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From shame...@apache.org
Subject [02/13] airavata git commit: merge
Date Tue, 12 Jul 2016 17:49:09 GMT
merge


Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/7cd9457e
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/7cd9457e
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/7cd9457e

Branch: refs/heads/develop
Commit: 7cd9457e9293a56cc2384a0f722a7b642086c86b
Parents: 518868a 2d398cf
Author: scnakandala <supun.nakandala@gmail.com>
Authored: Fri Jul 8 17:19:01 2016 -0400
Committer: scnakandala <supun.nakandala@gmail.com>
Committed: Fri Jul 8 17:19:01 2016 -0400

----------------------------------------------------------------------
 .travis.yml                                     |    14 +
 README                                          |     1 -
 .../airavata/api/server/AiravataAPIServer.java  |    30 +-
 .../server/handler/AiravataServerHandler.java   |   881 +-
 .../DefaultAiravataSecurityManager.java         |   164 +-
 .../server/security/authzcache/AuthzCache.java  |     8 +-
 .../security/authzcache/AuthzCacheIndex.java    |    20 +-
 .../security/interceptor/SecurityModule.java    |    10 +-
 .../handler/AiravataServerHandlerTest.java      |    65 +-
 .../java/org/apache/airavata/api/Airavata.java  | 18413 +++++++++--------
 .../main/resources/lib/airavata/Airavata.cpp    | 16712 +++++++--------
 .../src/main/resources/lib/airavata/Airavata.h  |  2409 +--
 .../lib/airavata/Airavata_server.skeleton.cpp   |   325 +-
 .../lib/airavata/airavata_data_models_types.h   |     1 +
 .../application_interface_model_types.cpp       |    22 +
 .../application_interface_model_types.h         |    12 +-
 .../airavata/application_io_models_types.cpp    |     4 +-
 .../lib/airavata/application_io_models_types.h  |     5 +-
 .../lib/airavata/experiment_model_types.cpp     |    10 +
 .../lib/airavata/experiment_model_types.h       |     9 +
 .../gateway_resource_profile_model_types.cpp    |    44 +
 .../gateway_resource_profile_model_types.h      |    20 +-
 .../lib/airavata/scheduling_model_types.cpp     |    66 +
 .../lib/airavata/scheduling_model_types.h       |    28 +-
 .../airavata/user_profile_model_constants.cpp   |    36 +
 .../lib/airavata/user_profile_model_constants.h |    42 +
 .../lib/airavata/user_profile_model_types.cpp   |   981 +
 .../lib/airavata/user_profile_model_types.h     |   373 +
 .../lib/airavata/workspace_model_types.cpp      |   259 +
 .../lib/airavata/workspace_model_types.h        |   107 +
 .../resources/lib/Airavata/API/Airavata.php     |  4435 ++--
 .../Model/AppCatalog/AppInterface/Types.php     |    23 +
 .../Model/AppCatalog/GatewayProfile/Types.php   |    50 +
 .../lib/Airavata/Model/Application/Io/Types.php |    10 +-
 .../lib/Airavata/Model/Experiment/Types.php     |     9 +
 .../lib/Airavata/Model/Scheduling/Types.php     |    69 +
 .../resources/lib/Airavata/Model/User/Types.php |  1079 +
 .../lib/Airavata/Model/Workspace/Types.php      |   247 +
 .../lib/apache/airavata/api/Airavata-remote     |   120 +-
 .../lib/apache/airavata/api/Airavata.py         |  4226 ++--
 .../model/appcatalog/appinterface/ttypes.py     |    15 +-
 .../model/appcatalog/gatewayprofile/ttypes.py   |    32 +-
 .../airavata/model/application/io/ttypes.py     |    15 +-
 .../apache/airavata/model/experiment/ttypes.py  |    14 +
 .../apache/airavata/model/scheduling/ttypes.py  |    41 +-
 .../lib/apache/airavata/model/ttypes.py         |     1 +
 .../lib/apache/airavata/model/user/__init__.py  |     1 +
 .../lib/apache/airavata/model/user/constants.py |    12 +
 .../lib/apache/airavata/model/user/ttypes.py    |   738 +
 .../apache/airavata/model/workspace/ttypes.py   |   179 +
 .../client/samples/CancelExperiments.java       |     3 +-
 .../client/samples/CreateLaunchBES.java         |    75 -
 .../client/samples/CreateLaunchExperiment.java  |    76 -
 .../apache/airavata/model/ComponentStatus.java  |     2 +-
 .../org/apache/airavata/model/EdgeModel.java    |     2 +-
 .../org/apache/airavata/model/NodeModel.java    |     2 +-
 .../org/apache/airavata/model/PortModel.java    |     2 +-
 .../apache/airavata/model/WorkflowModel.java    |     2 +-
 .../apache/airavata/model/WorkflowStatus.java   |     2 +-
 .../ApplicationDeploymentDescription.java       |     2 +-
 .../appdeployment/ApplicationModule.java        |     2 +-
 .../appcatalog/appdeployment/CommandObject.java |     2 +-
 .../appcatalog/appdeployment/SetEnvPaths.java   |     2 +-
 .../ApplicationInterfaceDescription.java        |   109 +-
 .../appcatalog/computeresource/BatchQueue.java  |     2 +-
 .../computeresource/CloudJobSubmission.java     |     2 +-
 .../ComputeResourceDescription.java             |     2 +-
 .../computeresource/GlobusJobSubmission.java    |     2 +-
 .../computeresource/JobSubmissionInterface.java |     2 +-
 .../computeresource/LOCALSubmission.java        |     2 +-
 .../computeresource/ResourceJobManager.java     |     2 +-
 .../computeresource/SSHJobSubmission.java       |     2 +-
 .../computeresource/UnicoreJobSubmission.java   |     2 +-
 .../ComputeResourcePreference.java              |     2 +-
 .../gatewayprofile/GatewayResourceProfile.java  |   226 +-
 .../gatewayprofile/StoragePreference.java       |     2 +-
 .../StorageResourceDescription.java             |     2 +-
 .../airavata/model/application/io/DataType.java |     9 +-
 .../application/io/InputDataObjectType.java     |     2 +-
 .../application/io/OutputDataObjectType.java    |     2 +-
 .../airavata/model/commons/ErrorModel.java      |     2 +-
 .../model/commons/ValidationResults.java        |     2 +-
 .../airavata/model/commons/ValidatorResult.java |     2 +-
 .../data/movement/DataMovementInterface.java    |     2 +-
 .../data/movement/GridFTPDataMovement.java      |     2 +-
 .../model/data/movement/LOCALDataMovement.java  |     2 +-
 .../model/data/movement/SCPDataMovement.java    |     2 +-
 .../data/movement/UnicoreDataMovement.java      |     2 +-
 .../model/data/replica/DataProductModel.java    |     2 +-
 .../data/replica/DataReplicaLocationModel.java  |     2 +-
 .../model/error/AiravataClientException.java    |     2 +-
 .../model/error/AiravataSystemException.java    |     2 +-
 .../model/error/AuthenticationException.java    |     2 +-
 .../model/error/AuthorizationException.java     |     2 +-
 .../error/ExperimentNotFoundException.java      |     2 +-
 .../model/error/InvalidRequestException.java    |     2 +-
 .../model/error/LaunchValidationException.java  |     2 +-
 .../model/error/ProjectNotFoundException.java   |     2 +-
 .../airavata/model/error/TimedOutException.java |     2 +-
 .../airavata/model/error/ValidationResults.java |     2 +-
 .../airavata/model/error/ValidatorResult.java   |     2 +-
 .../model/experiment/ExperimentModel.java       |     2 +-
 .../model/experiment/ExperimentStatistics.java  |     2 +-
 .../experiment/ExperimentSummaryModel.java      |     2 +-
 .../model/experiment/ProjectSearchFields.java   |    62 +
 .../experiment/UserConfigurationDataModel.java  |     2 +-
 .../org/apache/airavata/model/job/JobModel.java |     2 +-
 .../event/ExperimentStatusChangeEvent.java      |     2 +-
 .../model/messaging/event/JobIdentifier.java    |     2 +-
 .../messaging/event/JobStatusChangeEvent.java   |     2 +-
 .../event/JobStatusChangeRequestEvent.java      |     2 +-
 .../airavata/model/messaging/event/Message.java |     2 +-
 .../messaging/event/ProcessIdentifier.java      |     2 +-
 .../event/ProcessStatusChangeEvent.java         |     2 +-
 .../event/ProcessStatusChangeRequestEvent.java  |     2 +-
 .../messaging/event/ProcessSubmitEvent.java     |     2 +-
 .../messaging/event/ProcessTerminateEvent.java  |     2 +-
 .../model/messaging/event/TaskIdentifier.java   |     2 +-
 .../messaging/event/TaskOutputChangeEvent.java  |     2 +-
 .../messaging/event/TaskStatusChangeEvent.java  |     2 +-
 .../event/TaskStatusChangeRequestEvent.java     |     2 +-
 .../airavata/model/process/ProcessModel.java    |     2 +-
 .../ComputationalResourceSchedulingModel.java   |   328 +-
 .../airavata/model/security/AuthzToken.java     |     2 +-
 .../airavata/model/status/ExperimentStatus.java |     2 +-
 .../apache/airavata/model/status/JobStatus.java |     2 +-
 .../airavata/model/status/ProcessStatus.java    |     2 +-
 .../airavata/model/status/TaskStatus.java       |     2 +-
 .../model/task/DataStagingTaskModel.java        |     2 +-
 .../model/task/EnvironmentSetupTaskModel.java   |     2 +-
 .../model/task/JobSubmissionTaskModel.java      |     2 +-
 .../airavata/model/task/MonitorTaskModel.java   |     2 +-
 .../apache/airavata/model/task/TaskModel.java   |     2 +-
 .../airavata/model/user/NSFDemographics.java    |  1007 +
 .../org/apache/airavata/model/user/Status.java  |    98 +
 .../airavata/model/user/USCitizenship.java      |    69 +
 .../apache/airavata/model/user/UserProfile.java |  2766 +++
 .../apache/airavata/model/user/disability.java  |    68 +
 .../apache/airavata/model/user/ethnicity.java   |    67 +
 .../org/apache/airavata/model/user/race.java    |    86 +
 .../model/user/user_profile_modelConstants.java |    58 +
 .../airavata/model/workspace/Gateway.java       |     2 +-
 .../apache/airavata/model/workspace/Group.java  |     2 +-
 .../airavata/model/workspace/Notification.java  |  1137 +
 .../model/workspace/NotificationPriority.java   |    65 +
 .../airavata/model/workspace/Project.java       |     2 +-
 .../apache/airavata/model/workspace/User.java   |     2 +-
 .../main/resources/bin/airavata-server-start.sh |   122 +
 .../main/resources/bin/airavata-server-stop.sh  |    71 +
 .../src/main/resources/bin/airavata-server.sh   |   116 -
 .../src/main/resources/bin/api-server.sh        |   116 -
 .../src/main/resources/bin/gfac-server.sh       |   116 -
 .../main/resources/bin/orchestrator-server.sh   |   116 -
 .../src/main/resources/bin/workflow-server.sh   |   116 -
 modules/cloud/ansible-playbooks/README          |     1 +
 modules/cloud/cloud-provisioning/README         |    13 +
 modules/cloud/cloud-provisioning/pom.xml        |    60 +
 .../airavata/cloud/intf/CloudInterface.java     |   151 +
 .../cloud/intf/impl/OpenstackIntfImpl.java      |   497 +
 .../cloud/openstack/OS4JClientProvider.java     |   117 +
 .../apache/airavata/cloud/util/CloudRef.java    |    40 +
 .../apache/airavata/cloud/util/Constants.java   |    56 +
 .../org/apache/airavata/cloud/util/IPType.java  |    39 +
 .../airavata/cloud/util/OpenstackIntfUtil.java  |    49 +
 .../main/resources/jetstream_openrc.properties  |    33 +
 .../airavata/cloud/test/CloudIntfTest.java      |   200 +
 .../src/test/resources/test_data.properties     |    32 +
 modules/cloud/pom.xml                           |    23 +
 .../org/apache/airavata/cloud/CloudMain.java    |    28 +
 modules/commons/pom.xml                         |     2 +-
 .../apache/airavata/common/utils/Constants.java |     3 +-
 .../airavata/common/utils/ServerSettings.java   |    25 +-
 .../resources/airavata-default-xacml-policy.xml |   195 +-
 .../main/resources/airavata-server.properties   |    23 +-
 .../server/src/main/resources/gfac-config.yaml  |     4 +-
 .../impl/password/PasswordCredential.java       |    11 +-
 .../server/CredentialStoreServerHandler.java    |    74 +-
 .../test/resources/airavata-server.properties   |   274 -
 .../store/cpi/CredentialStoreService.java       |  2249 +-
 .../store/datamodel/CertificateCredential.java  |     2 +-
 .../store/datamodel/CommunityUser.java          |     2 +-
 .../store/datamodel/PasswordCredential.java     |   482 +-
 .../store/datamodel/SSHCredential.java          |     2 +-
 .../exception/CredentialStoreException.java     |     2 +-
 .../apache/airavata/gfac/cpi/GfacService.java   |     2 +-
 modules/gfac/gfac-core/pom.xml                  |    16 +-
 .../airavata/gfac/core/GFacConstants.java       |     2 +-
 .../apache/airavata/gfac/core/GFacUtils.java    |    14 +
 .../gfac/core/context/ProcessContext.java       |     8 +-
 .../org/apache/airavata/gfac/impl/Factory.java  |    43 +-
 .../airavata/gfac/impl/GFacEngineImpl.java      |    28 +-
 .../airavata/gfac/impl/HPCRemoteCluster.java    |    91 +-
 .../org/apache/airavata/gfac/impl/SSHUtils.java |     6 +-
 .../gfac/impl/task/BESJobSubmissionTask.java    |    10 +-
 .../airavata/gfac/impl/task/DataStageTask.java  |     3 +-
 .../impl/task/DefaultJobSubmissionTask.java     |    14 +-
 .../gfac/impl/task/SCPDataStageTask.java        |     3 +-
 .../impl/task/utils/bes/DataTransferrer.java    |     2 +
 .../apache/airavata/gfac/server/GfacServer.java |    12 +-
 .../src/test/resources/expcatalog-derby.sql     |   391 -
 modules/monitoring/pom.xml                      |    18 +
 .../airavata/monitoring/MessageExtract.java     |   109 +
 .../org/apache/airavata/monitoring/Util.java    |    54 +
 .../monitoring/consumer/StatusConsumer.java     |    84 +
 .../monitoring/consumer/StatusReceiver.java     |    60 +
 .../monitoring/mailbox/GmailSMTPMailBox.java    |    78 +
 .../airavata/monitoring/mailbox/MailBox.java    |    19 +
 .../airavata/monitoring/mailbox/MailConfig.java |    79 +
 .../producer/RabbitMQEmailPublisher.java        |    94 +
 .../monitoring/simulator/FetchPublish.java      |    41 +
 .../monitoring/simulator/Simulator.java         |    50 +
 .../orchestrator/cpi/OrchestratorService.java   |     2 +-
 .../core/utils/OrchestratorUtils.java           |    34 +
 .../cpi/impl/SimpleOrchestratorImpl.java        |    15 +-
 .../src/test/resources/expcatalog-derby.sql     |   391 -
 .../orchestrator/server/OrchestratorServer.java |    19 +-
 .../server/OrchestratorServerHandler.java       |    40 +-
 .../src/test/resources/expcatalog-derby.sql     |   391 -
 .../core/app/catalog/impl/AppCatalogImpl.java   |     7 +-
 .../catalog/impl/ApplicationInterfaceImpl.java  |     2 +
 .../catalog/impl/GwyClientCredentialImpl.java   |   104 -
 .../catalog/impl/GwyResourceProfileImpl.java    |     8 +
 .../app/catalog/model/ApplicationInterface.java |    10 +
 .../catalog/model/GatewayClientCredential.java  |    63 -
 .../core/app/catalog/model/GatewayProfile.java  |    22 +
 .../catalog/resources/AppInterfaceResource.java |    11 +
 .../GatewayClientCredentialResource.java        |   389 -
 .../resources/GatewayProfileResource.java       |    52 +-
 .../app/catalog/util/AppCatalogJPAUtils.java    |    20 +-
 .../catalog/util/AppCatalogResourceType.java    |     1 -
 .../util/AppCatalogThriftConversion.java        |    21 +-
 .../experiment/catalog/ExpCatResourceUtils.java |    31 +
 .../core/experiment/catalog/ResourceType.java   |     1 +
 .../catalog/impl/ExperimentCatalogImpl.java     |    64 +
 .../catalog/impl/ExperimentRegistry.java        |    56 +-
 .../impl/LoggingExperimentCatalogImpl.java      |    97 -
 .../catalog/impl/NotificationRegistry.java      |    91 +
 .../catalog/impl/ProjectRegistry.java           |    49 +-
 .../catalog/impl/RegistryFactory.java           |     7 -
 .../core/experiment/catalog/impl/UserReg.java   |    41 -
 .../experiment/catalog/impl/UserRegistry.java   |    41 +
 .../experiment/catalog/model/Notification.java  |   118 +
 .../catalog/model/ProcessResourceSchedule.java  |    30 +
 .../catalog/model/UserConfigurationData.java    |    30 +
 .../core/experiment/catalog/model/Users.java    |    10 +
 .../resources/AbstractExpCatResource.java       |     7 +
 .../catalog/resources/NotificationResource.java |   289 +
 .../ProcessResourceScheduleResource.java        |    30 +
 .../UserConfigurationDataResource.java          |    60 +-
 .../catalog/resources/UserResource.java         |     1 +
 .../experiment/catalog/resources/Utils.java     |    29 +
 .../catalog/resources/WorkerResource.java       |    26 +-
 .../utils/ThriftDataModelConversion.java        |    30 +
 .../src/main/resources/META-INF/persistence.xml |     2 +-
 .../src/main/resources/appcatalog-derby.sql     |    10 +-
 .../src/main/resources/appcatalog-mysql.sql     |    10 +-
 .../src/main/resources/expcatalog-derby.sql     |    17 +
 .../src/main/resources/expcatalog-mysql.sql     |    17 +
 .../catalog/GatewayClientCredentialTest.java    |    69 -
 .../airavata/registry/cpi/AppCatalog.java       |     7 -
 .../registry/cpi/ExpCatParentDataType.java      |     3 +-
 .../registry/cpi/ExperimentCatalog.java         |    16 +
 .../cpi/ExperimentCatalogModelType.java         |     1 +
 .../org/apache/airavata/server/ServerMain.java  |    78 +-
 modules/simstream/README.md                     |    18 +
 modules/simstream/example/README.md             |     9 +
 .../simstream/example/logfile_checker/README.md |    23 +
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 .../application/alanine_dipeptide.py            |    55 +
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 modules/simstream/simstream/simstream.py        |   167 +
 modules/user-profile/pom.xml                    |    21 +
 modules/user-profile/user-profile-core/pom.xml  |    80 +
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 .../src/main/resources/images/registry.png      |   Bin 0 -> 3419 bytes
 .../xbaya/src/main/resources/images/service.png |   Bin 0 -> 871 bytes
 .../src/main/resources/images/services.png      |   Bin 0 -> 899 bytes
 .../xbaya/src/main/resources/images/step.gif    |   Bin 0 -> 211 bytes
 .../xbaya/src/main/resources/images/stop.jpeg   |   Bin 0 -> 497 bytes
 .../src/main/resources/images/workflow.png      |   Bin 0 -> 601 bytes
 .../resources/images/workflow_templates.png     |   Bin 0 -> 710 bytes
 .../src/main/resources/images/workflows.png     |   Bin 0 -> 778 bytes
 .../xbaya/src/main/resources/views/home.fxml    |   587 +
 .../test/java/org/airavata/xbaya/AppTest.java   |    38 +
 pom.xml                                         |     2 +
 .../airavata-apis/airavata_api.thrift           |   338 +-
 .../component-cpis/credential-store-cpi.thrift  |     3 +
 .../credential_store_data_models.thrift         |    18 +-
 .../data-models/airavata_data_models.thrift     |     1 +
 .../application_interface_model.thrift          |     3 +-
 .../application_io_models.thrift                |     1 +
 .../experiment_model.thrift                     |     6 +
 .../scheduling_model.thrift                     |     5 +-
 .../workspace_model.thrift                      |    17 +
 .../gateway_resource_profile_model.thrift       |     8 +-
 .../user-group-models/group_manager_cpi.thrift  |    95 +
 .../group_manager_model.thrift                  |    88 +
 .../user-group-models/user_profile_model.thrift |   184 +
 381 files changed, 46456 insertions(+), 27330 deletions(-)
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