Outage tasks for 2022-11-10

geneontology / noctua

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

http://noctua.geneontology.org/

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

36 stars 13 forks source link

Outage tasks for 2022-11-10 #798

Closed kltm closed 1 year ago

kltm commented 1 year ago

[x] Run noctua-models-migration pipeline for @vanaukenk (day before? morning of?) to get report
[x] ~~Merge in https://github.com/geneontology/minerva/pull/505~~ Tests not passing
[x] Refresh minerva code with latest from minerva master
[x] Merge reactome updates https://github.com/geneontology/noctua-models/pull/247
[x] Fix models with incorrect reactome schema: https://github.com/geneontology/go-site/issues/1924
[x] Run replaced_by term update on blazegraph (@vanaukenk)
[x] Cycle minerva to get latest ontology
[x] Cycle barista to get latest groups.yaml (update groups.yaml too) https://github.com/geneontology/go-site/issues/1924
[x] ~~Update NEO~~ canceled due to apparent timeout failure; machine too busy? Not too bad as we updated out of sync last week
[x] Prep ticket for next outage: https://github.com/geneontology/noctua/issues/803

dustine32 commented 1 year ago

PR to come later today: apply https://github.com/geneontology/reactome-go-cams/pull/9 to noctua-models/master (drop-n-reload of Reactome models). @kltm Would this be OK for Thursday?

ukemi commented 1 year ago

Thanks @dustine32 !!!!

dustine32 commented 1 year ago

Reactome models PR is in! https://github.com/geneontology/noctua-models/pull/247

dustine32 commented 1 year ago

@ukemi No prob, and thank you for nudging me - I meant to get this in place last week!

kltm commented 1 year ago

@dustine32 I have no problem with this and am adding it to the list, but will leave overriding either way to @vanaukenk (who may be out, so we'll treat merging as default @suzialeksander ).

suzialeksander commented 1 year ago

Confirming that @vanaukenk has left me to do the reviewing. As long as it's a basic "do the new Reactome models exist and do they look reasonably complete" I can definitely review this as part of the regular outage tasks.

ukemi commented 1 year ago

@suzialeksander. The models are currently loaded into dev if you need a spot-check comparison. They all have Reactome in the title. For some reason there are still issues searching by group. Hopefully we can track that down by the next load.

dustine32 commented 1 year ago

@ukemi I think I just figured out the group thing and explained it further in https://github.com/geneontology/noctua-models/pull/247#issuecomment-1307747993.

kltm commented 1 year ago

@suzialeksander Diff ready: http://skyhook.berkeleybop.org/noctua-models-migrations/reports/ontology-replaced-by.diff