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geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services
http://noctua.geneontology.org/
BSD 3-Clause "New" or "Revised" License
37 stars 13 forks source link

Function companion does not return evidence properly -> ShEx violations and GPAD export errors #745

Open vanaukenk opened 2 years ago

vanaukenk commented 2 years ago

The current iteration of the Function companion workbench in the graph editor doesn't return evidence properly when there are multiple pipe-separated With/From entries and multiple, pipe-separated references. This leads to ShEx evidence model violations and incorrect evidence on the GPAD export.

I don't know how many people still use the Function companion, but perhaps we should consider retiring it (with sufficient advance notice) to avoid errors.

The equivalent functionality is available in the Noctua form and doesn't create ShEx violations or GPAD export errors.

@kltm @ukemi - what do you think?

ukemi commented 2 years ago

I think retirement and replacement with the from capability is a great idea. I used to use the function companion, but I think the form version is better and it maintains a consistent look and feel across tools.

kltm commented 2 years ago

Retirement is as easy as removing the workbench and restarting, so can be accomplished at short notice and little prep.

vanaukenk commented 2 years ago

@kltm - how about removing the function companion from the graph editor for the June 23rd maintenance outage?

We could also remove the Macromolecular complex creator as this functionality is now available in the VPE.

kltm commented 2 years ago

@vanaukenk Anything that is a "legacy" workbench is pretty trivial to clip out on demand--all that is necessary is a configuration change and a noctua restart, a non-disrupting outage of about 30 seconds.

vanaukenk commented 2 years ago

Okay, thanks, @kltm Maybe the week of 6/20; that way I can announce this on an annotation call before we do it.