fix(ENGKNOW-3353): pgor write randomly fails in sm#121
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gmagnu
commented
Jun 2, 2026
gmagnu
commented
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- Fix missing files if pgor | write was overwriting existing gord.
- Add retry in S3 start upload.
- Dont write empty files into gord.
…ites pgor rewrites each partition's write target from `ref_af.gord/` (folder mode) to a specific `ref_af.gord/<signature>.gorz` (single-file mode). ForkWrite was creating empty gorz files for every chromosome partition that produced no rows (e.g. gorrows with a fixed range hits only 2 of ~48 partitions). These ~46 unnecessary S3 multipart uploads caused random throttling failures. Fix 1 (ForkWrite): skip empty-file creation when the write target is inside a gord folder. Empty partitions in pgor writes should produce no file; the GORDICTFOLDER step builds the dictionary from meta files and correctly excludes empty entries. Fix 2 (S3MultipartOutputStream): add retry loop to initiateMultipartUpload() matching the existing uploadWithRetry pattern, so transient S3 errors during upload initiation don't cause permanent failures. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…write-randomly-fails-in-sm
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Interrupted thread reset the interrupt flag but kept looping and retrying instead of bailing out. Throw IOException on InterruptedException in both initiateMultipartUpload and uploadWithRetry. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
janeliutw
approved these changes
Jun 8, 2026
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