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gks-anvil / vrs_anvil_toolkit

Extract clinical variant interpretations from VCF using GA4GH VRS IDs
MIT License
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feature/specialized-error-handling #33

Open quinnwai opened 8 months ago

quinnwai commented 8 months ago

When we create VRS IDs or query metakb, we need to have error handling that describes the problem (network error, translation error, no matches found, etc). In some cases like within annotate_all, there can be non-descript messages outputted in the command line.

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is it good enough for an error? Do we just have to redirect them to the logs file everytime?

quinnwai commented 7 months ago

Still might need more work, as some logs can be misleading and we may want to suppress them: below the main problem is that the validation error is occurring but the traceback mentions a "timestamp_str" KeyError.

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