feat: remove http based file ingest#108
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jennifer-bowser
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July 9, 2026 17:51
jsstevenson
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I know this is leftover code, but there are a few things that I think we should not carry over from the previous endpoint
- file size limit -- the current max is too low to really be usable anyway, but I don't think a CLI needs to enforce a file size limit on itself. Since this is non-public, there's no reason why we need to be defensive against ourselves.
- validate gzip -- pysam can also read non-gzipped VCFs just fine, I don't think we should be introducing additional validation beyond what it thinks it can handle (ditto for the filename).
- the
_raise_vcf_ingestion_errorfunction -- I think this might be an unnecessary additional layer, in several cases it is re-logging exceptions that have already been logged, and also makes the stack trace that prints to the console even longer.- with respect to point # 2 above -- pysam will raise a ValueError if you try to give it an unreadable file. I think we should be catching this, logging, and reraising it directly in the service function instead of doing a big catch block in the CLI
…est_validate_vcf_header_missing_required_fields'
jennifer-bowser
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Jul 17, 2026
jennifer-bowser
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Jul 17, 2026
…nstead of having the CLI handle it; use pysam instead of gzip
jennifer-bowser
marked this pull request as draft
July 20, 2026 16:21
jennifer-bowser
marked this pull request as ready for review
July 20, 2026 16:21
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closes #103