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Posted to commits@airavata.apache.org by sc...@apache.org on 2017/05/24 21:34:55 UTC
[45/61] [abbrv] airavata git commit: Merge remote-tracking branch
'upstream/develop' into develop
Merge remote-tracking branch 'upstream/develop' into develop
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/9f57e1f3
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/9f57e1f3
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/9f57e1f3
Branch: refs/heads/master
Commit: 9f57e1f3d03d14423d142ee64c0815b6721d2e4e
Parents: 7177cac e988672
Author: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Authored: Wed May 17 13:59:04 2017 -0400
Committer: Ajinkya Dhamnaskar <ad...@umail.iu.edu>
Committed: Wed May 17 13:59:04 2017 -0400
----------------------------------------------------------------------
README | 3 -
airavata-api/airavata-api-server/pom.xml | 51 +-
.../airavata/api/server/AiravataAPIServer.java | 12 +-
.../api/server/AiravataDerbyServer.java | 4 +-
.../server/handler/AiravataServerHandler.java | 193 +-
.../AiravataExperimentStatusUpdator.java | 6 +-
.../listener/ExperimentStatusChangedEvent.java | 19 +
.../security/AiravataSecurityManager.java | 43 -
.../DefaultAiravataSecurityManager.java | 273 -
.../api/server/security/IdentityContext.java | 44 -
.../airavata/api/server/security/Main.java | 179 -
.../server/security/SecurityManagerFactory.java | 60 -
.../server/security/authzcache/AuthzCache.java | 61 -
.../security/authzcache/AuthzCacheEntry.java | 63 -
.../security/authzcache/AuthzCacheIndex.java | 90 -
.../security/authzcache/AuthzCacheManager.java | 80 -
.../authzcache/AuthzCacheManagerFactory.java | 60 -
.../security/authzcache/AuthzCachedStatus.java | 34 -
.../authzcache/DefaultAuthzCacheManager.java | 106 -
.../security/interceptor/SecurityCheck.java | 36 -
.../interceptor/SecurityInterceptor.java | 83 -
.../security/interceptor/SecurityModule.java | 43 -
.../security/oauth/DefaultOAuthClient.java | 91 -
.../server/security/xacml/DefaultPAPClient.java | 125 -
.../server/security/xacml/DefaultXACMLPEP.java | 133 -
.../airavata/api/server/util/Constants.java | 4 +-
.../api/server/util/ThriftClientPool.java | 5 +-
airavata-api/airavata-api-stubs/pom.xml | 31 +-
.../java/org/apache/airavata/api/Airavata.java | 55575 ++++++++++-------
.../api/client/AiravataClientFactory.java | 4 +-
.../airavata-cpp-sdk/pom.xml | 27 +-
.../src/main/assembly/bin-assembly.xml | 29 +-
.../main/resources/lib/airavata/Airavata.cpp | 17236 ++---
.../src/main/resources/lib/airavata/Airavata.h | 1230 +-
.../lib/airavata/Airavata_server.skeleton.cpp | 30 +
.../resources/lib/airavata/airavata_api_types.h | 1 +
.../lib/airavata/airavata_data_models_types.h | 2 +
.../lib/airavata/airavata_errors_types.cpp | 205 +-
.../lib/airavata/airavata_errors_types.h | 44 +
.../application_deployment_model_types.cpp | 24 +-
.../application_deployment_model_types.h | 12 +-
.../airavata/compute_resource_model_types.cpp | 88 +
.../lib/airavata/compute_resource_model_types.h | 36 +-
.../lib/airavata/db_event_model_constants.cpp | 34 +
.../lib/airavata/db_event_model_constants.h | 41 +
.../lib/airavata/db_event_model_types.cpp | 627 +
.../lib/airavata/db_event_model_types.h | 318 +
.../lib/airavata/messaging_events_types.cpp | 8 +-
.../lib/airavata/messaging_events_types.h | 3 +-
.../airavata/replica_catalog_models_types.cpp | 726 +-
.../lib/airavata/replica_catalog_models_types.h | 274 +-
.../airavata/tenant_profile_model_constants.cpp | 34 +
.../airavata/tenant_profile_model_constants.h | 41 +
.../lib/airavata/tenant_profile_model_types.cpp | 541 +
.../lib/airavata/tenant_profile_model_types.h | 244 +
.../lib/airavata/user_profile_model_types.cpp | 239 +-
.../lib/airavata/user_profile_model_types.h | 59 +-
.../airavata-php-sdk/pom.xml | 27 +-
.../src/main/assembly/bin-assembly.xml | 29 +-
.../resources/lib/Airavata/API/Airavata.php | 11335 ++--
.../resources/lib/Airavata/API/Error/Types.php | 82 +
.../Model/AppCatalog/AppDeployment/Types.php | 25 +-
.../Model/AppCatalog/ComputeResource/Types.php | 94 +-
.../lib/Airavata/Model/Application/Io/Types.php | 6 +-
.../lib/Airavata/Model/Data/Replica/Types.php | 572 +-
.../lib/Airavata/Model/Dbevent/Types.php | 573 +
.../Airavata/Model/Messaging/Event/Types.php | 2 +
.../lib/Airavata/Model/Tenant/Types.php | 528 +
.../resources/lib/Airavata/Model/User/Types.php | 279 +-
.../src/main/resources/lib/Types.php | 13 +
.../airavata-python-sdk/pom.xml | 27 +-
.../src/main/assembly/bin-assembly.xml | 29 +-
.../lib/apache/airavata/api/Airavata-remote | 42 +
.../lib/apache/airavata/api/Airavata.py | 8090 ++-
.../lib/apache/airavata/api/error/ttypes.py | 76 +
.../resources/lib/apache/airavata/api/ttypes.py | 1 +
.../model/appcatalog/appdeployment/ttypes.py | 19 +-
.../model/appcatalog/computeresource/ttypes.py | 54 +-
.../airavata/model/data/replica/ttypes.py | 430 +-
.../apache/airavata/model/dbevent/__init__.py | 1 +
.../apache/airavata/model/dbevent/constants.py | 11 +
.../lib/apache/airavata/model/dbevent/ttypes.py | 494 +
.../airavata/model/messaging/event/ttypes.py | 3 +
.../apache/airavata/model/tenant/__init__.py | 1 +
.../apache/airavata/model/tenant/constants.py | 11 +
.../lib/apache/airavata/model/tenant/ttypes.py | 352 +
.../lib/apache/airavata/model/ttypes.py | 2 +
.../lib/apache/airavata/model/user/ttypes.py | 231 +-
.../java-client-samples/pom.xml | 26 +-
.../client/samples/CancelExperiments.java | 4 +-
.../client/samples/CreateLaunchBES.java | 3 +-
.../client/samples/CreateLaunchExperiment.java | 4 +-
.../samples/CreateLaunchExperimentUS3.java | 2 +-
.../client/samples/ReplicaCatalogSample.java | 5 +-
.../client/samples/SampleEchoExperiment.java | 4 +-
.../client/OAuthAppRegisteringClient.java | 3 +-
.../client/OAuthTokenRetrievalClient.java | 3 +-
.../client/secure/client/Properties.java | 3 +-
.../client/secure/client/SecureClient.java | 3 +-
.../tools/RegisterOGCEUS3Application.java | 6 +-
.../tools/RegisterSampleApplications.java | 5 +-
.../tools/RegisterSampleApplicationsUtils.java | 19 +
.../client/tools/RegisterUS3Application.java | 6 +-
airavata-api/airavata-client-sdks/pom.xml | 26 +-
airavata-api/airavata-data-models/pom.xml | 31 +-
.../ApplicationDeploymentDescription.java | 117 +-
.../application_deployment_modelConstants.java | 28 +-
.../application_interface_modelConstants.java | 28 +-
.../ComputeResourceDescription.java | 404 +-
.../computeresource/ResourceJobManagerType.java | 4 +
.../compute_resource_modelConstants.java | 28 +-
.../gatewayprofile/DataStoragePreference.java | 28 +-
.../application/io/InputDataObjectType.java | 63 +-
.../credential/store/SSHCredentialSummary.java | 28 +-
.../model/data/replica/DataProductModel.java | 84 +-
.../data/replica/DataReplicaLocationModel.java | 44 +-
.../apache/airavata/model/dbevent/CrudType.java | 68 +
.../airavata/model/dbevent/DBEventMessage.java | 622 +
.../model/dbevent/DBEventMessageContext.java | 387 +
.../model/dbevent/DBEventPublisher.java | 411 +
.../model/dbevent/DBEventPublisherContext.java | 641 +
.../model/dbevent/DBEventSubscriber.java | 406 +
.../airavata/model/dbevent/DBEventType.java | 62 +
.../airavata/model/dbevent/EntityType.java | 80 +
.../model/error/DuplicateEntryException.java | 413 +
.../model/messaging/event/MessageType.java | 5 +-
.../model/messaging/event/TaskSubmitEvent.java | 28 +-
.../messaging/event/TaskTerminateEvent.java | 28 +-
.../event/messaging_eventsConstants.java | 28 +-
.../apache/airavata/model/tenant/Tenant.java | 2322 +
.../model/tenant/TenantApprovalStatus.java | 77 +
.../airavata/model/user/NSFDemographics.java | 149 +-
.../apache/airavata/model/user/UserProfile.java | 882 +-
.../model/workflow_data_modelConstants.java | 28 +-
airavata-api/airavata-model-utils/pom.xml | 31 +-
.../airavata/model/util/AppDeploymentUtil.java | 4 +-
.../airavata/model/util/AppInterfaceUtil.java | 4 +-
.../model/util/ComputeResourceUtil.java | 4 +-
.../airavata/model/util/ExecutionType.java | 4 +-
.../model/util/ExperimentModelUtil.java | 4 +-
.../airavata/model/util/ProjectModelUtil.java | 2 +-
airavata-api/pom.xml | 26 +-
airavata-services/pom.xml | 70 +
.../iam-admin-services-core/pom.xml | 62 +
.../core/impl/TenantManagementKeycloakImpl.java | 351 +
.../interfaces/TenantManagementInterface.java | 101 +
.../services/core/tests/SetupNewGateway.java | 117 +
airavata-services/profile-service/pom.xml | 39 +
.../java-client-samples/pom.xml | 37 +
.../client/samples/TenantProfileSample.java | 61 +
.../client/samples/UserProfileSample.java | 124 +
.../client/util/ProfileServiceClientUtil.java | 47 +
.../resources/profile-client-sample.properties | 29 +
.../profile-service-client-sdks/pom.xml | 34 +
.../profile-service-commons/pom.xml | 117 +
.../repositories/AbstractRepository.java | 106 +
.../commons/tenant/entities/GatewayEntity.java | 254 +
.../user/entities/NSFDemographicsEntity.java | 108 +
.../user/entities/UserProfileEntity.java | 334 +
.../profile/commons/utils/Committer.java | 27 +
.../profile/commons/utils/JPAConstants.java | 34 +
.../service/profile/commons/utils/JPAUtils.java | 79 +
.../commons/utils/ObjectMapperSingleton.java | 39 +
.../profile/commons/utils/QueryConstants.java | 23 +
.../service/profile/commons/utils/Utils.java | 147 +
.../src/main/resources/META-INF/persistence.xml | 35 +
.../profile-service-server/pom.xml | 59 +
.../handlers/IamAdminServicesHandler.java | 131 +
.../handlers/TenantProfileServiceHandler.java | 194 +
.../handlers/UserProfileServiceHandler.java | 173 +
.../profile/server/ProfileServiceServer.java | 181 +
.../profile/utils/ProfileServiceUtils.java | 70 +
.../profile-service-stubs/pom.xml | 37 +
.../client/ProfileServiceClientFactory.java | 63 +
.../admin/services/cpi/IamAdminServices.java | 8240 +++
.../exception/IamAdminServicesException.java | 407 +
.../cpi/iam_admin_services_cpiConstants.java | 59 +
.../tenant/cpi/TenantProfileService.java | 8359 +++
.../TenantProfileServiceException.java | 407 +
.../tenant/cpi/profile_tenant_cpiConstants.java | 59 +
.../profile/user/cpi/UserProfileService.java | 7894 +++
.../exception/UserProfileServiceException.java | 407 +
.../user/cpi/profile_user_cpiConstants.java | 59 +
.../profile-service/profile-tenant-core/pom.xml | 40 +
.../repositories/TenantProfileRepository.java | 71 +
.../profile-service/profile-user-core/pom.xml | 85 +
.../UserProfileRegistryException.java | 28 +
.../repositories/UserProfileRepository.java | 91 +
.../src/main/resources/user_profile_catalog.sql | 84 +
.../repositories/WorkspaceRepositoryTest.java | 176 +
airavata-services/services-security/pom.xml | 92 +
.../security/AiravataSecurityManager.java | 43 +
.../DefaultAiravataSecurityManager.java | 273 +
.../service/security/IdentityContext.java | 44 +
.../security/KeyCloakSecurityManager.java | 289 +
.../apache/airavata/service/security/Main.java | 179 +
.../security/SecurityManagerFactory.java | 60 +
.../service/security/authzcache/AuthzCache.java | 61 +
.../security/authzcache/AuthzCacheEntry.java | 63 +
.../security/authzcache/AuthzCacheIndex.java | 90 +
.../security/authzcache/AuthzCacheManager.java | 80 +
.../authzcache/AuthzCacheManagerFactory.java | 60 +
.../security/authzcache/AuthzCachedStatus.java | 34 +
.../authzcache/DefaultAuthzCacheManager.java | 106 +
.../security/interceptor/SecurityCheck.java | 37 +
.../interceptor/SecurityInterceptor.java | 83 +
.../security/interceptor/SecurityModule.java | 43 +
.../security/oauth/DefaultOAuthClient.java | 91 +
.../security/xacml/DefaultPAPClient.java | 125 +
.../service/security/xacml/DefaultXACMLPEP.java | 133 +
dev-tools/ansible/.gitignore | 2 +
dev-tools/ansible/README.md | 10 +-
dev-tools/ansible/airavata-iam-setup.yml | 8 +
dev-tools/ansible/airavata.yml | 59 +
dev-tools/ansible/ansible.cfg | 2 +
dev-tools/ansible/dev_airavata_deploy.yml | 20 +
dev-tools/ansible/dev_pga_deploy.yml | 20 +
dev-tools/ansible/group_vars/.gitignore | 1 -
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dev-tools/ansible/group_vars/dev-pga.yml | 3 -
dev-tools/ansible/group_vars/local.yml.template | 4 -
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.../StorageResourceRegister.java | 19 +
.../TestFrameworkProps.java | 6 +-
.../utils/ApplicationProperties.java | 19 +
.../utils/ComputeResourceProperties.java | 19 +
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.../utils/PropertyFileType.java | 6 +-
.../utils/PropertyReader.java | 6 +-
.../utils/TestFrameworkConstants.java | 6 +-
.../main/resources/airavata-server.properties | 31 +-
modules/test-suite/pom.xml | 26 +-
modules/user-profile-migration/pom.xml | 33 +-
.../apache/airavata/ISLoginCredentialsDAO.java | 59 -
.../apache/airavata/IdentityServerClient.java | 118 -
.../airavata/KeycloakIdentityServerClient.java | 77 +
.../org/apache/airavata/MigrationManager.java | 46 +-
.../UserProfileAiravataThriftClient.java | 12 +-
.../org/apache/airavata/UserProfileDAO.java | 4 +-
.../airavata/Wso2ISLoginCredentialsDAO.java | 78 +
.../airavata/Wso2IdentityServerClient.java | 137 +
modules/user-profile/pom.xml | 29 -
.../user-profile/user-profile-service/pom.xml | 29 -
.../user/profile/server/UserProfileServer.java | 159 -
.../server/UserProfileServiceHandler.java | 139 -
modules/user-profile/user-profile-stubs/pom.xml | 63 -
.../userprofile/cpi/UserProfileService.java | 7504 ---
.../client/UserProfileServiceClientFactory.java | 43 -
.../exception/UserProfileServiceException.java | 407 -
.../cpi/user_profile_cpiConstants.java | 57 -
modules/workflow-model/pom.xml | 26 +-
modules/workflow-model/workflow-engine/pom.xml | 26 +-
.../catalog/WorkflowCatalogFactory.java | 4 +-
.../workflow/engine/WorkflowEngine.java | 4 +-
.../engine/WorkflowEngineException.java | 4 +-
.../workflow/engine/WorkflowEngineFactory.java | 4 +-
.../workflow/engine/WorkflowEngineImpl.java | 4 +-
.../airavata/workflow/engine/WorkflowUtils.java | 4 +-
.../engine/concurrent/PredicatedExecutable.java | 5 +-
.../engine/concurrent/PredicatedTaskRunner.java | 5 +-
.../engine/core/amazon/AmazonCredential.java | 4 +-
.../engine/core/amazon/EC2InstanceResult.java | 19 +
.../engine/core/generators/XmlBeansFiler.java | 4 +-
.../core/workflow/ParameterListModel.java | 4 +-
.../engine/datadriven/WorkflowHarvester.java | 4 +-
.../engine/file/XBayaPathConstants.java | 4 +-
.../engine/gfac/GFacRegistryClient.java | 4 +-
.../workflow/engine/gfac/SimpleWSClient.java | 4 +-
.../engine/globus/FileTransferConstants.java | 4 +-
.../globus/GridFTPFileTransferClient.java | 19 +
.../engine/graph/controller/NodeController.java | 19 +
.../engine/interpretor/DoWhileHandler.java | 3 +-
.../engine/interpretor/HeaderConstants.java | 4 +-
.../SSWorkflowInterpreterInteractorImpl.java | 4 +-
.../interpretor/SystemComponentInvoker.java | 4 +-
.../WorkFlowInterpreterException.java | 4 +-
.../interpretor/WorkflowExecutionMessage.java | 4 +-
.../engine/interpretor/WorkflowInterpreter.java | 4 +-
.../WorkflowInterpreterConfiguration.java | 4 +-
.../WorkflowInterpreterInteractor.java | 4 +-
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.../WorkflowInterpreterSkeleton2.java | 19 +
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.../workflow/engine/invoker/SimpleInvoker.java | 4 +-
.../engine/invoker/WorkflowInputUtil.java | 5 +-
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.../airavata/workflow/engine/util/Data.java | 4 +-
.../workflow/engine/util/GOConstants.java | 4 +-
.../workflow/engine/util/GlobusOnlineUtils.java | 19 +
.../workflow/engine/util/InterpreterUtil.java | 3 +-
.../engine/util/ProxyMonitorPublisher.java | 4 +-
.../workflow/engine/util/RegistryConstants.java | 4 +-
.../workflow/engine/util/TransferFile.java | 4 +-
.../workflow/engine/util/XBayaUtil.java | 4 +-
.../workflow/WorkflowEngineException.java | 4 +-
.../engine/workflow/proxy/ProxyWSDL.java | 4 +-
.../engine/workflow/proxy/WorkflowClient.java | 4 +-
.../engine/workflow/proxy/WorkflowContext.java | 4 +-
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.../interpreter/ComplexForEachWorkflowTest.java | 19 +
.../xbaya/interpreter/ComplexMathService.java | 4 +-
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.../airavata/xbaya/interpreter/EchoService.java | 3 +-
.../xbaya/interpreter/ForEachWorkflowTest.java | 19 +
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.../xbaya/interpreter/NotificationSender.java | 19 +
.../xbaya/interpreter/RegistryServiceTest.java | 19 +
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.../xbaya/interpreter/WorkflowTrackingTest.java | 19 +
.../xbaya/interpreter/XBayaClientTest.java | 5 +-
.../interpreter/XBayaConsolidatedTestSuite.java | 19 +
.../xbaya/interpreter/utils/ConfigKeys.java | 5 +-
.../xbaya/interpreter/utils/TestUtilServer.java | 19 +
.../interpreter/utils/WorkflowTestUtils.java | 19 +
.../workflow-model-component/pom.xml | 26 +-
.../registry/JCRComponentReference.java | 4 +-
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.../workflow-model/workflow-model-core/pom.xml | 26 +-
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.../amazon/AmazonComponentRegistry.java | 4 +-
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.../component/url/URLComponentReference.java | 4 +-
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.../component/web/WebComponentRegistry.java | 4 +-
.../model/component/ws/WSComponent.java | 4 +-
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.../model/component/ws/WSComponentPort.java | 4 +-
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.../model/component/ws/WorkflowComponent.java | 4 +-
.../exceptions/LazyLoadedDataException.java | 4 +-
.../model/exceptions/UtilsException.java | 4 +-
.../model/exceptions/WorkflowException.java | 4 +-
.../exceptions/WorkflowRuntimeException.java | 4 +-
.../airavata/workflow/model/gpel/DSCUtil.java | 4 +-
.../workflow/model/gpel/script/BPELScript.java | 4 +-
.../model/gpel/script/BPELScriptType.java | 4 +-
.../model/gpel/script/WorkflowWSDL.java | 4 +-
.../workflow/model/graph/ControlEdge.java | 4 +-
.../workflow/model/graph/ControlPort.java | 4 +-
.../airavata/workflow/model/graph/DataEdge.java | 4 +-
.../airavata/workflow/model/graph/DataPort.java | 4 +-
.../airavata/workflow/model/graph/EPRPort.java | 4 +-
.../airavata/workflow/model/graph/Edge.java | 4 +-
.../model/graph/ForEachExecutableNode.java | 5 +-
.../airavata/workflow/model/graph/Graph.java | 4 +-
.../workflow/model/graph/GraphException.java | 4 +-
.../workflow/model/graph/GraphFactory.java | 4 +-
.../workflow/model/graph/GraphPiece.java | 4 +-
.../workflow/model/graph/GraphSchema.java | 4 +-
.../airavata/workflow/model/graph/Node.java | 4 +-
.../airavata/workflow/model/graph/Port.java | 4 +-
.../model/graph/amazon/InstanceDataPort.java | 4 +-
.../model/graph/amazon/InstanceNode.java | 4 +-
.../model/graph/amazon/ResourceNode.java | 4 +-
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.../model/graph/dynamic/DynamicPort.java | 4 +-
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.../model/graph/dynamic/SchemaCompilerUtil.java | 4 +-
.../workflow/model/graph/impl/EdgeImpl.java | 4 +-
.../workflow/model/graph/impl/GraphImpl.java | 4 +-
.../workflow/model/graph/impl/NodeImpl.java | 4 +-
.../workflow/model/graph/impl/PortImpl.java | 4 +-
.../graph/subworkflow/SubWorkflowNode.java | 4 +-
.../workflow/model/graph/system/BlockNode.java | 4 +-
.../model/graph/system/ConstantNode.java | 4 +-
.../model/graph/system/DifferedInputNode.java | 7 +-
.../model/graph/system/DoWhileNode.java | 4 +-
.../model/graph/system/EndBlockNode.java | 4 +-
.../model/graph/system/EndDoWhileNode.java | 4 +-
.../model/graph/system/EndForEachNode.java | 4 +-
.../workflow/model/graph/system/EndifNode.java | 4 +-
.../workflow/model/graph/system/ExitNode.java | 4 +-
.../model/graph/system/ForEachNode.java | 4 +-
.../workflow/model/graph/system/IfNode.java | 4 +-
.../workflow/model/graph/system/InputNode.java | 4 +-
.../workflow/model/graph/system/MemoNode.java | 4 +-
.../workflow/model/graph/system/OutputNode.java | 4 +-
.../model/graph/system/ParameterNode.java | 4 +-
.../model/graph/system/ReceiveNode.java | 4 +-
.../model/graph/system/S3InputNode.java | 4 +-
.../model/graph/system/StreamSourceNode.java | 4 +-
.../model/graph/system/SystemDataPort.java | 4 +-
.../workflow/model/graph/system/SystemNode.java | 4 +-
.../workflow/model/graph/util/GraphUtil.java | 4 +-
.../workflow/model/graph/ws/WSGraph.java | 4 +-
.../workflow/model/graph/ws/WSGraphFactory.java | 4 +-
.../workflow/model/graph/ws/WSNode.java | 4 +-
.../workflow/model/graph/ws/WSPort.java | 4 +-
.../workflow/model/graph/ws/WorkflowNode.java | 4 +-
.../workflow/model/ode/ODEBPELTransformer.java | 19 +
.../airavata/workflow/model/ode/ODEClient.java | 19 +
.../model/ode/ODEDeploymentDescriptor.java | 19 +
.../workflow/model/ode/ODEWSDLTransformer.java | 19 +
.../workflow/model/ode/WSDLCleaner.java | 19 +
.../model/utils/ApplicationVersion.java | 4 +-
.../workflow/model/utils/FileConstants.java | 4 +-
.../workflow/model/utils/MessageConstants.java | 4 +-
.../workflow/model/utils/WorkflowConstants.java | 4 +-
.../model/wf/InvalidDataFormatException.java | 4 +-
.../workflow/model/wf/TridentTransformer.java | 4 +-
.../airavata/workflow/model/wf/Workflow.java | 4 +-
.../workflow/model/wf/WorkflowData.java | 4 +-
.../model/wf/WorkflowExecutionState.java | 4 +-
.../workflow/model/wf/WorkflowInput.java | 4 +-
.../workflow/model/xsd/GFacSimpleTypesXSD.java | 4 +-
.../model/xsd/LeadContextHeaderXSD.java | 4 +-
.../workflow/model/xsd/LeadCrosscutXSD.java | 4 +-
modules/workflow/pom.xml | 31 +-
modules/workflow/workflow-core/pom.xml | 31 +-
.../airavata/workflow/core/WorkflowBuilder.java | 4 +-
.../workflow/core/WorkflowEnactmentService.java | 4 +-
.../airavata/workflow/core/WorkflowFactory.java | 4 +-
.../airavata/workflow/core/WorkflowInfo.java | 3 +-
.../workflow/core/WorkflowInterpreter.java | 4 +-
.../apache/airavata/workflow/core/XMLUtil.java | 4 +-
.../airavata/workflow/core/XmlFormatter.java | 4 +-
.../workflow/core/dag/edge/DirectedEdge.java | 4 +-
.../airavata/workflow/core/dag/edge/Edge.java | 4 +-
.../core/dag/nodes/ApplicationNode.java | 4 +-
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.../workflow/core/dag/nodes/InputNode.java | 4 +-
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.../workflow/core/dag/nodes/NodeType.java | 4 +-
.../workflow/core/dag/nodes/OutputNode.java | 4 +-
.../workflow/core/dag/nodes/OutputNodeImpl.java | 4 +-
.../workflow/core/dag/nodes/WorkflowNode.java | 4 +-
.../airavata/workflow/core/dag/port/InPort.java | 4 +-
.../workflow/core/dag/port/InputPortIml.java | 4 +-
.../workflow/core/dag/port/OutPort.java | 4 +-
.../workflow/core/dag/port/OutPortImpl.java | 4 +-
.../airavata/workflow/core/dag/port/Port.java | 4 +-
.../core/parser/JsonWorkflowParser.java | 4 +-
.../workflow/core/parser/ParserException.java | 3 +-
.../workflow/core/parser/WorkflowParser.java | 4 +-
.../airavata/workflow/core/XMLUtilTest.java | 5 +-
.../core/parser/JsonWorkflowParserTest.java | 4 +-
modules/xbaya-gui/pom.xml | 26 +-
.../apache/airavata/xbaya/ThriftClientData.java | 4 +-
.../airavata/xbaya/ThriftServiceType.java | 4 +-
.../java/org/apache/airavata/xbaya/XBaya.java | 4 +-
.../airavata/xbaya/XBayaConfiguration.java | 4 +-
.../apache/airavata/xbaya/XBayaConstants.java | 4 +-
.../org/apache/airavata/xbaya/XBayaEngine.java | 4 +-
.../org/apache/airavata/xbaya/XBayaVersion.java | 4 +-
.../component/registry/ComponentController.java | 4 +-
.../registry/ComponentRegistryLoader.java | 4 +-
.../xbaya/concurrent/PredicatedExecutable.java | 5 +-
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.../xbaya/core/amazon/AmazonCredential.java | 4 +-
.../xbaya/core/amazon/EC2InstanceResult.java | 4 +-
.../xbaya/core/generators/BPELFiler.java | 4 +-
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.../xbaya/core/generators/JythonFiler.java | 4 +-
.../xbaya/core/generators/ODEScriptFiler.java | 4 +-
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.../xbaya/core/generators/WorkflowFiler.java | 4 +-
.../xbaya/core/generators/XmlBeansFiler.java | 4 +-
.../core/ide/XBayaExecutionModeListener.java | 4 +-
.../xbaya/core/workflow/ParameterListModel.java | 4 +-
.../xbaya/datadriven/WorkflowHarvester.java | 4 +-
.../airavata/xbaya/file/XBayaPathConstants.java | 4 +-
.../airavata/xbaya/gfac/GFacRegistryClient.java | 4 +-
.../airavata/xbaya/gfac/SimpleWSClient.java | 4 +-
.../xbaya/globus/FileTransferConstants.java | 4 +-
.../xbaya/globus/GridFTPFileTransferClient.java | 19 +
.../xbaya/graph/controller/NodeController.java | 4 +-
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.../GUIWorkflowInterpreterInteractorImpl.java | 19 +
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.../SSWorkflowInterpreterInteractorImpl.java | 19 +
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.../WorkFlowInterpreterException.java | 4 +-
.../interpretor/WorkflowExecutionMessage.java | 4 +-
.../interpretor/WorkflowExecutionTemplate.java | 19 +
.../xbaya/interpretor/WorkflowInterpreter.java | 19 +
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.../WorkflowInterpreterInteractor.java | 19 +
.../interpretor/WorkflowInterpreterInvoker.java | 4 +-
.../WorkflowInterpretorEventListener.java | 19 +
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.../xbaya/jython/lib/GFacServiceCreator.java | 4 +-
.../xbaya/jython/lib/NotificationSender.java | 19 +
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.../xbaya/jython/lib/WorkflowNotifiable.java | 4 +-
.../xbaya/jython/runner/JythonClassLoader.java | 4 +-
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.../jython/runner/JythonOneTimeRunnerImpl.java | 4 +-
.../xbaya/jython/runner/JythonRunner.java | 4 +-
.../xbaya/jython/script/JythonScript.java | 4 +-
.../xbaya/menues/tools/ToolsMenuItem.java | 4 +-
.../airavata/xbaya/messaging/EventData.java | 4 +-
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.../xbaya/messaging/EventDataRepository.java | 4 +-
.../airavata/xbaya/messaging/Monitor.java | 4 +-
.../xbaya/messaging/MonitorException.java | 4 +-
.../xbaya/messaging/NotificationHandler.java | 4 +-
.../airavata/xbaya/messaging/event/Event.java | 4 +-
.../xbaya/messaging/event/EventListener.java | 4 +-
.../xbaya/messaging/event/EventProducer.java | 4 +-
.../xbaya/modifier/WorkflowModifier.java | 4 +-
.../xbaya/registry/PasswordCallbackImpl.java | 19 +
.../xbaya/scufl/script/ScuflScript.java | 19 +
.../xbaya/test/util/WorkflowCreator.java | 19 +
.../org/apache/airavata/xbaya/ui/XBayaGUI.java | 4 +-
.../ui/actions/AbstractBrowserActionItem.java | 4 +-
.../ui/actions/registry/browser/AddAction.java | 4 +-
.../actions/registry/browser/BrowserAction.java | 4 +-
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.../actions/registry/browser/ImportAction.java | 4 +-
.../actions/registry/browser/RefreshAction.java | 4 +-
.../ui/actions/registry/browser/ViewAction.java | 4 +-
.../airavata/xbaya/ui/dialogs/AboutWindow.java | 4 +-
.../airavata/xbaya/ui/dialogs/ErrorWindow.java | 4 +-
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.../airavata/xbaya/ui/dialogs/TextWindow.java | 4 +-
.../airavata/xbaya/ui/dialogs/WaitDialog.java | 4 +-
.../airavata/xbaya/ui/dialogs/XBayaDialog.java | 4 +-
.../dialogs/amazon/AmazonEC2InvokerWindow.java | 4 +-
.../ui/dialogs/amazon/AmazonS3UtilsWindow.java | 4 +-
.../xbaya/ui/dialogs/amazon/BucketsLoader.java | 4 +-
.../dialogs/amazon/ChangeCredentialWindow.java | 4 +-
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.../ui/dialogs/amazon/InstancesLoader.java | 4 +-
.../xbaya/ui/dialogs/amazon/S3Downloader.java | 4 +-
.../xbaya/ui/dialogs/amazon/S3Uploader.java | 4 +-
.../ui/dialogs/component/URLRegistryWindow.java | 4 +-
.../ui/dialogs/component/WebResigtryWindow.java | 4 +-
.../amazon/InstanceConfigurationDialog.java | 4 +-
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.../graph/system/DoWhileConfigrationDialog.java | 4 +-
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.../graph/system/MemoConfigurationDialog.java | 4 +-
.../graph/system/OutputConfigurationDialog.java | 4 +-
.../system/ReceiveConfigurationDialog.java | 4 +-
.../ui/dialogs/graph/system/S3FileChooser.java | 4 +-
.../system/StreamSourceConfigurationDialog.java | 4 +-
.../graph/ws/ServiceInteractionWindow.java | 4 +-
.../xbaya/ui/dialogs/graph/ws/WSNodeWindow.java | 4 +-
.../monitor/MonitorConfigurationWindow.java | 4 +-
.../xbaya/ui/dialogs/monitor/MonitorWindow.java | 4 +-
.../dialogs/registry/NewRegistryUserDialog.java | 4 +-
.../ui/dialogs/registry/RegistryWindow.java | 4 +-
.../registry/browser/JCRBrowserDialog.java | 4 +-
.../workflow/ParameterPropertyWindow.java | 4 +-
.../dialogs/workflow/WorkflowImportWindow.java | 4 +-
.../workflow/WorkflowPropertyWindow.java | 4 +-
.../xbaya/ui/experiment/ExperimentMenu.java | 4 +-
.../ui/experiment/LaunchApplicationWindow.java | 4 +-
.../ui/experiment/RegistrySearchResult.java | 4 +-
.../RegistryWorkflowPublisherWindow.java | 4 +-
.../WorkflowInterpreterLaunchWindow.java | 4 +-
.../apache/airavata/xbaya/ui/graph/EdgeGUI.java | 4 +-
.../airavata/xbaya/ui/graph/GraphCanvas.java | 4 +-
.../xbaya/ui/graph/GraphCanvasEvent.java | 4 +-
.../xbaya/ui/graph/GraphCanvasListener.java | 4 +-
.../airavata/xbaya/ui/graph/GraphGUI.java | 4 +-
.../airavata/xbaya/ui/graph/GraphPieceGUI.java | 4 +-
.../apache/airavata/xbaya/ui/graph/NodeGUI.java | 4 +-
.../airavata/xbaya/ui/graph/Paintable.java | 4 +-
.../apache/airavata/xbaya/ui/graph/PortGUI.java | 4 +-
.../xbaya/ui/graph/amazon/InstanceNodeGUI.java | 4 +-
.../graph/amazon/TerminateInstanceNodeGUI.java | 4 +-
.../graph/subworkflow/SubWorkflowNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/BlockNodeGUI.java | 4 +-
.../ui/graph/system/ConfigurableNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ConstantNodeGUI.java | 4 +-
.../ui/graph/system/DifferedInputHandler.java | 3 +-
.../ui/graph/system/DifferedInputNodeGUI.java | 3 +-
.../xbaya/ui/graph/system/DoWhileNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/EndBlockNodeGUI.java | 4 +-
.../ui/graph/system/EndDoWhileNodeGUI.java | 4 +-
.../ui/graph/system/EndForEachNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/EndifNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ExitNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ForEachNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/IfNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/InputNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/MemoNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/OutputNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ReceiveNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/S3InputNodeGUI.java | 4 +-
.../ui/graph/system/StreamSourceNodeGUI.java | 4 +-
.../airavata/xbaya/ui/graph/ws/WSNodeGUI.java | 4 +-
.../xbaya/ui/graph/ws/WorkflowNodeGUI.java | 4 +-
.../xbaya/ui/menues/AmazonEC2MenuItem.java | 4 +-
.../xbaya/ui/menues/ApplicationMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/EditMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/MenuIcons.java | 4 +-
.../xbaya/ui/menues/RegistryMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/RunMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/ViewMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/XBayaMenu.java | 4 +-
.../airavata/xbaya/ui/menues/XBayaMenuItem.java | 4 +-
.../xbaya/ui/monitor/MonitorEventHandler.java | 4 +-
.../xbaya/ui/monitor/MonitorStarter.java | 4 +-
.../xbaya/ui/monitor/ResourcePaintable.java | 4 +-
.../airavata/xbaya/ui/utils/Cancelable.java | 4 +-
.../airavata/xbaya/ui/utils/DrawUtils.java | 4 +-
.../airavata/xbaya/ui/utils/ErrorMessages.java | 4 +-
.../xbaya/ui/views/ComponentViewer.java | 4 +-
.../xbaya/ui/views/JCRBrowserPanel.java | 19 +
.../airavata/xbaya/ui/views/MonitorPanel.java | 4 +-
.../xbaya/ui/views/ParameterPropertyPanel.java | 4 +-
.../airavata/xbaya/ui/views/PortViewer.java | 4 +-
.../airavata/xbaya/ui/widgets/GridPanel.java | 4 +-
.../airavata/xbaya/ui/widgets/ScrollPanel.java | 4 +-
.../xbaya/ui/widgets/TabLabelButton.java | 4 +-
.../xbaya/ui/widgets/TableRenderable.java | 4 +-
.../xbaya/ui/widgets/ToolbarButton.java | 4 +-
.../xbaya/ui/widgets/XBayaComboBox.java | 4 +-
.../xbaya/ui/widgets/XBayaComponent.java | 4 +-
.../airavata/xbaya/ui/widgets/XBayaLabel.java | 3 +-
.../xbaya/ui/widgets/XBayaLinkButton.java | 4 +-
.../airavata/xbaya/ui/widgets/XBayaList.java | 4 +-
.../xbaya/ui/widgets/XBayaTextArea.java | 4 +-
.../xbaya/ui/widgets/XBayaTextComponent.java | 4 +-
.../xbaya/ui/widgets/XBayaTextField.java | 4 +-
.../airavata/xbaya/ui/widgets/XBayaToolBar.java | 4 +-
.../xbaya/ui/widgets/XbayaEnhancedList.java | 4 +-
.../xbaya/ui/widgets/amazon/S3Tree.java | 4 +-
.../xbaya/ui/widgets/amazon/S3TreeModel.java | 4 +-
.../ui/widgets/component/ComponentSelector.java | 4 +-
.../component/ComponentSelectorEvent.java | 4 +-
.../component/ComponentSelectorListener.java | 4 +-
.../component/ComponentSourceTransferable.java | 4 +-
.../widgets/component/ComponentTreeModel.java | 4 +-
.../ui/widgets/component/ComponentTreeNode.java | 4 +-
.../apache/airavata/xbaya/util/AmazonUtil.java | 4 +-
.../org/apache/airavata/xbaya/util/Data.java | 4 +-
.../apache/airavata/xbaya/util/GOConstants.java | 4 +-
.../airavata/xbaya/util/GlobusOnlineUtils.java | 19 +
.../airavata/xbaya/util/RegistryConstants.java | 4 +-
.../airavata/xbaya/util/TransferFile.java | 4 +-
.../apache/airavata/xbaya/util/XBayaUtil.java | 4 +-
.../airavata/xbaya/workflow/WorkflowClient.java | 4 +-
.../xbaya/workflow/WorkflowEngineException.java | 4 +-
.../xbaya/workflow/proxy/ProxyWSDL.java | 4 +-
.../xbaya/workflow/proxy/WorkflowClient.java | 4 +-
.../xbaya/workflow/proxy/WorkflowContext.java | 4 +-
.../workflow/proxy/WorkflowProxyException.java | 4 +-
.../interpreter/ComplexForEachWorkflowTest.java | 19 +
.../xbaya/interpreter/ComplexMathService.java | 4 +-
.../interpreter/ComplexMathWorkflowTest.java | 19 +
.../interpreter/CrossProductWorkflowTest.java | 19 +
.../airavata/xbaya/interpreter/EchoService.java | 3 +-
.../xbaya/interpreter/ForEachWorkflowTest.java | 19 +
.../interpreter/LevenshteinDistanceService.java | 4 +-
.../airavata/xbaya/interpreter/Listener.java | 19 +
.../xbaya/interpreter/NotificationSender.java | 19 +
.../xbaya/interpreter/RegistryServiceTest.java | 19 +
.../interpreter/SimpleForEachWorkflowTest.java | 19 +
.../interpreter/SimpleMathWorkflowTest.java | 19 +
.../xbaya/interpreter/WorkflowTest.java | 19 +
.../xbaya/interpreter/WorkflowTrackingTest.java | 19 +
.../xbaya/interpreter/XBayaClientTest.java | 5 +-
.../interpreter/XBayaConsolidatedTestSuite.java | 19 +
.../xbaya/interpreter/utils/ConfigKeys.java | 5 +-
.../xbaya/interpreter/utils/TestUtilServer.java | 19 +
.../interpreter/utils/WorkflowTestUtils.java | 19 +
pom.xml | 102 +-
sandbox/amqpwstunnel/python/amqpwstunnel.py | 20 +
sandbox/amqpwstunnel/wstest.html | 21 +
sandbox/job-status-rest-server/api_test.py | 20 +
sandbox/job-status-rest-server/app.py | 20 +
.../example/logfile_checker/generate_logs.sh | 20 +
.../example/logfile_checker/log_consumer.py | 20 +
.../example/logfile_checker/log_streamer.py | 20 +
.../simstream/example/logfile_checker/test.txt | 20 +
.../example/mem_streamer/memory_consumption.py | 20 +
.../example/mem_streamer/memory_streamer.py | 20 +
.../application/alanine_dipeptide.py | 20 +
.../example/openmm_example/openmm_consumer.py | 20 +
.../openmm_example/openmm_log_consumer.py | 20 +
.../openmm_example/openmm_rmsd_consumer.py | 20 +
.../example/openmm_example/openmm_streamer.py | 20 +
.../simstream/example/openmm_example/test.txt | 20 +
sandbox/simstream/setup.py | 20 +
sandbox/simstream/simstream/__init__.py | 20 +
sandbox/simstream/simstream/datacollector.py | 20 +
sandbox/simstream/simstream/datareporter.py | 20 +
sandbox/simstream/simstream/eventhandler.py | 20 +
sandbox/simstream/simstream/eventmonitor.py | 20 +
.../simstream/simstream/pikaasyncconsumer.py | 20 +
sandbox/simstream/simstream/pikaproducer.py | 20 +
sandbox/simstream/simstream/simstream.py | 20 +
.../airavata-apis/airavata_api.thrift | 42 +-
.../airavata-apis/airavata_errors.thrift | 9 +
.../airavata-apis/db_event_model.thrift | 81 +
.../airavata-apis/messaging_events.thrift | 3 +-
.../component-cpis/generate-cpi-stubs.sh | 32 +-
.../component-cpis/registry-api.thrift | 20 +-
.../component-cpis/user-profile-cpi.thrift | 2 +-
.../data-models/airavata_data_models.thrift | 6 +-
.../application_deployment_model.thrift | 3 +-
.../replica_catalog_models.thrift | 31 +-
.../compute_resource_model.thrift | 6 +-
.../user_resource_profile_model.thrift | 2 +-
.../group_manager_model.thrift | 48 -
.../user-group-models/user_profile_model.thrift | 185 -
.../group_manager_model.thrift | 48 +
.../tenant_profile_model.thrift | 58 +
.../user_profile_model.thrift | 196 +
.../generate-thrift-stubs.sh | 42 +-
.../service-cpis/generate-service-cpi-stubs.sh | 181 +
.../iam-admin-services-cpi.thrift | 81 +
.../iam_admin_services_cpi_errors.thrift | 32 +
.../profile-service/profile-service-cpi.thrift | 34 +
.../profile-tenant/profile-tenant-cpi.thrift | 70 +
.../profile_tenant_cpi_errors.thrift | 32 +
.../profile-user/profile-user-cpi.thrift | 74 +
.../profile-user/profile_user_cpi_errors.thrift | 32 +
tools/gsissh-cli-tools/README.txt | 20 +
tools/gsissh-cli-tools/pom.xml | 29 +-
.../ssh/cli/SSHApiClientWithMyProxyAuth.java | 4 +-
tools/phoebus-integration/pom.xml | 26 +-
.../impl/PhoebusGridConfigurationHandler.java | 4 +-
.../airavata/core/gfac/utils/PhoebusUtils.java | 4 +-
tools/pom.xml | 26 +-
tools/rabbitmq-download-start.sh | 20 +
1792 files changed, 137341 insertions(+), 66743 deletions(-)
----------------------------------------------------------------------