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From samin...@apache.org
Subject [50/50] [abbrv] git commit: Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata into workflow-support
Date Tue, 22 Jul 2014 15:06:15 GMT
Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata into workflow-support

Conflicts:
	airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
	pom.xml


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/16cd757f
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/16cd757f
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/16cd757f

Branch: refs/heads/workflow-support
Commit: 16cd757f2bee40aa8407ea76b012389d72d2dea7
Parents: 92838e4 d5b1b2d
Author: Saminda Wijeratne <samindaw@gmail.com>
Authored: Tue Jul 22 11:04:00 2014 -0400
Committer: Saminda Wijeratne <samindaw@gmail.com>
Committed: Tue Jul 22 11:04:00 2014 -0400

----------------------------------------------------------------------
 airavata-api/airavata-api-server/pom.xml        |     2 +-
 .../server/handler/AiravataServerHandler.java   |    14 +-
 airavata-api/airavata-api-stubs/pom.xml         |     2 +-
 .../java/org/apache/airavata/api/Airavata.java  |    33 +-
 .../airavata/api/airavataAPIConstants.java      |    33 +-
 .../apache/airavata/api/workflow/Workflow.java  |    33 +-
 .../api/workflow/workflowAPIConstants.java      |    33 +-
 .../airavata-cpp-sdk/pom.xml                    |     8 +-
 .../airavata-client-properties.ini              |     4 +
 .../main/resources/client_samples/compile.sh    |    21 +
 .../client_samples/createExperiment.cpp         |   174 +
 .../resources/client_samples/createProject.cpp  |   117 +
 .../client_samples/getExperimentOutputs.cpp     |   121 +
 .../client_samples/getExperimentStatus.cpp      |   118 +
 .../client_samples/launchExperiment.cpp         |   116 +
 .../src/main/resources/lib/Airavata.cpp         | 26734 ----------------
 .../src/main/resources/lib/Airavata.h           | 11188 -------
 .../resources/lib/Airavata_server.skeleton.cpp  |   399 -
 .../resources/lib/ApplicationCatalogAPI.cpp     |  9387 ------
 .../main/resources/lib/ApplicationCatalogAPI.h  |  4069 ---
 .../ApplicationCatalogAPI_server.skeleton.cpp   |   169 -
 .../src/main/resources/lib/Workflow.cpp         |  2497 --
 .../src/main/resources/lib/Workflow.h           |  1154 -
 .../resources/lib/Workflow_server.skeleton.cpp  |    74 -
 .../main/resources/lib/airavata/Airavata.cpp    | 26751 +++++++++++++++++
 .../src/main/resources/lib/airavata/Airavata.h  | 11205 +++++++
 .../lib/airavata/Airavata_server.skeleton.cpp   |   416 +
 .../main/resources/lib/airavata/Workflow.cpp    |  2514 ++
 .../src/main/resources/lib/airavata/Workflow.h  |  1171 +
 .../lib/airavata/Workflow_server.skeleton.cpp   |    91 +
 .../lib/airavata/airavataAPI_constants.cpp      |    36 +
 .../lib/airavata/airavataAPI_constants.h        |    42 +
 .../lib/airavata/airavataAPI_types.cpp          |    30 +
 .../resources/lib/airavata/airavataAPI_types.h  |    47 +
 .../airavata/airavataDataModel_constants.cpp    |    34 +
 .../lib/airavata/airavataDataModel_constants.h  |    41 +
 .../lib/airavata/airavataDataModel_types.cpp    |    30 +
 .../lib/airavata/airavataDataModel_types.h      |    41 +
 .../lib/airavata/airavataErrors_constants.cpp   |    34 +
 .../lib/airavata/airavataErrors_constants.h     |    41 +
 .../lib/airavata/airavataErrors_types.cpp       |   837 +
 .../lib/airavata/airavataErrors_types.h         |   526 +
 .../applicationDeploymentModel_constants.cpp    |    36 +
 .../applicationDeploymentModel_constants.h      |    42 +
 .../applicationDeploymentModel_types.cpp        |   514 +
 .../airavata/applicationDeploymentModel_types.h |   292 +
 .../applicationInterfaceModel_constants.cpp     |    36 +
 .../applicationInterfaceModel_constants.h       |    42 +
 .../applicationInterfaceModel_types.cpp         |   487 +
 .../airavata/applicationInterfaceModel_types.h  |   315 +
 .../airavata/computeResourceModel_constants.cpp |    36 +
 .../airavata/computeResourceModel_constants.h   |    42 +
 .../lib/airavata/computeResourceModel_types.cpp |  1728 ++
 .../lib/airavata/computeResourceModel_types.h   |   961 +
 .../lib/airavata/experimentModel_constants.cpp  |    40 +
 .../lib/airavata/experimentModel_constants.h    |    44 +
 .../lib/airavata/experimentModel_types.cpp      |  3356 +++
 .../lib/airavata/experimentModel_types.cpp~     |  3339 ++
 .../lib/airavata/experimentModel_types.h        |  2094 ++
 .../gatewayResourceProfileModel_constants.cpp   |    36 +
 .../gatewayResourceProfileModel_constants.h     |    42 +
 .../gatewayResourceProfileModel_types.cpp       |   310 +
 .../gatewayResourceProfileModel_types.h         |   214 +
 .../lib/airavata/workflowAPI_constants.cpp      |    36 +
 .../lib/airavata/workflowAPI_constants.h        |    42 +
 .../lib/airavata/workflowAPI_types.cpp          |    30 +
 .../resources/lib/airavata/workflowAPI_types.h  |    47 +
 .../airavata/workflowDataModel_constants.cpp    |    36 +
 .../lib/airavata/workflowDataModel_constants.h  |    42 +
 .../lib/airavata/workflowDataModel_types.cpp    |   125 +
 .../lib/airavata/workflowDataModel_types.h      |    99 +
 .../lib/airavata/workspaceModel_constants.cpp   |    34 +
 .../lib/airavata/workspaceModel_constants.h     |    41 +
 .../lib/airavata/workspaceModel_types.cpp       |   481 +
 .../lib/airavata/workspaceModel_types.h         |   290 +
 .../resources/lib/airavataAPI_constants.cpp     |    19 -
 .../main/resources/lib/airavataAPI_constants.h  |    25 -
 .../main/resources/lib/airavataAPI_types.cpp    |    13 -
 .../src/main/resources/lib/airavataAPI_types.h  |    30 -
 .../lib/airavataDataModel_constants.cpp         |    17 -
 .../resources/lib/airavataDataModel_constants.h |    24 -
 .../resources/lib/airavataDataModel_types.cpp   |    13 -
 .../resources/lib/airavataDataModel_types.h     |    24 -
 .../resources/lib/airavataErrors_constants.cpp  |    17 -
 .../resources/lib/airavataErrors_constants.h    |    24 -
 .../main/resources/lib/airavataErrors_types.cpp |   820 -
 .../main/resources/lib/airavataErrors_types.h   |   509 -
 .../lib/applicationCatalogAPI_constants.cpp     |    19 -
 .../lib/applicationCatalogAPI_constants.h       |    25 -
 .../lib/applicationCatalogAPI_types.cpp         |    13 -
 .../resources/lib/applicationCatalogAPI_types.h |    27 -
 .../applicationCatalogDataModel_constants.cpp   |    19 -
 .../lib/applicationCatalogDataModel_constants.h |    25 -
 .../lib/applicationCatalogDataModel_types.cpp   |  1327 -
 .../lib/applicationCatalogDataModel_types.h     |   713 -
 .../applicationDeploymentModel_constants.cpp    |    19 -
 .../lib/applicationDeploymentModel_constants.h  |    25 -
 .../lib/applicationDeploymentModel_types.cpp    |   497 -
 .../lib/applicationDeploymentModel_types.h      |   275 -
 .../lib/applicationInterfaceModel_constants.cpp |    19 -
 .../lib/applicationInterfaceModel_constants.h   |    25 -
 .../lib/applicationInterfaceModel_types.cpp     |   470 -
 .../lib/applicationInterfaceModel_types.h       |   298 -
 .../lib/computeResourceModel_constants.cpp      |    19 -
 .../lib/computeResourceModel_constants.h        |    25 -
 .../lib/computeResourceModel_types.cpp          |  1515 -
 .../resources/lib/computeResourceModel_types.h  |   842 -
 .../resources/lib/experimentModel_constants.cpp |    23 -
 .../resources/lib/experimentModel_constants.h   |    27 -
 .../resources/lib/experimentModel_types.cpp     |  3339 --
 .../main/resources/lib/experimentModel_types.h  |  2077 --
 .../lib/gatewayProfileModel_constants.cpp       |    19 -
 .../lib/gatewayProfileModel_constants.h         |    25 -
 .../resources/lib/gatewayProfileModel_types.cpp |   293 -
 .../resources/lib/gatewayProfileModel_types.h   |   197 -
 .../gatewayResourceProfileModel_constants.cpp   |    19 -
 .../lib/gatewayResourceProfileModel_constants.h |    25 -
 .../lib/gatewayResourceProfileModel_types.cpp   |   293 -
 .../lib/gatewayResourceProfileModel_types.h     |   197 -
 .../lib/thrift/TApplicationException.cpp        |    80 +
 .../lib/thrift/TApplicationException.h          |   115 +
 .../resources/lib/thrift/TDispatchProcessor.h   |   142 +
 .../src/main/resources/lib/thrift/TLogging.h    |   193 +
 .../src/main/resources/lib/thrift/TProcessor.h  |   233 +
 .../resources/lib/thrift/TReflectionLocal.h     |    96 +
 .../src/main/resources/lib/thrift/Thrift.cpp    |   125 +
 .../src/main/resources/lib/thrift/Thrift.h      |   202 +
 .../resources/lib/thrift/VirtualProfiling.cpp   |   455 +
 .../lib/thrift/async/TAsyncBufferProcessor.h    |    46 +
 .../lib/thrift/async/TAsyncChannel.cpp          |    34 +
 .../resources/lib/thrift/async/TAsyncChannel.h  |    66 +
 .../lib/thrift/async/TAsyncDispatchProcessor.h  |   149 +
 .../lib/thrift/async/TAsyncProcessor.h          |    97 +
 .../thrift/async/TAsyncProtocolProcessor.cpp    |    51 +
 .../lib/thrift/async/TAsyncProtocolProcessor.h  |    57 +
 .../lib/thrift/async/TEvhttpClientChannel.cpp   |   162 +
 .../lib/thrift/async/TEvhttpClientChannel.h     |    76 +
 .../lib/thrift/async/TEvhttpServer.cpp          |   169 +
 .../resources/lib/thrift/async/TEvhttpServer.h  |    71 +
 .../lib/thrift/concurrency/BoostMonitor.cpp     |   211 +
 .../lib/thrift/concurrency/BoostMutex.cpp       |    56 +
 .../thrift/concurrency/BoostThreadFactory.cpp   |   180 +
 .../lib/thrift/concurrency/BoostThreadFactory.h |    75 +
 .../lib/thrift/concurrency/Exception.h          |    64 +
 .../lib/thrift/concurrency/FunctionRunner.h     |   121 +
 .../lib/thrift/concurrency/Monitor.cpp          |   221 +
 .../resources/lib/thrift/concurrency/Monitor.h  |   130 +
 .../resources/lib/thrift/concurrency/Mutex.cpp  |   353 +
 .../resources/lib/thrift/concurrency/Mutex.h    |   188 +
 .../thrift/concurrency/PlatformThreadFactory.h  |    44 +
 .../thrift/concurrency/PosixThreadFactory.cpp   |   341 +
 .../lib/thrift/concurrency/PosixThreadFactory.h |   130 +
 .../lib/thrift/concurrency/StdMonitor.cpp       |   217 +
 .../lib/thrift/concurrency/StdMutex.cpp         |    55 +
 .../lib/thrift/concurrency/StdThreadFactory.cpp |   171 +
 .../lib/thrift/concurrency/StdThreadFactory.h   |    72 +
 .../resources/lib/thrift/concurrency/Thread.h   |   152 +
 .../lib/thrift/concurrency/ThreadManager.cpp    |   583 +
 .../lib/thrift/concurrency/ThreadManager.h      |   202 +
 .../lib/thrift/concurrency/TimerManager.cpp     |   305 +
 .../lib/thrift/concurrency/TimerManager.h       |   130 +
 .../resources/lib/thrift/concurrency/Util.cpp   |    41 +
 .../resources/lib/thrift/concurrency/Util.h     |   152 +
 .../src/main/resources/lib/thrift/config.h      |   427 +
 .../main/resources/lib/thrift/cxxfunctional.h   |   126 +
 .../lib/thrift/processor/PeekProcessor.cpp      |   127 +
 .../lib/thrift/processor/PeekProcessor.h        |    78 +
 .../lib/thrift/processor/StatsProcessor.h       |   266 +
 .../thrift/processor/TMultiplexedProcessor.h    |   218 +
 .../lib/thrift/protocol/TBase64Utils.cpp        |    79 +
 .../lib/thrift/protocol/TBase64Utils.h          |    42 +
 .../lib/thrift/protocol/TBinaryProtocol.h       |   282 +
 .../lib/thrift/protocol/TBinaryProtocol.tcc     |   465 +
 .../lib/thrift/protocol/TCompactProtocol.h      |   289 +
 .../lib/thrift/protocol/TCompactProtocol.tcc    |   818 +
 .../lib/thrift/protocol/TDebugProtocol.cpp      |   358 +
 .../lib/thrift/protocol/TDebugProtocol.h        |   227 +
 .../lib/thrift/protocol/TDenseProtocol.cpp      |   768 +
 .../lib/thrift/protocol/TDenseProtocol.h        |   254 +
 .../lib/thrift/protocol/TJSONProtocol.cpp       |  1023 +
 .../lib/thrift/protocol/TJSONProtocol.h         |   339 +
 .../thrift/protocol/TMultiplexedProtocol.cpp    |    47 +
 .../lib/thrift/protocol/TMultiplexedProtocol.h  |   103 +
 .../resources/lib/thrift/protocol/TProtocol.h   |   697 +
 .../lib/thrift/protocol/TProtocolDecorator.h    |   133 +
 .../lib/thrift/protocol/TProtocolException.h    |   104 +
 .../lib/thrift/protocol/TProtocolTap.h          |   188 +
 .../lib/thrift/protocol/TVirtualProtocol.h      |   564 +
 .../lib/thrift/qt/TQIODeviceTransport.cpp       |   179 +
 .../lib/thrift/qt/TQIODeviceTransport.h         |    64 +
 .../resources/lib/thrift/qt/TQTcpServer.cpp     |   157 +
 .../main/resources/lib/thrift/qt/TQTcpServer.h  |    72 +
 .../resources/lib/thrift/qt/moc_TQTcpServer.cpp |   100 +
 .../lib/thrift/server/TNonblockingServer.cpp    |  1567 +
 .../lib/thrift/server/TNonblockingServer.h      |   944 +
 .../resources/lib/thrift/server/TServer.cpp     |    47 +
 .../main/resources/lib/thrift/server/TServer.h  |   315 +
 .../lib/thrift/server/TSimpleServer.cpp         |   153 +
 .../resources/lib/thrift/server/TSimpleServer.h |   102 +
 .../lib/thrift/server/TThreadPoolServer.cpp     |   211 +
 .../lib/thrift/server/TThreadPoolServer.h       |   136 +
 .../lib/thrift/server/TThreadedServer.cpp       |   241 +
 .../lib/thrift/server/TThreadedServer.h         |   145 +
 .../src/main/resources/lib/thrift/stamp-h2      |     1 +
 .../main/resources/lib/thrift/thrift-config.h   |    24 +
 .../lib/thrift/transport/PlatformSocket.h       |    96 +
 .../lib/thrift/transport/TBufferTransports.cpp  |   391 +
 .../lib/thrift/transport/TBufferTransports.h    |   735 +
 .../lib/thrift/transport/TFDTransport.cpp       |    97 +
 .../lib/thrift/transport/TFDTransport.h         |    75 +
 .../lib/thrift/transport/TFileTransport.cpp     |  1069 +
 .../lib/thrift/transport/TFileTransport.h       |   474 +
 .../lib/thrift/transport/THttpClient.cpp        |   117 +
 .../lib/thrift/transport/THttpClient.h          |    49 +
 .../lib/thrift/transport/THttpServer.cpp        |   152 +
 .../lib/thrift/transport/THttpServer.h          |    64 +
 .../lib/thrift/transport/THttpTransport.cpp     |   252 +
 .../lib/thrift/transport/THttpTransport.h       |   107 +
 .../resources/lib/thrift/transport/TPipe.cpp    |   217 +
 .../main/resources/lib/thrift/transport/TPipe.h |    96 +
 .../lib/thrift/transport/TPipeServer.cpp        |   402 +
 .../lib/thrift/transport/TPipeServer.h          |    93 +
 .../lib/thrift/transport/TSSLServerSocket.cpp   |    47 +
 .../lib/thrift/transport/TSSLServerSocket.h     |    59 +
 .../lib/thrift/transport/TSSLSocket.cpp         |   671 +
 .../resources/lib/thrift/transport/TSSLSocket.h |   315 +
 .../lib/thrift/transport/TServerSocket.cpp      |   490 +
 .../lib/thrift/transport/TServerSocket.h        |    86 +
 .../lib/thrift/transport/TServerTransport.h     |    92 +
 .../lib/thrift/transport/TShortReadTransport.h  |    97 +
 .../thrift/transport/TSimpleFileTransport.cpp   |    67 +
 .../lib/thrift/transport/TSimpleFileTransport.h |    41 +
 .../resources/lib/thrift/transport/TSocket.cpp  |   813 +
 .../resources/lib/thrift/transport/TSocket.h    |   309 +
 .../lib/thrift/transport/TSocketPool.cpp        |   254 +
 .../lib/thrift/transport/TSocketPool.h          |   196 +
 .../resources/lib/thrift/transport/TTransport.h |   270 +
 .../thrift/transport/TTransportException.cpp    |    31 +
 .../lib/thrift/transport/TTransportException.h  |   115 +
 .../lib/thrift/transport/TTransportUtils.cpp    |   178 +
 .../lib/thrift/transport/TTransportUtils.h      |   330 +
 .../lib/thrift/transport/TVirtualTransport.h    |   146 +
 .../lib/thrift/transport/TZlibTransport.cpp     |   399 +
 .../lib/thrift/transport/TZlibTransport.h       |   249 +
 .../lib/thrift/windows/GetTimeOfDay.cpp         |   112 +
 .../resources/lib/thrift/windows/GetTimeOfDay.h |    43 +
 .../resources/lib/thrift/windows/Operators.h    |    40 +
 .../resources/lib/thrift/windows/SocketPair.cpp |   102 +
 .../resources/lib/thrift/windows/SocketPair.h   |    37 +
 .../resources/lib/thrift/windows/StdAfx.cpp     |     0
 .../main/resources/lib/thrift/windows/StdAfx.h  |     0
 .../lib/thrift/windows/TWinsockSingleton.cpp    |    73 +
 .../lib/thrift/windows/TWinsockSingleton.h      |    88 +
 .../lib/thrift/windows/TargetVersion.h          |     0
 .../resources/lib/thrift/windows/WinFcntl.cpp   |   104 +
 .../resources/lib/thrift/windows/WinFcntl.h     |    48 +
 .../main/resources/lib/thrift/windows/config.h  |    90 +
 .../resources/lib/thrift/windows/force_inc.h    |     0
 .../resources/lib/thrift/windows/tr1/functional |     0
 .../resources/lib/workflowAPI_constants.cpp     |    19 -
 .../main/resources/lib/workflowAPI_constants.h  |    25 -
 .../main/resources/lib/workflowAPI_types.cpp    |    13 -
 .../src/main/resources/lib/workflowAPI_types.h  |    30 -
 .../lib/workflowDataModel_constants.cpp         |    19 -
 .../resources/lib/workflowDataModel_constants.h |    25 -
 .../resources/lib/workflowDataModel_types.cpp   |   108 -
 .../resources/lib/workflowDataModel_types.h     |    82 -
 .../resources/lib/workspaceModel_constants.cpp  |    17 -
 .../resources/lib/workspaceModel_constants.h    |    24 -
 .../main/resources/lib/workspaceModel_types.cpp |   464 -
 .../main/resources/lib/workspaceModel_types.h   |   273 -
 .../airavata-php-sdk/pom.xml                    |     2 +-
 .../src/main/assembly/bin-assembly.xml          |     3 +-
 .../airavata-php-sdk/src/main/resources/INSTALL |    31 -
 .../airavata-php-sdk/src/main/resources/LICENSE |  1866 --
 .../airavata-php-sdk/src/main/resources/NOTICE  |   160 +-
 .../conf/airavata-client-properties.ini         |     4 +-
 .../resources/conf/app-catalog-identifiers.ini  |    20 +-
 .../Model/AppCatalog/ComputeResource/Types.php  |   224 +
 .../airavata-client-api-tester.php              |   132 +-
 .../php-cli-samples/cloneExperiment.php         |    20 +
 .../php-cli-samples/createExperiment.php        |   187 +-
 .../resources/php-cli-samples/createProject.php |    64 +-
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 .../getAllApplicationInterfaceNames.php         |    20 +
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 ...getAvailableAppInterfaceComputeResources.php |    20 +
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 .../getGatewayComputeResourcePreference.php     |    82 +
 .../php-cli-samples/launchExperiment.php        |    69 +-
 .../registerApplicationDeployment.php           |    20 +
 .../registerApplicationInterface.php            |    22 +
 .../registerApplicationModule.php               |    20 +
 .../php-cli-samples/registerComputeResource.php |    20 +
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 .../java-client-samples/pom.xml                 |     2 +-
 .../samples/CreateLaunchExperimentUS3.java      |    19 +
 .../tools/RegisterSampleApplications.java       |   189 +-
 airavata-api/airavata-client-sdks/pom.xml       |     2 +-
 airavata-api/airavata-data-models/pom.xml       |     2 +-
 .../org/apache/airavata/model/Workflow.java     |    33 +-
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 .../airavata/model/error/ValidationResults.java |    33 +-
 .../airavata/model/error/ValidatorResult.java   |    33 +-
 .../model/workflowDataModelConstants.java       |    33 +-
 .../airavata/model/workspace/Gateway.java       |    33 +-
 .../apache/airavata/model/workspace/Group.java  |    33 +-
 .../airavata/model/workspace/Project.java       |    33 +-
 .../apache/airavata/model/workspace/User.java   |    33 +-
 .../workspace/experiment/ActionableGroup.java   |    33 +-
 .../experiment/AdvancedInputDataHandling.java   |    33 +-
 .../experiment/AdvancedOutputDataHandling.java  |    33 +-
 .../workspace/experiment/ApplicationStatus.java |    33 +-
 .../ComputationalResourceScheduling.java        |    33 +-
 .../workspace/experiment/CorrectiveAction.java  |    33 +-
 .../workspace/experiment/DataObjectType.java    |    33 +-
 .../experiment/DataTransferDetails.java         |    33 +-
 .../model/workspace/experiment/DataType.java    |    33 +-
 .../workspace/experiment/ErrorCategory.java     |    33 +-
 .../workspace/experiment/ErrorDetails.java      |    33 +-
 .../workspace/experiment/ExecutionUnit.java     |    33 +-
 .../model/workspace/experiment/Experiment.java  |    33 +-
 .../workspace/experiment/ExperimentState.java   |    33 +-
 .../workspace/experiment/ExperimentStatus.java  |    33 +-
 .../workspace/experiment/ExperimentSummary.java |    33 +-
 .../model/workspace/experiment/JobDetails.java  |    33 +-
 .../model/workspace/experiment/JobState.java    |    33 +-
 .../model/workspace/experiment/JobStatus.java   |    33 +-
 .../experiment/QualityOfServiceParams.java      |    33 +-
 .../model/workspace/experiment/TaskDetails.java |    33 +-
 .../model/workspace/experiment/TaskState.java   |    33 +-
 .../model/workspace/experiment/TaskStatus.java  |    33 +-
 .../workspace/experiment/TransferState.java     |    33 +-
 .../workspace/experiment/TransferStatus.java    |    33 +-
 .../experiment/UserConfigurationData.java       |    33 +-
 .../workspace/experiment/ValidationResults.java |    33 +-
 .../workspace/experiment/ValidatorResult.java   |    33 +-
 .../experiment/WorkflowNodeDetails.java         |    33 +-
 .../workspace/experiment/WorkflowNodeState.java |    33 +-
 .../experiment/WorkflowNodeStatus.java          |    33 +-
 .../experiment/experimentModelConstants.java    |    33 +-
 airavata-api/airavata-model-utils/pom.xml       |     2 +-
 .../airavata/model/util/ProjectModelUtil.java   |    19 +
 airavata-api/generate-thrift-files.sh           |    52 +-
 airavata-api/pom.xml                            |     2 +-
 .../computeResourceModel.thrift                 |    26 +
 modules/airavata-client/pom.xml                 |     2 +-
 .../airavata/client/AiravataAPIFactory.java     |     4 +-
 .../client/tools/DocumentCreatorNew.java        |     8 +-
 .../client/tools/UltrascanDocumentCreator.java  |    19 +
 modules/app-catalog/app-catalog-cpi/pom.xml     |     5 +-
 .../org/airavata/appcatalog/cpi/AppCatalog.java |    19 +
 .../appcatalog/cpi/AppCatalogException.java     |    19 +
 .../appcatalog/cpi/ApplicationDeployment.java   |    19 +
 .../appcatalog/cpi/ApplicationInterface.java    |    19 +
 .../appcatalog/cpi/ComputeResource.java         |    19 +
 .../appcatalog/cpi/GwyResourceProfile.java      |    19 +
 modules/app-catalog/app-catalog-data/pom.xml    |     2 +-
 .../resources/ApplicationInputResource.java     |    19 +
 .../resources/ApplicationOutputResource.java    |    19 +
 .../resources/DataMovementProtocolResource.java |    19 +
 .../data/resources/GSISSHExportResource.java    |    19 +
 .../resources/GSISSHPostJobCommandResource.java |    19 +
 .../resources/GSISSHPreJobCommandResource.java  |    19 +
 .../resources/GSISSHSubmissionResource.java     |    19 +
 .../data/resources/GatewayProfileResource.java  |    19 +
 .../resources/GlobusGKEndpointResource.java     |    19 +
 .../resources/GlobusJobSubmissionResource.java  |    19 +
 .../resources/GridftpDataMovementResource.java  |    19 +
 .../data/resources/GridftpEndpointResource.java |    19 +
 .../data/resources/HostAliasResource.java       |    19 +
 .../data/resources/HostIPAddressResource.java   |    19 +
 .../JobSubmissionProtocolResource.java          |    19 +
 .../data/resources/ScpDataMovementResource.java |    19 +
 .../resources/SshJobSubmissionResource.java     |    19 +
 .../app/catalog/test/AppDeploymentTest.java     |   147 +
 .../app/catalog/test/AppInterfaceTest.java      |   173 +
 .../app/catalog/test/ComputeResourceTest.java   |   278 +
 .../app/catalog/test/GatewayProfileTest.java    |   127 +
 .../app/catalog/test/util/Initialize.java       |   321 +
 modules/app-catalog/pom.xml                     |     2 +-
 modules/commons/gfac-schema/pom.xml             |     2 +-
 modules/commons/pom.xml                         |     2 +-
 modules/commons/utils/pom.xml                   |     5 +-
 .../commons/workflow-execution-context/pom.xml  |     2 +-
 modules/commons/workflow-tracking/pom.xml       |     2 +-
 modules/configuration/client/pom.xml            |     2 +-
 modules/configuration/pom.xml                   |     2 +-
 modules/configuration/server/pom.xml            |     2 +-
 .../server/src/main/resources/PBSTemplate.xslt  |    10 +-
 .../credential-store-webapp/pom.xml             |     2 +-
 .../credential-store/pom.xml                    |     2 +-
 modules/credential-store-service/pom.xml        |     2 +-
 modules/distribution/client/java/pom.xml        |     2 +-
 modules/distribution/client/pom.xml             |     2 +-
 modules/distribution/pom.xml                    |     2 +-
 modules/distribution/release/pom.xml            |     2 +-
 modules/distribution/server/pom.xml             |     2 +-
 modules/gfac/airavata-gfac-service/pom.xml      |     2 +-
 .../src/test/resources/monitor.properties       |    20 +
 modules/gfac/gfac-bes/pom.xml                   |     2 +-
 modules/gfac/gfac-core/pom.xml                  |     2 +-
 .../AiravataWorkflowNodeStatusUpdator.java      |     2 +-
 .../airavata/gfac/core/monitor/MonitorID.java   |    21 +-
 modules/gfac/gfac-ec2/pom.xml                   |     2 +-
 modules/gfac/gfac-gram/pom.xml                  |     2 +-
 modules/gfac/gfac-gsissh/pom.xml                |     2 +-
 modules/gfac/gfac-hadoop/pom.xml                |     2 +-
 modules/gfac/gfac-local/pom.xml                 |     2 +-
 modules/gfac/gfac-monitor/pom.xml               |     5 +-
 .../monitor/impl/pull/qstat/HPCPullMonitor.java |    15 +-
 .../airavata/gfac/monitor/util/CommonUtils.java |     1 +
 modules/gfac/gfac-ssh/pom.xml                   |     5 +-
 modules/gfac/pom.xml                            |     2 +-
 .../airavata-orchestrator-service/pom.xml       |     2 +-
 .../orchestrator-client-sdks/pom.xml            |     2 +-
 modules/orchestrator/orchestrator-core/pom.xml  |     2 +-
 .../core/model/ExperimentConfigurationData.java |    19 +
 .../core/model/ResourceScheduling.java          |    19 +
 modules/orchestrator/pom.xml                    |     2 +-
 modules/registry/airavata-jpa-registry/pom.xml  |     2 +-
 .../registry/jpa/impl/ProjectRegistry.java      |     1 +
 .../registry/jpa/TaskDetailResourceTest.java    |    19 +
 .../jpa/WorkflowNodeDetailResourceTest.java     |    19 +
 modules/registry/pom.xml                        |     2 +-
 modules/registry/registry-api/pom.xml           |     2 +-
 .../api/orchestrator/OrchestratorData.java      |    19 +
 .../orchestrator/impl/OrchestratorDataImpl.java |    19 +
 modules/registry/registry-cpi/pom.xml           |     2 +-
 .../airavata/registry/cpi/ChildDataType.java    |    19 +
 .../airavata/registry/cpi/ParentDataType.java   |    19 +
 .../apache/airavata/registry/cpi/Registry.java  |    19 +
 .../registry/cpi/RegistryModelType.java         |    19 +
 .../airavata/registry/cpi/utils/StatusType.java |    19 +
 modules/security/pom.xml                        |     2 +-
 modules/server/pom.xml                          |     2 +-
 modules/test-suite/pom.xml                      |     2 +-
 modules/workflow-model/pom.xml                  |     2 +-
 .../workflow-model/workflow-model-core/pom.xml  |     2 +-
 modules/ws-messenger/client/pom.xml             |     2 +-
 modules/ws-messenger/commons/pom.xml            |     2 +-
 modules/ws-messenger/message-monitor/pom.xml    |     2 +-
 modules/ws-messenger/pom.xml                    |     2 +-
 pom.xml                                         |     2 +-
 tools/gsissh/pom.xml                            |     2 +-
 .../src/main/resources/SLURMTemplate.xslt       |     4 +-
 tools/pom.xml                                   |     2 +-
 tools/registry-tool/pom.xml                     |     2 +-
 509 files changed, 94550 insertions(+), 75256 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/airavata/blob/16cd757f/airavata-api/airavata-api-server/pom.xml
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/airavata/blob/16cd757f/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
----------------------------------------------------------------------
diff --cc airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
index 3c610f0,873c4f2..90f4857
--- a/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
+++ b/airavata-api/airavata-api-server/src/main/java/org/apache/airavata/api/server/handler/AiravataServerHandler.java
@@@ -45,8 -45,8 +45,9 @@@ import org.apache.aiaravata.application
  import org.apache.aiaravata.application.catalog.data.util.AppCatalogThriftConversion;
  import org.apache.airavata.api.Airavata;
  import org.apache.airavata.api.airavataAPIConstants;
 +import org.apache.airavata.api.server.util.DataModelUtils;
  import org.apache.airavata.common.exception.ApplicationSettingsException;
+ import org.apache.airavata.common.utils.AiravataUtils;
  import org.apache.airavata.common.utils.ServerSettings;
  import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription;
  import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule;

http://git-wip-us.apache.org/repos/asf/airavata/blob/16cd757f/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
----------------------------------------------------------------------
diff --cc airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
index 1374f9f,781c216..1f28d88
--- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
+++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java
@@@ -249,22 -248,22 +249,22 @@@ public class RegisterSampleApplication
  //        registerAutoDockInterface();
  
          //Registering Espresso
- //        registerEspressoInterface();
+         registerEspressoInterface();
  
          //Registering Gromacs
- //        registerGromacsInterface();
+         registerGromacsInterface();
  
          //Registering Lammps
- //        registerLammpsInterface();
+         registerLammpsInterface();
  
          //Registering NWChem
- //        registerNWChemInterface();
+         registerNWChemInterface();
  
          //Registering Trinity
- //        registerTrinityInterface();
+         registerTrinityInterface();
  
          //Registering WRF
 -        registerWRFInterface();
 +//        registerWRFInterface();
  
      }
  
@@@ -930,27 -794,33 +937,31 @@@
      }
  
      public static void writeIdPropertyFile() {
- //
- //        try {
- //            Properties properties = new Properties();
- //            properties.setProperty("stampedeResourceId", stampedeResourceId);
- //            properties.setProperty("trestlesResourceId", trestlesResourceId);
- //            properties.setProperty("bigredResourceId", bigredResourceId);
- //
- //            properties.setProperty("echoInterfaceId", echoInterfaceId);
- //            properties.setProperty("amberInterfaceId", amberInterfaceId);
- //            properties.setProperty("wrfInterfaceId", wrfInterfaceId);
- //
- //            File file = new File("airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini");
- //            FileOutputStream fileOut = new FileOutputStream(file);
- //            properties.store(fileOut, "Apache Airavata Gateway to Airavata Deployment
Identifiers");
- //            fileOut.close();
- //        } catch (FileNotFoundException e) {
- //            e.printStackTrace();
- //        } catch (IOException e) {
- //            e.printStackTrace();
- //        }
--
+         try {
+             Properties properties = new Properties();
+             properties.setProperty("stampedeResourceId", stampedeResourceId);
+             properties.setProperty("trestlesResourceId", trestlesResourceId);
+             properties.setProperty("bigredResourceId", bigredResourceId);
+ 
+             properties.setProperty("echoInterfaceId", echoInterfaceId);
+             properties.setProperty("amberInterfaceId", amberInterfaceId);
+             properties.setProperty("autoDockInterfaceId", autoDockInterfaceId);
+             properties.setProperty("espressoInterfaceId", espressoInterfaceId);
+             properties.setProperty("gromacsInterfaceId", gromacsInterfaceId);
+             properties.setProperty("lammpsInterfaceId", lammpsInterfaceId);
+             properties.setProperty("nwChemInterfaceId", nwChemInterfaceId);
+             properties.setProperty("trinityInterfaceId", trinityInterfaceId);
+             properties.setProperty("wrfInterfaceId", wrfInterfaceId);
+ 
+             File file = new File("airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini");
+             FileOutputStream fileOut = new FileOutputStream(file);
+             properties.store(fileOut, "Apache Airavata Gateway to Airavata Deployment Identifiers");
+             fileOut.close();
+         } catch (FileNotFoundException e) {
+             e.printStackTrace();
+         } catch (IOException e) {
+             e.printStackTrace();
+         }
 -
      }
  }
  

http://git-wip-us.apache.org/repos/asf/airavata/blob/16cd757f/modules/commons/utils/pom.xml
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/airavata/blob/16cd757f/modules/distribution/server/pom.xml
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/airavata/blob/16cd757f/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/monitor/AiravataWorkflowNodeStatusUpdator.java
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/airavata/blob/16cd757f/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
----------------------------------------------------------------------
diff --cc modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
index 4208c85,599446a..5150b49
--- a/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
+++ b/modules/gfac/gfac-monitor/src/main/java/org/apache/airavata/gfac/monitor/impl/pull/qstat/HPCPullMonitor.java
@@@ -179,13 -178,11 +179,13 @@@ public class HPCPullMonitor extends Pul
                              } catch (GFacException e) {
                              	publisher.publish(new TaskStatusChangeRequest(new TaskIdentity(iMonitorID.getExperimentID(),
iMonitorID.getWorkflowNodeID(),
  										iMonitorID.getTaskID()), TaskState.FAILED));
 -                            	publisher.publish(new ExperimentStatusChangeRequest(new ExperimentIdentity(iMonitorID.getExperimentID()),
 -										ExperimentState.FAILED));
 +                            	//FIXME this is a case where the output retrieving fails even
if the job execution was a success. Thus updating the task status 
 +                            	//should be done understanding whole workflow of job submission
and data transfer
 +//                            	publisher.publish(new ExperimentStatusChangedEvent(new ExperimentIdentity(iMonitorID.getExperimentID()),
 +//										ExperimentState.FAILED));
                                  logger.info(e.getLocalizedMessage(), e);
                              }
-                         } else if (iMonitorID.getFailedCount() > 2 && iMonitorID.getStatus().equals(JobState.UNKNOWN))
{
+                         } else if (iMonitorID.getFailedCount() > 2) {
                              logger.error("Tried to monitor the job with ID " + iMonitorID.getJobID()
+ " But failed 3 times, so skip this Job from Monitor");
                              iMonitorID.setLastMonitored(new Timestamp((new Date()).getTime()));
                              completedJobs.add(iMonitorID);

http://git-wip-us.apache.org/repos/asf/airavata/blob/16cd757f/modules/workflow-model/pom.xml
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/airavata/blob/16cd757f/modules/workflow-model/workflow-model-core/pom.xml
----------------------------------------------------------------------

http://git-wip-us.apache.org/repos/asf/airavata/blob/16cd757f/pom.xml
----------------------------------------------------------------------


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