Return-Path: X-Original-To: archive-asf-public-internal@cust-asf2.ponee.io Delivered-To: archive-asf-public-internal@cust-asf2.ponee.io Received: from cust-asf.ponee.io (cust-asf.ponee.io [163.172.22.183]) by cust-asf2.ponee.io (Postfix) with ESMTP id 1B05F200C8B for ; Mon, 22 May 2017 18:19:15 +0200 (CEST) Received: by cust-asf.ponee.io (Postfix) id 19A6C160BBF; Mon, 22 May 2017 16:19:15 +0000 (UTC) Delivered-To: archive-asf-public@cust-asf.ponee.io Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by cust-asf.ponee.io (Postfix) with SMTP id 7185F160BA5 for ; Mon, 22 May 2017 18:19:12 +0200 (CEST) Received: (qmail 6063 invoked by uid 500); 22 May 2017 16:19:11 -0000 Mailing-List: contact commits-help@airavata.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: dev@airavata.apache.org Delivered-To: mailing list commits@airavata.apache.org Received: (qmail 6041 invoked by uid 99); 22 May 2017 16:19:11 -0000 Received: from git1-us-west.apache.org (HELO git1-us-west.apache.org) (140.211.11.23) by apache.org (qpsmtpd/0.29) with ESMTP; Mon, 22 May 2017 16:19:11 +0000 Received: by git1-us-west.apache.org (ASF Mail Server at git1-us-west.apache.org, from userid 33) id 5F5D1DFA33; Mon, 22 May 2017 16:19:11 +0000 (UTC) Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit From: scnakandala@apache.org To: commits@airavata.apache.org Date: Mon, 22 May 2017 16:19:16 -0000 Message-Id: <746f55316f014ac6a6a3ca81f72ce224@git.apache.org> In-Reply-To: <762d3624631547b4a6160e81988acfd5@git.apache.org> References: <762d3624631547b4a6160e81988acfd5@git.apache.org> X-Mailer: ASF-Git Admin Mailer Subject: [06/12] airavata git commit: Merge remote-tracking branch 'upstream/develop' into develop archived-at: Mon, 22 May 2017 16:19:15 -0000 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/develop Commit: 9f57e1f3d03d14423d142ee64c0815b6721d2e4e Parents: 7177cac e988672 Author: Ajinkya Dhamnaskar Authored: Wed May 17 13:59:04 2017 -0400 Committer: Ajinkya Dhamnaskar 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 - 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+- .../app/catalog/model/ResourceJobManager.java | 4 +- .../core/app/catalog/model/ScpDataMovement.java | 4 +- .../app/catalog/model/SshJobSubmission.java | 4 +- .../app/catalog/model/StorageInterface.java | 4 +- .../app/catalog/model/StorageInterface_PK.java | 4 +- .../app/catalog/model/StoragePreference.java | 4 +- .../app/catalog/model/StoragePreferencePK.java | 4 +- .../core/app/catalog/model/StorageResource.java | 4 +- .../app/catalog/model/UnicoreDataMovement.java | 6 +- .../app/catalog/model/UnicoreJobSubmission.java | 6 +- .../model/UserComputeResourcePreference.java | 10 +- .../model/UserComputeResourcePreferencePK.java | 28 +- .../app/catalog/model/UserResourceProfile.java | 4 +- .../catalog/model/UserResourceProfilePK.java | 4 +- .../catalog/model/UserStoragePreference.java | 10 +- .../catalog/model/UserStoragePreferencePK.java | 26 +- .../resources/AppCatAbstractResource.java | 4 +- .../catalog/resources/AppCatalogResource.java | 19 + 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+- .../src/main/resources/appcatalog-derby.sql | 5 + .../src/main/resources/appcatalog-mysql.sql | 5 + .../main/resources/workflowcatalog-mysql.sql | 3 +- .../airavata/app/catalog/AppDeploymentTest.java | 4 +- .../airavata/app/catalog/AppInterfaceTest.java | 4 +- ...puteAppCatalogExperimentCatResourceTest.java | 4 +- .../app/catalog/GatewayProfileTest.java | 4 +- .../catalog/StorageResourceAppCatalogTest.java | 4 +- .../app/catalog/UserResourceProfileTest.java | 4 +- .../airavata/app/catalog/util/Initialize.java | 4 +- .../catalog/AbstractResourceTest.java | 4 +- .../catalog/ExperimentInputResourceTest.java | 19 + .../catalog/ExperimentOutputResourceTest.java | 19 + .../catalog/ExperimentResourceTest.java | 19 + .../experiment/catalog/GatewayResourceTest.java | 19 + .../experiment/catalog/JobResourceTest.java | 2 +- .../experiment/catalog/ProcessResourceTest.java | 2 +- .../catalog/QueueStatusResourceTest.java | 19 + .../experiment/catalog/TaskResourceTest.java | 2 +- 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.../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(-) ----------------------------------------------------------------------