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/f200d50b Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/f200d50b Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/f200d50b Branch: refs/heads/master Commit: f200d50be55bd435e367494482d67881f4f19f51 Parents: aa2fab5 636a733 Author: Supun Nakandala <[email protected]> Authored: Thu Jun 25 20:55:13 2015 +0530 Committer: Supun Nakandala <[email protected]> Committed: Thu Jun 25 20:55:13 2015 +0530 ---------------------------------------------------------------------- .../java/org/apache/airavata/api/Airavata.java | 2 +- .../Airavata/Model/Messaging/Event/Types.php | 379 +++++- .../airavata/model/messaging/event/ttypes.py | 335 +++++- .../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/LaunchValidationException.java | 2 +- .../model/error/ProjectNotFoundException.java | 2 +- .../airavata/model/error/TimedOutException.java | 2 +- .../airavata/model/error/ValidationResults.java | 2 +- .../airavata/model/error/ValidatorResult.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/ProcessIdentifier.java | 2 +- .../event/ProcessStatusChangeEvent.java | 2 +- .../event/ProcessStatusChangeRequestEvent.java | 2 +- .../messaging/event/ProcessSubmitEvent.java | 112 +- .../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 | 2 +- .../ComputationalResourceSchedulingModel.java | 2 +- .../airavata/model/security/AuthzToken.java | 2 +- .../airavata/model/status/ExperimentStatus.java | 2 +- .../apache/airavata/model/status/JobStatus.java | 2 +- .../airavata/model/status/ProcessState.java | 36 +- .../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 +- distribution/pom.xml | 9 +- .../gaussian/handler/GaussianHandler.java | 326 ++--- .../org/apache/airavata/gfac/core/GFac.java | 10 +- .../apache/airavata/gfac/core/GFacUtils.java | 44 +- .../SSHPublicKeyAuthentication.java | 2 +- .../SSHPublicKeyFileAuthentication.java | 2 +- .../gfac/core/context/JobExecutionContext.java | 988 +++++++-------- .../gfac/core/context/ProcessContext.java | 6 + .../airavata/gfac/core/monitor/MonitorID.java | 30 +- .../java/com/jcraft/jsch/GSSContextX509.java | 205 ++++ .../UserAuthGSSAPIWithMICGSSCredentials.java | 1 - .../apache/airavata/gfac/impl/GFacWorker.java | 47 +- .../gfac/impl/job/PBSJobConfiguration.java | 112 +- .../gfac/impl/task/SSHJobSubmissionTask.java | 26 +- .../handler/LocalDirectorySetupHandler.java | 124 +- .../gfac/local/handler/LocalInputHandler.java | 184 +-- .../gfac/local/provider/impl/LocalProvider.java | 618 +++++----- .../gfac/local/utils/LocalProviderUtil.java | 102 +- .../ssh/handler/AdvancedSCPInputHandler.java | 454 +++---- .../ssh/handler/AdvancedSCPOutputHandler.java | 450 +++---- .../gfac/ssh/handler/NewSSHOutputHandler.java | 156 +-- .../ssh/handler/SSHDirectorySetupHandler.java | 238 ++-- .../gfac/ssh/handler/SSHInputHandler.java | 386 +++--- .../gfac/ssh/handler/SSHOutputHandler.java | 510 ++++---- .../gfac/ssh/provider/impl/SSHProvider.java | 946 +++++++-------- .../airavata/gfac/ssh/util/GFACSSHUtils.java | 1124 +++++++++--------- .../airavata/gfac/ssh/util/HandleOutputs.java | 192 +-- .../apache/airavata/gfac/server/GfacServer.java | 4 +- .../orchestrator/cpi/OrchestratorService.java | 314 ++--- .../cpi/orchestrator_cpi_serviceConstants.java | 2 +- .../core/validator/JobMetadataValidator.java | 9 +- .../validator/impl/BatchQueueValidator.java | 14 +- .../impl/ExperimentStatusValidator.java | 12 +- .../airavata/orchestrator/cpi/Orchestrator.java | 20 +- .../cpi/impl/SimpleOrchestratorImpl.java | 104 +- .../orchestrator/orchestrator-service/pom.xml | 5 - .../server/OrchestratorServerHandler.java | 577 ++++----- .../orchestrator/util/DataModelUtils.java | 4 +- .../OrchestratorServerThreadPoolExecutor.java | 6 +- .../engine/interpretor/WorkflowInterpreter.java | 28 +- .../engine/invoker/WorkflowInputUtil.java | 2 +- .../model/component/ComponentDataPort.java | 2 +- .../amazon/InstanceComponentDataPort.java | 2 +- .../component/dynamic/DynamicComponentPort.java | 2 +- .../component/ws/WSComponentApplication.java | 6 +- .../ws/WSComponentApplicationParameter.java | 3 +- .../model/component/ws/WSComponentPort.java | 2 +- .../airavata/workflow/model/graph/DataPort.java | 2 +- .../airavata/workflow/model/graph/EPRPort.java | 2 +- .../model/graph/amazon/InstanceDataPort.java | 2 +- .../model/graph/dynamic/DynamicPort.java | 2 +- .../model/graph/system/ConstantNode.java | 2 +- .../model/graph/system/DifferedInputNode.java | 2 +- .../model/graph/system/EndBlockNode.java | 2 +- .../model/graph/system/EndDoWhileNode.java | 2 +- .../model/graph/system/EndForEachNode.java | 2 +- .../workflow/model/graph/system/EndifNode.java | 2 +- .../workflow/model/graph/system/OutputNode.java | 2 +- .../model/graph/system/ParameterNode.java | 3 +- .../model/graph/system/SystemDataPort.java | 3 +- .../workflow/model/graph/system/SystemNode.java | 3 +- .../workflow/model/graph/ws/WSPort.java | 2 +- .../workflow/model/wf/WorkflowInput.java | 3 +- .../core/dag/nodes/WorkflowInputNode.java | 2 +- .../core/dag/nodes/WorkflowInputNodeImpl.java | 2 +- .../core/dag/nodes/WorkflowOutputNode.java | 2 +- .../core/dag/nodes/WorkflowOutputNodeImpl.java | 2 +- .../airavata/workflow/core/dag/port/InPort.java | 2 +- .../workflow/core/dag/port/InputPortIml.java | 2 +- .../workflow/core/dag/port/OutPort.java | 2 +- .../workflow/core/dag/port/OutPortImpl.java | 2 +- .../core/parser/AiravataWorkflowParser.java | 16 +- .../core/parser/AiravataWorkflowParserTest.java | 6 +- pom.xml | 8 +- .../airavata-api/messaging_events.thrift | 2 +- .../airavata-api/status_models.thrift | 6 + .../orchestrator.cpi.service.thrift | 8 +- 151 files changed, 5121 insertions(+), 4389 deletions(-) ----------------------------------------------------------------------
