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From sma...@apache.org
Subject [47/47] git commit: Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata into HEAD
Date Sat, 12 Jul 2014 04:09:05 GMT
Merge branch 'master' of https://git-wip-us.apache.org/repos/asf/airavata into HEAD


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/69769b8d
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/69769b8d
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/69769b8d

Branch: refs/heads/master
Commit: 69769b8df043dc9173261832851a453f19dc457a
Parents: c9af283 a0f5419
Author: Suresh Marru <smarru@apache.org>
Authored: Sat Jul 12 00:07:33 2014 -0400
Committer: Suresh Marru <smarru@apache.org>
Committed: Sat Jul 12 00:07:33 2014 -0400

----------------------------------------------------------------------
 .../server/handler/AiravataServerHandler.java   |   15 +
 .../airavata-php-sdk/pom.xml                    |    2 +-
 .../conf/airavata-client-properties.ini         |    1 +
 .../resources/conf/app-catalog-identifiers.ini  |    8 +
 .../php-cli-samples/createExperiment.php        |   16 +-
 .../php-cli-samples/deleteComputeResource.php   |   49 +
 .../getAllComputeResourceNames.php              |   39 +
 .../resources/php-cli-samples/getAppModule.php  |   68 -
 .../getApplicationDeployment.php                |   46 +
 .../php-cli-samples/getApplicationModule.php    |   68 +
 .../php-cli-samples/getComputeResource.php      |   46 +
 .../php-cli-samples/launchExperiment.php        |    2 +-
 .../updateApplicationInterface.php              |   32 +-
 .../client/samples/CreateLaunchExperiment.java  |  331 +-
 .../tools/RegisterSampleApplications.java       |  813 +++++
 .../tools/RegisterSampleApplicationsUtils.java  |  158 +
 .../applicationDeploymentModel.thrift           |    2 +-
 .../client/tools/DocumentCreatorNew.java        |  511 ++-
 .../data/impl/ApplicationDeploymentImpl.java    |   32 +-
 .../data/impl/ApplicationInterfaceImpl.java     |   47 +-
 .../catalog/data/impl/ComputeResourceImpl.java  |   15 +-
 .../catalog/data/util/AppCatalogJPAUtils.java   |  368 ++-
 .../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 --
 .../server/src/main/resources/PBSTemplate.xslt  |   14 +-
 .../src/main/resources/SLURMTemplate.xslt       |    5 +
 .../main/resources/airavata-server.properties   |    4 +-
 .../server/src/main/resources/gfac-config.xml   |    2 +-
 .../airavata/gfac/server/GfacServerHandler.java |    6 +-
 .../airavata/gfac/core/cpi/BetterGfacImpl.java  |  232 +-
 .../apache/airavata/gfac/core/cpi/GFacImpl.java |    4 +-
 .../AiravataExperimentStatusUpdator.java        |    2 +-
 .../AiravataWorkflowNodeStatusUpdator.java      |    2 +-
 .../airavata/gfac/core/utils/GFacUtils.java     | 1917 ++++++-----
 .../gfac/gsissh/util/GFACGSISSHUtils.java       |    2 +-
 .../monitor/impl/pull/qstat/HPCPullMonitor.java |   11 +
 .../gfac/ssh/handler/SSHOutputHandler.java      |   20 +
 .../airavata/gfac/ssh/util/GFACSSHUtils.java    |    1 +
 .../airavata/integration/SimpleEchoIT.java      |    8 +-
 .../SingleAppIntegrationTestBase.java           |    2 +-
 .../cpi/impl/AbstractOrchestrator.java          |   12 +-
 .../orchestrator/core/BaseOrchestratorTest.java |    8 +-
 .../registry/jpa/impl/ExperimentRegistry.java   |   70 +-
 .../registry/jpa/impl/RegistryImpl.java         |   44 +-
 .../registry/jpa/resources/Utils.java           |   17 +-
 .../registry/jpa/resources/WorkerResource.java  |   18 +-
 .../resources/WorkflowNodeDetailResource.java   |    3 +-
 .../jpa/utils/ThriftDataModelConversion.java    |   24 +-
 modules/xbaya-gui/pom.xml                       |   20 +-
 .../apache/airavata/xbaya/ThriftClientData.java |   70 +
 .../airavata/xbaya/ThriftServiceType.java       |   27 +
 .../java/org/apache/airavata/xbaya/XBaya.java   |   42 -
 .../airavata/xbaya/XBayaConfiguration.java      |  140 +-
 .../org/apache/airavata/xbaya/XBayaEngine.java  |   99 +-
 .../registry/ComponentRegistryLoader.java       |   15 +-
 .../xbaya/core/generators/ScuflFiler.java       |   89 +-
 .../xbaya/interpretor/DoWhileHandler.java       |    9 +-
 .../xbaya/interpretor/ExperimentTemplate.java   |   74 +-
 .../GUIWorkflowInterpreterInteractorImpl.java   |  418 +--
 .../SSWorkflowInterpreterInteractorImpl.java    |  232 +-
 .../interpretor/WorkflowExecutionTemplate.java  |  102 +-
 .../xbaya/interpretor/WorkflowInterpreter.java  | 3008 +++++++++---------
 .../WorkflowInterpreterConfiguration.java       |  464 +--
 .../WorkflowInterpreterInteractor.java          |  180 +-
 .../WorkflowInterpretorEventListener.java       |  772 ++---
 ...WorkflowInterpretorMessageReceiverInOut.java |  524 +--
 .../WorkflowInterpretorSkeleton.java            | 1135 ++++---
 .../xbaya/invoker/EmbeddedGFacInvoker.java      | 1364 ++++----
 .../xbaya/jython/script/JythonScript.java       |    1 -
 .../xbaya/lead/LeadContextHeaderHelper.java     |    1 -
 .../registrybrowser/AiravataConfigurations.java |   54 -
 .../ApplicationDeploymentDescriptionWrap.java   |   98 -
 .../ApplicationDeploymentDescriptions.java      |  107 -
 .../registrybrowser/EventingServiceURL.java     |   54 -
 .../registrybrowser/EventingServiceURLs.java    |   54 -
 .../xbaya/model/registrybrowser/GFacURL.java    |   54 -
 .../xbaya/model/registrybrowser/GFacURLs.java   |   56 -
 .../model/registrybrowser/HostDescriptions.java |   50 -
 .../model/registrybrowser/InputParameters.java  |   36 -
 .../registrybrowser/InterpreterServiceURL.java  |   54 -
 .../registrybrowser/InterpreterServiceURLs.java |   56 -
 .../model/registrybrowser/MessageBoxURL.java    |   54 -
 .../model/registrybrowser/MessageBoxURLs.java   |   54 -
 .../model/registrybrowser/NodeParameter.java    |   60 -
 .../model/registrybrowser/OutputParameters.java |   36 -
 .../registrybrowser/ServiceDescriptions.java    |   50 -
 .../registrybrowser/ServiceParameters.java      |   57 -
 .../model/registrybrowser/XBayaWorkflow.java    |   94 -
 .../XBayaWorkflowExperiment.java                |   81 -
 .../XBayaWorkflowExperiments.java               |   65 -
 .../XBayaWorkflowNodeElement.java               |  107 -
 .../registrybrowser/XBayaWorkflowTemplate.java  |   50 -
 .../registrybrowser/XBayaWorkflowTemplates.java |   63 -
 .../xbaya/provenance/ProvenanceReader.java      |   64 -
 .../xbaya/provenance/ProvenanceWrite.java       |  217 --
 .../provenance/WorkflowNodeStatusUpdater.java   |  135 -
 .../xbaya/provenance/WorkflowStatusUpdater.java |  103 -
 .../xbaya/registry/RegistryAccesser.java        |  212 --
 .../nodes/AbstractAiravataTreeNode.java         |  255 --
 .../nodes/AiravataConfigurationsNode.java       |   94 -
 .../nodes/AiravataTreeNodeFactory.java          |  112 -
 .../ApplicationDeploymentDescriptionNode.java   |  131 -
 .../ApplicationDeploymentDescriptionsNode.java  |  139 -
 .../nodes/EventingServiceURLNode.java           |   98 -
 .../nodes/EventingServiceURLsNode.java          |   91 -
 .../registrybrowser/nodes/GFacURLNode.java      |   98 -
 .../registrybrowser/nodes/GFacURLsNode.java     |   91 -
 .../nodes/HostDescriptionNode.java              |  127 -
 .../nodes/HostDescriptionsNode.java             |  131 -
 .../nodes/InputParametersNode.java              |   46 -
 .../nodes/InterpreterServiceURLNode.java        |   98 -
 .../nodes/InterpreterServiceURLsNode.java       |   90 -
 .../registrybrowser/nodes/JCRBrowserIcons.java  |   50 -
 .../nodes/MessageBoxURLNode.java                |   98 -
 .../nodes/MessageBoxURLsNode.java               |   90 -
 .../nodes/OutputParametersNode.java             |   46 -
 .../registrybrowser/nodes/ParameterNode.java    |  136 -
 .../nodes/ParameterValueNode.java               |   90 -
 .../registrybrowser/nodes/ParametersNode.java   |   90 -
 .../registrybrowser/nodes/RegistryNode.java     |  130 -
 .../nodes/RegistryTreeCellRenderer.java         |   43 -
 .../nodes/ServiceDescriptionNode.java           |  142 -
 .../nodes/ServiceDescriptionsNode.java          |  137 -
 .../nodes/XBayaWorkflowExperimentNode.java      |  141 -
 .../nodes/XBayaWorkflowExperimentsNode.java     |   89 -
 .../nodes/XBayaWorkflowNode.java                |  107 -
 .../nodes/XBayaWorkflowNodeElementNode.java     |  101 -
 .../nodes/XBayaWorkflowTemplateNode.java        |  130 -
 .../nodes/XBayaWorkflowTemplatesNode.java       |   99 -
 .../xbaya/scufl/script/ScuflScript.java         | 1078 +++----
 .../airavata/xbaya/test/BPELScriptTestCase.java |  209 --
 .../airavata/xbaya/test/BrowserTestCase.java    |   38 -
 .../apache/airavata/xbaya/test/DSCTestCase.java |  131 -
 .../airavata/xbaya/test/DSCUtilTestCase.java    |   79 -
 .../xbaya/test/GFacServiceCreaterTestCase.java  |  120 -
 .../airavata/xbaya/test/GraphTestCase.java      |   54 -
 .../airavata/xbaya/test/MetadataTestCase.java   |  221 --
 .../airavata/xbaya/test/MonitorTestCase.java    |   67 -
 .../xbaya/test/ResourceNotifierTestCase.java    |   59 -
 .../airavata/xbaya/test/StringUtilTestCase.java |   55 -
 .../airavata/xbaya/test/WSDLTestCase.java       |   92 -
 .../airavata/xbaya/test/WSDLUtilTestCase.java   |   51 -
 .../airavata/xbaya/test/WSIFTestCase.java       |   53 -
 .../airavata/xbaya/test/WaitDialogTestCase.java |  282 --
 .../WebComponentRegistryClientTestCase.java     |  173 -
 .../test/WorkflowModificationTestCase.java      |  373 ---
 .../airavata/xbaya/test/WorkflowTestCase.java   |  120 -
 .../xbaya/test/XBayaSecurityTestCase.java       |   68 -
 .../airavata/xbaya/test/XBayaTestCase.java      |   77 -
 .../apache/airavata/xbaya/test/XppTestCase.java |   71 -
 .../test/jython/JythonClassLoaderTestCase.java  |   44 -
 .../xbaya/test/jython/JythonLibraryTest.java    |  115 -
 .../jython/JythonOneTimeRunnerTestCase.java     |   70 -
 .../xbaya/test/jython/JythonRunnerTestCase.java |   74 -
 .../xbaya/test/jython/JythonScriptTestCase.java |  131 -
 .../xbaya/test/service/AllServices.java         |  115 -
 .../airavata/xbaya/test/service/Service.java    |   44 -
 .../test/service/ServiceNotificationSender.java |  161 -
 .../xbaya/test/service/adder/Adder.java         |   54 -
 .../xbaya/test/service/adder/AdderClient.java   |  114 -
 .../xbaya/test/service/adder/AdderImpl.java     |   79 -
 .../xbaya/test/service/adder/AdderService.java  |  131 -
 .../xbaya/test/service/approver/Approver.java   |   54 -
 .../test/service/approver/ApproverClient.java   |  113 -
 .../test/service/approver/ApproverImpl.java     |   74 -
 .../test/service/approver/ApproverService.java  |  131 -
 .../test/service/arrayadder/ArrayAdder.java     |   54 -
 .../service/arrayadder/ArrayAdderClient.java    |  121 -
 .../test/service/arrayadder/ArrayAdderImpl.java |   83 -
 .../service/arrayadder/ArrayAdderService.java   |  131 -
 .../test/service/arraygen/ArrayGenerator.java   |   54 -
 .../service/arraygen/ArrayGeneratorClient.java  |  113 -
 .../service/arraygen/ArrayGeneratorImpl.java    |   77 -
 .../service/arraygen/ArrayGeneratorService.java |  131 -
 .../airavata/xbaya/test/service/echo/Echo.java  |   54 -
 .../xbaya/test/service/echo/EchoClient.java     |  116 -
 .../xbaya/test/service/echo/EchoImpl.java       |   73 -
 .../xbaya/test/service/echo/EchoService.java    |  113 -
 .../test/service/multiplier/Multiplier.java     |   54 -
 .../test/service/multiplier/MultiplierImpl.java |   80 -
 .../service/multiplier/MultiplierService.java   |  132 -
 .../xbaya/test/util/WorkflowCreator.java        | 1482 ++++-----
 .../org/apache/airavata/xbaya/ui/XBayaGUI.java  |   72 +-
 ...licationDescriptionAdvancedOptionDialog.java |  358 ---
 .../ApplicationDescriptionDialog.java           |  822 -----
 ...tionDescriptionHostAdvancedOptionDialog.java |  459 ---
 .../DeploymentDescriptionDialog.java            |  816 -----
 .../descriptors/DescriptorEditorDialog.java     |  424 ---
 .../descriptors/DescriptorListDialog.java       |  261 --
 .../descriptors/HostDeploymentDialog.java       |  617 ----
 .../descriptors/HostDescriptionDialog.java      |  592 ----
 .../descriptors/ServiceDescriptionDialog.java   |  727 -----
 .../dynamic/DynamicWorkflowRunnerWindow.java    |  774 ++---
 .../xbaya/ui/dialogs/graph/ws/WSNodeWindow.java |   12 +-
 .../ui/dialogs/registry/RegistryWindow.java     |  268 +-
 .../registry/browser/JCRBrowserDialog.java      |    3 +-
 .../xbaya/ui/experiment/ExperimentMenu.java     |   45 +-
 .../ui/experiment/RegistryLoaderWindow.java     |  239 --
 .../WorkflowInterpreterLaunchWindow.java        |   69 +-
 .../airavata/xbaya/ui/menues/EditMenuItem.java  |   91 +-
 .../airavata/xbaya/ui/menues/RunMenuItem.java   |   56 +-
 .../airavata/xbaya/ui/menues/ViewMenuItem.java  |   22 +-
 .../airavata/xbaya/ui/menues/XBayaMenuItem.java |  177 +-
 .../xbaya/ui/views/JCRBrowserPanel.java         |  574 ++--
 .../airavata/xbaya/util/InterpreterUtil.java    |   42 +-
 .../apache/airavata/xbaya/util/XBayaUtil.java   |  154 +-
 .../interpreter/ComplexForEachWorkflowTest.java |  146 +-
 .../interpreter/ComplexMathWorkflowTest.java    |  142 +-
 .../interpreter/CrossProductWorkflowTest.java   |  142 +-
 .../xbaya/interpreter/ForEachWorkflowTest.java  |  146 +-
 .../xbaya/interpreter/RegistryServiceTest.java  |  210 +-
 .../interpreter/SimpleForEachWorkflowTest.java  |  144 +-
 .../interpreter/SimpleMathWorkflowTest.java     |  146 +-
 .../xbaya/interpreter/WorkflowTest.java         |  148 +-
 .../xbaya/interpreter/WorkflowTrackingTest.java |  210 +-
 .../interpreter/XBayaConsolidatedTestSuite.java |  134 +-
 .../xbaya/interpreter/utils/TestUtilServer.java |  486 +--
 .../interpreter/utils/WorkflowTestUtils.java    |  194 +-
 .../airavata/gsi/ssh/api/job/JobDescriptor.java |    8 +
 .../gsi/ssh/impl/StandardOutReader.java         |    6 +
 .../src/main/resources/SLURMTemplate.xslt       |    5 +
 .../main/resources/schemas/PBSJobDescriptor.xsd |    1 +
 225 files changed, 11432 insertions(+), 26777 deletions(-)
----------------------------------------------------------------------



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