Clinical-Genomics / cg

Glue between Clinical Genomics apps

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No TB analysis is created for cases with no associated order even though jobs start running

beatrizsavinhas opened this issue · comments

Description

When starting a case that, for some reason, does not have an associated order, the start command fails with the following error:

Could not run analysis: list index out of range
Aborted!

But the jobs are created and start running while no analysis is created on Trailblazer.

Suggested solution

  • Prevent the analysis from starting in situations like this and print a more explanative error.

This can be closed when

  • Analyses that do not have an associated order are prevented from starting and the error is communicated to the user.

Blocked by

Nothing, to my knowledge.

A bit uncertain if we just want to print a warning. Given that such cases should not be able to exist, I feel like we should not implement checks for it, rather we should get to the bottom of why these cases were malformed in the first place.

@beatrizsavinhas How could this case be created? We should make sure it cannot happen.

This happened with cases that were created manually by us in production, which happens somewhat frequently. I see that now though, when creating a new case with the cli command cg add case, the new case is automatically connected to an order, so this is not an issue anymore.

new_case.orders.append(order)

Great! Thx!