Undo/Redo in Graph Editor Breaks Save Functionality

[tmushayahama]

If an undo/redo action is performed in the Graph Editor and changes are not saved there but saved in the Standard Annotation or Pathway Editor instead, the changes fail to save. This appears to occur because the contributor and other meta tags ,maybe group is missing in the save request, so it will have false save. I want to mark it as critical because receiving an wrong model makes the model corrupted and not savable.

Steps to Reproduce:

Perform undo/redo in the Graph Editor.
Do not save changes in the Graph Editor.
You can see that there is no group or contributor on the panel
Attempt to save in Standard Annotation or Pathway Editor.

Expected Behavior:
Changes should save correctly, contributors and groups should not disappear

Actual Behavior:
Cannot save, contributors and groups disappear, making an error that cannot save without contributor

For Developers:

Undo request not returning correct model annotations

[{"entity":"model","operation":"undo","arguments":{"model-id":"gomodel:677c8e3400000330"}}]

Response without contributor:

Normal request when it is working

cc @kltm @vanaukenk @balhoff

[kltm]

@tmushayahama Hm. Just to confirm what is going on, without leaving the Legacy Graph Editor world, are you saying here that the use of the undo/redo stack is removing model annotations that already exist?
For example:

• Go to: http://noctua-dev.berkeleybop.org/editor/graph/gomodel:67299f1a00000020
• Note sole contributor "https://orcid.org/0000-0002-1706-4196", "https://orcid.org/0000-0001-8244-1536" under [Model] -> [Edit annotations]
• Save model with [Model] -> [Save]
• Note two contributors, "https://orcid.org/0000-0002-1706-4196" and , under [Model] -> [Edit annotations]
• Undo with [Model] -> [Undo last]
• • Note sole contributor "https://orcid.org/0000-0002-1706-4196", "https://orcid.org/0000-0001-8244-1536" under [Model] -> [Edit annotations]
• Save model with [Model] -> [Save]

That's pretty much what I'd expect. (Although, honestly, even for what I just did above, as I thought saving wiped out the undo/redo stack, I would have guessed it wouldn't work that way.) No apparent data damage.

I guess what I'm trying to confirm is if this is something that can be reproduced solely in the Legacy Graph Editor, or is this an interaction problem?

[vanaukenk]

I've put this on the agenda for the 2025-01-09 workbenches call so we can touch base and decide what needs to be done.

[kltm]

From discussion today, it seems likely that this is a minerva issue.
@tmushayahama will produce steps to reproduce, at the request level so that @balhoff can simulate/create tests, and create a minerva ticket.