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Posted to commits@airavata.apache.org by la...@apache.org on 2014/03/12 19:31:43 UTC
[1/2] git commit: fixing issue with output data handling
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 <la...@apache.org>
Authored: Wed Mar 12 14:30:04 2014 -0400
Committer: lahiru <la...@apache.org>
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(-)
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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
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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();
[2/2] git commit: Merge branch 'master' of
https://git-wip-us.apache.org/repos/asf/airavata
Posted by la...@apache.org.
Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/0c08b94b
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/0c08b94b
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/0c08b94b
Branch: refs/heads/master
Commit: 0c08b94b859913d9b295b0732fd546ad25fa0f36
Parents: c0f2084 e8a6d41
Author: lahiru <la...@apache.org>
Authored: Wed Mar 12 14:31:27 2014 -0400
Committer: lahiru <la...@apache.org>
Committed: Wed Mar 12 14:31:27 2014 -0400
----------------------------------------------------------------------
.../airavata-cpp-sdk/README | 7 +
.../airavata-stubs/Airavata.cpp | 6268 ++++++++++++++++++
.../airavata-cpp-sdk/airavata-stubs/Airavata.h | 2714 ++++++++
.../airavata-stubs/Airavata_server.skeleton.cpp | 129 +
.../airavata-stubs/airavataAPI_constants.cpp | 19 +
.../airavata-stubs/airavataAPI_constants.h | 25 +
.../airavata-stubs/airavataAPI_types.cpp | 13 +
.../airavata-stubs/airavataAPI_types.h | 26 +
.../airavataDataModel_constants.cpp | 17 +
.../airavataDataModel_constants.h | 24 +
.../airavata-stubs/airavataDataModel_types.cpp | 13 +
.../airavata-stubs/airavataDataModel_types.h | 23 +
.../airavata-stubs/airavataErrors_constants.cpp | 17 +
.../airavata-stubs/airavataErrors_constants.h | 24 +
.../airavata-stubs/airavataErrors_types.cpp | 511 ++
.../airavata-stubs/airavataErrors_types.h | 341 +
.../experimentModel_constants.cpp | 23 +
.../airavata-stubs/experimentModel_constants.h | 27 +
.../airavata-stubs/experimentModel_types.cpp | 2867 ++++++++
.../airavata-stubs/experimentModel_types.h | 1801 +++++
.../airavata-stubs/workspaceModel_constants.cpp | 17 +
.../airavata-stubs/workspaceModel_constants.h | 24 +
.../airavata-stubs/workspaceModel_types.cpp | 464 ++
.../airavata-stubs/workspaceModel_types.h | 273 +
.../airavata-php-sdk/README | 5 +
.../lib/Airavata/API/Airavata.php | 4849 ++++++++++++++
.../lib/Airavata/API/Error/Types.php | 583 ++
.../airavata-php-sdk/lib/Airavata/API/Types.php | 22 +
.../lib/Airavata/Model/Types.php | 20 +
.../Model/Workspace/Experiment/Types.php | 3670 ++++++++++
.../lib/Airavata/Model/Workspace/Types.php | 568 ++
.../airavata-php-sdk/lib/Thrift/Base/TBase.php | 367 +
.../Thrift/ClassLoader/ThriftClassLoader.php | 223 +
.../Thrift/Exception/TApplicationException.php | 72 +
.../lib/Thrift/Exception/TException.php | 369 ++
.../lib/Thrift/Exception/TProtocolException.php | 48 +
.../Thrift/Exception/TTransportException.php | 41 +
.../Thrift/Factory/TBinaryProtocolFactory.php | 43 +
.../Thrift/Factory/TCompactProtocolFactory.php | 39 +
.../lib/Thrift/Factory/TJSONProtocolFactory.php | 41 +
.../lib/Thrift/Factory/TProtocolFactory.php | 35 +
.../lib/Thrift/Factory/TStringFuncFactory.php | 63 +
.../lib/Thrift/Factory/TTransportFactory.php | 16 +
.../lib/Thrift/Protocol/JSON/BaseContext.php | 39 +
.../lib/Thrift/Protocol/JSON/ListContext.php | 52 +
.../Thrift/Protocol/JSON/LookaheadReader.php | 54 +
.../lib/Thrift/Protocol/JSON/PairContext.php | 60 +
.../lib/Thrift/Protocol/TBinaryProtocol.php | 396 ++
.../Protocol/TBinaryProtocolAccelerated.php | 47 +
.../lib/Thrift/Protocol/TCompactProtocol.php | 669 ++
.../lib/Thrift/Protocol/TJSONProtocol.php | 694 ++
.../lib/Thrift/Protocol/TProtocol.php | 340 +
.../lib/Thrift/Serializer/TBinarySerializer.php | 73 +
.../lib/Thrift/Server/TForkingServer.php | 119 +
.../lib/Thrift/Server/TServer.php | 101 +
.../lib/Thrift/Server/TServerSocket.php | 98 +
.../lib/Thrift/Server/TServerTransport.php | 54 +
.../lib/Thrift/Server/TSimpleServer.php | 57 +
.../lib/Thrift/StringFunc/Core.php | 38 +
.../lib/Thrift/StringFunc/Mbstring.php | 45 +
.../lib/Thrift/StringFunc/TStringFunc.php | 27 +
.../lib/Thrift/Transport/TBufferedTransport.php | 165 +
.../lib/Thrift/Transport/TFramedTransport.php | 183 +
.../lib/Thrift/Transport/THttpClient.php | 221 +
.../lib/Thrift/Transport/TMemoryBuffer.php | 89 +
.../lib/Thrift/Transport/TNullTransport.php | 50 +
.../lib/Thrift/Transport/TPhpStream.php | 114 +
.../lib/Thrift/Transport/TSocket.php | 326 +
.../lib/Thrift/Transport/TSocketPool.php | 295 +
.../lib/Thrift/Transport/TTransport.php | 93 +
.../lib/Thrift/Type/TMessageType.php | 33 +
.../airavata-php-sdk/lib/Thrift/Type/TType.php | 46 +
.../java-client-samples/pom.xml | 7 +-
.../client/samples/CreateLaunchExperiment.java | 131 +-
.../samples/CreateLaunchExperimentUS3.java | 348 +
airavata-api/generate-thrift-files.sh | 61 +-
.../airavata/client/tools/DocumentCreator.java | 377 +-
.../client/tools/UltrascanDocumentCreator.java | 428 ++
.../job/monitor/AiravataJobStatusUpdator.java | 24 +-
modules/gfac/gfac-core/README.txt | 1 -
.../client/OrchestratorClientFactoryTest.java | 2 +-
.../client/sample/OrchestratorClientSample.java | 2 +-
.../orchestrator/core/BaseOrchestratorTest.java | 2 +-
.../registry/jpa/impl/ExperimentRegistry.java | 33 +-
.../registry/jpa/impl/RegistryImpl.java | 4 +-
.../jpa/resources/TaskDetailResource.java | 1 +
86 files changed, 32214 insertions(+), 526 deletions(-)
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