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

EVA-3587: Semantic metadata checks #43

Merged
merged 11 commits into from
Jul 15, 2024

Conversation

apriltuesday
Copy link
Contributor

@apriltuesday apriltuesday commented Jul 8, 2024

ENA refget endpoint is misbehaving so a few tests are still failing, I've raised it with ENA but meanwhile this can be reviewed.

This adds the following semantic metadata checks:

  • valid taxonomy IDs in project and samples
  • valid public project accessions for project links
  • analysis alias coherence among analysis, sample, and files

It also modifies the BioSamples characteristic conversion to JSON and modifies the sample schema to allow lists of analysis aliases to be consistent with the spreadsheet.

@apriltuesday apriltuesday marked this pull request as ready for review July 9, 2024 15:20
@apriltuesday apriltuesday requested review from nitin-ebi and tcezard July 9, 2024 15:20
}
},
{
"analysisAlias": "VD5",
Copy link
Contributor Author

Choose a reason for hiding this comment

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

I'm not sure if there was a reason for having samples exploded by analysis like this, I would be worried about brokering the same sample twice or something...

eva_sub_cli/nextflow/nextflow.config Outdated Show resolved Hide resolved
eva_sub_cli/semantic_metadata.py Outdated Show resolved Hide resolved
@apriltuesday apriltuesday merged commit d12c158 into EBIvariation:main Jul 15, 2024
1 check passed
@apriltuesday apriltuesday deleted the EVA-3587 branch July 15, 2024 14:15
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