Sometimes results are not reported back to pephub using pipestat and phc
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- Dominant language
- Python
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Description
I noticed that when using a PEP as input and updating that same PEP with a downstream result using pipestat, that sometimes results will not be reported back or, more alarmingly, existing data will be nulled.
using this pep:
https://pephub.databio.org/donaldcampbelljr/mouse_seqcol_digests?tag=default
and this pipeline: https://github.com/refgenie/refgenomes.databio.org/blob/donald_PEP_additions/scripts/seq_col_comparison/pipeline/seq_col_jsons.py
This happened to a couple of samples and it happened to me twice today on two different PEPs. I'm using looper to run the samples in parallel on the HPC.
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Research direction
Start with scripts/seq_col_comparison/pipeline/seq_col_jsons.py and trace how pipestat and phc update the PEP at the PEPhub URL. Reproduce the issue with parallel looper runs on the referenced PEPs, then verify that every downstream result is reported and existing PEP data is preserved.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend-api-design, databases
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100