[23.1] Fix DataResult type

[mvdbeek]

None isn't valid for List[Any].
Fixes:

ValidationError

1 validation error for DataResult
data
  Input should be a valid list [type=list_type, input_value=None, input_type=NoneType]
    For further information visit https://errors.pydantic.dev/2.5/v/list_type

from https://sentry.galaxyproject.org/share/issue/ed6da4c9029649cc9cc4b9a30e5144fe/

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[davelopez]

Ouch... I wonder why mypy didn't complain about this... 🤔
Sorry about that.

[ahmedhamidawan]

It is still possible to get this error:

File "./galaxy/lib/galaxy/webapps/galaxy/services/datasets.py", line 910, in _data
    stats = indexer.get_data(chrom, low, high, stats=True)
AttributeError: 'NoneType' object has no attribute 'get_data'

in case

indexer = self.data_provider_registry.get_data_provider(trans, original_dataset=dataset, source="index")

produces indexer = None
Is that expected behavior or should we be considering that case?

[mvdbeek]

I don't know, what's the stack trace ? It's probably a good idea to raise a RequestInvalidException or something like this if there's no indexer for a given dataset.

[ahmedhamidawan]

For the api call:

/api/datasets/f158df71bb77bb86?data_type=data&chrom=tb_ncbiRefSeq&low=0&high=50

You get:

Traceback (most recent call last):
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/uvicorn/protocols/http/h11_impl.py", line 412, in run_asgi
    |     result = await app(  # type: ignore[func-returns-value]
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/uvicorn/middleware/proxy_headers.py", line 84, in __call__
    |     return await self.app(scope, receive, send)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/fastapi/applications.py", line 1054, in __call__
    |     await super().__call__(scope, receive, send)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/applications.py", line 123, in __call__
    |     await self.middleware_stack(scope, receive, send)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/middleware/errors.py", line 186, in __call__
    |     raise exc
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/middleware/errors.py", line 164, in __call__
    |     await self.app(scope, receive, _send)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette_context/middleware/raw_middleware.py", line 92, in __call__
    |     await self.app(scope, receive, send_wrapper)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/middleware/base.py", line 189, in __call__
    |     with collapse_excgroups():
    |   File "/usr/lib/python3.10/contextlib.py", line 153, in __exit__
    |     self.gen.throw(typ, value, traceback)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/_utils.py", line 93, in collapse_excgroups
    |     raise exc
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/middleware/base.py", line 191, in __call__
    |     response = await self.dispatch_func(request, call_next)
    |   File "/home/ahmedhamidawan/repos/galaxy/lib/galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options
    |     response = await call_next(request)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/middleware/base.py", line 165, in call_next
    |     raise app_exc
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/middleware/base.py", line 151, in coro
    |     await self.app(scope, receive_or_disconnect, send_no_error)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/middleware/exceptions.py", line 62, in __call__
    |     await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
    |     raise exc
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
    |     await app(scope, receive, sender)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/routing.py", line 758, in __call__
    |     await self.middleware_stack(scope, receive, send)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/routing.py", line 778, in app
    |     await route.handle(scope, receive, send)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/routing.py", line 299, in handle
    |     await self.app(scope, receive, send)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/routing.py", line 79, in app
    |     await wrap_app_handling_exceptions(app, request)(scope, receive, send)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/_exception_handler.py", line 64, in wrapped_app
    |     raise exc
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/_exception_handler.py", line 53, in wrapped_app
    |     await app(scope, receive, sender)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/routing.py", line 74, in app
    |     response = await func(request)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/fastapi/routing.py", line 278, in app
    |     raw_response = await run_endpoint_function(
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/fastapi/routing.py", line 193, in run_endpoint_function
    |     return await run_in_threadpool(dependant.call, **values)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/starlette/concurrency.py", line 42, in run_in_threadpool
    |     return await anyio.to_thread.run_sync(func, *args)
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/anyio/to_thread.py", line 56, in run_sync
    |     return await get_async_backend().run_sync_in_worker_thread(
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/anyio/_backends/_asyncio.py", line 2144, in run_sync_in_worker_thread
    |     return await future
    |   File "/home/ahmedhamidawan/repos/galaxy/.venv/lib/python3.10/site-packages/anyio/_backends/_asyncio.py", line 851, in run
    |     result = context.run(func, *args)
    |   File "/home/ahmedhamidawan/repos/galaxy/lib/galaxy/webapps/galaxy/api/datasets.py", line 445, in show
    |     return self.service.show(trans, dataset_id, hda_ldda, serialization_params, data_type, **extra_params)
    |   File "/home/ahmedhamidawan/repos/galaxy/lib/galaxy/webapps/galaxy/services/datasets.py", line 381, in show
    |     rval = self._data(trans, dataset, **extra_params)
    |   File "/home/ahmedhamidawan/repos/galaxy/lib/galaxy/webapps/galaxy/services/datasets.py", line 910, in _data
    |     stats = indexer.get_data(chrom, low, high, stats=True)
    | AttributeError: 'NoneType' object has no attribute 'get_data'

I think at the very least, we should raise the RequestInvalidException or something similar like you said instead of it just being an Internal Server Error. I can do that in a PR if needed?

[mvdbeek]

Sounds good to me, thank you!