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From scnakand...@apache.org
Subject [05/17] airavata git commit: Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata
Date Thu, 18 Jun 2015 20:51:12 GMT
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/f7156973
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/f7156973
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/f7156973

Branch: refs/heads/master
Commit: f715697318e4127f1e158bfb33fe4dc1d00e3b94
Parents: 8a0e6ce f6d34cc
Author: Supun Nakandala <scnakandala@apache.org>
Authored: Wed Jun 17 19:12:57 2015 +0530
Committer: Supun Nakandala <scnakandala@apache.org>
Committed: Wed Jun 17 19:12:57 2015 +0530

----------------------------------------------------------------------
 .../AiravataExperimentStatusUpdator.java        |    4 +-
 .../listener/ExperimentStatusChangedEvent.java  |    2 +-
 .../util/AiravataServerThreadPoolExecutor.java  |    6 +-
 .../api/server/util/DataModelUtils.java         |   10 +-
 .../handler/AiravataServerHandlerTest.java      |   57 +-
 .../java/org/apache/airavata/api/Airavata.java  |    2 +-
 .../api/client/AiravataClientFactory.java       |    8 +-
 .../client/samples/CreateLaunchBES.java         |   55 +-
 .../client/samples/CreateLaunchExperiment.java  |  177 +-
 .../samples/CreateLaunchExperimentUS3.java      |    2 +-
 .../client/samples/RegisterSampleData.java      |   12 +-
 .../samples/TestCreateLaunchExperiment.java     |    2 +-
 .../tools/RegisterOGCEUS3Application.java       |    6 +-
 .../tools/RegisterSampleApplications.java       |    4 +-
 .../tools/RegisterSampleApplicationsUtils.java  |    4 +-
 .../client/tools/RegisterUS3Application.java    |    6 +-
 .../org/apache/airavata/model/Workflow.java     |    2 +-
 .../ApplicationDeploymentDescription.java       |    2 +-
 .../appdeployment/ApplicationModule.java        |    2 +-
 .../appcatalog/appdeployment/SetEnvPaths.java   |    2 +-
 .../ApplicationInterfaceDescription.java        |    2 +-
 .../appcatalog/computeresource/BatchQueue.java  |    2 +-
 .../computeresource/CloudJobSubmission.java     |    2 +-
 .../ComputeResourceDescription.java             |    2 +-
 .../computeresource/DataMovementInterface.java  |    2 +-
 .../computeresource/GlobusJobSubmission.java    |    2 +-
 .../computeresource/GridFTPDataMovement.java    |    2 +-
 .../computeresource/JobSubmissionInterface.java |    2 +-
 .../computeresource/LOCALDataMovement.java      |    2 +-
 .../computeresource/LOCALSubmission.java        |    2 +-
 .../computeresource/ResourceJobManager.java     |    2 +-
 .../computeresource/SCPDataMovement.java        |    2 +-
 .../computeresource/SSHJobSubmission.java       |    2 +-
 .../computeresource/UnicoreDataMovement.java    |    2 +-
 .../computeresource/UnicoreJobSubmission.java   |    2 +-
 .../ComputeResourcePreference.java              |    2 +-
 .../gatewayprofile/GatewayResourceProfile.java  |    2 +-
 .../application/io/InputDataObjectType.java     |    2 +-
 .../application/io/OutputDataObjectType.java    |    2 +-
 .../airavata/model/commons/ErrorModel.java      |    2 +-
 .../model/commons/ValidationResults.java        |    2 +-
 .../airavata/model/commons/ValidatorResult.java |    2 +-
 .../model/error/AiravataClientException.java    |    2 +-
 .../model/error/AiravataSystemException.java    |    2 +-
 .../model/error/AuthenticationException.java    |    2 +-
 .../model/error/AuthorizationException.java     |    2 +-
 .../error/ExperimentNotFoundException.java      |    2 +-
 .../model/error/InvalidRequestException.java    |    2 +-
 .../model/error/ProjectNotFoundException.java   |    2 +-
 .../airavata/model/error/TimedOutException.java |    2 +-
 .../model/experiment/ExperimentModel.java       |    2 +-
 .../model/experiment/ExperimentStatistics.java  |    2 +-
 .../experiment/ExperimentSummaryModel.java      |    2 +-
 .../experiment/UserConfigurationDataModel.java  |    2 +-
 .../org/apache/airavata/model/job/JobModel.java |    2 +-
 .../event/ExperimentStatusChangeEvent.java      |    2 +-
 .../model/messaging/event/JobIdentifier.java    |    2 +-
 .../messaging/event/JobStatusChangeEvent.java   |    2 +-
 .../event/JobStatusChangeRequestEvent.java      |    2 +-
 .../airavata/model/messaging/event/Message.java |    2 +-
 .../messaging/event/ProcessSubmitEvent.java     |    2 +-
 .../model/messaging/event/TaskIdentifier.java   |    2 +-
 .../messaging/event/TaskOutputChangeEvent.java  |    2 +-
 .../messaging/event/TaskStatusChangeEvent.java  |    2 +-
 .../event/TaskStatusChangeRequestEvent.java     |    2 +-
 .../model/messaging/event/TaskSubmitEvent.java  |    2 +-
 .../messaging/event/TaskTerminateEvent.java     |    2 +-
 .../airavata/model/process/ProcessModel.java    |  610 ++++-
 .../ComputationalResourceSchedulingModel.java   |  116 +-
 .../airavata/model/security/AuthzToken.java     |    2 +-
 .../airavata/model/status/ExperimentStatus.java |    2 +-
 .../apache/airavata/model/status/JobStatus.java |    2 +-
 .../airavata/model/status/ProcessStatus.java    |    2 +-
 .../airavata/model/status/TaskStatus.java       |    2 +-
 .../model/task/DataStagingTaskModel.java        |    2 +-
 .../apache/airavata/model/task/TaskModel.java   |    2 +-
 .../airavata/model/workspace/Gateway.java       |    2 +-
 .../apache/airavata/model/workspace/Group.java  |    2 +-
 .../airavata/model/workspace/Project.java       |    2 +-
 .../apache/airavata/model/workspace/User.java   |    2 +-
 .../airavata/model/util/AppInterfaceUtil.java   |    6 +-
 .../model/util/ExperimentModelUtil.java         |  161 +-
 .../apache/airavata/common/utils/Constants.java |    5 +
 .../gaussian/handler/GaussianHandler.java       |    2 +-
 .../gfac/bes/handlers/AbstractSMSHandler.java   |    4 +-
 .../gfac/bes/provider/impl/BESProvider.java     |    4 +-
 .../bes/security/UNICORESecurityContext.java    |    2 +-
 .../gfac/bes/utils/DataTransferrer.java         |    2 +-
 .../gfac/bes/utils/ResourceProcessor.java       |    4 +-
 modules/gfac/gfac-core/pom.xml                  |    6 +
 .../core/AbstractJobManagerConfiguration.java   |   40 +
 .../airavata/gfac/core/GFacConfiguration.java   |  289 ---
 .../airavata/gfac/core/GFacConstants.java       |    2 +
 .../apache/airavata/gfac/core/GFacEngine.java   |   41 +
 .../apache/airavata/gfac/core/GFacUtils.java    | 1382 ++++++-----
 .../airavata/gfac/core/JobSubmissionFault.java  |   98 -
 .../apache/airavata/gfac/core/Scheduler.java    |  230 --
 .../airavata/gfac/core/ToolsException.java      |   35 -
 .../core/authentication/AuthenticationInfo.java |    9 +-
 .../authentication/SSHKeyAuthentication.java    |   45 +-
 .../SSHPasswordAuthentication.java              |   29 +-
 .../core/cluster/AbstractRemoteCluster.java     |   39 +
 .../airavata/gfac/core/cluster/JobStatus.java   |  110 -
 .../gfac/core/cluster/OutputParser.java         |    1 +
 .../gfac/core/cluster/RemoteCluster.java        |  234 +-
 .../core/config/DataTransferTaskConfig.java     |   44 +
 .../gfac/core/config/GFacYamlConfigruation.java |  124 +
 .../core/config/JobSubmitterTaskConfig.java     |   44 +
 .../gfac/core/config/ResourceConfig.java        |   64 +
 .../gfac/core/context/JobExecutionContext.java  |    8 +-
 .../gfac/core/context/ProcessContext.java       |  128 +
 .../airavata/gfac/core/context/TaskContext.java |   49 +
 .../gfac/core/handler/AbstractHandler.java      |   76 -
 .../core/handler/AppDescriptorCheckHandler.java |   81 -
 .../airavata/gfac/core/handler/GFacHandler.java |   60 -
 .../gfac/core/handler/GFacHandlerConfig.java    |   52 -
 .../gfac/core/handler/GFacHandlerException.java |   49 -
 .../gfac/core/handler/ThreadedHandler.java      |   31 -
 .../core/monitor/GfacInternalStatusUpdator.java |  103 -
 .../airavata/gfac/core/monitor/JobMonitor.java  |   39 +
 .../gfac/core/monitor/JobStatusResult.java      |    3 +-
 .../airavata/gfac/core/monitor/MonitorID.java   |   16 +-
 .../state/GfacExperimentStateChangeRequest.java |   74 -
 .../core/monitor/state/PublisherMessage.java    |   26 -
 .../gfac/core/provider/AbstractProvider.java    |   58 -
 .../gfac/core/provider/GFacProvider.java        |   78 -
 .../gfac/core/provider/GFacProviderConfig.java  |   51 -
 .../core/provider/GFacProviderException.java    |   50 -
 .../gfac/core/provider/utils/DataIDType.java    |   95 -
 .../gfac/core/provider/utils/ProviderUtils.java |   58 -
 .../provider/utils/ResourceRequirement.java     |   34 -
 .../scheduler/impl/SimpleHostScheduler.java     |   33 -
 .../gfac/core/states/GfacExperimentState.java   |   89 -
 .../gfac/core/states/GfacHandlerState.java      |   65 -
 .../gfac/core/task/JobSubmissionTask.java       |   28 +
 .../apache/airavata/gfac/core/task/Task.java    |   57 +
 .../airavata/gfac/core/task/TaskException.java  |   45 +
 .../src/main/resources/gfac-config.yaml         |   79 +
 .../apache/airavata/job/GFacConfigXmlTest.java  |  126 -
 .../apache/airavata/job/TestGlobalHandler.java  |   38 -
 .../org/apache/airavata/job/TestInHandler.java  |   38 -
 .../org/apache/airavata/job/TestOutHandler.java |   38 -
 .../org/apache/airavata/job/TestProvider.java   |   58 -
 .../airavata/job/TestThreadedHandler.java       |   45 -
 modules/gfac/gfac-impl/pom.xml                  |    5 +
 .../airavata/gfac/gsi/ssh/GSSContextX509.java   |  210 --
 .../gfac/gsi/ssh/api/CommandExecutor.java       |  295 ---
 .../apache/airavata/gfac/gsi/ssh/api/Core.java  |   59 -
 .../apache/airavata/gfac/gsi/ssh/api/Node.java  |  104 -
 .../gsi/ssh/api/job/LSFJobConfiguration.java    |  123 -
 .../gfac/gsi/ssh/api/job/LSFOutputParser.java   |  132 -
 .../gsi/ssh/api/job/PBSJobConfiguration.java    |  121 -
 .../gfac/gsi/ssh/api/job/PBSOutputParser.java   |  218 --
 .../gsi/ssh/api/job/SlurmJobConfiguration.java  |  119 -
 .../gfac/gsi/ssh/api/job/SlurmOutputParser.java |  192 --
 .../gsi/ssh/api/job/UGEJobConfiguration.java    |  121 -
 .../gfac/gsi/ssh/api/job/UGEOutputParser.java   |  190 --
 .../gfac/gsi/ssh/config/ConfigReader.java       |   76 -
 .../ssh/impl/DefaultJobSubmissionListener.java  |   43 -
 .../gsi/ssh/impl/GSISSHAbstractCluster.java     |  770 ------
 .../gfac/gsi/ssh/impl/HPCRemoteCluster.java     |   46 -
 .../airavata/gfac/gsi/ssh/impl/SSHUserInfo.java |   63 -
 .../gfac/gsi/ssh/impl/StandardOutReader.java    |   79 -
 .../gfac/gsi/ssh/impl/SystemCommandOutput.java  |   78 -
 .../DefaultPasswordAuthenticationInfo.java      |   48 -
 .../DefaultPublicKeyAuthentication.java         |   68 -
 .../DefaultPublicKeyFileAuthentication.java     |   70 -
 .../MyProxyAuthenticationInfo.java              |  108 -
 .../gfac/gsi/ssh/jsch/ExtendedJSch.java         |   64 -
 .../gsi/ssh/listener/JobSubmissionListener.java |   81 -
 .../airavata/gfac/gsi/ssh/util/CommonUtils.java |   83 -
 .../ssh/util/SSHAPIUIKeyboardInteractive.java   |   73 -
 .../gsi/ssh/util/SSHKeyPasswordHandler.java     |   68 -
 .../airavata/gfac/gsi/ssh/util/SSHUtils.java    |  760 ------
 .../handler/GSISSHDirectorySetupHandler.java    |  118 -
 .../gfac/gsissh/handler/GSISSHInputHandler.java |  213 --
 .../gsissh/handler/GSISSHOutputHandler.java     |  323 ---
 .../gsissh/handler/NewGSISSHOutputHandler.java  |   83 -
 .../gsissh/provider/impl/GSISSHProvider.java    |  344 ---
 .../gsissh/security/GSISecurityContext.java     |   67 -
 .../security/TokenizedMyProxyAuthInfo.java      |  304 ---
 .../gfac/gsissh/util/GFACGSISSHUtils.java       |  367 ---
 .../gfac/impl/AiravataJobStatusUpdator.java     |    3 +-
 .../gfac/impl/AiravataTaskStatusUpdator.java    |    3 +-
 .../impl/AiravataWorkflowNodeStatusUpdator.java |    6 +-
 .../airavata/gfac/impl/BetterGfacImpl.java      |   19 +-
 .../gfac/impl/DefaultHostScheduler.java         |   37 +
 .../org/apache/airavata/gfac/impl/Factory.java  |  154 ++
 .../apache/airavata/gfac/impl/GFacEngine.java   |   53 -
 .../airavata/gfac/impl/GFacEngineImpl.java      |  128 +
 .../apache/airavata/gfac/impl/GFacWorker.java   |   84 +-
 .../gfac/impl/GfacInternalStatusUpdator.java    |  104 -
 .../airavata/gfac/impl/HPCRemoteCluster.java    |  332 +++
 .../airavata/gfac/impl/InputHandlerWorker.java  |   52 -
 .../airavata/gfac/impl/OutHandlerWorker.java    |   88 -
 .../apache/airavata/gfac/impl/OutputUtils.java  |  110 -
 .../org/apache/airavata/gfac/impl/SSHUtils.java |  441 ++++
 .../airavata/gfac/impl/StandardOutReader.java   |   79 +
 .../gfac/impl/job/LSFJobConfiguration.java      |  123 +
 .../airavata/gfac/impl/job/LSFOutputParser.java |  133 +
 .../gfac/impl/job/PBSJobConfiguration.java      |  121 +
 .../airavata/gfac/impl/job/PBSOutputParser.java |  219 ++
 .../gfac/impl/job/SlurmJobConfiguration.java    |  119 +
 .../gfac/impl/job/SlurmOutputParser.java        |  193 ++
 .../gfac/impl/job/UGEJobConfiguration.java      |  121 +
 .../airavata/gfac/impl/job/UGEOutputParser.java |  191 ++
 .../gfac/impl/task/AbstractSCPTask.java         |   62 +
 .../gfac/impl/task/JobSubmissionTaskImpl.java   |  108 +
 .../gfac/impl/task/SCPInputDataStageTask.java   |   78 +
 .../gfac/impl/task/SCPOutputDataStatgeTask.java |   70 +
 .../gfac/impl/task/SSHEnvironmentSetupTask.java |   55 +
 .../gfac/local/provider/impl/LocalProvider.java |    6 +-
 .../airavata/gfac/monitor/HPCMonitorID.java     |  107 -
 .../airavata/gfac/monitor/HostMonitorData.java  |   88 -
 .../airavata/gfac/monitor/UserMonitorData.java  |   76 -
 .../command/ExperimentCancelRequest.java        |   38 -
 .../gfac/monitor/command/TaskCancelRequest.java |   52 -
 .../monitor/core/AiravataAbstractMonitor.java   |   37 -
 .../gfac/monitor/core/MessageParser.java        |   43 -
 .../airavata/gfac/monitor/core/Monitor.java     |   30 -
 .../airavata/gfac/monitor/core/PullMonitor.java |   64 -
 .../airavata/gfac/monitor/core/PushMonitor.java |   60 -
 .../gfac/monitor/email/EmailBasedMonitor.java   |  105 +-
 .../gfac/monitor/email/EmailMonitorFactory.java |   47 -
 .../monitor/email/parser/LSFEmailParser.java    |    2 +-
 .../monitor/email/parser/PBSEmailParser.java    |    2 +-
 .../monitor/email/parser/SLURMEmailParser.java  |    2 +-
 .../monitor/email/parser/UGEEmailParser.java    |    2 +-
 .../handlers/GridPullMonitorHandler.java        |  139 --
 .../handlers/GridPushMonitorHandler.java        |  107 -
 .../monitor/impl/pull/qstat/HPCPullMonitor.java |  471 ----
 .../impl/pull/qstat/ResourceConnection.java     |  154 --
 .../monitor/impl/push/amqp/AMQPMonitor.java     |  280 ---
 .../monitor/impl/push/amqp/BasicConsumer.java   |   87 -
 .../impl/push/amqp/ComputingActivity.java       |   19 -
 .../impl/push/amqp/JSONMessageParser.java       |   77 -
 .../impl/push/amqp/SimpleJobFinishConsumer.java |   86 -
 .../impl/push/amqp/UnRegisterWorker.java        |   67 -
 .../gfac/monitor/util/AMQPConnectionUtil.java   |   80 -
 .../airavata/gfac/monitor/util/CommonUtils.java |  280 ---
 .../airavata/gfac/monitor/util/X509Helper.java  |  164 --
 .../ssh/handler/AdvancedSCPInputHandler.java    |    2 +-
 .../ssh/handler/AdvancedSCPOutputHandler.java   |    4 +-
 .../gfac/ssh/handler/NewSSHOutputHandler.java   |    4 +-
 .../ssh/handler/SSHDirectorySetupHandler.java   |    2 +-
 .../gfac/ssh/handler/SSHInputHandler.java       |    2 +-
 .../gfac/ssh/handler/SSHOutputHandler.java      |   12 +-
 .../gfac/ssh/provider/impl/SSHProvider.java     |   12 +-
 .../airavata/gfac/ssh/util/GFACSSHUtils.java    |   10 +-
 .../services/impl/BigRed2TestWithSSHAuth.java   |    2 +-
 .../impl/GSISSHProviderTestWithMyProxyAuth.java |    2 +-
 .../gfac/services/impl/LocalProviderTest.java   |    8 +-
 .../impl/DefaultSSHApiTestWithMyProxyAuth.java  |    2 +-
 .../gfac/ssh/impl/VanilaTestWithSSHAuth.java    |    2 +-
 .../apache/airavata/job/AMQPMonitorTest.java    |    2 +-
 .../airavata/gfac/server/GfacServerHandler.java |   51 +-
 .../apache/airavata/integration/BaseCaseIT.java |   10 +-
 .../airavata/integration/DataRetrievalIT.java   |    2 +-
 .../airavata/integration/SimpleEchoIT.java      |    6 +-
 .../SingleAppIntegrationTestBase.java           |    6 +-
 .../WorkflowIntegrationTestBase.java            |    2 +-
 .../sample/OrchestratorClientSample.java        |    6 +-
 .../core/validator/JobMetadataValidator.java    |    6 +-
 .../validator/impl/BatchQueueValidator.java     |    2 +-
 .../impl/ExperimentStatusValidator.java         |    8 +-
 .../airavata/orchestrator/cpi/Orchestrator.java |    6 +-
 .../cpi/impl/SimpleOrchestratorImpl.java        |    2 +-
 .../orchestrator/core/ValidatorTest.java        |    2 +-
 .../orchestrator/core/util/SecondValidator.java |    6 +-
 .../orchestrator/core/util/TestValidator.java   |    6 +-
 .../server/OrchestratorServerHandler.java       |   18 +-
 .../orchestrator/util/DataModelUtils.java       |    2 +-
 .../catalog/impl/ApplicationInterfaceImpl.java  |   10 +-
 .../app/catalog/impl/ComputeResourceImpl.java   |    2 +-
 .../catalog/impl/GwyResourceProfileImpl.java    |    3 +-
 .../app/catalog/impl/WorkflowCatalogImpl.java   |    4 +-
 .../util/AppCatalogThriftConversion.java        |    3 +
 .../catalog/impl/ExperimentCatalogImpl.java     |  238 +-
 .../catalog/impl/ExperimentRegistry.java        | 2307 +++++++++---------
 .../catalog/resources/WorkerResource.java       |    2 +-
 .../utils/ThriftDataModelConversion.java        |  393 ++-
 .../catalog/ExperimentUseCaseTest.java          |    2 +-
 .../catalog/TaskDetailResourceTest.java         |    2 +-
 .../airavata/registry/cpi/WorkflowCatalog.java  |    3 +-
 .../ExperimentExecution.java                    |    2 +-
 .../workflow/engine/WorkflowEngineImpl.java     |    2 +-
 .../airavata/workflow/engine/WorkflowUtils.java |    2 +-
 .../engine/interpretor/WorkflowInterpreter.java |    2 +-
 .../WorkflowInterpreterSkeleton2.java           |    2 +-
 .../airavata/workflow/core/ProcessContext.java  |    4 +-
 .../core/SimpleWorkflowInterpreter.java         |   14 +-
 .../core/parser/AiravataWorkflowParser.java     |    2 +-
 .../core/parser/AiravataWorkflowParserTest.java |    2 +-
 .../airavata/xbaya/messaging/Monitor.java       |    2 +-
 .../ui/experiment/LaunchApplicationWindow.java  |    6 +-
 .../WorkflowInterpreterLaunchWindow.java        |    6 +-
 .../xbaya/ui/monitor/MonitorEventHandler.java   |    2 +-
 pom.xml                                         |    1 +
 .../airavata/api/samples/ExperimentSample.java  |   10 +-
 .../airavata-api/process_model.thrift           |   16 +-
 .../airavata-api/scheduling_model.thrift        |    1 +
 301 files changed, 7204 insertions(+), 14613 deletions(-)
----------------------------------------------------------------------



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