Microsalt cases are not storing

[SofiaOtero]

Description

Microsalt cases are stuck on "Running" in statusdb which is causing them to not store in housekeeper.

Suggested solution

Set cases to "Empty" in statusdb when they have completed in trailblazer.

This can be closed when

Cases are stored in housekeeper again.

Blocked by

Nothing

[Vince-janv]

Decision

• [x] Temporarily disable MicroSalt QC service until we have time to fix it https://github.com/Clinical-Genomics/cg/pull/2505
• [x] Make sure storing works as previously for microsalt cases

[SofiaOtero]

It is not possible to store the current cases as we get an issue with the negative control samples in the cases:

Error storing deliverables for case <case_name> - /home/proj/production/microbial/results//<sample_id>_2023.9.20_1.9.31/<sample_id>/assembly/quast/<sample_id>_report.tsv

Has something changed with handling negative controls for microsalt?

[Vince-janv]

It is not possible to store the current cases as we get an issue with the negative control samples in the cases:

Error storing deliverables for case <case_name> - /home/proj/production/microbial/results//<sample_id>_2023.9.20_1.9.31/<sample_id>/assembly/quast/<sample_id>_report.tsv

Has something changed with handling negative controls for microsalt?

Hmm, I think the actions we decided upon will not solve the root issue. Will need to look a bit deeper at this

[Vince-janv]

Bug found

The remove_missing_files validator method of CGDeliverables is not working properly. It is suposed to remove non-mandatory files if they are missing. This is not done, and hence an error is thrown when trying to store them in housekeeper.

@islean Could you work on a patch tomorrow? I have an example file I can show you.

[islean]

Command has been run and succeeded after the merging of #2522.