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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
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@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.

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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.

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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

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VCF annotator should not check for GRCh38

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