[BUG] Prompt re-registration for assay when linked study is removed

[Brilator]

Is your feature request related to a problem? Please describe. When removing a study (arc s remove -s) the linked assay is properly unregistered from the isa.investigation file, but not removed from the ARC (for good reason). However, it's then flying around unlinked (to study and inv) and also doesn't appear in arc a list.

Describe the solution you'd like a) When removing studies throw a warning that an assay is linked b) Suggest alternative studies to link the assay to (if exists), e.g. via message arc a register -s <existing s id> -a

[Brilator]

Would it also makes sense to let arc a list / arc s list display unregistered assays / studies, in case people just copy-dump them in there? Or is this part of validation during arc update?

[HLWeil]

Hey @Brilator, I think your a),b) suggestions for the initial problem would be the best way to assist the user.

Also showing unregistered assays and studies when using list seems also sensible.

Thanks for your input

[HLWeil]

Proposed solution for the first problem:

[HLWeil]

And the second problem:

Study list

Assay list