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

Fix commas that shouldn't be in biotools_mappings.tsv #18919

Merged
merged 3 commits into from
Oct 4, 2024

Conversation

jmchilton
Copy link
Member

Fixes #18903

How to test the changes?

(Select all options that apply)

  • Instructions for manual testing are as follows:
    1. I don't know - check the file for commas after the commit I guess 😅

License

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

Copy link
Member

@mvdbeek mvdbeek left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I guess these are coming from an upstream source https://github.com/bio-tools/content if i can believe galaxy.yml.sample ? That repo doesn't exist anymore though, so ... :shipit: ?

@jmchilton jmchilton marked this pull request as ready for review October 1, 2024 18:12
@github-actions github-actions bot added this to the 24.2 milestone Oct 1, 2024
@hexylena
Copy link
Member

hexylena commented Oct 1, 2024

@mvdbeek https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://github.com/bio-tools/content at least they warned us 😆

IMPORTANT : this repo is a sandbox: do not use it for production purposes! It's entire contents may change, be reorganised or even deleted without notice.

@jmchilton you might also be missing the ones with spaces? e.g. L263 rxlr_motifs. And in that case i would argue both biotools xrefs are relevant. do we need to pick one? is there a way to have both annotations?

@bgruening
Copy link
Member

I guess these are coming from an upstream source https://github.com/bio-tools/content if i can believe galaxy.yml.sample ? That repo doesn't exist anymore though, so ... :shipit: ?

Its redirecting to https://github.com/research-software-ecosystem/content ... is the redirect not working for you?

@hexylena
Copy link
Member

hexylena commented Oct 2, 2024

https://github.com/galaxyproject/galaxy/pull/18919/files#diff-fd14abe36b9effe9869962313d1b668af331e9cd4234faa4a08bab8115eed210L135 last one, I think (sam_merge2 is on two lines, the first "broken link in toolshed", the second looks more correct.)

@jmchilton
Copy link
Member Author

I think (sam_merge2 is on two lines, the first "broken link in toolshed", the second looks more correct.)

It looks like it already had an entry - so I think we're fine to just delete it.

@bgruening bgruening merged commit d18bc68 into galaxyproject:dev Oct 4, 2024
52 of 54 checks passed
@bgruening
Copy link
Member

Thanks @jmchilton

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

Successfully merging this pull request may close these issues.

biotools_mappings.tsv includes comma and space separated values leading to incorrect bio.tools IDs.
4 participants