Re-upload misses added VCFs

[dnil]

On a recently rerun case (quicktapir), added VCFs since last MIP version (MEI) were found missing. They are present in the CG-generated scout load config, so presumably the issue is with scout load.

[dnil]

I'm going to manually load the VCFs for the case in question on this case, but should be possible to reproduce locally.

[northwestwitch]

Was it research variants that were missing or both clinical and research?

[dnil]

Both for MEI:

[northwestwitch]

I can't seem to reproduce locally with the demo config file? What I'm doing is:

• Commenting out the mei-related VCF files line
• Loading the case with scout setup demo
• Mei clinical variants are not loaded and path is missing from case document (as it should be)

Then:

• Un-comment the mei lines on config file
• scout --demo load case scout/demo/643594.config.yaml --update --keep-actions
• mei clinical variants are present (as I would expect). Research variants are not shown because it's not a is_research case.

🤔

[dnil]

Interesting?! Some interaction with the research? Sounds odd. Have you checked the working load command against what the cg app is using?

[dnil]

How about the pydantic idea - case loaded with old pre pydantic change, without mei, then load with current?

[northwestwitch]

We checked other cases re-runned lately and couldn't find any other similar case. For instance this one worked fine

[northwestwitch]

The weird thing is that the upload date for the case in question is one year old:

[northwestwitch]

Shall we close this one, we can re-open if it happens again?