nextstrain / ncov-ingest

A pipeline that ingests SARS-CoV-2 (i.e. nCoV) data from GISAID and Genbank, transforms it, stores it on S3, and triggers Nextstrain nCoV rebuilds.
MIT License
36 stars 20 forks source link

fix: make legacy mapping use `{clade} (Omicron)` by default #473

Closed corneliusroemer closed 3 months ago

corneliusroemer commented 3 months ago

Resolves #471

I forgot to update the clade-legacy-mapping.yml with the last clade update (24C). As a result, the Nextstrain_clade output for 24C was wrong (? instead of 24C (Omicron)).

To reduce maintenance effort, we now use {value} (Omicron) as the default mapping. This means one less file to update when clades are updated. If there's ever a non-Omicron again, we'd have to updated clade-legacy-mapping.yml but WHO has stopped giving variant names and there's nothing left that's not Omicron. So this should work into the indefinite future (until Emma stops using Nextstrain_clade - she's possibly the only user of that backwards-compat column)

Checklist

corneliusroemer commented 3 months ago

Merging this as I have high confidence this change will work - if not we can revert and/or fix tomorrow

corneliusroemer commented 3 months ago

Famous last words - of course there was an issue: I forgot the parens around (Omicron), fixed in https://github.com/nextstrain/ncov-ingest/commit/8276d2206a21540d81595a5671ae0040e6ea3491

corneliusroemer commented 3 months ago

Running ingest (without fetch):