Replace tuswsgi with tuspyserver

[mvdbeek]

This should resolve #21031 ... not having a middleware implementation of tus should also be more performant.

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• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
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[nsoranzo]

It looks like fastapi is still installed (in addition to fastapi-slim) though. May need to patch tuspyserver upstream?

[nsoranzo]

It looks like fastapi is still installed (in addition to fastapi-slim) though. May need to patch tuspyserver upstream?

Actually, I think you just forgot to add

fastapi==0.120.2 ; sys_platform == 'never'

to lib/galaxy/dependencies/pinned-requirements.txt .

[mvdbeek]

Hmm, let me check what the update script did. However, are we really on the right track with fastapi-slim? It seems that a lot of external packages want to bring fastapi, which has caused mayhem in our production venv already

[nsoranzo]

Hmm, let me check what the update script did. However, are we really on the right track with fastapi-slim? It seems that a lot of external packages want to bring fastapi, which has caused mayhem in our production venv already

Actually we don't need to use fastapi-slim any more, since 0.112.0 the 2 are equivalent and the ~30 extra dependencies can be installed with fastapi[standard].

[kysrpex]

Are my eyes seeing ASGI middleware for TUS? I commented on #20235:

Endpoints dedicated to TUS uploads work in tandem with the WSGI middleware TusMiddleware from the tuswsgi package. WSGI middlewares and endpoints are injected into the FastAPI app after FastAPI routes as a single sub-application wsgi_handler using app.mount("/", wsgi_handler), meaning that requests are passed to the wsgi_handler sub-application (and thus to TusMiddleware) only if there was no FastAPI endpoint defined to handle them. Therefore, they cannot be migrated to FastAPI unless TusMiddleware is also migrated to ASGI.

This would allow all endpoints to be migrated to FastAPI I guess 🎉.

[nsoranzo]

Thanks! There's still https://github.com/galaxyproject/galaxy/pull/21201/files#r2477632100 pending, LGTM otherwise.

[nsoranzo]

Galaxy package tests failure are relevant, you need to update the web_apps package requirements.

[github-actions]

This PR was merged without a "kind/" label, please correct.