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Roll back (and then forward) "problematic" upstream files from selected resources #373

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kltm opened this issue Apr 17, 2024 · 13 comments
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kltm commented Apr 17, 2024

We have four files that we want to roll back to the last "good" source, as represented in the last release.

Fastest path to get out fix for geneontology/amigo#716

Tagging @pgaudet @dustine32

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kltm commented Apr 18, 2024

Blocked by #374 for the moment.

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kltm commented Apr 18, 2024

snapshot started.

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kltm commented Apr 18, 2024

I have confirmed with @vanaukenk that the FTP (and downloads HTTP) are down for WB. Adding them to the list above.

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kltm commented Apr 22, 2024

Talking to @pgaudet last week, we"ll be holding like this while she researches the issues (delta WB).

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kltm commented Apr 23, 2024

Noting that WB FTP still seems to be out of action. @vanaukenk, could I ask you to update here if that status changes?

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kltm commented Apr 25, 2024

Note from @vanaukenk that WB has recovered.

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kltm commented Apr 25, 2024

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kltm commented Apr 28, 2024

@vanaukenk WB failing again:

01:10:56  Download of ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_association/c_elegans.PRJNA13758.current.gene_association.wb.gz failed:  - Trying again

Reverting to our "safe" version.

kltm added a commit to geneontology/go-site that referenced this issue Apr 28, 2024
Failures occurring again upstream.
geneontology/pipeline#373 (comment)
@pgaudet pgaudet moved this to Next release in GO releases QC - 2024 Apr 29, 2024
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kltm commented Apr 30, 2024

Ah, I missed that the GPI is grabbed later for (the now unavailable) WB GPI. Reverting that as well.

kltm added a commit to geneontology/go-site that referenced this issue Apr 30, 2024
@vanaukenk
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@kltm - I just tried the WB ftp site again and can manually download all of our files in the wb.yaml, so I"m not sure what"s going on and if this is an intermittent thing.

If you want to look at this together in case I"m missing something, let me know.

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kltm commented Apr 30, 2024

@vanaukenk I can confirm that it"s still not working for me and the pipeline machine, but I cannot confirm if there are firewall rules at my end or your end (yet). I"m happy to explore this with you at some point; hopefully we can deal with it at our leisure as your release frequency is low?

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Okay, thanks @kltm and very sorry for the continued trouble with the WB files.

Let me know when you"d like to meet and I could try to wrangle one of the WB developers, too, as that might also be a help.

vanaukenk added a commit to geneontology/go-site that referenced this issue May 1, 2024
Adding new https source links for WB GAF and GPI files to try to address geneontology/pipeline#373

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kltm added a commit to geneontology/go-site that referenced this issue Jun 10, 2024
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kltm commented Jul 8, 2024

I think MGI is good because we are now testing with our "internal" "upstream" source.

@kltm kltm closed this as completed Jul 8, 2024
@pgaudet pgaudet moved this from Next release to 2024-06-17 Snapshot in GO releases QC - 2024 Jul 18, 2024
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