2024-09-26 - 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

2024-09-26 #916

Closed kltm closed 1 month ago

kltm commented 2 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] update workbenches as https://github.com/geneontology/noctua/issues/916#issuecomment-2378004754
[x] Update NEO
[x] Prep ticket for next outage

kltm commented 2 months ago

@suzialeksander @vanaukenk Diff done, empty.

tmushayahama commented 1 month ago

update NSA cd noctua-standard-annotations git pull origin main

cc @vanaukenk @kltm

suzialeksander commented 1 month ago

Noting that @tmushayahama's comment should address https://github.com/geneontology/noctua-standard-annotations/issues/47

kltm commented 1 month ago

Some issues during the SOP:

remote: Enumerating objects: 52526, done.
remote: Counting objects: 100% (52526/52526), done.
remote: Compressing objects: 100% (16/16), done.
error: RPC failed; curl 18 transfer closed with outstanding read data remaining
fatal: The remote end hung up unexpectedly
fatal: early EOF
fatal: index-pack failed

This did not clear with multiple tries. In the end, I switch to a fresh shallow clone:

git clone --depth 1 https://github.com/geneontology/noctua-models.git

Proceeded as normal afterwards.

suzialeksander commented 1 month ago

outage-over-email sent. Looks like fix for NOT is in place, just asked KC to confirm on that ticket (linked above)