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Posted to commits@airavata.apache.org by ma...@apache.org on 2017/04/28 15:23:31 UTC
[50/50] [abbrv] airavata git commit: Merge branch 'master' into
develop
Merge branch 'master' into develop
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/7a779933
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/7a779933
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/7a779933
Branch: refs/heads/develop
Commit: 7a779933e7e6b89d722f11ef5c80026210e63dd1
Parents: b37882a 10d7c02
Author: Marcus Christie <ma...@apache.org>
Authored: Fri Apr 28 11:20:49 2017 -0400
Committer: Marcus Christie <ma...@apache.org>
Committed: Fri Apr 28 11:20:49 2017 -0400
----------------------------------------------------------------------
airavata-api/airavata-api-server/pom.xml | 31 +++--
.../airavata/api/server/AiravataAPIServer.java | 4 +-
.../api/server/AiravataDerbyServer.java | 4 +-
.../server/handler/AiravataServerHandler.java | 4 +-
.../AiravataExperimentStatusUpdator.java | 6 +-
.../listener/ExperimentStatusChangedEvent.java | 19 +++
.../security/AiravataSecurityManager.java | 3 +-
.../DefaultAiravataSecurityManager.java | 3 +-
.../api/server/security/IdentityContext.java | 4 +-
.../airavata/api/server/security/Main.java | 5 +-
.../server/security/SecurityManagerFactory.java | 3 +-
.../server/security/authzcache/AuthzCache.java | 3 +-
.../security/authzcache/AuthzCacheEntry.java | 3 +-
.../security/authzcache/AuthzCacheIndex.java | 3 +-
.../security/authzcache/AuthzCacheManager.java | 3 +-
.../authzcache/AuthzCacheManagerFactory.java | 3 +-
.../security/authzcache/AuthzCachedStatus.java | 3 +-
.../authzcache/DefaultAuthzCacheManager.java | 3 +-
.../security/interceptor/SecurityCheck.java | 3 +-
.../interceptor/SecurityInterceptor.java | 3 +-
.../security/interceptor/SecurityModule.java | 3 +-
.../security/oauth/DefaultOAuthClient.java | 3 +-
.../server/security/xacml/DefaultPAPClient.java | 3 +-
.../server/security/xacml/DefaultXACMLPEP.java | 3 +-
.../airavata/api/server/util/Constants.java | 4 +-
.../api/server/util/ThriftClientPool.java | 5 +-
airavata-api/airavata-api-stubs/pom.xml | 31 +++--
.../java/org/apache/airavata/api/Airavata.java | 28 ++--
.../airavata/api/airavata_apiConstants.java | 28 ++--
.../api/client/AiravataClientFactory.java | 4 +-
.../airavata-cpp-sdk/pom.xml | 27 +++-
.../src/main/assembly/bin-assembly.xml | 29 ++--
.../airavata-php-sdk/pom.xml | 27 +++-
.../src/main/assembly/bin-assembly.xml | 29 ++--
.../airavata-python-sdk/pom.xml | 27 +++-
.../src/main/assembly/bin-assembly.xml | 29 ++--
.../java-client-samples/pom.xml | 26 +++-
.../client/samples/CancelExperiments.java | 4 +-
.../client/samples/CreateLaunchBES.java | 3 +-
.../client/samples/CreateLaunchExperiment.java | 4 +-
.../samples/CreateLaunchExperimentUS3.java | 2 +-
.../client/samples/ReplicaCatalogSample.java | 5 +-
.../client/samples/SampleEchoExperiment.java | 4 +-
.../client/OAuthAppRegisteringClient.java | 3 +-
.../client/OAuthTokenRetrievalClient.java | 3 +-
.../client/secure/client/Properties.java | 3 +-
.../client/secure/client/SecureClient.java | 3 +-
.../tools/RegisterOGCEUS3Application.java | 6 +-
.../tools/RegisterSampleApplications.java | 5 +-
.../tools/RegisterSampleApplicationsUtils.java | 19 +++
.../client/tools/RegisterUS3Application.java | 6 +-
airavata-api/airavata-client-sdks/pom.xml | 26 +++-
airavata-api/airavata-data-models/pom.xml | 31 +++--
.../apache/airavata/model/ComponentState.java | 28 ++--
.../apache/airavata/model/ComponentStatus.java | 28 ++--
.../org/apache/airavata/model/EdgeModel.java | 28 ++--
.../org/apache/airavata/model/NodeModel.java | 28 ++--
.../org/apache/airavata/model/PortModel.java | 28 ++--
.../apache/airavata/model/WorkflowModel.java | 28 ++--
.../apache/airavata/model/WorkflowState.java | 28 ++--
.../apache/airavata/model/WorkflowStatus.java | 28 ++--
.../ApplicationDeploymentDescription.java | 28 ++--
.../appdeployment/ApplicationModule.java | 28 ++--
.../appcatalog/appdeployment/CommandObject.java | 28 ++--
.../appcatalog/appdeployment/SetEnvPaths.java | 28 ++--
.../application_deployment_modelConstants.java | 28 ++--
.../ApplicationInterfaceDescription.java | 28 ++--
.../application_interface_modelConstants.java | 28 ++--
.../appcatalog/computeresource/BatchQueue.java | 28 ++--
.../computeresource/CloudJobSubmission.java | 28 ++--
.../ComputeResourceDescription.java | 28 ++--
.../appcatalog/computeresource/DMType.java | 28 ++--
.../appcatalog/computeresource/FileSystems.java | 28 ++--
.../computeresource/GlobusJobSubmission.java | 28 ++--
.../computeresource/JobManagerCommand.java | 28 ++--
.../computeresource/JobSubmissionInterface.java | 28 ++--
.../computeresource/JobSubmissionProtocol.java | 28 ++--
.../computeresource/LOCALSubmission.java | 28 ++--
.../appcatalog/computeresource/MonitorMode.java | 28 ++--
.../computeresource/ProviderName.java | 28 ++--
.../computeresource/ResourceJobManager.java | 28 ++--
.../computeresource/ResourceJobManagerType.java | 28 ++--
.../computeresource/SSHJobSubmission.java | 28 ++--
.../computeresource/UnicoreJobSubmission.java | 28 ++--
.../compute_resource_modelConstants.java | 28 ++--
.../ComputeResourcePreference.java | 28 ++--
.../gatewayprofile/DataStoragePreference.java | 28 ++--
.../gatewayprofile/GatewayResourceProfile.java | 28 ++--
.../gatewayprofile/StoragePreference.java | 28 ++--
.../StorageResourceDescription.java | 28 ++--
.../UserComputeResourcePreference.java | 28 ++--
.../UserResourceProfile.java | 28 ++--
.../UserStoragePreference.java | 28 ++--
.../airavata/model/application/io/DataType.java | 28 ++--
.../application/io/InputDataObjectType.java | 28 ++--
.../application/io/OutputDataObjectType.java | 28 ++--
.../airavata/model/commons/ErrorModel.java | 28 ++--
.../model/commons/ValidationResults.java | 28 ++--
.../airavata/model/commons/ValidatorResult.java | 28 ++--
.../commons/airavata_commonsConstants.java | 28 ++--
.../credential/store/CertificateCredential.java | 28 ++--
.../model/credential/store/CommunityUser.java | 28 ++--
.../credential/store/CredentialOwnerType.java | 28 ++--
.../credential/store/CredentialSummary.java | 28 ++--
.../credential/store/PasswordCredential.java | 28 ++--
.../model/credential/store/SSHCredential.java | 28 ++--
.../credential/store/SSHCredentialSummary.java | 28 ++--
.../model/credential/store/SummaryType.java | 28 ++--
.../credential_store_data_modelsConstants.java | 28 ++--
.../airavata/model/data/movement/DMType.java | 28 ++--
.../data/movement/DataMovementInterface.java | 28 ++--
.../data/movement/DataMovementProtocol.java | 28 ++--
.../data/movement/GridFTPDataMovement.java | 28 ++--
.../model/data/movement/LOCALDataMovement.java | 28 ++--
.../model/data/movement/SCPDataMovement.java | 28 ++--
.../model/data/movement/SecurityProtocol.java | 28 ++--
.../data/movement/UnicoreDataMovement.java | 28 ++--
.../model/data/replica/DataProductModel.java | 28 ++--
.../model/data/replica/DataProductType.java | 28 ++--
.../data/replica/DataReplicaLocationModel.java | 28 ++--
.../data/replica/ReplicaLocationCategory.java | 28 ++--
.../data/replica/ReplicaPersistentType.java | 28 ++--
.../model/error/AiravataClientException.java | 28 ++--
.../airavata/model/error/AiravataErrorType.java | 28 ++--
.../model/error/AiravataSystemException.java | 28 ++--
.../model/error/AuthenticationException.java | 28 ++--
.../model/error/AuthorizationException.java | 28 ++--
.../error/ExperimentNotFoundException.java | 28 ++--
.../model/error/InvalidRequestException.java | 28 ++--
.../model/error/LaunchValidationException.java | 28 ++--
.../model/error/ProjectNotFoundException.java | 28 ++--
.../airavata/model/error/TimedOutException.java | 28 ++--
.../airavata/model/error/ValidationResults.java | 28 ++--
.../airavata/model/error/ValidatorResult.java | 28 ++--
.../model/experiment/ExperimentModel.java | 28 ++--
.../experiment/ExperimentSearchFields.java | 28 ++--
.../model/experiment/ExperimentStatistics.java | 28 ++--
.../experiment/ExperimentSummaryModel.java | 28 ++--
.../model/experiment/ExperimentType.java | 28 ++--
.../model/experiment/ProjectSearchFields.java | 28 ++--
.../experiment/UserConfigurationDataModel.java | 28 ++--
.../apache/airavata/model/group/GroupModel.java | 28 ++--
.../model/group/ResourcePermissionType.java | 28 ++--
.../airavata/model/group/ResourceType.java | 28 ++--
.../org/apache/airavata/model/job/JobModel.java | 28 ++--
.../event/ExperimentStatusChangeEvent.java | 28 ++--
.../messaging/event/ExperimentSubmitEvent.java | 28 ++--
.../model/messaging/event/JobIdentifier.java | 28 ++--
.../messaging/event/JobStatusChangeEvent.java | 28 ++--
.../event/JobStatusChangeRequestEvent.java | 28 ++--
.../airavata/model/messaging/event/Message.java | 28 ++--
.../model/messaging/event/MessageLevel.java | 28 ++--
.../model/messaging/event/MessageType.java | 28 ++--
.../messaging/event/ProcessIdentifier.java | 28 ++--
.../event/ProcessStatusChangeEvent.java | 28 ++--
.../event/ProcessStatusChangeRequestEvent.java | 28 ++--
.../messaging/event/ProcessSubmitEvent.java | 28 ++--
.../messaging/event/ProcessTerminateEvent.java | 28 ++--
.../model/messaging/event/TaskIdentifier.java | 28 ++--
.../messaging/event/TaskOutputChangeEvent.java | 28 ++--
.../messaging/event/TaskStatusChangeEvent.java | 28 ++--
.../event/TaskStatusChangeRequestEvent.java | 28 ++--
.../model/messaging/event/TaskSubmitEvent.java | 28 ++--
.../messaging/event/TaskTerminateEvent.java | 28 ++--
.../event/messaging_eventsConstants.java | 28 ++--
.../parallelism/ApplicationParallelismType.java | 28 ++--
.../airavata/model/process/ProcessModel.java | 28 ++--
.../ComputationalResourceSchedulingModel.java | 28 ++--
.../airavata/model/security/AuthzToken.java | 28 ++--
.../airavata/model/status/ExperimentState.java | 28 ++--
.../airavata/model/status/ExperimentStatus.java | 28 ++--
.../apache/airavata/model/status/JobState.java | 28 ++--
.../apache/airavata/model/status/JobStatus.java | 28 ++--
.../airavata/model/status/ProcessState.java | 28 ++--
.../airavata/model/status/ProcessStatus.java | 28 ++--
.../airavata/model/status/QueueStatusModel.java | 28 ++--
.../apache/airavata/model/status/TaskState.java | 28 ++--
.../airavata/model/status/TaskStatus.java | 28 ++--
.../airavata/model/task/DataStageType.java | 28 ++--
.../model/task/DataStagingTaskModel.java | 28 ++--
.../model/task/EnvironmentSetupTaskModel.java | 28 ++--
.../model/task/JobSubmissionTaskModel.java | 28 ++--
.../airavata/model/task/MonitorTaskModel.java | 28 ++--
.../apache/airavata/model/task/TaskModel.java | 28 ++--
.../apache/airavata/model/task/TaskTypes.java | 28 ++--
.../airavata/model/user/NSFDemographics.java | 28 ++--
.../org/apache/airavata/model/user/Status.java | 28 ++--
.../airavata/model/user/USCitizenship.java | 28 ++--
.../apache/airavata/model/user/UserProfile.java | 28 ++--
.../apache/airavata/model/user/disability.java | 28 ++--
.../apache/airavata/model/user/ethnicity.java | 28 ++--
.../org/apache/airavata/model/user/race.java | 28 ++--
.../model/user/user_profile_modelConstants.java | 28 ++--
.../model/workflow_data_modelConstants.java | 28 ++--
.../airavata/model/workspace/Gateway.java | 28 ++--
.../model/workspace/GatewayApprovalStatus.java | 28 ++--
.../apache/airavata/model/workspace/Group.java | 28 ++--
.../airavata/model/workspace/Notification.java | 28 ++--
.../model/workspace/NotificationPriority.java | 28 ++--
.../airavata/model/workspace/Project.java | 28 ++--
.../apache/airavata/model/workspace/User.java | 28 ++--
airavata-api/airavata-model-utils/pom.xml | 31 +++--
.../airavata/model/util/AppDeploymentUtil.java | 4 +-
.../airavata/model/util/AppInterfaceUtil.java | 4 +-
.../model/util/ComputeResourceUtil.java | 4 +-
.../airavata/model/util/ExecutionType.java | 4 +-
.../model/util/ExperimentModelUtil.java | 4 +-
.../airavata/model/util/ProjectModelUtil.java | 2 +-
airavata-api/pom.xml | 26 +++-
.../commons/tenant/entities/GatewayEntity.java | 2 +-
.../commons/utils/ObjectMapperSingleton.java | 2 +-
.../UserProfileRegistryException.java | 2 +-
.../security/interceptor/SecurityModule.java | 2 +-
dev-tools/ansible/airavata.yml | 20 +++
dev-tools/ansible/ansible.cfg | 2 +-
dev-tools/ansible/dev_airavata_deploy.yml | 20 +++
dev-tools/ansible/dev_pga_deploy.yml | 20 +++
.../inventories/develop/group_vars/all.yml | 20 +++
.../develop/group_vars/dev-airavata.yml | 20 +++
.../inventories/develop/group_vars/dev-pga.yml | 20 +++
.../geogateway-dev/group_vars/pga/vars.yml | 22 ++-
.../scigap/production/files/airavata.jks | 76 ++++++++++
.../scigap/production/files/airavata_sym.jks | 30 ++++
.../production/files/client_truststore.jks | 126 +++++++++++++++++
.../scigap/production/group_vars/all/vars.yml | 123 +++++++++++++++++
.../scigap/production/group_vars/all/vault.yml | 20 +++
.../ansible/inventories/scigap/production/hosts | 20 +++
.../production/pga_config/brandeis/vars.yml | 51 +++++++
.../production/pga_config/brandeis/vault.yml | 18 +++
.../production/pga_config/cinetvtech/vars.yml | 55 ++++++++
.../production/pga_config/cinetvtech/vault.yml | 18 +++
.../cornell-dnasequence/pga-ssl-vhost.conf.j2 | 31 +++++
.../pga_config/cornell-dnasequence/vars.yml | 63 +++++++++
.../pga_config/cornell-dnasequence/vault.yml | 18 +++
.../production/pga_config/georgiastate/vars.yml | 55 ++++++++
.../pga_config/georgiastate/vault.yml | 18 +++
.../production/pga_config/iugateway/vars.yml | 55 ++++++++
.../production/pga_config/iugateway/vault.yml | 18 +++
.../scigap/production/pga_config/lsu/vars.yml | 51 +++++++
.../scigap/production/pga_config/lsu/vault.yml | 18 +++
.../scigap/production/pga_config/nsg/vars.yml | 56 ++++++++
.../scigap/production/pga_config/nsg/vault.yml | 18 +++
.../production/pga_config/oiitandy/vars.yml | 55 ++++++++
.../production/pga_config/oiitandy/vault.yml | 18 +++
.../scigap/production/pga_config/oscer/vars.yml | 55 ++++++++
.../production/pga_config/oscer/vault.yml | 18 +++
.../production/pga_config/phasta/vars.yml | 55 ++++++++
.../production/pga_config/phasta/vault.yml | 18 +++
.../production/pga_config/scigap/vars.yml | 56 ++++++++
.../production/pga_config/scigap/vault.yml | 18 +++
.../production/pga_config/seagrid/vars.yml | 56 ++++++++
.../production/pga_config/seagrid/vault.yml | 18 +++
.../production/pga_config/simvascular/vars.yml | 55 ++++++++
.../production/pga_config/simvascular/vault.yml | 18 +++
.../production/pga_config/southdakota/vars.yml | 55 ++++++++
.../production/pga_config/southdakota/vault.yml | 18 +++
.../pga_config/southernillinois/vars.yml | 55 ++++++++
.../pga_config/southernillinois/vault.yml | 18 +++
.../production/pga_config/testdrive/vars.yml | 56 ++++++++
.../production/pga_config/testdrive/vault.yml | 18 +++
.../production/pga_config/ultrascan/vars.yml | 64 +++++++++
.../production/pga_config/ultrascan/vault.yml | 18 +++
.../scigap/production/pga_config/utah/vars.yml | 55 ++++++++
.../scigap/production/pga_config/utah/vault.yml | 18 +++
.../testing-0.17-scigap/group_vars/all/vars.yml | 20 +++
.../testing-0.17-scigap/group_vars/pga/vars.yml | 22 ++-
.../group_vars/all/vars.yml | 20 +++
.../group_vars/pga/vars.yml | 25 +++-
.../testing-0.17/group_vars/all/vars.yml | 20 +++
.../testing-0.17/group_vars/pga/vars.yml | 22 ++-
dev-tools/ansible/local_airavata_deploy.yml | 20 +++
dev-tools/ansible/pga-scigap-prod.yml | 41 ++++++
dev-tools/ansible/pga-single-vhost.yml | 37 +++++
dev-tools/ansible/pga.yml | 20 +++
.../ansible/roles/airavata_build/tasks/main.yml | 20 +++
.../roles/airavata_deploy/defaults/main.yml | 20 +++
.../roles/airavata_deploy/handlers/main.yml | 20 +++
.../roles/airavata_deploy/tasks/main.yml | 20 +++
.../ansible/roles/api-orch/defaults/main.yml | 22 +++
.../ansible/roles/api-orch/handlers/main.yml | 20 +++
dev-tools/ansible/roles/api-orch/tasks/main.yml | 42 +++++-
.../api-orch/templates/gfac-config.yaml.j2 | 6 +
.../roles/api-orch/templates/logback.xml.j2 | 55 ++++++++
.../ansible/roles/common/defaults/main.yml | 20 +++
dev-tools/ansible/roles/common/tasks/main.yml | 20 +++
dev-tools/ansible/roles/common/vars/main.yml | 20 +++
.../ansible/roles/database/defaults/main.yml | 21 +++
.../ansible/roles/database/files/mysql-tmp.te | 9 ++
.../ansible/roles/database/handlers/main.yml | 20 +++
dev-tools/ansible/roles/database/tasks/main.yml | 70 +++++++++-
.../roles/database/tasks/secure_install.yml | 20 +++
dev-tools/ansible/roles/database/vars/main.yml | 21 ++-
.../ansible/roles/env_setup/tasks/main.yml | 20 +++
.../ansible/roles/env_setup/tasks/redhat.yml | 20 +++
dev-tools/ansible/roles/gfac/defaults/main.yml | 21 +++
dev-tools/ansible/roles/gfac/handlers/main.yml | 20 +++
dev-tools/ansible/roles/gfac/tasks/main.yml | 34 ++++-
.../roles/gfac/templates/gfac-config.yaml.j2 | 7 +
.../ansible/roles/gfac/templates/logback.xml.j2 | 55 ++++++++
dev-tools/ansible/roles/java/tasks/main.yml | 20 +++
dev-tools/ansible/roles/java/vars/main.yml | 20 +++
dev-tools/ansible/roles/pga/defaults/main.yml | 37 ++++-
dev-tools/ansible/roles/pga/files/default.conf | 5 +
dev-tools/ansible/roles/pga/handlers/main.yml | 24 +++-
.../roles/pga/tasks/install_deps_CentOS_7.yml | 20 +++
.../roles/pga/tasks/install_deps_Ubuntu_14.yml | 20 +++
.../roles/pga/tasks/install_deps_Ubuntu_16.yml | 20 +++
dev-tools/ansible/roles/pga/tasks/main.yml | 137 +++++++++++++++----
.../roles/pga/templates/pga-ssl-vhost.conf.j2 | 29 ++++
.../roles/pga/templates/pga-vhost.conf.j2 | 3 +
.../roles/pga/templates/pga_config.php.j2 | 16 +--
.../ansible/roles/pga_deploy/handlers/main.yml | 20 +++
.../ansible/roles/pga_deploy/tasks/main.yml | 20 +++
.../ansible/roles/rabbitmq/handlers/main.yml | 20 +++
dev-tools/ansible/roles/rabbitmq/tasks/main.yml | 20 +++
dev-tools/ansible/roles/rabbitmq/vars/main.yml | 20 +++
dev-tools/ansible/roles/registry/tasks/main.yml | 20 +++
dev-tools/ansible/roles/wso2_is/tasks/main.yml | 20 +++
dev-tools/ansible/roles/wso2_is/vars/main.yml | 20 +++
.../ansible/roles/zookeeper/handlers/main.yml | 20 +++
.../ansible/roles/zookeeper/tasks/main.yml | 20 +++
dev-tools/ansible/roles/zookeeper/vars/main.yml | 20 +++
dev-tools/ansible/site.yml | 20 +++
modules/cloud/cloud-provisioning/pom.xml | 5 -
modules/cluster-monitoring/pom.xml | 25 +++-
.../monitoring/ClusterStatusMonitorJob.java | 5 +-
.../ClusterStatusMonitorJobScheduler.java | 5 +-
modules/commons/pom.xml | 30 ++--
.../airavata/common/utils/BuildConstant.java | 4 +-
.../airavata/common/context/RequestContext.java | 4 +-
.../common/context/WorkflowContext.java | 4 +-
.../AiravataConfigurationException.java | 4 +-
.../common/exception/AiravataException.java | 4 +-
.../exception/AiravataStartupException.java | 4 +-
.../exception/ApplicationSettingsException.java | 4 +-
.../airavata/common/logging/Exception.java | 3 +-
.../airavata/common/logging/LogEntry.java | 3 +-
.../airavata/common/logging/MDCConstants.java | 3 +-
.../apache/airavata/common/logging/MDCUtil.java | 19 +++
.../airavata/common/logging/ServerId.java | 3 +-
.../common/logging/kafka/KafkaAppender.java | 3 +-
.../airavata/common/utils/AiravataJobState.java | 5 +-
.../airavata/common/utils/AiravataUtils.java | 4 +-
.../airavata/common/utils/AiravataZKUtils.java | 5 +-
.../common/utils/ApplicationSettings.java | 4 +-
.../airavata/common/utils/AwsMetadata.java | 3 +-
.../airavata/common/utils/BrowserLauncher.java | 4 +-
.../airavata/common/utils/ClientSettings.java | 4 +-
.../apache/airavata/common/utils/Constants.java | 4 +-
.../apache/airavata/common/utils/DBUtil.java | 4 +-
.../common/utils/DatabaseTestCases.java | 4 +-
.../utils/DefaultKeyStorePasswordCallback.java | 4 +-
.../apache/airavata/common/utils/DerbyUtil.java | 4 +-
.../airavata/common/utils/ExecutionMode.java | 4 +-
.../apache/airavata/common/utils/IOUtil.java | 4 +-
.../apache/airavata/common/utils/IServer.java | 4 +-
.../apache/airavata/common/utils/JSONUtil.java | 4 +-
.../common/utils/KeyStorePasswordCallback.java | 19 +++
.../common/utils/LocalEventPublisher.java | 5 +-
.../airavata/common/utils/NameValidator.java | 4 +-
.../org/apache/airavata/common/utils/Pair.java | 4 +-
.../airavata/common/utils/SecurityUtil.java | 4 +-
.../airavata/common/utils/ServerSettings.java | 4 +-
.../airavata/common/utils/ServiceUtils.java | 19 +++
.../airavata/common/utils/StringUtil.java | 4 +-
.../apache/airavata/common/utils/SwingUtil.java | 4 +-
.../airavata/common/utils/ThriftUtils.java | 4 +-
.../apache/airavata/common/utils/Version.java | 4 +-
.../airavata/common/utils/WSConstants.java | 4 +-
.../apache/airavata/common/utils/WSDLUtil.java | 4 +-
.../airavata/common/utils/ZkConstants.java | 3 +-
.../listener/AbstractActivityListener.java | 4 +-
.../listener/AbstractStateChangeRequest.java | 4 +-
.../common/utils/listener/PublisherMessage.java | 4 +-
.../common/utils/ApplicationSettingsTest.java | 4 +-
.../airavata/common/utils/SecurityUtilTest.java | 4 +-
modules/configuration/client/pom.xml | 26 +++-
modules/configuration/pom.xml | 26 +++-
modules/configuration/server/pom.xml | 26 +++-
.../src/main/resources/LSF_Groovy.template | 3 +
.../src/main/resources/UGE_Groovy.template | 3 +-
.../server/src/main/resources/log4j.properties | 48 -------
.../server/src/main/resources/logback.xml | 70 ++++++----
.../credential-store-service/pom.xml | 33 +++--
.../credential/store/credential/AuditInfo.java | 4 +-
.../store/credential/CommunityUser.java | 4 +-
.../credential/store/credential/Credential.java | 4 +-
.../store/credential/CredentialOwnerType.java | 19 +++
.../impl/certificate/CertificateAuditInfo.java | 6 +-
.../impl/certificate/CertificateCredential.java | 4 +-
.../impl/password/PasswordCredential.java | 4 +-
.../credential/impl/ssh/SSHCredential.java | 4 +-
.../impl/ssh/SSHCredentialGenerator.java | 4 +-
.../store/notifier/CredentialStoreNotifier.java | 19 +++
.../store/notifier/NotificationMessage.java | 4 +-
.../store/notifier/NotifierBootstrap.java | 4 +-
.../notifier/impl/EmailNotificationMessage.java | 4 +-
.../store/notifier/impl/EmailNotifier.java | 4 +-
.../impl/EmailNotifierConfiguration.java | 4 +-
.../store/server/CredentialStoreServer.java | 3 +-
.../server/CredentialStoreServerHandler.java | 3 +-
.../store/servlet/CredentialBootstrapper.java | 4 +-
.../servlet/CredentialStoreCallbackServlet.java | 4 +-
.../servlet/CredentialStoreStartServlet.java | 4 +-
.../store/store/CredentialReader.java | 4 +-
.../store/store/CredentialReaderFactory.java | 4 +-
.../store/store/CredentialStoreException.java | 4 +-
.../store/store/CredentialWriter.java | 4 +-
.../store/impl/CertificateCredentialWriter.java | 4 +-
.../store/store/impl/CredentialReaderImpl.java | 4 +-
.../store/store/impl/SSHCredentialWriter.java | 4 +-
.../store/store/impl/db/CommunityUserDAO.java | 4 +-
.../store/store/impl/db/CredentialsDAO.java | 4 +-
.../store/store/impl/db/ParentDAO.java | 4 +-
.../store/store/impl/util/ConnectionPool.java | 5 +-
.../impl/util/CredentialStoreInitUtil.java | 5 +-
.../store/store/impl/util/DatabaseCreator.java | 5 +-
.../store/store/impl/util/JdbcStorage.java | 5 +-
.../store/util/ConfigurationReader.java | 4 +-
.../store/util/CredentialStoreConstants.java | 4 +-
.../credential/store/util/PrivateKeyStore.java | 4 +-
.../credential/store/util/TokenGenerator.java | 4 +-
.../airavata/credential/store/util/Utility.java | 4 +-
.../cpi/SSHSummaryTest/SSHSummaryTest.java | 19 +++
.../store/notifier/impl/EmailNotifierTest.java | 4 +-
.../store/impl/db/CommunityUserDAOTest.java | 4 +-
.../store/store/impl/db/CredentialsDAOTest.java | 4 +-
.../store/store/impl/db/SSHCredentialTest.java | 4 +-
.../store/util/ConfigurationReaderTest.java | 4 +-
.../store/util/TokenGeneratorTest.java | 4 +-
.../credential-store-stubs/pom.xml | 31 +++--
.../client/CredentialStoreClientFactory.java | 4 +-
.../credential/store/client/TestSSLClient.java | 3 +-
.../store/cpi/CredentialStoreService.java | 19 +++
.../cpi/credential_store_cpiConstants.java | 19 +++
.../exception/CredentialStoreException.java | 19 +++
modules/credential-store/pom.xml | 26 +++-
.../db/event/manager/utils/Constants.java | 2 +-
modules/distribution/pom.xml | 46 +++++--
.../src/main/assembly/bin-assembly.xml | 32 +++--
.../src/main/assembly/src-assembly.xml | 37 ++---
.../main/resources/bin/airavata-server-start.sh | 17 ++-
.../gfac-application-specific-handlers/pom.xml | 31 +++--
.../gaussian/handler/GaussianHandler.java | 19 +++
modules/gfac/gfac-bes/pom.xml | 29 ++--
.../gfac/bes/handlers/AbstractSMSHandler.java | 19 +++
.../gfac/bes/handlers/SMSByteIOInHandler.java | 19 +++
.../gfac/bes/handlers/SMSByteIOOutHandler.java | 19 +++
.../gfac/bes/handlers/SMSDirectoryHandler.java | 19 +++
.../gfac/bes/provider/impl/BESProvider.java | 3 +-
.../bes/security/UNICORESecurityContext.java | 19 +++
.../gfac/bes/security/X509SecurityContext.java | 5 +-
.../airavata/gfac/bes/utils/ActivityInfo.java | 19 +++
.../gfac/bes/utils/ApplicationProcessor.java | 4 +-
.../airavata/gfac/bes/utils/BESConstants.java | 19 +++
.../gfac/bes/utils/DataTransferrer.java | 4 +-
.../airavata/gfac/bes/utils/FileDownloader.java | 4 +-
.../gfac/bes/utils/FileTransferBase.java | 4 +-
.../airavata/gfac/bes/utils/FileUploader.java | 4 +-
.../airavata/gfac/bes/utils/JSDLGenerator.java | 3 +-
.../airavata/gfac/bes/utils/JSDLUtils.java | 4 +-
.../apache/airavata/gfac/bes/utils/Mode.java | 4 +-
.../airavata/gfac/bes/utils/MyProxyLogon.java | 19 +++
.../airavata/gfac/bes/utils/OSRequirement.java | 4 +-
.../apache/airavata/gfac/bes/utils/OSType.java | 4 +-
.../gfac/bes/utils/ProcessorRequirement.java | 6 +-
.../airavata/gfac/bes/utils/RangeValueType.java | 4 +-
.../gfac/bes/utils/ResourceProcessor.java | 4 +-
.../airavata/gfac/bes/utils/SPMDProcessor.java | 4 +-
.../airavata/gfac/bes/utils/SPMDVariations.java | 4 +-
.../airavata/gfac/bes/utils/SecurityUtils.java | 19 +++
.../airavata/gfac/bes/utils/StorageCreator.java | 4 +-
.../gfac/bes/utils/UASDataStagingProcessor.java | 4 +-
.../airavata/gfac/bes/utils/URIUtils.java | 4 +-
.../impl/JSDLGeneratorTestWithMyProxyAuth.java | 4 +-
modules/gfac/gfac-client/pom.xml | 31 +++--
.../airavata/gfac/client/GFACInstance.java | 5 +-
.../airavata/gfac/client/GFacClientFactory.java | 5 +-
.../apache/airavata/gfac/cpi/GfacService.java | 19 +++
.../airavata/gfac/cpi/gfac_cpiConstants.java | 19 +++
modules/gfac/gfac-impl/pom.xml | 26 +++-
.../java/com/jcraft/jsch/ExtendedSession.java | 4 +-
.../com/jcraft/jsch/GSISSHIdentityFile.java | 4 +-
.../jcraft/jsch/GSISSHIdentityRepository.java | 4 +-
.../java/com/jcraft/jsch/GSSContextX509.java | 4 +-
.../UserAuthGSSAPIWithMICGSSCredentials.java | 4 +-
.../apache/airavata/gfac/impl/AuroraUtils.java | 3 +-
.../airavata/gfac/impl/BESRemoteCluster.java | 6 +-
.../gfac/impl/DefaultHostScheduler.java | 3 +-
.../org/apache/airavata/gfac/impl/Factory.java | 3 +-
.../airavata/gfac/impl/GFacEngineImpl.java | 6 +-
.../apache/airavata/gfac/impl/GFacWorker.java | 4 +-
.../airavata/gfac/impl/HPCRemoteCluster.java | 5 +-
.../apache/airavata/gfac/impl/HTTPUtils.java | 19 +++
.../airavata/gfac/impl/LocalCommandOutput.java | 3 +-
.../airavata/gfac/impl/LocalRemoteCluster.java | 3 +-
.../org/apache/airavata/gfac/impl/SSHUtils.java | 3 +-
.../airavata/gfac/impl/StandardOutReader.java | 5 +-
.../job/AiravataCustomCommandOutputParser.java | 6 +-
.../gfac/impl/job/ForkJobConfiguration.java | 6 +-
.../gfac/impl/job/ForkOutputParser.java | 6 +-
.../apache/airavata/gfac/impl/job/JobUtil.java | 3 +-
.../gfac/impl/job/LSFJobConfiguration.java | 5 +-
.../airavata/gfac/impl/job/LSFOutputParser.java | 5 +-
.../gfac/impl/job/PBSJobConfiguration.java | 5 +-
.../airavata/gfac/impl/job/PBSOutputParser.java | 5 +-
.../gfac/impl/job/SlurmJobConfiguration.java | 5 +-
.../gfac/impl/job/SlurmOutputParser.java | 5 +-
.../gfac/impl/job/UGEJobConfiguration.java | 5 +-
.../airavata/gfac/impl/job/UGEOutputParser.java | 5 +-
.../airavata/gfac/impl/task/ArchiveTask.java | 3 +-
.../gfac/impl/task/AuroraJobSubmissionTask.java | 3 +-
.../gfac/impl/task/BESJobSubmissionTask.java | 19 +++
.../airavata/gfac/impl/task/DataStageTask.java | 3 +-
.../gfac/impl/task/DataStreamingTask.java | 6 +-
.../impl/task/DefaultJobSubmissionTask.java | 6 +-
.../gfac/impl/task/EnvironmentSetupTask.java | 3 +-
.../gfac/impl/task/ForkJobSubmissionTask.java | 6 +-
.../gfac/impl/task/LocalJobSubmissionTask.java | 6 +-
.../gfac/impl/task/SCPDataStageTask.java | 3 +-
.../airavata/gfac/impl/task/TaskUtils.java | 3 +-
.../gfac/impl/task/utils/StreamData.java | 6 +-
.../gfac/impl/task/utils/bes/ActivityInfo.java | 19 +++
.../task/utils/bes/ApplicationProcessor.java | 4 +-
.../gfac/impl/task/utils/bes/BESConstants.java | 19 +++
.../impl/task/utils/bes/DataTransferrer.java | 4 +-
.../impl/task/utils/bes/FileDownloader.java | 4 +-
.../impl/task/utils/bes/FileTransferBase.java | 4 +-
.../gfac/impl/task/utils/bes/FileUploader.java | 4 +-
.../gfac/impl/task/utils/bes/JSDLGenerator.java | 3 +-
.../gfac/impl/task/utils/bes/JSDLUtils.java | 4 +-
.../airavata/gfac/impl/task/utils/bes/Mode.java | 4 +-
.../gfac/impl/task/utils/bes/MyProxyLogon.java | 19 +++
.../gfac/impl/task/utils/bes/OSType.java | 4 +-
.../task/utils/bes/ProcessorRequirement.java | 6 +-
.../impl/task/utils/bes/RangeValueType.java | 4 +-
.../impl/task/utils/bes/ResourceProcessor.java | 4 +-
.../task/utils/bes/ResourceRequirement.java | 4 +-
.../impl/task/utils/bes/SPMDVariations.java | 4 +-
.../gfac/impl/task/utils/bes/SecurityUtils.java | 19 +++
.../impl/task/utils/bes/StorageCreator.java | 4 +-
.../task/utils/bes/UASDataStagingProcessor.java | 4 +-
.../task/utils/bes/UNICORESecurityContext.java | 19 +++
.../gfac/impl/task/utils/bes/URIUtils.java | 4 +-
.../task/utils/bes/X509SecurityContext.java | 5 +-
.../impl/watcher/CancelRequestWatcherImpl.java | 3 +-
.../watcher/RedeliveryRequestWatcherImpl.java | 3 +-
.../handler/LocalDirectorySetupHandler.java | 19 +++
.../gfac/local/handler/LocalInputHandler.java | 19 +++
.../gfac/local/provider/impl/LocalProvider.java | 19 +++
.../local/utils/InputStreamToFileWriter.java | 5 +-
.../airavata/gfac/local/utils/InputUtils.java | 5 +-
.../gfac/local/utils/LocalProviderUtil.java | 19 +++
.../gfac/monitor/cloud/AuroraJobMonitor.java | 3 +-
.../gfac/monitor/email/EmailBasedMonitor.java | 5 +-
.../email/parser/AiravataCustomMailParser.java | 5 +-
.../monitor/email/parser/LSFEmailParser.java | 5 +-
.../monitor/email/parser/PBSEmailParser.java | 5 +-
.../monitor/email/parser/SLURMEmailParser.java | 5 +-
.../monitor/email/parser/UGEEmailParser.java | 5 +-
.../exception/AiravataMonitorException.java | 5 +-
.../gfac/ssh/context/SSHAuthWrapper.java | 5 +-
.../gfac/ssh/security/SSHSecurityContext.java | 3 +-
.../gfac/ssh/security/TokenizedSSHAuthInfo.java | 5 +-
.../services/impl/BigRed2TestWithSSHAuth.java | 19 +++
.../gfac/services/impl/CredentialStoreTest.java | 19 +++
.../impl/GSISSHProviderTestWithMyProxyAuth.java | 19 +++
.../gfac/services/impl/LocalProviderTest.java | 19 +++
.../impl/SSHProviderTestWithSSHAuth.java | 19 +++
.../GSISecurityContextTestWithMyProxyAuth.java | 19 +++
.../email/parser/PBSEmailParserTest.java | 19 +++
.../gfac/ssh/config/ConfigReaderTest.java | 19 +++
.../impl/DefaultSSHApiTestWithMyProxyAuth.java | 19 +++
.../gfac/ssh/impl/VanilaTestWithSSHAuth.java | 19 +++
.../apache/airavata/job/AMQPMonitorTest.java | 19 +++
.../job/QstatMonitorTestWithMyProxyAuth.java | 19 +++
modules/gfac/gfac-service/pom.xml | 31 +++--
.../apache/airavata/gfac/server/GfacServer.java | 5 +-
.../airavata/gfac/server/GfacServerHandler.java | 5 +-
.../gfac/client/GfacClientFactoryTest.java | 6 +-
.../airavata/gfac/client/util/Initialize.java | 4 +-
modules/gfac/pom.xml | 26 +++-
modules/integration-tests/pom.xml | 26 +++-
.../org/apache/airavata/integration/Man.java | 4 +-
.../integration/AbstractIntegrationTest.java | 4 +-
.../apache/airavata/integration/BaseCaseIT.java | 4 +-
.../airavata/integration/DataRetrievalIT.java | 4 +-
.../airavata/integration/ForEachCaseIT.java | 4 +-
.../apache/airavata/integration/OsUtils.java | 4 +-
.../integration/PasswordCallbackImpl.java | 19 +++
.../airavata/integration/SimpleEchoIT.java | 4 +-
.../SingleAppIntegrationTestBase.java | 3 +-
.../WorkflowIntegrationTestBase.java | 4 +-
.../integration/WorkflowSamplesCaseIT.java | 4 +-
.../integration/tools/DocumentCreatorNew.java | 5 +-
.../integration/tools/DocumentCreatorUtils.java | 4 +-
.../integration-tests/src/test/java/suite.xml | 30 ++--
modules/messaging/client/pom.xml | 26 +++-
.../messaging/client/RabbitMQListener.java | 4 +-
.../airavata/messaging/client/TestReader.java | 3 +-
modules/messaging/core/pom.xml | 29 ++--
.../airavata/messaging/core/MessageContext.java | 4 +-
.../airavata/messaging/core/MessageHandler.java | 4 +-
.../messaging/core/MessagingConstants.java | 4 +-
.../messaging/core/MessagingFactory.java | 3 +-
.../airavata/messaging/core/Publisher.java | 4 +-
.../messaging/core/PublisherFactory.java | 19 +++
.../messaging/core/RabbitMQProperties.java | 3 +-
.../airavata/messaging/core/Subscriber.java | 4 +-
.../airavata/messaging/core/TestClient.java | 4 +-
.../apache/airavata/messaging/core/Type.java | 3 +-
.../messaging/core/impl/ExperimentConsumer.java | 3 +-
.../messaging/core/impl/ProcessConsumer.java | 3 +-
.../impl/RabbitMQProcessLaunchConsumer.java | 19 +++
.../impl/RabbitMQProcessLaunchPublisher.java | 19 +++
.../messaging/core/impl/RabbitMQProducer.java | 19 +++
.../messaging/core/impl/RabbitMQPublisher.java | 3 +-
.../core/impl/RabbitMQStatusPublisher.java | 19 +++
.../core/impl/RabbitMQStatusSubscriber.java | 19 +++
.../messaging/core/impl/RabbitMQSubscriber.java | 4 +-
.../messaging/core/impl/StatusConsumer.java | 3 +-
.../messaging/core/stats/CountWriterTask.java | 3 +-
.../messaging/core/stats/LatencyWriterTask.java | 3 +-
.../messaging/core/stats/StatCounter.java | 3 +-
modules/messaging/pom.xml | 26 +++-
modules/monitoring/pom.xml | 31 +++--
.../org/apache/airavata/monitoring/Main.java | 3 +-
.../airavata/monitoring/MessageExtract.java | 3 +-
.../org/apache/airavata/monitoring/Util.java | 3 +-
.../monitoring/consumer/StatusConsumer.java | 3 +-
.../monitoring/consumer/StatusReceiver.java | 3 +-
.../monitoring/mailbox/GmailSMTPMailBox.java | 3 +-
.../airavata/monitoring/mailbox/MailBox.java | 3 +-
.../airavata/monitoring/mailbox/MailConfig.java | 3 +-
.../producer/RabbitMQEmailPublisher.java | 3 +-
.../monitoring/simulator/FetchPublish.java | 3 +-
.../monitoring/simulator/Simulator.java | 3 +-
modules/orchestrator/NULL | 1 -
.../orchestrator/orchestrator-client/pom.xml | 31 +++--
.../client/OrchestratorClientFactory.java | 4 +-
.../orchestrator/cpi/OrchestratorService.java | 19 +++
.../cpi/orchestrator_cpiConstants.java | 19 +++
.../sample/OrchestratorClientSample.java | 6 +-
modules/orchestrator/orchestrator-core/pom.xml | 31 +++--
.../core/OrchestratorConfiguration.java | 5 +-
.../core/context/OrchestratorContext.java | 5 +-
.../core/exception/OrchestratorException.java | 5 +-
.../core/impl/GFACPassiveJobSubmitter.java | 5 +-
.../orchestrator/core/job/JobSubmitter.java | 5 +-
.../core/utils/OrchestratorConstants.java | 5 +-
.../core/utils/OrchestratorUtils.java | 5 +-
.../core/validator/JobMetadataValidator.java | 5 +-
.../validator/impl/BatchQueueValidator.java | 5 +-
.../impl/ExperimentStatusValidator.java | 5 +-
.../airavata/orchestrator/cpi/Orchestrator.java | 5 +-
.../cpi/impl/AbstractOrchestrator.java | 5 +-
.../cpi/impl/SimpleOrchestratorImpl.java | 5 +-
.../orchestrator/core/BaseOrchestratorTest.java | 5 +-
.../orchestrator/core/NewOrchestratorTest.java | 5 +-
.../core/OrchestratorTestWithGRAM.java | 5 +-
.../core/OrchestratorTestWithMyProxyAuth.java | 5 +-
.../orchestrator/core/ValidatorTest.java | 19 +++
.../orchestrator/core/util/Initialize.java | 4 +-
.../orchestrator/core/util/SecondValidator.java | 19 +++
.../orchestrator/core/util/TestValidator.java | 19 +++
.../orchestrator/orchestrator-service/pom.xml | 31 +++--
.../orchestrator/server/OrchestratorServer.java | 4 +-
.../server/OrchestratorServerHandler.java | 4 +-
.../airavata/orchestrator/util/Constants.java | 4 +-
.../OrchestratorServerThreadPoolExecutor.java | 4 +-
.../orchestrator/util/OrchestratorUtils.java | 3 +-
.../client/OrchestratorClientFactoryTest.java | 6 +-
.../orchestrator/client/util/Initialize.java | 4 +-
modules/orchestrator/pom.xml | 26 +++-
modules/registry/pom.xml | 26 +++-
modules/registry/registry-core/pom.xml | 26 +++-
.../core/app/catalog/impl/AppCatalogImpl.java | 4 +-
.../catalog/impl/ApplicationDeploymentImpl.java | 4 +-
.../catalog/impl/ApplicationInterfaceImpl.java | 4 +-
.../app/catalog/impl/ComputeResourceImpl.java | 4 +-
.../catalog/impl/GwyResourceProfileImpl.java | 4 +-
.../app/catalog/impl/StorageResourceImpl.java | 4 +-
.../catalog/impl/UsrResourceProfileImpl.java | 4 +-
.../core/app/catalog/model/AppEnvironment.java | 4 +-
.../app/catalog/model/AppEnvironment_PK.java | 4 +-
.../core/app/catalog/model/AppInput_PK.java | 4 +-
.../app/catalog/model/AppModuleMapping.java | 4 +-
.../app/catalog/model/AppModuleMapping_PK.java | 4 +-
.../core/app/catalog/model/AppOutput_PK.java | 4 +-
.../catalog/model/ApplicationDeployment.java | 4 +-
.../app/catalog/model/ApplicationIntInput.java | 4 +-
.../app/catalog/model/ApplicationIntOutput.java | 4 +-
.../app/catalog/model/ApplicationInterface.java | 4 +-
.../app/catalog/model/ApplicationModule.java | 4 +-
.../core/app/catalog/model/BatchQueue.java | 4 +-
.../core/app/catalog/model/BatchQueue_PK.java | 4 +-
.../app/catalog/model/CloudJobSubmission.java | 5 +-
.../core/app/catalog/model/ComputeResource.java | 4 +-
.../model/ComputeResourceFileSystem.java | 4 +-
.../model/ComputeResourceFileSystem_PK.java | 4 +-
.../model/ComputeResourcePreference.java | 4 +-
.../model/ComputeResourcePreferencePK.java | 4 +-
.../core/app/catalog/model/Configuration.java | 19 +++
.../app/catalog/model/Configuration_PK.java | 4 +-
.../catalog/model/DataMovementInterface.java | 4 +-
.../catalog/model/DataMovementInterface_PK.java | 4 +-
.../app/catalog/model/DataStorageResource.java | 4 +-
.../core/app/catalog/model/GSISSHExport.java | 4 +-
.../core/app/catalog/model/GSISSHExportPK.java | 4 +-
.../app/catalog/model/GSISSHSubmission.java | 4 +-
.../core/app/catalog/model/GatewayProfile.java | 4 +-
.../app/catalog/model/GlobusGKEndPointPK.java | 4 +-
.../app/catalog/model/GlobusGKEndpoint.java | 4 +-
.../app/catalog/model/GlobusJobSubmission.java | 4 +-
.../app/catalog/model/GridftpDataMovement.java | 4 +-
.../core/app/catalog/model/GridftpEndpoint.java | 4 +-
.../app/catalog/model/GridftpEndpoint_PK.java | 4 +-
.../core/app/catalog/model/HostAlias.java | 4 +-
.../core/app/catalog/model/HostAliasPK.java | 4 +-
.../core/app/catalog/model/HostIPAddress.java | 4 +-
.../core/app/catalog/model/HostIPAddressPK.java | 4 +-
.../app/catalog/model/JobManagerCommand.java | 4 +-
.../app/catalog/model/JobManagerCommand_PK.java | 4 +-
.../catalog/model/JobSubmissionInterface.java | 4 +-
.../model/JobSubmissionInterface_PK.java | 4 +-
.../app/catalog/model/LibraryApendPath.java | 4 +-
.../app/catalog/model/LibraryApendPath_PK.java | 4 +-
.../app/catalog/model/LibraryPrepandPath.java | 4 +-
.../catalog/model/LibraryPrepandPath_PK.java | 4 +-
.../app/catalog/model/LocalDataMovement.java | 4 +-
.../core/app/catalog/model/LocalSubmission.java | 4 +-
.../core/app/catalog/model/ModuleLoadCmd.java | 4 +-
.../app/catalog/model/ModuleLoadCmd_PK.java | 4 +-
.../catalog/model/ParallelismPrefixCommand.java | 4 +-
.../model/ParallelismPrefixCommand_PK.java | 4 +-
.../core/app/catalog/model/PostJobCommand.java | 4 +-
.../app/catalog/model/PostJobCommandPK.java | 4 +-
.../core/app/catalog/model/PreJobCommand.java | 4 +-
.../core/app/catalog/model/PreJobCommandPK.java | 4 +-
.../app/catalog/model/ResourceJobManager.java | 4 +-
.../core/app/catalog/model/ScpDataMovement.java | 4 +-
.../app/catalog/model/SshJobSubmission.java | 4 +-
.../app/catalog/model/StorageInterface.java | 4 +-
.../app/catalog/model/StorageInterface_PK.java | 4 +-
.../app/catalog/model/StoragePreference.java | 4 +-
.../app/catalog/model/StoragePreferencePK.java | 4 +-
.../core/app/catalog/model/StorageResource.java | 4 +-
.../app/catalog/model/UnicoreDataMovement.java | 6 +-
.../app/catalog/model/UnicoreJobSubmission.java | 6 +-
.../model/UserComputeResourcePreference.java | 4 +-
.../model/UserComputeResourcePreferencePK.java | 4 +-
.../app/catalog/model/UserResourceProfile.java | 4 +-
.../catalog/model/UserResourceProfilePK.java | 4 +-
.../catalog/model/UserStoragePreference.java | 4 +-
.../catalog/model/UserStoragePreferencePK.java | 4 +-
.../resources/AppCatAbstractResource.java | 4 +-
.../catalog/resources/AppCatalogResource.java | 19 +++
.../resources/AppDeploymentResource.java | 4 +-
.../resources/AppEnvironmentResource.java | 4 +-
.../catalog/resources/AppInterfaceResource.java | 4 +-
...ppModuleMappingAppCatalogResourceAppCat.java | 4 +-
.../catalog/resources/AppModuleResource.java | 4 +-
.../resources/ApplicationInputResource.java | 2 +-
.../resources/ApplicationOutputResource.java | 2 +-
.../catalog/resources/BatchQueueResource.java | 4 +-
.../resources/CloudSubmissionResource.java | 5 +-
.../ComputeHostPreferenceResource.java | 4 +-
.../ComputeResourceFileSystemResource.java | 4 +-
.../resources/ComputeResourceResource.java | 4 +-
.../DataMovementInterfaceResource.java | 4 +-
.../catalog/resources/GSISSHExportResource.java | 2 +-
.../resources/GSISSHSubmissionResource.java | 2 +-
.../resources/GatewayProfileResource.java | 2 +-
.../resources/GlobusGKEndpointResource.java | 2 +-
.../resources/GlobusJobSubmissionResource.java | 2 +-
.../resources/GridftpDataMovementResource.java | 2 +-
.../resources/GridftpEndpointResource.java | 2 +-
.../catalog/resources/HostAliasAppResource.java | 2 +-
.../resources/HostIPAddressResource.java | 2 +-
.../resources/JobManagerCommandResource.java | 4 +-
.../JobSubmissionInterfaceResource.java | 4 +-
.../resources/LibraryApendPathResource.java | 4 +-
.../resources/LibraryPrepandPathResource.java | 4 +-
.../resources/LocalDataMovementResource.java | 4 +-
.../resources/LocalSubmissionResource.java | 4 +-
.../resources/ModuleLoadCmdResource.java | 4 +-
.../ParallelismPrefixCommandResource.java | 4 +-
.../resources/PostJobCommandResource.java | 2 +-
.../resources/PreJobCommandResource.java | 2 +-
.../resources/ResourceJobManagerResource.java | 4 +-
.../resources/ScpDataMovementResource.java | 2 +-
.../resources/SshJobSubmissionResource.java | 2 +-
.../resources/StorageInterfaceResource.java | 4 +-
.../resources/StoragePreferenceResource.java | 4 +-
.../resources/StorageResourceResource.java | 4 +-
.../resources/UnicoreDataMovementResource.java | 6 +-
.../resources/UnicoreJobSubmissionResource.java | 6 +-
.../UserComputeHostPreferenceResource.java | 4 +-
.../resources/UserResourceProfileResource.java | 2 +-
.../UserStoragePreferenceResource.java | 4 +-
.../app/catalog/util/AppCatalogJPAUtils.java | 4 +-
.../catalog/util/AppCatalogQueryGenerator.java | 4 +-
.../catalog/util/AppCatalogResourceType.java | 4 +-
.../util/AppCatalogThriftConversion.java | 4 +-
.../core/app/catalog/util/AppCatalogUtils.java | 4 +-
.../experiment/catalog/ExpCatResourceUtils.java | 5 +-
.../catalog/ExperimentCatResource.java | 5 +-
.../core/experiment/catalog/JPAConstants.java | 4 +-
.../core/experiment/catalog/ResourceType.java | 5 +-
.../catalog/impl/ExperimentCatalogImpl.java | 4 +-
.../catalog/impl/ExperimentRegistry.java | 4 +-
.../catalog/impl/GatewayRegistry.java | 4 +-
.../catalog/impl/NotificationRegistry.java | 4 +-
.../catalog/impl/ProjectRegistry.java | 4 +-
.../catalog/impl/RegistryFactory.java | 4 +-
.../experiment/catalog/impl/UserRegistry.java | 4 +-
.../experiment/catalog/model/Experiment.java | 5 +-
.../catalog/model/ExperimentError.java | 5 +-
.../catalog/model/ExperimentErrorPK.java | 5 +-
.../catalog/model/ExperimentInput.java | 5 +-
.../catalog/model/ExperimentInputPK.java | 5 +-
.../catalog/model/ExperimentOutput.java | 5 +-
.../catalog/model/ExperimentOutputPK.java | 5 +-
.../catalog/model/ExperimentStatus.java | 5 +-
.../catalog/model/ExperimentStatusPK.java | 5 +-
.../catalog/model/ExperimentSummary.java | 5 +-
.../core/experiment/catalog/model/Gateway.java | 5 +-
.../experiment/catalog/model/GatewayWorker.java | 5 +-
.../catalog/model/GatewayWorkerPK.java | 5 +-
.../core/experiment/catalog/model/Job.java | 5 +-
.../core/experiment/catalog/model/JobPK.java | 5 +-
.../experiment/catalog/model/JobStatus.java | 5 +-
.../experiment/catalog/model/JobStatusPK.java | 5 +-
.../experiment/catalog/model/Notification.java | 5 +-
.../core/experiment/catalog/model/Process.java | 5 +-
.../experiment/catalog/model/ProcessError.java | 5 +-
.../catalog/model/ProcessErrorPK.java | 5 +-
.../experiment/catalog/model/ProcessInput.java | 5 +-
.../catalog/model/ProcessInputPK.java | 5 +-
.../experiment/catalog/model/ProcessOutput.java | 5 +-
.../catalog/model/ProcessOutputPK.java | 5 +-
.../catalog/model/ProcessResourceSchedule.java | 5 +-
.../experiment/catalog/model/ProcessStatus.java | 5 +-
.../catalog/model/ProcessStatusPK.java | 5 +-
.../core/experiment/catalog/model/Project.java | 5 +-
.../experiment/catalog/model/ProjectUser.java | 5 +-
.../experiment/catalog/model/ProjectUserPK.java | 5 +-
.../experiment/catalog/model/QueueStatus.java | 5 +-
.../experiment/catalog/model/QueueStatusPK.java | 5 +-
.../core/experiment/catalog/model/Task.java | 5 +-
.../experiment/catalog/model/TaskError.java | 5 +-
.../experiment/catalog/model/TaskErrorPK.java | 5 +-
.../experiment/catalog/model/TaskStatus.java | 5 +-
.../experiment/catalog/model/TaskStatusPK.java | 5 +-
.../catalog/model/UserConfigurationData.java | 5 +-
.../core/experiment/catalog/model/UserPK.java | 5 +-
.../core/experiment/catalog/model/Users.java | 5 +-
.../resources/AbstractExpCatResource.java | 3 +-
.../resources/ExperimentErrorResource.java | 4 +-
.../resources/ExperimentInputResource.java | 4 +-
.../resources/ExperimentOutputResource.java | 4 +-
.../catalog/resources/ExperimentResource.java | 4 +-
.../resources/ExperimentStatisticsResource.java | 5 +-
.../resources/ExperimentStatusResource.java | 4 +-
.../resources/ExperimentSummaryResource.java | 5 +-
.../catalog/resources/GatewayResource.java | 5 +-
.../catalog/resources/JobResource.java | 4 +-
.../catalog/resources/JobStatusResource.java | 4 +-
.../catalog/resources/NotificationResource.java | 5 +-
.../catalog/resources/ProcessErrorResource.java | 4 +-
.../catalog/resources/ProcessInputResource.java | 4 +-
.../resources/ProcessOutputResource.java | 4 +-
.../catalog/resources/ProcessResource.java | 4 +-
.../ProcessResourceScheduleResource.java | 4 +-
.../resources/ProcessStatusResource.java | 4 +-
.../catalog/resources/ProjectResource.java | 5 +-
.../catalog/resources/ProjectUserResource.java | 4 +-
.../catalog/resources/QueueStatusResource.java | 5 +-
.../catalog/resources/TaskErrorResource.java | 4 +-
.../catalog/resources/TaskResource.java | 4 +-
.../catalog/resources/TaskStatusResource.java | 4 +-
.../UserConfigurationDataResource.java | 4 +-
.../catalog/resources/UserResource.java | 5 +-
.../experiment/catalog/resources/Utils.java | 3 +-
.../catalog/resources/WorkerResource.java | 9 +-
.../catalog/utils/QueryGenerator.java | 4 +-
.../utils/ThriftDataModelConversion.java | 19 +++
.../registry/core/impl/RegistryImpl.java | 6 +-
.../catalog/impl/ReplicaCatalogImpl.java | 4 +-
.../replica/catalog/model/Configuration.java | 19 +++
.../replica/catalog/model/Configuration_PK.java | 4 +-
.../core/replica/catalog/model/DataProduct.java | 5 +-
.../catalog/model/DataProductMetaData.java | 5 +-
.../catalog/model/DataProductMetaData_PK.java | 5 +-
.../catalog/model/DataReplicaLocation.java | 5 +-
.../catalog/model/DataReplicaMetaData.java | 5 +-
.../catalog/model/DataReplicaMetaData_PK.java | 5 +-
.../catalog/utils/ReplicaCatalogConstants.java | 3 +-
.../catalog/utils/ReplicaCatalogJPAUtils.java | 4 +-
.../utils/ReplicaCatalogQueryGenerator.java | 4 +-
.../utils/ThriftDataModelConversion.java | 19 +++
.../catalog/impl/WorkflowCatalogImpl.java | 4 +-
.../workflow/catalog/model/ComponentStatus.java | 4 +-
.../core/workflow/catalog/model/Edge.java | 4 +-
.../core/workflow/catalog/model/Edge_PK.java | 4 +-
.../core/workflow/catalog/model/Node.java | 4 +-
.../core/workflow/catalog/model/Node_PK.java | 4 +-
.../core/workflow/catalog/model/Port.java | 4 +-
.../core/workflow/catalog/model/Port_PK.java | 4 +-
.../core/workflow/catalog/model/Workflow.java | 4 +-
.../workflow/catalog/model/WorkflowInput.java | 4 +-
.../catalog/model/WorkflowInput_PK.java | 4 +-
.../workflow/catalog/model/WorkflowOutput.java | 4 +-
.../catalog/model/WorkflowOutput_PK.java | 4 +-
.../workflow/catalog/model/WorkflowStatus.java | 4 +-
.../catalog/model/WorkflowStatus_PK.java | 4 +-
.../resources/ComponentStatusResource.java | 2 +-
.../catalog/resources/EdgeResource.java | 2 +-
.../catalog/resources/NodeResource.java | 2 +-
.../catalog/resources/PortResource.java | 2 +-
.../resources/WorkflowCatAbstractResource.java | 4 +-
.../resources/WorkflowCatalogResource.java | 19 +++
.../resources/WorkflowInputResource.java | 2 +-
.../resources/WorkflowOutputResource.java | 2 +-
.../catalog/resources/WorkflowResource.java | 4 +-
.../resources/WorkflowStatusResource.java | 2 +-
.../catalog/utils/WorkflowCatalogJPAUtils.java | 4 +-
.../utils/WorkflowCatalogQueryGenerator.java | 4 +-
.../utils/WorkflowCatalogResourceType.java | 4 +-
.../utils/WorkflowCatalogThriftConversion.java | 4 +-
.../catalog/utils/WorkflowCatalogUtils.java | 4 +-
.../airavata/app/catalog/AppDeploymentTest.java | 4 +-
.../airavata/app/catalog/AppInterfaceTest.java | 4 +-
...puteAppCatalogExperimentCatResourceTest.java | 4 +-
.../app/catalog/GatewayProfileTest.java | 4 +-
.../catalog/StorageResourceAppCatalogTest.java | 4 +-
.../app/catalog/UserResourceProfileTest.java | 4 +-
.../airavata/app/catalog/util/Initialize.java | 4 +-
.../catalog/AbstractResourceTest.java | 4 +-
.../catalog/ExperimentInputResourceTest.java | 19 +++
.../catalog/ExperimentOutputResourceTest.java | 19 +++
.../catalog/ExperimentResourceTest.java | 19 +++
.../experiment/catalog/GatewayResourceTest.java | 19 +++
.../experiment/catalog/JobResourceTest.java | 2 +-
.../experiment/catalog/ProcessResourceTest.java | 2 +-
.../catalog/QueueStatusResourceTest.java | 19 +++
.../experiment/catalog/TaskResourceTest.java | 2 +-
.../catalog/UserConfigurationDataTest.java | 4 +-
.../experiment/catalog/UserResourceTest.java | 19 +++
.../experiment/catalog/util/Initialize.java | 4 +-
.../replica/catalog/ReplicaCatalogTest.java | 5 +-
.../replica/catalog/util/Initialize.java | 4 +-
modules/registry/registry-cpi/pom.xml | 26 +++-
.../airavata/registry/cpi/AppCatalog.java | 2 +-
.../registry/cpi/AppCatalogException.java | 2 +-
.../registry/cpi/ApplicationDeployment.java | 2 +-
.../registry/cpi/ApplicationInterface.java | 2 +-
.../registry/cpi/CompositeIdentifier.java | 4 +-
.../airavata/registry/cpi/ComputeResource.java | 2 +-
.../registry/cpi/ExpCatChildDataType.java | 2 +-
.../registry/cpi/ExpCatParentDataType.java | 2 +-
.../registry/cpi/ExperimentCatalog.java | 2 +-
.../cpi/ExperimentCatalogException.java | 6 +-
.../cpi/ExperimentCatalogModelType.java | 2 +-
.../registry/cpi/GwyClientCredential.java | 2 +-
.../registry/cpi/GwyResourceProfile.java | 2 +-
.../apache/airavata/registry/cpi/Registry.java | 6 +-
.../registry/cpi/RegistryException.java | 4 +-
.../airavata/registry/cpi/ReplicaCatalog.java | 2 +-
.../registry/cpi/ReplicaCatalogException.java | 2 +-
.../airavata/registry/cpi/ResultOrderType.java | 19 +++
.../airavata/registry/cpi/StorageResource.java | 8 +-
.../registry/cpi/UsrResourceProfile.java | 2 +-
.../airavata/registry/cpi/WorkflowCatalog.java | 6 +-
.../registry/cpi/WorkflowCatalogException.java | 2 +-
.../airavata/registry/cpi/utils/Constants.java | 4 +-
.../airavata/registry/cpi/utils/StatusType.java | 2 +-
modules/registry/registry-server/pom.xml | 28 +++-
.../registry-api-service/pom.xml | 21 +++
.../registry/api/service/RegistryAPIServer.java | 5 +-
.../service/handler/RegistryServerHandler.java | 5 +-
.../api/service/util/AppCatalogInitUtil.java | 19 +++
.../api/service/util/ConnectionPool.java | 6 +-
.../registry/api/service/util/Constants.java | 4 +-
.../api/service/util/DatabaseCreator.java | 5 +-
.../service/util/ExperimentCatalogInitUtil.java | 19 +++
.../registry/api/service/util/JdbcStorage.java | 5 +-
.../service/util/ReplicaCatalogInitUtil.java | 19 +++
.../service/util/WorkflowCatalogInitUtil.java | 19 +++
.../registry-server/registry-api-stubs/pom.xml | 21 +++
.../airavata/registry/api/RegistryService.java | 19 +++
.../client/RegistryServiceClientFactory.java | 4 +-
.../api/exception/RegistryServiceException.java | 19 +++
.../registry/api/registry_apiConstants.java | 19 +++
modules/registry/registry-tools/jpa-gen/pom.xml | 26 +++-
.../computeresource/BatchQueueGenerator.java | 4 +-
.../ComputeResourceDescriptionGenerator.java | 4 +-
.../DataMovementInterfaceGenerator.java | 4 +-
.../computeresource/FileSystemsGenerator.java | 4 +-
.../GridFTPDataMovementGenerator.java | 4 +-
.../GridFTPEndpointsGenerator.java | 4 +-
.../JobManagerCommandGenerator.java | 4 +-
.../JobSubmissionInterfaceGenerator.java | 4 +-
.../LocalDataMovementGenerator.java | 4 +-
.../LocalSubmissionGenerator.java | 4 +-
.../computeresource/ModuleCMDGenerator.java | 4 +-
.../ResourceJobManagerGenerator.java | 4 +-
.../SCPDataMovementGenerator.java | 4 +-
.../SSHJobSubmissionGenerator.java | 4 +-
.../main/java/generators/AbstractGenerator.java | 19 +++
.../main/java/generators/JPAClassGenerator.java | 19 +++
.../generators/JPAResourceClassGenerator.java | 19 +++
.../src/main/java/generators/SQLGenerator.java | 19 +++
.../src/main/java/model/JPAClassField.java | 19 +++
.../src/main/java/model/JPAClassModel.java | 19 +++
.../src/main/java/model/JPAPKClassModel.java | 19 +++
.../main/java/model/JPAResourceClassModel.java | 19 +++
.../jpa-gen/src/main/java/model/SQLData.java | 19 +++
.../jpa-gen/src/main/java/test/Test.java | 19 +++
modules/registry/registry-tools/pom.xml | 26 +++-
.../registry-tools/registry-tool/pom.xml | 26 +++-
.../airavata/registry/tool/DBMigrator.java | 4 +-
.../DeltaScripts/appCatalog_schema_delta.sql | 20 +++
.../credentialStore_schema_delta.sql | 20 +++
.../DeltaScripts/expCatalog_schema_delta.sql | 20 +++
.../replicaCatalog_schema_delta.sql | 20 +++
.../DeltaScripts/workFlow_schema_delta.sql | 20 +++
modules/security/pom.xml | 30 ++--
.../security/AbstractAuthenticator.java | 4 +-
.../security/AbstractDatabaseAuthenticator.java | 4 +-
.../security/AiravataSecurityException.java | 3 +-
.../security/AuthenticationException.java | 4 +-
.../apache/airavata/security/Authenticator.java | 4 +-
.../apache/airavata/security/Authoriser.java | 4 +-
.../org/apache/airavata/security/UserStore.java | 4 +-
.../airavata/security/UserStoreException.java | 4 +-
.../AbstractConfigurationReader.java | 4 +-
.../AuthenticatorConfigurationReader.java | 4 +-
.../userstore/AbstractJDBCUserStore.java | 4 +-
.../security/userstore/JDBCUserStore.java | 4 +-
.../security/userstore/LDAPUserStore.java | 4 +-
.../security/userstore/SessionDBUserStore.java | 4 +-
.../security/util/PasswordDigester.java | 4 +-
.../security/util/TrustStoreManager.java | 3 +-
.../AuthenticatorConfigurationReaderTest.java | 4 +-
.../configurations/TestDBAuthenticator1.java | 4 +-
.../configurations/TestDBAuthenticator2.java | 4 +-
.../configurations/TestDBAuthenticator3.java | 4 +-
.../security/configurations/TestUserStore.java | 36 +++--
.../security/userstore/JDBCUserStoreTest.java | 36 +++--
.../security/userstore/LDAPUserStoreTest.java | 36 +++--
.../userstore/SessionDBUserStoreTest.java | 36 +++--
modules/server/pom.xml | 30 ++--
.../org/apache/airavata/server/ServerMain.java | 3 +-
modules/sharing-registry/pom.xml | 21 +++
.../sharing-data-migrator/pom.xml | 21 +++
.../migrator/airavata/AiravataDataMigrator.java | 5 +-
.../migrator/airavata/ConnectionFactory.java | 5 +-
.../sharing-registry-distribution/pom.xml | 21 +++
.../src/main/assembly/bin-assembly.xml | 37 ++---
.../sharing-registry-server/pom.xml | 27 ++++
.../registry/db/entities/DomainEntity.java | 5 +-
.../registry/db/entities/EntityEntity.java | 5 +-
.../sharing/registry/db/entities/EntityPK.java | 5 +-
.../registry/db/entities/EntityTypeEntity.java | 5 +-
.../registry/db/entities/EntityTypePK.java | 5 +-
.../db/entities/GroupMembershipEntity.java | 5 +-
.../registry/db/entities/GroupMembershipPK.java | 5 +-
.../db/entities/PermissionTypeEntity.java | 5 +-
.../registry/db/entities/PermissionTypePK.java | 5 +-
.../registry/db/entities/SharingEntity.java | 5 +-
.../sharing/registry/db/entities/SharingPK.java | 5 +-
.../registry/db/entities/UserEntity.java | 5 +-
.../registry/db/entities/UserGroupEntity.java | 5 +-
.../registry/db/entities/UserGroupPK.java | 5 +-
.../sharing/registry/db/entities/UserPK.java | 5 +-
.../db/repositories/AbstractRepository.java | 5 +-
.../db/repositories/DomainRepository.java | 5 +-
.../db/repositories/EntityRepository.java | 5 +-
.../db/repositories/EntityTypeRepository.java | 5 +-
.../repositories/GroupMembershipRepository.java | 5 +-
.../repositories/PermissionTypeRepository.java | 5 +-
.../db/repositories/SharingRepository.java | 5 +-
.../db/repositories/UserGroupRepository.java | 5 +-
.../db/repositories/UserRepository.java | 5 +-
.../sharing/registry/db/utils/Committer.java | 5 +-
.../registry/db/utils/ConnectionPool.java | 5 +-
.../sharing/registry/db/utils/DBConstants.java | 5 +-
.../registry/db/utils/DatabaseCreator.java | 5 +-
.../sharing/registry/db/utils/JPAUtils.java | 5 +-
.../sharing/registry/db/utils/JdbcStorage.java | 5 +-
.../db/utils/ObjectMapperSingleton.java | 5 +-
.../sharing/registry/server/ServerMain.java | 5 +-
.../registry/server/SharingRegistryServer.java | 5 +-
.../server/SharingRegistryServerHandler.java | 5 +-
.../airavata/sharing/registry/CipresTest.java | 5 +-
.../SharingRegistryServerHandlerTest.java | 5 +-
.../registry/SharingRegistryServiceTest.java | 5 +-
.../sharing/registry/util/Initialize.java | 4 +-
.../sharing-registry-stubs/pom.xml | 21 +++
.../SharingRegistryServiceClientFactory.java | 5 +-
.../sharing/registry/models/Domain.java | 19 +++
.../sharing/registry/models/Entity.java | 19 +++
.../registry/models/EntitySearchField.java | 19 +++
.../sharing/registry/models/EntityType.java | 19 +++
.../registry/models/GroupCardinality.java | 19 +++
.../sharing/registry/models/GroupChildType.java | 19 +++
.../registry/models/GroupMembership.java | 19 +++
.../sharing/registry/models/GroupType.java | 19 +++
.../sharing/registry/models/PermissionType.java | 19 +++
.../registry/models/SearchCondition.java | 19 +++
.../sharing/registry/models/SearchCriteria.java | 19 +++
.../sharing/registry/models/Sharing.java | 19 +++
.../models/SharingRegistryException.java | 19 +++
.../sharing/registry/models/SharingType.java | 19 +++
.../airavata/sharing/registry/models/User.java | 19 +++
.../sharing/registry/models/UserGroup.java | 19 +++
.../models/sharing_modelsConstants.java | 19 +++
.../service/cpi/SharingRegistryService.java | 19 +++
.../sharing-service-docs/api-docs/index.html | 21 +++
.../api-docs/sharing_cpi.html | 21 +++
.../api-docs/sharing_models.html | 21 +++
.../sharing-service-docs/api-docs/style.css | 22 ++-
.../sharing-service-docs/index.html | 21 +++
.../sharing-service-docs/style.css | 22 ++-
.../thrift_models/thrift-gen.sh | 20 +++
.../test-suite/multi-tenanted-airavata/pom.xml | 26 +++-
.../multitenantedairavata/AiravataClient.java | 6 +-
.../multitenantedairavata/AiravataIT.java | 6 +-
.../ApplicationRegister.java | 6 +-
.../ComputeResourceRegister.java | 6 +-
.../ExperimentExecution.java | 6 +-
.../FrameworkBootstrapping.java | 19 +++
.../multitenantedairavata/FrameworkSetup.java | 6 +-
.../multitenantedairavata/GatewayRegister.java | 6 +-
.../StorageResourceRegister.java | 19 +++
.../TestFrameworkProps.java | 6 +-
.../utils/ApplicationProperties.java | 19 +++
.../utils/ComputeResourceProperties.java | 19 +++
.../utils/FrameworkUtils.java | 6 +-
.../utils/PropertyFileType.java | 6 +-
.../utils/PropertyReader.java | 6 +-
.../utils/TestFrameworkConstants.java | 6 +-
modules/test-suite/pom.xml | 26 +++-
modules/user-profile-migration/pom.xml | 31 +++--
.../apache/airavata/ISLoginCredentialsDAO.java | 19 +++
.../apache/airavata/IdentityServerClient.java | 19 +++
.../org/apache/airavata/MigrationManager.java | 4 +-
.../UserProfileAiravataThriftClient.java | 4 +-
.../org/apache/airavata/UserProfileDAO.java | 4 +-
modules/user-profile/pom.xml | 31 +++--
modules/user-profile/user-profile-core/pom.xml | 21 +++
.../core/UserProfileRegistryException.java | 2 +-
.../core/entities/NSFDemographicsEntity.java | 2 +-
.../core/entities/UserProfileEntity.java | 2 +-
.../core/repositories/AbstractRepository.java | 2 +-
.../repositories/UserProfileRepository.java | 2 +-
.../user/registry/core/utils/Committer.java | 2 +-
.../user/registry/core/utils/JPAUtils.java | 2 +-
.../core/utils/ObjectMapperSingleton.java | 2 +-
.../registry/core/utils/QueryConstants.java | 19 +++
.../user/registry/core/utils/Utils.java | 3 +-
.../user-profile/user-profile-service/pom.xml | 21 +++
.../user/profile/server/UserProfileServer.java | 6 +-
.../server/UserProfileServiceHandler.java | 5 +-
modules/user-profile/user-profile-stubs/pom.xml | 31 +++--
.../userprofile/cpi/UserProfileService.java | 19 +++
.../client/UserProfileServiceClientFactory.java | 3 +-
.../exception/UserProfileServiceException.java | 19 +++
.../cpi/user_profile_cpiConstants.java | 19 +++
modules/workflow-model/pom.xml | 26 +++-
modules/workflow-model/workflow-engine/pom.xml | 26 +++-
.../catalog/WorkflowCatalogFactory.java | 4 +-
.../workflow/engine/WorkflowEngine.java | 4 +-
.../engine/WorkflowEngineException.java | 4 +-
.../workflow/engine/WorkflowEngineFactory.java | 4 +-
.../workflow/engine/WorkflowEngineImpl.java | 4 +-
.../airavata/workflow/engine/WorkflowUtils.java | 4 +-
.../engine/concurrent/PredicatedExecutable.java | 5 +-
.../engine/concurrent/PredicatedTaskRunner.java | 5 +-
.../engine/core/amazon/AmazonCredential.java | 4 +-
.../engine/core/amazon/EC2InstanceResult.java | 19 +++
.../engine/core/generators/XmlBeansFiler.java | 4 +-
.../core/workflow/ParameterListModel.java | 4 +-
.../engine/datadriven/WorkflowHarvester.java | 4 +-
.../engine/file/XBayaPathConstants.java | 4 +-
.../engine/gfac/GFacRegistryClient.java | 4 +-
.../workflow/engine/gfac/SimpleWSClient.java | 4 +-
.../engine/globus/FileTransferConstants.java | 4 +-
.../globus/GridFTPFileTransferClient.java | 19 +++
.../engine/graph/controller/NodeController.java | 19 +++
.../engine/interpretor/DoWhileHandler.java | 3 +-
.../engine/interpretor/HeaderConstants.java | 4 +-
.../SSWorkflowInterpreterInteractorImpl.java | 4 +-
.../interpretor/SystemComponentInvoker.java | 4 +-
.../WorkFlowInterpreterException.java | 4 +-
.../interpretor/WorkflowExecutionMessage.java | 4 +-
.../engine/interpretor/WorkflowInterpreter.java | 4 +-
.../WorkflowInterpreterConfiguration.java | 4 +-
.../WorkflowInterpreterInteractor.java | 4 +-
.../interpretor/WorkflowInterpreterInvoker.java | 4 +-
.../WorkflowInterpreterSkeleton2.java | 19 +++
.../engine/invoker/AsynchronousInvoker.java | 4 +-
.../workflow/engine/invoker/DynamicInvoker.java | 4 +-
.../workflow/engine/invoker/Invoker.java | 4 +-
.../invoker/MsgBoxWsaResponsesCorrelator.java | 19 +++
.../workflow/engine/invoker/SimpleInvoker.java | 4 +-
.../engine/invoker/WorkflowInputUtil.java | 5 +-
.../workflow/engine/util/AmazonUtil.java | 4 +-
.../airavata/workflow/engine/util/Data.java | 4 +-
.../workflow/engine/util/GOConstants.java | 4 +-
.../workflow/engine/util/GlobusOnlineUtils.java | 19 +++
.../workflow/engine/util/InterpreterUtil.java | 3 +-
.../engine/util/ProxyMonitorPublisher.java | 4 +-
.../workflow/engine/util/RegistryConstants.java | 4 +-
.../workflow/engine/util/TransferFile.java | 4 +-
.../workflow/engine/util/XBayaUtil.java | 4 +-
.../workflow/WorkflowEngineException.java | 4 +-
.../engine/workflow/proxy/ProxyWSDL.java | 4 +-
.../engine/workflow/proxy/WorkflowClient.java | 4 +-
.../engine/workflow/proxy/WorkflowContext.java | 4 +-
.../workflow/proxy/WorkflowProxyException.java | 4 +-
.../interpreter/ComplexForEachWorkflowTest.java | 19 +++
.../xbaya/interpreter/ComplexMathService.java | 4 +-
.../interpreter/ComplexMathWorkflowTest.java | 19 +++
.../interpreter/CrossProductWorkflowTest.java | 19 +++
.../airavata/xbaya/interpreter/EchoService.java | 3 +-
.../xbaya/interpreter/ForEachWorkflowTest.java | 19 +++
.../interpreter/LevenshteinDistanceService.java | 4 +-
.../airavata/xbaya/interpreter/Listener.java | 19 +++
.../xbaya/interpreter/NotificationSender.java | 19 +++
.../xbaya/interpreter/RegistryServiceTest.java | 19 +++
.../interpreter/SimpleForEachWorkflowTest.java | 19 +++
.../interpreter/SimpleMathWorkflowTest.java | 19 +++
.../xbaya/interpreter/WorkflowTest.java | 19 +++
.../xbaya/interpreter/WorkflowTrackingTest.java | 19 +++
.../xbaya/interpreter/XBayaClientTest.java | 5 +-
.../interpreter/XBayaConsolidatedTestSuite.java | 19 +++
.../xbaya/interpreter/utils/ConfigKeys.java | 5 +-
.../xbaya/interpreter/utils/TestUtilServer.java | 19 +++
.../interpreter/utils/WorkflowTestUtils.java | 19 +++
.../workflow-model-component/pom.xml | 26 +++-
.../registry/JCRComponentReference.java | 4 +-
.../registry/JCRComponentRegistry.java | 4 +-
.../workflow-model/workflow-model-core/pom.xml | 26 +++-
.../workflow/model/component/Component.java | 4 +-
.../model/component/ComponentControlPort.java | 4 +-
.../model/component/ComponentDataPort.java | 4 +-
.../model/component/ComponentEPRPort.java | 4 +-
.../model/component/ComponentException.java | 4 +-
.../component/ComponentOperationReference.java | 4 +-
.../workflow/model/component/ComponentPort.java | 4 +-
.../model/component/ComponentReference.java | 4 +-
.../model/component/ComponentRegistry.java | 4 +-
.../component/ComponentRegistryException.java | 4 +-
.../amazon/AmazonComponentRegistry.java | 4 +-
.../component/amazon/InstanceComponent.java | 4 +-
.../amazon/InstanceComponentDataPort.java | 4 +-
.../amazon/TerminateInstanceComponent.java | 4 +-
.../component/dynamic/DynamicComponent.java | 4 +-
.../component/dynamic/DynamicComponentPort.java | 4 +-
.../local/LocalComponentReference.java | 4 +-
.../component/local/LocalComponentRegistry.java | 4 +-
.../model/component/system/BlockComponent.java | 4 +-
.../component/system/ConstantComponent.java | 4 +-
.../system/DifferedInputComponent.java | 8 +-
.../component/system/DoWhileComponent.java | 4 +-
.../component/system/EndBlockComponent.java | 4 +-
.../component/system/EndDoWhileComponent.java | 4 +-
.../component/system/EndForEachComponent.java | 4 +-
.../model/component/system/EndifComponent.java | 4 +-
.../model/component/system/ExitComponent.java | 4 +-
.../component/system/ForEachComponent.java | 4 +-
.../model/component/system/IfComponent.java | 4 +-
.../model/component/system/InputComponent.java | 4 +-
.../model/component/system/MemoComponent.java | 4 +-
.../model/component/system/OutputComponent.java | 4 +-
.../component/system/ReceiveComponent.java | 4 +-
.../component/system/S3InputComponent.java | 4 +-
.../component/system/StreamSourceComponent.java | 4 +-
.../component/system/SubWorkflowComponent.java | 4 +-
.../model/component/system/SystemComponent.java | 4 +-
.../system/SystemComponentDataPort.java | 4 +-
.../system/SystemComponentReference.java | 4 +-
.../system/SystemComponentRegistry.java | 4 +-
.../component/url/URLComponentReference.java | 4 +-
.../component/url/URLComponentRegistry.java | 4 +-
.../component/web/WebComponentReference.java | 4 +-
.../component/web/WebComponentRegistry.java | 4 +-
.../model/component/ws/WSComponent.java | 4 +-
.../component/ws/WSComponentApplication.java | 4 +-
.../ws/WSComponentApplicationParameter.java | 4 +-
.../model/component/ws/WSComponentFactory.java | 4 +-
.../model/component/ws/WSComponentKey.java | 4 +-
.../model/component/ws/WSComponentPort.java | 4 +-
.../component/ws/WSComponentReference.java | 4 +-
.../model/component/ws/WSComponentRegistry.java | 4 +-
.../model/component/ws/WorkflowComponent.java | 4 +-
.../exceptions/LazyLoadedDataException.java | 4 +-
.../model/exceptions/UtilsException.java | 4 +-
.../model/exceptions/WorkflowException.java | 4 +-
.../exceptions/WorkflowRuntimeException.java | 4 +-
.../airavata/workflow/model/gpel/DSCUtil.java | 4 +-
.../workflow/model/gpel/script/BPELScript.java | 4 +-
.../model/gpel/script/BPELScriptType.java | 4 +-
.../model/gpel/script/WorkflowWSDL.java | 4 +-
.../workflow/model/graph/ControlEdge.java | 4 +-
.../workflow/model/graph/ControlPort.java | 4 +-
.../airavata/workflow/model/graph/DataEdge.java | 4 +-
.../airavata/workflow/model/graph/DataPort.java | 4 +-
.../airavata/workflow/model/graph/EPRPort.java | 4 +-
.../airavata/workflow/model/graph/Edge.java | 4 +-
.../model/graph/ForEachExecutableNode.java | 5 +-
.../airavata/workflow/model/graph/Graph.java | 4 +-
.../workflow/model/graph/GraphException.java | 4 +-
.../workflow/model/graph/GraphFactory.java | 4 +-
.../workflow/model/graph/GraphPiece.java | 4 +-
.../workflow/model/graph/GraphSchema.java | 4 +-
.../airavata/workflow/model/graph/Node.java | 4 +-
.../airavata/workflow/model/graph/Port.java | 4 +-
.../model/graph/amazon/InstanceDataPort.java | 4 +-
.../model/graph/amazon/InstanceNode.java | 4 +-
.../model/graph/amazon/ResourceNode.java | 4 +-
.../graph/amazon/TerminateInstanceNode.java | 4 +-
.../model/graph/dynamic/BasicTypeMapping.java | 4 +-
.../model/graph/dynamic/DynamicNode.java | 4 +-
.../model/graph/dynamic/DynamicPort.java | 4 +-
.../model/graph/dynamic/PortAddable.java | 4 +-
.../model/graph/dynamic/SchemaCompilerUtil.java | 4 +-
.../workflow/model/graph/impl/EdgeImpl.java | 4 +-
.../workflow/model/graph/impl/GraphImpl.java | 4 +-
.../workflow/model/graph/impl/NodeImpl.java | 4 +-
.../workflow/model/graph/impl/PortImpl.java | 4 +-
.../graph/subworkflow/SubWorkflowNode.java | 4 +-
.../workflow/model/graph/system/BlockNode.java | 4 +-
.../model/graph/system/ConstantNode.java | 4 +-
.../model/graph/system/DifferedInputNode.java | 7 +-
.../model/graph/system/DoWhileNode.java | 4 +-
.../model/graph/system/EndBlockNode.java | 4 +-
.../model/graph/system/EndDoWhileNode.java | 4 +-
.../model/graph/system/EndForEachNode.java | 4 +-
.../workflow/model/graph/system/EndifNode.java | 4 +-
.../workflow/model/graph/system/ExitNode.java | 4 +-
.../model/graph/system/ForEachNode.java | 4 +-
.../workflow/model/graph/system/IfNode.java | 4 +-
.../workflow/model/graph/system/InputNode.java | 4 +-
.../workflow/model/graph/system/MemoNode.java | 4 +-
.../workflow/model/graph/system/OutputNode.java | 4 +-
.../model/graph/system/ParameterNode.java | 4 +-
.../model/graph/system/ReceiveNode.java | 4 +-
.../model/graph/system/S3InputNode.java | 4 +-
.../model/graph/system/StreamSourceNode.java | 4 +-
.../model/graph/system/SystemDataPort.java | 4 +-
.../workflow/model/graph/system/SystemNode.java | 4 +-
.../workflow/model/graph/util/GraphUtil.java | 4 +-
.../workflow/model/graph/ws/WSGraph.java | 4 +-
.../workflow/model/graph/ws/WSGraphFactory.java | 4 +-
.../workflow/model/graph/ws/WSNode.java | 4 +-
.../workflow/model/graph/ws/WSPort.java | 4 +-
.../workflow/model/graph/ws/WorkflowNode.java | 4 +-
.../workflow/model/ode/ODEBPELTransformer.java | 19 +++
.../airavata/workflow/model/ode/ODEClient.java | 19 +++
.../model/ode/ODEDeploymentDescriptor.java | 19 +++
.../workflow/model/ode/ODEWSDLTransformer.java | 19 +++
.../workflow/model/ode/WSDLCleaner.java | 19 +++
.../model/utils/ApplicationVersion.java | 4 +-
.../workflow/model/utils/FileConstants.java | 4 +-
.../workflow/model/utils/MessageConstants.java | 4 +-
.../workflow/model/utils/WorkflowConstants.java | 4 +-
.../model/wf/InvalidDataFormatException.java | 4 +-
.../workflow/model/wf/TridentTransformer.java | 4 +-
.../airavata/workflow/model/wf/Workflow.java | 4 +-
.../workflow/model/wf/WorkflowData.java | 4 +-
.../model/wf/WorkflowExecutionState.java | 4 +-
.../workflow/model/wf/WorkflowInput.java | 4 +-
.../workflow/model/xsd/GFacSimpleTypesXSD.java | 4 +-
.../model/xsd/LeadContextHeaderXSD.java | 4 +-
.../workflow/model/xsd/LeadCrosscutXSD.java | 4 +-
modules/workflow/pom.xml | 31 +++--
modules/workflow/workflow-core/pom.xml | 31 +++--
.../airavata/workflow/core/WorkflowBuilder.java | 4 +-
.../workflow/core/WorkflowEnactmentService.java | 4 +-
.../airavata/workflow/core/WorkflowFactory.java | 4 +-
.../airavata/workflow/core/WorkflowInfo.java | 3 +-
.../workflow/core/WorkflowInterpreter.java | 4 +-
.../apache/airavata/workflow/core/XMLUtil.java | 4 +-
.../airavata/workflow/core/XmlFormatter.java | 4 +-
.../workflow/core/dag/edge/DirectedEdge.java | 4 +-
.../airavata/workflow/core/dag/edge/Edge.java | 4 +-
.../core/dag/nodes/ApplicationNode.java | 4 +-
.../core/dag/nodes/ApplicationNodeImpl.java | 4 +-
.../workflow/core/dag/nodes/InputNode.java | 4 +-
.../workflow/core/dag/nodes/InputNodeImpl.java | 4 +-
.../workflow/core/dag/nodes/NodeType.java | 4 +-
.../workflow/core/dag/nodes/OutputNode.java | 4 +-
.../workflow/core/dag/nodes/OutputNodeImpl.java | 4 +-
.../workflow/core/dag/nodes/WorkflowNode.java | 4 +-
.../airavata/workflow/core/dag/port/InPort.java | 4 +-
.../workflow/core/dag/port/InputPortIml.java | 4 +-
.../workflow/core/dag/port/OutPort.java | 4 +-
.../workflow/core/dag/port/OutPortImpl.java | 4 +-
.../airavata/workflow/core/dag/port/Port.java | 4 +-
.../core/parser/JsonWorkflowParser.java | 4 +-
.../workflow/core/parser/ParserException.java | 3 +-
.../workflow/core/parser/WorkflowParser.java | 4 +-
.../airavata/workflow/core/XMLUtilTest.java | 5 +-
.../core/parser/JsonWorkflowParserTest.java | 4 +-
modules/xbaya-gui/pom.xml | 26 +++-
.../apache/airavata/xbaya/ThriftClientData.java | 4 +-
.../airavata/xbaya/ThriftServiceType.java | 4 +-
.../java/org/apache/airavata/xbaya/XBaya.java | 4 +-
.../airavata/xbaya/XBayaConfiguration.java | 4 +-
.../apache/airavata/xbaya/XBayaConstants.java | 4 +-
.../org/apache/airavata/xbaya/XBayaEngine.java | 4 +-
.../org/apache/airavata/xbaya/XBayaVersion.java | 4 +-
.../component/registry/ComponentController.java | 4 +-
.../registry/ComponentRegistryLoader.java | 4 +-
.../xbaya/concurrent/PredicatedExecutable.java | 5 +-
.../xbaya/concurrent/PredicatedTaskRunner.java | 5 +-
.../xbaya/core/amazon/AmazonCredential.java | 4 +-
.../xbaya/core/amazon/EC2InstanceResult.java | 4 +-
.../xbaya/core/generators/BPELFiler.java | 4 +-
.../xbaya/core/generators/ImageFiler.java | 4 +-
.../xbaya/core/generators/JythonFiler.java | 4 +-
.../xbaya/core/generators/ODEScriptFiler.java | 4 +-
.../xbaya/core/generators/ScuflFiler.java | 4 +-
.../xbaya/core/generators/WorkflowFiler.java | 4 +-
.../xbaya/core/generators/XmlBeansFiler.java | 4 +-
.../core/ide/XBayaExecutionModeListener.java | 4 +-
.../xbaya/core/workflow/ParameterListModel.java | 4 +-
.../xbaya/datadriven/WorkflowHarvester.java | 4 +-
.../airavata/xbaya/file/XBayaPathConstants.java | 4 +-
.../airavata/xbaya/gfac/GFacRegistryClient.java | 4 +-
.../airavata/xbaya/gfac/SimpleWSClient.java | 4 +-
.../xbaya/globus/FileTransferConstants.java | 4 +-
.../xbaya/globus/GridFTPFileTransferClient.java | 19 +++
.../xbaya/graph/controller/NodeController.java | 4 +-
.../xbaya/interpretor/ExperimentTemplate.java | 19 +++
.../GUIWorkflowInterpreterInteractorImpl.java | 19 +++
.../xbaya/interpretor/HeaderConstants.java | 4 +-
.../SSWorkflowInterpreterInteractorImpl.java | 19 +++
.../StandaloneNotificationSender.java | 4 +-
.../WorkFlowInterpreterException.java | 4 +-
.../interpretor/WorkflowExecutionMessage.java | 4 +-
.../interpretor/WorkflowExecutionTemplate.java | 19 +++
.../xbaya/interpretor/WorkflowInterpreter.java | 19 +++
.../WorkflowInterpreterConfiguration.java | 19 +++
.../WorkflowInterpreterInteractor.java | 19 +++
.../interpretor/WorkflowInterpreterInvoker.java | 4 +-
.../WorkflowInterpretorEventListener.java | 19 +++
...WorkflowInterpretorMessageReceiverInOut.java | 19 +++
.../WorkflowInterpretorSkeleton.java | 19 +++
.../xbaya/jython/lib/GFacServiceCreator.java | 4 +-
.../xbaya/jython/lib/NotificationSender.java | 19 +++
.../xbaya/jython/lib/ServiceNotifiable.java | 4 +-
.../jython/lib/ServiceNotificationSender.java | 19 +++
.../StandaloneServiceNotificationSender.java | 4 +-
.../xbaya/jython/lib/WorkflowNotifiable.java | 4 +-
.../xbaya/jython/runner/JythonClassLoader.java | 4 +-
.../jython/runner/JythonOneTimeRunner.java | 4 +-
.../jython/runner/JythonOneTimeRunnerImpl.java | 4 +-
.../xbaya/jython/runner/JythonRunner.java | 4 +-
.../xbaya/jython/script/JythonScript.java | 4 +-
.../xbaya/menues/tools/ToolsMenuItem.java | 4 +-
.../airavata/xbaya/messaging/EventData.java | 4 +-
.../xbaya/messaging/EventDataListener.java | 4 +-
.../xbaya/messaging/EventDataRepository.java | 4 +-
.../airavata/xbaya/messaging/Monitor.java | 4 +-
.../xbaya/messaging/MonitorException.java | 4 +-
.../xbaya/messaging/NotificationHandler.java | 4 +-
.../airavata/xbaya/messaging/event/Event.java | 4 +-
.../xbaya/messaging/event/EventListener.java | 4 +-
.../xbaya/messaging/event/EventProducer.java | 4 +-
.../xbaya/modifier/WorkflowModifier.java | 4 +-
.../xbaya/registry/PasswordCallbackImpl.java | 19 +++
.../xbaya/scufl/script/ScuflScript.java | 19 +++
.../xbaya/test/util/WorkflowCreator.java | 19 +++
.../org/apache/airavata/xbaya/ui/XBayaGUI.java | 4 +-
.../ui/actions/AbstractBrowserActionItem.java | 4 +-
.../ui/actions/registry/browser/AddAction.java | 4 +-
.../actions/registry/browser/BrowserAction.java | 4 +-
.../ui/actions/registry/browser/CopyAction.java | 4 +-
.../actions/registry/browser/DeleteAction.java | 4 +-
.../ui/actions/registry/browser/EditAction.java | 4 +-
.../actions/registry/browser/ImportAction.java | 4 +-
.../actions/registry/browser/RefreshAction.java | 4 +-
.../ui/actions/registry/browser/ViewAction.java | 4 +-
.../airavata/xbaya/ui/dialogs/AboutWindow.java | 4 +-
.../airavata/xbaya/ui/dialogs/ErrorWindow.java | 4 +-
.../ui/dialogs/GlobusFileTransferWindow.java | 19 +++
.../airavata/xbaya/ui/dialogs/TextWindow.java | 4 +-
.../airavata/xbaya/ui/dialogs/WaitDialog.java | 4 +-
.../airavata/xbaya/ui/dialogs/XBayaDialog.java | 4 +-
.../dialogs/amazon/AmazonEC2InvokerWindow.java | 4 +-
.../ui/dialogs/amazon/AmazonS3UtilsWindow.java | 4 +-
.../xbaya/ui/dialogs/amazon/BucketsLoader.java | 4 +-
.../dialogs/amazon/ChangeCredentialWindow.java | 4 +-
.../amazon/EC2InstancesManagementWindow.java | 4 +-
.../ui/dialogs/amazon/EC2LaunchWindow.java | 4 +-
.../ui/dialogs/amazon/InstancesLoader.java | 4 +-
.../xbaya/ui/dialogs/amazon/S3Downloader.java | 4 +-
.../xbaya/ui/dialogs/amazon/S3Uploader.java | 4 +-
.../ui/dialogs/component/URLRegistryWindow.java | 4 +-
.../ui/dialogs/component/WebResigtryWindow.java | 4 +-
.../amazon/InstanceConfigurationDialog.java | 4 +-
.../system/ConstantConfigurationDialog.java | 4 +-
.../DifferedInputConfigurationDialog.java | 4 +-
.../graph/system/DoWhileConfigrationDialog.java | 4 +-
.../system/EndBlockConfigurationDialog.java | 4 +-
.../system/EndDoWhileConfigurationDialog.java | 4 +-
.../system/EndForEachConfigurationDialog.java | 4 +-
.../graph/system/EndifConfigurationDialog.java | 4 +-
.../system/ForEachConfigurationDialog.java | 4 +-
.../graph/system/IfConfigurationDialog.java | 4 +-
.../graph/system/InputConfigurationDialog.java | 4 +-
.../graph/system/MemoConfigurationDialog.java | 4 +-
.../graph/system/OutputConfigurationDialog.java | 4 +-
.../system/ReceiveConfigurationDialog.java | 4 +-
.../ui/dialogs/graph/system/S3FileChooser.java | 4 +-
.../system/StreamSourceConfigurationDialog.java | 4 +-
.../graph/ws/ServiceInteractionWindow.java | 4 +-
.../xbaya/ui/dialogs/graph/ws/WSNodeWindow.java | 4 +-
.../monitor/MonitorConfigurationWindow.java | 4 +-
.../xbaya/ui/dialogs/monitor/MonitorWindow.java | 4 +-
.../dialogs/registry/NewRegistryUserDialog.java | 4 +-
.../ui/dialogs/registry/RegistryWindow.java | 4 +-
.../registry/browser/JCRBrowserDialog.java | 4 +-
.../workflow/ParameterPropertyWindow.java | 4 +-
.../dialogs/workflow/WorkflowImportWindow.java | 4 +-
.../workflow/WorkflowPropertyWindow.java | 4 +-
.../xbaya/ui/experiment/ExperimentMenu.java | 4 +-
.../ui/experiment/LaunchApplicationWindow.java | 4 +-
.../ui/experiment/RegistrySearchResult.java | 4 +-
.../RegistryWorkflowPublisherWindow.java | 4 +-
.../WorkflowInterpreterLaunchWindow.java | 4 +-
.../apache/airavata/xbaya/ui/graph/EdgeGUI.java | 4 +-
.../airavata/xbaya/ui/graph/GraphCanvas.java | 4 +-
.../xbaya/ui/graph/GraphCanvasEvent.java | 4 +-
.../xbaya/ui/graph/GraphCanvasListener.java | 4 +-
.../airavata/xbaya/ui/graph/GraphGUI.java | 4 +-
.../airavata/xbaya/ui/graph/GraphPieceGUI.java | 4 +-
.../apache/airavata/xbaya/ui/graph/NodeGUI.java | 4 +-
.../airavata/xbaya/ui/graph/Paintable.java | 4 +-
.../apache/airavata/xbaya/ui/graph/PortGUI.java | 4 +-
.../xbaya/ui/graph/amazon/InstanceNodeGUI.java | 4 +-
.../graph/amazon/TerminateInstanceNodeGUI.java | 4 +-
.../graph/subworkflow/SubWorkflowNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/BlockNodeGUI.java | 4 +-
.../ui/graph/system/ConfigurableNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ConstantNodeGUI.java | 4 +-
.../ui/graph/system/DifferedInputHandler.java | 3 +-
.../ui/graph/system/DifferedInputNodeGUI.java | 3 +-
.../xbaya/ui/graph/system/DoWhileNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/EndBlockNodeGUI.java | 4 +-
.../ui/graph/system/EndDoWhileNodeGUI.java | 4 +-
.../ui/graph/system/EndForEachNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/EndifNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ExitNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ForEachNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/IfNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/InputNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/MemoNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/OutputNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/ReceiveNodeGUI.java | 4 +-
.../xbaya/ui/graph/system/S3InputNodeGUI.java | 4 +-
.../ui/graph/system/StreamSourceNodeGUI.java | 4 +-
.../airavata/xbaya/ui/graph/ws/WSNodeGUI.java | 4 +-
.../xbaya/ui/graph/ws/WorkflowNodeGUI.java | 4 +-
.../xbaya/ui/menues/AmazonEC2MenuItem.java | 4 +-
.../xbaya/ui/menues/ApplicationMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/EditMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/MenuIcons.java | 4 +-
.../xbaya/ui/menues/RegistryMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/RunMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/ViewMenuItem.java | 4 +-
.../airavata/xbaya/ui/menues/XBayaMenu.java | 4 +-
.../airavata/xbaya/ui/menues/XBayaMenuItem.java | 4 +-
.../xbaya/ui/monitor/MonitorEventHandler.java | 4 +-
.../xbaya/ui/monitor/MonitorStarter.java | 4 +-
.../xbaya/ui/monitor/ResourcePaintable.java | 4 +-
.../airavata/xbaya/ui/utils/Cancelable.java | 4 +-
.../airavata/xbaya/ui/utils/DrawUtils.java | 4 +-
.../airavata/xbaya/ui/utils/ErrorMessages.java | 4 +-
.../xbaya/ui/views/ComponentViewer.java | 4 +-
.../xbaya/ui/views/JCRBrowserPanel.java | 19 +++
.../airavata/xbaya/ui/views/MonitorPanel.java | 4 +-
.../xbaya/ui/views/ParameterPropertyPanel.java | 4 +-
.../airavata/xbaya/ui/views/PortViewer.java | 4 +-
.../airavata/xbaya/ui/widgets/GridPanel.java | 4 +-
.../airavata/xbaya/ui/widgets/ScrollPanel.java | 4 +-
.../xbaya/ui/widgets/TabLabelButton.java | 4 +-
.../xbaya/ui/widgets/TableRenderable.java | 4 +-
.../xbaya/ui/widgets/ToolbarButton.java | 4 +-
.../xbaya/ui/widgets/XBayaComboBox.java | 4 +-
.../xbaya/ui/widgets/XBayaComponent.java | 4 +-
.../airavata/xbaya/ui/widgets/XBayaLabel.java | 3 +-
.../xbaya/ui/widgets/XBayaLinkButton.java | 4 +-
.../airavata/xbaya/ui/widgets/XBayaList.java | 4 +-
.../xbaya/ui/widgets/XBayaTextArea.java | 4 +-
.../xbaya/ui/widgets/XBayaTextComponent.java | 4 +-
.../xbaya/ui/widgets/XBayaTextField.java | 4 +-
.../airavata/xbaya/ui/widgets/XBayaToolBar.java | 4 +-
.../xbaya/ui/widgets/XbayaEnhancedList.java | 4 +-
.../xbaya/ui/widgets/amazon/S3Tree.java | 4 +-
.../xbaya/ui/widgets/amazon/S3TreeModel.java | 4 +-
.../ui/widgets/component/ComponentSelector.java | 4 +-
.../component/ComponentSelectorEvent.java | 4 +-
.../component/ComponentSelectorListener.java | 4 +-
.../component/ComponentSourceTransferable.java | 4 +-
.../widgets/component/ComponentTreeModel.java | 4 +-
.../ui/widgets/component/ComponentTreeNode.java | 4 +-
.../apache/airavata/xbaya/util/AmazonUtil.java | 4 +-
.../org/apache/airavata/xbaya/util/Data.java | 4 +-
.../apache/airavata/xbaya/util/GOConstants.java | 4 +-
.../airavata/xbaya/util/GlobusOnlineUtils.java | 19 +++
.../airavata/xbaya/util/RegistryConstants.java | 4 +-
.../airavata/xbaya/util/TransferFile.java | 4 +-
.../apache/airavata/xbaya/util/XBayaUtil.java | 4 +-
.../airavata/xbaya/workflow/WorkflowClient.java | 4 +-
.../xbaya/workflow/WorkflowEngineException.java | 4 +-
.../xbaya/workflow/proxy/ProxyWSDL.java | 4 +-
.../xbaya/workflow/proxy/WorkflowClient.java | 4 +-
.../xbaya/workflow/proxy/WorkflowContext.java | 4 +-
.../workflow/proxy/WorkflowProxyException.java | 4 +-
.../interpreter/ComplexForEachWorkflowTest.java | 19 +++
.../xbaya/interpreter/ComplexMathService.java | 4 +-
.../interpreter/ComplexMathWorkflowTest.java | 19 +++
.../interpreter/CrossProductWorkflowTest.java | 19 +++
.../airavata/xbaya/interpreter/EchoService.java | 3 +-
.../xbaya/interpreter/ForEachWorkflowTest.java | 19 +++
.../interpreter/LevenshteinDistanceService.java | 4 +-
.../airavata/xbaya/interpreter/Listener.java | 19 +++
.../xbaya/interpreter/NotificationSender.java | 19 +++
.../xbaya/interpreter/RegistryServiceTest.java | 19 +++
.../interpreter/SimpleForEachWorkflowTest.java | 19 +++
.../interpreter/SimpleMathWorkflowTest.java | 19 +++
.../xbaya/interpreter/WorkflowTest.java | 19 +++
.../xbaya/interpreter/WorkflowTrackingTest.java | 19 +++
.../xbaya/interpreter/XBayaClientTest.java | 5 +-
.../interpreter/XBayaConsolidatedTestSuite.java | 19 +++
.../xbaya/interpreter/utils/ConfigKeys.java | 5 +-
.../xbaya/interpreter/utils/TestUtilServer.java | 19 +++
.../interpreter/utils/WorkflowTestUtils.java | 19 +++
pom.xml | 99 +++++++++++---
sandbox/amqpwstunnel/python/amqpwstunnel.py | 20 +++
sandbox/amqpwstunnel/wstest.html | 21 +++
sandbox/job-status-rest-server/api_test.py | 20 +++
sandbox/job-status-rest-server/app.py | 20 +++
.../example/logfile_checker/generate_logs.sh | 20 +++
.../example/logfile_checker/log_consumer.py | 20 +++
.../example/logfile_checker/log_streamer.py | 20 +++
.../simstream/example/logfile_checker/test.txt | 20 +++
.../example/mem_streamer/memory_consumption.py | 20 +++
.../example/mem_streamer/memory_streamer.py | 20 +++
.../application/alanine_dipeptide.py | 20 +++
.../example/openmm_example/openmm_consumer.py | 20 +++
.../openmm_example/openmm_log_consumer.py | 20 +++
.../openmm_example/openmm_rmsd_consumer.py | 20 +++
.../example/openmm_example/openmm_streamer.py | 20 +++
.../simstream/example/openmm_example/test.txt | 20 +++
sandbox/simstream/setup.py | 20 +++
sandbox/simstream/simstream/__init__.py | 20 +++
sandbox/simstream/simstream/datacollector.py | 20 +++
sandbox/simstream/simstream/datareporter.py | 20 +++
sandbox/simstream/simstream/eventhandler.py | 20 +++
sandbox/simstream/simstream/eventmonitor.py | 20 +++
.../simstream/simstream/pikaasyncconsumer.py | 20 +++
sandbox/simstream/simstream/pikaproducer.py | 20 +++
sandbox/simstream/simstream/simstream.py | 20 +++
.../component-cpis/generate-cpi-stubs.sh | 30 ++--
.../generate-thrift-stubs.sh | 30 ++--
tools/gsissh-cli-tools/README.txt | 20 +++
tools/gsissh-cli-tools/pom.xml | 29 ++--
.../ssh/cli/SSHApiClientWithMyProxyAuth.java | 4 +-
tools/phoebus-integration/pom.xml | 26 +++-
.../impl/PhoebusGridConfigurationHandler.java | 4 +-
.../airavata/core/gfac/utils/PhoebusUtils.java | 4 +-
tools/pom.xml | 26 +++-
tools/rabbitmq-download-start.sh | 20 +++
1679 files changed, 12712 insertions(+), 5992 deletions(-)
----------------------------------------------------------------------