Code Consensus

Author: Nicholas Sunderland ([email protected])

Collaborative phenotype coding toolkit: Vue + PrimeVue frontend (Netlify) and FastAPI backend (Fly.io) with Supabase auth/DB.

Structure

• frontend/: Vue 3 + Vite app (PrimeVue UI). Routes: / home, /accordion consensus tool, /examples gallery, /terms legal, /flow flow view.
• backend/: FastAPI API, Supabase DB access, seed/utility scripts (db/). Example endpoint /api/example-phenotypes.
• backend/db/schema.sql: Supabase schema (phenotypes, selections, consensus, codes).
• backend/db/ukb_cooccurrence.py: Generates co-occurrence metrics (jaccard/lift/counts) CSV for import.

Quickstart

Backend (FastAPI):

cd backend
python -m venv venv && source venv/bin/activate
pip install -r requirements.txt
uvicorn main:app --reload

Frontend (Vue):

cd frontend
npm install
npm run dev

Environment

Create .env files:

• backend/.env: DATABASE_URL=..., EXAMPLE_PROJECT_IDS=uuid1,uuid2, ORIGIN=http://localhost:5173, etc.
• frontend/.env: VITE_API_URL=http://localhost:8000, VITE_SUPABASE_URL=..., VITE_SUPABASE_ANON_KEY=....

Supabase auth setup (short)

1. In Supabase: enable GitHub/Google providers; set Site URL http://localhost:5173 (and production URL), redirect URLs include both local and production.
2. Copy project.supabase.co URL and anon key into frontend/.env.
3. Backend uses DATABASE_URL (service role) and EXAMPLE_PROJECT_IDS for public examples.
4. RLS: ensure read-only policies for vocab tables; project/phenotype/selection policies already in schema.sql.

Seeding data

From backend/db:

• Seed test data: python seed_db_testing.py
• Seed production sample: python seed_db.py
• Generate co-occurrence CSV: python ukb_cooccurrence.py (reads backend/.env, outputs ~/Downloads/cooccurrence_web_summary.csv) Import CSV into code_cooccurrence (ordered pairs enforced).

Deploy

• Frontend (Netlify): set env vars (VITE_API_URL, VITE_SUPABASE_URL, VITE_SUPABASE_ANON_KEY); build command npm run build, publish frontend/dist.
• Backend (Fly.io): set VITE_DATABASE_URL, EXAMPLE_PROJECT_IDS, CORS ORIGIN; run fly deploy from backend/.

Tests

• Frontend: cd frontend && npm test (Vitest).
• Backend: cd backend && python -m unittest discover -s tests.

Notes

• Do not store PHI/PII in free-text fields; code selections should reference vocab only.
• Counts metric suppresses low numbers (<100). Service role bypasses RLS; public exposure should use curated endpoints only.