Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata into data-manager
# Conflicts: # airavata-api/airavata-api-stubs/src/main/java/org/apache/airavata/api/Airavata.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/Workflow.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/appdeployment/ApplicationDeploymentDescription.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/appdeployment/ApplicationModule.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/appdeployment/CommandObject.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/appdeployment/SetEnvPaths.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/appinterface/ApplicationInterfaceDescription.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/BatchQueue.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/CloudJobSubmission.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/ComputeResourceDescription.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/GlobusJobSubmission.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/JobSubmissionInterface.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/LOCALSubmission.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/ResourceJobManager.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/SSHJobSubmission.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/UnicoreJobSubmission.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/ComputeResourcePreference.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/GatewayResourceProfile.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/StoragePreference.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/storageresource/StorageResourceDescription.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/application/io/InputDataObjectType.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/application/io/OutputDataObjectType.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/commons/ErrorModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/commons/ValidationResults.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/commons/ValidatorResult.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/data/movement/DataMovementInterface.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/data/movement/GridFTPDataMovement.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/data/movement/LOCALDataMovement.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/data/movement/SCPDataMovement.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/data/movement/UnicoreDataMovement.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/data/replica/FileReplicaModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/data/resource/DataResourceModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/AiravataClientException.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/AiravataSystemException.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/AuthenticationException.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/AuthorizationException.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/ExperimentNotFoundException.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/InvalidRequestException.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/LaunchValidationException.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/ProjectNotFoundException.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/TimedOutException.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/ValidationResults.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/error/ValidatorResult.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/experiment/ExperimentModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/experiment/ExperimentStatistics.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/experiment/ExperimentSummaryModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/experiment/UserConfigurationDataModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/job/JobModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/ExperimentStatusChangeEvent.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/JobIdentifier.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/JobStatusChangeEvent.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/JobStatusChangeRequestEvent.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/Message.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/ProcessIdentifier.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/ProcessStatusChangeEvent.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/ProcessStatusChangeRequestEvent.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/ProcessSubmitEvent.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/ProcessTerminateEvent.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/TaskIdentifier.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/TaskOutputChangeEvent.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/TaskStatusChangeEvent.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/TaskStatusChangeRequestEvent.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/process/ProcessModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/scheduling/ComputationalResourceSchedulingModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/security/AuthzToken.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/ExperimentStatus.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/JobStatus.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/ProcessStatus.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/status/TaskStatus.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/DataStagingTaskModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/EnvironmentSetupTaskModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/JobSubmissionTaskModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/MonitorTaskModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/task/TaskModel.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Gateway.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Group.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/Project.java # airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workspace/User.java Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/4fb928e1 Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/4fb928e1 Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/4fb928e1 Branch: refs/heads/data-manager Commit: 4fb928e18471d39dde50f4cf11ed436a6439c3dd Parents: e89f3ea e43b6d9 Author: scnakandala <[email protected]> Authored: Tue Jan 12 11:06:08 2016 -0500 Committer: scnakandala <[email protected]> Committed: Tue Jan 12 11:06:08 2016 -0500 ---------------------------------------------------------------------- .../server/handler/AiravataServerHandler.java | 257 +- .../java/org/apache/airavata/api/Airavata.java | 45811 ++++++++++------- .../lib/airavata/experiment_model_types.cpp | 22 + .../lib/airavata/experiment_model_types.h | 12 +- .../lib/airavata/process_model_types.cpp | 22 + .../lib/airavata/process_model_types.h | 12 +- .../lib/Airavata/Model/Experiment/Types.php | 23 + .../lib/Airavata/Model/Process/Types.php | 23 + .../apache/airavata/model/experiment/ttypes.py | 15 +- .../lib/apache/airavata/model/process/ttypes.py | 15 +- .../org/apache/airavata/model/Workflow.java | 2 +- .../ApplicationDeploymentDescription.java | 2 +- .../appdeployment/ApplicationModule.java | 2 +- .../appcatalog/appdeployment/CommandObject.java | 2 +- .../appcatalog/appdeployment/SetEnvPaths.java | 2 +- .../ApplicationInterfaceDescription.java | 2 +- .../appcatalog/computeresource/BatchQueue.java | 2 +- .../computeresource/CloudJobSubmission.java | 2 +- .../ComputeResourceDescription.java | 2 +- .../computeresource/GlobusJobSubmission.java | 2 +- .../computeresource/JobSubmissionInterface.java | 2 +- .../computeresource/LOCALSubmission.java | 2 +- .../computeresource/ResourceJobManager.java | 2 +- .../computeresource/SSHJobSubmission.java | 2 +- .../computeresource/UnicoreJobSubmission.java | 2 +- .../ComputeResourcePreference.java | 2 +- .../gatewayprofile/GatewayResourceProfile.java | 154 +- .../gatewayprofile/StoragePreference.java | 2 +- .../StorageResourceDescription.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 +- .../data/movement/DataMovementInterface.java | 2 +- .../data/movement/GridFTPDataMovement.java | 2 +- .../model/data/movement/LOCALDataMovement.java | 2 +- .../model/data/movement/SCPDataMovement.java | 2 +- .../data/movement/UnicoreDataMovement.java | 2 +- .../model/data/replica/FileReplicaModel.java | 1143 +- .../model/data/resource/DataResourceModel.java | 1837 + .../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 | 116 +- .../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 | 2 +- .../messaging/event/ProcessTerminateEvent.java | 2 +- .../model/messaging/event/TaskIdentifier.java | 2 +- .../messaging/event/TaskOutputChangeEvent.java | 2 +- .../messaging/event/TaskStatusChangeEvent.java | 2 +- .../event/TaskStatusChangeRequestEvent.java | 2 +- .../airavata/model/process/ProcessModel.java | 116 +- .../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/ProcessStatus.java | 2 +- .../airavata/model/status/TaskStatus.java | 2 +- .../model/task/DataStagingTaskModel.java | 2 +- .../model/task/EnvironmentSetupTaskModel.java | 2 +- .../model/task/JobSubmissionTaskModel.java | 2 +- .../airavata/model/task/MonitorTaskModel.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 +- .../model/util/ExperimentModelUtil.java | 1 + .../airavata/common/utils/AiravataUtils.java | 4 +- .../gfac/core/cluster/JobSubmissionOutput.java | 18 + .../gfac/core/cluster/OutputParser.java | 8 + .../gfac/core/context/ProcessContext.java | 9 + .../airavata/gfac/impl/GFacEngineImpl.java | 120 +- .../apache/airavata/gfac/impl/GFacWorker.java | 68 +- .../airavata/gfac/impl/HPCRemoteCluster.java | 6 + .../gfac/impl/job/ForkOutputParser.java | 5 + .../airavata/gfac/impl/job/LSFOutputParser.java | 5 + .../airavata/gfac/impl/job/PBSOutputParser.java | 5 + .../gfac/impl/job/SlurmOutputParser.java | 7 + .../airavata/gfac/impl/job/UGEOutputParser.java | 5 + .../impl/task/DefaultJobSubmissionTask.java | 123 +- .../gfac/impl/task/SCPDataStageTask.java | 17 +- .../gfac/monitor/email/EmailBasedMonitor.java | 26 +- .../airavata/gfac/server/GfacServerHandler.java | 72 +- .../cpi/impl/SimpleOrchestratorImpl.java | 1 + .../server/OrchestratorServerHandler.java | 33 +- .../catalog/impl/ExperimentRegistry.java | 4 + .../core/experiment/catalog/model/Process.java | 10 + .../core/experiment/catalog/model/Project.java | 11 - .../catalog/model/UserConfigurationData.java | 11 + .../catalog/resources/ProcessResource.java | 10 + .../catalog/resources/ProjectResource.java | 10 +- .../UserConfigurationDataResource.java | 10 + .../experiment/catalog/resources/Utils.java | 4 +- .../utils/ThriftDataModelConversion.java | 2 + .../src/main/resources/expcatalog-derby.sql | 14 +- .../src/main/resources/expcatalog-mysql.sql | 17 +- .../experiment_model.thrift | 1 + .../process_model.thrift | 3 +- 119 files changed, 31120 insertions(+), 19242 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/4fb928e1/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java ----------------------------------------------------------------------
