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From shame...@apache.org
Subject [39/39] airavata git commit: Refactored gfac sub modules, merged gfac-ssh, gfac-gsissh, gfac-local, gfac-monitor and gsissh modules and create gface-impl, removed implementation from gfac-core to gfac-impl
Date Wed, 03 Jun 2015 18:14:56 GMT
Refactored gfac sub modules, merged  gfac-ssh, gfac-gsissh, gfac-local, gfac-monitor and gsissh
 modules and create gface-impl, removed implementation from gfac-core to gfac-impl


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/7b809747
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/7b809747
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/7b809747

Branch: refs/heads/moduleRefactor
Commit: 7b809747658c5b5e5703540395884c580e8d1f8f
Parents: 82773c7
Author: Shameera Rathanyaka <shameerainfo@gmail.com>
Authored: Wed Jun 3 14:14:00 2015 -0400
Committer: Shameera Rathanyaka <shameerainfo@gmail.com>
Committed: Wed Jun 3 14:14:00 2015 -0400

----------------------------------------------------------------------
 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 ---
 .../src/main/resources/gsissh.properties        |   26 -
 .../gfac/client/GfacClientFactoryTest.java      |  103 -
 .../airavata/gfac/client/util/Initialize.java   |  330 --
 .../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 -
 modules/gfac/airavata-gfac-stubs/pom.xml        |   60 -
 .../airavata/gfac/client/GFACInstance.java      |   62 -
 .../airavata/gfac/client/GFacClientFactory.java |   42 -
 .../apache/airavata/gfac/cpi/GfacService.java   | 2867 ----------------
 .../gfac/cpi/gfac_cpi_serviceConstants.java     |   55 -
 .../gfac/bes/handlers/AbstractSMSHandler.java   |    2 +-
 .../gfac/bes/provider/impl/BESProvider.java     |    7 +-
 .../airavata/gfac/bes/utils/SecurityUtils.java  |    2 +-
 modules/gfac/gfac-client/pom.xml                |   60 +
 .../airavata/gfac/client/GFACInstance.java      |   62 +
 .../airavata/gfac/client/GFacClientFactory.java |   42 +
 .../apache/airavata/gfac/cpi/GfacService.java   | 2867 ++++++++++++++++
 .../gfac/cpi/gfac_cpi_serviceConstants.java     |   55 +
 .../org/apache/airavata/gfac/Scheduler.java     |    2 +-
 .../org/apache/airavata/gfac/core/GFac.java     |   77 +
 .../gfac/core/GFacThreadPoolExecutor.java       |   57 +
 .../apache/airavata/gfac/core/GFacUtils.java    |  708 ++++
 .../core/authentication/AuthenticationInfo.java |   32 +
 .../authentication/GSIAuthenticationInfo.java   |   43 +
 .../authentication/SSHKeyAuthentication.java    |   46 +
 .../SSHPasswordAuthentication.java              |   43 +
 .../SSHPublicKeyAuthentication.java             |   54 +
 .../SSHPublicKeyFileAuthentication.java         |   52 +
 .../gfac/core/context/JobExecutionContext.java  |   13 +-
 .../airavata/gfac/core/cpi/BetterGfacImpl.java  | 1158 -------
 .../org/apache/airavata/gfac/core/cpi/GFac.java |   77 -
 .../apache/airavata/gfac/core/cpi/GFacImpl.java |  798 -----
 .../gfac/core/handler/AbstractHandler.java      |    2 +-
 .../core/handler/AppDescriptorCheckHandler.java |    2 +-
 .../core/monitor/AiravataJobStatusUpdator.java  |  123 -
 .../core/monitor/AiravataTaskStatusUpdator.java |  162 -
 .../AiravataWorkflowNodeStatusUpdator.java      |  130 -
 .../airavata/gfac/core/monitor/EmailParser.java |   35 +
 .../gfac/core/monitor/ExperimentIdentity.java   |   36 -
 .../airavata/gfac/core/monitor/JobIdentity.java |   39 -
 .../gfac/core/monitor/JobStatusResult.java      |   55 +
 .../gfac/core/monitor/TaskIdentity.java         |   38 -
 .../gfac/core/monitor/WorkflowNodeIdentity.java |   37 -
 .../monitor/state/JobStatusChangeRequest.java   |   81 -
 .../monitor/state/JobStatusChangedEvent.java    |   81 -
 .../state/TaskOutputDataChangedEvent.java       |   64 -
 .../monitor/state/TaskStatusChangeRequest.java  |   62 -
 .../monitor/state/TaskStatusChangedEvent.java   |   62 -
 .../state/WorkflowNodeStatusChangedEvent.java   |   64 -
 .../gfac/core/notification/GFacNotifier.java    |   42 -
 .../core/notification/MonitorPublisher.java     |   47 -
 .../notification/events/ExecutionFailEvent.java |   35 -
 .../events/FinishExecutionEvent.java            |   29 -
 .../events/FinishScheduleEvent.java             |   29 -
 .../core/notification/events/GFacEvent.java     |   39 -
 .../core/notification/events/JobIDEvent.java    |   35 -
 .../events/StartExecutionEvent.java             |   29 -
 .../notification/events/StartScheduleEvent.java |   29 -
 .../notification/events/StatusChangeEvent.java  |   33 -
 .../notification/events/UnicoreJobIDEvent.java  |   35 -
 .../notification/listeners/LoggingListener.java |   57 -
 .../listeners/WorkflowTrackingListener.java     |  133 -
 .../airavata/gfac/core/persistence/JobData.java |   55 -
 .../core/persistence/JobPersistenceManager.java |   76 -
 .../gfac/core/provider/AbstractProvider.java    |    2 -
 .../gfac/core/utils/GFacThreadPoolExecutor.java |   57 -
 .../airavata/gfac/core/utils/GFacUtils.java     |  708 ----
 .../gfac/core/utils/InputHandlerWorker.java     |   52 -
 .../gfac/core/utils/OutHandlerWorker.java       |   87 -
 .../airavata/gfac/core/utils/OutputUtils.java   |  111 -
 modules/gfac/gfac-gsissh/pom.xml                |  117 -
 .../handler/GSISSHDirectorySetupHandler.java    |  118 -
 .../gfac/gsissh/handler/GSISSHInputHandler.java |  213 --
 .../gsissh/handler/GSISSHOutputHandler.java     |  323 --
 .../gsissh/handler/NewGSISSHOutputHandler.java  |   83 -
 .../gsissh/provider/impl/GSISSHProvider.java    |  351 --
 .../gsissh/security/GSISecurityContext.java     |   86 -
 .../security/TokenizedMyProxyAuthInfo.java      |  305 --
 .../gfac/gsissh/util/GFACGSISSHUtils.java       |  367 --
 .../src/main/resources/errors.properties        |  197 --
 .../src/main/resources/service.properties       |   58 -
 .../impl/GSISSHProviderTestWithMyProxyAuth.java |  229 --
 .../GSISecurityContextTestWithMyProxyAuth.java  |  163 -
 .../src/test/resources/PBSTemplate.xslt         |   78 -
 .../src/test/resources/logging.properties       |   42 -
 modules/gfac/gfac-impl/pom.xml                  |   65 +
 .../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 +
 .../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 +++++
 .../handler/GSISSHDirectorySetupHandler.java    |  118 +
 .../gfac/gsissh/handler/GSISSHInputHandler.java |  213 ++
 .../gsissh/handler/GSISSHOutputHandler.java     |  323 ++
 .../gsissh/handler/NewGSISSHOutputHandler.java  |   83 +
 .../gsissh/provider/impl/GSISSHProvider.java    |  346 ++
 .../gsissh/security/GSISecurityContext.java     |   74 +
 .../security/TokenizedMyProxyAuthInfo.java      |  304 ++
 .../gfac/gsissh/util/GFACGSISSHUtils.java       |  367 ++
 .../gfac/impl/AiravataJobStatusUpdator.java     |  120 +
 .../gfac/impl/AiravataTaskStatusUpdator.java    |  166 +
 .../impl/AiravataWorkflowNodeStatusUpdator.java |  129 +
 .../airavata/gfac/impl/BetterGfacImpl.java      | 1151 +++++++
 .../gfac/impl/GfacInternalStatusUpdator.java    |  104 +
 .../airavata/gfac/impl/InputHandlerWorker.java  |   52 +
 .../airavata/gfac/impl/OutHandlerWorker.java    |   88 +
 .../apache/airavata/gfac/impl/OutputUtils.java  |  111 +
 .../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 +
 .../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 +
 .../gfac/monitor/email/EmailBasedMonitor.java   |  344 ++
 .../gfac/monitor/email/EmailMonitorFactory.java |   49 +
 .../monitor/email/parser/LSFEmailParser.java    |   75 +
 .../monitor/email/parser/PBSEmailParser.java    |  105 +
 .../monitor/email/parser/SLURMEmailParser.java  |   83 +
 .../monitor/email/parser/UGEEmailParser.java    |  103 +
 .../exception/AiravataMonitorException.java     |   37 +
 .../handlers/GridPullMonitorHandler.java        |  139 +
 .../handlers/GridPushMonitorHandler.java        |  107 +
 .../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 +
 .../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     |  467 +++
 .../gfac/ssh/security/SSHSecurityContext.java   |  118 +
 .../gfac/ssh/security/TokenizedSSHAuthInfo.java |  184 +
 .../airavata/gfac/ssh/util/GFACSSHUtils.java    |  561 ++++
 .../airavata/gfac/ssh/util/HandleOutputs.java   |   96 +
 .../src/main/resources/LSFTemplate.xslt         |   93 +
 .../src/main/resources/PBSTemplate.xslt         |   82 +
 .../src/main/resources/SLURMTemplate.xslt       |   78 +
 .../src/main/resources/UGETemplate.xslt         |   74 +
 .../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 +
 .../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       |   37 +
 .../impl/DefaultSSHApiTestWithMyProxyAuth.java  |   77 +
 .../gfac/ssh/impl/VanilaTestWithSSHAuth.java    |  262 ++
 .../apache/airavata/job/AMQPMonitorTest.java    |  207 ++
 .../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 -
 .../gfac/gfac-monitor/gfac-hpc-monitor/pom.xml  |  158 -
 .../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               |   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 +++
 .../src/main/resources/gsissh.properties        |   26 +
 .../gfac/client/GfacClientFactoryTest.java      |  103 +
 .../airavata/gfac/client/util/Initialize.java   |  330 ++
 .../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 -
 modules/gfac/pom.xml                            |    9 +-
 .../core/impl/GFACEmbeddedJobSubmitter.java     |   12 +-
 .../core/impl/GFACPassiveJobSubmitter.java      |    2 +-
 .../server/OrchestratorServerHandler.java       |    2 +-
 pom.xml                                         |    1 -
 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 --
 488 files changed, 36116 insertions(+), 32978 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/7b809747/modules/gfac/airavata-gfac-service/pom.xml
----------------------------------------------------------------------
diff --git a/modules/gfac/airavata-gfac-service/pom.xml b/modules/gfac/airavata-gfac-service/pom.xml
deleted file mode 100644
index 224537f..0000000
--- a/modules/gfac/airavata-gfac-service/pom.xml
+++ /dev/null
@@ -1,95 +0,0 @@
-<?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 (theƏ "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/xsd/maven-4.0.0.xsd">
-
-    <modelVersion>4.0.0</modelVersion>
-
-    <parent>
-        <artifactId>gfac</artifactId>
-        <groupId>org.apache.airavata</groupId>
-        <version>0.16-SNAPSHOT</version>
-        <relativePath>../pom.xml</relativePath>
-    </parent>
-
-    <name>Airavata Gfac Service</name>
-    <artifactId>airavata-gfac-service</artifactId>
-    <packaging>jar</packaging>
-    <url>http://airavata.apache.org/</url>
-
-    <dependencies>
-        <dependency>
-            <groupId>org.apache.thrift</groupId>
-            <artifactId>libthrift</artifactId>
-            <version>${thrift.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-log4j12</artifactId>
-            <version>${org.slf4j.version}</version>
-        </dependency>
-        <!--<dependency>-->
-            <!--<groupId>org.apache.airavata</groupId>-->
-            <!--<artifactId>airavata-client-api</artifactId>-->
-            <!--<version>${project.version}</version>-->
-        <!--</dependency>-->
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-common-utils</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-registry-cpi</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-jpa-registry</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-core</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-	    <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-model-utils</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-api-stubs</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-         <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-gfac-stubs</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-	    <dependency>
-            <groupId>org.apache.airavata</groupId>
-            <artifactId>airavata-server-configuration</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.curator</groupId>
-            <artifactId>curator-framework</artifactId>
-            <version>${curator.version}</version>
-        </dependency>
-    </dependencies>
-
-    <properties>
-        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-    </properties>
-    
-</project>


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