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hivdb / chiro-frontend

Coronavirus frontend, CoV-Rx-DB,
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Switch mutation-viewer page to use data source from DRDB #30

Open philiptzou opened 2 years ago

philiptzou commented 2 years ago

Problem: The current mutation-viewer page requires heavy manual maintenance when a variant is updated / a new variant is named. The most time consuming part is to organize a set of mutation lists for all variants and submit them to hivdb/chiro-cms.

Solution: DRDB has a table named variant_consensus, which includes an automatic set of mutation lists of variants that listed in variants table. It can be easily updated by just running the command make sync-varcons from the root directory of hivdb/covid-drdb. We can switch the data source to DRDB to reduce manual maintenance and manual errors.

Task and time estimate:

philiptzou commented 2 years ago

@KaimingTao Please comment, since you are maintaining the variant mutation lists.

KaimingTao commented 2 years ago

It seems that outbreak.info hasn't updated the mutations list for omicron yet. https://outbreak.info/situation-reports?pango=B.1.1.529. If we want to show it now we still need some manual work.

KaimingTao commented 2 years ago

Outbreak.info uses 75% consensus to generate the mutation list, it's not a stable list when new sequences are added in the calculation as I remember. Is it ok?

philiptzou commented 2 years ago

They updated it now but have an issue with the 212-214 insertion. See outbreak-info/outbreak.info#477.

philiptzou commented 2 years ago

Outbreak.info uses 75% consensus to generate the mutation list, it's not a stable list when new sequences are added in the calculation as I remember. Is it ok?

I think it's fine. Yes they are not stable, but we have the git-diff tool to review the mutation lists before we pushed it to our repo. If you found a bug or just anything weird, just report to them: https://github.com/outbreak-info/outbreak.info/issues.