Merge moduleRefactor branch
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/b4ede9cb Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/b4ede9cb Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/b4ede9cb Branch: refs/heads/master Commit: b4ede9cbec6089b32d0dc856cc57aea27616197b Parents: 4d9ed53 08e3a87 Author: Shameera Rathanyaka <[email protected]> Authored: Thu Jun 4 16:14:48 2015 -0400 Committer: Shameera Rathanyaka <[email protected]> Committed: Thu Jun 4 16:14:48 2015 -0400 ---------------------------------------------------------------------- airavata-api/airavata-api-server/pom.xml | 2 +- airavata-api/generate-thrift-files.sh | 305 -- .../airavataAPI.thrift | 2064 -------- .../airavataDataModel.thrift | 38 - .../airavataErrors.thrift | 172 - .../appCatalogModels.thrift | 24 - .../applicationDeploymentModel.thrift | 132 - .../applicationInterfaceModel.thrift | 146 - .../computeResourceModel.thrift | 445 -- .../experimentModel.thrift | 411 -- .../gatewayResourceProfileModel.thrift | 83 - .../messagingEvents.thrift | 149 - .../securityModel.thrift | 35 - .../workflowAPI.thrift | 82 - .../workflowDataModel.thrift | 43 - .../workspaceModel.thrift | 63 - .../airavata-api/airavataAPI.thrift | 2064 ++++++++ .../airavata-api/airavataDataModel.thrift | 38 + .../airavata-api/airavataErrors.thrift | 172 + .../airavata-api/appCatalogModels.thrift | 24 + .../applicationDeploymentModel.thrift | 132 + .../applicationInterfaceModel.thrift | 146 + .../airavata-api/computeResourceModel.thrift | 445 ++ .../airavata-api/experimentModel.thrift | 411 ++ .../gatewayResourceProfileModel.thrift | 83 + .../airavata-api/generate-thrift-files.sh | 305 ++ .../airavata-api/messagingEvents.thrift | 149 + .../airavata-api/securityModel.thrift | 35 + .../airavata-api/workflowAPI.thrift | 82 + .../airavata-api/workflowDataModel.thrift | 43 + .../airavata-api/workspaceModel.thrift | 63 + .../gfac/generate-gfac-stubs.sh | 134 + .../gfac/gfac.cpi.service.thrift | 68 + .../gfac/gfacDataModel.thrift | 64 + .../orchestrator/generate-orchestrator-stubs.sh | 132 + .../orchestrator.cpi.service.thrift | 78 + distribution/pom.xml | 581 +++ distribution/src/main/assembly/bin-assembly.xml | 189 + distribution/src/main/assembly/src-assembly.xml | 75 + distribution/src/main/resources/INSTALL | 30 + distribution/src/main/resources/LICENSE | 2387 +++++++++ distribution/src/main/resources/NOTICE | 163 + distribution/src/main/resources/README | 145 + .../src/main/resources/bin/airavata-server.bat | 55 + .../src/main/resources/bin/airavata-server.sh | 118 + .../src/main/resources/bin/api-server.sh | 118 + distribution/src/main/resources/bin/derby.sh | 23 + .../src/main/resources/bin/gfac-server.sh | 118 + distribution/src/main/resources/bin/logo.txt | 34 + .../main/resources/bin/orchestrator-server.sh | 118 + distribution/src/main/resources/bin/setenv.bat | 43 + distribution/src/main/resources/bin/setenv.sh | 77 + 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39 - .../src/main/assembly/api-server-component.xml | 35 - .../new-dist/src/main/assembly/src-assembly.xml | 75 - .../new-dist/src/main/resources/INSTALL | 30 - .../new-dist/src/main/resources/LICENSE | 2387 --------- .../new-dist/src/main/resources/NOTICE | 163 - .../new-dist/src/main/resources/README | 145 - .../src/main/resources/bin/airavata-server.bat | 55 - .../src/main/resources/bin/airavata-server.sh | 118 - .../new-dist/src/main/resources/bin/derby.sh | 23 - .../new-dist/src/main/resources/bin/logo.txt | 34 - .../new-dist/src/main/resources/bin/setenv.bat | 43 - .../new-dist/src/main/resources/bin/setenv.sh | 77 - .../src/main/resources/bin/startNetworkServer | 189 - .../main/resources/samples/registerSample.sh | 25 - .../src/main/resources/samples/scripts/add.sh | 21 - .../src/main/resources/samples/scripts/echo.sh | 22 - .../main/resources/samples/scripts/multiply.sh | 22 - .../main/resources/samples/scripts/subtract.sh | 22 - .../distribution/orchestrator-server/pom.xml | 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.../xbaya-gui/src/main/resources/README | 101 - .../src/main/resources/airavata-logo.gif | Bin 13895 -> 0 bytes .../xbaya-gui/src/main/resources/bin/setenv.bat | 42 - .../xbaya-gui/src/main/resources/bin/setenv.sh | 77 - .../src/main/resources/bin/xbaya-gui.bat | 23 - .../src/main/resources/bin/xbaya-gui.sh | 22 - .../src/main/resources/conf/log4j.properties | 40 - .../xbaya-gui/src/main/resources/jnlp/INSTALL | 48 - .../xbaya-gui/src/main/resources/jnlp/LICENSE | 2272 --------- .../xbaya-gui/src/main/resources/jnlp/NOTICE | 163 - .../xbaya-gui/src/main/resources/jnlp/README | 91 - .../src/main/resources/jnlp/xbaya.jnlp | 42 - .../xbaya-gui/src/main/resources/xbaya.jks | Bin 2234 -> 0 bytes modules/gfac/airavata-gfac-service/pom.xml | 95 - .../apache/airavata/gfac/cpi/GfacService.java | 3170 ------------ .../gfac/cpi/gfac_cpi_serviceConstants.java | 55 - .../apache/airavata/gfac/server/GfacServer.java | 143 - .../airavata/gfac/server/GfacServerHandler.java | 421 -- 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.../src/main/resources/schema/Resource.json | 27 + .../src/main/resources/schema/Service.json | 75 + .../src/main/resources/schema/Share.json | 45 + .../resources/schema/StorageAccessProtocol.json | 32 + .../main/resources/schema/StorageEndpoint.json | 8 + .../main/resources/schema/StorageManager.json | 8 + .../main/resources/schema/StorageService.json | 22 + .../schema/StorageServiceCapacity.json | 33 + .../src/main/resources/schema/StorageShare.json | 65 + .../resources/schema/StorageShareCapacity.json | 33 + .../resources/schema/ToComputingService.json | 32 + .../main/resources/schema/ToStorageService.json | 25 + .../src/main/resources/schema/UserDomain.json | 58 + .../main/resources/schemas/PBSJobDescriptor.xsd | 114 + .../resources/schemas/gsissh-schemas.xsdconfig | 14 + .../src/main/resources/service.properties | 58 + .../services/impl/BigRed2TestWithSSHAuth.java | 252 + .../gfac/services/impl/CredentialStoreTest.java | 135 + .../impl/GSISSHProviderTestWithMyProxyAuth.java | 229 + .../gfac/services/impl/LocalProviderTest.java | 184 + .../impl/SSHProviderTestWithSSHAuth.java | 172 + .../GSISecurityContextTestWithMyProxyAuth.java | 163 + .../gfac/ssh/config/ConfigReaderTest.java | 38 + .../impl/DefaultSSHApiTestWithMyProxyAuth.java | 84 + .../gfac/ssh/impl/VanilaTestWithSSHAuth.java | 264 + .../apache/airavata/job/AMQPMonitorTest.java | 208 + .../job/QstatMonitorTestWithMyProxyAuth.java | 172 + .../src/test/resources/PBSTemplate.xslt | 73 + .../gfac/gfac-impl/src/test/resources/echo.bat | 22 + .../src/test/resources/gsissh.properties | 26 + .../src/test/resources/log4j.properties | 34 + .../src/test/resources/logging.properties | 42 + .../gfac/gfac-impl/src/test/resources/sleep.pbs | 32 + .../gfac/gfac-impl/src/test/resources/test.pbs | 30 + modules/gfac/gfac-local/pom.xml | 65 - .../handler/LocalDirectorySetupHandler.java | 62 - .../gfac/local/handler/LocalInputHandler.java | 92 - .../gfac/local/provider/impl/LocalProvider.java | 311 -- .../local/utils/InputStreamToFileWriter.java | 68 - .../airavata/gfac/local/utils/InputUtils.java | 46 - .../gfac/local/utils/LocalProviderUtil.java | 51 - .../src/main/resources/errors.properties | 197 - .../src/main/resources/service.properties | 58 - .../gfac/services/impl/LocalProviderTest.java | 184 - .../src/test/resources/PBSTemplate.xslt | 73 - .../src/test/resources/logging.properties | 42 - .../gfac-monitor/gfac-email-monitor/pom.xml | 35 - .../gfac/monitor/email/EmailBasedMonitor.java | 345 -- .../gfac/monitor/email/EmailMonitorFactory.java | 49 - .../gfac/monitor/email/JobStatusResult.java | 55 - .../gfac/monitor/email/parser/EmailParser.java | 36 - .../monitor/email/parser/LSFEmailParser.java | 74 - .../monitor/email/parser/PBSEmailParser.java | 104 - .../monitor/email/parser/SLURMEmailParser.java | 82 - .../monitor/email/parser/UGEEmailParser.java | 102 - .../airavata/gfac/monitor/HPCMonitorID.java | 107 - .../airavata/gfac/monitor/HostMonitorData.java | 88 - .../airavata/gfac/monitor/UserMonitorData.java | 76 - .../command/ExperimentCancelRequest.java | 38 - .../gfac/monitor/command/TaskCancelRequest.java | 52 - .../monitor/core/AiravataAbstractMonitor.java | 38 - .../gfac/monitor/core/MessageParser.java | 43 - .../airavata/gfac/monitor/core/Monitor.java | 30 - .../airavata/gfac/monitor/core/PullMonitor.java | 64 - .../airavata/gfac/monitor/core/PushMonitor.java | 60 - .../exception/AiravataMonitorException.java | 37 - .../handlers/GridPullMonitorHandler.java | 145 - .../handlers/GridPushMonitorHandler.java | 108 - .../monitor/impl/pull/qstat/HPCPullMonitor.java | 471 -- .../impl/pull/qstat/ResourceConnection.java | 154 - .../monitor/impl/push/amqp/AMQPMonitor.java | 280 -- .../monitor/impl/push/amqp/BasicConsumer.java | 87 - .../impl/push/amqp/JSONMessageParser.java | 78 - .../impl/push/amqp/SimpleJobFinishConsumer.java | 86 - .../impl/push/amqp/UnRegisterWorker.java | 67 - .../gfac/monitor/util/AMQPConnectionUtil.java | 80 - .../airavata/gfac/monitor/util/CommonUtils.java | 280 -- .../airavata/gfac/monitor/util/X509Helper.java | 164 - .../src/main/resources/errors.properties | 197 - .../src/main/resources/schema/AccessPolicy.json | 13 - .../src/main/resources/schema/Activity.json | 31 - .../src/main/resources/schema/AdminDomain.json | 51 - .../schema/ApplicationEnvironment.json | 86 - .../resources/schema/ApplicationHandle.json | 21 - .../src/main/resources/schema/Benchmark.json | 21 - .../resources/schema/ComputingActivity.json | 165 - .../resources/schema/ComputingEndpoint.json | 44 - .../main/resources/schema/ComputingManager.json | 117 - .../main/resources/schema/ComputingService.json | 32 - .../main/resources/schema/ComputingShare.json | 182 - .../src/main/resources/schema/Contact.json | 32 - .../src/main/resources/schema/DataStore.json | 30 - .../src/main/resources/schema/Domain.json | 30 - .../src/main/resources/schema/Endpoint.json | 147 - .../src/main/resources/schema/Entity.json | 35 - .../resources/schema/ExecutionEnvironment.json | 115 - .../src/main/resources/schema/Glue2.json | 246 - .../src/main/resources/schema/Location.json | 47 - .../src/main/resources/schema/Manager.json | 28 - .../main/resources/schema/MappingPolicy.json | 13 - .../src/main/resources/schema/Policy.json | 27 - .../src/main/resources/schema/Resource.json | 27 - .../src/main/resources/schema/Service.json | 75 - .../src/main/resources/schema/Share.json | 45 - .../resources/schema/StorageAccessProtocol.json | 32 - .../main/resources/schema/StorageEndpoint.json | 8 - .../main/resources/schema/StorageManager.json | 8 - .../main/resources/schema/StorageService.json | 22 - .../schema/StorageServiceCapacity.json | 33 - .../src/main/resources/schema/StorageShare.json | 65 - .../resources/schema/StorageShareCapacity.json | 33 - .../resources/schema/ToComputingService.json | 32 - .../main/resources/schema/ToStorageService.json | 25 - .../src/main/resources/schema/UserDomain.json | 58 - .../src/main/resources/service.properties | 58 - .../apache/airavata/job/AMQPMonitorTest.java | 207 - .../job/QstatMonitorTestWithMyProxyAuth.java | 172 - .../src/test/resources/PBSTemplate.xslt | 73 - .../src/test/resources/echo.bat | 22 - .../src/test/resources/logging.properties | 42 - modules/gfac/gfac-monitor/pom.xml | 29 - modules/gfac/gfac-service/pom.xml | 100 + .../apache/airavata/gfac/server/GfacServer.java | 143 + .../airavata/gfac/server/GfacServerHandler.java | 421 ++ .../src/main/resources/gsissh.properties | 26 + .../gfac/client/GfacClientFactoryTest.java | 88 + .../airavata/gfac/client/util/Initialize.java | 329 ++ .../src/test/resources/gsissh.properties | 26 + .../src/test/resources/monitor.properties | 30 + .../src/test/resources/orchestrator.properties | 26 + .../src/test/resources/registry-derby.sql | 361 ++ .../gfac-service/src/test/resources/zoo.cfg | 22 + modules/gfac/gfac-ssh/pom.xml | 114 - .../gfac/ssh/context/SSHAuthWrapper.java | 50 - .../ssh/handler/AdvancedSCPInputHandler.java | 229 - .../ssh/handler/AdvancedSCPOutputHandler.java | 225 - .../gfac/ssh/handler/NewSSHOutputHandler.java | 78 - .../ssh/handler/SSHDirectorySetupHandler.java | 119 - .../gfac/ssh/handler/SSHInputHandler.java | 198 - .../gfac/ssh/handler/SSHOutputHandler.java | 256 - .../gfac/ssh/provider/impl/SSHProvider.java | 473 -- .../gfac/ssh/security/SSHSecurityContext.java | 118 - .../gfac/ssh/security/TokenizedSSHAuthInfo.java | 184 - .../airavata/gfac/ssh/util/GFACSSHUtils.java | 562 --- .../airavata/gfac/ssh/util/HandleOutputs.java | 96 - .../src/main/resources/errors.properties | 197 - .../src/main/resources/service.properties | 58 - .../services/impl/BigRed2TestWithSSHAuth.java | 252 - .../gfac/services/impl/CredentialStoreTest.java | 135 - .../impl/SSHProviderTestWithSSHAuth.java | 172 - .../src/test/resources/PBSTemplate.xslt | 75 - .../src/test/resources/logging.properties | 42 - .../generate-gfac-stubs.sh | 134 - .../gfac.cpi.service.thrift | 68 - .../gfacDataModel.thrift | 64 - modules/gfac/pom.xml | 11 +- .../airavata-orchestrator-service/pom.xml | 85 - .../orchestrator/server/OrchestratorServer.java | 160 - .../server/OrchestratorServerHandler.java | 643 --- .../airavata/orchestrator/util/Constants.java | 29 - .../orchestrator/util/DataModelUtils.java | 55 - .../OrchestratorServerThreadPoolExecutor.java | 56 - .../src/main/resources/gsissh.properties | 26 - .../client/OrchestratorClientFactoryTest.java | 77 - .../orchestrator/client/util/Initialize.java | 329 -- .../src/test/resources/gsissh.properties | 26 - .../src/test/resources/monitor.properties | 30 - .../src/test/resources/orchestrator.properties | 26 - .../src/test/resources/registry-derby.sql | 361 -- .../src/test/resources/zoo.cfg | 22 - .../airavata-orchestrator-stubs/pom.xml | 60 - .../client/OrchestratorClientFactory.java | 44 - .../orchestrator/cpi/OrchestratorService.java | 4669 ------------------ .../cpi/orchestrator_cpi_serviceConstants.java | 55 - .../sample/OrchestratorClientSample.java | 136 - .../orchestrator/orchestrator-client/pom.xml | 60 + .../client/OrchestratorClientFactory.java | 44 + .../orchestrator/cpi/OrchestratorService.java | 4669 ++++++++++++++++++ .../cpi/orchestrator_cpi_serviceConstants.java | 55 + .../sample/OrchestratorClientSample.java | 136 + modules/orchestrator/orchestrator-core/pom.xml | 20 +- .../core/impl/GFACEmbeddedJobSubmitter.java | 12 +- .../core/impl/GFACPassiveJobSubmitter.java | 2 +- .../orchestrator/orchestrator-service/pom.xml | 85 + .../orchestrator/server/OrchestratorServer.java | 160 + .../server/OrchestratorServerHandler.java | 643 +++ .../airavata/orchestrator/util/Constants.java | 29 + .../orchestrator/util/DataModelUtils.java | 55 + .../OrchestratorServerThreadPoolExecutor.java | 56 + .../src/main/resources/gsissh.properties | 26 + .../client/OrchestratorClientFactoryTest.java | 77 + .../orchestrator/client/util/Initialize.java | 329 ++ .../src/test/resources/gsissh.properties | 26 + .../src/test/resources/monitor.properties | 30 + .../src/test/resources/orchestrator.properties | 26 + .../src/test/resources/registry-derby.sql | 361 ++ .../src/test/resources/zoo.cfg | 22 + .../generate-orchestrator-stubs.sh | 132 - .../orchestrator.cpi.service.thrift | 78 - modules/orchestrator/pom.xml | 4 +- modules/server/pom.xml | 2 +- modules/workflow-model/workflow-engine/pom.xml | 4 +- modules/xbaya-gui/pom.xml | 7 +- pom.xml | 88 +- tools/gsissh-cli-tools/README.txt | 2 +- .../ssh/cli/SSHApiClientWithMyProxyAuth.java | 25 +- tools/gsissh/src/main/java/SSHDemo.java | 4 +- .../java/com/jcraft/jsch/ExtendedSession.java | 2 +- .../UserAuthGSSAPIWithMICGSSCredentials.java | 4 +- .../airavata/gfac/gsi/ssh/GSSContextX509.java | 210 + .../airavata/gfac/gsi/ssh/api/Cluster.java | 162 + .../gfac/gsi/ssh/api/CommandExecutor.java | 278 ++ .../airavata/gfac/gsi/ssh/api/CommandInfo.java | 34 + .../gfac/gsi/ssh/api/CommandOutput.java | 49 + .../apache/airavata/gfac/gsi/ssh/api/Core.java | 59 + .../apache/airavata/gfac/gsi/ssh/api/Node.java | 104 + .../gfac/gsi/ssh/api/SSHApiException.java | 36 + .../airavata/gfac/gsi/ssh/api/ServerInfo.java | 65 + .../api/authentication/AuthenticationInfo.java | 32 + .../authentication/GSIAuthenticationInfo.java | 43 + .../authentication/SSHKeyAuthentication.java | 46 + .../SSHPasswordAuthentication.java | 43 + .../SSHPublicKeyAuthentication.java | 54 + .../SSHPublicKeyFileAuthentication.java | 52 + .../gfac/gsi/ssh/api/job/JobDescriptor.java | 473 ++ .../ssh/api/job/JobManagerConfiguration.java | 51 + .../airavata/gfac/gsi/ssh/api/job/JobType.java | 32 + .../gsi/ssh/api/job/LSFJobConfiguration.java | 121 + .../gfac/gsi/ssh/api/job/LSFOutputParser.java | 130 + .../gfac/gsi/ssh/api/job/OutputParser.java | 67 + .../gsi/ssh/api/job/PBSJobConfiguration.java | 119 + .../gfac/gsi/ssh/api/job/PBSOutputParser.java | 212 + .../gsi/ssh/api/job/SlurmJobConfiguration.java | 117 + .../gfac/gsi/ssh/api/job/SlurmOutputParser.java | 190 + .../gsi/ssh/api/job/UGEJobConfiguration.java | 119 + .../gfac/gsi/ssh/api/job/UGEOutputParser.java | 188 + .../gfac/gsi/ssh/config/ConfigReader.java | 76 + .../ssh/impl/DefaultJobSubmissionListener.java | 42 + .../gsi/ssh/impl/GSISSHAbstractCluster.java | 767 +++ .../airavata/gfac/gsi/ssh/impl/JobStatus.java | 110 + .../airavata/gfac/gsi/ssh/impl/PBSCluster.java | 45 + .../gfac/gsi/ssh/impl/RawCommandInfo.java | 55 + .../airavata/gfac/gsi/ssh/impl/SSHUserInfo.java | 63 + .../gfac/gsi/ssh/impl/StandardOutReader.java | 79 + .../gfac/gsi/ssh/impl/SystemCommandOutput.java | 78 + .../DefaultPasswordAuthenticationInfo.java | 48 + .../DefaultPublicKeyAuthentication.java | 68 + .../DefaultPublicKeyFileAuthentication.java | 70 + .../MyProxyAuthenticationInfo.java | 108 + .../gfac/gsi/ssh/jsch/ExtendedJSch.java | 64 + .../gsi/ssh/listener/JobSubmissionListener.java | 81 + .../airavata/gfac/gsi/ssh/util/CommonUtils.java | 81 + .../ssh/util/SSHAPIUIKeyboardInteractive.java | 73 + .../gsi/ssh/util/SSHKeyPasswordHandler.java | 68 + .../airavata/gfac/gsi/ssh/util/SSHUtils.java | 757 +++ .../apache/airavata/gsi/ssh/GSSContextX509.java | 214 - .../apache/airavata/gsi/ssh/api/Cluster.java | 162 - .../airavata/gsi/ssh/api/CommandExecutor.java | 278 -- .../airavata/gsi/ssh/api/CommandInfo.java | 34 - .../airavata/gsi/ssh/api/CommandOutput.java | 49 - .../org/apache/airavata/gsi/ssh/api/Core.java | 59 - .../org/apache/airavata/gsi/ssh/api/Node.java | 104 - .../airavata/gsi/ssh/api/SSHApiException.java | 36 - .../apache/airavata/gsi/ssh/api/ServerInfo.java | 65 - .../api/authentication/AuthenticationInfo.java | 32 - .../authentication/GSIAuthenticationInfo.java | 43 - .../authentication/SSHKeyAuthentication.java | 46 - .../SSHPasswordAuthentication.java | 43 - .../SSHPublicKeyAuthentication.java | 54 - .../SSHPublicKeyFileAuthentication.java | 52 - .../airavata/gsi/ssh/api/job/JobDescriptor.java | 473 -- .../ssh/api/job/JobManagerConfiguration.java | 51 - .../airavata/gsi/ssh/api/job/JobType.java | 32 - .../gsi/ssh/api/job/LSFJobConfiguration.java | 121 - .../gsi/ssh/api/job/LSFOutputParser.java | 130 - .../airavata/gsi/ssh/api/job/OutputParser.java | 68 - .../gsi/ssh/api/job/PBSJobConfiguration.java | 119 - .../gsi/ssh/api/job/PBSOutputParser.java | 214 - .../gsi/ssh/api/job/SlurmJobConfiguration.java | 117 - .../gsi/ssh/api/job/SlurmOutputParser.java | 190 - .../gsi/ssh/api/job/UGEJobConfiguration.java | 119 - .../gsi/ssh/api/job/UGEOutputParser.java | 188 - .../airavata/gsi/ssh/config/ConfigReader.java | 81 - .../ssh/impl/DefaultJobSubmissionListener.java | 42 - .../gsi/ssh/impl/GSISSHAbstractCluster.java | 768 --- .../apache/airavata/gsi/ssh/impl/JobStatus.java | 112 - .../airavata/gsi/ssh/impl/PBSCluster.java | 46 - .../airavata/gsi/ssh/impl/RawCommandInfo.java | 55 - .../airavata/gsi/ssh/impl/SSHUserInfo.java | 63 - .../gsi/ssh/impl/StandardOutReader.java | 80 - .../gsi/ssh/impl/SystemCommandOutput.java | 78 - .../DefaultPasswordAuthenticationInfo.java | 50 - .../DefaultPublicKeyAuthentication.java | 68 - .../DefaultPublicKeyFileAuthentication.java | 70 - .../MyProxyAuthenticationInfo.java | 108 - .../airavata/gsi/ssh/jsch/ExtendedJSch.java | 64 - .../gsi/ssh/listener/JobSubmissionListener.java | 81 - .../airavata/gsi/ssh/util/CommonUtils.java | 81 - .../ssh/util/SSHAPIUIKeyboardInteractive.java | 73 - .../gsi/ssh/util/SSHKeyPasswordHandler.java | 68 - .../apache/airavata/gsi/ssh/util/SSHUtils.java | 758 --- .../resources/schemas/gsissh-schemas.xsdconfig | 2 +- .../gfac/ssh/config/ConfigReaderTest.java | 37 + .../impl/DefaultSSHApiTestWithMyProxyAuth.java | 77 + .../gfac/ssh/impl/VanilaTestWithSSHAuth.java | 262 + .../gsi/ssh/config/ConfigReaderTest.java | 37 - .../impl/DefaultSSHApiTestWithMyProxyAuth.java | 88 - .../gsi/ssh/impl/VanilaTestWithSSHAuth.java | 263 - 721 files changed, 58879 insertions(+), 71470 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/b4ede9cb/airavata-api/airavata-api-server/pom.xml ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/b4ede9cb/distribution/pom.xml ---------------------------------------------------------------------- diff --cc distribution/pom.xml index 0000000,cf33308..d934b9e mode 000000,100644..100644 --- a/distribution/pom.xml +++ b/distribution/pom.xml @@@ -1,0 -1,581 +1,581 @@@ + <?xml version="1.0" encoding="UTF-8"?> + + <!--Licensed to the Apache Software Foundation (ASF) under one or more contributor + license agreements. See the NOTICE file distributed with this work for additional + information regarding copyright ownership. The ASF licenses this file to + you under the Apache License, Version 2.0 (theà "License"); you may not use + this file except in compliance with the License. You may obtain a copy of + the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required + by applicable law or agreed to in writing, software distributed under the + License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS + OF ANY ~ KIND, either express or implied. See the License for the specific + language governing permissions and limitations under the License. --> + + <project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> + + <parent> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata</artifactId> + <version>0.16-SNAPSHOT</version> + <relativePath>../pom.xml</relativePath> + </parent> + + <modelVersion>4.0.0</modelVersion> + <artifactId>apache-airavata-distribution</artifactId> + <name>Airavata server distribution</name> + <packaging>pom</packaging> + <url>http://airavata.apache.org/</url> + + <build> + <plugins> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-dependency-plugin</artifactId> + <version>2.8</version> + <executions> + <execution> + <id>unpack</id> + <phase>compile</phase> + <goals> + <goal>unpack</goal> + </goals> + <configuration> + <artifactItems> + <artifactItem> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-server-configuration</artifactId> + <version>${project.version}</version> + <type>jar</type> + </artifactItem> + </artifactItems> + <!--includes>**/*.war</includes --> + <outputDirectory>${project.build.directory}/conf</outputDirectory> + </configuration> + </execution> + </executions> + </plugin> + + <plugin> + <groupId>org.codehaus.gmaven</groupId> + <artifactId>gmaven-plugin</artifactId> + <version>1.4</version> + <executions> + <execution> + <id>generate-timestamp</id> + <phase>package</phase> + <goals> + <goal>execute</goal> + </goals> + <configuration> + <source> + import java.util.Date + import java.text.MessageFormat + + project.properties['buildTimestamp'] = + MessageFormat.format("{0,date,dd-MM-yyyy}", new + Date()) + </source> + </configuration> + </execution> + </executions> + </plugin> + <plugin> + <groupId>org.apache.maven.plugins</groupId> + <artifactId>maven-assembly-plugin</artifactId> + <executions> + <execution> + <id>distribution-package</id> + <phase>package</phase> + <goals> + <goal>single</goal> + </goals> + <configuration> + <finalName>${archieve.name}-${project.version}</finalName> + <descriptors> + <descriptor>src/main/assembly/bin-assembly.xml</descriptor> + <!-- <descriptor>src/main/assembly/src-assembly.xml</descriptor> --> + </descriptors> + <attach>false</attach> + </configuration> + </execution> + </executions> + </plugin> + + <plugin> + <groupId>org.codehaus.mojo</groupId> + <artifactId>build-helper-maven-plugin</artifactId> + <version>1.7</version> + <executions> + <execution> + <id>attach-artifacts</id> + <phase>package</phase> + <goals> + <goal>attach-artifact</goal> + </goals> + <configuration> + <artifacts> + <artifact> + <file>${airavata.bin.zip}</file> + <type>zip</type> + <classifier>bin</classifier> + </artifact> + <artifact> + <file>${airavata.bin.tar.gz}</file> + <type>tar.gz</type> + <classifier>bin</classifier> + </artifact> + </artifacts> + </configuration> + </execution> + </executions> + </plugin> + </plugins> + </build> + + <dependencies> + <dependency> + <groupId>org.apache.derby</groupId> + <artifactId>derby</artifactId> + <version>${derby.version}</version> + </dependency> + <dependency> + <groupId>org.apache.derby</groupId> + <artifactId>derbyclient</artifactId> + <version>${derby.version}</version> + </dependency> + <dependency> + <groupId>org.apache.derby</groupId> + <artifactId>derbynet</artifactId> + <version>${derby.version}</version> + </dependency> + <dependency> + <groupId>org.apache.derby</groupId> + <artifactId>derbytools</artifactId> + <version>${derby.version}</version> + </dependency> + <dependency> + <groupId>org.slf4j</groupId> + <artifactId>slf4j-api</artifactId> + </dependency> + <dependency> + <groupId>org.slf4j</groupId> + <artifactId>jcl-over-slf4j</artifactId> + </dependency> + <dependency> + <groupId>org.slf4j</groupId> + <artifactId>slf4j-log4j12</artifactId> + </dependency> + <dependency> + <groupId>log4j</groupId> + <artifactId>log4j</artifactId> + </dependency> + <dependency> + <groupId>com.amazonaws</groupId> + <artifactId>aws-java-sdk</artifactId> + <version>1.9.0</version> + <exclusions> + <exclusion> + <groupId>org.apache.httpcomponents</groupId> + <artifactId>httpclient</artifactId> + </exclusion> + </exclusions> + </dependency> + <dependency> + <groupId>net.java.dev.jets3t</groupId> + <artifactId>jets3t</artifactId> + <version>0.8.0</version> + </dependency> + <dependency> + <groupId>commons-collections</groupId> + <artifactId>commons-collections</artifactId> + <version>3.2.1</version> + </dependency> + <dependency> + <groupId>commons-lang</groupId> + <artifactId>commons-lang</artifactId> + <version>2.4</version> + </dependency> + <dependency> + <groupId>commons-io</groupId> + <artifactId>commons-io</artifactId> + <version>2.4</version> + </dependency> + <dependency> + <groupId>commons-codec</groupId> + <artifactId>commons-codec</artifactId> + <version>1.6</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-standalone-server</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>app-catalog-cpi</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-messaging-core</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>app-catalog-data</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-common-utils</artifactId> + <version>${project.version}</version> + <exclusions> + <exclusion> + <groupId>org.apache.ws.commons.schema</groupId> + <artifactId>XmlSchema</artifactId> + </exclusion> + <exclusion> + <groupId>xerces</groupId> + <artifactId>xmlParserAPIs</artifactId> + </exclusion> + <exclusion> + <groupId>org.apache.neethi</groupId> + <artifactId>neethi</artifactId> + </exclusion> + </exclusions> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-orchestrator-service</artifactId> + <version>${project.version}</version> + <exclusions> + <exclusion> + <groupId>org.apache.ws.commons.schema</groupId> + <artifactId>XmlSchema</artifactId> + </exclusion> + <exclusion> + <groupId>xerces</groupId> + <artifactId>xmlParserAPIs</artifactId> + </exclusion> + <exclusion> + <groupId>org.apache.neethi</groupId> + <artifactId>neethi</artifactId> + </exclusion> + </exclusions> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-orchestrator-client</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-gfac-client</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-orchestrator-core</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-registry-cpi</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> - <artifactId>airavata-jpa-registry</artifactId> ++ <artifactId>airavata-experiment-catalog</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-data-models</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-credential-store</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-gfac-impl</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-gfac-bes</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-gfac-core</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-gfac-service</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-workflow-model-core</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-model-utils</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-api-server</artifactId> + <version>${project.version}</version> + </dependency> + <dependency> + <groupId>org.bouncycastle</groupId> + <artifactId>bcprov-jdk15on</artifactId> + </dependency> + <dependency> + <groupId>org.apache.openjpa</groupId> + <artifactId>openjpa-all</artifactId> + <version>2.2.0</version> + </dependency> + + <dependency> + <groupId>org.apache.shiro</groupId> + <artifactId>shiro-core</artifactId> + <version>1.2.1</version> + </dependency> + <dependency> + <groupId>com.sun.jersey</groupId> + <artifactId>jersey-client</artifactId> + <version>${jersey.version}</version> + </dependency> + <dependency> + <groupId>javax.servlet</groupId> + <artifactId>javax.servlet-api</artifactId> + <version>3.0.1</version> + <scope>provided</scope> + </dependency> + <dependency> + <groupId>org.apache.tomcat.embed</groupId> + <artifactId>tomcat-embed-logging-juli</artifactId> + <version>7.0.22</version> + </dependency> + <dependency> + <groupId>org.apache.tomcat.embed</groupId> + <artifactId>tomcat-embed-jasper</artifactId> + <version>7.0.22</version> + </dependency> + <dependency> + <groupId>com.sun.jersey</groupId> + <artifactId>jersey-servlet</artifactId> + <version>${jersey.version}</version> + </dependency> + <dependency> + <groupId>com.sun.jersey</groupId> + <artifactId>jersey-json</artifactId> + <version>${jersey.version}</version> + <exclusions> + <exclusion> + <groupId>stax</groupId> + <artifactId>stax-api</artifactId> + </exclusion> + </exclusions> + + </dependency> + <dependency> + <groupId>com.sun.jersey.contribs</groupId> + <artifactId>jersey-multipart</artifactId> + <version>${jersey.version}</version> + </dependency> + <dependency> + <groupId>com.sun.jersey</groupId> + <artifactId>jersey-server</artifactId> + <version>${jersey.version}</version> + </dependency> + <!--dependency> <groupId>com.sun.jersey</groupId> <artifactId>jersey-client</artifactId> + <version>${jersey.version}</version> </dependency --> + <dependency> + <groupId>org.codehaus.jackson</groupId> + <artifactId>jackson-mapper-asl</artifactId> + <version>1.9.2</version> + </dependency> + <dependency> + <groupId>org.codehaus.jackson</groupId> + <artifactId>jackson-xc</artifactId> + <version>1.9.2</version> + </dependency> + <dependency> + <groupId>org.codehaus.jackson</groupId> + <artifactId>jackson-jaxrs</artifactId> + <version>1.9.2</version> + </dependency> + <dependency> + <groupId>org.codehaus.jackson</groupId> + <artifactId>jackson-core-asl</artifactId> + <version>1.9.2</version> + </dependency> + <dependency> + <groupId>xerces</groupId> + <artifactId>xercesImpl</artifactId> + <version>2.9.1</version> + <exclusions> + <exclusion> + <groupId>xml-apis</groupId> + <artifactId>xml-apis</artifactId> + </exclusion> + </exclusions> + </dependency> + <dependency> + <groupId>com.ibm.icu</groupId> + <artifactId>icu4j</artifactId> + <version>3.4.4</version> + </dependency> + <dependency> + <groupId>com.google.guava</groupId> + <artifactId>guava</artifactId> + <version>12.0</version> + </dependency> + + <!-- Hadoop provider related dependencies --> + <dependency> + <groupId>org.apache.hadoop</groupId> + <artifactId>hadoop-core</artifactId> + <version>1.0.3</version> + </dependency> + <dependency> + <groupId>org.apache.hadoop</groupId> + <artifactId>hadoop-client</artifactId> + <version>1.0.3</version> + </dependency> + <dependency> + <groupId>org.apache.whirr</groupId> + <artifactId>whirr-core</artifactId> + <version>0.7.1</version> + <exclusions> + <exclusion> + <groupId>org.bouncycastle</groupId> + <artifactId>bcprov-jdk16</artifactId> + </exclusion> + <exclusion> + <groupId>org.jclouds.driver</groupId> + <artifactId>jclouds-bouncycastle</artifactId> + </exclusion> + </exclusions> + </dependency> + <dependency> + <groupId>org.apache.whirr</groupId> + <artifactId>whirr-hadoop</artifactId> + <version>0.7.1</version> + </dependency> + <dependency> + <groupId>org.hamcrest</groupId> + <artifactId>hamcrest-all</artifactId> + <version>1.1</version> + </dependency> + <dependency> + <groupId>org.mockito</groupId> + <artifactId>mockito-all</artifactId> + <version>1.8.5</version> + </dependency> + <dependency> + <groupId>commons-configuration</groupId> + <artifactId>commons-configuration</artifactId> + <version>1.7</version> + </dependency> + <dependency> + <groupId>net.sf.jopt-simple</groupId> + <artifactId>jopt-simple</artifactId> + <version>3.2</version> + </dependency> + <dependency> + <groupId>org.ebaysf.web</groupId> + <artifactId>cors-filter</artifactId> + <version>${ebay.cors.filter}</version> + </dependency> + <dependency> + <groupId>com.jcraft</groupId> + <artifactId>jsch</artifactId> + <version>0.1.50</version> + </dependency> + <!-- dependency> <groupId>org.ogce</groupId> <artifactId>bcgss</artifactId> + <version>146</version> </dependency> --> + <dependency> + <groupId>org.apache.xmlbeans</groupId> + <artifactId>xmlbeans</artifactId> + <version>${xmlbeans.version}</version> + <exclusions> + <exclusion> + <groupId>stax</groupId> + <artifactId>stax-api</artifactId> + </exclusion> + </exclusions> + </dependency> + <dependency> + <groupId>org.apache.thrift</groupId> + <artifactId>libthrift</artifactId> + <version>0.9.1</version> + </dependency> + <dependency> + <groupId>com.fasterxml.jackson.core</groupId> + <artifactId>jackson-databind</artifactId> + <version>2.0.0</version> + </dependency> + <dependency> + <groupId>com.fasterxml.jackson.core</groupId> + <artifactId>jackson-core</artifactId> + <version>2.0.0</version> + </dependency> + <dependency> + <groupId>com.fasterxml.jackson.core</groupId> + <artifactId>jackson-annotations</artifactId> + <version>2.0.0</version> + </dependency> + <!-- zookeeper dependencies --> + + <dependency> + <groupId>org.apache.zookeeper</groupId> + <artifactId>zookeeper</artifactId> + <version>3.4.0</version> + </dependency> + <dependency> + <groupId>commons-cli</groupId> + <artifactId>commons-cli</artifactId> + <version>1.2</version> + </dependency> + + <dependency> + <groupId>com.rabbitmq</groupId> + <artifactId>amqp-client</artifactId> + <version>${amqp.client.version}</version> + </dependency> + <dependency> + <groupId>org.apache.curator</groupId> + <artifactId>curator-framework</artifactId> + <version>${curator.version}</version> + </dependency> + + <!-- ======================== Sample =================== --> + <dependency> + <groupId>org.apache.airavata</groupId> + <artifactId>airavata-client-samples</artifactId> + <version>${project.version}</version> + </dependency> + </dependencies> + + + <properties> + <jersey.version>1.13</jersey.version> + <grizzly.version>2.0.0-M3</grizzly.version> + <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> + <archieve.name>apache-airavata-server</archieve.name> + <airavata.dist.name>${archieve.name}-${project.version}</airavata.dist.name> + <airavata.work.dir>${project.build.directory}/tests/${airavata.dist.name}</airavata.work.dir> + <airavata.bin.zip>${project.build.directory}/${airavata.dist.name}-bin.zip</airavata.bin.zip> + <airavata.bin.tar.gz>${project.build.directory}/${airavata.dist.name}-bin.tar.gz</airavata.bin.tar.gz> + </properties> + </project> http://git-wip-us.apache.org/repos/asf/airavata/blob/b4ede9cb/modules/gfac/gfac-bes/src/main/java/org/apache/airavata/gfac/bes/provider/impl/BESProvider.java ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/b4ede9cb/modules/gfac/gfac-core/pom.xml ---------------------------------------------------------------------- diff --cc modules/gfac/gfac-core/pom.xml index 037cef6,d2741a1..079fe36 --- a/modules/gfac/gfac-core/pom.xml +++ b/modules/gfac/gfac-core/pom.xml @@@ -47,9 -47,14 +47,14 @@@ </dependency> <dependency> <groupId>org.apache.airavata</groupId> - <artifactId>airavata-jpa-registry</artifactId> + <artifactId>airavata-experiment-catalog</artifactId> <version>${project.version}</version> </dependency> + <dependency> + <groupId>org.apache.xmlbeans</groupId> + <artifactId>xmlbeans</artifactId> + <version>${xmlbeans.version}</version> + </dependency> <!-- Credential Store --> <dependency> <groupId>org.apache.airavata</groupId>
