feat: add outbreaks.json (#484) #490
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Pull Request Overview
This PR adds support for serializing outbreak descriptions via next-mdx-remote while refactoring the catalog build process into separate files. Key changes include the fix for outbreak definition issues (escaping a “<” character and correcting a file path), splitting build-catalog.ts into modular files, and adding outbreak types to the common entities.
Reviewed Changes
Copilot reviewed 12 out of 13 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| catalog/source/outbreaks/mpox.md | Fixed escaping for the “<” character in the mortality line. |
| catalog/source/outbreaks.yml | Updated the path for the malaria outbreak definition. |
| catalog/build/ts/utils.ts | Introduced new helper functions for file operations. |
| catalog/build/ts/build-workflows.ts | Added workflow build logic. |
| catalog/build/ts/build-outbreaks.ts | Added outbreak build logic using MDX serialization. |
| catalog/build/ts/build-organisms.ts | Constructed organisms from genome data. |
| catalog/build/ts/build-catalog.ts | Refactored to leverage new build modules. |
| catalog/build/ts/build-assemblies.ts | Moved assembly-building logic from the consolidated file. |
| app/apis/catalog/brc-analytics-catalog/common/schema-entities.ts | Exported outbreak priority and resource type enums. |
| app/apis/catalog/brc-analytics-catalog/common/entities.ts | Added outbreak interfaces to the common entities. |
Files not reviewed (1)
- package.json: Language not supported
Comments suppressed due to low confidence (2)
catalog/source/outbreaks.yml:103
- [nitpick] Confirm that the updated file name 'plasmodium_falciparum.md' is correct and consistent with the outbreak naming conventions used elsewhere in the project.
+ path: outbreaks/plasmodium_falciparum.md
catalog/source/outbreaks/mpox.md:13
- Ensure that escaping the '<' character with a backslash is necessary for MDX serialization to render the content as intended. If not, consider removing the escape to improve readability.
+- **Mortality**: Case-fatality rate \<0.1% in non-endemic countries (2022), ~10% in Africa for more virulent clades
d-callan
approved these changes
Apr 30, 2025
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Closes #484
next-mdx-remotebuild-catalog.tsinto multiple files because I felt it was getting a bit too busy --build-assemblies.ts,build-organisms.ts, andbuild-workflows.tsare all just existing code<in the mpox description and fixing the description path for Plasmodium falciparum malaria)