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clingen-data-model / genegraph

Presents an RDF triplestore of gene information using GraphQL APIs
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Issue with link generated from GCI to Website #750

Closed tnavatar closed 1 year ago

tnavatar commented 1 year ago

Report from Phil

Hi guys. We're running into some problems with the new GDV timestamp. Although it did not cause me any issues, it's causing a lot for the GCI. The problem is that they saved the old links in the GCI, and now they don't resolve. At first, I thought I could just reformat on my end, and that does work for some. But the new timestamp includes microseconds, whereas the old did not. There is no way I can know what microseconds to add. I think we're going to need genegraph to add a backward compatibility feature that allows it to correctly map something like https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_bb7755df-a1e3-4398-a771-cd6c2d112b68--2021-01-13T19:42:10 to the correct curation.

Will reach out to Gloria to confirm issue and discuss solutions.

tnavatar commented 1 year ago

From Gloria:

Hi Tristan, there was an issue from GCI but Phil has fixed to support the old links on website so it’s good now. Thanks.

Will loop back with Phil and close issue if nothing more needs to be done.

tnavatar commented 1 year ago

Tristan Nelson 3:21 PM Hi Phil, I looped back around with Gloria, she mentioned you made a change to the website to support the old links and that things are OK now. Can you confirm?

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Phillip Weller 3:24 PM No, I tried, but it only helped with a few. The ones Gloria originally gave me all had milliseconds set to 001. However, the last one was something like 160, so the assumption that a mapping was possible was incorrect. Once the backward compatibility is supported in genegraph, I'll have to remove my stuff completely.

tnavatar commented 1 year ago

I'd think I'd rather deal with the issue at the source. Let's see if we can't get the GCI generating links that work.

tnavatar commented 1 year ago

Tristan Nelson 3:30 PM Phil tells me he's still having issues. Could I ask, are you generating links dynamically to get back to the website? There may be a format that would work better going forward.

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Gloria Cheung 3:31 PM yes, we are. If you give us the new format, we can update to generate it.

Tristan Nelson 3:33 PM Sure, the new one should be simpler, simply CGGV:, for example https://search.clinicalgenome.org/kb/gene-validity/CGGV:bb7755df-a1e3-4398-a771-cd6c2d112b68 3:34 I think Phil is still choosing to generate links with the previous style, but this should get you to the latest curation for the snapshot id. 3:34 Once we figure out the business with versioning we can discuss how to support that.

Gloria Cheung 3:35 PM ok. will update and test. Thanks. :+1: 1

tnavatar commented 1 year ago

Moving to Review pending confirmation of resolution.