Filter annotations by evidence is not working

[vanaukenk]

When viewing a list of annotations in AmiGO, it is no longer possible to filter by Evidence.

Clicking on the Evidence facet says 'Nothing to filter'.

This may also be related to an issue with the Noctua Search Annotations functionality reported today by @pmasson55

https://github.com/geneontology/noctua-visual-pathway-editor/issues/75

[pgaudet]

Thanks for reporting this Kimberly. I also got that problem; it was in amigo.staging - did something happen in the last release/snapshot?

[kltm]

After the last GO release, evidence filters are no longer working in AmiGO.

To reproduce:

• Go to: https://amigo.geneontology.org/amigo/search/annotation
• Open Evidence filter
• it is empty

The evidence filter should contain a fair number of entries.

[kltm]

Seems specific to "Evidence" only. Hm.

[kltm]

Noting that the loaded ontology would have been ontology/extensions/go-amigo.owl

There have been no changes to the loading software since the last release, so I think it's safe to put that to the side.

The likely fruitful paths are:

• there was something that happened in the pipeline changes (which seems unlikely as everything seems to have been fine except evidence)
• there was a change in ECO that had some effect
• there was a change in the ontology build or build of go-amigo.owl that had some effect

I'm still digging around on the first on that list, but so far nothing. We likely need to slide into damage control for the moment: leave as-is or revert to last AmiGO index (and add warning note).

[balhoff]

@kltm related to this? https://github.com/geneontology/noctua/issues/860

[kltm]

@balhoff Yes, could be, but it looks like we have not dug down very far in that ticket. Talking to @pgaudet , she is leery about jumping back to the previous (~2m/o) index to "fix" things as a temporary measure. If we want to go with the ECO-not-getting-through theory, we would either need to dig in there or go back to loading files separately (at least in the short term).

[kltm]

With @balhoff 's PR in, I'd proposed we start a rebuild and check on staging.

[kltm]

snapshot attempt underway. If things go well, we could maybe have product to look at later tomorrow.

[kltm]

Noting report from @raymond91125 about the knock-on effects to go-annotation reports.

[kltm]

We have tested @balhoff 's fix, which seems good for the "Evidence" filter, but are waiting on shifting to a release due to other issues.

[suzialeksander]

@kltm (or @dustine32 might know) do we have an ETA for a fix? Does this need to wait for next week's outage or is there a chance it will be fixed before that?

[kltm]

@suzialeksander This independent on any outage--it is tied to a new release. We have discussed how to proceed with some "problematic sources" that occurred since last release (see https://github.com/geneontology/pipeline/issues/373) and have just started a run that could potentially fix everything. The soonest possible deployment would be Friday or into the weekend, but that would depend on other sources, etc., being as we expect.

[kltm]

Now in production.

[kltm]

@vanaukenk When you have time, can you check the expression of this in Noctua?

[pgaudet]

Noctua's "Search annotation" functionality works for me.

[vanaukenk]

Yes, this looks to be working again in Noctua.

Thanks @balhoff @kltm