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loculus-project / loculus

An open-source software package to power microbial genomic databases
https://loculus.org
GNU Affero General Public License v3.0
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fix: don't ingest region as geoLocAdmin2 (it's continent) #2833

Closed corneliusroemer closed 1 day ago

corneliusroemer commented 1 day ago

Relates to #2788

Might require pp values.yaml changes - need to check

https://fix-continent.loculus.org

theosanderson commented 1 day ago

This will indeed have no effect on PP without changing its values. I guess it will also trigger a bunch of new versions? (Which we've made peace with)

theosanderson commented 1 day ago

Maybe we roll out name reordering and this together on PP? [Aha - great minds https://github.com/loculus-project/loculus/issues/2830 ]

theosanderson commented 1 day ago

Do we want to ingest this as something else?

corneliusroemer commented 1 day ago

Good point @theosanderson about whether we want to ingest as something else.

The answer is no I think. We will want to eventually have a "continent/region" field - but we should derive this in prepro from the countries through a mapping, rather than rely on users settings this (extra work and they might get it wrong). I'll make an issue for that.