2024-09-12 - Githubissues

geneontology / noctua

Graph-based modeling environment for biology, including prototype editor and services

http://noctua.geneontology.org/

BSD 3-Clause "New" or "Revised" License

38 stars 12 forks source link

2024-09-12 #913

Closed kltm closed 2 months ago

kltm commented 3 months ago

[x] Send reminder email to go-consortium mailing list
[x] Run noctua-models-migration pipeline for (@vanaukenk) (automated to day before) to get report
http://skyhook.berkeleybop.org/noctua-models-migrations/reports/
[x] Refresh minerva code with latest from minerva master
[x] Run replaced_by term update on blazegraph (@vanaukenk)
[x] Cycle minerva to get latest ontology
[x] Follow instructions below to update noctua SAF
[x] Update NEO
[x] Prep ticket for next outage

kltm commented 2 months ago

@balhoff to add instructions for migration discussed on slack.

dustine32 commented 2 months ago

@kltm Forgot to ask this yesterday. Can we schedule the pull of the Alliance pathway preview workbench changes (basically the changes in https://github.com/geneontology/noctua-alliance-pathway-preview/pull/15; a PR into master will be made by @tmushayahama) into Noctua prod?

kltm commented 2 months ago

@dustine32 @tmushayahama It should all be fine as we can always roll back. Just add necessary instructions to the list above and merge any PRs that are necessary.

kltm commented 2 months ago

@vanaukenk migrations run, diff available.

kltm commented 2 months ago

Note to @vanaukenk : in preparation, I'm running the commands up through the failure from last time around to see if it happens again. I'll report here if it does.

vanaukenk commented 2 months ago

Extra large diff file this time, but all changes are consistent with recent ontology updates wrt enzymatic activities, transporter activities, and GPI-related BP terms.

Also noting that in one case, a term merge will result in two identical annotations. I'm not sure we've encountered this before, so I'll put a ticket in the noctua tracker as a placeholder to discuss and investigate what we want to do about those annotations. https://github.com/geneontology/noctua/issues/917

tmushayahama commented 2 months ago

git pull origin noctua-landing-page master branch

cd noctua-standard-annotations
git pull origin noctua-standard-annotations
git checkout main

kltm commented 2 months ago

As a note from @tmushayahama during the meeting, the workbench addition can be added anywhere, so I will add it to the bottom of the list.