README.md

collection-seeding

Seeds the backend with example collections:

• covid-resistance-mutations — resistance mutation data for 3CLpro, RdRp, and Spike mAb
• covid-pango-lineages — one collection per pango lineage, with nucleotide substitutions as variants
• covid-pango-lineages-sample — same as above but limited to 10 lineages, for quick testing

The script is idempotent — re-running it will create new collections or update existing ones (matched by name). If a collection's name changes in the source, the old entry is orphaned and a new one is created.

Use --repeat-interval-hours N (or $REPEAT_INTERVAL_HOURS) to run on a loop — re-seeds every N hours. Without it, the script runs once and exits.

Via Docker Compose

The seeder runs automatically as part of Docker Compose:

BACKEND_TAG=latest WEBSITE_TAG=latest SEEDER_TAG=latest docker compose up

Running locally

Requires pixi. Install dependencies once:

pixi install

Then use the provided tasks:

pixi run seed                    # all sources
pixi run seed-resistance         # resistance mutations only
pixi run seed-lineages           # pango lineages only
pixi run seed-lineages-sample    # first 10 pango lineages (quick test)

To target a different backend:

pixi run seed --url http://localhost:4321

Run pixi run seed --help for all options, including --source, --list, --repeat-interval-hours, and --url.

Adding a new source

1. Create sources/your_source.py and implement the Source ABC:

   from sources import Source
   from models import Collection
   
   class YourSource(Source):
       name = "your-source-name"  # used with --source flag
   
       def get_collections(self) -> list[Collection]:
           ...

2. Register it in sources/registry.py by adding it to ALL_SOURCES.