Skip to content

Conversation

@theferrit32
Copy link
Contributor

Close #530

@theferrit32 theferrit32 requested review from a team as code owners July 23, 2025 18:20
@larrybabb larrybabb requested a review from jsstevenson July 23, 2025 18:21
@larrybabb
Copy link
Contributor

@jsstevenson would you please review this. the think-tank group decided the healthcheck() was not necessary so we removed it. If you have a counter arg, please make it, otherwise we will move forward.

@jsstevenson
Copy link
Contributor

jsstevenson commented Jul 23, 2025

I'd be fine with removal for now. The bigger problem is that the VCF annotator suppresses all exceptions and just dumps them verbatim onto the VCF in an ERRORS info field. I think we ideally should be more specific about exception handling, such that some things get recognized as annotation-related errors (like coordinate wonkiness or something) and suppressed + logged, and other things should just interrupt annotation entirely (like a SeqRepoRestDataProxy HTTP error). This was a bandaid for the latter.

@theferrit32
Copy link
Contributor Author

After discussion we decided that at least the filesystem and the REST based dataproxies should work the same way, in that they will fail at construction time if the underlying data source is not accessible. This latest commit adds a call to the /ping endpoint in the __init__ function of the REST dataproxy and throws an exception if it fails

@theferrit32 theferrit32 force-pushed the remove-annotator-healthcheck branch from cb4f975 to 499f173 Compare December 17, 2025 19:57
@theferrit32
Copy link
Contributor Author

I have no idea why the tests are failing because they run locally with I do pytest --vcr-record=none

@theferrit32
Copy link
Contributor Author

theferrit32 commented Dec 17, 2025

I think the problem is the vcr decorator on test functions does not record any requests made by fixture initialization functions run prior to the test function itself. So when we construct a REST dataproxy in a test fixture in conftest.py, the ping request is not being recorded.

@theferrit32 theferrit32 merged commit e28852f into main Dec 17, 2025
16 checks passed
@theferrit32 theferrit32 deleted the remove-annotator-healthcheck branch December 17, 2025 21:20
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.

VCF annotator should not check for GRCh38

4 participants