SACGF / SACGF/variantgrid

Annotation run retry fails: refuses to overwrite stale variantannotation_0.tsv scratch file

Open
#1,596 1 comment 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
30
Forks
3
Avg merge
9h 28m
Merged PRs (30d)
42

Description

🤖 Written by Claude

Retrying an annotation run aborts with `ValueError: We don't want to overwrite '.../annotation_run_NNNNN/annotation_run_annotation_variantannotation_0.tsv'` because the leftover scratch `.tsv` from the prior run is still present and `write_sql_copy_csv` refuses to overwrite it. The retry can never succeed until the file is removed by hand.

Seen on **shariant prod**. Suggest cleaning the run's scratch files before re-running (or overwriting deliberately).

Location: `annotation/vcf_files/bulk_vep_vcf_annotation_inserter.py:650` (finish) → `upload/vcf/sql_copy_files.py:92`

**Rollbar:**
- https://app.rollbar.com/a/jimmy.andrews/fix/item/VariantGrid/7074

_(Filed from a 6-month Rollbar triage.)_

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.