This is an automated email from the ASF dual-hosted git repository.
lahirujayathilake pushed a change to branch agent-framework-refactoring
in repository https://gitbox.apache.org/repos/asf/airavata.git
omit 1e1db46bc2 fixed the source generation when building from the project
root
omit d5d876a8ff symlinked the proto directory and updated the proto-java
build plugin to generate sources correctly
add 3e97c3aeb7 Agent service - fixed source generation issues
add 8665a46540 run spotless:apply, add style-check github action
add 19c4efd33d update spotless github action
add a33929942a Add details about the airavata ecosystem into README.md
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Summary of changes:
.github/workflows/style-check.yml | 36 +
README.md | 36 +
airavata-api/airavata-api-client/pom.xml | 36 +-
.../airavata/api/client/AiravataClientFactory.java | 81 +-
airavata-api/airavata-api-server/pom.xml | 32 +-
.../airavata/api/server/AiravataAPIServer.java | 292 +--
.../api/server/handler/AiravataServerHandler.java | 2680 +++++++++++++-------
.../apache/airavata/api/server/util/Constants.java | 38 +-
.../airavata-client-sdks/airavata-cpp-sdk/pom.xml | 32 +-
.../airavata-client-sdks/airavata-php-sdk/pom.xml | 32 +-
.../java-client-samples/pom.xml | 32 +-
.../airavata/client/samples/CancelExperiments.java | 52 +-
.../airavata/client/samples/CreateLaunchBES.java | 164 +-
.../client/samples/CreateLaunchExperiment.java | 853 ++++---
.../client/samples/CreateLaunchExperimentUS3.java | 498 ++--
.../client/samples/ReplicaCatalogSample.java | 39 +-
.../client/samples/SampleEchoExperiment.java | 140 +-
.../airavata/client/secure/client/Properties.java | 47 +-
.../client/secure/client/SecureClient.java | 46 +-
.../client/tools/RegisterOGCEUS3Application.java | 514 ++--
.../client/tools/RegisterSampleApplications.java | 1787 ++++++++-----
.../tools/RegisterSampleApplicationsUtils.java | 131 +-
.../client/tools/RegisterUS3Application.java | 530 ++--
airavata-api/airavata-client-sdks/pom.xml | 36 +-
airavata-api/airavata-data-models/pom.xml | 32 +-
airavata-api/airavata-model-utils/pom.xml | 36 +-
.../airavata/model/util/AppDeploymentUtil.java | 55 +-
.../airavata/model/util/AppInterfaceUtil.java | 69 +-
.../apache/airavata/model/util/ExecutionType.java | 42 +-
.../airavata/model/util/ExperimentModelUtil.java | 107 +-
.../util/GroupComputeResourcePreferenceUtil.java | 43 +-
.../airavata/model/util/ProjectModelUtil.java | 39 +-
.../GroupComputeResourcePreferenceUtilTest.java | 117 +-
airavata-api/pom.xml | 36 +-
airavata-services/pom.xml | 32 +-
.../iam-admin-services-core/pom.xml | 32 +-
.../core/impl/TenantManagementKeycloakImpl.java | 397 +--
.../core/interfaces/TenantManagementInterface.java | 82 +-
.../admin/services/core/tests/SetupNewGateway.java | 210 +-
airavata-services/profile-service/pom.xml | 36 +-
.../java-client-samples/pom.xml | 36 +-
.../profile/client/samples/GroupManagerSample.java | 37 +-
.../client/samples/TenantProfileSample.java | 43 +-
.../profile/client/samples/UserProfileSample.java | 53 +-
.../client/util/ProfileServiceClientUtil.java | 38 +-
.../profile-service-client-sdks/pom.xml | 36 +-
.../profile-service-commons/pom.xml | 32 +-
.../commons/repositories/AbstractRepository.java | 64 +-
.../commons/tenant/entities/GatewayEntity.java | 87 +-
.../user/entities/CustomizedDashboardEntity.java | 92 +-
.../user/entities/NSFDemographicsEntity.java | 55 +-
.../commons/user/entities/UserProfileEntity.java | 115 +-
.../service/profile/commons/utils/Committer.java | 40 +-
.../profile/commons/utils/JPAConstants.java | 54 +-
.../service/profile/commons/utils/JPAUtils.java | 46 +-
.../commons/utils/ObjectMapperSingleton.java | 49 +-
.../commons/utils/ProfileServiceJDBCConfig.java | 40 +-
.../profile/commons/utils/QueryConstants.java | 68 +-
.../service/profile/commons/utils/Utils.java | 99 +-
.../profile-service/profile-service-server/pom.xml | 32 +-
.../handlers/GroupManagerServiceHandler.java | 185 +-
.../profile/handlers/IamAdminServicesHandler.java | 124 +-
.../handlers/TenantProfileServiceHandler.java | 100 +-
.../handlers/UserProfileServiceHandler.java | 110 +-
.../profile/server/ProfileServiceServer.java | 89 +-
.../profile-service/profile-service-stubs/pom.xml | 32 +-
.../client/ProfileServiceClientFactory.java | 62 +-
.../profile-service/profile-tenant-core/pom.xml | 36 +-
.../core/repositories/TenantProfileRepository.java | 64 +-
.../profile-service/profile-user-core/pom.xml | 32 +-
.../exceptions/UserProfileRegistryException.java | 40 +-
.../core/repositories/UserProfileRepository.java | 96 +-
.../core/utils/UserProfileCatalogDBInitConfig.java | 39 +-
.../core/utils/UserProfileCatalogJDBCConfig.java | 39 +-
.../core/repositories/WorkspaceRepositoryTest.java | 342 +--
airavata-services/services-security/pom.xml | 32 +-
.../service/security/AiravataSecurityManager.java | 43 +-
.../service/security/GatewayGroupsInitializer.java | 88 +-
.../airavata/service/security/IdentityContext.java | 43 +-
.../service/security/KeyCloakSecurityManager.java | 320 +--
.../service/security/SecurityManagerFactory.java | 39 +-
.../apache/airavata/service/security/UserInfo.java | 39 +-
.../service/security/authzcache/AuthzCache.java | 43 +-
.../security/authzcache/AuthzCacheEntry.java | 42 +-
.../security/authzcache/AuthzCacheIndex.java | 42 +-
.../security/authzcache/AuthzCacheManager.java | 40 +-
.../authzcache/AuthzCacheManagerFactory.java | 44 +-
.../security/authzcache/AuthzCachedStatus.java | 36 +-
.../authzcache/DefaultAuthzCacheManager.java | 48 +-
.../security/interceptor/SecurityCheck.java | 40 +-
.../security/interceptor/SecurityInterceptor.java | 57 +-
.../security/interceptor/SecurityModule.java | 43 +-
.../security/GatewayGroupsInitializerTest.java | 123 +-
.../security/KeyCloakSecurityManagerTest.java | 340 ++-
modules/agent-framework/agent-service/pom.xml | 34 +-
.../service/AgentServiceApplication.java | 37 +-
.../agent/connection/service/UserContext.java | 43 +-
.../service/config/AuthzTokenFilter.java | 46 +-
.../service/config/ClusterApplicationConfig.java | 41 +-
.../service/controllers/AgentController.java | 102 +-
.../service/controllers/ExperimentController.java | 51 +-
.../service/controllers/PlanController.java | 42 +-
.../service/db/entity/AgentDeploymentInfo.java | 42 +-
.../service/db/entity/AgentExecution.java | 41 +-
.../service/db/entity/AgentExecutionStatus.java | 38 +-
.../agent/connection/service/db/entity/Plan.java | 38 +-
.../service/db/repo/AgentDeploymentInfoRepo.java | 40 +-
.../service/db/repo/AgentExecutionRepo.java | 40 +-
.../service/db/repo/AgentExecutionStatusRepo.java | 40 +-
.../agent/connection/service/db/repo/PlanRepo.java | 40 +-
.../service/handlers/AgentConnectionHandler.java | 303 ++-
.../service/handlers/AgentManagementHandler.java | 127 +-
.../connection/service/handlers/FuseFSHandler.java | 125 +-
.../connection/service/handlers/PlanHandler.java | 42 +-
.../models/AgentAsyncCommandExecutionRequest.java | 37 +-
.../models/AgentAsyncCommandExecutionResponse.java | 37 +-
.../models/AgentAsyncCommandListRequest.java | 37 +-
.../models/AgentAsyncCommandListResponse.java | 37 +-
.../models/AgentAsyncCommandTerminateRequest.java | 37 +-
.../models/AgentAsyncCommandTerminateResponse.java | 37 +-
.../service/models/AgentCommandExecutionAck.java | 39 +-
.../models/AgentCommandExecutionRequest.java | 37 +-
.../models/AgentCommandExecutionResponse.java | 37 +-
.../service/models/AgentEnvSetupAck.java | 39 +-
.../service/models/AgentEnvSetupRequest.java | 38 +-
.../service/models/AgentEnvSetupResponse.java | 37 +-
.../service/models/AgentInfoResponse.java | 39 +-
.../service/models/AgentJupyterExecutionAck.java | 40 +-
.../models/AgentJupyterExecutionRequest.java | 37 +-
.../models/AgentJupyterExecutionResponse.java | 37 +-
.../service/models/AgentKernelRestartAck.java | 40 +-
.../service/models/AgentKernelRestartRequest.java | 37 +-
.../service/models/AgentKernelRestartResponse.java | 37 +-
.../service/models/AgentLaunchRequest.java | 38 +-
.../service/models/AgentLaunchResponse.java | 37 +-
.../service/models/AgentPythonExecutionAck.java | 40 +-
.../models/AgentPythonExecutionRequest.java | 37 +-
.../models/AgentPythonExecutionResponse.java | 37 +-
.../service/models/AgentTerminateResponse.java | 37 +-
.../connection/service/models/AgentTunnelAck.java | 37 +-
.../service/models/AgentTunnelCreateRequest.java | 37 +-
.../service/models/AgentTunnelCreateResponse.java | 37 +-
.../models/AgentTunnelTerminateRequest.java | 37 +-
.../models/AgentTunnelTerminateResponse.java | 40 +-
.../connection/service/models/AsyncCommand.java | 37 +-
.../connection/service/models/DirectoryInfo.java | 37 +-
.../service/models/ExperimentStorageResponse.java | 37 +-
.../agent/connection/service/models/FileInfo.java | 37 +-
.../service/services/AiravataFileService.java | 78 +-
.../service/services/AiravataService.java | 111 +-
modules/agent-framework/pom.xml | 34 +-
modules/airavata-helix/agent-api/pom.xml | 32 +-
.../apache/airavata/agents/api/AdaptorParams.java | 39 +-
.../java/org/apache/airavata/agents/api/Agent.java | 41 +-
.../apache/airavata/agents/api/AgentAdaptor.java | 44 +-
.../apache/airavata/agents/api/AgentException.java | 38 +-
.../org/apache/airavata/agents/api/AgentUtils.java | 23 +-
.../apache/airavata/agents/api/CommandOutput.java | 48 +-
.../apache/airavata/agents/api/FileMetadata.java | 38 +-
.../airavata/agents/api/JobSubmissionOutput.java | 38 +-
.../agents/api/StorageResourceAdaptor.java | 52 +-
.../airavata/agents/streaming/TransferResult.java | 42 +-
.../agents/streaming/VirtualInputStream.java | 46 +-
.../agents/streaming/VirtualOutputStream.java | 40 +-
.../agents/streaming/VirtualStreamProducer.java | 38 +-
modules/airavata-helix/agent-impl/pom.xml | 32 +-
.../airavata-helix/agent-impl/ssh-agent/pom.xml | 19 +-
.../airavata/helix/agent/ssh/SshAdaptorParams.java | 41 +-
.../airavata/helix/agent/ssh/SshAgentAdaptor.java | 189 +-
.../helix/agent/ssh/StandardOutReader.java | 42 +-
.../agent/storage/StorageResourceAdaptorImpl.java | 59 +-
.../airavata-helix/agent-impl/sshj-agent/pom.xml | 36 +-
.../airavata/helix/adaptor/PoolingSSHJClient.java | 133 +-
.../airavata/helix/adaptor/SSHJAgentAdaptor.java | 280 +-
.../airavata/helix/adaptor/SSHJStorageAdaptor.java | 87 +-
.../adaptor/wrapper/SCPFileTransferWrapper.java | 48 +-
.../helix/adaptor/wrapper/SFTPClientWrapper.java | 44 +-
.../helix/adaptor/wrapper/SSHClientWrapper.java | 19 +
.../helix/adaptor/wrapper/SessionWrapper.java | 57 +-
modules/airavata-helix/helix-spectator/pom.xml | 32 +-
.../helix/impl/controller/HelixController.java | 71 +-
.../impl/controller/WorkflowCleanupAgent.java | 54 +-
.../helix/impl/participant/GlobalParticipant.java | 86 +-
.../airavata/helix/impl/task/AiravataTask.java | 181 +-
.../airavata/helix/impl/task/TaskContext.java | 335 +--
.../helix/impl/task/TaskOnFailException.java | 38 +-
.../impl/task/cancel/CancelCompletingTask.java | 34 +-
.../task/cancel/RemoteJobCancellationTask.java | 114 +-
.../impl/task/cancel/WorkflowCancellationTask.java | 61 +-
.../helix/impl/task/completing/CompletingTask.java | 46 +-
.../airavata/helix/impl/task/env/EnvSetupTask.java | 66 +-
.../airavata/helix/impl/task/mock/MockTask.java | 25 +-
.../helix/impl/task/parsing/DataParsingTask.java | 313 ++-
.../impl/task/parsing/ParsingTriggeringTask.java | 41 +-
.../task/parsing/ProcessCompletionMessage.java | 19 +
.../ProcessCompletionMessageDeserializer.java | 30 +-
.../kafka/ProcessCompletionMessageSerializer.java | 30 +-
.../impl/task/parsing/models/ParsingTaskInput.java | 19 +
.../task/parsing/models/ParsingTaskInputs.java | 22 +-
.../task/parsing/models/ParsingTaskOutput.java | 19 +
.../task/parsing/models/ParsingTaskOutputs.java | 22 +-
.../helix/impl/task/staging/ArchiveTask.java | 122 +-
.../helix/impl/task/staging/DataStagingTask.java | 155 +-
.../impl/task/staging/InputDataStagingTask.java | 72 +-
.../impl/task/staging/JobVerificationTask.java | 69 +-
.../impl/task/staging/OutputDataStagingTask.java | 142 +-
.../task/submission/DefaultJobSubmissionTask.java | 134 +-
.../task/submission/ForkJobSubmissionTask.java | 74 +-
.../impl/task/submission/JobSubmissionTask.java | 177 +-
.../task/submission/LocalJobSubmissionTask.java | 55 +-
.../task/submission/config/GroovyMapBuilder.java | 160 +-
.../impl/task/submission/config/GroovyMapData.java | 58 +-
.../impl/task/submission/config/JobFactory.java | 134 +-
.../submission/config/JobManagerConfiguration.java | 44 +-
.../impl/task/submission/config/OutputParser.java | 44 +-
.../task/submission/config/RawCommandInfo.java | 38 +-
.../impl/task/submission/config/ScriptTag.java | 39 +-
.../config/app/ForkJobConfiguration.java | 62 +-
.../config/app/HTCondorJobConfiguration.java | 73 +-
.../impl/task/submission/config/app/JobUtil.java | 105 +-
.../submission/config/app/LSFJobConfiguration.java | 64 +-
.../submission/config/app/PBSJobConfiguration.java | 238 +-
.../config/app/SlurmJobConfiguration.java | 83 +-
.../submission/config/app/UGEJobConfiguration.java | 65 +-
.../parser/AiravataCustomCommandOutputParser.java | 41 +-
.../config/app/parser/ForkOutputParser.java | 48 +-
.../config/app/parser/HTCondorOutputParser.java | 62 +-
.../config/app/parser/LSFOutputParser.java | 86 +-
.../config/app/parser/PBSOutputParser.java | 80 +-
.../config/app/parser/SlurmOutputParser.java | 79 +-
.../config/app/parser/UGEOutputParser.java | 115 +-
.../helix/impl/workflow/ParserWorkflowManager.java | 203 +-
.../helix/impl/workflow/PostWorkflowManager.java | 249 +-
.../helix/impl/workflow/PreWorkflowManager.java | 123 +-
.../helix/impl/workflow/WorkflowManager.java | 62 +-
modules/airavata-helix/pom.xml | 32 +-
modules/airavata-helix/task-api/pom.xml | 32 +-
.../apache/airavata/helix/task/api/TaskHelper.java | 38 +-
.../airavata/helix/task/api/TaskParamType.java | 20 +
.../helix/task/api/annotation/TaskDef.java | 38 +-
.../helix/task/api/annotation/TaskOutPort.java | 38 +-
.../helix/task/api/annotation/TaskParam.java | 40 +-
.../helix/task/api/support/AdaptorSupport.java | 48 +-
modules/airavata-helix/task-core/pom.xml | 32 +-
.../apache/airavata/helix/core/AbstractTask.java | 74 +-
.../org/apache/airavata/helix/core/OutPort.java | 39 +-
.../helix/core/participant/HelixParticipant.java | 87 +-
.../helix/core/support/TaskHelperImpl.java | 38 +-
.../core/support/adaptor/AdaptorSupportImpl.java | 101 +-
.../helix/core/support/adaptor/AgentStore.java | 98 +-
.../airavata/helix/core/util/MonitoringUtil.java | 31 +-
.../airavata/helix/core/util/PropertyResolver.java | 38 +-
.../apache/airavata/helix/core/util/TaskUtil.java | 74 +-
modules/airavata-helix/workflow-impl/pom.xml | 32 +-
.../airavata/helix/workflow/QueueOperator.java | 72 +-
.../airavata/helix/workflow/WorkflowOperator.java | 93 +-
.../metadata-analyzer/pom.xml | 19 +-
.../metadata/analyzer/DataInterpreterService.java | 40 +-
.../metadata/analyzer/impl/DataAnalyzerImpl.java | 43 +-
.../metadata/analyzer/utils/Constants.java | 21 +-
.../metascheduler-core/pom.xml | 19 +-
.../metascheduler/core/api/ProcessScheduler.java | 30 +-
.../engine/ComputeResourceSelectionPolicy.java | 27 +-
.../metascheduler/core/engine/DataAnalyzer.java | 24 +-
.../metascheduler/core/engine/ProcessScanner.java | 24 +-
.../metascheduler/core/engine/ReScheduler.java | 19 +
.../airavata/metascheduler/core/utils/Utils.java | 57 +-
modules/airavata-metascheduler/pom.xml | 19 +-
.../process-scheduler/pom.xml | 19 +-
.../scheduling/api/ProcessSchedulerImpl.java | 74 +-
.../ComputeResourceSelectionPolicyImpl.java | 32 +-
.../DefaultComputeResourceSelectionPolicy.java | 39 +-
.../selection/MultipleComputeResourcePolicy.java | 83 +-
.../rescheduler/ExponentialBackOffReScheduler.java | 110 +-
.../rescheduler/ProcessReschedulingService.java | 40 +-
.../engine/rescheduler/ProcessScannerImpl.java | 30 +-
.../process/scheduling/utils/Constants.java | 21 +-
modules/cluster-monitoring/pom.xml | 32 +-
.../monitoring/ClusterStatusMonitorJob.java | 145 +-
.../ClusterStatusMonitorJobScheduler.java | 53 +-
modules/commons/pom.xml | 32 +-
.../airavata/common/context/RequestContext.java | 37 +-
.../airavata/common/context/WorkflowContext.java | 42 +-
.../exception/AiravataConfigurationException.java | 57 +-
.../common/exception/AiravataException.java | 58 +-
.../common/exception/AiravataStartupException.java | 39 +-
.../exception/ApplicationSettingsException.java | 52 +-
.../apache/airavata/common/logging/Exception.java | 37 +-
.../airavata/common/logging/MDCConstants.java | 37 +-
.../apache/airavata/common/logging/MDCUtil.java | 42 +-
.../airavata/common/utils/AiravataJobState.java | 37 +-
.../airavata/common/utils/AiravataUtils.java | 42 +-
.../airavata/common/utils/ApplicationSettings.java | 409 +--
.../apache/airavata/common/utils/Constants.java | 43 +-
.../common/utils/DBEventManagerConstants.java | 54 +-
.../airavata/common/utils/DBEventService.java | 40 +-
.../apache/airavata/common/utils/DBInitConfig.java | 43 +-
.../airavata/common/utils/DBInitializer.java | 49 +-
.../org/apache/airavata/common/utils/DBUtil.java | 87 +-
.../airavata/common/utils/DatabaseCreator.java | 74 +-
.../airavata/common/utils/DatabaseTestCases.java | 64 +-
.../utils/DefaultKeyStorePasswordCallback.java | 41 +-
.../airavata/common/utils/DerbyTestUtil.java | 113 +-
.../apache/airavata/common/utils/DerbyUtil.java | 60 +-
.../airavata/common/utils/ExecutionMode.java | 42 +-
.../org/apache/airavata/common/utils/IOUtil.java | 53 +-
.../org/apache/airavata/common/utils/IServer.java | 92 +-
.../apache/airavata/common/utils/JDBCConfig.java | 43 +-
.../org/apache/airavata/common/utils/JPAUtils.java | 44 +-
.../org/apache/airavata/common/utils/JSONUtil.java | 85 +-
.../common/utils/KeyStorePasswordCallback.java | 77 +-
.../airavata/common/utils/LocalEventPublisher.java | 43 +-
.../airavata/common/utils/NameValidator.java | 39 +-
.../org/apache/airavata/common/utils/Pair.java | 49 +-
.../apache/airavata/common/utils/SecurityUtil.java | 94 +-
.../airavata/common/utils/ServerSettings.java | 113 +-
.../apache/airavata/common/utils/StringUtil.java | 611 ++---
.../apache/airavata/common/utils/SwingUtil.java | 134 +-
.../airavata/common/utils/ThriftClientPool.java | 85 +-
.../apache/airavata/common/utils/ThriftUtils.java | 93 +-
.../org/apache/airavata/common/utils/Version.java | 219 +-
.../apache/airavata/common/utils/WSConstants.java | 64 +-
.../org/apache/airavata/common/utils/WSDLUtil.java | 821 +++---
.../apache/airavata/common/utils/ZkConstants.java | 51 +-
.../common/utils/ApplicationSettingsTest.java | 42 +-
.../airavata/common/utils/SecurityUtilTest.java | 60 +-
.../common/utils/ThriftClientPoolTest.java | 60 +-
modules/compute-account-provisioning/pom.xml | 32 +-
.../airavata/accountprovisioning/ConfigParam.java | 36 +-
.../accountprovisioning/InvalidSetupException.java | 39 +-
.../InvalidUsernameException.java | 39 +-
.../accountprovisioning/SSHAccountManager.java | 180 +-
.../accountprovisioning/SSHAccountProvisioner.java | 36 +-
.../SSHAccountProvisionerFactory.java | 44 +-
.../SSHAccountProvisionerProvider.java | 38 +-
.../airavata/accountprovisioning/SSHUtil.java | 65 +-
.../provisioner/IULdapSSHAccountProvisioner.java | 120 +-
.../IULdapSSHAccountProvisionerProvider.java | 57 +-
.../SSHAccountProvisionerFactoryTest.java | 60 +-
.../provisioner/TestSSHAccountProvisioner.java | 42 +-
.../TestSSHAccountProvisionerProvider.java | 49 +-
.../computer-resource-monitoring-service/pom.xml | 19 +-
.../ComputationalResourceMonitoringService.java | 54 +-
.../monitoring/job/ComputeResourceMonitor.java | 107 +-
.../resource/monitoring/job/MonitoringJob.java | 115 +-
.../monitoring/job/output/OutputParser.java | 23 +-
.../monitoring/job/output/OutputParserImpl.java | 27 +-
.../resource/monitoring/utils/Constants.java | 25 +-
modules/configuration/client/pom.xml | 32 +-
modules/configuration/pom.xml | 32 +-
modules/configuration/server/pom.xml | 32 +-
.../credential-store-service/pom.xml | 32 +-
.../credential/store/credential/AuditInfo.java | 43 +-
.../credential/store/credential/CommunityUser.java | 36 +-
.../credential/store/credential/Credential.java | 46 +-
.../store/credential/CredentialOwnerType.java | 36 +-
.../impl/certificate/CertificateAuditInfo.java | 41 +-
.../impl/certificate/CertificateCredential.java | 44 +-
.../impl/password/PasswordCredential.java | 36 +-
.../store/credential/impl/ssh/SSHCredential.java | 69 +-
.../store/notifier/CredentialStoreNotifier.java | 78 +-
.../store/notifier/NotificationMessage.java | 37 +-
.../store/notifier/NotifierBootstrap.java | 64 +-
.../notifier/impl/EmailNotificationMessage.java | 37 +-
.../store/notifier/impl/EmailNotifier.java | 44 +-
.../notifier/impl/EmailNotifierConfiguration.java | 50 +-
.../store/server/CredentialStoreServer.java | 59 +-
.../store/server/CredentialStoreServerHandler.java | 361 ++-
.../store/servlet/CredentialBootstrapper.java | 43 +-
.../servlet/CredentialStoreCallbackServlet.java | 99 +-
.../store/servlet/CredentialStoreStartServlet.java | 90 +-
.../credential/store/store/CredentialReader.java | 55 +-
.../store/store/CredentialReaderFactory.java | 41 +-
.../store/store/CredentialStoreException.java | 36 +-
.../credential/store/store/CredentialWriter.java | 39 +-
.../store/impl/CertificateCredentialWriter.java | 67 +-
.../store/store/impl/CredentialReaderImpl.java | 81 +-
.../store/store/impl/SSHCredentialWriter.java | 48 +-
.../store/store/impl/db/CommunityUserDAO.java | 47 +-
.../store/store/impl/db/CredentialsDAO.java | 101 +-
.../credential/store/store/impl/db/ParentDAO.java | 41 +-
.../impl/util/CredentialStoreDBInitConfig.java | 38 +-
.../store/impl/util/CredentialStoreJDBCConfig.java | 39 +-
.../credential/store/util/ConfigurationReader.java | 67 +-
.../store/util/CredentialStoreConstants.java | 37 +-
.../credential/store/util/PrivateKeyStore.java | 39 +-
.../credential/store/util/TokenGenerator.java | 47 +-
.../airavata/credential/store/util/Utility.java | 63 +-
.../store/cpi/SSHSummaryTest/SSHSummaryTest.java | 68 +-
.../store/notifier/impl/EmailNotifierTest.java | 52 +-
.../store/store/impl/db/CommunityUserDAOTest.java | 46 +-
.../store/store/impl/db/CredentialsDAOTest.java | 159 +-
.../store/store/impl/db/SSHCredentialTest.java | 49 +-
.../store/util/ConfigurationReaderTest.java | 39 +-
.../credential/store/util/TokenGeneratorTest.java | 40 +-
.../credential-store-stubs/pom.xml | 32 +-
.../store/client/CredentialStoreClientFactory.java | 46 +-
.../credential/store/client/TestSSLClient.java | 90 +-
modules/credential-store/pom.xml | 36 +-
modules/db-event-manager/pom.xml | 36 +-
.../db/event/manager/DBEventManagerRunner.java | 47 +-
.../manager/messaging/DBEventManagerException.java | 37 +-
.../messaging/DBEventManagerMessagingFactory.java | 56 +-
.../messaging/impl/DBEventMessageHandler.java | 71 +-
.../airavata/db/event/manager/utils/Constants.java | 40 +-
.../event/manager/utils/DbEventManagerZkUtils.java | 87 +-
modules/db-event-manager/src/test/java/Test.java | 42 +-
modules/distribution/pom.xml | 32 +-
modules/file-server/pom.xml | 18 +
.../file/server/FileServerApplication.java | 23 +-
.../file/server/FileServerConfiguration.java | 27 +-
.../file/server/controller/FileController.java | 46 +-
.../file/server/model/AiravataDirectory.java | 20 +-
.../airavata/file/server/model/AiravataFile.java | 40 +-
.../file/server/model/FileUploadResponse.java | 19 +
.../file/server/service/AirvataFileService.java | 64 +-
.../file/server/service/ProcessDataManager.java | 31 +-
modules/ide-integration/pom.xml | 19 +-
.../airavata/ide/integration/APIServerStarter.java | 19 +
.../airavata/ide/integration/JobEngineStarter.java | 31 +-
.../ide/integration/JobMonitorStarter.java | 19 +
modules/job-monitor/email-monitor/pom.xml | 31 +-
.../airavata/monitor/email/EmailBasedMonitor.java | 113 +-
.../email/parser/AiravataCustomMailParser.java | 56 +-
.../airavata/monitor/email/parser/EmailParser.java | 44 +-
.../monitor/email/parser/HTCondorEmailParser.java | 89 +-
.../monitor/email/parser/LSFEmailParser.java | 56 +-
.../monitor/email/parser/PBSEmailParser.java | 58 +-
.../monitor/email/parser/ResourceConfig.java | 81 +-
.../monitor/email/parser/SLURMEmailParser.java | 59 +-
.../monitor/email/parser/UGEEmailParser.java | 59 +-
modules/job-monitor/job-monitor-api/pom.xml | 31 +-
.../apache/airavata/monitor/AbstractMonitor.java | 45 +-
.../apache/airavata/monitor/JobStateValidator.java | 51 +-
.../apache/airavata/monitor/JobStatusResult.java | 38 +-
.../airavata/monitor/MonitoringException.java | 22 +-
.../monitor/kafka/JobStatusResultDeserializer.java | 51 +-
.../monitor/kafka/JobStatusResultSerializer.java | 56 +-
.../airavata/monitor/kafka/MessageProducer.java | 59 +-
modules/job-monitor/pom.xml | 31 +-
modules/job-monitor/real-time-monitor/pom.xml | 31 +-
.../airavata/monitor/realtime/RealtimeMonitor.java | 46 +-
.../realtime/parser/RealtimeJobStatusParser.java | 54 +-
modules/messaging/client/pom.xml | 32 +-
.../messaging/client/RabbitMQListener.java | 115 +-
.../airavata/messaging/client/TestReader.java | 120 +-
modules/messaging/core/pom.xml | 32 +-
.../airavata/messaging/core/MessageContext.java | 54 +-
.../airavata/messaging/core/MessageHandler.java | 36 +-
.../messaging/core/MessagingConstants.java | 42 +-
.../airavata/messaging/core/MessagingFactory.java | 96 +-
.../apache/airavata/messaging/core/Publisher.java | 38 +-
.../messaging/core/RabbitMQProperties.java | 38 +-
.../apache/airavata/messaging/core/Subscriber.java | 45 +-
.../apache/airavata/messaging/core/TestClient.java | 82 +-
.../org/apache/airavata/messaging/core/Type.java | 36 +-
.../messaging/core/impl/ExperimentConsumer.java | 87 +-
.../messaging/core/impl/MessageConsumer.java | 67 +-
.../messaging/core/impl/ProcessConsumer.java | 84 +-
.../messaging/core/impl/RabbitMQPublisher.java | 71 +-
.../messaging/core/impl/RabbitMQSubscriber.java | 92 +-
.../messaging/core/impl/StatusConsumer.java | 82 +-
.../messaging/core/stats/CountWriterTask.java | 40 +-
.../messaging/core/stats/LatencyWriterTask.java | 41 +-
.../airavata/messaging/core/stats/StatCounter.java | 45 +-
.../messaging/core/util/DBEventPublisherUtils.java | 53 +-
modules/messaging/pom.xml | 36 +-
modules/orchestrator/orchestrator-client/pom.xml | 32 +-
.../client/OrchestratorClientFactory.java | 41 +-
.../sample/OrchestratorClientSample.java | 128 +-
modules/orchestrator/orchestrator-core/pom.xml | 32 +-
.../core/OrchestratorConfiguration.java | 37 +-
.../core/context/OrchestratorContext.java | 36 +-
.../core/exception/OrchestratorException.java | 38 +-
.../core/impl/GFACPassiveJobSubmitter.java | 74 +-
.../orchestrator/core/job/JobSubmitter.java | 41 +-
.../core/schedule/DefaultHostScheduler.java | 40 +-
.../orchestrator/core/schedule/HostScheduler.java | 39 +-
.../core/utils/OrchestratorConstants.java | 38 +-
.../orchestrator/core/utils/OrchestratorUtils.java | 192 +-
.../core/validator/JobMetadataValidator.java | 37 +-
.../core/validator/impl/BatchQueueValidator.java | 134 +-
.../validator/impl/ExperimentStatusValidator.java | 44 +-
.../impl/GroupResourceProfileValidator.java | 101 +-
.../airavata/orchestrator/cpi/Orchestrator.java | 48 +-
.../cpi/impl/AbstractOrchestrator.java | 99 +-
.../cpi/impl/SimpleOrchestratorImpl.java | 421 +--
.../orchestrator/core/BaseOrchestratorTest.java | 41 +-
.../orchestrator/core/NewOrchestratorTest.java | 184 +-
.../core/OrchestratorTestWithGRAM.java | 147 +-
.../core/OrchestratorTestWithMyProxyAuth.java | 153 +-
modules/orchestrator/orchestrator-service/pom.xml | 32 +-
.../orchestrator/server/OrchestratorServer.java | 77 +-
.../server/OrchestratorServerHandler.java | 484 ++--
.../airavata/orchestrator/util/Constants.java | 37 +-
.../util/OrchestratorServerThreadPoolExecutor.java | 77 +-
.../orchestrator/util/OrchestratorUtils.java | 132 +-
.../client/OrchestratorClientFactoryTest.java | 46 +-
modules/orchestrator/pom.xml | 36 +-
modules/platform-monitoring/pom.xml | 30 +-
.../airavata/patform/monitoring/CountMonitor.java | 46 +-
.../airavata/patform/monitoring/GaugeMonitor.java | 41 +-
.../patform/monitoring/MonitoringServer.java | 46 +-
modules/registry/pom.xml | 32 +-
modules/registry/registry-core/pom.xml | 32 +-
.../airavata/registry/core/RegistryException.java | 41 +-
.../AiravataWorkflowEntity.java | 71 +-
.../AiravataWorkflowErrorEntity.java | 42 +-
.../AiravataWorkflowErrorPK.java | 45 +-
.../AiravataWorkflowStatusEntity.java | 44 +-
.../AiravataWorkflowStatusPK.java | 45 +-
.../ApplicationErrorEntity.java | 40 +-
.../ApplicationErrorPK.java | 45 +-
.../ApplicationStatusEntity.java | 44 +-
.../ApplicationStatusPK.java | 45 +-
.../HandlerErrorEntity.java | 46 +-
.../airavataworkflowcatalog/HandlerErrorPK.java | 45 +-
.../HandlerInputEntity.java | 49 +-
.../airavataworkflowcatalog/HandlerInputPK.java | 45 +-
.../HandlerOutputEntity.java | 49 +-
.../airavataworkflowcatalog/HandlerOutputPK.java | 45 +-
.../HandlerStatusEntity.java | 45 +-
.../airavataworkflowcatalog/HandlerStatusPK.java | 45 +-
.../WorkflowApplicationEntity.java | 55 +-
.../WorkflowApplicationPK.java | 45 +-
.../WorkflowConnectionEntity.java | 44 +-
.../WorkflowConnectionPK.java | 45 +-
.../WorkflowDataBlockEntity.java | 47 +-
.../WorkflowHandlerEntity.java | 68 +-
.../airavataworkflowcatalog/WorkflowHandlerPK.java | 45 +-
.../entities/appcatalog/AppEnvironmentEntity.java | 47 +-
.../core/entities/appcatalog/AppEnvironmentPK.java | 43 +-
.../appcatalog/AppModuleMappingEntity.java | 122 +-
.../entities/appcatalog/AppModuleMappingPK.java | 114 +-
.../appcatalog/ApplicationDeploymentEntity.java | 92 +-
.../appcatalog/ApplicationInputEntity.java | 314 ++-
.../entities/appcatalog/ApplicationInputPK.java | 114 +-
.../appcatalog/ApplicationInterfaceEntity.java | 253 +-
.../appcatalog/ApplicationModuleEntity.java | 158 +-
.../appcatalog/ApplicationOutputEntity.java | 50 +-
.../entities/appcatalog/ApplicationOutputPK.java | 114 +-
.../core/entities/appcatalog/BatchQueueEntity.java | 46 +-
.../core/entities/appcatalog/BatchQueuePK.java | 114 +-
.../appcatalog/BatchQueueResourcePolicyEntity.java | 45 +-
.../appcatalog/CloudJobSubmissionEntity.java | 49 +-
.../entities/appcatalog/ComputeResourceEntity.java | 68 +-
.../ComputeResourceFileSystemEntity.java | 125 +-
.../appcatalog/ComputeResourceFileSystemPK.java | 118 +-
.../appcatalog/ComputeResourcePolicyEntity.java | 50 +-
.../ComputeResourcePreferenceEntity.java | 57 +-
.../appcatalog/ComputeResourcePreferencePK.java | 48 +-
.../ComputeResourceReservationEntity.java | 58 +-
.../appcatalog/DataMovementInterfaceEntity.java | 45 +-
.../appcatalog/DataMovementInterfacePK.java | 49 +-
.../entities/appcatalog/GatewayGroupsEntity.java | 43 +-
.../entities/appcatalog/GatewayProfileEntity.java | 57 +-
.../appcatalog/GlobusGkEndpointEntity.java | 85 +-
.../entities/appcatalog/GlobusGkEndpointPK.java | 114 +-
.../appcatalog/GlobusSubmissionEntity.java | 99 +-
.../appcatalog/GridftpDataMovementEntity.java | 47 +-
.../entities/appcatalog/GridftpEndpointEntity.java | 45 +-
.../entities/appcatalog/GridftpEndpointPK.java | 49 +-
.../appcatalog/GroupComputeResourcePrefEntity.java | 67 +-
.../appcatalog/GroupComputeResourcePrefPK.java | 45 +-
.../appcatalog/GroupResourceProfileEntity.java | 63 +-
.../GroupSSHAccountProvisionerConfig.java | 54 +-
.../GroupSSHAccountProvisionerConfigPK.java | 47 +-
.../entities/appcatalog/GsisshExportEntity.java | 43 +-
.../core/entities/appcatalog/GsisshExportPK.java | 114 +-
.../appcatalog/GsisshPostjobcommandEntity.java | 83 +-
.../appcatalog/GsisshPostjobcommandPK.java | 110 +-
.../appcatalog/GsisshPrejobcommandEntity.java | 43 +-
.../entities/appcatalog/GsisshPrejobcommandPK.java | 114 +-
.../appcatalog/GsisshSubmissionEntity.java | 128 +-
.../appcatalog/JobManagerCommandEntity.java | 47 +-
.../entities/appcatalog/JobManagerCommandPK.java | 52 +-
.../appcatalog/JobSubmissionInterfaceEntity.java | 45 +-
.../appcatalog/JobSubmissionInterfacePK.java | 49 +-
.../appcatalog/LibraryApendPathEntity.java | 49 +-
.../entities/appcatalog/LibraryAppendPathPK.java | 41 +-
.../appcatalog/LibraryPrependPathEntity.java | 127 +-
.../entities/appcatalog/LibraryPrependPathPK.java | 39 +-
.../appcatalog/LocalDataMovementEntity.java | 43 +-
.../entities/appcatalog/LocalSubmissionEntity.java | 47 +-
.../entities/appcatalog/ModuleLoadCmdEntity.java | 46 +-
.../core/entities/appcatalog/ModuleLoadCmdPK.java | 41 +-
.../appcatalog/ParallelismCommandEntity.java | 47 +-
.../entities/appcatalog/ParallelismCommandPK.java | 52 +-
.../entities/appcatalog/ParserConnectorEntity.java | 47 +-
.../appcatalog/ParserConnectorInputEntity.java | 39 +-
.../core/entities/appcatalog/ParserEntity.java | 55 +-
.../entities/appcatalog/ParserInputEntity.java | 39 +-
.../entities/appcatalog/ParserOutputEntity.java | 39 +-
.../entities/appcatalog/ParsingTemplateEntity.java | 55 +-
.../appcatalog/ParsingTemplateInputEntity.java | 39 +-
.../entities/appcatalog/PostjobCommandEntity.java | 57 +-
.../core/entities/appcatalog/PostjobCommandPK.java | 42 +-
.../entities/appcatalog/PrejobCommandEntity.java | 57 +-
.../core/entities/appcatalog/PrejobCommandPK.java | 114 +-
.../appcatalog/ResourceJobManagerEntity.java | 45 +-
.../SSHAccountProvisionerConfiguration.java | 48 +-
.../SSHAccountProvisionerConfigurationPK.java | 37 +-
.../entities/appcatalog/ScpDataMovementEntity.java | 46 +-
.../appcatalog/SshJobSubmissionEntity.java | 174 +-
.../appcatalog/StorageInterfaceEntity.java | 49 +-
.../entities/appcatalog/StorageInterfacePK.java | 115 +-
.../appcatalog/StoragePreferenceEntity.java | 40 +-
.../entities/appcatalog/StoragePreferencePK.java | 48 +-
.../entities/appcatalog/StorageResourceEntity.java | 49 +-
.../appcatalog/UnicoreDatamovementEntity.java | 102 +-
.../appcatalog/UnicoreSubmissionEntity.java | 102 +-
.../UserComputeResourcePreferenceEntity.java | 45 +-
.../UserComputeResourcePreferencePK.java | 52 +-
.../appcatalog/UserResourceProfileEntity.java | 60 +-
.../entities/appcatalog/UserResourceProfilePK.java | 48 +-
.../appcatalog/UserStoragePreferenceEntity.java | 46 +-
.../appcatalog/UserStoragePreferencePK.java | 52 +-
.../ComputationalResourceSchedulingEntity.java | 24 +-
.../ComputationalResourceSchedulingPK.java | 34 +-
.../core/entities/expcatalog/ExperimentEntity.java | 91 +-
.../entities/expcatalog/ExperimentErrorEntity.java | 44 +-
.../entities/expcatalog/ExperimentErrorPK.java | 48 +-
.../entities/expcatalog/ExperimentInputEntity.java | 63 +-
.../entities/expcatalog/ExperimentInputPK.java | 48 +-
.../expcatalog/ExperimentOutputEntity.java | 44 +-
.../entities/expcatalog/ExperimentOutputPK.java | 48 +-
.../expcatalog/ExperimentStatusEntity.java | 45 +-
.../entities/expcatalog/ExperimentStatusPK.java | 48 +-
.../expcatalog/ExperimentSummaryEntity.java | 39 +-
.../core/entities/expcatalog/GatewayEntity.java | 49 +-
.../GatewayUsageReportingCommandEntity.java | 40 +-
.../expcatalog/GatewayUsageReportingPK.java | 47 +-
.../entities/expcatalog/GatewayWorkerEntity.java | 42 +-
.../core/entities/expcatalog/GatewayWorkerPK.java | 46 +-
.../core/entities/expcatalog/JobEntity.java | 47 +-
.../registry/core/entities/expcatalog/JobPK.java | 47 +-
.../core/entities/expcatalog/JobStatusEntity.java | 45 +-
.../core/entities/expcatalog/JobStatusPK.java | 52 +-
.../entities/expcatalog/NotificationEntity.java | 45 +-
.../core/entities/expcatalog/ProcessEntity.java | 90 +-
.../entities/expcatalog/ProcessErrorEntity.java | 43 +-
.../core/entities/expcatalog/ProcessErrorPK.java | 48 +-
.../entities/expcatalog/ProcessInputEntity.java | 59 +-
.../core/entities/expcatalog/ProcessInputPK.java | 48 +-
.../entities/expcatalog/ProcessOutputEntity.java | 43 +-
.../core/entities/expcatalog/ProcessOutputPK.java | 48 +-
.../expcatalog/ProcessResourceScheduleEntity.java | 40 +-
.../entities/expcatalog/ProcessStatusEntity.java | 45 +-
.../core/entities/expcatalog/ProcessStatusPK.java | 48 +-
.../entities/expcatalog/ProcessWorkflowEntity.java | 20 +-
.../entities/expcatalog/ProcessWorkflowPK.java | 23 +-
.../core/entities/expcatalog/ProjectEntity.java | 44 +-
.../entities/expcatalog/ProjectUserEntity.java | 42 +-
.../core/entities/expcatalog/ProjectUserPK.java | 46 +-
.../entities/expcatalog/QueueStatusEntity.java | 42 +-
.../core/entities/expcatalog/QueueStatusPK.java | 51 +-
.../core/entities/expcatalog/TaskEntity.java | 62 +-
.../core/entities/expcatalog/TaskErrorEntity.java | 43 +-
.../core/entities/expcatalog/TaskErrorPK.java | 48 +-
.../core/entities/expcatalog/TaskStatusEntity.java | 45 +-
.../core/entities/expcatalog/TaskStatusPK.java | 48 +-
.../expcatalog/UserConfigurationDataEntity.java | 54 +-
.../core/entities/expcatalog/UserEntity.java | 19 +
.../registry/core/entities/expcatalog/UserPK.java | 23 +-
.../replicacatalog/ConfigurationEntity.java | 38 +-
.../entities/replicacatalog/ConfigurationPK.java | 47 +-
.../entities/replicacatalog/DataProductEntity.java | 58 +-
.../replicacatalog/DataProductMetadataEntity.java | 38 +-
.../replicacatalog/DataProductMetadataPK.java | 47 +-
.../replicacatalog/DataReplicaLocationEntity.java | 44 +-
.../replicacatalog/DataReplicaMetadataEntity.java | 38 +-
.../replicacatalog/DataReplicaMetadataPK.java | 44 +-
.../workflowcatalog/ComponentStatusEntity.java | 43 +-
.../core/entities/workflowcatalog/EdgeEntity.java | 45 +-
.../core/entities/workflowcatalog/EdgePK.java | 48 +-
.../core/entities/workflowcatalog/NodeEntity.java | 45 +-
.../core/entities/workflowcatalog/NodePK.java | 48 +-
.../core/entities/workflowcatalog/PortEntity.java | 46 +-
.../core/entities/workflowcatalog/PortPK.java | 114 +-
.../entities/workflowcatalog/WorkflowEntity.java | 65 +-
.../workflowcatalog/WorkflowInputEntity.java | 42 +-
.../entities/workflowcatalog/WorkflowInputPK.java | 48 +-
.../workflowcatalog/WorkflowOutputEntity.java | 246 +-
.../entities/workflowcatalog/WorkflowOutputPK.java | 114 +-
.../workflowcatalog/WorkflowStatusEntity.java | 42 +-
.../entities/workflowcatalog/WorkflowStatusPK.java | 48 +-
.../core/repositories/AbstractRepository.java | 111 +-
.../appcatalog/AppCatAbstractRepository.java | 40 +-
.../ApplicationDeploymentRepository.java | 170 +-
.../appcatalog/ApplicationInputRepository.java | 42 +-
.../appcatalog/ApplicationInterfaceRepository.java | 165 +-
.../appcatalog/ApplicationModuleRepository.java | 42 +-
.../appcatalog/ApplicationOutputRepository.java | 42 +-
.../appcatalog/BatchQueuePolicyRepository.java | 39 +-
.../appcatalog/BatchQueueRepository.java | 36 +-
.../ComputeResourcePolicyRepository.java | 39 +-
.../appcatalog/ComputeResourcePrefRepository.java | 61 +-
.../appcatalog/ComputeResourceRepository.java | 294 ++-
.../appcatalog/DataMovementRepository.java | 42 +-
.../appcatalog/GatewayGroupsRepository.java | 39 +-
.../appcatalog/GroupResourceProfileRepository.java | 100 +-
.../appcatalog/GrpComputePrefRepository.java | 40 +-
.../appcatalog/GwyResourceProfileRepository.java | 131 +-
.../JobSubmissionInterfaceRepository.java | 43 +-
.../appcatalog/ParserInputRepository.java | 21 +-
.../appcatalog/ParserOutputRepository.java | 23 +-
.../repositories/appcatalog/ParserRepository.java | 28 +-
.../appcatalog/ParsingTemplateRepository.java | 29 +-
.../appcatalog/ResourceJobManagerRepository.java | 75 +-
.../appcatalog/StoragePrefRepository.java | 39 +-
.../appcatalog/StorageResourceRepository.java | 145 +-
.../UserComputeResourcePreferenceRepository.java | 43 +-
.../appcatalog/UserResourceProfileRepository.java | 121 +-
.../UserStoragePreferenceRepository.java | 42 +-
.../expcatalog/ExpCatAbstractRepository.java | 22 +-
.../expcatalog/ExperimentErrorRepository.java | 49 +-
.../expcatalog/ExperimentInputRepository.java | 60 +-
.../expcatalog/ExperimentOutputRepository.java | 56 +-
.../expcatalog/ExperimentRepository.java | 102 +-
.../expcatalog/ExperimentStatusRepository.java | 87 +-
.../expcatalog/ExperimentSummaryRepository.java | 337 ++-
.../repositories/expcatalog/GatewayRepository.java | 65 +-
.../GatewayUsageReportingCommandRepository.java | 60 +-
.../repositories/expcatalog/JobRepository.java | 70 +-
.../expcatalog/JobStatusRepository.java | 77 +-
.../expcatalog/NotificationRepository.java | 66 +-
.../expcatalog/ProcessErrorRepository.java | 53 +-
.../expcatalog/ProcessInputRepository.java | 57 +-
.../expcatalog/ProcessOutputRepository.java | 60 +-
.../repositories/expcatalog/ProcessRepository.java | 103 +-
.../expcatalog/ProcessStatusRepository.java | 80 +-
.../expcatalog/ProcessWorkflowRepository.java | 32 +-
.../repositories/expcatalog/ProjectRepository.java | 110 +-
.../expcatalog/QueueStatusRepository.java | 53 +-
.../expcatalog/TaskErrorRepository.java | 29 +-
.../repositories/expcatalog/TaskRepository.java | 63 +-
.../expcatalog/TaskStatusRepository.java | 52 +-
.../repositories/expcatalog/UserRepository.java | 52 +-
.../replicacatalog/DataProductRepository.java | 76 +-
.../DataReplicaLocationRepository.java | 70 +-
.../replicacatalog/RepCatAbstractRepository.java | 40 +-
.../WorkflowCatAbstractRepository.java | 40 +-
.../workflowcatalog/WorkflowRepository.java | 119 +-
.../core/utils/AppCatalogDBInitConfig.java | 41 +-
.../registry/core/utils/AppCatalogJDBCConfig.java | 40 +-
.../registry/core/utils/AppCatalogUtils.java | 38 +-
.../airavata/registry/core/utils/Committer.java | 41 +-
.../registry/core/utils/CustomBeanFactory.java | 50 +-
.../airavata/registry/core/utils/DBConstants.java | 46 +-
.../utils/DozerConverter/CsvStringConverter.java | 42 +-
.../utils/DozerConverter/StorageDateConverter.java | 45 +-
.../core/utils/ExpCatalogDBInitConfig.java | 38 +-
.../registry/core/utils/ExpCatalogJDBCConfig.java | 39 +-
.../registry/core/utils/ExpCatalogUtils.java | 38 +-
.../core/utils/JPAUtil/AppCatalogJPAUtils.java | 41 +-
.../core/utils/JPAUtil/ExpCatalogJPAUtils.java | 40 +-
.../core/utils/JPAUtil/RepCatalogJPAUtils.java | 43 +-
.../utils/JPAUtil/WorkflowCatalogJPAUtils.java | 40 +-
.../registry/core/utils/ObjectMapperSingleton.java | 77 +-
.../registry/core/utils/QueryConstants.java | 383 +--
.../core/utils/ReplicaCatalogDBInitConfig.java | 38 +-
.../core/utils/ReplicaCatalogJDBCConfig.java | 38 +-
.../core/utils/WorkflowCatalogDBInitConfig.java | 38 +-
.../core/utils/WorkflowCatalogJDBCConfig.java | 38 +-
.../registry/core/utils/WorkflowCatalogUtils.java | 38 +-
.../core/utils/migration/MappingToolRunner.java | 25 +-
.../utils/migration/MigrationSchemaGenerator.java | 41 +-
.../ApplicationDeploymentRepositoryTest.java | 168 +-
.../ApplicationInterfaceRepositoryTest.java | 165 +-
.../appcatalog/ComputeResourceRepositoryTest.java | 154 +-
.../appcatalog/GatewayGroupsRepositoryTest.java | 41 +-
.../appcatalog/GatewayProfileRepositoryTest.java | 80 +-
.../GroupResourceProfileRepositoryTest.java | 251 +-
.../JobSubmissionInterfaceRepositoryTest.java | 43 +-
.../appcatalog/StorageResourceRepositoryTest.java | 73 +-
.../UserResourceProfileRepositoryTest.java | 65 +-
.../core/repositories/common/TestBase.java | 45 +-
.../expcatalog/ExperimentErrorRepositoryTest.java | 46 +-
.../expcatalog/ExperimentInputRepositoryTest.java | 57 +-
.../expcatalog/ExperimentOutputRepositoryTest.java | 61 +-
.../expcatalog/ExperimentRepositoryTest.java | 76 +-
.../expcatalog/ExperimentStatusRepositoryTest.java | 61 +-
.../ExperimentSummaryRepositoryTest.java | 150 +-
.../expcatalog/GatewayRepositoryTest.java | 54 +-
.../repositories/expcatalog/JobRepositoryTest.java | 49 +-
.../expcatalog/JobStatusRepositoryTest.java | 44 +-
.../expcatalog/NotificationRepositoryTest.java | 47 +-
.../expcatalog/ProcessErrorRepositoryTest.java | 46 +-
.../expcatalog/ProcessInputRepositoryTest.java | 49 +-
.../expcatalog/ProcessOutputRepositoryTest.java | 48 +-
.../expcatalog/ProcessRepositoryTest.java | 70 +-
.../expcatalog/ProcessStatusRepositoryTest.java | 56 +-
.../expcatalog/ProjectRepositoryTest.java | 61 +-
.../expcatalog/QueueStatusRepositoryTest.java | 48 +-
.../expcatalog/TaskErrorRepositoryTest.java | 46 +-
.../expcatalog/TaskRepositoryTest.java | 48 +-
.../expcatalog/TaskStatusRepositoryTest.java | 26 +-
.../expcatalog/UserRepositoryTest.java | 56 +-
.../replicacatalog/DataProductRepositoryTest.java | 63 +-
.../DataReplicaLocationRepositoryTest.java | 82 +-
.../workflowcatalog/WorkflowRepositoryTest.java | 54 +-
.../registry/core/utils/CustomBeanFactoryTest.java | 60 +-
.../core/utils/ObjectMapperSingletonTest.java | 55 +-
modules/registry/registry-cpi/pom.xml | 36 +-
.../apache/airavata/registry/cpi/AppCatalog.java | 36 +-
.../airavata/registry/cpi/AppCatalogException.java | 38 +-
.../registry/cpi/ApplicationDeployment.java | 70 +-
.../registry/cpi/ApplicationInterface.java | 67 +-
.../airavata/registry/cpi/CompositeIdentifier.java | 48 +-
.../airavata/registry/cpi/ComputeResource.java | 187 +-
.../registry/cpi/DataProductInterface.java | 27 +-
.../registry/cpi/DataReplicaLocationInterface.java | 23 +-
.../airavata/registry/cpi/ExpCatChildDataType.java | 38 +-
.../registry/cpi/ExpCatParentDataType.java | 39 +-
.../airavata/registry/cpi/ExperimentCatalog.java | 98 +-
.../registry/cpi/ExperimentCatalogException.java | 36 +-
.../registry/cpi/ExperimentCatalogModelType.java | 36 +-
.../airavata/registry/cpi/GwyClientCredential.java | 36 +-
.../airavata/registry/cpi/GwyResourceProfile.java | 60 +-
.../org/apache/airavata/registry/cpi/Registry.java | 42 +-
.../airavata/registry/cpi/RegistryException.java | 36 +-
.../airavata/registry/cpi/ReplicaCatalog.java | 37 +-
.../registry/cpi/ReplicaCatalogException.java | 38 +-
.../airavata/registry/cpi/ResultOrderType.java | 74 +-
.../airavata/registry/cpi/StorageResource.java | 46 +-
.../airavata/registry/cpi/UsrResourceProfile.java | 65 +-
.../airavata/registry/cpi/WorkflowCatalog.java | 48 +-
.../registry/cpi/WorkflowCatalogException.java | 38 +-
.../airavata/registry/cpi/utils/Constants.java | 36 +-
.../airavata/registry/cpi/utils/StatusType.java | 36 +-
modules/registry/registry-server/pom.xml | 36 +-
.../registry-server/registry-api-service/pom.xml | 32 +-
.../registry/api/service/RegistryAPIServer.java | 67 +-
.../api/service/handler/RegistryServerHandler.java | 1499 +++++++----
.../messaging/RegistryServiceDBEventHandler.java | 65 +-
.../RegistryServiceDBEventMessagingFactory.java | 65 +-
.../registry/api/service/util/Constants.java | 53 +-
.../registry-server/registry-api-stubs/pom.xml | 32 +-
.../api/client/RegistryServiceClientFactory.java | 41 +-
modules/registry/registry-tools/jpa-gen/pom.xml | 36 +-
.../computeresource/BatchQueueGenerator.java | 149 +-
.../ComputeResourceDescriptionGenerator.java | 131 +-
.../DataMovementInterfaceGenerator.java | 143 +-
.../computeresource/FileSystemsGenerator.java | 141 +-
.../GridFTPDataMovementGenerator.java | 131 +-
.../computeresource/GridFTPEndpointsGenerator.java | 140 +-
.../JobManagerCommandGenerator.java | 144 +-
.../JobSubmissionInterfaceGenerator.java | 143 +-
.../LocalDataMovementGenerator.java | 128 +-
.../computeresource/LocalSubmissionGenerator.java | 139 +-
.../computeresource/ModuleCMDGenerator.java | 54 +-
.../ResourceJobManagerGenerator.java | 139 +-
.../computeresource/SCPDataMovementGenerator.java | 134 +-
.../computeresource/SSHJobSubmissionGenerator.java | 145 +-
.../main/java/generators/AbstractGenerator.java | 224 +-
.../main/java/generators/JPAClassGenerator.java | 434 ++--
.../java/generators/JPAResourceClassGenerator.java | 1123 ++++----
.../src/main/java/generators/SQLGenerator.java | 124 +-
.../jpa-gen/src/main/java/model/JPAClassField.java | 89 +-
.../jpa-gen/src/main/java/model/JPAClassModel.java | 54 +-
.../src/main/java/model/JPAPKClassModel.java | 46 +-
.../src/main/java/model/JPAResourceClassModel.java | 47 +-
.../jpa-gen/src/main/java/model/SQLData.java | 144 +-
.../jpa-gen/src/main/java/test/Test.java | 129 +-
modules/registry/registry-tools/pom.xml | 36 +-
.../registry/registry-tools/registry-tool/pom.xml | 32 +-
.../apache/airavata/registry/tool/DBMigrator.java | 142 +-
modules/research-framework/pom.xml | 35 +-
.../research-framework/research-service/pom.xml | 35 +-
.../airavata/research/service/AiravataService.java | 41 +-
.../service/ResearchServiceApplication.java | 37 +-
.../research/service/config/AuthzTokenFilter.java | 73 +-
.../service/config/DevDataInitializer.java | 108 +-
.../research/service/config/OpenApiConfig.java | 51 +-
.../research/service/config/WebMvcConfig.java | 37 +-
.../controller/GlobalExceptionController.java | 54 +-
.../service/controller/ProjectController.java | 43 +-
.../service/controller/ResearchHubController.java | 41 +-
.../service/controller/ResourceController.java | 76 +-
.../service/controller/SessionController.java | 47 +-
.../research/service/dto/CreateProjectRequest.java | 37 +-
.../service/dto/CreateResourceRequest.java | 40 +-
.../service/dto/ModifyResourceRequest.java | 37 +-
.../research/service/dto/RedirectResponse.java | 37 +-
.../research/service/dto/ResourceResponse.java | 37 +-
.../research/service/enums/PrivacyEnum.java | 37 +-
.../research/service/enums/ResourceTypeEnum.java | 38 +-
.../research/service/enums/SessionStatusEnum.java | 37 +-
.../research/service/enums/StatusEnum.java | 37 +-
.../research/service/exception/ErrorResponse.java | 37 +-
.../service/exception/GlobalExceptionHandler.java | 44 +-
.../research/service/handlers/ProjectHandler.java | 53 +-
.../service/handlers/ResearchHubHandler.java | 91 +-
.../research/service/handlers/ResourceHandler.java | 66 +-
.../research/service/handlers/SessionHandler.java | 50 +-
.../research/service/model/UserContext.java | 37 +-
.../service/model/entity/DatasetResource.java | 37 +-
.../service/model/entity/ModelResource.java | 37 +-
.../service/model/entity/NotebookResource.java | 37 +-
.../research/service/model/entity/Project.java | 47 +-
.../service/model/entity/RepositoryResource.java | 37 +-
.../research/service/model/entity/Resource.java | 52 +-
.../research/service/model/entity/Session.java | 43 +-
.../research/service/model/entity/Tag.java | 37 +-
.../service/model/repo/ProjectRepository.java | 42 +-
.../service/model/repo/ResourceRepository.java | 54 +-
.../service/model/repo/SessionRepository.java | 45 +-
.../research/service/model/repo/TagRepository.java | 37 +-
modules/security/pom.xml | 32 +-
.../airavata/security/AbstractAuthenticator.java | 55 +-
.../security/AbstractDatabaseAuthenticator.java | 45 +-
.../security/AiravataSecurityException.java | 37 +-
.../airavata/security/AuthenticationException.java | 37 +-
.../apache/airavata/security/Authenticator.java | 55 +-
.../org/apache/airavata/security/Authoriser.java | 39 +-
.../org/apache/airavata/security/UserStore.java | 38 +-
.../airavata/security/UserStoreException.java | 38 +-
.../AbstractConfigurationReader.java | 41 +-
.../AuthenticatorConfigurationReader.java | 86 +-
.../security/userstore/AbstractJDBCUserStore.java | 46 +-
.../airavata/security/userstore/JDBCUserStore.java | 71 +-
.../airavata/security/userstore/LDAPUserStore.java | 47 +-
.../security/userstore/SessionDBUserStore.java | 57 +-
.../airavata/security/util/PasswordDigester.java | 49 +-
.../airavata/security/util/TrustStoreManager.java | 50 +-
.../AuthenticatorConfigurationReaderTest.java | 74 +-
.../configurations/TestDBAuthenticator1.java | 36 +-
.../configurations/TestDBAuthenticator2.java | 36 +-
.../configurations/TestDBAuthenticator3.java | 36 +-
.../security/configurations/TestUserStore.java | 42 +-
.../security/userstore/JDBCUserStoreTest.java | 73 +-
.../security/userstore/LDAPUserStoreTest.java | 46 +-
.../security/userstore/SessionDBUserStoreTest.java | 58 +-
modules/server/pom.xml | 32 +-
.../org/apache/airavata/server/ServerMain.java | 795 +++---
modules/sharing-registry/pom.xml | 36 +-
.../sharing-registry/sharing-data-migrator/pom.xml | 32 +-
.../migrator/airavata/AiravataDataMigrator.java | 477 ++--
.../migrator/airavata/ConnectionFactory.java | 56 +-
.../sharing-registry-distribution/pom.xml | 32 +-
.../sharing-registry-server/pom.xml | 32 +-
.../sharing/registry/db/entities/DomainEntity.java | 43 +-
.../sharing/registry/db/entities/EntityEntity.java | 60 +-
.../sharing/registry/db/entities/EntityPK.java | 46 +-
.../registry/db/entities/EntityTypeEntity.java | 48 +-
.../sharing/registry/db/entities/EntityTypePK.java | 51 +-
.../registry/db/entities/GroupAdminEntity.java | 28 +-
.../sharing/registry/db/entities/GroupAdminPK.java | 28 +-
.../db/entities/GroupMembershipEntity.java | 43 +-
.../registry/db/entities/GroupMembershipPK.java | 45 +-
.../registry/db/entities/PermissionTypeEntity.java | 49 +-
.../registry/db/entities/PermissionTypePK.java | 51 +-
.../registry/db/entities/SharingEntity.java | 49 +-
.../sharing/registry/db/entities/SharingPK.java | 58 +-
.../sharing/registry/db/entities/UserEntity.java | 45 +-
.../registry/db/entities/UserGroupEntity.java | 52 +-
.../sharing/registry/db/entities/UserGroupPK.java | 48 +-
.../sharing/registry/db/entities/UserPK.java | 48 +-
.../db/repositories/AbstractRepository.java | 95 +-
.../registry/db/repositories/DomainRepository.java | 42 +-
.../registry/db/repositories/EntityRepository.java | 148 +-
.../db/repositories/EntityTypeRepository.java | 40 +-
.../db/repositories/GroupAdminRepository.java | 22 +-
.../db/repositories/GroupMembershipRepository.java | 106 +-
.../db/repositories/PermissionTypeRepository.java | 52 +-
.../db/repositories/SharingRepository.java | 75 +-
.../db/repositories/UserGroupRepository.java | 93 +-
.../registry/db/repositories/UserRepository.java | 90 +-
.../sharing/registry/db/utils/Committer.java | 40 +-
.../sharing/registry/db/utils/DBConstants.java | 40 +-
.../sharing/registry/db/utils/JPAUtils.java | 40 +-
.../registry/db/utils/ObjectMapperSingleton.java | 49 +-
.../db/utils/SharingRegistryDBInitConfig.java | 38 +-
.../db/utils/SharingRegistryJDBCConfig.java | 39 +-
.../messaging/SharingServiceDBEventHandler.java | 225 +-
.../SharingServiceDBEventMessagingFactory.java | 69 +-
.../sharing/registry/server/ServerMain.java | 97 +-
.../registry/server/SharingRegistryServer.java | 61 +-
.../server/SharingRegistryServerHandler.java | 598 +++--
.../airavata/sharing/registry/utils/Constants.java | 53 +-
.../registry/utils/ThriftDataModelConversion.java | 39 +-
.../airavata/sharing/registry/CipresTest.java | 408 +--
.../registry/SharingRegistryServerHandlerTest.java | 174 +-
.../registry/SharingRegistryServiceTest.java | 268 +-
.../sharing-registry-stubs/pom.xml | 32 +-
.../SharingRegistryServiceClientFactory.java | 43 +-
pom.xml | 4 +-
tools/load-client/pom.xml | 19 +-
.../apache/airavata/tools/load/Authenticator.java | 47 +-
.../apache/airavata/tools/load/Configuration.java | 35 +-
.../apache/airavata/tools/load/Configurations.java | 21 +-
.../org/apache/airavata/tools/load/LoadClient.java | 91 +-
.../airavata/tools/load/SecurityManager.java | 45 +-
.../apache/airavata/tools/load/StatusMonitor.java | 97 +-
.../tools/load/StorageResourceManager.java | 60 +-
.../org/apache/airavata/tools/load/UnitLoad.java | 79 +-
tools/pom.xml | 36 +-
997 files changed, 41292 insertions(+), 35210 deletions(-)
create mode 100644 .github/workflows/style-check.yml
