOutHandlers(); for (GFacHandlerConfig handlerClassName : handlers) { http://git-wip-us.apache.org/repos/asf/airavata/blob/c0f20842/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java index d33e1a3..db5c29a 100644 --- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java +++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/provider/impl/GSISSHProvider.java @@ -90,7 +90,7 @@ public class GSISSHProvider extends AbstractProvider implements GFacProvider{ } // This installed path is a mandetory field, because this could change based on the computing resource JobDescriptor jobDescriptor = new JobDescriptor(); - jobDescriptor.setWorkingDirectory(app.getStaticWorkingDirectory() ); + jobDescriptor.setWorkingDirectory(app.getStaticWorkingDirectory()); jobDescriptor.setShellName("/bin/bash"); Random random = new Random(); int i = random.nextInt();
