Re-map score sets with mapped variants that have neither a mapping nor an error #820
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app: backendTask implementation touches the backendTask implementation touches the backendapp: mapperTask implementation touches the mapperTask implementation touches the mapper
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Problem
Three of the 1,170 mapped score sets in the public dump have mapped variants with both post_mapped and error_message null. They came from dcd-mapping runs that were killed during BLAT alignment, most likely out of memory, before the mapper could report a reason, and the worker stored null for the missing error.
Both causes are gone on the code shipping in 2026.3.0:
- dcd_mapping2 runs BLAT with
shell=False, a timeout and an output file (align.py:185), so BLAT's output is no longer held in memory. - RT (the allele-centric mapping work on
feature/bencap/allele-centric-mapping-and-storage)'s mapping job requires a typedoutcomeon every mapped record and fails the job when one is missing (worker/jobs/variant_processing/mapping.py), so a null/null row can't be written.
Scope
- After 2026.3.0 deploys, find the score sets whose current mappings have neither a mapping nor an error.
- Re-run mapping for those score sets.
Acceptance criteria
- The query for current mapping records with no post-mapped allele and no error returns no rows in prod.
- The affected score sets are listed in this issue, with their re-mapping job ids.
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app: backendTask implementation touches the backendTask implementation touches the backendapp: mapperTask implementation touches the mapperTask implementation touches the mapper
Activity
[-]Mapping worker can silently persist error_message: null on total mapping failure (BLAT OOM)[/-][+]Re-map score sets with mapped variants that have neither a mapping nor an error[/+]