HGNC ids not being looked up properly

[nathandunn]

The is affecting all of the ribbon code using human data.

No work with hgnc id: HGNC:11204

https://api.monarchinitiative.org/api/bioentityset/slimmer/function?&slim=GO:0003824&slim=GO:0004872&slim=GO:0005102&slim=GO:0005215&slim=GO:0005198&slim=GO:0008092&slim=GO:0003677&slim=GO:0003723&slim=GO:0001071&slim=GO:0036094&slim=GO:0046872&slim=GO:0030246&slim=GO:0003674&slim=GO:0008283&slim=GO:0071840&slim=GO:0051179&slim=GO:0032502&slim=GO:0000003&slim=GO:0002376&slim=GO:0050877&slim=GO:0050896&slim=GO:0023052&slim=GO:0010467&slim=GO:0019538&slim=GO:0006259&slim=GO:0044281&slim=GO:0050789&slim=GO:0042592&slim=GO:0007610&slim=GO:0008150&slim=GO:0005576&slim=GO:0005737&slim=GO:0005856&slim=GO:0005739&slim=GO:0005634&slim=GO:0005694&slim=GO:0016020&slim=GO:0031982&slim=GO:0071944&slim=GO:0030054&slim=GO:0042995&slim=GO:0032991&slim=GO:0045202&slim=GO:0005575&subject=HGNC:11204

Works with UniprotKB ID mapped to the same gene:

https://api.monarchinitiative.org/api/bioentityset/slimmer/function?&slim=GO:0003824&slim=GO:0004872&slim=GO:0005102&slim=GO:0005215&slim=GO:0005198&slim=GO:0008092&slim=GO:0003677&slim=GO:0003723&slim=GO:0001071&slim=GO:0036094&slim=GO:0046872&slim=GO:0030246&slim=GO:0003674&slim=GO:0008283&slim=GO:0071840&slim=GO:0051179&slim=GO:0032502&slim=GO:0000003&slim=GO:0002376&slim=GO:0050877&slim=GO:0050896&slim=GO:0023052&slim=GO:0010467&slim=GO:0019538&slim=GO:0006259&slim=GO:0044281&slim=GO:0050789&slim=GO:0042592&slim=GO:0007610&slim=GO:0008150&slim=GO:0005576&slim=GO:0005737&slim=GO:0005856&slim=GO:0005739&slim=GO:0005634&slim=GO:0005694&slim=GO:0016020&slim=GO:0031982&slim=GO:0071944&slim=GO:0030054&slim=GO:0042995&slim=GO:0032991&slim=GO:0045202&slim=GO:0005575&subject=UniProtKB:H9GEA7

[deepakunni3]

@nathandunn Looks like the lookup from HGNC to UniProtKB yields no result. This is unusual since this was working before.

Will keep looking...

[deepakunni3]

@nathandunn This bug was a result of the slimmer referring to https://scigraph-data-dev.monarchinitiative.org/scigraph/, which I am assuming was taken down recently as a result of migration of Monarch servers.

That URL was temporary to begin with and we should have been using https://scigraph-data.monarchinitiative.org/scigraph/ as defined in config.yaml.

[nathandunn]

@deepakunni3 Great. Should I bug @kshefchek to update the API server?

[deepakunni3]

Yes, @kshefchek would be able to help with updating the production server. Although, I still am not able to get the desired behavior from the api-dev. But it works properly on a local instance.

[nathandunn]

Ah okay. Weird.

On Sep 18, 2018, at 5:08 PM, Deepak notifications@github.com wrote:

Yes, @kshefchek https://github.com/kshefchek would be able to help with updating the production server. Although, I still am not able to get the desired behavior from the api-dev. But it works properly on a local instance.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/biolink/biolink-api/issues/226#issuecomment-422600719, or mute the thread https://github.com/notifications/unsubscribe-auth/AAt2qnWXSfaHUsUkZYDnfZpSHHB7jj8cks5ucYsagaJpZM4Wu2h3.

[deepakunni3]

Oh wait. nevermind. The build is running.

If I have a success on api-dev then I can trigger an update myself for the prod API.

[nathandunn]

Its working here and on production. Thanks @deepakunni3 !

[deepakunni3]

Thanks to @kshefchek

This was happening because we had an exception being thrown server side (related to Ontobio). Kent had a workaround for it which fixed the issue on master but its still an issue on dev. But the fix is temporary and will need to be removed when we release next version of Ontobio.