This is an automated email from the ASF dual-hosted git repository.
yasith pushed a change to branch feat/server-collapse
in repository https://gitbox.apache.org/repos/asf/airavata.git
from 886c72cf16 style: apply spotless formatting
add 3420655304 refactor: consolidate 6 persistence units into single
Spring-managed EntityManagerFactory
add c0393b6313 fix: resolve Hibernate 6 entity mapping errors for @IdClass
entities
add d4ce4111bd refactor: restore non-Java modules at top level, move proto
to src/main/proto
add 6f2df6f3ea build: configure surefire to fail on first error
(skipAfterFailureCount=1)
add 72ba47c9ac fix: resolve all integration test failures for Hibernate 6
No new revisions were added by this update.
Summary of changes:
airavata-agent/.gitignore | 6 +
.../Dockerfile | 19 +-
airavata-agent/Makefile | 159 ++
airavata-agent/README.md | 235 ++
airavata-agent/agent-communication.proto | 1 +
airavata-agent/agent.go | 254 ++
airavata-agent/agent.sh | 119 +
airavata-agent/application/README.md | 19 +
airavata-agent/application/alphafold2.sh | 91 +
airavata-agent/application/gaussian16.sh | 256 +++
airavata-agent/application/gromacs.sh | 165 ++
airavata-agent/application/namd.sh | 130 ++
airavata-agent/application/pmemd_cuda.sh | 4 +
airavata-agent/application/pmemd_mpi.sh | 4 +
airavata-agent/application/psi4.sh | 4 +
airavata-agent/go.mod | 73 +
airavata-agent/kernel.py | 163 ++
airavata-agent/pkg/jupyter.go | 251 ++
airavata-agent/pkg/python.go | 54 +
airavata-agent/pkg/shell.go | 213 ++
airavata-agent/pkg/tunnel.go | 115 +
airavata-agent/pkg/types.go | 25 +
airavata-agent/protos/agent-communication.pb.go | 2419 ++++++++++++++++++++
.../protos/agent-communication_grpc.pb.go | 133 ++
airavata-api/agent-service/pom.xml | 2 +-
.../{ => src/main}/proto/agent-communication.proto | 0
.../{ => src/main}/proto/airavata-fuse.proto | 0
.../db/EntityManagerFactoryHolder.java} | 27 +-
...zer.java => EntityManagerFactoryRegistrar.java} | 29 +-
.../org/apache/airavata/common/db/JPAUtils.java | 102 -
.../compute/model/AppEnvironmentEntity.java | 5 +-
.../compute/model/AppModuleMappingEntity.java | 4 +-
.../compute/model/ApplicationInputEntity.java | 5 +-
.../compute/model/ApplicationInterfaceEntity.java | 2 +-
.../compute/model/ApplicationOutputEntity.java | 5 +-
.../airavata/compute/model/BatchQueueEntity.java | 2 +-
.../model/BatchQueueResourcePolicyEntity.java | 2 +-
.../compute/model/ComputeResourceEntity.java | 5 +-
.../model/ComputeResourceFileSystemEntity.java | 2 +-
.../compute/model/ComputeResourcePolicyEntity.java | 4 +-
.../model/ComputeResourceReservationEntity.java | 2 +-
.../model/GroupSSHAccountProvisionerConfig.java | 8 +-
.../compute/model/JobManagerCommandEntity.java | 2 +-
.../model/JobSubmissionInterfaceEntity.java | 2 +-
.../compute/model/LibraryApendPathEntity.java | 5 +-
.../compute/model/LibraryPrependPathEntity.java | 5 +-
.../compute/model/LocalSubmissionEntity.java | 2 +-
.../compute/model/ModuleLoadCmdEntity.java | 5 +-
.../compute/model/ParallelismCommandEntity.java | 2 +-
.../compute/model/ParserConnectorEntity.java | 6 +-
.../compute/model/ParserConnectorInputEntity.java | 6 +-
.../airavata/compute/model/ParserInputEntity.java | 2 +-
.../airavata/compute/model/ParserOutputEntity.java | 2 +-
.../compute/model/ParsingTemplateInputEntity.java | 4 +-
.../compute/model/PostjobCommandEntity.java | 5 +-
.../compute/model/PrejobCommandEntity.java | 5 +-
.../model/SSHAccountProvisionerConfiguration.java | 4 +-
.../model/UserComputeResourcePreferenceEntity.java | 5 +-
.../repository/AppCatAbstractRepository.java | 36 -
.../ApplicationDeploymentRepository.java | 3 +-
.../repository/ApplicationInputRepository.java | 3 +-
.../repository/ApplicationInterfaceRepository.java | 3 +-
.../repository/ApplicationModuleRepository.java | 3 +-
.../repository/ApplicationOutputRepository.java | 3 +-
.../repository/BatchQueuePolicyRepository.java | 3 +-
.../compute/repository/BatchQueueRepository.java | 3 +-
.../ComputeResourcePolicyRepository.java | 3 +-
.../repository/ComputeResourcePrefRepository.java | 3 +-
.../repository/ComputeResourceRepository.java | 44 +-
.../repository/GatewayGroupsRepository.java | 3 +-
.../repository/GroupResourceProfileRepository.java | 3 +-
.../repository/GrpComputePrefRepository.java | 3 +-
.../repository/GwyResourceProfileRepository.java | 4 +-
.../JobSubmissionInterfaceRepository.java | 4 +-
.../compute/repository/ParserInputRepository.java | 3 +-
.../compute/repository/ParserOutputRepository.java | 3 +-
.../compute/repository/ParserRepository.java | 3 +-
.../repository/ParsingTemplateRepository.java | 4 +-
.../repository/ResourceJobManagerRepository.java | 3 +-
.../UserComputeResourcePreferenceRepository.java | 3 +-
.../repository/UserResourceProfileRepository.java | 3 +-
.../ComputationalResourceSchedulingEntity.java | 2 +-
.../execution/model/ExperimentErrorEntity.java | 2 +-
.../execution/model/ExperimentInputEntity.java | 2 +-
.../execution/model/ExperimentOutputEntity.java | 2 +-
.../execution/model/ExperimentStatusEntity.java | 2 +-
.../apache/airavata/execution/model/JobEntity.java | 2 +-
.../airavata/execution/model/JobStatusEntity.java | 4 +-
.../airavata/execution/model/ProcessEntity.java | 2 +-
.../execution/model/ProcessErrorEntity.java | 2 +-
.../execution/model/ProcessInputEntity.java | 2 +-
.../execution/model/ProcessOutputEntity.java | 2 +-
.../execution/model/ProcessStatusEntity.java | 2 +-
.../execution/model/ProcessWorkflowEntity.java | 2 +-
.../execution/model/ProjectUserEntity.java | 2 +-
.../airavata/execution/model/TaskEntity.java | 2 +-
.../airavata/execution/model/TaskErrorEntity.java | 2 +-
.../airavata/execution/model/TaskStatusEntity.java | 2 +-
.../airavata/execution/model/UserEntity.java | 2 +-
.../workflow/AiravataWorkflowErrorEntity.java | 2 +-
.../workflow/AiravataWorkflowStatusEntity.java | 2 +-
.../model/workflow/ApplicationErrorEntity.java | 2 +-
.../model/workflow/ApplicationStatusEntity.java | 2 +-
.../model/workflow/HandlerErrorEntity.java | 7 +-
.../model/workflow/HandlerInputEntity.java | 7 +-
.../model/workflow/HandlerOutputEntity.java | 7 +-
.../model/workflow/HandlerStatusEntity.java | 7 +-
.../model/workflow/WorkflowApplicationEntity.java | 2 +-
.../model/workflow/WorkflowConnectionEntity.java | 4 +-
.../model/workflow/WorkflowDataBlockEntity.java | 2 +-
.../model/workflow/WorkflowHandlerEntity.java | 2 +-
.../model/workflow/WorkflowInputEntity.java | 2 +-
.../model/workflow/WorkflowOutputEntity.java | 2 +-
.../repository/ExpCatAbstractRepository.java | 36 -
.../repository/ExperimentErrorRepository.java | 3 +-
.../repository/ExperimentInputRepository.java | 3 +-
.../repository/ExperimentOutputRepository.java | 3 +-
.../execution/repository/ExperimentRepository.java | 3 +-
.../repository/ExperimentStatusRepository.java | 3 +-
.../repository/ExperimentSummaryRepository.java | 3 +-
.../execution/repository/GatewayRepository.java | 3 +-
.../GatewayUsageReportingCommandRepository.java | 3 +-
.../execution/repository/JobRepository.java | 3 +-
.../execution/repository/JobStatusRepository.java | 3 +-
.../repository/NotificationRepository.java | 3 +-
.../repository/ProcessErrorRepository.java | 3 +-
.../repository/ProcessInputRepository.java | 3 +-
.../repository/ProcessOutputRepository.java | 3 +-
.../execution/repository/ProcessRepository.java | 22 +-
.../repository/ProcessStatusRepository.java | 4 +-
.../repository/ProcessWorkflowRepository.java | 3 +-
.../execution/repository/ProjectRepository.java | 3 +-
.../repository/QueueStatusRepository.java | 3 +-
.../execution/repository/TaskErrorRepository.java | 3 +-
.../execution/repository/TaskRepository.java | 14 +-
.../execution/repository/TaskStatusRepository.java | 3 +-
.../execution/repository/UserRepository.java | 3 +-
.../repository/WorkflowCatAbstractRepository.java | 36 -
.../execution/repository/WorkflowRepository.java | 3 +-
.../execution/util/AbstractRepository.java | 100 +-
.../execution/util/AppCatalogDBInitConfig.java | 2 +-
.../execution/util/AppCatalogJDBCConfig.java | 65 -
.../execution/util/AppCatalogJPAUtils.java | 49 -
.../execution/util/ExpCatalogDBInitConfig.java | 2 +-
.../execution/util/ExpCatalogJDBCConfig.java | 65 -
.../execution/util/ExpCatalogJPAUtils.java | 46 -
.../airavata/execution/util/QueryConstants.java | 2 +-
.../execution/util/RepCatalogJPAUtils.java | 49 -
.../execution/util/ReplicaCatalogDBInitConfig.java | 2 +-
.../execution/util/ReplicaCatalogJDBCConfig.java | 65 -
.../util/WorkflowCatalogDBInitConfig.java | 2 +-
.../execution/util/WorkflowCatalogJDBCConfig.java | 65 -
.../execution/util/WorkflowCatalogJPAUtils.java | 47 -
.../commons/repositories/AbstractRepository.java | 37 +-
.../commons/tenant/entities/GatewayEntity.java | 2 +-
.../user/entities/NSFDemographicsEntity.java | 2 +-
.../commons/user/entities/UserProfileEntity.java | 2 +-
.../security/profile/commons/utils/JPAUtils.java | 63 -
.../commons/utils/ProfileServiceJDBCConfig.java | 50 -
.../profile/commons/utils/QueryConstants.java | 6 +-
.../core/repositories/UserProfileRepository.java | 3 +-
.../core/utils/UserProfileCatalogDBInitConfig.java | 2 +-
.../core/utils/UserProfileCatalogJDBCConfig.java | 51 -
.../airavata/sharing/model/GroupAdminEntity.java | 4 +-
.../apache/airavata/sharing/model/UserEntity.java | 2 +-
.../airavata/sharing/model/UserGroupEntity.java | 2 +-
.../sharing/repository/AbstractRepository.java | 30 +-
.../sharing/repository/EntityRepository.java | 22 +-
.../repository/GroupMembershipRepository.java | 3 +-
.../sharing/repository/UserRepository.java | 4 +-
.../sharing/util/SharingRegistryDBInitConfig.java | 2 +-
.../sharing/util/SharingRegistryJDBCConfig.java | 66 -
.../storage/model/DataMovementInterfaceEntity.java | 2 +-
.../airavata/storage/model/DataProductEntity.java | 2 +-
.../storage/model/DataReplicaLocationEntity.java | 4 +-
.../storage/model/GridftpEndpointEntity.java | 2 +-
.../storage/model/StorageInterfaceEntity.java | 2 +-
.../storage/model/UserStoragePreferenceEntity.java | 5 +-
.../storage/repository/DataMovementRepository.java | 4 +-
.../storage/repository/DataProductRepository.java | 32 +-
.../repository/DataReplicaLocationRepository.java | 24 +-
.../repository/RepCatAbstractRepository.java | 36 -
.../storage/repository/StoragePrefRepository.java | 4 +-
.../repository/StorageResourceRepository.java | 4 +-
.../UserStoragePreferenceRepository.java | 4 +-
.../execution/util/common/SharedMariaDB.java | 29 +-
.../SharedMariaDBLauncherSessionListener.java | 2 +-
.../DataReplicaLocationRepositoryTest.java | 13 +-
.../src/test/resources/META-INF/persistence.xml | 176 ++
airavata-fuse/.gitignore | 4 +
.../bin/file-service.sh => airavata-fuse/Makefile | 30 +-
.../test.txt => airavata-fuse/README.md | 23 +-
airavata-fuse/src/grpcfs/adapters.go | 81 +
airavata-fuse/src/grpcfs/fs.go | 249 ++
airavata-fuse/src/grpcfs/go.mod | 18 +
airavata-fuse/src/grpcfs/go.sum | 33 +
airavata-fuse/src/grpcfs/grpc.go | 129 ++
airavata-fuse/src/grpcfs/inode.go | 166 ++
airavata-fuse/src/grpcfs/pb/grpcfs.pb.go | 2319 +++++++++++++++++++
airavata-fuse/src/grpcfs/pb/grpcfs_grpc.pb.go | 396 ++++
airavata-fuse/src/grpcfs_client/go.mod | 19 +
airavata-fuse/src/grpcfs_client/go.sum | 32 +
airavata-fuse/src/grpcfs_client/main.go | 82 +
airavata-fuse/src/grpcfs_server/go.mod | 20 +
airavata-fuse/src/grpcfs_server/go.sum | 26 +
airavata-fuse/src/grpcfs_server/main.go | 239 ++
airavata-fuse/src/proto/grpcfs.proto | 137 ++
airavata-jupyterhub/Dockerfile | 14 +
airavata-jupyterhub/custom_templates/login.html | 52 +
airavata-jupyterhub/docker-compose.yaml | 24 +
airavata-jupyterhub/jupyterhub_config.py | 139 ++
airavata-jupyterhub/user-container/Dockerfile | 12 +
airavata-jupyterhub/user-container/Makefile | 3 +
airavata-jupyterhub/user-container/init.sh | 28 +
.../apache/airavata/server/AiravataServerMain.java | 2 +-
airavata-server/src/main/resources/application.yml | 3 +
dev-tools/simexr_mod/.gitignore | 199 ++
dev-tools/simexr_mod/FINAL_REPORT.md | 144 ++
dev-tools/simexr_mod/README.md | 450 ++++
dev-tools/simexr_mod/api/__init__.py | 13 +
dev-tools/simexr_mod/api/config.py | 34 +
dev-tools/simexr_mod/api/dependencies.py | 63 +
dev-tools/simexr_mod/api/main.py | 115 +
dev-tools/simexr_mod/api/models.py | 182 ++
dev-tools/simexr_mod/api/routers/__init__.py | 1 +
dev-tools/simexr_mod/api/routers/database.py | 438 ++++
dev-tools/simexr_mod/api/routers/health.py | 407 ++++
dev-tools/simexr_mod/api/routers/reasoning.py | 268 +++
dev-tools/simexr_mod/api/routers/simulation.py | 510 +++++
dev-tools/simexr_mod/app.py | 1071 +++++++++
dev-tools/simexr_mod/code/__init__.py | 8 +
dev-tools/simexr_mod/code/extract/llm_extract.py | 131 ++
dev-tools/simexr_mod/code/helpers/ast_helpers.py | 116 +
.../simexr_mod/code/helpers/locate_helpers.py | 44 +
.../simexr_mod/code/inject/inject_overrides.py | 137 ++
dev-tools/simexr_mod/code/locate/locate.py | 27 +
.../simexr_mod/code/locate/param_usage_visitor.py | 70 +
dev-tools/simexr_mod/code/models/param_ref.py | 10 +
dev-tools/simexr_mod/code/refactor/llm_refactor.py | 99 +
dev-tools/simexr_mod/code/test/__init__.py | 5 +
.../simexr_mod/code/test/simulation_refiner.py | 46 +
dev-tools/simexr_mod/code/utils/github_utils.py | 26 +
dev-tools/simexr_mod/code/utils/notebook_utils.py | 36 +
dev-tools/simexr_mod/config.yaml.example | 15 +
dev-tools/simexr_mod/core/__init__.py | 1 +
dev-tools/simexr_mod/core/interfaces.py | 224 ++
dev-tools/simexr_mod/core/parser.py | 65 +
dev-tools/simexr_mod/core/patterns.py | 686 ++++++
dev-tools/simexr_mod/core/services.py | 691 ++++++
dev-tools/simexr_mod/db/__init__.py | 174 ++
dev-tools/simexr_mod/db/base.py | 117 +
dev-tools/simexr_mod/db/config/__init__.py | 5 +
dev-tools/simexr_mod/db/config/database.py | 63 +
dev-tools/simexr_mod/db/models/__init__.py | 6 +
dev-tools/simexr_mod/db/models/base.py | 34 +
dev-tools/simexr_mod/db/models/simulation.py | 43 +
dev-tools/simexr_mod/db/repositories/__init__.py | 7 +
dev-tools/simexr_mod/db/repositories/base.py | 43 +
dev-tools/simexr_mod/db/repositories/reasoning.py | 24 +
dev-tools/simexr_mod/db/repositories/simulation.py | 114 +
dev-tools/simexr_mod/db/services/__init__.py | 7 +
dev-tools/simexr_mod/db/services/reasoning.py | 29 +
dev-tools/simexr_mod/db/services/results.py | 147 ++
dev-tools/simexr_mod/db/services/store.py | 127 +
dev-tools/simexr_mod/db/utils/__init__.py | 7 +
dev-tools/simexr_mod/db/utils/hash_utils.py | 24 +
dev-tools/simexr_mod/db/utils/json_utils.py | 78 +
dev-tools/simexr_mod/db/utils/transform_utils.py | 87 +
dev-tools/simexr_mod/execute/__init__.py | 84 +
dev-tools/simexr_mod/execute/base.py | 80 +
dev-tools/simexr_mod/execute/loader/__init__.py | 6 +
.../simexr_mod/execute/loader/simulate_loader.py | 55 +
.../simexr_mod/execute/loader/transform_code.py | 83 +
dev-tools/simexr_mod/execute/logging/__init__.py | 5 +
dev-tools/simexr_mod/execute/logging/run_logger.py | 51 +
dev-tools/simexr_mod/execute/model/__init__.py | 5 +
.../simexr_mod/execute/model/smoke_test_result.py | 7 +
.../simexr_mod/execute/persistence/__init__.py | 5 +
.../simexr_mod/execute/persistence/save_script.py | 34 +
dev-tools/simexr_mod/execute/run/__init__.py | 6 +
dev-tools/simexr_mod/execute/run/batch_runner.py | 89 +
.../simexr_mod/execute/run/simulation_runner.py | 170 ++
dev-tools/simexr_mod/execute/test/__init__.py | 8 +
dev-tools/simexr_mod/execute/test/fix_agent.py | 57 +
.../simexr_mod/execute/test/simulation_refiner.py | 61 +
dev-tools/simexr_mod/execute/test/smoke_tester.py | 45 +
dev-tools/simexr_mod/execute/utils/__init__.py | 17 +
.../simexr_mod/execute/utils/black_formatter.py | 24 +
.../simexr_mod/execute/utils/error_context.py | 30 +
dev-tools/simexr_mod/execute/utils/json_utlils.py | 30 +
dev-tools/simexr_mod/execute/utils/model_utils.py | 42 +
dev-tools/simexr_mod/execute/utils/python_utils.py | 32 +
.../execute/utils/requirements_manager.py | 65 +
dev-tools/simexr_mod/llm/local_llm.py | 52 +
dev-tools/simexr_mod/llm/prompt_templates.py | 192 ++
dev-tools/simexr_mod/pages/param_annotations.py | 453 ++++
dev-tools/simexr_mod/reasoning/__init__.py | 81 +
dev-tools/simexr_mod/reasoning/agent/__init__.py | 5 +
dev-tools/simexr_mod/reasoning/agent/loop.py | 266 +++
dev-tools/simexr_mod/reasoning/base.py | 94 +
dev-tools/simexr_mod/reasoning/config/__init__.py | 5 +
dev-tools/simexr_mod/reasoning/config/tools.py | 76 +
dev-tools/simexr_mod/reasoning/helpers/__init__.py | 6 +
.../simexr_mod/reasoning/helpers/chat_utils.py | 27 +
dev-tools/simexr_mod/reasoning/helpers/prompts.py | 29 +
.../simexr_mod/reasoning/messages/__init__.py | 7 +
.../simexr_mod/reasoning/messages/llm_client.py | 7 +
dev-tools/simexr_mod/reasoning/messages/model.py | 8 +
.../simexr_mod/reasoning/messages/openai_client.py | 36 +
dev-tools/simexr_mod/reasoning/model/__init__.py | 5 +
.../simexr_mod/reasoning/model/reasoning_result.py | 10 +
dev-tools/simexr_mod/reasoning/tools/__init__.py | 7 +
.../simexr_mod/reasoning/tools/final_answer.py | 58 +
.../simexr_mod/reasoning/tools/python_exec.py | 167 ++
.../simexr_mod/reasoning/tools/simulate_exec.py | 132 ++
dev-tools/simexr_mod/reasoning/utils/__init__.py | 8 +
.../simexr_mod/reasoning/utils/extract_code_map.py | 20 +
dev-tools/simexr_mod/reasoning/utils/history.py | 26 +
dev-tools/simexr_mod/reasoning/utils/json_utils.py | 9 +
.../simexr_mod/reasoning/utils/load_results.py | 56 +
dev-tools/simexr_mod/requirements.txt | 43 +
dev-tools/simexr_mod/setup.sh | 128 ++
dev-tools/simexr_mod/start_api.py | 89 +
dev-tools/simexr_mod/start_streamlit.py | 87 +
dev-tools/simexr_mod/test_all_apis.py | 405 ++++
dev-tools/simexr_mod/utils/config.py | 153 ++
dev-tools/simexr_mod/utils/logger.py | 11 +
dev-tools/simexr_mod/utils/openai_config.py | 50 +
pom.xml | 2 +
329 files changed, 21254 insertions(+), 1243 deletions(-)
create mode 100644 airavata-agent/.gitignore
copy dev-tools/ansible/roles/api-orch/tasks/haproxy/install_deps_Centos_7.yml
=> airavata-agent/Dockerfile (73%)
create mode 100644 airavata-agent/Makefile
create mode 100644 airavata-agent/README.md
create mode 120000 airavata-agent/agent-communication.proto
create mode 100644 airavata-agent/agent.go
create mode 100755 airavata-agent/agent.sh
create mode 100644 airavata-agent/application/README.md
create mode 100644 airavata-agent/application/alphafold2.sh
create mode 100644 airavata-agent/application/gaussian16.sh
create mode 100644 airavata-agent/application/gromacs.sh
create mode 100644 airavata-agent/application/namd.sh
create mode 100644 airavata-agent/application/pmemd_cuda.sh
create mode 100644 airavata-agent/application/pmemd_mpi.sh
create mode 100644 airavata-agent/application/psi4.sh
create mode 100644 airavata-agent/go.mod
create mode 100644 airavata-agent/kernel.py
create mode 100644 airavata-agent/pkg/jupyter.go
create mode 100644 airavata-agent/pkg/python.go
create mode 100644 airavata-agent/pkg/shell.go
create mode 100644 airavata-agent/pkg/tunnel.go
create mode 100644 airavata-agent/pkg/types.go
create mode 100644 airavata-agent/protos/agent-communication.pb.go
create mode 100644 airavata-agent/protos/agent-communication_grpc.pb.go
rename airavata-api/agent-service/{ =>
src/main}/proto/agent-communication.proto (100%)
rename airavata-api/agent-service/{ => src/main}/proto/airavata-fuse.proto
(100%)
rename
airavata-api/src/main/java/org/apache/airavata/{sharing/util/JPAUtils.java =>
common/db/EntityManagerFactoryHolder.java} (61%)
copy
airavata-api/src/main/java/org/apache/airavata/common/db/{DBInitializer.java =>
EntityManagerFactoryRegistrar.java} (54%)
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/common/db/JPAUtils.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/compute/repository/AppCatAbstractRepository.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/execution/repository/ExpCatAbstractRepository.java
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airavata-api/src/main/java/org/apache/airavata/execution/repository/WorkflowCatAbstractRepository.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/execution/util/AppCatalogJDBCConfig.java
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airavata-api/src/main/java/org/apache/airavata/execution/util/AppCatalogJPAUtils.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/execution/util/ExpCatalogJDBCConfig.java
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airavata-api/src/main/java/org/apache/airavata/execution/util/ExpCatalogJPAUtils.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/execution/util/RepCatalogJPAUtils.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/execution/util/ReplicaCatalogJDBCConfig.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/execution/util/WorkflowCatalogJDBCConfig.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/execution/util/WorkflowCatalogJPAUtils.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/security/profile/commons/utils/JPAUtils.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/security/profile/commons/utils/ProfileServiceJDBCConfig.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/security/profile/user/core/utils/UserProfileCatalogJDBCConfig.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/sharing/util/SharingRegistryJDBCConfig.java
delete mode 100644
airavata-api/src/main/java/org/apache/airavata/storage/repository/RepCatAbstractRepository.java
create mode 100644 airavata-api/src/test/resources/META-INF/persistence.xml
create mode 100644 airavata-fuse/.gitignore
copy
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