README.md

October 16, 2025 · View on GitHub

PETadex.io [Under construction]

PETadex.io is an open‑source platform for exploring plastic‑degrading enzymes. The repository has two‑tiers

petadex.io/
├── backend/     - Node/Express API (PostgreSQL – fastaa table)
├── frontend/    - Gatsby static site (served by GitHub Pages)
├── .github/     - Workflows & AI helpers
└── docs/        - OpenAPI spec & misc assets

Local quick start (development server)

clone & enter repo

git clone https://github.com/ababaian/petadex.io.git && cd petadex.io

backend → http://localhost:3001

 cd backend && cp .env.example .env  # fill in DB creds
 npm ci && npm run dev

frontend → http://localhost:8000

 <!-- Do the following in new terminal  -->
 cd ../frontend && npm ci
 npm run develop

Production architecture

┌───────────────┐        HTTPS           ┌────────────────┐       TCP 5432      ┌───────────────┐
│  GitHub Pages │     petadex.net    ─▶  │  NGINX @ EC2   │  ──►   AWS RDS      │ PostgreSQL DB │
│  (Gatsby)     │                        │ api.petadex.net│                     │   petadex     │
└───────────────┘                        └────────────────┘                     └───────────────┘
                                              │
                                              └─> PM2‑managed Node/Express (backend/)
  • GitHub Pages hosts the static site built from /frontend.
  • EC2 runs NGINX which terminates SSL (/etc/letsencrypt/live/api.petadex.net/*) and proxies /api/* to the Express server on port 3001.
  • PostgreSQL RDS stores enzyme sequences (fastaa table) and future datasets.

CI/CD overview

WorkflowPathPurpose
frontend-ci-deploy.yml.github/workflowsBuilds Gatsby from /frontend, injects GATSBY_API_URL, deploys to GitHub Pages.
backend-deploy.yml.github/workflowsSSHes into EC2, pulls latest /backend code, npm ci, pm2 restart.

All sensitive values (DB creds, API URL, EC2 SSH key) live in GitHub Secrets.

Contributing

PETadex community — feel free to open issues & PRs!

  1. Fork & branch from main.
  2. Run npm run lint in both sub‑projects.
  3. Add or update unit tests (backend/tests, frontend/src/__tests__).
  4. PR → CI must pass.