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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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Pipeline failure on being unable to find MGI upstream #372

Closed kltm closed 2 months ago

kltm commented 2 months ago

The main build is now failing with the error:

18:09:08   - Trying again
18:09:22  Downloading http://www.informatics.jax.org/downloads/reports/gene_association_nonoctua.mgi.gz
18:09:22  Download of http://www.informatics.jax.org/downloads/reports/gene_association_nonoctua.mgi.gz failed: http://www.informatics.jax.org/downloads/reports/gene_association_nonoctua.mgi.gz:
18:09:22  2024-04-08 18:09:22 ERROR 404: Not Found.

Looking at http://www.informatics.jax.org/downloads/reports/, it just seems to be removed.

I'm assuming this is a consequence of the ongoing MGI "remainders" project, but I'm not sure what this would be connected to. I would have assumed that gene_association_nonoctua.mgi.gz would be available until the final parts of the switchover have been completed?

Tagging @sierra-moxon @pgaudet @leemdi @LiNiMGI

leemdi commented 2 months ago

this report was removed as part of the MGI-GOC project. Now, GOC is generating the mgi.gpad and mgi.gaf file. And we are not generating gene_association_nonoctua.mgi.gz, anymore. if this needs to be discussed further, let me know (that is, a Zoom call).

P.S. since we are now static, the last gene_association_nonctua.mgi.gz that you downloaded would be the last one anyway. That is, we cannot generate that file any longer anyway.

kltm commented 2 months ago

@leemdi Good to know. My understanding was that things were going to be static (as in not change) until we completed

https://github.com/geneontology/pipeline/issues/369 https://github.com/geneontology/go-site/issues/2285

and reported back. No worries, we can proceed with wrapping those up first.

leemdi commented 2 months ago

The MGI-GO data is static. But we removed the reports that we used to generate. David said it was OK to remove those public reports. Li agreed. This was all passed MGI-GO as part of our testing. The reports are part of our MGI/GO pipeline. so we removed them. If you still have the old gene_association_nonoctua.mgi.gz, then just use that. I cannot product that file anymore.

When I said things would remain "static", I wasn't talking about the public reports. Sorry for the misunderstanding.

kltm commented 2 months ago

@leemdi Understood--not a problem :) We're going ahead with manually getting https://github.com/geneontology/pipeline/issues/369 out the door, so we'll have our own SoT while we finish the transition.

kltm commented 2 months ago

Closing in favor of https://github.com/geneontology/pipeline/issues/373