This is an automated email from the ASF dual-hosted git repository.
yasith pushed a change to branch cybershuttle-dev
in repository https://gitbox.apache.org/repos/asf/airavata.git
from 23c31506cc move portal to research-framework
new 1f2e18be3b consolidate POM deps to non-deprecated versions
new 46197be2ea partially update deprecated code
new a02e87b430 deprecation fixing round 2. cleanup unused imports of most
files.
new 80b4bd40e4 no functional changes - just removing unused imports and
reordering them.
new 3f7df10a72 fix rabbitmq deprecation
new a650ea74df fix dozer deprecations, add httpclient dep
new eec2402b5b fix api server assembly after the dependency update.
The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "add" were already present in the repository and have only
been added to this reference.
Summary of changes:
airavata-api/airavata-api-server/pom.xml | 21 -
.../api/server/handler/AiravataServerHandler.java | 23 +-
airavata-api/airavata-api-stubs/pom.xml | 27 -
.../airavata/api/client/AiravataClientFactory.java | 3 +-
airavata-api/airavata-base-api/pom.xml | 2 -
.../java-client-samples/pom.xml | 11 -
.../airavata/client/samples/CancelExperiments.java | 7 +-
.../tools/RegisterSampleApplicationsUtils.java | 3 +-
airavata-api/airavata-data-models/pom.xml | 29 -
airavata-api/airavata-model-utils/pom.xml | 2 -
.../airavata/model/util/ComputeResourceUtil.java | 4 -
.../GroupComputeResourcePreferenceUtilTest.java | 8 +-
airavata-services/pom.xml | 2 -
.../iam-admin-services-core/pom.xml | 36 +-
airavata-services/profile-service/pom.xml | 1 -
.../profile/client/samples/UserProfileSample.java | 3 -
.../profile-service-commons/pom.xml | 28 +-
.../commons/repositories/AbstractRepository.java | 16 +-
.../commons/tenant/entities/GatewayEntity.java | 3 +-
.../user/entities/NSFDemographicsEntity.java | 1 +
.../commons/user/entities/UserProfileEntity.java | 1 +
.../service/profile/commons/utils/JPAUtils.java | 1 -
.../commons/utils/ObjectMapperSingleton.java | 18 +-
.../commons/utils/ProfileServiceJDBCConfig.java | 1 -
.../handlers/GroupManagerServiceHandler.java | 8 +-
.../profile/handlers/IamAdminServicesHandler.java | 6 +-
.../handlers/UserProfileServiceHandler.java | 3 +-
.../profile/server/ProfileServiceServer.java | 6 +-
.../profile-service/profile-tenant-core/pom.xml | 1 -
.../profile-service/profile-user-core/pom.xml | 8 +-
.../core/repositories/UserProfileRepository.java | 4 +-
airavata-services/services-security/pom.xml | 60 +-
modules/agent-framework/agent-service/pom.xml | 20 +-
.../service/controllers/AgentController.java | 26 +-
.../service/controllers/ExperimentController.java | 11 +-
.../service/controllers/PlanController.java | 8 +-
.../service/db/entity/AgentExecution.java | 3 +-
.../service/handlers/AgentConnectionHandler.java | 46 +-
.../service/handlers/AgentManagementHandler.java | 10 +-
.../service/models/AgentLaunchRequest.java | 4 +-
.../service/services/AiravataFileService.java | 24 +-
.../service/services/AiravataService.java | 13 +-
modules/airavata-helix/agent-api/pom.xml | 33 +-
.../apache/airavata/agents/api/AdaptorParams.java | 2 +-
.../apache/airavata/agents/api/AgentAdaptor.java | 3 -
.../apache/airavata/agents/api/CommandOutput.java | 2 -
.../airavata-helix/agent-impl/ssh-agent/pom.xml | 1 -
.../airavata/helix/agent/ssh/SshAdaptorParams.java | 4 +-
.../airavata/helix/agent/ssh/SshAgentAdaptor.java | 4 +-
.../helix/agent/ssh/StandardOutReader.java | 5 +-
.../airavata/helix/adaptor/PoolingSSHJClient.java | 4 +-
.../airavata/helix/adaptor/SSHJAgentAdaptor.java | 8 +-
modules/airavata-helix/helix-spectator/pom.xml | 26 +-
.../helix/impl/controller/HelixController.java | 2 -
.../airavata/helix/impl/task/AiravataTask.java | 41 +-
.../airavata/helix/impl/task/TaskContext.java | 19 +-
.../impl/task/cancel/CancelCompletingTask.java | 1 -
.../helix/impl/task/completing/CompletingTask.java | 2 -
.../helix/impl/task/parsing/DataParsingTask.java | 6 +-
.../impl/task/parsing/ParsingTriggeringTask.java | 2 +-
.../impl/task/staging/OutputDataStagingTask.java | 4 -
.../task/submission/DefaultJobSubmissionTask.java | 17 +-
.../impl/task/submission/JobSubmissionTask.java | 3 +-
.../task/submission/LocalJobSubmissionTask.java | 8 -
.../task/submission/config/GroovyMapBuilder.java | 6 +-
.../config/app/ForkJobConfiguration.java | 4 +-
.../config/app/HTCondorJobConfiguration.java | 6 +-
.../submission/config/app/LSFJobConfiguration.java | 4 +-
.../submission/config/app/PBSJobConfiguration.java | 4 +-
.../config/app/SlurmJobConfiguration.java | 8 +-
.../submission/config/app/UGEJobConfiguration.java | 4 +-
.../config/app/parser/HTCondorOutputParser.java | 1 -
.../helix/impl/workflow/ParserWorkflowManager.java | 3 +-
.../helix/impl/workflow/PostWorkflowManager.java | 14 +-
.../helix/impl/workflow/PreWorkflowManager.java | 4 +-
modules/airavata-helix/task-api/pom.xml | 43 +-
.../helix/task/api/support/AdaptorSupport.java | 6 +-
.../task-api/src/main/resources/logback.xml | 28 +
modules/airavata-helix/task-core/pom.xml | 14 -
.../org/apache/airavata/helix/core/OutPort.java | 1 -
.../helix/core/participant/HelixParticipant.java | 6 +-
.../core/support/adaptor/AdaptorSupportImpl.java | 4 +-
.../helix/core/support/adaptor/AgentStore.java | 1 -
.../apache/airavata/helix/core/util/TaskUtil.java | 5 +-
modules/airavata-helix/workflow-impl/pom.xml | 16 -
.../metadata/analyzer/impl/DataAnalyzerImpl.java | 1 -
.../metascheduler/core/api/ProcessScheduler.java | 4 -
.../airavata/metascheduler/core/utils/Utils.java | 1 -
.../scheduling/api/ProcessSchedulerImpl.java | 1 -
.../ComputeResourceSelectionPolicyImpl.java | 1 -
.../DefaultComputeResourceSelectionPolicy.java | 1 -
.../selection/MultipleComputeResourcePolicy.java | 6 +-
.../rescheduler/ExponentialBackOffReScheduler.java | 1 -
.../engine/rescheduler/ProcessScannerImpl.java | 2 -
.../monitoring/ClusterStatusMonitorJob.java | 2 +-
.../ClusterStatusMonitorJobScheduler.java | 12 +-
modules/commons/pom.xml | 73 +--
.../airavata/common/utils/ApplicationSettings.java | 6 +-
.../common/utils/DBEventManagerConstants.java | 2 -
.../airavata/common/utils/DatabaseCreator.java | 7 +-
.../airavata/common/utils/DerbyTestUtil.java | 16 +-
.../apache/airavata/common/utils/DerbyUtil.java | 8 +-
.../org/apache/airavata/common/utils/IOUtil.java | 14 +-
.../org/apache/airavata/common/utils/JPAUtils.java | 8 +-
.../org/apache/airavata/common/utils/JSONUtil.java | 13 +-
.../apache/airavata/common/utils/StringUtil.java | 147 ++---
.../apache/airavata/common/utils/SwingUtil.java | 18 +-
.../airavata/common/utils/ThriftClientPool.java | 6 +-
.../apache/airavata/common/utils/WSConstants.java | 7 -
.../org/apache/airavata/common/utils/WSDLUtil.java | 525 +++--------------
.../airavata/common/utils/SecurityUtilTest.java | 1 -
.../common/utils/ThriftClientPoolTest.java | 12 +-
.../ComputationalResourceMonitoringService.java | 1 -
.../monitoring/job/ComputeResourceMonitor.java | 2 -
.../resource/monitoring/job/MonitoringJob.java | 1 -
.../src/main/resources/airavata-server.properties | 299 ++++------
.../server/src/main/resources/logback.xml | 53 ++
.../credential-store-service/pom.xml | 78 +--
.../impl/certificate/CertificateCredential.java | 1 +
.../store/credential/impl/ssh/SSHCredential.java | 1 +
.../store/notifier/NotifierBootstrap.java | 5 +-
.../store/notifier/impl/EmailNotifier.java | 5 +-
.../store/server/CredentialStoreServerHandler.java | 7 +-
.../store/servlet/CredentialBootstrapper.java | 34 +-
.../servlet/CredentialStoreCallbackServlet.java | 280 ++++-----
.../store/servlet/CredentialStoreStartServlet.java | 181 +++---
.../store/impl/CertificateCredentialWriter.java | 4 +-
.../store/store/impl/CredentialReaderImpl.java | 2 +-
.../store/store/impl/SSHCredentialWriter.java | 6 +-
.../credential/store/store/impl/db/ParentDAO.java | 1 -
.../credential/store/util/TokenGenerator.java | 1 -
.../store/notifier/impl/EmailNotifierTest.java | 1 -
.../credential-store-stubs/pom.xml | 38 --
.../store/client/CredentialStoreClientFactory.java | 2 -
.../credential/store/client/TestSSLClient.java | 5 +-
.../db/event/manager/DBEventManagerRunner.java | 6 +-
.../messaging/DBEventManagerMessagingFactory.java | 1 -
.../messaging/impl/DBEventMessageHandler.java | 4 -
.../airavata/db/event/manager/utils/Constants.java | 4 -
.../event/manager/utils/DbEventManagerZkUtils.java | 1 -
modules/distribution/pom.xml | 82 +--
.../src/main/assembly/api-server-bin-assembly.xml | 60 +-
.../src/main/assembly/api-server-src-assembly.xml | 78 ---
.../src/main/assembly/controller-bin-assembly.xml | 75 +--
.../main/assembly/email-monitor-bin-assembly.xml | 17 +-
.../src/main/assembly/parser-wm-bin-assembly.xml | 73 +--
.../src/main/assembly/participant-bin-assembly.xml | 77 +--
.../src/main/assembly/post-wm-bin-assembly.xml | 55 +-
.../src/main/assembly/pre-wm-bin-assembly.xml | 50 +-
.../assembly/realtime-monitor-bin-assembly.xml | 20 +-
modules/file-server/pom.xml | 8 +-
.../file/server/FileServerApplication.java | 1 -
.../file/server/FileServerConfiguration.java | 1 -
.../file/server/controller/FileController.java | 1 -
modules/ide-integration/pom.xml | 4 +
.../app/tests/selenium/pom.xml | 21 +-
modules/job-monitor/email-monitor/pom.xml | 1 +
.../airavata/monitor/email/EmailBasedMonitor.java | 15 +-
.../email/parser/AiravataCustomMailParser.java | 4 +-
.../airavata/monitor/email/parser/EmailParser.java | 5 +-
.../monitor/email/parser/HTCondorEmailParser.java | 5 +-
.../monitor/email/parser/LSFEmailParser.java | 4 +-
.../monitor/email/parser/PBSEmailParser.java | 5 +-
.../monitor/email/parser/SLURMEmailParser.java | 4 +-
.../monitor/email/parser/UGEEmailParser.java | 4 +-
modules/job-monitor/job-monitor-api/pom.xml | 1 -
.../apache/airavata/monitor/JobStateValidator.java | 10 +-
.../monitor/kafka/JobStatusResultDeserializer.java | 2 +-
modules/job-monitor/pom.xml | 2 -
.../src/main/resources/log4j.properties | 28 -
.../src/main/resources/log4j2.xml | 53 --
.../src/main/resources/logback.xml | 35 ++
modules/messaging/client/pom.xml | 8 +-
.../messaging/client/RabbitMQListener.java | 12 +-
.../airavata/messaging/client/TestReader.java | 3 -
modules/messaging/core/pom.xml | 12 +-
.../airavata/messaging/core/MessagingFactory.java | 9 +-
.../apache/airavata/messaging/core/TestClient.java | 1 -
.../messaging/core/impl/ExperimentConsumer.java | 30 +-
.../messaging/core/impl/MessageConsumer.java | 29 +-
.../messaging/core/impl/ProcessConsumer.java | 28 +-
.../messaging/core/impl/RabbitMQPublisher.java | 7 +-
.../messaging/core/impl/RabbitMQSubscriber.java | 9 +-
.../messaging/core/impl/StatusConsumer.java | 16 +-
.../messaging/core/stats/LatencyWriterTask.java | 1 -
.../airavata/messaging/core/stats/StatCounter.java | 2 +-
.../messaging/core/util/DBEventPublisherUtils.java | 8 +-
modules/orchestrator/orchestrator-client/pom.xml | 13 +-
modules/orchestrator/orchestrator-core/pom.xml | 26 -
.../orchestrator/core/schedule/HostScheduler.java | 4 +-
.../orchestrator/core/utils/OrchestratorUtils.java | 5 +-
.../core/validator/JobMetadataValidator.java | 1 -
.../core/validator/impl/BatchQueueValidator.java | 3 +-
modules/orchestrator/orchestrator-service/pom.xml | 16 +-
.../server/OrchestratorServerHandler.java | 2 +-
.../util/OrchestratorServerThreadPoolExecutor.java | 7 +-
modules/platform-monitoring/pom.xml | 2 +-
modules/registry/registry-core/pom.xml | 65 +-
.../AiravataWorkflowEntity.java | 1 +
.../AiravataWorkflowErrorEntity.java | 1 +
.../AiravataWorkflowStatusEntity.java | 2 +-
.../ApplicationErrorEntity.java | 1 +
.../ApplicationStatusEntity.java | 2 +-
.../HandlerErrorEntity.java | 1 +
.../HandlerInputEntity.java | 2 +-
.../HandlerOutputEntity.java | 2 +-
.../HandlerStatusEntity.java | 1 +
.../WorkflowApplicationEntity.java | 3 +-
.../WorkflowConnectionEntity.java | 2 +-
.../WorkflowDataBlockEntity.java | 1 +
.../WorkflowHandlerEntity.java | 2 +-
.../entities/appcatalog/AppEnvironmentEntity.java | 1 +
.../appcatalog/AppModuleMappingEntity.java | 1 +
.../appcatalog/ApplicationDeploymentEntity.java | 2 +-
.../appcatalog/ApplicationInputEntity.java | 2 +-
.../appcatalog/ApplicationInterfaceEntity.java | 1 +
.../appcatalog/ApplicationModuleEntity.java | 1 +
.../appcatalog/ApplicationOutputEntity.java | 2 +-
.../core/entities/appcatalog/BatchQueueEntity.java | 1 +
.../appcatalog/CloudJobSubmissionEntity.java | 2 +-
.../entities/appcatalog/ComputeResourceEntity.java | 2 +-
.../ComputeResourceFileSystemEntity.java | 2 +-
.../ComputeResourcePreferenceEntity.java | 2 +-
.../ComputeResourceReservationEntity.java | 14 +-
.../appcatalog/DataMovementInterfaceEntity.java | 2 +-
.../entities/appcatalog/GatewayGroupsEntity.java | 1 +
.../entities/appcatalog/GatewayProfileEntity.java | 1 +
.../appcatalog/GlobusGkEndpointEntity.java | 1 +
.../appcatalog/GlobusSubmissionEntity.java | 2 +-
.../appcatalog/GridftpDataMovementEntity.java | 2 +-
.../entities/appcatalog/GridftpEndpointEntity.java | 1 +
.../appcatalog/GroupComputeResourcePrefEntity.java | 15 +-
.../appcatalog/GroupResourceProfileEntity.java | 9 +-
.../GroupSSHAccountProvisionerConfig.java | 11 +-
.../entities/appcatalog/GsisshExportEntity.java | 1 +
.../appcatalog/GsisshPostjobcommandEntity.java | 1 +
.../appcatalog/GsisshPrejobcommandEntity.java | 1 +
.../appcatalog/GsisshSubmissionEntity.java | 1 +
.../appcatalog/JobManagerCommandEntity.java | 2 +-
.../appcatalog/JobSubmissionInterfaceEntity.java | 2 +-
.../appcatalog/LibraryApendPathEntity.java | 1 +
.../appcatalog/LibraryPrependPathEntity.java | 1 +
.../appcatalog/LocalDataMovementEntity.java | 1 +
.../entities/appcatalog/LocalSubmissionEntity.java | 2 +-
.../entities/appcatalog/ModuleLoadCmdEntity.java | 2 +
.../appcatalog/ParallelismCommandEntity.java | 2 +-
.../entities/appcatalog/ParserConnectorEntity.java | 1 +
.../appcatalog/ParserConnectorInputEntity.java | 1 +
.../core/entities/appcatalog/ParserEntity.java | 1 +
.../entities/appcatalog/ParserInputEntity.java | 1 +
.../entities/appcatalog/ParserOutputEntity.java | 1 +
.../entities/appcatalog/ParsingTemplateEntity.java | 1 +
.../appcatalog/ParsingTemplateInputEntity.java | 1 +
.../entities/appcatalog/PostjobCommandEntity.java | 1 +
.../entities/appcatalog/PrejobCommandEntity.java | 1 +
.../appcatalog/ResourceJobManagerEntity.java | 2 +-
.../entities/appcatalog/ScpDataMovementEntity.java | 2 +-
.../appcatalog/SshJobSubmissionEntity.java | 2 +-
.../appcatalog/StorageInterfaceEntity.java | 2 +-
.../appcatalog/StoragePreferenceEntity.java | 1 +
.../entities/appcatalog/StorageResourceEntity.java | 1 +
.../appcatalog/UnicoreDatamovementEntity.java | 7 +-
.../appcatalog/UnicoreSubmissionEntity.java | 2 +-
.../UserComputeResourcePreferenceEntity.java | 1 +
.../appcatalog/UserResourceProfileEntity.java | 3 +-
.../ComputationalResourceSchedulingEntity.java | 1 +
.../core/entities/expcatalog/ExperimentEntity.java | 2 +-
.../entities/expcatalog/ExperimentErrorEntity.java | 2 +-
.../entities/expcatalog/ExperimentInputEntity.java | 2 +-
.../expcatalog/ExperimentOutputEntity.java | 2 +-
.../expcatalog/ExperimentStatusEntity.java | 2 +-
.../expcatalog/ExperimentSummaryEntity.java | 5 +-
.../core/entities/expcatalog/GatewayEntity.java | 2 +-
.../GatewayUsageReportingCommandEntity.java | 1 +
.../entities/expcatalog/GatewayWorkerEntity.java | 1 +
.../core/entities/expcatalog/JobEntity.java | 1 +
.../core/entities/expcatalog/JobStatusEntity.java | 2 +-
.../entities/expcatalog/NotificationEntity.java | 2 +-
.../core/entities/expcatalog/ProcessEntity.java | 1 +
.../entities/expcatalog/ProcessErrorEntity.java | 2 +-
.../entities/expcatalog/ProcessInputEntity.java | 2 +-
.../entities/expcatalog/ProcessOutputEntity.java | 2 +-
.../expcatalog/ProcessResourceScheduleEntity.java | 1 +
.../entities/expcatalog/ProcessStatusEntity.java | 2 +-
.../entities/expcatalog/ProcessWorkflowPK.java | 2 -
.../core/entities/expcatalog/ProjectEntity.java | 7 +-
.../entities/expcatalog/ProjectUserEntity.java | 1 +
.../entities/expcatalog/QueueStatusEntity.java | 2 +-
.../core/entities/expcatalog/QueueStatusPK.java | 1 -
.../core/entities/expcatalog/TaskEntity.java | 2 +-
.../core/entities/expcatalog/TaskErrorEntity.java | 2 +-
.../core/entities/expcatalog/TaskStatusEntity.java | 2 +-
.../expcatalog/UserConfigurationDataEntity.java | 1 +
.../replicacatalog/ConfigurationEntity.java | 1 +
.../entities/replicacatalog/DataProductEntity.java | 2 +-
.../replicacatalog/DataProductMetadataEntity.java | 1 +
.../replicacatalog/DataReplicaLocationEntity.java | 2 +-
.../replicacatalog/DataReplicaMetadataEntity.java | 1 +
.../workflowcatalog/ComponentStatusEntity.java | 1 +
.../core/entities/workflowcatalog/EdgeEntity.java | 2 +-
.../core/entities/workflowcatalog/NodeEntity.java | 2 +-
.../core/entities/workflowcatalog/PortEntity.java | 2 +-
.../entities/workflowcatalog/WorkflowEntity.java | 7 +-
.../workflowcatalog/WorkflowInputEntity.java | 1 +
.../workflowcatalog/WorkflowOutputEntity.java | 1 +
.../workflowcatalog/WorkflowStatusEntity.java | 1 +
.../core/repositories/AbstractRepository.java | 2 +-
.../appcatalog/AppCatAbstractRepository.java | 3 +-
.../ApplicationDeploymentRepository.java | 4 +-
.../appcatalog/ApplicationInterfaceRepository.java | 4 +-
.../appcatalog/ComputeResourceRepository.java | 37 +-
.../appcatalog/DataMovementRepository.java | 2 +-
.../appcatalog/GroupResourceProfileRepository.java | 6 +-
.../appcatalog/GwyResourceProfileRepository.java | 2 +-
.../JobSubmissionInterfaceRepository.java | 2 +-
.../repositories/appcatalog/ParserRepository.java | 2 +-
.../appcatalog/ResourceJobManagerRepository.java | 6 +-
.../appcatalog/StorageResourceRepository.java | 3 +-
.../UserComputeResourcePreferenceRepository.java | 2 -
.../appcatalog/UserResourceProfileRepository.java | 8 +-
.../UserStoragePreferenceRepository.java | 2 -
.../expcatalog/ExpCatAbstractRepository.java | 3 +-
.../expcatalog/ExperimentErrorRepository.java | 2 +-
.../expcatalog/ExperimentInputRepository.java | 2 +-
.../expcatalog/ExperimentOutputRepository.java | 2 +-
.../expcatalog/ExperimentRepository.java | 4 +-
.../expcatalog/ExperimentStatusRepository.java | 2 +-
.../expcatalog/ExperimentSummaryRepository.java | 9 +-
.../repositories/expcatalog/GatewayRepository.java | 2 +-
.../GatewayUsageReportingCommandRepository.java | 2 +-
.../repositories/expcatalog/JobRepository.java | 2 +-
.../expcatalog/JobStatusRepository.java | 5 +-
.../expcatalog/NotificationRepository.java | 2 +-
.../expcatalog/ProcessErrorRepository.java | 9 +-
.../expcatalog/ProcessInputRepository.java | 4 +-
.../expcatalog/ProcessOutputRepository.java | 4 +-
.../repositories/expcatalog/ProcessRepository.java | 2 +-
.../expcatalog/ProcessStatusRepository.java | 3 +-
.../expcatalog/ProcessWorkflowRepository.java | 2 +-
.../repositories/expcatalog/ProjectRepository.java | 7 +-
.../expcatalog/QueueStatusRepository.java | 2 +-
.../expcatalog/TaskErrorRepository.java | 2 +-
.../repositories/expcatalog/TaskRepository.java | 2 +-
.../expcatalog/TaskStatusRepository.java | 2 +-
.../replicacatalog/DataProductRepository.java | 9 +-
.../DataReplicaLocationRepository.java | 2 +-
.../replicacatalog/RepCatAbstractRepository.java | 3 +-
.../WorkflowCatAbstractRepository.java | 3 +-
.../workflowcatalog/WorkflowRepository.java | 7 +-
.../core/utils/AppCatalogDBInitConfig.java | 2 -
.../registry/core/utils/CustomBeanFactory.java | 22 +-
.../utils/DozerConverter/CsvStringConverter.java | 4 +-
.../utils/DozerConverter/StorageDateConverter.java | 2 +-
.../core/utils/JPAUtil/AppCatalogJPAUtils.java | 1 -
.../core/utils/JPAUtil/ExpCatalogJPAUtils.java | 1 -
.../core/utils/JPAUtil/RepCatalogJPAUtils.java | 1 -
.../utils/JPAUtil/WorkflowCatalogJPAUtils.java | 1 -
.../registry/core/utils/ObjectMapperSingleton.java | 25 +-
.../registry/core/utils/QueryConstants.java | 4 -
.../core/utils/migration/MappingToolRunner.java | 3 +-
.../utils/migration/MigrationSchemaGenerator.java | 10 +-
.../ApplicationDeploymentRepositoryTest.java | 53 +-
.../appcatalog/GatewayProfileRepositoryTest.java | 4 +-
.../GroupResourceProfileRepositoryTest.java | 12 +-
.../appcatalog/StorageResourceRepositoryTest.java | 6 +-
.../UserResourceProfileRepositoryTest.java | 4 +-
.../core/repositories/common/TestBase.java | 6 +-
.../expcatalog/ExperimentErrorRepositoryTest.java | 1 +
.../expcatalog/ExperimentInputRepositoryTest.java | 1 +
.../expcatalog/ExperimentOutputRepositoryTest.java | 1 +
.../expcatalog/GatewayRepositoryTest.java | 4 +-
.../repositories/expcatalog/JobRepositoryTest.java | 5 +-
.../expcatalog/ProcessErrorRepositoryTest.java | 1 +
.../expcatalog/ProcessInputRepositoryTest.java | 1 +
.../expcatalog/ProcessOutputRepositoryTest.java | 1 +
.../expcatalog/ProcessStatusRepositoryTest.java | 4 +-
.../expcatalog/QueueStatusRepositoryTest.java | 1 +
.../replicacatalog/DataProductRepositoryTest.java | 10 +-
.../DataReplicaLocationRepositoryTest.java | 1 -
.../core/utils/ObjectMapperSingletonTest.java | 25 +
modules/registry/registry-cpi/pom.xml | 2 -
.../airavata/registry/cpi/UsrResourceProfile.java | 3 +-
.../airavata/registry/cpi/WorkflowCatalog.java | 3 -
.../registry-server/registry-api-service/pom.xml | 8 -
.../registry/api/service/RegistryAPIServer.java | 8 +-
.../api/service/handler/RegistryServerHandler.java | 3 +-
.../registry-server/registry-api-stubs/pom.xml | 3 -
.../computeresource/BatchQueueGenerator.java | 5 +-
.../ComputeResourceDescriptionGenerator.java | 5 +-
.../DataMovementInterfaceGenerator.java | 5 +-
.../computeresource/FileSystemsGenerator.java | 5 +-
.../GridFTPDataMovementGenerator.java | 5 +-
.../computeresource/GridFTPEndpointsGenerator.java | 5 +-
.../JobManagerCommandGenerator.java | 5 +-
.../JobSubmissionInterfaceGenerator.java | 5 +-
.../LocalDataMovementGenerator.java | 5 +-
.../computeresource/LocalSubmissionGenerator.java | 5 +-
.../ResourceJobManagerGenerator.java | 5 +-
.../computeresource/SCPDataMovementGenerator.java | 5 +-
.../computeresource/SSHJobSubmissionGenerator.java | 5 +-
.../main/java/generators/JPAClassGenerator.java | 5 +-
.../java/generators/JPAResourceClassGenerator.java | 5 +-
.../src/main/java/generators/SQLGenerator.java | 6 +-
.../jpa-gen/src/main/java/test/Test.java | 5 +-
.../registry/registry-tools/registry-tool/pom.xml | 21 -
.../apache/airavata/registry/tool/DBMigrator.java | 4 +-
.../research-framework/research-service/pom.xml | 59 +-
.../service/config/DevDataInitializer.java | 6 +-
.../research/service/config/OpenApiConfig.java | 7 -
.../service/controller/ResearchHubController.java | 11 -
.../service/controller/ResourceController.java | 15 +-
.../service/controller/SessionController.java | 4 -
.../research/service/handlers/ProjectHandler.java | 2 -
.../service/handlers/ResearchHubHandler.java | 2 +-
.../research/service/handlers/ResourceHandler.java | 1 -
.../research/service/model/entity/Project.java | 11 +-
.../research/service/model/entity/Resource.java | 18 +-
.../research/service/model/entity/Session.java | 12 +-
.../research/service/model/entity/Tag.java | 6 +-
modules/security/pom.xml | 2 -
.../airavata/security/AbstractAuthenticator.java | 2 -
.../security/userstore/AbstractJDBCUserStore.java | 1 -
.../airavata/security/userstore/JDBCUserStore.java | 2 +-
.../security/userstore/SessionDBUserStore.java | 2 +-
.../airavata/security/util/TrustStoreManager.java | 4 +-
modules/server/pom.xml | 3 +-
.../org/apache/airavata/server/ServerMain.java | 17 +-
.../sharing-registry/sharing-data-migrator/pom.xml | 9 +-
.../sharing-registry-distribution/pom.xml | 22 +-
.../sharing-registry-server/pom.xml | 29 +-
.../sharing/registry/db/entities/DomainEntity.java | 3 +-
.../sharing/registry/db/entities/EntityEntity.java | 3 +-
.../sharing/registry/db/entities/EntityPK.java | 4 +-
.../registry/db/entities/EntityTypeEntity.java | 3 +-
.../sharing/registry/db/entities/EntityTypePK.java | 4 +-
.../registry/db/entities/GroupAdminEntity.java | 3 +-
.../sharing/registry/db/entities/GroupAdminPK.java | 4 +-
.../db/entities/GroupMembershipEntity.java | 3 +-
.../registry/db/entities/GroupMembershipPK.java | 4 +-
.../registry/db/entities/PermissionTypeEntity.java | 3 +-
.../registry/db/entities/PermissionTypePK.java | 4 +-
.../registry/db/entities/SharingEntity.java | 3 +-
.../sharing/registry/db/entities/SharingPK.java | 4 +-
.../sharing/registry/db/entities/UserEntity.java | 3 +-
.../registry/db/entities/UserGroupEntity.java | 2 +-
.../sharing/registry/db/entities/UserGroupPK.java | 4 +-
.../sharing/registry/db/entities/UserPK.java | 4 +-
.../db/repositories/AbstractRepository.java | 14 +-
.../registry/db/repositories/EntityRepository.java | 5 +-
.../db/repositories/PermissionTypeRepository.java | 2 +-
.../db/repositories/SharingRepository.java | 3 +-
.../sharing/registry/db/utils/JPAUtils.java | 1 -
.../registry/db/utils/ObjectMapperSingleton.java | 18 +-
.../messaging/SharingServiceDBEventHandler.java | 6 +-
.../server/SharingRegistryServerHandler.java | 2 +-
.../registry/SharingRegistryServerHandlerTest.java | 2 +-
.../sharing-registry-stubs/pom.xml | 23 +-
pom.xml | 653 ++++++++++++++-------
tools/load-client/pom.xml | 27 +-
.../apache/airavata/tools/load/Configurations.java | 2 -
.../org/apache/airavata/tools/load/LoadClient.java | 8 +-
.../airavata/tools/load/SecurityManager.java | 10 +-
.../org/apache/airavata/tools/load/UnitLoad.java | 2 -
463 files changed, 2128 insertions(+), 3655 deletions(-)
create mode 100644
modules/airavata-helix/task-api/src/main/resources/logback.xml
create mode 100644 modules/configuration/server/src/main/resources/logback.xml
delete mode 100644
modules/distribution/src/main/assembly/api-server-src-assembly.xml
delete mode 100644
modules/job-monitor/real-time-monitor/src/main/resources/log4j.properties
delete mode 100644
modules/job-monitor/real-time-monitor/src/main/resources/log4j2.xml
create mode 100644
modules/job-monitor/real-time-monitor/src/main/resources/logback.xml
