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Posted to commits@airavata.apache.org by la...@apache.org on 2025/05/22 12:58:22 UTC
(airavata) branch cybershuttle-staging updated (0a4ac25c2b -> 2eb180795d)
This is an automated email from the ASF dual-hosted git repository.
lahirujayathilake pushed a change to branch cybershuttle-staging
in repository https://gitbox.apache.org/repos/asf/airavata.git
omit 0a4ac25c2b update messages in python sdk. polish messaging and flow.
omit 1e1a4721b0 ui for adding repos
omit daf4f86054 update DevDataInitializer projects/paths, update the application.yml bundled with research-service.
omit 156257d9b1 Condense to single resource page + allow unauthenticated routes
omit 1c6b505132 Homepage + redirecting logins
omit c0f9ea0606 Support logout
omit 2b46e574d7 Add auth to swagger
omit 18411f75fc refactoring UI and responsive changes
omit f9597dee62 rename platform x86_64 -> amd64. fix issues in cyberfaces dockerfile. update notebooks. move environment files.
omit 7f5b6064f8 organize code, add other deployment files, partially redo airavata_jupyter_magic for runtime switching
omit 17d5431256 cleanup airavata_sdk wrappers, error-handling in airavata_experiments
omit e89254ac66 regenerate thrift specs
omit 078513067f refine Makefiles, move app-scripts to agent-framework/, fix bugs in agent.go and sample Dockerfile
omit e895397580 venv support for agent, update notebooks, show tables as pandas df, update dir refs, fix bugs.
omit dd95d0e1f2 initial experiment sdk implementation
omit b8b14141c6 revise jupyterhub spawned notebooks, add makefiles
omit 0a487c3007 reorganize agent-framework related code. make airavata-magics a python package.
omit 6ff5872519 add airavata magics to dev-tools/, make airavata-agent/ build generic
omit 88538e5a94 included license headers in research service sources
omit 7746ee9477 update messages in python sdk. polish messaging and flow.
omit 6a44933f47 ui for adding repos
omit 1363ae493f update DevDataInitializer projects/paths, update the application.yml bundled with research-service.
omit 8f30d87e9f Cybershuttle.org homepage copy
omit a8bd217bf2 Condense to single resource page + allow unauthenticated routes
omit 3985e66871 Homepage + redirecting logins
omit 225ff9eca4 Support logout
omit b9abe6ee55 Add auth to swagger
omit 7a415a6b15 refactoring UI and responsive changes
omit 9abac93a3c Setup complete
omit 070b5047ee gkeyll agent image and notebook sample
omit ac59cdaefc rename platform x86_64 -> amd64. fix issues in cyberfaces dockerfile. update notebooks. move environment files.
omit 4acab98139 organize code, add other deployment files, partially redo airavata_jupyter_magic for runtime switching
omit 2cdb164be9 cleanup imports, fix bugs found by type checker
omit 2d62b9596d cleanup airavata_sdk wrappers, error-handling in airavata_experiments
omit 6f727d0809 regenerate thrift specs
omit a6f47785f7 refine Makefiles, move app-scripts to agent-framework/, fix bugs in agent.go and sample Dockerfile
omit ce8ce645b8 venv support for agent, update notebooks, show tables as pandas df, update dir refs, fix bugs.
omit d0df70328d improve auth flow, add python code invocation, add plan crud apis and file ul/dl apis, reduce settings.ini deps, fix bugs
omit ceed624849 initial experiment sdk implementation
omit ed10663c17 revise jupyterhub spawned notebooks, add makefiles
omit 4eb8c6d674 reorganize agent-framework related code. make airavata-magics a python package.
omit d3562319a5 add airavata magics to dev-tools/, make airavata-agent/ build generic
omit 9ed694f3da temp commit to get cyberfaces meeting poc
omit 2140e05758 add file ops to jupyter magics, cleanup code, update agent.sh
This update removed existing revisions from the reference, leaving the
reference pointing at a previous point in the repository history.
* -- * -- N refs/heads/cybershuttle-staging (2eb180795d)
\
O -- O -- O (0a4ac25c2b)
Any revisions marked "omit" are not gone; other references still
refer to them. Any revisions marked "discard" are gone forever.
No new revisions were added by this update.
Summary of changes:
.../airavata-python-sdk/.gitignore | 5 +-
.../airavata_experiments/__init__.py | 124 +-
.../airavata_experiments/airavata.py | 138 +-
.../airavata_experiments/auth/__init__.py | 2 +-
.../airavata_experiments/auth/device_auth.py | 216 +-
.../airavata_experiments/base.py | 18 +-
.../airavata_experiments/md/__init__.py | 11 +-
.../airavata_experiments/md/applications.py | 183 +-
.../airavata_experiments/plan.py | 46 +-
.../airavata_experiments/runtime.py | 248 +-
.../airavata_experiments/sftp.py | 112 +-
.../airavata_experiments/task.py | 54 +-
.../airavata_jupyter_magic/__init__.py | 834 +-
.../airavata_sdk/clients/api_server_client.py | 28 +-
.../clients/credential_store_client.py | 26 +-
.../airavata_sdk/clients/file_handling_client.py | 9 +-
.../airavata_sdk/clients/group_manager_client.py | 23 +-
.../airavata_sdk/clients/iam_admin_client.py | 25 +-
.../airavata_sdk/clients/keycloak_token_fetcher.py | 83 +-
.../clients/sftp_file_handling_client.py | 10 +-
.../clients/sharing_registry_client.py | 23 +-
.../airavata_sdk/clients/tenant_profile_client.py | 23 +-
.../airavata_sdk/clients/user_profile_client.py | 22 +-
.../clients/utils/api_server_client_util.py | 34 +-
.../clients/utils/data_model_creation_util.py | 75 +-
.../clients/utils/experiment_handler_util.py | 70 +-
.../airavata_sdk/transport/settings.py | 17 +-
.../airavata-python-sdk/pyproject.toml | 2 +-
.../airavata-python-sdk/samples/annotations.py | 70 -
.../airavata-python-sdk/samples/data/b4pull.pdb | 97198 ------------
.../samples/data/b4pull.restart.coor | Bin 2332708 -> 0 bytes
.../samples/data/b4pull.restart.vel | Bin 2332708 -> 0 bytes
.../samples/data/b4pull.restart.xsc | 3 -
.../samples/data/par_all36_water.prm | 115 -
.../samples/data/par_all36m_prot.prm | 3435 -
.../airavata-python-sdk/samples/data/pull_cpu.conf | 100 -
.../airavata-python-sdk/samples/data/pull_gpu.conf | 100 -
.../airavata-python-sdk/samples/data/structure.pdb | 97198 ------------
.../airavata-python-sdk/samples/data/structure.psf | 147335 ------------------
.../airavata-python-sdk/samples/poc.ipynb | 384 -
.../airavata-python-sdk/samples/settings.ini | 17 -
.../airavata-python-sdk/samples/smd_cpu.ipynb | 401 -
modules/agent-framework/airavata-agent/Dockerfile | 20 +
modules/agent-framework/airavata-agent/agent.go | 624 +-
modules/agent-framework/airavata-agent/agent.sh | 123 +
.../airavata-jupyter-magic/.gitignore | 2 -
.../airavata_jupyter_magic.py | 617 -
.../airavata-jupyter-magic/pyproject.toml | 30 -
.../deployments/agent-cerebrum/Makefile | 10 -
.../deployments/agent-cyberfaces/Dockerfile | 55 -
.../deployments/agent-cyberfaces/Makefile | 17 -
.../deployments/agent-i-guide/Makefile | 10 -
.../agent-framework/deployments/agent-md/Makefile | 10 -
.../deployments/agent-sample/Dockerfile | 9 -
.../deployments/agent-sample/Makefile | 10 -
.../deployments/jupyterhub/Dockerfile-jl-base | 28 -
.../deployments/jupyterhub/Dockerfile-jl-iguide | 30 -
.../cyberfaces/Solution_DA3_DEM_Access_v4.ipynb | 601 -
.../Solution_DP6_DEM_Processing_v2.ipynb | 882 -
.../jupyterhub/data/gkeyll/plotE_z.ipynb | 157 -
.../deployments/jupyterhub/jupyterhub_config.py | 71 -
modules/research-framework/pom.xml | 18 -
.../research-framework/portal/package-lock.json | 15 +-
modules/research-framework/portal/package.json | 1 +
modules/research-framework/portal/src/App.tsx | 2 +
.../portal/src/components/add/AddGitUrl.tsx | 30 +-
.../portal/src/components/add/AddRepoMaster.tsx | 21 +-
.../src/components/auth/ProtectedComponent.tsx | 5 -
.../portal/src/components/auth/UserMenu.tsx | 29 +-
.../src/components/home/CybershuttleLanding.tsx | 236 +-
.../portal/src/components/resources/index.tsx | 179 +-
.../portal/src/layouts/NavBar.tsx | 2 +-
.../compose/user-container/bootstrap.sh | 1 +
.../research-framework/research-service/README.md | 19 -
.../research-framework/research-service/pom.xml | 18 -
.../airavata/research/service/AiravataService.java | 17 +-
.../service/ResearchServiceApplication.java | 17 +-
.../research/service/config/AuthzTokenFilter.java | 22 +-
.../service/config/DevDataInitializer.java | 144 +-
.../research/service/config/OpenApiConfig.java | 19 -
.../controller/GlobalExceptionController.java | 17 +-
.../service/controller/ProjectController.java | 58 +-
.../service/controller/ResearchHubController.java | 17 +-
.../service/controller/ResourceController.java | 17 +-
.../service/controller/SessionController.java | 19 -
.../research/service/dto/CreateProjectRequest.java | 19 -
.../service/dto/CreateResourceRequest.java | 19 -
.../service/dto/ModifyResourceRequest.java | 19 -
.../research/service/dto/RedirectResponse.java | 19 -
.../research/service/dto/ResourceResponse.java | 19 -
.../research/service/enums/PrivacyEnum.java | 19 -
.../research/service/enums/ResourceTypeEnum.java | 19 -
.../research/service/enums/SessionStatusEnum.java | 19 -
.../research/service/enums/StatusEnum.java | 19 -
.../research/service/exception/ErrorResponse.java | 19 -
.../service/exception/GlobalExceptionHandler.java | 19 -
.../research/service/handlers/ProjectHandler.java | 17 +-
.../service/handlers/ResearchHubHandler.java | 17 +-
.../research/service/handlers/ResourceHandler.java | 17 +-
.../research/service/handlers/SessionHandler.java | 17 +-
.../research/service/model/UserContext.java | 17 +-
.../service/model/entity/DatasetResource.java | 17 +-
.../service/model/entity/ModelResource.java | 17 +-
.../service/model/entity/NotebookResource.java | 17 +-
.../research/service/model/entity/Project.java | 17 +-
.../service/model/entity/RepositoryResource.java | 17 +-
.../research/service/model/entity/Resource.java | 17 +-
.../research/service/model/entity/Session.java | 17 +-
.../research/service/model/entity/Tag.java | 17 +-
.../service/model/repo/ProjectRepository.java | 17 +-
.../service/model/repo/ResourceRepository.java | 17 +-
.../service/model/repo/SessionRepository.java | 17 +-
.../research/service/model/repo/TagRepository.java | 17 +-
.../src/main/proto/research-service.proto | 20 -
.../src/main/resources/application.yml | 44 +-
.../resources/distribution/conf/application.yml | 16 -
116 files changed, 2905 insertions(+), 350719 deletions(-)
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/annotations.py
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/b4pull.pdb
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/b4pull.restart.coor
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/b4pull.restart.vel
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/b4pull.restart.xsc
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/par_all36_water.prm
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/par_all36m_prot.prm
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/pull_cpu.conf
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/pull_gpu.conf
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/structure.pdb
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/structure.psf
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/poc.ipynb
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/settings.ini
delete mode 100644 airavata-api/airavata-client-sdks/airavata-python-sdk/samples/smd_cpu.ipynb
create mode 100755 modules/agent-framework/airavata-agent/agent.sh
delete mode 100644 modules/agent-framework/airavata-jupyter-magic/.gitignore
delete mode 100644 modules/agent-framework/airavata-jupyter-magic/airavata_jupyter_magic.py
delete mode 100644 modules/agent-framework/airavata-jupyter-magic/pyproject.toml
delete mode 100644 modules/agent-framework/deployments/agent-cerebrum/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-cyberfaces/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-cyberfaces/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-i-guide/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-md/Makefile
delete mode 100644 modules/agent-framework/deployments/agent-sample/Dockerfile
delete mode 100644 modules/agent-framework/deployments/agent-sample/Makefile
delete mode 100644 modules/agent-framework/deployments/jupyterhub/Dockerfile-jl-base
delete mode 100644 modules/agent-framework/deployments/jupyterhub/Dockerfile-jl-iguide
delete mode 100644 modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DA3_DEM_Access_v4.ipynb
delete mode 100644 modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DP6_DEM_Processing_v2.ipynb
delete mode 100644 modules/agent-framework/deployments/jupyterhub/data/gkeyll/plotE_z.ipynb
delete mode 100644 modules/agent-framework/deployments/jupyterhub/jupyterhub_config.py
create mode 100644 modules/research-framework/research-hub/compose/user-container/bootstrap.sh