fix: make legacy mapping use {clade} (Omicron) by default
#473
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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)
|
Merging this as I have high confidence this change will work - if not we can revert and/or fix tomorrow |
|
Famous last words - of course there was an issue: I forgot the parens around |
|
Running ingest (without fetch): |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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 of24C (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 updatedclade-legacy-mapping.ymlbut 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 usingNextstrain_clade- she's possibly the only user of that backwards-compat column)Checklist