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geneontology / pipeline

Declarative pipeline for the Gene Ontology.
https://build.geneontology.org/job/geneontology/job/pipeline/
BSD 3-Clause "New" or "Revised" License
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Test and merge PANTHER / PAINT 17 into pipeline #307

Closed kltm closed 1 year ago

kltm commented 1 year ago

Aim at metadata provided in https://github.com/geneontology/go-site/issues/1926 and test new PAINT release. Tagging @dustine32

kltm commented 1 year ago

Working branch is issue-307-panther-17. Tagging @dustine32 .

dustine32 commented 1 year ago

@kltm Thanks for creating the branch! I can update the Jenkinsfile for 17.0 following the change pattern we used in https://github.com/geneontology/pipeline/commit/3deaf006b6bf790c591ad19e1c8c5cf092ed905d.

kltm commented 1 year ago

@dustine32 That would be lovely--cheers! I'd crosscheck that GAF list against snapshot to make sure changes like xenbase are there.

dustine32 commented 1 year ago

@kltm Right, I had to add xenbase and japonicusdb to the GAF list.

dustine32 commented 1 year ago

Noting that I also had to remove aspgd from the GAF list to avoid another instance of #282 in the go-stats report.

dustine32 commented 1 year ago

@kltm So with the latest jenkins test run it looks like everything worked OK but the last stage "Produce derivatives" reported failure. I can't seem to figure out why exactly. No errors and it looks like all of the steps completed fine. I checked the go-stats go-annotation-changes.tsv report and the drop in IBAs matches what I was expecting to see (~316,000 IBAs).

If you're fine with this result then I'm ready to schedule the PANTHER_VERSION var switchover on the other pipeline branches master, snapshot, release along with the IBA GAF symlink switch on the PAINT FTP server.

dustine32 commented 1 year ago

@kltm Looks like the "Produce derivatives" stage rerun finally worked. I'm thinking about getting the switch in today for the snapshot starting tonight?

kltm commented 1 year ago

I think that's right. If you can get the change (directly) into master, I'll propagate it up.