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
from 2eb180795d included missing license headers
add 2140e05758 add file ops to jupyter magics, cleanup code, update
agent.sh
add 9ed694f3da temp commit to get cyberfaces meeting poc
add d3562319a5 add airavata magics to dev-tools/, make airavata-agent/
build generic
add 4eb8c6d674 reorganize agent-framework related code. make
airavata-magics a python package.
add ed10663c17 revise jupyterhub spawned notebooks, add makefiles
add ceed624849 initial experiment sdk implementation
add d0df70328d improve auth flow, add python code invocation, add plan
crud apis and file ul/dl apis, reduce settings.ini deps, fix bugs
add ce8ce645b8 venv support for agent, update notebooks, show tables as
pandas df, update dir refs, fix bugs.
add a6f47785f7 refine Makefiles, move app-scripts to agent-framework/, fix
bugs in agent.go and sample Dockerfile
add 6f727d0809 regenerate thrift specs
add 2d62b9596d cleanup airavata_sdk wrappers, error-handling in
airavata_experiments
add 2cdb164be9 cleanup imports, fix bugs found by type checker
add 4acab98139 organize code, add other deployment files, partially redo
airavata_jupyter_magic for runtime switching
add ac59cdaefc rename platform x86_64 -> amd64. fix issues in cyberfaces
dockerfile. update notebooks. move environment files.
add 070b5047ee gkeyll agent image and notebook sample
add 9abac93a3c Setup complete
add 7a415a6b15 refactoring UI and responsive changes
add b9abe6ee55 Add auth to swagger
add 225ff9eca4 Support logout
add 3985e66871 Homepage + redirecting logins
add a8bd217bf2 Condense to single resource page + allow unauthenticated
routes
add 8f30d87e9f Cybershuttle.org homepage copy
add 1363ae493f update DevDataInitializer projects/paths, update the
application.yml bundled with research-service.
add 6a44933f47 ui for adding repos
add 7746ee9477 update messages in python sdk. polish messaging and flow.
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 | 133 +-
.../airavata_experiments/auth/__init__.py | 2 +-
.../airavata_experiments/auth/device_auth.py | 16 +-
.../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/task.py | 20 +-
.../airavata_jupyter_magic/__init__.py | 834 +-
.../airavata-python-sdk/pyproject.toml | 2 +-
.../airavata-python-sdk/samples/data/b4pull.pdb | 97198 ++++++++++++
.../samples/data/b4pull.restart.coor | Bin 0 -> 2332708 bytes
.../samples/data/b4pull.restart.vel | Bin 0 -> 2332708 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 | 428 +
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 +
.../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 | 20 +-
.../portal/src/components/resources/index.tsx | 179 +-
.../portal/src/layouts/NavBar.tsx | 2 +-
.../research/service/config/AuthzTokenFilter.java | 5 -
.../service/config/DevDataInitializer.java | 144 +-
.../service/controller/ProjectController.java | 57 +-
.../src/main/resources/application.yml | 28 +-
59 files changed, 349774 insertions(+), 2025 deletions(-)
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/b4pull.pdb
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/b4pull.restart.coor
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/b4pull.restart.vel
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/b4pull.restart.xsc
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/par_all36_water.prm
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/par_all36m_prot.prm
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/pull_cpu.conf
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/pull_gpu.conf
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/structure.pdb
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/data/structure.psf
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/poc.ipynb
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/settings.ini
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airavata-api/airavata-client-sdks/airavata-python-sdk/samples/smd_cpu.ipynb
delete mode 100755 modules/agent-framework/airavata-agent/agent.sh
create mode 100644 modules/agent-framework/airavata-jupyter-magic/.gitignore
create mode 100644
modules/agent-framework/airavata-jupyter-magic/airavata_jupyter_magic.py
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modules/agent-framework/airavata-jupyter-magic/pyproject.toml
create mode 100644 modules/agent-framework/deployments/agent-cerebrum/Makefile
create mode 100644
modules/agent-framework/deployments/agent-cyberfaces/Dockerfile
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modules/agent-framework/deployments/agent-cyberfaces/Makefile
create mode 100644 modules/agent-framework/deployments/agent-i-guide/Makefile
create mode 100644 modules/agent-framework/deployments/agent-md/Makefile
create mode 100644 modules/agent-framework/deployments/agent-sample/Dockerfile
create mode 100644 modules/agent-framework/deployments/agent-sample/Makefile
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modules/agent-framework/deployments/jupyterhub/Dockerfile-jl-base
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modules/agent-framework/deployments/jupyterhub/Dockerfile-jl-iguide
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modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DA3_DEM_Access_v4.ipynb
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modules/agent-framework/deployments/jupyterhub/data/cyberfaces/Solution_DP6_DEM_Processing_v2.ipynb
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modules/agent-framework/deployments/jupyterhub/data/gkeyll/plotE_z.ipynb
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modules/agent-framework/deployments/jupyterhub/jupyterhub_config.py
