biokea.ai

The BioKEA website — Astro 6 + Tailwind 4, deploying to Cloudflare Workers.

BioKEA is an AI company with a wet-lab moat: a 5,000+ sq ft Berkeley lab and an AI pipeline from field sample to verifiable scientific claim. The LDC also runs as a molecular sequencing service for environmental-DNA and biodiversity-omics customers.

Run locally

npm install
npm run dev            # http://localhost:4321

Or, without a local Node install, via Docker (dev server only — the Cloudflare Worker deploy still goes through wrangler/CI):

docker compose up      # http://localhost:4321, live-reloads from ./src

Test

npm run check          # astro check (TypeScript + Astro diagnostics)
npm test               # vitest — unit tests
npm run test:e2e       # playwright — per-page smokes + API endpoints

CI runs the same three on every PR (.github/workflows/deploy.yml).

Build + preview

npm run build          # outputs to dist/
npm run preview

Deploy

Cloudflare Workers, via wrangler deploy. CI handles this automatically on push to main. Secrets:

wrangler secret put RESEND_API_KEY
# non-secret vars (CONTACT_FROM_EMAIL, CONTACT_TO_EMAIL) live in wrangler.toml

Migrations

Supabase schema changes live in migrations/*.sql, applied by hand:

• migrations/0005_quotes.sql
• migrations/0006_quote_payments.sql
• migrations/0007_shopify.sql

Apply in the Supabase Dashboard → SQL Editor, in order; 0006 must be applied before the first deploy of the payments code (existing quotes get status = 'quoted'), and 0007 before the first deploy of the Shopify gateway (renames the Stripe-era column names to provider-neutral ones — free, since nothing had reached production on the old names).

Payments (Shopify)

Customers configure a quote and pay in full either from /quote (or /quote/<token> for a saved quote) or from a service product page on store.biokea.ai — both host the same quote widget bundle. Under-shipping settles as a 12-month credit, not a refund — see the spec. Staff issue the balance invoice from /admin/quotes/<number> when more samples arrive than quoted. The payment rail is Shopify Draft Orders: no card data touches our infrastructure, and pricing stays authoritative on our Worker — Shopify never computes a service price. Design: docs/superpowers/specs/2026-08-17-shopify-store-design.md. Store setup (domain, custom app, webhooks, products, theme, Turnstile hostname): docs/shopify/STORE-SETUP.md.

Secrets:

wrangler secret put SHOPIFY_ADMIN_TOKEN     # custom app Admin API token — write_draft_orders, read_orders, read_products
wrangler secret put SHOPIFY_WEBHOOK_SECRET  # Settings → Notifications → Webhooks signing key

Vars (wrangler.toml): SHOPIFY_STORE_DOMAIN (biokea.myshopify.com), SHOPIFY_STORE_HANDLE (biokea — builds the admin.shopify.com/store/<handle>/… links on the admin quote page), SHOPIFY_PAYMENT_TERMS_TEMPLATE (optional, default NET_30 — net terms on the draft order for PO buyers).

Rollout order:

1. Apply migrations/0007_shopify.sql in Supabase (see Migrations, above).
2. Create the Cloudflare Access app and set CF_ACCESS_TEAM_DOMAIN / CF_ACCESS_AUD in wrangler.toml (unchanged from before payments): Zero Trust → Access → Applications → Add → Self-hosted; domain biokea.ai, paths /admin/* and /api/admin/*; policy Allow emails ending @biokea.ai.
3. Walk docs/shopify/STORE-SETUP.md steps 1–6: create the store, connect store.biokea.ai (DNS-only CNAME), create the biokea-website custom app and copy its Admin API token, create the four webhook topics pointed at https://biokea.ai/api/shopify/webhook and copy the signing key, confirm Net 30 payment terms are available, mark the service products non-taxable.
4. wrangler secret put SHOPIFY_ADMIN_TOKEN / SHOPIFY_WEBHOOK_SECRET, confirm the vars above, deploy.
5. STORE-SETUP.md steps 7–8: create the two service products (specimen-barcoding, edna-metabarcoding) and the eight placeholder goods; on the product.quote template, add a Custom Liquid section pasting in docs/shopify/product-quote-section.liquid — it mounts the same widget bundle served from biokea.ai/widget/quote.js and .css.
6. Add store.biokea.ai to the Turnstile widget's allowed hostnames (Cloudflare dashboard).
7. Walk the test-mode checklist with Shopify's Bogus Gateway (deposit → balance → paid, draft delete, net-30 invoice, refund, goods checkout, domain + TLS), then switch on Shopify Payments live.
8. Marketing CTAs (/pricing, /services, the Nav "Store" link) already point at the store — nothing left to flip.

Local dev: copy .dev.vars.example → .dev.vars — it lists every key the Worker reads, including a Shopify test-app token. npm run dev builds the widget bundle first (widget:build, gitignored output at public/widget/quote.{js,css}) and then starts the dev server. Set CF_ACCESS_DEV_EMAIL to reach /admin locally.

Architecture

src/
├── pages/
│   ├── *.astro                 # Routes (/, /mission, /lab, /pipeline, /projects,
│   │                           #         /agentis, /contact, 404)
│   └── api/
│       ├── contact.ts          # POST — contact form → Resend
│       ├── team.json.ts        # GET — static JSON of team
│       ├── projects.json.ts    # GET — static JSON of projects
│       └── capabilities.json.ts # GET — lab + services + equipment + partners
├── layouts/BaseLayout.astro    # Global chrome; accepts noindex prop
├── components/
│   ├── layout/                 # Nav, Footer, Seo
│   ├── sections/               # Hero, Thesis, Evidence, Ecosystem, Origin, CtaBand
│   └── ui/                     # Eyebrow, StatPill, PhotoCard, Portrait, PipelineStep,
│                               # PartnerMark, ProjectCard
├── data/                       # Typed content modules
│   ├── team.ts  partners.ts  projects.ts
│   ├── milestones.ts  stats.ts  pipeline.ts  equipment.ts
└── styles/                     # tokens.css (design tokens), global.css (Tailwind entry)

public/
├── llms.txt                    # Agent-first site summary (llmstxt.org)
├── assets/images/              # Logo, portraits, lab photos, illustrations
└── favicon.*, robots.txt, site.webmanifest

tests/
├── unit/                       # Vitest — content shape + contact endpoint
└── e2e/                        # Playwright — per-page + JSON-LD + /api/*.json

docs/                           # Briefs, references, source material, archive.
                                # See docs/README.md.

Agent-facing surface

• /llms.txt — agent-first site summary per llmstxt.org
• /api/team.json, /api/projects.json, /api/capabilities.json — machine-readable data
• Per-page JSON-LD @graph: Organization, Person, ResearchOrganization, Place, Service, SoftwareApplication, Dataset, SoftwareSourceCode, HowTo

Content changes

Most content lives in src/data/*.ts. Editing those files is usually enough — the pages + JSON-LD + /api/*.json endpoints all read from them.

See CONTRIBUTING.md for the full workflow.

Docs

docs/ is source material and planning, not shipped content. See docs/README.md for the layout.

• docs/briefs/ — LDC visual style guide, imagery production brief
• docs/references/ — external PDFs (AI-first bio-publishing deck, capabilities deck, CIBI Ecography proof)
• docs/source/ — raw inputs for public/assets/images/
• docs/imagery-production-pack/ — the delivered 13-asset cream-palette pack
• docs/superpowers/ — design spec + implementation plan for the Astro overhaul
• docs/archive/ — pre-Astro-migration artifacts (see archive/README.md for pointers to the old Next.js source in git history)

Known open items

• Cloudflare Web Analytics token — placeholder REPLACE_WITH_CF_BEACON_TOKEN in src/layouts/BaseLayout.astro
• Replace advisor placeholder portraits (portrait-placeholder.svg) with real photos for Sunit Jain and Greg Fedewa
• Dependabot is wired up (.github/dependabot.yml); review the initial wave of PRs when they land