merging with master
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/e197005d Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/e197005d Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/e197005d Branch: refs/heads/gfac-storm Commit: e197005dad3c38888fa929c3dc0f4e53bdc8a890 Parents: ce7e8f9 7f89880 Author: Lahiru Gunathilake <[email protected]> Authored: Fri Feb 6 11:05:08 2015 -0500 Committer: Lahiru Gunathilake <[email protected]> Committed: Fri Feb 6 11:05:08 2015 -0500 ---------------------------------------------------------------------- INSTALL | 12 +- README | 59 +- RELEASE_NOTES | 74 + airavata-api/airavata-api-server/pom.xml | 2 +- .../airavata/api/server/AiravataAPIServer.java | 2 +- .../api/server/AiravataDerbyServer.java | 2 +- .../server/handler/AiravataServerHandler.java | 30 +- .../util/AiravataServerThreadPoolExecutor.java | 24 +- .../api/server/util/ConnectionPool.java | 8 +- .../api/server/util/DataModelUtils.java | 10 +- .../airavata/api/server/util/JdbcStorage.java | 3 +- airavata-api/airavata-api-stubs/pom.xml | 2 +- .../java/org/apache/airavata/api/Airavata.java | 25087 +++++++++-------- .../airavata-cpp-sdk/pom.xml | 2 +- .../airavata-cpp-sdk/src/main/resources/INSTALL | 3 +- .../airavata-client-properties.ini | 17 + .../main/resources/lib/airavata/Airavata.cpp | 396 +- .../src/main/resources/lib/airavata/Airavata.h | 143 + .../lib/airavata/Airavata_server.skeleton.cpp | 5 + .../applicationDeploymentModel_types.cpp | 96 +- .../airavata/applicationDeploymentModel_types.h | 28 +- .../applicationInterfaceModel_types.cpp | 216 +- .../airavata/applicationInterfaceModel_types.h | 139 +- .../lib/airavata/experimentModel_types.cpp | 394 +- .../lib/airavata/experimentModel_types.h | 64 +- .../lib/airavata/messagingEvents_types.cpp | 4 +- .../lib/airavata/messagingEvents_types.h | 4 +- .../lib/airavata/workflowDataModel_types.cpp | 4 +- .../lib/airavata/workflowDataModel_types.h | 4 +- .../airavata-php-sdk/pom.xml | 2 +- .../conf/airavata-client-properties.ini | 21 + .../resources/conf/app-catalog-identifiers.ini | 17 + .../resources/lib/Airavata/API/Airavata.php | 294 +- .../Model/AppCatalog/AppDeployment/Types.php | 108 +- .../Model/AppCatalog/AppInterface/Types.php | 169 +- .../Model/Workspace/Experiment/Types.php | 416 +- .../resources/lib/AiravataClientFactory.php | 17 + .../java-client-samples/pom.xml | 5 +- .../client/samples/CreateLaunchExperiment.java | 1745 ++ .../client/samples/RegisterSampleData.java | 138 +- .../tools/RegisterOGCEUS3Application.java | 31 +- .../tools/RegisterSampleApplications.java | 204 +- .../tools/RegisterSampleApplicationsUtils.java | 30 +- .../client/tools/RegisterUS3Application.java | 33 +- airavata-api/airavata-client-sdks/pom.xml | 2 +- airavata-api/airavata-data-models/pom.xml | 2 +- .../ApplicationDeploymentDescription.java | 394 +- .../appinterface/CommandLineType.java | 62 - .../appinterface/InputDataObjectType.java | 258 +- .../appinterface/OutputDataObjectType.java | 562 +- .../appcatalog/appinterface/ValidityType.java | 62 - .../model/workspace/experiment/Experiment.java | 524 +- .../workspace/experiment/ExperimentSummary.java | 36 +- .../model/workspace/experiment/TaskDetails.java | 362 +- .../workspace/experiment/ValidationResults.java | 36 +- .../experiment/WorkflowNodeDetails.java | 144 +- airavata-api/airavata-model-utils/pom.xml | 2 +- .../model/util/ExperimentModelUtil.java | 10 + airavata-api/generate-thrift-files.sh | 2 +- airavata-api/pom.xml | 2 +- .../airavataAPI.thrift | 10 + .../applicationDeploymentModel.thrift | 2 + .../applicationInterfaceModel.thrift | 30 +- .../experimentModel.thrift | 22 +- modules/airavata-client/pom.xml | 88 - .../airavata/client/AiravataAPIFactory.java | 60 - .../airavata/client/AiravataAPIUtils.java | 86 - .../apache/airavata/client/AiravataClient.java | 353 - .../client/AiravataClientConfiguration.java | 106 - .../client/RegistryServiceCallbackHandler.java | 65 - 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.../airavata/ws/monitor/MonitorEvent.java | 33 - .../airavata/ws/monitor/MonitorEventData.java | 27 - .../ws/monitor/MonitorEventListener.java | 31 - .../airavata/ws/monitor/MonitorException.java | 62 - .../apache/airavata/ws/monitor/MonitorUtil.java | 627 - .../apache/airavata/ws/monitor/WsmgClient.java | 165 - .../apache/airavata/ws/monitor/event/Event.java | 84 - .../ws/monitor/event/EventListener.java | 35 - .../ws/monitor/event/EventProducer.java | 105 - .../ws-messenger/messagebox/maven-eclipse.xml | 16 - modules/ws-messenger/messagebox/pom.xml | 95 - .../wsmg/msgbox/MsgBoxServiceLifeCycle.java | 192 - .../MsgBoxServiceMessageReceiverInOut.java | 138 - .../wsmg/msgbox/MsgBoxServiceSkeleton.java | 186 - .../wsmg/msgbox/Storage/MsgBoxStorage.java | 59 - .../Storage/dbpool/DatabaseStorageImpl.java | 125 - .../msgbox/Storage/dbpool/MessageBoxDB.java | 265 - .../msgbox/Storage/memory/InMemoryImpl.java | 133 - .../wsmg/msgbox/StoreMessageHandler.java | 123 - .../airavata/wsmg/msgbox/util/ConfigKeys.java | 36 - 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.../wsmg/commons/util/OMElementComparator.java | 177 - .../airavata/wsmg/config/WSMGParameter.java | 48 - .../wsmg/config/WsmgConfigurationContext.java | 118 - .../wsmg/matching/AbstractMessageMatcher.java | 89 - .../wsmg/matching/XPath/YFilterInfo.java | 156 - .../matching/XPath/YFilterMessageMatcher.java | 183 - .../simpleTopic/DirectWsntMessageMatcher.java | 125 - .../wsmg/messenger/ConsumerUrlManager.java | 195 - .../airavata/wsmg/messenger/Deliverable.java | 32 - .../wsmg/messenger/DeliveryProcessor.java | 90 - .../airavata/wsmg/messenger/OutGoingQueue.java | 65 - .../airavata/wsmg/messenger/SenderUtils.java | 161 - .../messenger/protocol/DeliveryProtocol.java | 34 - .../messenger/protocol/SendingException.java | 37 - .../messenger/protocol/impl/Axis2Protocol.java | 156 - .../messenger/strategy/SendingStrategy.java | 33 - .../strategy/impl/ConsumerHandler.java | 71 - .../strategy/impl/FixedParallelSender.java | 185 - .../messenger/strategy/impl/LightweightMsg.java | 54 - .../messenger/strategy/impl/ParallelSender.java | 155 - .../messenger/strategy/impl/SerialSender.java | 75 - .../apache/airavata/wsmg/util/BrokerUtil.java | 121 - .../org/apache/airavata/wsmg/util/Counter.java | 77 - .../airavata/wsmg/util/RunTimeStatistics.java | 157 - .../apache/airavata/wsmg/util/TimerThread.java | 87 - .../wsmg/util/WsEventingOperations.java | 55 - .../wsmg/util/WsNotificationOperations.java | 56 - .../database_scripts/cleanDBScript.sql | 27 - .../database_scripts/msgBroker-derby.sql | 60 - .../database_scripts/msgBroker-mysql.sql | 61 - .../src/main/resources/services.xml | 125 - .../airavata/wsmg/broker/BrokerWSETest.java | 107 - .../airavata/wsmg/broker/BrokerWSNTTest.java | 108 - .../wsmg/commons/TestCommonRoutines.java | 57 - .../TestAddtionalWseXpathAndTopicScenarios.java | 151 - .../XPath/TestWseXpathAndTopicSubscription.java | 137 - .../XPath/TestWseXpathSubscription.java | 139 - .../matching/XPath/performance/XppXPath.java | 269 - .../rtt/NotificationManager.java | 151 - .../rtt/PerformanceTest.java | 399 - .../rtt/PublisherThread.java | 99 - .../rtt/StatCalculatorThread.java | 103 - .../rtt/StatContainer.java | 49 - .../performance_evaluator/rtt/Subscription.java | 107 - .../rtt/util/ConfigKeys.java | 43 - .../rtt/util/LoadMsgPayload.java | 66 - .../rtt/util/LoadXpath.java | 66 - .../airavata/wsmg/util/BrokerUtilTest.java | 167 - .../apache/airavata/wsmg/util/ConfigKeys.java | 34 - .../airavata/wsmg/util/TestUtilServer.java | 225 - .../src/test/resources/unit_tests.properties | 24 - modules/ws-messenger/pom.xml | 162 - modules/xbaya-gui/pom.xml | 2 +- .../java/org/apache/airavata/xbaya/XBaya.java | 5 +- .../airavata/xbaya/XBayaConfiguration.java | 4 +- .../org/apache/airavata/xbaya/XBayaEngine.java | 4 +- .../xbaya/concurrent/PredicatedTaskRunner.java | 6 +- .../xbaya/core/generators/ODEScriptFiler.java | 5 +- .../xbaya/globus/GridFTPFileTransferClient.java | 44 +- .../interpretor/SystemComponentInvoker.java | 6 +- .../airavata/xbaya/invoker/DynamicInvoker.java | 9 +- .../invoker/MsgBoxWsaResponsesCorrelator.java | 95 +- .../airavata/xbaya/invoker/SimpleInvoker.java | 2 +- .../xbaya/jython/lib/NotificationSender.java | 578 +- .../jython/lib/ServiceNotificationSender.java | 586 +- .../xbaya/jython/runner/JythonClassLoader.java | 8 +- .../xbaya/jython/script/JythonScript.java | 11 +- .../xbaya/lead/LeadContextHeaderHelper.java | 21 +- .../xbaya/lead/NotificationHandler.java | 49 +- .../xbaya/messaging/EventDataRepository.java | 15 +- .../airavata/xbaya/messaging/Monitor.java | 4 +- .../org/apache/airavata/xbaya/ui/XBayaGUI.java | 4 +- .../graph/dynamic/DynamicNodeWindow.java | 10 +- .../monitor/MonitorConfigurationWindow.java | 15 +- .../dialogs/registry/NewRegistryUserDialog.java | 1 - .../registry/browser/JCRBrowserDialog.java | 5 +- .../dialogs/workflow/WorkflowImportWindow.java | 14 +- .../ui/experiment/LaunchApplicationWindow.java | 58 +- .../RegistryWorkflowPublisherWindow.java | 1 - .../WorkflowInterpreterLaunchWindow.java | 2 +- .../airavata/xbaya/ui/graph/GraphCanvas.java | 2 +- .../xbaya/ui/menues/ApplicationMenuItem.java | 21 + .../xbaya/ui/monitor/MonitorEventHandler.java | 19 +- .../apache/airavata/xbaya/util/XBayaUtil.java | 2 +- .../airavata/xbaya/interpreter/Listener.java | 64 +- .../xbaya/interpreter/NotificationSender.java | 408 +- pom.xml | 726 + tools/gsissh/pom.xml | 2 +- tools/gsissh/src/main/java/SSHDemo.java | 7 +- .../illinois/ncsa/BCGSS/GlobusTlsClient.java | 7 +- .../apache/airavata/gsi/ssh/GSSContextX509.java | 5 +- .../airavata/gsi/ssh/api/job/JobDescriptor.java | 36 + .../gsi/ssh/impl/GSISSHAbstractCluster.java | 21 +- .../gsi/ssh/impl/StandardOutReader.java | 5 +- .../gsi/ssh/impl/SystemCommandOutput.java | 5 +- .../apache/airavata/gsi/ssh/util/SSHUtils.java | 51 +- .../gsissh/src/main/resources/PBSTemplate.xslt | 5 + .../src/main/resources/SLURMTemplate.xslt | 4 + .../main/resources/schemas/PBSJobDescriptor.xsd | 6 + .../impl/DefaultSSHApiTestWithMyProxyAuth.java | 4 +- tools/pom.xml | 2 +- tools/registry-tool/pom.xml | 2 +- .../airavata/registry/tool/DBMigrator.java | 9 +- 679 files changed, 37614 insertions(+), 64533 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/airavata-api/airavata-client-sdks/java-client-samples/pom.xml ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/app-catalog/app-catalog-data/src/main/java/org/apache/aiaravata/application/catalog/data/util/AppCatalogJPAUtils.java ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/commons/utils/src/main/java/org/apache/airavata/common/utils/ApplicationSettings.java ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/gfac/gfac-core/pom.xml ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java ---------------------------------------------------------------------- diff --cc modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java index c81a179,00d313c..67815f4 --- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java +++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/cpi/BetterGfacImpl.java @@@ -301,14 -297,8 +297,7 @@@ public class BetterGfacImpl implements // List<InputDataObjectType> experimentInputs = experiment.getExperimentInputs(); // jobExecutionContext.setInMessageContext(new MessageContext(GFacUtils.getInputParamMap(experimentInputs))); List<InputDataObjectType> taskInputs = taskData.getApplicationInputs(); - jobExecutionContext.setInMessageContext(new MessageContext(GFacUtils.getInputParamMap(taskInputs))); - // List<OutputDataObjectType> outputData = experiment.getExperimentOutputs(); - List<OutputDataObjectType> taskOutputs = taskData.getApplicationOutputs(); - if (taskOutputs == null || taskOutputs.isEmpty() ){ - taskOutputs = applicationInterface.getApplicationOutputs(); - } - jobExecutionContext.setOutMessageContext(new MessageContext(GFacUtils.getOuputParamMap(taskOutputs))); - jobExecutionContext.setProperty(Constants.PROP_TOPIC, experimentID); jobExecutionContext.setGfac(this); jobExecutionContext.setZk(zk); http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/utils/GFacUtils.java ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/gfac/gfac-ec2/pom.xml ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/gfac/gfac-local/pom.xml ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/gfac/pom.xml ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/orchestrator/orchestrator-core/pom.xml ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/ExperimentRegistry.java ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/RegistryImpl.java ---------------------------------------------------------------------- diff --cc modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/RegistryImpl.java index f619e1f,ec60bd4..8359044 --- a/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/RegistryImpl.java +++ b/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/impl/RegistryImpl.java @@@ -63,8 -62,8 +63,9 @@@ public class RegistryImpl implements Re experimentRegistry = new ExperimentRegistry(gatewayResource, user); projectRegistry = new ProjectRegistry(gatewayResource, user); } catch (ApplicationSettingsException e) { + e.printStackTrace(); logger.error("Unable to read airavata server properties..", e); + throw new RegistryException("Unable to read airavata server properties..", e); } } http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/modules/registry/airavata-jpa-registry/src/main/java/org/apache/airavata/persistance/registry/jpa/resources/AbstractResource.java ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/e197005d/tools/gsissh/pom.xml ----------------------------------------------------------------------
