Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Enable artifact.open() for tiledbsoma backends #114

Open
falexwolf opened this issue Nov 25, 2024 · 0 comments · May be fixed by #117
Open

Enable artifact.open() for tiledbsoma backends #114

falexwolf opened this issue Nov 25, 2024 · 0 comments · May be fixed by #117

Comments

@falexwolf
Copy link
Member

In the Python API, we allow to artifact.open() tiledbsoma stores.

It'd be great if we could replace the call of open_soma

census <- open_soma()

with this:

census <- artifact.open()

This is how it looks in Python: https://docs.lamin.ai/cellxgene#slice-a-concatenated-array

To make that happen, it'll only be a few lines of changes to the census package:

https://github.com/chanzuckerberg/cellxgene-census/blob/f32c2748e9664cc196bb1758acb22f5a460fe188/api/r/cellxgene.census/R/open.R#L24C1-L38C2

In particular, replacing the s3 path (uri in the code there) via artifact$path so that it works for any tiledbsoma store.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant