This is an automated email from the ASF dual-hosted git repository.
yasith pushed a change to branch refactor/phase3-execution-module
in repository https://gitbox.apache.org/repos/asf/airavata.git
from 936e43fa7d refactor: Phase 3 — reorganize execution module (registry,
helix, orchestrator, monitor, metascheduler)
add 9391f2ef1b style: apply spotless formatting after package
reorganization
add 26b8168cd8 fix: move test files to match new package structure, apply
spotless
No new revisions were added by this update.
Summary of changes:
.../common/server/KeyStorePasswordCallback.java | 38 ++++++------
.../airavata/common/server/MonitoringServer.java | 1 -
.../airavata/common/server/ServiceRegistry.java | 1 -
.../common/util/AiravataClientFactory.java | 2 +-
.../ApplicationDeploymentRepository.java | 6 +-
.../repository/ApplicationInputRepository.java | 2 +-
.../repository/ApplicationInterfaceRepository.java | 10 ++--
.../repository/ApplicationModuleRepository.java | 2 +-
.../repository/ApplicationOutputRepository.java | 2 +-
.../repository/BatchQueuePolicyRepository.java | 2 +-
.../compute/repository/BatchQueueRepository.java | 2 +-
.../ComputeResourcePolicyRepository.java | 2 +-
.../repository/ComputeResourcePrefRepository.java | 2 +-
.../repository/ComputeResourceRepository.java | 30 +++++-----
.../repository/GatewayGroupsRepository.java | 2 +-
.../repository/GroupResourceProfileRepository.java | 16 ++---
.../repository/GrpComputePrefRepository.java | 8 +--
.../repository/GwyResourceProfileRepository.java | 10 ++--
.../JobSubmissionInterfaceRepository.java | 2 +-
.../compute/repository/ParserInputRepository.java | 2 +-
.../compute/repository/ParserOutputRepository.java | 2 +-
.../compute/repository/ParserRepository.java | 2 +-
.../repository/ParsingTemplateRepository.java | 2 +-
.../repository/ResourceJobManagerRepository.java | 6 +-
.../UserComputeResourcePreferenceRepository.java | 2 +-
.../repository/UserResourceProfileRepository.java | 10 ++--
.../compute/service/ApplicationCatalogService.java | 12 ++--
.../service/GatewayResourceProfileService.java | 6 +-
.../service/GroupResourceProfileService.java | 12 ++--
.../airavata/compute/service/ParserService.java | 4 +-
.../airavata/compute/service/ResourceService.java | 9 ++-
.../service/UserResourceProfileService.java | 6 +-
.../task/AiravataCustomCommandOutputParser.java | 1 -
.../compute/task/CloudJobManagerConfiguration.java | 4 --
.../compute/task/DefaultJobSubmissionTask.java | 8 +--
.../compute/task/ForkJobConfiguration.java | 3 -
.../compute/task/ForkJobSubmissionTask.java | 6 +-
.../airavata/compute/task/ForkOutputParser.java | 1 -
.../compute/task/HTCondorJobConfiguration.java | 3 -
.../compute/task/HTCondorOutputParser.java | 2 -
.../apache/airavata/compute/task/JobFactory.java | 4 +-
.../airavata/compute/task/JobSubmissionTask.java | 10 +---
.../airavata/compute/task/LSFJobConfiguration.java | 3 -
.../airavata/compute/task/LSFOutputParser.java | 1 -
.../compute/task/LocalJobSubmissionTask.java | 3 +-
.../airavata/compute/task/PBSJobConfiguration.java | 3 -
.../airavata/compute/task/PBSOutputParser.java | 2 -
.../compute/task/SlurmJobConfiguration.java | 3 -
.../airavata/compute/task/SlurmOutputParser.java | 2 -
.../airavata/compute/task/UGEJobConfiguration.java | 3 -
.../airavata/compute/task/UGEOutputParser.java | 1 -
.../compute/task/aws/AWSCompletingTask.java | 3 +-
.../compute/task/aws/AWSJobSubmissionTask.java | 14 ++---
.../airavata/compute/task/aws/AWSTaskUtil.java | 1 -
.../compute/task/aws/CreateEC2InstanceTask.java | 3 +-
.../airavata/compute/task/aws/NoOperationTask.java | 2 +-
.../apache/airavata/compute/util/AgentUtils.java | 6 +-
.../airavata/compute/util/PoolingSSHJClient.java | 4 --
.../airavata/compute/util/SSHJAgentAdaptor.java | 7 +--
.../airavata/compute/util/SshAdaptorParams.java | 1 -
.../airavata/compute/util/SshAgentAdaptor.java | 3 +-
.../airavata/compute/util/StandardOutReader.java | 1 -
.../handler/CredentialStoreServerHandler.java | 69 +++++++---------------
.../credential/model/CertificateAuditInfo.java | 2 -
.../credential/model/CertificateCredential.java | 2 -
.../credential/model/PasswordCredential.java | 2 -
.../airavata/credential/model/SSHCredential.java | 1 -
.../repository/CertificateCredentialWriter.java | 6 +-
.../repository/CredentialReaderFactory.java | 3 +-
.../repository/CredentialReaderImpl.java | 8 +--
.../credential/repository/SSHCredentialWriter.java | 4 +-
.../credential/repository/db/CredentialsDAO.java | 2 +-
.../repository/util/CredentialStoreJDBCConfig.java | 4 +-
.../credential/service/CredentialService.java | 10 ++--
.../credential/service/SSHAccountService.java | 6 +-
.../service/provisioning/SSHAccountManager.java | 6 +-
.../airavata/credential/task/EnvSetupTask.java | 4 +-
.../airavata/credential/util/TestSSLClient.java | 2 +-
.../apache/airavata/credential/util/Utility.java | 4 +-
.../util/notifier/CredentialStoreNotifier.java | 38 ++++++------
.../util/notifier/NotifierBootstrap.java | 12 ++--
.../util/notifier/impl/EmailNotifier.java | 2 +-
.../execution/handler/RegistryServerHandler.java | 16 ++---
.../handler/RegistryServiceDBEventHandler.java | 4 +-
.../RegistryServiceDBEventMessagingFactory.java | 4 +-
.../monitor/AiravataCustomMailParser.java | 1 -
.../execution/monitor/ClusterStatusMonitorJob.java | 2 +-
.../monitor/ClusterStatusMonitorJobScheduler.java | 2 +-
.../ComputationalResourceMonitoringService.java | 4 +-
.../execution/monitor/EmailBasedMonitor.java | 10 +---
.../airavata/execution/monitor/EmailParser.java | 1 -
.../execution/monitor/HTCondorEmailParser.java | 1 -
.../monitor/JobStatusResultDeserializer.java | 1 -
.../monitor/JobStatusResultSerializer.java | 1 -
.../airavata/execution/monitor/LSFEmailParser.java | 1 -
.../execution/monitor/MessageProducer.java | 3 +-
.../airavata/execution/monitor/MonitoringJob.java | 7 +--
.../execution/monitor/OutputParserImpl.java | 1 -
.../airavata/execution/monitor/PBSEmailParser.java | 1 -
.../execution/monitor/RealtimeJobStatusParser.java | 1 -
.../execution/monitor/RealtimeMonitor.java | 7 +--
.../execution/monitor/SLURMEmailParser.java | 1 -
.../airavata/execution/monitor/UGEEmailParser.java | 1 -
.../orchestrator/AbstractOrchestrator.java | 7 +--
.../execution/orchestrator/AbstractTask.java | 8 +--
.../execution/orchestrator/AdaptorSupport.java | 2 +-
.../execution/orchestrator/AdaptorSupportImpl.java | 5 +-
.../execution/orchestrator/AgentStore.java | 2 +-
.../execution/orchestrator/AiravataTask.java | 10 +---
.../orchestrator/BatchQueueValidator.java | 5 +-
.../orchestrator/ExperimentStatusValidator.java | 1 -
.../orchestrator/GFACPassiveJobSubmitter.java | 6 +-
.../execution/orchestrator/GlobalParticipant.java | 4 +-
.../GroupResourceProfileValidator.java | 5 +-
.../execution/orchestrator/HelixController.java | 2 +-
.../execution/orchestrator/HelixParticipant.java | 5 +-
.../execution/orchestrator/JobSubmitter.java | 3 -
.../execution/orchestrator/Orchestrator.java | 1 -
.../orchestrator/OrchestratorClientSample.java | 2 +-
.../orchestrator/OrchestratorContext.java | 1 -
.../OrchestratorServerThreadPoolExecutor.java | 2 +-
.../orchestrator/OrchestratorServerUtils.java | 4 +-
.../execution/orchestrator/OrchestratorUtils.java | 8 +--
.../orchestrator/ParserWorkflowManager.java | 12 ++--
.../orchestrator/PostWorkflowManager.java | 18 +++---
.../execution/orchestrator/PreWorkflowManager.java | 13 ++--
.../execution/orchestrator/QueueOperator.java | 2 -
.../orchestrator/SimpleOrchestratorImpl.java | 12 +---
.../execution/orchestrator/SlurmTaskFactory.java | 6 +-
.../execution/orchestrator/TaskContext.java | 4 +-
.../execution/orchestrator/TaskHelper.java | 2 -
.../execution/orchestrator/TaskHelperImpl.java | 3 -
.../airavata/execution/orchestrator/TaskUtil.java | 5 --
.../orchestrator/WorkflowCleanupAgent.java | 2 +-
.../execution/orchestrator/WorkflowManager.java | 3 +-
.../execution/orchestrator/WorkflowOperator.java | 4 --
.../repository/ExperimentErrorRepository.java | 4 +-
.../repository/ExperimentInputRepository.java | 4 +-
.../repository/ExperimentOutputRepository.java | 4 +-
.../execution/repository/ExperimentRepository.java | 8 +--
.../repository/ExperimentStatusRepository.java | 6 +-
.../repository/ExperimentSummaryRepository.java | 6 +-
.../execution/repository/GatewayRepository.java | 4 +-
.../GatewayUsageReportingCommandRepository.java | 2 +-
.../execution/repository/JobRepository.java | 4 +-
.../execution/repository/JobStatusRepository.java | 6 +-
.../repository/NotificationRepository.java | 2 +-
.../repository/ProcessErrorRepository.java | 4 +-
.../repository/ProcessInputRepository.java | 4 +-
.../repository/ProcessOutputRepository.java | 4 +-
.../execution/repository/ProcessRepository.java | 10 ++--
.../repository/ProcessStatusRepository.java | 6 +-
.../repository/ProcessWorkflowRepository.java | 4 +-
.../execution/repository/ProjectRepository.java | 6 +-
.../repository/QueueStatusRepository.java | 2 +-
.../execution/repository/TaskErrorRepository.java | 4 +-
.../execution/repository/TaskRepository.java | 4 +-
.../execution/repository/TaskStatusRepository.java | 6 +-
.../execution/repository/UserRepository.java | 2 +-
.../execution/repository/WorkflowRepository.java | 4 +-
.../ComputeResourceSelectionPolicyImpl.java | 2 -
.../execution/scheduler/DataAnalyzerImpl.java | 2 -
.../scheduler/DataInterpreterService.java | 4 +-
.../scheduler/ExponentialBackOffReScheduler.java | 5 +-
.../scheduler/ProcessReschedulingService.java | 3 +-
.../execution/scheduler/ProcessScannerImpl.java | 3 -
.../execution/scheduler/ProcessSchedulerImpl.java | 3 -
.../apache/airavata/execution/scheduler/Utils.java | 2 +-
.../execution/service/ExperimentService.java | 14 ++---
.../airavata/execution/service/GatewayService.java | 8 +--
.../execution/service/NotificationService.java | 4 +-
.../airavata/execution/service/ProjectService.java | 10 +---
.../execution/task/CancelCompletingTask.java | 2 +-
.../airavata/execution/task/CompletingTask.java | 2 +-
.../airavata/execution/task/DataParsingTask.java | 20 +++----
.../execution/task/JobVerificationTask.java | 8 +--
.../apache/airavata/execution/task/MockTask.java | 2 +-
.../execution/task/ParsingTriggeringTask.java | 5 +-
.../task/ProcessCompletionMessageDeserializer.java | 1 -
.../task/ProcessCompletionMessageSerializer.java | 1 -
.../execution/task/RemoteJobCancellationTask.java | 8 +--
.../execution/task/WorkflowCancellationTask.java | 2 +-
.../execution/util/AbstractRepository.java | 3 -
.../execution/util/AppCatalogDBInitConfig.java | 4 +-
.../execution/util/AppCatalogJDBCConfig.java | 4 +-
.../execution/util/AppCatalogJPAUtils.java | 1 -
.../airavata/execution/util/CustomBeanFactory.java | 4 +-
.../execution/util/ExpCatalogDBInitConfig.java | 6 +-
.../execution/util/ExpCatalogJDBCConfig.java | 4 +-
.../execution/util/ExpCatalogJPAUtils.java | 1 -
.../airavata/execution/util/QueryConstants.java | 4 +-
.../execution/util/RepCatalogJPAUtils.java | 1 -
.../execution/util/ReplicaCatalogJDBCConfig.java | 4 +-
.../execution/util/WorkflowCatalogJDBCConfig.java | 4 +-
.../execution/util/WorkflowCatalogJPAUtils.java | 1 -
.../execution/util/cpi/ResultOrderType.java | 38 ++++++------
.../handler/DBEventManagerMessagingFactory.java | 3 +-
.../messaging/handler/DBEventManagerRunner.java | 1 -
.../messaging/handler/DBEventMessageHandler.java | 7 +--
.../messaging/handler/ExperimentConsumer.java | 2 +-
.../messaging/handler/ProcessConsumer.java | 2 +-
.../messaging/handler/RabbitMQListener.java | 2 +-
.../airavata/messaging/service/EventPublisher.java | 2 -
.../messaging/service/MessagingFactory.java | 6 +-
.../messaging/service/RabbitMQPublisher.java | 2 -
.../messaging/service/RabbitMQSubscriber.java | 1 -
.../messaging/util/DBEventPublisherUtils.java | 2 -
.../messaging/util/DbEventManagerZkUtils.java | 2 +-
.../security/profile/commons/utils/Utils.java | 2 +-
.../core/impl/TenantManagementKeycloakImpl.java | 4 +-
.../security/repository/AbstractJDBCUserStore.java | 2 +-
.../security/repository/JDBCUserStore.java | 2 +-
.../security/repository/LDAPUserStore.java | 2 +-
.../security/service/GatewayGroupsInitializer.java | 8 +--
.../security/service/KeyCloakSecurityManager.java | 10 ++--
.../security/service/SecurityManagerFactory.java | 2 +-
.../security/service/authzcache/AuthzCache.java | 2 +-
.../authzcache/AuthzCacheManagerFactory.java | 2 +-
.../service/interceptor/SecurityInterceptor.java | 6 +-
.../util/AuthenticatorConfigurationReader.java | 3 -
.../airavata/security/util/PasswordDigester.java | 2 -
.../handler/SharingRegistryServerHandler.java | 8 +--
.../handler/SharingServiceDBEventHandler.java | 4 +-
.../SharingServiceDBEventMessagingFactory.java | 4 +-
.../sharing/repository/AbstractRepository.java | 2 +-
.../sharing/repository/EntityRepository.java | 2 +-
.../repository/GroupMembershipRepository.java | 2 +-
.../repository/PermissionTypeRepository.java | 4 +-
.../sharing/repository/SharingRepository.java | 2 +-
.../sharing/repository/UserGroupRepository.java | 2 +-
.../sharing/repository/UserRepository.java | 2 +-
.../sharing/service/ResourceSharingService.java | 8 +--
.../airavata/sharing/service/SharingHelper.java | 4 +-
.../sharing/util/AiravataDataMigrator.java | 15 +++--
.../airavata/sharing/util/ConnectionFactory.java | 2 +-
.../sharing/util/SharingRegistryJDBCConfig.java | 4 +-
.../storage/model/DataMovementInterfaceEntity.java | 2 +-
.../storage/repository/DataMovementRepository.java | 4 +-
.../storage/repository/DataProductRepository.java | 6 +-
.../repository/DataReplicaLocationRepository.java | 6 +-
.../storage/repository/StoragePrefRepository.java | 2 +-
.../repository/StorageResourceRepository.java | 14 ++---
.../UserStoragePreferenceRepository.java | 2 +-
.../storage/service/DataProductService.java | 4 +-
.../apache/airavata/storage/task/ArchiveTask.java | 12 ++--
.../airavata/storage/task/DataStagingTask.java | 14 ++---
.../storage/task/InputDataStagingTask.java | 8 +--
.../storage/task/OutputDataStagingTask.java | 8 +--
.../storage/util/StorageResourceAdaptorImpl.java | 1 -
.../common/utils/ThriftClientPoolTest.java | 1 -
.../GroupComputeResourcePreferenceUtilTest.java | 0
.../repository/db/CommunityUserDAOTest.java | 2 +-
.../repository/db/CredentialsDAOTest.java | 4 +-
.../repository/db/SSHCredentialTest.java | 2 +-
.../credential/service/CredentialServiceTest.java | 6 +-
.../credential/service/SSHAccountServiceTest.java | 6 +-
.../store/cpi/SSHSummaryTest/SSHSummaryTest.java | 4 +-
.../util}/CustomBeanFactoryTest.java | 0
.../util}/ObjectMapperSingletonTest.java | 0
.../ExperimentRepositoryIntegrationTest.java | 8 +--
.../integration/SharingServiceIntegrationTest.java | 4 +-
.../ApplicationDeploymentRepositoryTest.java | 6 +-
.../ApplicationInterfaceRepositoryTest.java | 6 +-
.../appcatalog/ComputeResourceRepositoryTest.java | 6 +-
.../appcatalog/GatewayGroupsRepositoryTest.java | 2 +-
.../appcatalog/GatewayProfileRepositoryTest.java | 6 +-
.../GroupResourceProfileRepositoryTest.java | 4 +-
.../JobSubmissionInterfaceRepositoryTest.java | 6 +-
.../appcatalog/StorageResourceRepositoryTest.java | 4 +-
.../UserResourceProfileRepositoryTest.java | 4 +-
.../expcatalog/ExperimentErrorRepositoryTest.java | 4 +-
.../expcatalog/ExperimentInputRepositoryTest.java | 4 +-
.../expcatalog/ExperimentOutputRepositoryTest.java | 4 +-
.../expcatalog/ExperimentRepositoryTest.java | 4 +-
.../expcatalog/ExperimentStatusRepositoryTest.java | 4 +-
.../ExperimentSummaryRepositoryTest.java | 8 +--
.../expcatalog/GatewayRepositoryTest.java | 6 +-
.../repositories/expcatalog/JobRepositoryTest.java | 8 +--
.../expcatalog/JobStatusRepositoryTest.java | 6 +-
.../expcatalog/NotificationRepositoryTest.java | 4 +-
.../expcatalog/ProcessErrorRepositoryTest.java | 4 +-
.../expcatalog/ProcessInputRepositoryTest.java | 4 +-
.../expcatalog/ProcessOutputRepositoryTest.java | 4 +-
.../expcatalog/ProcessRepositoryTest.java | 6 +-
.../expcatalog/ProcessStatusRepositoryTest.java | 4 +-
.../expcatalog/ProjectRepositoryTest.java | 6 +-
.../expcatalog/QueueStatusRepositoryTest.java | 2 +-
.../expcatalog/TaskErrorRepositoryTest.java | 4 +-
.../expcatalog/TaskRepositoryTest.java | 6 +-
.../expcatalog/TaskStatusRepositoryTest.java | 4 +-
.../expcatalog/UserRepositoryTest.java | 4 +-
.../replicacatalog/DataProductRepositoryTest.java | 4 +-
.../DataReplicaLocationRepositoryTest.java | 4 +-
.../workflowcatalog/WorkflowRepositoryTest.java | 2 +-
.../security/repository/JDBCUserStoreTest.java | 2 +-
.../repository/SessionDBUserStoreTest.java | 2 +-
.../service/KeyCloakSecurityManagerTest.java | 8 +--
.../util/AuthenticatorConfigurationReaderTest.java | 1 -
.../security/util/TestDBAuthenticator1.java | 3 -
.../security/util/TestDBAuthenticator2.java | 2 -
.../security/util/TestDBAuthenticator3.java | 3 -
.../airavata/security/util/TestUserStore.java | 1 -
.../appcatalog/ApplicationCatalogServiceTest.java | 6 +-
.../dataproduct/DataProductServiceTest.java | 6 +-
.../service/experiment/ExperimentServiceTest.java | 7 +--
.../service/gateway/GatewayServiceTest.java | 3 +-
.../GroupResourceProfileServiceTest.java | 4 +-
.../notification/NotificationServiceTest.java | 3 +-
.../airavata/service/parser/ParserServiceTest.java | 4 +-
.../service/project/ProjectServiceTest.java | 5 +-
.../service/resource/ResourceServiceTest.java | 5 +-
.../GatewayResourceProfileServiceTest.java | 6 +-
.../UserResourceProfileServiceTest.java | 6 +-
.../airavata/sharing/registry/CipresTest.java | 2 +-
.../registry/SharingRegistryServerHandlerTest.java | 4 +-
.../service/ResourceSharingServiceTest.java | 4 +-
.../apache/airavata/api/server/AiravataServer.java | 34 +++++------
.../api/server/handler/AiravataServerHandler.java | 34 +++++------
.../airavata/api/server/handler/ThriftAdapter.java | 8 +--
.../server/OrchestratorServerHandler.java | 30 +++++-----
.../handlers/GroupManagerServiceHandler.java | 8 +--
.../profile/handlers/IamAdminServicesHandler.java | 14 ++---
.../handlers/TenantProfileServiceHandler.java | 8 +--
.../handlers/UserProfileServiceHandler.java | 18 +++---
.../file/server/FileServerConfiguration.java | 2 +-
.../file/server/service/AirvataFileService.java | 6 +-
.../file/server/service/ProcessDataManager.java | 6 +-
327 files changed, 723 insertions(+), 999 deletions(-)
rename airavata-api/src/test/java/org/apache/airavata/{model =>
compute}/util/GroupComputeResourcePreferenceUtilTest.java (100%)
rename airavata-api/src/test/java/org/apache/airavata/{registry/core/utils =>
execution/util}/CustomBeanFactoryTest.java (100%)
rename airavata-api/src/test/java/org/apache/airavata/{registry/core/utils =>
execution/util}/ObjectMapperSingletonTest.java (100%)
