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

Single meds entrypoint for command line tools #43

Closed
tompollard opened this issue Oct 28, 2024 · 2 comments
Closed

Single meds entrypoint for command line tools #43

tompollard opened this issue Oct 28, 2024 · 2 comments

Comments

@tompollard
Copy link
Contributor

tompollard commented Oct 28, 2024

It would be nice to have a single entrypoint for the meds command line tools. e.g.

meds convert --from omop --to meds [OMOP_PATH] [MEDS_PATH]
meds convert --from meds --to omop [MEDS_PATH] [OMOP_PATH]
meds convert --from mimic --to meds [MIMIC_PATH] [MEDS_PATH]

This would be more flexible and enable a single help command meds --help. Not sure how best to manage a single entrypoint across multiple repos.

@rafgia mentioned that he was interested in exploring possibility of converting from MEDS to other formats (e.g. MEDS -> MIMIC). Restructuring entrypoints might be an early step in implementing this?

@EthanSteinberg
Copy link
Collaborator

Yeah, this seems like a really good idea.

I probably wouldn't do a single entrypoint for meds in general, but a single entry point for meds_etl is a great suggestion.

@mmcdermott
Copy link

I think this is a nice idea, but given #50 and #51, should likely be closed for now as we are (potentially, though I advocate for) moving away from having a joint package for MIMIC and OMOP in favor of separate ETL packages per data source. Feel free to re-open if folks disagree.

@mmcdermott mmcdermott closed this as not planned Won't fix, can't repro, duplicate, stale Jan 7, 2025
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

No branches or pull requests

3 participants