This is an automated email from the ASF dual-hosted git repository.
lahirujayathilake pushed a change to branch cybershuttle-dev
in repository https://gitbox.apache.org/repos/asf/airavata.git
from 45243c04e4 jobmanager configs and included registry server properties
for real-time monitor
new 829bd328c7 partial solution for keycloak update in ide-integration
new 99504c30ab move self-signed certs to a single location
new fb4155084f create devcontainer.json and integrate with docker-compose
file. fix bugs.
new 27d2ba06d0 updated devcontainer and compose for easy use in vscode
new 56f28c3639 add AF2Complex notebook
new 13f4e46336 rename devcontainer to Airavata
new bd94c98f80 move docker-compose file to .devcontainer
new aeba381891 bump all jdk deps to 17. get devcontainer to working state.
add launch.json for vscode integration. add openjpa runtimeoptimization tag to
persistence.xml. bump mysql connector to 8.0.31. add dns tags to keystore
generation script (browser https compatibility), move keystores to top-level
and add build-time copy to project resources. fix Serializable warning in
UserPK.java
new 54f9d1d951 change protobuf plugin to a maintained one
new 9c700c7b0b update rabbitmq and proto versions, fix proto path in
agent-service
new 25e2fcc752 fix generated protos unused issue
new a5f2a0d1a1 fix pom issues when running in devcontainer
new e10321af33 migrate openjpa to 4.0.1. update javax.persistence to
jakarta.persistence.
new eaa1b7fd07 simplify devcontainer. unify maven-compiler plugin version.
new 8b9ca6c94e migrate javax.mail to jakarta.mail to fix email-monitor
bug. exclude conflicting angus-mail dependency. add missing @Deprecated tags.
new c6fc644ad8 regenerated thrift stubs with version 0.21.0 and fix issues
new e44acc9da5 parametrize pom versions. add maven-enforcer rule for
dependency convergence and fix version issues.
new eb9b50b12e migrate openjpa to hibernate, update pool and dbcp deps to
pool2 and dbcp2.
new b13e81da33 get hibernate orm to validate against test db. manually
specify catalog for conflicting entities.
new 3c2b9397bb fix issues with helix participant and job engine starter
new 22be98dcd9 cleanup code. add placeholders for job monitor email/pw in
airavata-server.properties
The 21 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:
.devcontainer/Dockerfile | 8 +
.devcontainer/devcontainer.json | 27 +
.devcontainer/docker-compose.yml | 142 +
.gitignore | 1 +
.vscode/launch.json | 25 +
airavata-api/airavata-api-server/pom.xml | 6 +-
.../java/org/apache/airavata/api/Airavata.java | 3876 +++++++++++++-----
.../apache/airavata/api/airavata_apiConstants.java | 2 +-
airavata-api/airavata-base-api/pom.xml | 6 +
.../java/org/apache/airavata/base/api/BaseAPI.java | 36 +-
.../airavata-client-sdks/airavata-cpp-sdk/pom.xml | 6 +-
.../airavata-client-sdks/airavata-php-sdk/pom.xml | 6 +-
.../java-client-samples/pom.xml | 4 +-
airavata-api/airavata-data-models/pom.xml | 5 +
.../org/apache/airavata/model/ComponentState.java | 4 +-
.../org/apache/airavata/model/ComponentStatus.java | 4 +-
.../java/org/apache/airavata/model/EdgeModel.java | 4 +-
.../java/org/apache/airavata/model/NodeModel.java | 4 +-
.../java/org/apache/airavata/model/PortModel.java | 4 +-
.../org/apache/airavata/model/WorkflowModel.java | 4 +-
.../org/apache/airavata/model/WorkflowState.java | 4 +-
.../org/apache/airavata/model/WorkflowStatus.java | 4 +-
.../accountprovisioning/SSHAccountProvisioner.java | 4 +-
.../SSHAccountProvisionerConfigParam.java | 4 +-
.../SSHAccountProvisionerConfigParamType.java | 4 +-
.../ApplicationDeploymentDescription.java | 4 +-
.../appdeployment/ApplicationModule.java | 4 +-
.../appcatalog/appdeployment/CommandObject.java | 4 +-
.../appcatalog/appdeployment/SetEnvPaths.java | 4 +-
.../application_deployment_modelConstants.java | 60 -
.../ApplicationInterfaceDescription.java | 4 +-
.../application_interface_modelConstants.java | 60 -
.../appcatalog/computeresource/BatchQueue.java | 4 +-
.../computeresource/CloudJobSubmission.java | 4 +-
.../ComputeResourceDescription.java | 4 +-
.../model/appcatalog/computeresource/DMType.java | 4 +-
.../appcatalog/computeresource/FileSystems.java | 4 +-
.../computeresource/GlobusJobSubmission.java | 4 +-
.../computeresource/JobManagerCommand.java | 4 +-
.../computeresource/JobSubmissionInterface.java | 4 +-
.../computeresource/JobSubmissionProtocol.java | 4 +-
.../computeresource/LOCALSubmission.java | 4 +-
.../appcatalog/computeresource/MonitorMode.java | 4 +-
.../appcatalog/computeresource/ProviderName.java | 4 +-
.../computeresource/ResourceJobManager.java | 4 +-
.../computeresource/ResourceJobManagerType.java | 4 +-
.../computeresource/SSHJobSubmission.java | 4 +-
.../computeresource/UnicoreJobSubmission.java | 4 +-
.../compute_resource_modelConstants.java | 60 -
.../appcatalog/gatewaygroups/GatewayGroups.java | 4 +-
.../gatewayprofile/ComputeResourcePreference.java | 4 +-
.../gatewayprofile/DataStoragePreference.java | 730 ----
.../gatewayprofile/GatewayResourceProfile.java | 4 +-
.../gatewayprofile/StoragePreference.java | 4 +-
.../BatchQueueResourcePolicy.java | 4 +-
.../ComputeResourcePolicy.java | 4 +-
.../ComputeResourceReservation.java | 4 +-
.../GroupAccountSSHProvisionerConfig.java | 4 +-
.../GroupComputeResourcePreference.java | 4 +-
.../groupresourceprofile/GroupResourceProfile.java | 4 +-
.../airavata/model/appcatalog/parser/IOType.java | 4 +-
.../airavata/model/appcatalog/parser/Parser.java | 4 +-
.../model/appcatalog/parser/ParserConnector.java | 4 +-
.../appcatalog/parser/ParserConnectorInput.java | 4 +-
.../appcatalog/parser/ParserDagInputMapping.java | 789 ----
.../model/appcatalog/parser/ParserInput.java | 4 +-
.../model/appcatalog/parser/ParserOutput.java | 4 +-
.../model/appcatalog/parser/ParsingTemplate.java | 4 +-
.../appcatalog/parser/ParsingTemplateInput.java | 4 +-
.../StorageResourceDescription.java | 4 +-
.../UserComputeResourcePreference.java | 4 +-
.../userresourceprofile/UserResourceProfile.java | 4 +-
.../userresourceprofile/UserStoragePreference.java | 4 +-
.../airavata/model/application/io/DataType.java | 4 +-
.../model/application/io/InputDataObjectType.java | 4 +-
.../model/application/io/OutputDataObjectType.java | 4 +-
.../apache/airavata/model/commons/ErrorModel.java | 4 +-
.../airavata/model/commons/ValidationResults.java | 4 +-
.../airavata/model/commons/ValidatorResult.java | 4 +-
.../model/commons/airavata_commonsConstants.java | 2 +-
.../credential/store/CertificateCredential.java | 4 +-
.../model/credential/store/CommunityUser.java | 4 +-
.../credential/store/CredentialOwnerType.java | 62 -
.../model/credential/store/CredentialSummary.java | 4 +-
.../model/credential/store/PasswordCredential.java | 4 +-
.../model/credential/store/SSHCredential.java | 4 +-
.../credential/store/SSHCredentialSummary.java | 929 -----
.../model/credential/store/SummaryType.java | 4 +-
....java => credential_store_modelsConstants.java} | 4 +-
.../airavata/model/data/movement/DMType.java | 4 +-
.../model/data/movement/DataMovementInterface.java | 4 +-
.../model/data/movement/DataMovementProtocol.java | 4 +-
.../model/data/movement/GridFTPDataMovement.java | 4 +-
.../model/data/movement/LOCALDataMovement.java | 4 +-
.../model/data/movement/SCPDataMovement.java | 4 +-
.../model/data/movement/SecurityProtocol.java | 4 +-
.../model/data/movement/UnicoreDataMovement.java | 4 +-
.../model/data/replica/DataProductModel.java | 4 +-
.../model/data/replica/DataProductType.java | 4 +-
.../data/replica/DataReplicaLocationModel.java | 4 +-
.../data/replica/ReplicaLocationCategory.java | 4 +-
.../model/data/replica/ReplicaPersistentType.java | 4 +-
.../apache/airavata/model/dbevent/CrudType.java | 4 +-
.../airavata/model/dbevent/DBEventMessage.java | 4 +-
.../model/dbevent/DBEventMessageContext.java | 4 +-
.../airavata/model/dbevent/DBEventPublisher.java | 4 +-
.../model/dbevent/DBEventPublisherContext.java | 4 +-
.../airavata/model/dbevent/DBEventSubscriber.java | 4 +-
.../apache/airavata/model/dbevent/DBEventType.java | 4 +-
.../apache/airavata/model/dbevent/EntityType.java | 4 +-
.../model/error/AiravataClientException.java | 4 +-
.../airavata/model/error/AiravataErrorType.java | 4 +-
.../model/error/AiravataSystemException.java | 4 +-
.../model/error/AuthenticationException.java | 4 +-
.../model/error/AuthorizationException.java | 4 +-
.../model/error/DuplicateEntryException.java | 4 +-
.../model/error/ExperimentNotFoundException.java | 4 +-
.../model/error/InvalidRequestException.java | 4 +-
.../model/error/LaunchValidationException.java | 4 +-
.../model/error/ProjectNotFoundException.java | 4 +-
.../airavata/model/error/TimedOutException.java | 4 +-
.../airavata/model/error/ValidationResults.java | 4 +-
.../airavata/model/error/ValidatorResult.java | 4 +-
.../airavata/model/experiment/ExperimentModel.java | 4 +-
.../model/experiment/ExperimentSearchFields.java | 4 +-
.../model/experiment/ExperimentStatistics.java | 4 +-
.../model/experiment/ExperimentSummaryModel.java | 4 +-
.../airavata/model/experiment/ExperimentType.java | 4 +-
.../model/experiment/ProjectSearchFields.java | 4 +-
.../experiment/UserConfigurationDataModel.java | 4 +-
.../apache/airavata/model/group/GroupModel.java | 4 +-
.../model/group/ResourcePermissionType.java | 4 +-
.../apache/airavata/model/group/ResourceType.java | 4 +-
.../org/apache/airavata/model/job/JobModel.java | 4 +-
.../event/ExperimentIntermediateOutputsEvent.java | 4 +-
.../event/ExperimentStatusChangeEvent.java | 4 +-
.../messaging/event/ExperimentSubmitEvent.java | 4 +-
.../model/messaging/event/JobIdentifier.java | 4 +-
.../messaging/event/JobStatusChangeEvent.java | 4 +-
.../event/JobStatusChangeRequestEvent.java | 4 +-
.../airavata/model/messaging/event/Message.java | 4 +-
.../model/messaging/event/MessageLevel.java | 4 +-
.../model/messaging/event/MessageType.java | 4 +-
.../model/messaging/event/ProcessIdentifier.java | 4 +-
.../messaging/event/ProcessStatusChangeEvent.java | 4 +-
.../event/ProcessStatusChangeRequestEvent.java | 4 +-
.../model/messaging/event/ProcessSubmitEvent.java | 4 +-
.../messaging/event/ProcessTerminateEvent.java | 4 +-
.../model/messaging/event/TaskIdentifier.java | 4 +-
.../messaging/event/TaskOutputChangeEvent.java | 4 +-
.../messaging/event/TaskStatusChangeEvent.java | 4 +-
.../event/TaskStatusChangeRequestEvent.java | 4 +-
.../model/messaging/event/TaskSubmitEvent.java | 711 ----
.../model/messaging/event/TaskTerminateEvent.java | 711 ----
.../messaging/event/messaging_eventsConstants.java | 60 -
.../parallelism/ApplicationParallelismType.java | 4 +-
.../airavata/model/process/ProcessModel.java | 4 +-
.../airavata/model/process/ProcessWorkflow.java | 4 +-
.../ComputationalResourceSchedulingModel.java | 4 +-
.../apache/airavata/model/security/AuthzToken.java | 4 +-
.../airavata/model/status/ExperimentState.java | 4 +-
.../airavata/model/status/ExperimentStatus.java | 4 +-
.../org/apache/airavata/model/status/JobState.java | 4 +-
.../apache/airavata/model/status/JobStatus.java | 4 +-
.../apache/airavata/model/status/ProcessState.java | 4 +-
.../airavata/model/status/ProcessStatus.java | 4 +-
.../airavata/model/status/QueueStatusModel.java | 4 +-
.../apache/airavata/model/status/TaskState.java | 4 +-
.../apache/airavata/model/status/TaskStatus.java | 4 +-
.../apache/airavata/model/task/DataStageType.java | 4 +-
.../airavata/model/task/DataStagingTaskModel.java | 4 +-
.../model/task/EnvironmentSetupTaskModel.java | 4 +-
.../model/task/JobSubmissionTaskModel.java | 4 +-
.../airavata/model/task/MonitorTaskModel.java | 4 +-
.../org/apache/airavata/model/task/TaskModel.java | 4 +-
.../org/apache/airavata/model/task/TaskTypes.java | 4 +-
.../org/apache/airavata/model/tenant/Tenant.java | 4 +-
.../model/tenant/TenantApprovalStatus.java | 4 +-
.../apache/airavata/model/tenant/TenantConfig.java | 4 +-
.../airavata/model/tenant/TenantPreferences.java | 4 +-
.../airavata/model/user/CustomDashboard.java | 4 +-
.../airavata/model/user/NSFDemographics.java | 4 +-
.../org/apache/airavata/model/user/Status.java | 4 +-
.../apache/airavata/model/user/USCitizenship.java | 4 +-
.../apache/airavata/model/user/UserProfile.java | 4 +-
.../org/apache/airavata/model/user/disability.java | 4 +-
.../org/apache/airavata/model/user/ethnicity.java | 4 +-
.../java/org/apache/airavata/model/user/race.java | 4 +-
.../model/user/user_profile_modelConstants.java | 2 +-
.../airavata/model/workflow/AiravataWorkflow.java | 4 +-
.../airavata/model/workflow/ApplicationState.java | 4 +-
.../airavata/model/workflow/ApplicationStatus.java | 4 +-
.../airavata/model/workflow/ComponentType.java | 4 +-
.../apache/airavata/model/workflow/DataBlock.java | 4 +-
.../airavata/model/workflow/HandlerState.java | 4 +-
.../airavata/model/workflow/HandlerStatus.java | 4 +-
.../airavata/model/workflow/HandlerType.java | 4 +-
.../airavata/model/workflow/NotificationEmail.java | 380 --
.../model/workflow/WorkflowApplication.java | 4 +-
.../model/workflow/WorkflowConnection.java | 4 +-
.../airavata/model/workflow/WorkflowHandler.java | 4 +-
.../airavata/model/workflow/WorkflowState.java | 4 +-
.../airavata/model/workflow/WorkflowStatus.java | 4 +-
.../model/workflow_data_modelConstants.java | 60 -
.../apache/airavata/model/workspace/Gateway.java | 4 +-
.../model/workspace/GatewayApprovalStatus.java | 4 +-
.../workspace/GatewayUsageReportingCommand.java | 4 +-
.../org/apache/airavata/model/workspace/Group.java | 4 +-
.../airavata/model/workspace/Notification.java | 4 +-
.../model/workspace/NotificationPriority.java | 4 +-
.../apache/airavata/model/workspace/Project.java | 4 +-
.../org/apache/airavata/model/workspace/User.java | 4 +-
airavata-services/pom.xml | 2 +-
.../iam-admin-services-core/pom.xml | 10 +-
.../profile-service-commons/pom.xml | 49 +-
.../commons/repositories/AbstractRepository.java | 2 +-
.../commons/tenant/entities/GatewayEntity.java | 9 +-
.../user/entities/CustomizedDashboardEntity.java | 2 +-
.../user/entities/NSFDemographicsEntity.java | 2 +-
.../commons/user/entities/UserProfileEntity.java | 2 +-
.../service/profile/commons/utils/JPAUtils.java | 4 +-
.../src/main/resources/META-INF/persistence.xml | 6 +-
.../groupmanager/cpi/GroupManagerService.java | 276 +-
.../exception/GroupManagerServiceException.java | 4 +-
.../cpi/group_manager_cpiConstants.java | 2 +-
.../iam/admin/services/cpi/IamAdminServices.java | 316 +-
.../cpi/exception/IamAdminServicesException.java | 4 +-
.../cpi/iam_admin_services_cpiConstants.java | 2 +-
.../profile/tenant/cpi/TenantProfileService.java | 156 +-
.../exception/TenantProfileServiceException.java | 4 +-
.../tenant/cpi/profile_tenant_cpiConstants.java | 2 +-
.../profile/user/cpi/UserProfileService.java | 156 +-
.../cpi/exception/UserProfileServiceException.java | 4 +-
.../user/cpi/profile_user_cpiConstants.java | 2 +-
.../profile-service/profile-tenant-core/pom.xml | 2 +-
.../profile-service/profile-user-core/pom.xml | 26 +-
airavata-services/services-security/pom.xml | 13 +-
dev-tools/ansible/roles/api-orch/defaults/main.yml | 2 +-
keystores/airavata.jks | Bin 0 -> 2848 bytes
keystores/client_truststore.jks | Bin 0 -> 2351 bytes
keystores/generate_keystore.sh | 14 +
modules/agent-framework/agent-service/pom.xml | 78 +-
.../service/controllers/AgentController.java | 11 +-
.../service/controllers/ExperimentController.java | 4 +-
.../agent-framework/agent-service/src/main/proto | 1 -
.../src/main/resources/application.yml | 2 +-
.../resources/distribution/conf/application.yml | 2 +-
.../data/af2complex/AF2Complex_notebook.ipynb | 1021 +++++
modules/agent-framework/pom.xml | 17 +-
modules/airavata-helix/agent-api/pom.xml | 2 +-
.../airavata-helix/agent-impl/ssh-agent/pom.xml | 6 +-
.../airavata-helix/agent-impl/sshj-agent/pom.xml | 3 +-
modules/airavata-helix/helix-spectator/pom.xml | 21 +-
.../helix/impl/controller/HelixController.java | 60 +-
.../helix/impl/participant/GlobalParticipant.java | 5 +-
.../airavata/helix/impl/task/AiravataTask.java | 2 +-
.../impl/task/parsing/ParsingTriggeringTask.java | 6 +-
modules/airavata-helix/task-api/pom.xml | 2 +-
modules/airavata-helix/task-core/pom.xml | 2 +-
.../helix/core/participant/HelixParticipant.java | 93 +-
modules/airavata-helix/workflow-impl/pom.xml | 2 +-
.../metadata-analyzer/pom.xml | 11 +-
.../metascheduler-core/pom.xml | 18 +-
modules/airavata-metascheduler/pom.xml | 4 +-
.../process-scheduler/pom.xml | 24 +-
modules/cluster-monitoring/pom.xml | 8 +-
modules/commons/pom.xml | 22 +-
.../airavata/common/utils/ApplicationSettings.java | 3 +
.../common/utils/DBConnectionProvider.java | 185 +
.../org/apache/airavata/common/utils/DBUtil.java | 2 +-
.../org/apache/airavata/common/utils/JPAUtils.java | 44 +-
modules/commons/src/test/resources/mykeystore.jks | Bin 498 -> 0 bytes
modules/compute-account-provisioning/pom.xml | 6 +-
.../computer-resource-monitoring-service/pom.xml | 13 +-
.../credential-store-service/pom.xml | 30 +-
.../store/credential/CredentialOwnerType.java | 23 +-
.../src/test/resources/keystore.jks | Bin 2230 -> 0 bytes
.../src/test/resources/mykeystore.jks | Bin 498 -> 0 bytes
.../credential-store-stubs/pom.xml | 2 +-
.../store/cpi/CredentialStoreService.java | 276 +-
.../store/cpi/credential_store_cpiConstants.java | 2 +-
.../store/exception/CredentialStoreException.java | 4 +-
modules/distribution/pom.xml | 74 +-
.../src/main/assembly/api-server-bin-assembly.xml | 2 +-
.../src/main/assembly/controller-bin-assembly.xml | 14 +-
.../main/assembly/email-monitor-bin-assembly.xml | 6 +-
.../src/main/assembly/parser-wm-bin-assembly.xml | 13 +-
.../src/main/assembly/participant-bin-assembly.xml | 20 +-
.../src/main/assembly/post-wm-bin-assembly.xml | 13 +-
.../src/main/assembly/pre-wm-bin-assembly.xml | 13 +-
.../assembly/realtime-monitor-bin-assembly.xml | 7 +-
.../src/main/docker/docker-compose.yml | 2 +-
modules/file-server/pom.xml | 3 +-
.../{src/main/containers => }/.gitignore | 0
modules/ide-integration/README.md | 43 +-
modules/ide-integration/pom.xml | 10 +-
.../src/main/containers/docker-compose.yml | 54 -
.../main/containers/keycloak/Default-export.json | 1508 -------
.../containers/keycloak/Default-export.json.bk | 1507 -------
.../src/main/containers/keycloak/keycloak.conf | 27 +
.../main/containers/keycloak/realm-default.json | 2649 ++++++++++++
.../src/main/containers/keycloak/standalone.xml | 521 ---
.../airavata-php-gateway/app/config/pga_config.php | 4 +-
.../app/tests/selenium/pom.xml | 37 +-
.../airavata/ide/integration/JobEngineStarter.java | 26 +-
.../src/main/resources/airavata-server.properties | 31 +-
.../src/main/resources/keystores/airavata.jks | Bin 2679 -> 0 bytes
.../src/main/resources/keystores/airavata_sym.jks | Bin 501 -> 0 bytes
.../main/resources/keystores/client_truststore.jks | Bin 2282 -> 0 bytes
.../ide-integration/src/main/resources/log4j2.xml | 4 +-
modules/job-monitor/email-monitor/pom.xml | 10 +-
.../airavata/monitor/email/EmailBasedMonitor.java | 29 +-
.../email/parser/AiravataCustomMailParser.java | 4 +-
.../airavata/monitor/email/parser/EmailParser.java | 4 +-
.../monitor/email/parser/HTCondorEmailParser.java | 4 +-
.../monitor/email/parser/LSFEmailParser.java | 4 +-
.../monitor/email/parser/PBSEmailParser.java | 4 +-
.../monitor/email/parser/SLURMEmailParser.java | 4 +-
.../monitor/email/parser/UGEEmailParser.java | 4 +-
modules/job-monitor/job-monitor-api/pom.xml | 3 +-
modules/job-monitor/pom.xml | 13 +-
modules/messaging/client/pom.xml | 1 +
.../core/impl/RabbitMQStatusSubscriber.java | 2 +-
.../messaging/core/impl/StatusConsumer.java | 24 +-
.../orchestrator/cpi/OrchestratorService.java | 116 +-
.../cpi/orchestrator_cpiConstants.java | 2 +-
modules/orchestrator/orchestrator-core/pom.xml | 2 +-
modules/orchestrator/orchestrator-service/pom.xml | 8 -
modules/platform-monitoring/pom.xml | 10 +-
modules/registry/registry-core/pom.xml | 57 +-
.../AiravataWorkflowEntity.java | 2 +-
.../AiravataWorkflowErrorEntity.java | 8 +-
.../AiravataWorkflowStatusEntity.java | 2 +-
.../ApplicationErrorEntity.java | 8 +-
.../ApplicationStatusEntity.java | 2 +-
.../HandlerErrorEntity.java | 8 +-
.../HandlerInputEntity.java | 12 +-
.../HandlerOutputEntity.java | 8 +-
.../HandlerStatusEntity.java | 2 +-
.../WorkflowApplicationEntity.java | 2 +-
.../WorkflowConnectionEntity.java | 2 +-
.../WorkflowDataBlockEntity.java | 2 +-
.../WorkflowHandlerEntity.java | 2 +-
.../entities/appcatalog/AppEnvironmentEntity.java | 8 +-
.../appcatalog/AppModuleMappingEntity.java | 2 +-
.../appcatalog/ApplicationDeploymentEntity.java | 2 +-
.../appcatalog/ApplicationInputEntity.java | 21 +-
.../appcatalog/ApplicationInterfaceEntity.java | 4 +-
.../appcatalog/ApplicationModuleEntity.java | 8 +-
.../appcatalog/ApplicationOutputEntity.java | 15 +-
.../core/entities/appcatalog/BatchQueueEntity.java | 2 +-
.../appcatalog/BatchQueueResourcePolicyEntity.java | 16 +-
.../appcatalog/CloudJobSubmissionEntity.java | 2 +-
.../entities/appcatalog/ComputeResourceEntity.java | 2 +-
.../ComputeResourceFileSystemEntity.java | 2 +-
.../appcatalog/ComputeResourcePolicyEntity.java | 19 +-
.../ComputeResourcePreferenceEntity.java | 6 +-
.../ComputeResourceReservationEntity.java | 28 +-
.../appcatalog/DataMovementInterfaceEntity.java | 2 +-
.../entities/appcatalog/GatewayGroupsEntity.java | 8 +-
.../entities/appcatalog/GatewayProfileEntity.java | 4 +-
.../appcatalog/GlobusGkEndpointEntity.java | 2 +-
.../appcatalog/GlobusSubmissionEntity.java | 2 +-
.../appcatalog/GridftpDataMovementEntity.java | 2 +-
.../entities/appcatalog/GridftpEndpointEntity.java | 2 +-
.../appcatalog/GroupComputeResourcePrefEntity.java | 37 +-
.../appcatalog/GroupResourceProfileEntity.java | 14 +-
.../GroupSSHAccountProvisionerConfig.java | 24 +-
.../entities/appcatalog/GsisshExportEntity.java | 2 +-
.../appcatalog/GsisshPostjobcommandEntity.java | 2 +-
.../appcatalog/GsisshPrejobcommandEntity.java | 2 +-
.../appcatalog/GsisshSubmissionEntity.java | 8 +-
.../appcatalog/JobManagerCommandEntity.java | 4 +-
.../appcatalog/JobSubmissionInterfaceEntity.java | 2 +-
.../appcatalog/LibraryApendPathEntity.java | 8 +-
.../appcatalog/LibraryPrependPathEntity.java | 8 +-
.../appcatalog/LocalDataMovementEntity.java | 8 +-
.../entities/appcatalog/LocalSubmissionEntity.java | 4 +-
.../entities/appcatalog/ModuleLoadCmdEntity.java | 9 +-
.../appcatalog/ParallelismCommandEntity.java | 4 +-
.../entities/appcatalog/ParserConnectorEntity.java | 8 +-
.../appcatalog/ParserConnectorInputEntity.java | 8 +-
.../core/entities/appcatalog/ParserEntity.java | 2 +-
.../entities/appcatalog/ParserInputEntity.java | 4 +-
.../entities/appcatalog/ParserOutputEntity.java | 4 +-
.../entities/appcatalog/ParsingTemplateEntity.java | 2 +-
.../appcatalog/ParsingTemplateInputEntity.java | 6 +-
.../entities/appcatalog/PostjobCommandEntity.java | 8 +-
.../entities/appcatalog/PrejobCommandEntity.java | 8 +-
.../appcatalog/ResourceJobManagerEntity.java | 2 +-
.../SSHAccountProvisionerConfiguration.java | 4 +-
.../entities/appcatalog/ScpDataMovementEntity.java | 2 +-
.../appcatalog/SshJobSubmissionEntity.java | 4 +-
.../appcatalog/StorageInterfaceEntity.java | 2 +-
.../appcatalog/StoragePreferenceEntity.java | 4 +-
.../entities/appcatalog/StorageResourceEntity.java | 4 +-
.../appcatalog/UnicoreDatamovementEntity.java | 12 +-
.../appcatalog/UnicoreSubmissionEntity.java | 2 +-
.../UserComputeResourcePreferenceEntity.java | 2 +-
.../appcatalog/UserResourceProfileEntity.java | 2 +-
.../appcatalog/UserStoragePreferenceEntity.java | 2 +-
.../ComputationalResourceSchedulingEntity.java | 2 +-
.../core/entities/expcatalog/ExperimentEntity.java | 4 +-
.../entities/expcatalog/ExperimentErrorEntity.java | 8 +-
.../entities/expcatalog/ExperimentInputEntity.java | 14 +-
.../expcatalog/ExperimentOutputEntity.java | 10 +-
.../expcatalog/ExperimentStatusEntity.java | 4 +-
.../expcatalog/ExperimentSummaryEntity.java | 4 +-
.../core/entities/expcatalog/GatewayEntity.java | 4 +-
.../GatewayUsageReportingCommandEntity.java | 4 +-
.../entities/expcatalog/GatewayWorkerEntity.java | 2 +-
.../core/entities/expcatalog/JobEntity.java | 8 +-
.../core/entities/expcatalog/JobStatusEntity.java | 4 +-
.../entities/expcatalog/NotificationEntity.java | 2 +-
.../core/entities/expcatalog/ProcessEntity.java | 12 +-
.../entities/expcatalog/ProcessErrorEntity.java | 8 +-
.../entities/expcatalog/ProcessInputEntity.java | 14 +-
.../entities/expcatalog/ProcessOutputEntity.java | 10 +-
.../expcatalog/ProcessResourceScheduleEntity.java | 2 +-
.../entities/expcatalog/ProcessStatusEntity.java | 4 +-
.../entities/expcatalog/ProcessWorkflowEntity.java | 8 +-
.../entities/expcatalog/ProcessWorkflowPK.java | 14 +-
.../core/entities/expcatalog/ProjectEntity.java | 2 +-
.../entities/expcatalog/ProjectUserEntity.java | 2 +-
.../entities/expcatalog/QueueStatusEntity.java | 6 +-
.../core/entities/expcatalog/TaskEntity.java | 8 +-
.../core/entities/expcatalog/TaskErrorEntity.java | 8 +-
.../core/entities/expcatalog/TaskStatusEntity.java | 4 +-
.../expcatalog/UserConfigurationDataEntity.java | 4 +-
.../core/entities/expcatalog/UserEntity.java | 2 +-
.../registry/core/entities/expcatalog/UserPK.java | 4 +-
.../replicacatalog/ConfigurationEntity.java | 2 +-
.../entities/replicacatalog/DataProductEntity.java | 2 +-
.../replicacatalog/DataProductMetadataEntity.java | 2 +-
.../replicacatalog/DataReplicaLocationEntity.java | 2 +-
.../replicacatalog/DataReplicaMetadataEntity.java | 2 +-
.../workflowcatalog/ComponentStatusEntity.java | 8 +-
.../core/entities/workflowcatalog/EdgeEntity.java | 2 +-
.../core/entities/workflowcatalog/NodeEntity.java | 2 +-
.../core/entities/workflowcatalog/PortEntity.java | 2 +-
.../entities/workflowcatalog/WorkflowEntity.java | 10 +-
.../workflowcatalog/WorkflowInputEntity.java | 14 +-
.../workflowcatalog/WorkflowOutputEntity.java | 6 +-
.../workflowcatalog/WorkflowStatusEntity.java | 2 +-
.../core/repositories/AbstractRepository.java | 4 +-
.../appcatalog/AppCatAbstractRepository.java | 2 +-
.../ApplicationDeploymentRepository.java | 4 +-
.../appcatalog/ApplicationInterfaceRepository.java | 6 +-
.../appcatalog/ComputeResourceRepository.java | 6 +-
.../appcatalog/ResourceJobManagerRepository.java | 2 +-
.../expcatalog/ExpCatAbstractRepository.java | 2 +-
.../expcatalog/ExperimentSummaryRepository.java | 2 +-
.../replicacatalog/RepCatAbstractRepository.java | 2 +-
.../WorkflowCatAbstractRepository.java | 2 +-
.../core/utils/JPAUtil/AppCatalogJPAUtils.java | 4 +-
.../core/utils/JPAUtil/ExpCatalogJPAUtils.java | 4 +-
.../core/utils/JPAUtil/RepCatalogJPAUtils.java | 4 +-
.../utils/JPAUtil/WorkflowCatalogJPAUtils.java | 4 +-
.../core/utils/migration/MappingToolRunner.java | 83 +-
.../src/main/resources/META-INF/persistence.xml | 17 +-
.../mysql/airavata-server.properties | 12 +-
.../ApplicationDeploymentRepositoryTest.java | 6 +-
.../registry-server/registry-api-service/pom.xml | 1 +
.../registry-server/registry-api-stubs/pom.xml | 1 +
.../airavata/registry/api/RegistryService.java | 4216 +++++++++++++++-----
.../api/exception/RegistryServiceException.java | 4 +-
.../registry/api/registry_apiConstants.java | 2 +-
.../main/java/generators/JPAClassGenerator.java | 4 +-
.../registry/registry-tools/registry-tool/pom.xml | 10 +-
modules/security/pom.xml | 10 +-
modules/server/pom.xml | 7 +-
.../sharing-registry/sharing-data-migrator/pom.xml | 13 +-
.../sharing-registry-distribution/pom.xml | 15 +-
.../sharing-registry-server/pom.xml | 69 +-
.../sharing/registry/db/entities/DomainEntity.java | 2 +-
.../sharing/registry/db/entities/EntityEntity.java | 12 +-
.../sharing/registry/db/entities/EntityPK.java | 4 +-
.../registry/db/entities/EntityTypeEntity.java | 2 +-
.../sharing/registry/db/entities/EntityTypePK.java | 4 +-
.../registry/db/entities/GroupAdminEntity.java | 2 +-
.../sharing/registry/db/entities/GroupAdminPK.java | 4 +-
.../db/entities/GroupMembershipEntity.java | 2 +-
.../registry/db/entities/GroupMembershipPK.java | 4 +-
.../registry/db/entities/PermissionTypeEntity.java | 2 +-
.../registry/db/entities/PermissionTypePK.java | 4 +-
.../registry/db/entities/SharingEntity.java | 2 +-
.../sharing/registry/db/entities/SharingPK.java | 4 +-
.../sharing/registry/db/entities/UserEntity.java | 12 +-
.../registry/db/entities/UserGroupEntity.java | 2 +-
.../sharing/registry/db/entities/UserGroupPK.java | 4 +-
.../sharing/registry/db/entities/UserPK.java | 4 +-
.../db/repositories/AbstractRepository.java | 6 +-
.../db/repositories/SharingRepository.java | 2 +-
.../sharing/registry/db/utils/JPAUtils.java | 4 +-
.../src/main/resources/META-INF/persistence.xml | 5 +-
.../src/main/resources/airavata.jks | Bin 1410 -> 0 bytes
.../src/main/resources/client_truststore.jks | Bin 5312 -> 0 bytes
.../src/test/resources/airavata.jks | Bin 1410 -> 0 bytes
.../src/test/resources/client_truststore.jks | Bin 5312 -> 0 bytes
.../sharing-registry-stubs/pom.xml | 5 +-
.../airavata/sharing/registry/models/Domain.java | 4 +-
.../registry/models/DuplicateEntryException.java | 4 +-
.../airavata/sharing/registry/models/Entity.java | 4 +-
.../sharing/registry/models/EntitySearchField.java | 4 +-
.../sharing/registry/models/EntityType.java | 4 +-
.../sharing/registry/models/GroupAdmin.java | 4 +-
.../sharing/registry/models/GroupCardinality.java | 4 +-
.../sharing/registry/models/GroupChildType.java | 4 +-
.../sharing/registry/models/GroupMembership.java | 4 +-
.../sharing/registry/models/GroupType.java | 4 +-
.../sharing/registry/models/PermissionType.java | 4 +-
.../sharing/registry/models/SearchCondition.java | 4 +-
.../sharing/registry/models/SearchCriteria.java | 4 +-
.../airavata/sharing/registry/models/Sharing.java | 4 +-
.../registry/models/SharingRegistryException.java | 4 +-
.../sharing/registry/models/SharingType.java | 4 +-
.../airavata/sharing/registry/models/User.java | 4 +-
.../sharing/registry/models/UserGroup.java | 4 +-
.../registry/models/sharing_modelsConstants.java | 2 +-
.../service/cpi/SharingRegistryService.java | 1156 ++++--
.../registry/service/cpi/sharing_cpiConstants.java | 2 +-
pom.xml | 433 +-
.../airavata-apis/airavata_api.thrift | 6 +-
.../component-cpis/credential-store-cpi.thrift | 24 +-
.../data-models/airavata_data_models.thrift | 19 +-
...odels.thrift => credential_store_models.thrift} | 0
.../experiment_catalog_models.thrift | 9 +-
.../experiment_model.thrift | 4 +-
.../user_tenant_group_models.thrift | 10 +-
.../workflow-models/workflow_data_model.thrift | 3 +-
.../workflow_model.thrift} | 0
.../generate-thrift-stubs.sh | 41 +-
.../iam-admin-services-cpi.thrift | 2 +-
tools/load-client/pom.xml | 16 +-
.../src/main/assembly/load-client-bin-assembly.xml | 2 +-
.../src/main/resources/client_truststore.jks | Bin 5312 -> 0 bytes
536 files changed, 13915 insertions(+), 12666 deletions(-)
create mode 100644 .devcontainer/Dockerfile
create mode 100644 .devcontainer/devcontainer.json
create mode 100644 .devcontainer/docker-compose.yml
create mode 100644 .vscode/launch.json
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/appdeployment/application_deployment_modelConstants.java
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/appinterface/application_interface_modelConstants.java
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/computeresource/compute_resource_modelConstants.java
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/gatewayprofile/DataStoragePreference.java
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/appcatalog/parser/ParserDagInputMapping.java
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/credential/store/CredentialOwnerType.java
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/credential/store/SSHCredentialSummary.java
rename
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/credential/store/{credential_store_data_modelsConstants.java
=> credential_store_modelsConstants.java} (91%)
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/TaskSubmitEvent.java
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/TaskTerminateEvent.java
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/messaging/event/messaging_eventsConstants.java
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workflow/NotificationEmail.java
delete mode 100644
airavata-api/airavata-data-models/src/main/java/org/apache/airavata/model/workflow_data_modelConstants.java
create mode 100644 keystores/airavata.jks
create mode 100644 keystores/client_truststore.jks
create mode 100755 keystores/generate_keystore.sh
delete mode 120000 modules/agent-framework/agent-service/src/main/proto
create mode 100644
modules/agent-framework/deployments/jupyterhub/data/af2complex/AF2Complex_notebook.ipynb
create mode 100644
modules/commons/src/main/java/org/apache/airavata/common/utils/DBConnectionProvider.java
delete mode 100644 modules/commons/src/test/resources/mykeystore.jks
delete mode 100644
modules/credential-store/credential-store-service/src/test/resources/keystore.jks
delete mode 100644
modules/credential-store/credential-store-service/src/test/resources/mykeystore.jks
rename modules/ide-integration/{src/main/containers => }/.gitignore (100%)
delete mode 100644
modules/ide-integration/src/main/containers/docker-compose.yml
delete mode 100644
modules/ide-integration/src/main/containers/keycloak/Default-export.json
delete mode 100644
modules/ide-integration/src/main/containers/keycloak/Default-export.json.bk
create mode 100644
modules/ide-integration/src/main/containers/keycloak/keycloak.conf
create mode 100644
modules/ide-integration/src/main/containers/keycloak/realm-default.json
delete mode 100644
modules/ide-integration/src/main/containers/keycloak/standalone.xml
delete mode 100644
modules/ide-integration/src/main/resources/keystores/airavata.jks
delete mode 100644
modules/ide-integration/src/main/resources/keystores/airavata_sym.jks
delete mode 100644
modules/ide-integration/src/main/resources/keystores/client_truststore.jks
delete mode 100644
modules/sharing-registry/sharing-registry-server/src/main/resources/airavata.jks
delete mode 100644
modules/sharing-registry/sharing-registry-server/src/main/resources/client_truststore.jks
delete mode 100644
modules/sharing-registry/sharing-registry-server/src/test/resources/airavata.jks
delete mode 100644
modules/sharing-registry/sharing-registry-server/src/test/resources/client_truststore.jks
rename
thrift-interface-descriptions/data-models/credential-store-models/{credential_store_data_models.thrift
=> credential_store_models.thrift} (100%)
copy
airavata-api/airavata-client-sdks/airavata-cpp-sdk/src/main/resources/lib/thrift/thrift-config.h
=>
thrift-interface-descriptions/data-models/experiment-catalog-models/experiment_catalog_models.thrift
(89%)
mode change 100755 => 100644
copy
airavata-api/airavata-client-sdks/airavata-cpp-sdk/src/main/resources/lib/thrift/thrift-config.h
=>
thrift-interface-descriptions/data-models/user-tenant-group-models/user_tenant_group_models.thrift
(87%)
mode change 100755 => 100644
rename
thrift-interface-descriptions/data-models/{experiment-catalog-models/airavata_workflow_model.thrift
=> workflow-models/workflow_model.thrift} (100%)
delete mode 100644 tools/load-client/src/main/resources/client_truststore.jks