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

Accession order fixes #330

Merged
merged 5 commits into from
Sep 27, 2024
Merged

Accession order fixes #330

merged 5 commits into from
Sep 27, 2024

Conversation

cbielow
Copy link
Contributor

@cbielow cbielow commented Sep 16, 2024

Enhances scripts/find_next_available_number.py to report the gap size and also now detects an unsorted CV (which would cause reporting of false positive gaps).

e.g.

Found gap of size 62: ('MS', 1000938) to ('MS', 1000999)
...
Found gap of size 1: ('MS', 1003236) to ('MS', 1003236)
Found gap of size 2: ('MS', 1003407) to ('MS', 1003408)               <-- false positive...
Found gap of size 2996587: ('MS', 1003413) to ('MS', 3999999)
Found gap of size 1: ('MS', 4000011) to ('MS', 4000011)
Found gap of size 25: ('MS', 4000025) to ('MS', 4000049)
CV is not sorted! MS:1003407 found after MS:4000181
Found gap of size 1000965: ('PEFF', 1036) to ('PEFF', 1002000)

Ordering of accessions is restored as well in this PR (eliminating CV is not sorted! MS:1003407 found after MS:4000181).

This might be worth adding to GH actions? i.e. fail if not sorted?

@cbielow
Copy link
Contributor Author

cbielow commented Sep 16, 2024

Do we need to increase the version number? It's just a re-ordering of terms. Content is identical.

Copy link
Contributor

@edeutsch edeutsch left a comment

Choose a reason for hiding this comment

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

yes, I think the GitHub actions/checking requires every change to have a bump in version number.

@cbielow
Copy link
Contributor Author

cbielow commented Sep 18, 2024

good to go

Copy link
Contributor

@mobiusklein mobiusklein left a comment

Choose a reason for hiding this comment

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

Good catch, I had not considered the CV being unsorted by accession when I wrote the niche finder.

It is highly improbable that this breaks things for people directly consuming the OBO file.

@mobiusklein mobiusklein added this pull request to the merge queue Sep 27, 2024
Merged via the queue into HUPO-PSI:master with commit a5157d0 Sep 27, 2024
3 checks passed
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 this pull request may close these issues.

3 participants