/genome: endless procedural double-helix viewer over the live CPIC gene catalogue

[AdaWorldAPI]

What

A new /genome route — an endless procedural double helix that visualises the GUID address space CPIC lives in, rather than a sized mesh. Standalone (GenomeHelix.tsx); shares nothing with the working /cpic CpicCockpit, so it can never break it (same isolation discipline as /helix vs /body).

The premise: the OGAR GUID address space is billions of slots (HEEL·HIP·TWIG cascade); CPIC fills almost none of it. So this isn't a fixed mesh — it's an infinite scaffold that is the address space, with the sparse real pharmacogenes lighting up loci in it.

How (cheap by construction — repetition placed by a function of the address)

• One instanced sugar-bead per strand + one instanced rung, a fixed pool of 240 base-pairs (THREE.InstancedMesh). Position is a pure function of the integer step: angle = step·goldenAngle, y = step·rise. No baked geometry, no forced shape.
• Endless: the 240 instances are a sliding window over an infinite strand — scroll advances, the same instances re-address higher steps, the ends fade into fog. Infinite length, constant instance count, no reallocation.
• Fractal: the wheel grows density; spacing subdivides ×16 per tier, so zoom descends the 16-ary cascade ("scale = the next cascade level"). The golden angle (most-irrational) makes the scaffold aperiodic — endless, not looped.

Real CPIC data (not placeholders)

• Loci come from GET /api/cpic/catalog (the live gene list); the canonical CPIC level-A list is only a fallback when the endpoint is absent (old deploy), so /genome always renders. The header shows live vs fallback + the real gene count.
• Each gene gets a stable FNV-1a address from its name (linear-probe on the rare collision) → same gene, same locus forever; addressability with zero storage.
• Click a lit gene (drag-aware, so orbiting never triggers it) raycasts the rung InstancedMesh and hands off to the working reasoner at /cpic?gene=<gene>.
• CpicCockpit now honors ?gene= as its initial gene (additive, backward-compatible — no param ⇒ the existing default), so the handoff lands on the clicked gene and its diplotype→phenotype→recommendation 2-hop.

Scope / safety

• New /genome route + GenomeHelix.tsx; the only edit to existing code is the additive ?gene= read in CpicCockpit.tsx. /cpic behaviour is unchanged when no param is present.
• Separate from the FMA body work (PR helix: 20260629b re-bake (vessel diameter + teeth→skeleton) + living-anatomy browser (search / x-ray / LOD) #66) — different feature, different branch.

Verification

• tsc --noEmit + vite build clean.
• /api/cpic/catalog + /api/cpic/reason are the existing endpoints the working /cpic cockpit already uses; /genome consumes the catalog read-only and deep-links into the reasoner.

Follow-ups (not in this PR)

• Hover-highlight + a small inline panel (gene → its CPIC drugs) so the payload is visible without leaving the helix.
• Literal per-rung 16-child expansion on deep zoom (the current zoom subdivides spacing; a true recursive node expansion is the next step).

🤖 Generated with Claude Code

https://claude.ai/code/session_01RhpwkHGgia2TuDFvdnuQdE

---

Generated by Claude Code

Summary by CodeRabbit

• New Features

  • Added a new genome visualization page with interactive orbit, zoom, and click-to-open gene navigation.
  • The CPIC view now opens with a gene from the URL when provided, making shared links more precise.

• Bug Fixes

  • Updated tissue and layer classification so connective structures are handled correctly in visualizations and analysis.
  • Refreshed embedded assets to the latest published version.

[coderabbitai]

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: ed099aab-4951-4783-a38f-e3aaf1307398

📥 Commits

Reviewing files that changed from the base of the PR and between e32429d and 360a386.

📒 Files selected for processing (8)

• Dockerfile
• cockpit/public/body.manifest.json
• cockpit/src/CpicCockpit.tsx
• cockpit/src/GenomeHelix.tsx
• cockpit/src/main.tsx
• crates/osint-bake/tools/audit_body_semantics.py
• crates/osint-bake/tools/bake_body_v3.py
• crates/osint-bake/tools/bake_torso_splat.py

---

📝 Walkthrough

Walkthrough

Adds a new connective tissue type (layer 7) to the body bake and audit pipeline tools. Introduces a GenomeHelix Three.js React page at /genome that renders an animated double-helix with CPIC gene loci, raycast picking, and navigation. Reads the gene URL param in CpicCockpit. Bumps wire asset downloads to version 20260629c.

Changes

Connective tissue layer 7 in bake pipeline

Layer / File(s)	Summary
Connective tissue classification and rendering params crates/osint-bake/tools/bake_torso_splat.py, crates/osint-bake/tools/bake_body_v3.py	TYPEKEYS gains a "connective" entry matching ligament/membrane/tendon/fascia/retinaculum keywords; SYSTEM_OF maps it to "musculoskeletal"; TISSUE_RGB, TISSUE_OPACITY, TISSUE_CONTAINERS extended; LAYER_OF in bake_body_v3 adds "connective": 7.
Audit layer mapping and QA-3 assertions crates/osint-bake/tools/audit_body_semantics.py	Adds "connective": 7 to LAYER_OF, fixes retina regex to word-boundary form, and asserts connective landmarks (interosseous membrane, tendons, ligaments) resolve to layer 7.

GenomeHelix page and asset bump

Layer / File(s)	Summary
Wire asset version bump to 20260629c Dockerfile, cockpit/public/body.manifest.json	Dockerfile curl URLs updated from 20260629b to 20260629c for both body SoA and helix SoA; manifest helix_latest and note updated to match.
GenomeHelix Three.js scene and helpers cockpit/src/GenomeHelix.tsx	New file: FNV-1a gene-to-step hashing (lociFrom), canvas label sprites, Three.js instanced strand/rung scene with scroll animation, raycast picking, drag-orbit, wheel zoom, and full GPU/listener cleanup on unmount.
GenomeHelix React component and /genome route cockpit/src/GenomeHelix.tsx, cockpit/src/main.tsx, cockpit/src/CpicCockpit.tsx	React component fetches /api/cpic/catalog with FALLBACK_GENES fallback, mounts renderer when genes are ready, renders overlay UI; /genome route added to router; CpicCockpit reads ?gene= URL param.

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~45 minutes

Possibly related PRs

• AdaWorldAPI/q2#52: Introduces bake_torso_splat.py, which this PR directly extends with the new "connective" tissue bucket.
• AdaWorldAPI/q2#65: Modifies the same helix_latest manifest field and Dockerfile helix SoA download that this PR advances to 20260629c.
• AdaWorldAPI/q2#66: Updates the same Dockerfile helix SoA download path and body.manifest.json helix_latest field for the prior version bump.

Poem

🐇 Hop along the double helix strand,
connective tissue now has layer seven planned,
the genome page spins up with Three.js might,
gene loci glow like stars in the night,
20260629c freshly baked and bright! 🧬

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

---

Thanks for using CodeRabbit! It's free for OSS, and your support helps us grow. If you like it, consider giving us a shout-out.

❤️ Share

• X
• Mastodon
• Reddit
• LinkedIn

_{Comment @coderabbitai help to get the list of available commands.}