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Posted to commits@airavata.apache.org by ch...@apache.org on 2014/11/11 20:11:01 UTC
[14/16] airavata git commit: merging gfac app catalog integration
branch with master - AIRAVATA-1511
merging gfac app catalog integration branch with master - AIRAVATA-1511
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/36938926
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/36938926
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/36938926
Branch: refs/heads/gfac_appcatalog_int
Commit: 36938926632e490d0a64e14e13277f74fd41c4df
Parents: 4286c8c 0b867da
Author: Chathuri Wimalasena <ka...@gmail.com>
Authored: Tue Nov 11 11:14:09 2014 -0500
Committer: Chathuri Wimalasena <ka...@gmail.com>
Committed: Tue Nov 11 11:14:09 2014 -0500
----------------------------------------------------------------------
.../server/handler/AiravataServerHandler.java | 72 +-
.../java/org/apache/airavata/api/Airavata.java | 58 +-
.../main/resources/lib/airavata/Airavata.cpp | 6 +-
.../src/main/resources/lib/airavata/Airavata.h | 16 +-
.../lib/airavata/Airavata_server.skeleton.cpp | 2 +-
.../applicationInterfaceModel_types.cpp | 10 +-
.../airavata/applicationInterfaceModel_types.h | 4 +-
.../lib/airavata/computeResourceModel_types.cpp | 218 ++--
.../lib/airavata/computeResourceModel_types.h | 28 +-
.../lib/airavata/experimentModel_types.cpp | 521 ++++-----
.../lib/airavata/experimentModel_types.h | 124 +-
.../gatewayResourceProfileModel_types.cpp | 48 +-
.../gatewayResourceProfileModel_types.h | 19 +-
.../lib/airavata/messagingEvents_types.cpp | 6 +-
.../lib/airavata/messagingEvents_types.h | 9 +-
.../resources/lib/Airavata/API/Airavata.php | 4 +-
.../Model/AppCatalog/AppInterface/Types.php | 4 +
.../Model/AppCatalog/ComputeResource/Types.php | 29 +
.../Model/AppCatalog/GatewayProfile/Types.php | 20 +-
.../Airavata/Model/Messaging/Event/Types.php | 4 +-
.../Model/Workspace/Experiment/Types.php | 171 +--
.../client/samples/CreateLaunchExperiment.java | 260 +++--
.../samples/CreateLaunchExperimentUS3.java | 139 +--
.../tools/RegisterSampleApplications.java | 8 +-
.../tools/RegisterSampleApplicationsUtils.java | 3 +-
.../model/appcatalog/appinterface/DataType.java | 8 +-
.../appcatalog/computeresource/MonitorMode.java | 73 ++
.../computeresource/SSHJobSubmission.java | 121 +-
.../ComputeResourcePreference.java | 68 +-
.../messaging/event/TaskOutputChangeEvent.java | 40 +-
.../workspace/experiment/DataObjectType.java | 719 ------------
.../model/workspace/experiment/DataType.java | 71 --
.../model/workspace/experiment/Experiment.java | 76 +-
.../model/workspace/experiment/TaskDetails.java | 76 +-
.../experiment/WorkflowNodeDetails.java | 76 +-
.../model/util/ExperimentModelUtil.java | 15 +-
.../airavataAPI.thrift | 2 +-
.../applicationInterfaceModel.thrift | 4 +-
.../computeResourceModel.thrift | 19 +-
.../experimentModel.thrift | 32 +-
.../gatewayResourceProfileModel.thrift | 5 +-
.../messagingEvents.thrift | 3 +-
.../client/tools/DocumentCreatorUtils.java | 4 +-
.../data/impl/GwyResourceProfileImpl.java | 19 +-
.../data/util/AppCatalogThriftConversion.java | 4 +-
.../app/catalog/test/GatewayProfileTest.java | 8 +-
.../server/src/main/resources/gfac-config.xml | 6 +-
.../gfac/bes/handlers/AbstractSMSHandler.java | 74 +-
.../gfac/bes/provider/impl/BESProvider.java | 378 +++---
.../bes/security/UNICORESecurityContext.java | 4 +-
.../gfac/bes/utils/ApplicationProcessor.java | 212 ++--
.../org/apache/airavata/gfac/Constants.java | 3 +
.../org/apache/airavata/gfac/Scheduler.java | 103 +-
.../gfac/core/context/ApplicationContext.java | 44 +-
.../gfac/core/context/JobExecutionContext.java | 185 ++-
.../airavata/gfac/core/cpi/BetterGfacImpl.java | 405 +++----
.../handler/AbstractRecoverableHandler.java | 4 +-
.../core/handler/AppDescriptorCheckHandler.java | 56 +-
.../airavata/gfac/core/monitor/MonitorID.java | 20 +-
.../gfac/core/provider/utils/ProviderUtils.java | 18 +-
.../airavata/gfac/core/utils/GFacUtils.java | 1101 ++++++++++--------
.../airavata/gfac/core/utils/OutputUtils.java | 72 +-
.../apache/airavata/job/GFacConfigXmlTest.java | 78 +-
.../apache/airavata/gfac/ec2/EC2Provider.java | 61 +-
.../airavata/gfac/ec2/EC2ProviderTest.java | 366 +++---
.../gfac/gram/handler/GridFTPOutputHandler.java | 5 +-
.../handler/GSISSHDirectorySetupHandler.java | 11 +-
.../gfac/gsissh/handler/GSISSHInputHandler.java | 86 +-
.../gsissh/handler/GSISSHOutputHandler.java | 116 +-
.../gsissh/provider/impl/GSISSHProvider.java | 77 +-
.../gfac/gsissh/util/GFACGSISSHUtils.java | 203 ++--
.../impl/GSISSHProviderTestWithMyProxyAuth.java | 465 ++++----
.../handler/LocalDirectorySetupHandler.java | 19 +-
.../gfac/local/provider/impl/LocalProvider.java | 54 +-
.../gfac/local/utils/LocalProviderUtil.java | 15 +-
.../gfac/services/impl/LocalProviderTest.java | 368 +++---
.../airavata/gfac/monitor/HPCMonitorID.java | 13 +-
.../airavata/gfac/monitor/HostMonitorData.java | 40 +-
.../handlers/GridPullMonitorHandler.java | 2 +-
.../monitor/impl/pull/qstat/HPCPullMonitor.java | 28 +-
.../impl/pull/qstat/ResourceConnection.java | 6 +-
.../monitor/impl/push/amqp/AMQPMonitor.java | 57 +-
.../airavata/gfac/monitor/util/CommonUtils.java | 32 +-
.../apache/airavata/job/AMQPMonitorTest.java | 64 +-
.../job/QstatMonitorTestWithMyProxyAuth.java | 344 +++---
.../ssh/handler/AdvancedSCPOutputHandler.java | 34 +-
.../ssh/handler/SSHDirectorySetupHandler.java | 11 +-
.../gfac/ssh/handler/SSHInputHandler.java | 5 +-
.../gfac/ssh/handler/SSHOutputHandler.java | 185 ++-
.../gfac/ssh/provider/impl/SSHProvider.java | 79 +-
.../airavata/gfac/ssh/util/GFACSSHUtils.java | 300 +++--
.../services/impl/BigRed2TestWithSSHAuth.java | 504 ++++----
.../impl/SSHProviderTestWithSSHAuth.java | 342 +++---
modules/gfac/pom.xml | 6 +-
.../apache/airavata/integration/BaseCaseIT.java | 49 +-
.../airavata/integration/DataRetrievalIT.java | 15 +-
.../airavata/integration/SimpleEchoIT.java | 23 +-
.../integration/tools/DocumentCreatorUtils.java | 4 +-
.../sample/OrchestratorClientSample.java | 22 +-
.../registry/jpa/impl/ExperimentRegistry.java | 126 +-
.../registry/jpa/impl/RegistryImpl.java | 13 +-
.../jpa/utils/ThriftDataModelConversion.java | 101 +-
.../engine/interpretor/WorkflowInterpreter.java | 81 +-
.../ui/experiment/LaunchApplicationWindow.java | 58 +-
.../WorkflowInterpreterLaunchWindow.java | 17 +-
.../airavata/gsi/ssh/api/job/JobDescriptor.java | 7 +
106 files changed, 4861 insertions(+), 5542 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
----------------------------------------------------------------------
diff --cc airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
index f039988,63fe5ad..2d7768b
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/CreateLaunchExperiment.java
@@@ -53,9 -56,9 +56,9 @@@ public class CreateLaunchExperiment
private static final String DEFAULT_GATEWAY = "default.registry.gateway";
private static Airavata.Client airavataClient;
- private static String echoAppId = "Echo_636b4530-6fb2-4c9e-998a-b41e648aa70f";
- private static String wrfAppId = "WRF_d41bdc86-e280-4eb6-a045-708f69a8c116";
- private static String amberAppId = "Amber_b23ee051-90d6-4892-827e-622a2f6c95ee";
- private static String echoAppId = "Echo_647ba0c5-64ef-4efe-9786-2d28f4d5acc9";
++ private static String echoAppId = "Echo_1869465f-f002-43a9-b243-c091f63ab059";
+ private static String wrfAppId = "WRF_a458df70-6808-4d5d-ae32-c49082f2a6cc";
+ private static String amberAppId = "Amber_1b99f73b-a88d-44e3-b04e-4f56ba95ed6f";
private static String localHost = "localhost";
private static String trestlesHostName = "trestles.sdsc.xsede.org";
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/Constants.java
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
index 1f84490,b2790c9..b2c40a7
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHDirectorySetupHandler.java
@@@ -47,8 -47,7 +47,8 @@@ public class GSISSHDirectorySetupHandle
public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
try {
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
- if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
++ String hostAddress = jobExecutionContext.getHostName();
+ if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
}
} catch (Exception e) {
@@@ -65,26 -64,24 +65,25 @@@
makeDirectory(jobExecutionContext);
}
private void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
- Cluster cluster = null;
- try {
- cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
- if (cluster == null) {
- try {
- GFacUtils.saveErrorDetails(jobExecutionContext, "Security context is not set properly", CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
- } catch (GFacException e1) {
- log.error(e1.getLocalizedMessage());
- }
- throw new GFacHandlerException("Security context is not set properly");
- } else {
- log.info("Successfully retrieved the Security Context");
- }
+ Cluster cluster = null;
+ try {
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
++ String hostAddress = jobExecutionContext.getHostName();
+ cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
+ if (cluster == null) {
+ try {
+ GFacUtils.saveErrorDetails(jobExecutionContext, "Security context is not set properly", CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
+ } catch (GFacException e1) {
+ log.error(e1.getLocalizedMessage());
+ }
+ throw new GFacHandlerException("Security context is not set properly");
+ } else {
+ log.info("Successfully retrieved the Security Context");
+ }
- ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
- String workingDirectory = app.getScratchWorkingDirectory();
+ String workingDirectory = jobExecutionContext.getWorkingDir();
cluster.makeDirectory(workingDirectory);
- cluster.makeDirectory(app.getInputDataDirectory());
- cluster.makeDirectory(app.getOutputDataDirectory());
+ cluster.makeDirectory(jobExecutionContext.getInputDir());
+ cluster.makeDirectory(jobExecutionContext.getOutputDir());
DataTransferDetails detail = new DataTransferDetails();
TransferStatus status = new TransferStatus();
status.setTransferState(TransferState.DIRECTORY_SETUP);
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
index 01dc712,39f8df1..c297b2a
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHInputHandler.java
@@@ -67,12 -69,11 +69,12 @@@ public class GSISSHInputHandler extend
Cluster cluster = null;
try {
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
- if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
- cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
- } else {
- cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
++ String hostAddress = jobExecutionContext.getHostName();
+ if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
+ GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
}
+
+ cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
if (cluster == null) {
throw new GFacException("Security context is not set properly");
} else {
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
index eff0164,a25e66a..68273b8
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/handler/GSISSHOutputHandler.java
@@@ -67,39 -61,9 +61,9 @@@ public class GSISSHOutputHandler extend
int oldIndex = 0;
List<String> oldFiles = new ArrayList<String>();
StringBuffer data = new StringBuffer("|");
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
- if (jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof GsisshHostType) { // this is because we don't have the right jobexecution context
- // so attempting to get it from the registry
- if (Constants.PUSH.equals(((GsisshHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType()).getMonitorMode())) {
- log.warn("During the out handler chain jobExecution context came null, so trying to handler");
- ApplicationDescription applicationDeploymentDescription = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
- TaskDetails taskData = null;
- try {
- taskData = (TaskDetails) jobExecutionContext.getRegistry().get(RegistryModelType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
- } catch (RegistryException e) {
- log.error("Error retrieving job details from Registry");
- throw new GFacHandlerException("Error retrieving job details from Registry", e);
- }
- JobDetails jobDetails = taskData.getJobDetailsList().get(0);
- String jobDescription = jobDetails.getJobDescription();
- if (jobDescription != null) {
- JobDescriptor jobDescriptor = null;
- try {
- jobDescriptor = JobDescriptor.fromXML(jobDescription);
- } catch (XmlException e1) {
- e1.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
- }
- applicationDeploymentDescription.getType().setScratchWorkingDirectory(
- jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory());
- applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getInputDirectory());
- applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getOutputDirectory());
- applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile());
- applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile());
- }
- }
- }
++ String hostAddress = jobExecutionContext.getHostName();
try {
- if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
-
+ if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
}
} catch (Exception e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
index 87e0fb4,92a50e4..d26d31b
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/provider/impl/GSISSHProvider.java
@@@ -61,8 -70,7 +70,8 @@@ public class GSISSHProvider extends Abs
public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
super.initialize(jobExecutionContext);
try {
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
- if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
++ String hostAddress = jobExecutionContext.getHostName();
+ if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
}
} catch (ApplicationSettingsException e) {
@@@ -77,16 -85,20 +86,19 @@@
log.info("Invoking GSISSH Provider Invoke ...");
StringBuffer data = new StringBuffer();
jobExecutionContext.getNotifier().publish(new StartExecutionEvent());
- HostDescriptionType host = jobExecutionContext.getApplicationContext().
- getHostDescription().getType();
- HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) jobExecutionContext.getApplicationContext().
- getApplicationDeploymentDescription().getType();
+ ComputeResourceDescription computeResourceDescription = jobExecutionContext.getApplicationContext()
+ .getComputeResourceDescription();
+ ApplicationDeploymentDescription appDeployDesc = jobExecutionContext.getApplicationContext()
+ .getApplicationDeploymentDescription();
JobDetails jobDetails = new JobDetails();
Cluster cluster = null;
-
+
try {
- if (jobExecutionContext.getSecurityContext(host.getHostAddress()) != null) {
- cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(host.getHostAddress())).getPbsCluster();
+ AppCatalog appCatalog = AppCatalogFactory.getAppCatalog();
+ SSHJobSubmission sshJobSubmission = appCatalog.getComputeResource().getSSHJobSubmission(
+ jobExecutionContext.getPreferredJobSubmissionInterface().getJobSubmissionInterfaceId());
-
- if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) != null) {
- cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
++ if (jobExecutionContext.getSecurityContext(jobExecutionContext.getHostName()) != null) {
++ cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(jobExecutionContext.getHostName())).getPbsCluster();
}
if (cluster == null) {
throw new GFacProviderException("Security context is not set properly");
@@@ -209,15 -221,13 +221,14 @@@
public void cancelJob(JobExecutionContext jobExecutionContext) throws GFacProviderException,GFacException {
//To change body of implemented methods use File | Settings | File Templates.
log.info("canceling the job status in GSISSHProvider!!!!!");
- HostDescriptionType host = jobExecutionContext.getApplicationContext().
- getHostDescription().getType();
JobDetails jobDetails = jobExecutionContext.getJobDetails();
++ String hostName = jobExecutionContext.getHostName();
try {
Cluster cluster = null;
- if (jobExecutionContext.getSecurityContext(host.getHostAddress()) == null) {
- if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
++ if (jobExecutionContext.getSecurityContext(hostName) == null) {
GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
}
- cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(host.getHostAddress())).getPbsCluster();
- cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT)).getPbsCluster();
++ cluster = ((GSISecurityContext) jobExecutionContext.getSecurityContext(hostName)).getPbsCluster();
if (cluster == null) {
throw new GFacProviderException("Security context is not set properly");
} else {
@@@ -256,8 -266,8 +267,9 @@@
public void recover(JobExecutionContext jobExecutionContext) throws GFacProviderException,GFacException {
// have to implement the logic to recover a gfac failure
log.info("Invoking Recovering for the Experiment: " + jobExecutionContext.getExperimentID());
- HostDescriptionType host = jobExecutionContext.getApplicationContext().
- getHostDescription().getType();
+ ComputeResourceDescription computeResourceDescription = jobExecutionContext.getApplicationContext()
+ .getComputeResourceDescription();
++ String hostName = jobExecutionContext.getHostName();
String jobId = "";
String jobDesc = "";
try {
@@@ -299,7 -309,7 +311,7 @@@
jobDetails.setJobDescription(jobDesc);
jobDetails.setJobID(jobId);
jobExecutionContext.setJobDetails(jobDetails);
- if (jobExecutionContext.getSecurityContext(host.getHostAddress()) == null) {
- if (jobExecutionContext.getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT) == null) {
++ if (jobExecutionContext.getSecurityContext(hostName) == null) {
try {
GFACGSISSHUtils.addSecurityContext(jobExecutionContext);
} catch (ApplicationSettingsException e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
index 58efb56,3c2e839..45ef1b8
--- a/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
+++ b/modules/gfac/gfac-gsissh/src/main/java/org/apache/airavata/gfac/gsissh/util/GFACGSISSHUtils.java
@@@ -160,10 -159,11 +159,11 @@@ public class GFACGSISSHUtils
clusters.put(key, pbsClusters);
}
}
- } catch (Exception e) {
- throw new GFacException("An error occurred while creating GSI security context", e);
+
- jobExecutionContext.addSecurityContext(Constants.GSI_SECURITY_CONTEXT, context);
++ jobExecutionContext.addSecurityContext(jobExecutionContext.getHostName(), context);
}
- jobExecutionContext.addSecurityContext(registeredHost.getType().getHostAddress(), context);
+ } catch (Exception e) {
+ throw new GFacException("An error occurred while creating GSI security context", e);
}
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/HPCMonitorID.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/HPCMonitorID.java
index 3a15d39,c788ace..12b7ad9
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/HPCMonitorID.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/HPCMonitorID.java
@@@ -62,8 -63,7 +63,8 @@@ public class HPCMonitorID extends Monit
this.authenticationInfo = authenticationInfo;
if (this.authenticationInfo != null) {
try {
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
- SecurityContext securityContext = jobExecutionContext.getSecurityContext(Constants.GSI_SECURITY_CONTEXT);
++ String hostAddress = jobExecutionContext.getHostName();
+ SecurityContext securityContext = jobExecutionContext.getSecurityContext(hostAddress);
ServerInfo serverInfo = null;
if (securityContext != null) {
serverInfo = (((GSISecurityContext) securityContext).getPbsCluster()).getServerInfo();
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
index 9f93dc6,feaaa2d..25113fd
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
@@@ -25,6 -25,6 +25,7 @@@ import org.apache.airavata.common.logge
import org.apache.airavata.common.logger.AiravataLoggerFactory;
import org.apache.airavata.common.utils.MonitorPublisher;
import org.apache.airavata.common.utils.ServerSettings;
++import org.apache.airavata.gfac.monitor.util.CommonUtils;
import org.apache.airavata.commons.gfac.type.HostDescription;
import org.apache.airavata.gfac.core.cpi.GFac;
import org.apache.airavata.gfac.core.monitor.MonitorID;
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/ResourceConnection.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/ResourceConnection.java
index 121cc59,73c05b7..e7a081b
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/ResourceConnection.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/ResourceConnection.java
@@@ -49,13 -49,11 +49,13 @@@ public class ResourceConnection
public ResourceConnection(HostMonitorData hostMonitorData,AuthenticationInfo authInfo) throws SSHApiException {
MonitorID monitorID = hostMonitorData.getMonitorIDs().get(0);
try {
- GSISecurityContext securityContext = (GSISecurityContext) monitorID.getJobExecutionContext().getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT);
+ GSISecurityContext securityContext = (GSISecurityContext)
- monitorID.getJobExecutionContext().getSecurityContext(monitorID.getHost().getType().getHostAddress());
++ monitorID.getJobExecutionContext().getSecurityContext(monitorID.getComputeResourceDescription().getHostName());
if(securityContext != null) {
cluster = (PBSCluster) securityContext.getPbsCluster();
}else {
- SSHSecurityContext sshSecurityContext = (SSHSecurityContext) monitorID.getJobExecutionContext().getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT);
+ SSHSecurityContext sshSecurityContext = (SSHSecurityContext)
- monitorID.getJobExecutionContext().getSecurityContext(monitorID.getHost().getType().getHostAddress());
++ monitorID.getJobExecutionContext().getSecurityContext(monitorID.getComputeResourceDescription().getHostName());
cluster = (PBSCluster)sshSecurityContext.getPbsCluster();
}
@@@ -70,8 -68,7 +70,8 @@@
public ResourceConnection(HostMonitorData hostMonitorData) throws SSHApiException {
MonitorID monitorID = hostMonitorData.getMonitorIDs().get(0);
try {
- GSISecurityContext securityContext = (GSISecurityContext) monitorID.getJobExecutionContext().getSecurityContext(GSISecurityContext.GSI_SECURITY_CONTEXT);
+ GSISecurityContext securityContext = (GSISecurityContext)
- monitorID.getJobExecutionContext().getSecurityContext(monitorID.getHost().getType().getHostAddress());
++ monitorID.getJobExecutionContext().getSecurityContext(monitorID.getComputeResourceDescription().getHostName());
cluster = (PBSCluster) securityContext.getPbsCluster();
// we just use cluster configuration from the incoming request and construct a new cluster because for monitoring
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
index 6152505,a503154..219db22
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/util/CommonUtils.java
@@@ -148,7 -156,7 +156,6 @@@ public class CommonUtils
/**
* This method doesn't have to be synchronized because it will be invoked by HPCPullMonitor which already synchronized
-- * @param queue
* @param monitorID
* @throws AiravataMonitorException
*/
@@@ -169,11 -180,15 +176,10 @@@
// could be different, thats why we check the jobID
iterator2.remove();
logger.infoId(monitorID.getJobID(), "Removed the jobId: {} JobName: {} from monitoring last " +
- "status:{}", monitorID.getJobID(),monitorID.getJobName(), monitorID.getStatus().toString());
+ "status:{}", monitorID.getJobID(), monitorID.getJobName(), monitorID.getStatus().toString());
if (iHostMonitorID.getMonitorIDs().size() == 0) {
iterator1.remove();
- logger.debug("Removed host {} from monitoring queue", iHostMonitorID.getHost()
- .getType().getHostAddress());
+ logger.debug("Removed host {} from monitoring queue", iHostMonitorID.getComputeResourceDescription().getHostName());
- if (hostMonitorData.size() == 0) {
- // no useful data so we have to remove the element from the queue
- queue.remove(next);
- logger.debug("Removed user {} from monitoring.", next.getUserName());
- }
}
return;
}
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
index c0416f5,e46dfa5..caefe7a
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/AdvancedSCPOutputHandler.java
@@@ -110,10 -107,22 +107,23 @@@ public class AdvancedSCPOutputHandler e
this.passPhrase);
}
try {
- ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
- .getApplicationDeploymentDescription().getType();
- String standardError = app.getStandardError();
- String standardOutput = app.getStandardOutput();
- if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null) {
++ String hostName = jobExecutionContext.getHostName();
++ if (jobExecutionContext.getSecurityContext(hostName) == null) {
+ try {
+ GFACSSHUtils.addSecurityContext(jobExecutionContext);
+ } catch (ApplicationSettingsException e) {
+ log.error(e.getMessage());
+ try {
+ GFacUtils.saveErrorDetails(jobExecutionContext, e.getLocalizedMessage(), CorrectiveAction.CONTACT_SUPPORT, ErrorCategory.AIRAVATA_INTERNAL_ERROR);
+ } catch (GFacException e1) {
+ log.error(e1.getLocalizedMessage());
+ }
+ throw new GFacHandlerException("Error while creating SSHSecurityContext", e, e.getLocalizedMessage());
+ }
+ }
- pbsCluster = ((SSHSecurityContext)jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
++ pbsCluster = ((SSHSecurityContext)jobExecutionContext.getSecurityContext(hostName)).getPbsCluster();
+ String standardError = jobExecutionContext.getStandardError();
+ String standardOutput = jobExecutionContext.getStandardOutput();
super.invoke(jobExecutionContext);
// Server info
if(jobExecutionContext.getTaskData().getAdvancedOutputDataHandling() != null && jobExecutionContext.getTaskData().getAdvancedOutputDataHandling().getOutputDataDir() != null){
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHDirectorySetupHandler.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHDirectorySetupHandler.java
index 9dcdefe,f7cbcc0..1baed57
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHDirectorySetupHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHDirectorySetupHandler.java
@@@ -46,8 -46,7 +46,8 @@@ public class SSHDirectorySetupHandler e
public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
try {
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
- if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null) {
++ String hostAddress = jobExecutionContext.getHostName();
+ if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
GFACSSHUtils.addSecurityContext(jobExecutionContext);
}
} catch (Exception e) {
@@@ -68,8 -67,7 +68,8 @@@
private void makeDirectory(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
Cluster cluster = null;
try{
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
- cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
++ String hostAddress = jobExecutionContext.getHostName();
+ cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
if (cluster == null) {
throw new GFacHandlerException("Security context is not set properly");
} else {
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
index c279378,b0367f3..dd27d6b
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHInputHandler.java
@@@ -66,8 -66,13 +66,8 @@@ public class SSHInputHandler extends Ab
Cluster cluster = null;
try {
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
- cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
- if (cluster == null) {
- throw new GFacException("Security context is not set properly");
- } else {
- log.info("Successfully retrieved the Security Context");
- }
- if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null) {
++ String hostAddress = jobExecutionContext.getHostName();
+ if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
try {
GFACSSHUtils.addSecurityContext(jobExecutionContext);
} catch (ApplicationSettingsException e) {
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHOutputHandler.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHOutputHandler.java
index 0780084,94f667e..bf01aff
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHOutputHandler.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/handler/SSHOutputHandler.java
@@@ -58,40 -53,9 +53,9 @@@ public class SSHOutputHandler extends A
private static final Logger log = LoggerFactory.getLogger(SSHOutputHandler.class);
public void invoke(JobExecutionContext jobExecutionContext) throws GFacHandlerException {
- if (jobExecutionContext.getApplicationContext().getHostDescription().getType() instanceof GsisshHostType) { // this is because we don't have the right jobexecution context
- // so attempting to get it from the registry
- if (Constants.PUSH.equals(((GsisshHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType()).getMonitorMode())) { // this is because we don't have the right jobexecution context
- // so attempting to get it from the registry
- log.warn("During the out handler chain jobExecution context came null, so trying to handler");
- ApplicationDescription applicationDeploymentDescription = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription();
- TaskDetails taskData = null;
- try {
- taskData = (TaskDetails) registry.get(RegistryModelType.TASK_DETAIL, jobExecutionContext.getTaskData().getTaskID());
- } catch (RegistryException e) {
- log.error("Error retrieving job details from Registry");
- throw new GFacHandlerException("Error retrieving job details from Registry", e);
- }
- JobDetails jobDetails = taskData.getJobDetailsList().get(0);
- String jobDescription = jobDetails.getJobDescription();
- if (jobDescription != null) {
- JobDescriptor jobDescriptor = null;
- try {
- jobDescriptor = JobDescriptor.fromXML(jobDescription);
- } catch (XmlException e1) {
- e1.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
- }
- applicationDeploymentDescription.getType().setScratchWorkingDirectory(
- jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getWorkingDirectory());
- applicationDeploymentDescription.getType().setInputDataDirectory(jobDescriptor.getInputDirectory());
- applicationDeploymentDescription.getType().setOutputDataDirectory(jobDescriptor.getOutputDirectory());
- applicationDeploymentDescription.getType().setStandardError(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardErrorFile());
- applicationDeploymentDescription.getType().setStandardOutput(jobDescriptor.getJobDescriptorDocument().getJobDescriptor().getStandardOutFile());
- }
- }
- }
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
++ String hostAddress = jobExecutionContext.getHostName();
try {
- if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null) {
-
+ if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
GFACSSHUtils.addSecurityContext(jobExecutionContext);
}
} catch (Exception e) {
@@@ -108,11 -72,9 +72,9 @@@
DataTransferDetails detail = new DataTransferDetails();
TransferStatus status = new TransferStatus();
- ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext()
- .getApplicationDeploymentDescription().getType();
Cluster cluster = null;
try {
- cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
+ cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
if (cluster == null) {
throw new GFacProviderException("Security context is not set properly");
} else {
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
index 8e46d1b,573ddf0..ff2267c
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/provider/impl/SSHProvider.java
@@@ -76,8 -78,7 +78,8 @@@ public class SSHProvider extends Abstra
public void initialize(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
super.initialize(jobExecutionContext);
- String hostAddress = jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress();
- if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) == null) {
++ String hostAddress = jobExecutionContext.getHostName();
+ if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
try {
GFACSSHUtils.addSecurityContext(jobExecutionContext);
} catch (ApplicationSettingsException e) {
@@@ -87,12 -88,12 +89,12 @@@
}
taskID = jobExecutionContext.getTaskData().getTaskID();
- if (!((SSHHostType) jobExecutionContext.getApplicationContext().getHostDescription().getType()).getHpcResource()) {
- jobID = "SSH_" + jobExecutionContext.getApplicationContext().getHostDescription().getType().getHostAddress() + "_" + Calendar.getInstance().getTimeInMillis();
+ JobSubmissionProtocol preferredJobSubmissionProtocol = jobExecutionContext.getPreferredJobSubmissionProtocol();
+ if (preferredJobSubmissionProtocol == JobSubmissionProtocol.SSH) {
+ jobID = "SSH_" + jobExecutionContext.getHostName() + "_" + Calendar.getInstance().getTimeInMillis();
- cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
+ cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
- ApplicationDeploymentDescriptionType app = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType();
- String remoteFile = app.getStaticWorkingDirectory() + File.separatorChar + Constants.EXECUTABLE_NAME;
+ String remoteFile = jobExecutionContext.getWorkingDir() + File.separatorChar + Constants.EXECUTABLE_NAME;
details.setJobID(taskID);
details.setJobDescription(remoteFile);
jobExecutionContext.setJobDetails(details);
@@@ -140,17 -140,12 +141,14 @@@
} else {
try {
jobExecutionContext.getNotifier().publish(new StartExecutionEvent());
- HostDescriptionType host = jobExecutionContext.getApplicationContext().
- getHostDescription().getType();
- HpcApplicationDeploymentType app = (HpcApplicationDeploymentType) jobExecutionContext.getApplicationContext().
- getApplicationDeploymentDescription().getType();
JobDetails jobDetails = new JobDetails();
++ String hostAddress = jobExecutionContext.getHostName();
try {
Cluster cluster = null;
- if (jobExecutionContext.getSecurityContext(host.getHostAddress()) == null) {
- if (jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT) != null) {
- cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
++ if (jobExecutionContext.getSecurityContext(hostAddress) == null) {
+ GFACSSHUtils.addSecurityContext(jobExecutionContext);
}
- cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(host.getHostAddress())).getPbsCluster();
++ cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
if (cluster == null) {
throw new GFacProviderException("Security context is not set properly");
} else {
@@@ -201,13 -196,11 +199,12 @@@
public void cancelJob(JobExecutionContext jobExecutionContext) throws GFacProviderException, GFacException {
JobDetails jobDetails = jobExecutionContext.getJobDetails();
- HostDescriptionType host = jobExecutionContext.getApplicationContext().
- getHostDescription().getType();
StringBuffer data = new StringBuffer();
++ String hostAddress = jobExecutionContext.getHostName();
if (!hpcType) {
throw new NotImplementedException();
} else {
- Cluster cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(host.getHostAddress())).getPbsCluster();
- Cluster cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(SSHSecurityContext.SSH_SECURITY_CONTEXT)).getPbsCluster();
++ Cluster cluster = ((SSHSecurityContext) jobExecutionContext.getSecurityContext(hostAddress)).getPbsCluster();
if (cluster == null) {
throw new GFacProviderException("Security context is not set properly");
} else {
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
index c756026,f726024..05cdf31
--- a/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
+++ b/modules/gfac/gfac-ssh/src/main/java/org/apache/airavata/gfac/ssh/util/GFACSSHUtils.java
@@@ -72,77 -73,84 +73,84 @@@ public class GFACSSHUtils
* @throws ApplicationSettingsException
*/
public static void addSecurityContext(JobExecutionContext jobExecutionContext) throws GFacException, ApplicationSettingsException {
- HostDescription registeredHost = jobExecutionContext.getApplicationContext().getHostDescription();
- if (registeredHost.getType() instanceof GlobusHostType || registeredHost.getType() instanceof UnicoreHostType) {
+ JobSubmissionProtocol preferredJobSubmissionProtocol = jobExecutionContext.getPreferredJobSubmissionProtocol();
+ JobSubmissionInterface preferredJobSubmissionInterface = jobExecutionContext.getPreferredJobSubmissionInterface();
+ if (preferredJobSubmissionProtocol == JobSubmissionProtocol.GLOBUS || preferredJobSubmissionProtocol == JobSubmissionProtocol.UNICORE) {
logger.error("This is a wrong method to invoke to non ssh host types,please check your gfac-config.xml");
- } else if (registeredHost.getType() instanceof SSHHostType
- || registeredHost.getType() instanceof GsisshHostType) {
- SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
- String credentialStoreToken = jobExecutionContext.getCredentialStoreToken(); // this is set by the framework
- RequestData requestData = new RequestData(ServerSettings.getDefaultUserGateway());
- requestData.setTokenId(credentialStoreToken);
-
- ServerInfo serverInfo = new ServerInfo(null, registeredHost.getType().getHostAddress());
- Cluster pbsCluster = null;
+ } else if (preferredJobSubmissionProtocol == JobSubmissionProtocol.SSH) {
try {
- TokenizedSSHAuthInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(requestData);
- String installedParentPath = ((HpcApplicationDeploymentType)
- jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getType()).getInstalledParentPath();
- if (installedParentPath == null) {
- installedParentPath = "/";
- }
+ AppCatalog appCatalog = AppCatalogFactory.getAppCatalog();
+ SSHJobSubmission sshJobSubmission = appCatalog.getComputeResource().getSSHJobSubmission(preferredJobSubmissionInterface.getJobSubmissionInterfaceId());
+ if (sshJobSubmission.getSecurityProtocol() == SecurityProtocol.GSI) {
+ SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
+ String credentialStoreToken = jobExecutionContext.getCredentialStoreToken(); // this is set by the framework
+ RequestData requestData = new RequestData(ServerSettings.getDefaultUserGateway());
+ requestData.setTokenId(credentialStoreToken);
- SSHCredential credentials = tokenizedSSHAuthInfo.getCredentials();// this is just a call to get and set credentials in to this object,data will be used
- serverInfo.setUserName(credentials.getPortalUserName());
- jobExecutionContext.getExperiment().setUserName(credentials.getPortalUserName());
- // inside the pbsCluser object
+ ServerInfo serverInfo = new ServerInfo(null, jobExecutionContext.getHostName());
- String key = credentials.getPortalUserName() + registeredHost.getType().getHostAddress() +
- serverInfo.getPort();
- boolean recreate = false;
- synchronized (clusters) {
- if (clusters.containsKey(key) && clusters.get(key).size() < maxClusterCount) {
- recreate = true;
- } else if (clusters.containsKey(key)) {
- int i = new Random().nextInt(Integer.MAX_VALUE) % maxClusterCount;
- if (clusters.get(key).get(i).getSession().isConnected()) {
- pbsCluster = clusters.get(key).get(i);
- } else {
- clusters.get(key).remove(i);
- recreate = true;
+ Cluster pbsCluster = null;
+ try {
+ TokenizedSSHAuthInfo tokenizedSSHAuthInfo = new TokenizedSSHAuthInfo(requestData);
+ String installedParentPath = jobExecutionContext.getApplicationContext().getApplicationDeploymentDescription().getExecutablePath();
+ if (installedParentPath == null) {
+ installedParentPath = "/";
}
- if (!recreate) {
- try {
- pbsCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate
- } catch (Exception e) {
- clusters.get(key).remove(i);
- logger.info("Connection found the connection map is expired, so we create from the scratch");
- maxClusterCount++;
- recreate = true; // we make the pbsCluster to create again if there is any exception druing connection
+
+ SSHCredential credentials = tokenizedSSHAuthInfo.getCredentials();// this is just a call to get and set credentials in to this object,data will be used
+ serverInfo.setUserName(credentials.getPortalUserName());
+ jobExecutionContext.getExperiment().setUserName(credentials.getPortalUserName());
+ // inside the pbsCluser object
+
+ String key = credentials.getPortalUserName() + jobExecutionContext.getHostName() + serverInfo.getPort();
+ boolean recreate = false;
+ synchronized (clusters) {
+ if (clusters.containsKey(key) && clusters.get(key).size() < maxClusterCount) {
+ recreate = true;
+ } else if (clusters.containsKey(key)) {
+ int i = new Random().nextInt(Integer.MAX_VALUE) % maxClusterCount;
+ if (clusters.get(key).get(i).getSession().isConnected()) {
+ pbsCluster = clusters.get(key).get(i);
+ } else {
+ clusters.get(key).remove(i);
+ recreate = true;
+ }
+ if (!recreate) {
+ try {
+ pbsCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate
+ } catch (Exception e) {
+ clusters.get(key).remove(i);
+ logger.info("Connection found the connection map is expired, so we create from the scratch");
+ maxClusterCount++;
+ recreate = true; // we make the pbsCluster to create again if there is any exception druing connection
+ }
+ }
+ logger.info("Re-using the same connection used with the connection string:" + key);
+ } else {
+ recreate = true;
+ }
+ if (recreate) {
+ pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo,
+ CommonUtils.getPBSJobManager(installedParentPath));
+ List<Cluster> pbsClusters = null;
+ if (!(clusters.containsKey(key))) {
+ pbsClusters = new ArrayList<Cluster>();
+ } else {
+ pbsClusters = clusters.get(key);
+ }
+ pbsClusters.add(pbsCluster);
+ clusters.put(key, pbsClusters);
}
}
- logger.info("Re-using the same connection used with the connection string:" + key);
- } else {
- recreate = true;
- }
- if (recreate) {
- pbsCluster = new PBSCluster(serverInfo, tokenizedSSHAuthInfo,
- CommonUtils.getPBSJobManager(installedParentPath));
- List<Cluster> pbsClusters = null;
- if (!(clusters.containsKey(key))) {
- pbsClusters = new ArrayList<Cluster>();
- } else {
- pbsClusters = clusters.get(key);
- }
- pbsClusters.add(pbsCluster);
- clusters.put(key, pbsClusters);
+ } catch (Exception e) {
+ throw new GFacException("Error occurred...", e);
}
+ sshSecurityContext.setPbsCluster(pbsCluster);
- jobExecutionContext.addSecurityContext(Constants.SSH_SECURITY_CONTEXT, sshSecurityContext);
++ jobExecutionContext.addSecurityContext(jobExecutionContext.getHostName(), sshSecurityContext);
}
- } catch (Exception e) {
- e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ } catch (AppCatalogException e) {
+ throw new GFacException("Error while getting SSH Submission object from app catalog", e);
}
- sshSecurityContext.setPbsCluster(pbsCluster);
- jobExecutionContext.addSecurityContext(registeredHost.getType().getHostAddress(), sshSecurityContext);
}
}
@@@ -154,61 -162,61 +162,61 @@@
* @throws ApplicationSettingsException
*/
public static void addSecurityContext(JobExecutionContext jobExecutionContext,SSHAuthWrapper sshAuth) throws GFacException, ApplicationSettingsException {
- try {
- if(sshAuth== null) {
- throw new GFacException("Error adding security Context, because sshAuthWrapper is null");
- }
- SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
- Cluster pbsCluster = null;
- String key=sshAuth.getKey();
- boolean recreate = false;
- synchronized (clusters) {
- if (clusters.containsKey(key) && clusters.get(key).size() < maxClusterCount) {
- recreate = true;
- } else if (clusters.containsKey(key)) {
- int i = new Random().nextInt(Integer.MAX_VALUE) % maxClusterCount;
- if (clusters.get(key).get(i).getSession().isConnected()) {
- pbsCluster = clusters.get(key).get(i);
- } else {
- clusters.get(key).remove(i);
- recreate = true;
- }
- if (!recreate) {
- try {
- pbsCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate
- } catch (Exception e) {
- clusters.get(key).remove(i);
- logger.info("Connection found the connection map is expired, so we create from the scratch");
- maxClusterCount++;
- recreate = true; // we make the pbsCluster to create again if there is any exception druing connection
- }
- }
- logger.info("Re-using the same connection used with the connection string:" + key);
+ try {
+ if(sshAuth== null) {
+ throw new GFacException("Error adding security Context, because sshAuthWrapper is null");
+ }
+ SSHSecurityContext sshSecurityContext = new SSHSecurityContext();
+ Cluster pbsCluster = null;
+ String key=sshAuth.getKey();
+ boolean recreate = false;
+ synchronized (clusters) {
+ if (clusters.containsKey(key) && clusters.get(key).size() < maxClusterCount) {
+ recreate = true;
+ } else if (clusters.containsKey(key)) {
+ int i = new Random().nextInt(Integer.MAX_VALUE) % maxClusterCount;
+ if (clusters.get(key).get(i).getSession().isConnected()) {
+ pbsCluster = clusters.get(key).get(i);
} else {
+ clusters.get(key).remove(i);
recreate = true;
}
- if (recreate) {
- pbsCluster = new PBSCluster(sshAuth.getServerInfo(), sshAuth.getAuthenticationInfo(),null);
- key = sshAuth.getKey();
- List<Cluster> pbsClusters = null;
- if (!(clusters.containsKey(key))) {
- pbsClusters = new ArrayList<Cluster>();
- } else {
- pbsClusters = clusters.get(key);
+ if (!recreate) {
+ try {
+ pbsCluster.listDirectory("~/"); // its hard to trust isConnected method, so we try to connect if it works we are good,else we recreate
+ } catch (Exception e) {
+ clusters.get(key).remove(i);
+ logger.info("Connection found the connection map is expired, so we create from the scratch");
+ maxClusterCount++;
+ recreate = true; // we make the pbsCluster to create again if there is any exception druing connection
}
- pbsClusters.add(pbsCluster);
- clusters.put(key, pbsClusters);
}
+ logger.info("Re-using the same connection used with the connection string:" + key);
+ } else {
+ recreate = true;
+ }
+ if (recreate) {
+ pbsCluster = new PBSCluster(sshAuth.getServerInfo(), sshAuth.getAuthenticationInfo(),null);
+ key = sshAuth.getKey();
+ List<Cluster> pbsClusters = null;
+ if (!(clusters.containsKey(key))) {
+ pbsClusters = new ArrayList<Cluster>();
+ } else {
+ pbsClusters = clusters.get(key);
+ }
+ pbsClusters.add(pbsCluster);
+ clusters.put(key, pbsClusters);
}
- sshSecurityContext.setPbsCluster(pbsCluster);
- jobExecutionContext.addSecurityContext(key, sshSecurityContext);
- } catch (Exception e) {
- e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
+ sshSecurityContext.setPbsCluster(pbsCluster);
- jobExecutionContext.addSecurityContext(Constants.SSH_SECURITY_CONTEXT+key, sshSecurityContext);
++ jobExecutionContext.addSecurityContext(key, sshSecurityContext);
+ } catch (Exception e) {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ }
}
- public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext,
- ApplicationDeploymentDescriptionType app, Cluster cluster) {
+
+ public static JobDescriptor createJobDescriptor(JobExecutionContext jobExecutionContext, Cluster cluster) {
JobDescriptor jobDescriptor = new JobDescriptor();
// this is common for any application descriptor
jobDescriptor.setCallBackIp(ServerSettings.getIp());
http://git-wip-us.apache.org/repos/asf/airavata/blob/36938926/modules/xbaya-gui/src/main/java/org/apache/airavata/xbaya/ui/experiment/WorkflowInterpreterLaunchWindow.java
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