Test WormBase manually curated data in pipeline and output

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 WormBase manually curated data in pipeline and output #238

Open kltm opened 3 years ago

kltm commented 3 years ago

Add a testing pipeline for WormBase manually curated data in the pipeline system for testing.

Tagging @vanaukenk @ukemi

kltm commented 3 years ago

Noting https://github.com/geneontology/go-site/tree/issue-pipeline-238-wormbase-test-pipeline This go-site branch is where we want to add the non-manual annotation file that will be used for our upstream, instead of the usual upstream GAF.

kltm commented 3 years ago

I'm starting a basic test to make sure it runs, even before we get the final upstream. If successful, the products will be available at: http://skyhook.berkeleybop.org/issue-238-wormbase-test-pipeline/

vanaukenk commented 3 years ago

@kltm Just checking to see whose court the WB Noctua GPAD ball is currently in.

I don't see our imported annotations in the Noctua GPAD in the products directory of the wormbase-test-pipeline, but I don't know if there are any data issues on our side that are preventing this or we need to do a pipeline run to generate the test GPAD file.

At least spot-checking the latest imported annotation models on noctua-dev hasn't revealed any systematic errors.

Thx.

vanaukenk commented 3 years ago

Update: I'm looking at the WB file generated in the MGI ticket. It seems to have our imported annotations.

kltm commented 3 years ago

@vanaukenk As far as I know, the ball isn't in my court--the testing pipeline seems to be running and can complete. From here outputs can be checked and inputs can be changed, for example: new non-curated upstreams or merging/unmerging of noctua annotations. I believe that we are either:

waiting for changes to the metadata so we can get a more exact view of how it will be in the "final" state or
waiting on reports of output GPAD quality so changes can be made there

(Also, if you can give me a static IP address or an address block, I can add you to the whitelist so you can watch Jenkins directly. I may also be able to release the blackout on it soon.)