feat(collection-seeder): add descriptions to covid pango lineage variant types - #1363
Open
fhennig wants to merge 1 commit into
Open
feat(collection-seeder): add descriptions to covid pango lineage variant types#1363fhennig wants to merge 1 commit into
fhennig wants to merge 1 commit into
Conversation
…ant types Explains what 'Nucleotide substitutions' vs 'New nucleotide substitutions' means for each lineage collection. The parent lineage name is included in the description of the 'New' variants. These descriptions surface in the collection detail page and as tooltips in the queries-over-time table. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
|
The latest updates on your projects. Learn more about Vercel for GitHub.
|
Contributor
There was a problem hiding this comment.
Pull request overview
Adds user-facing variant descriptions to COVID Pango lineage collections in the collection seeder so the UI can better explain “(New) nucleotide/amino acid substitutions” on collection detail pages and in tooltips (per #1357).
Changes:
- Add
descriptionfields to the four variant types generated byCovidPangoLineagesSource. - Minor whitespace cleanup in an influenza resistance mutations test file.
Reviewed changes
Copilot reviewed 2 out of 2 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| collection-seeding/sources/covid_pango_lineages.py | Adds per-variant descriptions for (new) nucleotide/amino acid substitution variants. |
| collection-seeding/tests/test_influenza_resistance_mutations.py | Removes an extraneous blank line. |
Suppressed comments (1)
collection-seeding/sources/covid_pango_lineages.py:68
- Same issue as above: for lineages without a known parent, this will render "parent lineage (—)" in the UI. It would be clearer to omit the parent clause when it’s unknown.
"description": f"Amino acid substitutions not present in the parent lineage ({parent}).",
| { | ||
| "type": "filterObject", | ||
| "name": "New nucleotide substitutions", | ||
| "description": f"Nucleotide substitutions not present in the parent lineage ({parent}).", |
Comment on lines
47
to
51
| { | ||
| "type": "filterObject", | ||
| "name": "Nucleotide substitutions", | ||
| "description": "All nucleotide substitutions that define this lineage.", | ||
| "filterObject": {"nucleotideMutations": nuc_subs}, |
This file contains hidden or 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
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 #1357
Summary
Explains what 'Nucleotide substitutions' vs 'New nucleotide substitutions' means for each lineage collection. The parent lineage name is included in the description of the 'New' variants. These descriptions surface in the collection detail page and as tooltips in the queries-over-time table.
Screenshot
PR Checklist
All necessary documentation has been adapted.The implemented feature is covered by an appropriate test.