---
phase: 01-genome-migration-cleanup
verified: 2026-02-26T22:00:00Z
status: passed
score: 5/5 must-haves verified
re_verification: false
---

# Phase 1: Genome Migration Cleanup Verification Report

**Phase Goal:** Genome data reads from the correct directory and all stale digital-twin references are eliminated
**Verified:** 2026-02-26
**Status:** PASSED
**Re-verification:** No — initial verification

## Goal Achievement

### Observable Truths

| # | Truth | Status | Evidence |
|---|-------|--------|----------|
| 1 | All route comments in genome.js reference `/api/meatspace/genome/` (zero digital-twin references) | VERIFIED | 19 occurrences of `meatspace/genome` in `server/routes/genome.js`, 0 occurrences of `digital-twin`; grep returns exit 1 (no matches) |
| 2 | IdentityTab "View Full Genome" button navigates to `/meatspace/genome` (a live route) | VERIFIED | Line 190: `onClick={() => navigate('/meatspace/genome')}` confirmed; `MeatSpace.jsx` line 29 confirms `case 'genome'` is live |
| 3 | genome.js, clinvar.js, and epigenetic.js read/write data from `data/meatspace/` directory | VERIFIED | genome.js line 7: `GENOME_DIR = PATHS.meatspace`; clinvar.js line 9: `GENOME_DIR = PATHS.meatspace`; epigenetic.js line 6: `DATA_DIR = PATHS.meatspace`; zero `PATHS.digitalTwin` remaining |
| 4 | Genome data files (genome.json, genome-raw.txt, clinvar-index.json, clinvar-meta.json) exist in `data/meatspace/` | VERIFIED | All four files confirmed on disk: genome.json (82KB), genome-raw.txt (16MB), clinvar-index.json (44MB), clinvar-meta.json (142B) |
| 5 | No genome data files remain in `data/digital-twin/` | VERIFIED | `ls data/digital-twin/genome.json data/digital-twin/genome-raw.txt data/digital-twin/clinvar-index.json data/digital-twin/clinvar-meta.json` → "No such file or directory" for all four |

**Score:** 5/5 truths verified

### Required Artifacts

| Artifact | Expected | Status | Details |
|----------|----------|--------|---------|
| `server/routes/genome.js` | Corrected route comments containing `/api/meatspace/genome` | VERIFIED | 19 meatspace references, 0 digital-twin references |
| `server/services/genome.js` | Correct data directory via `PATHS.meatspace` | VERIFIED | Line 7: `const GENOME_DIR = PATHS.meatspace;` |
| `server/services/clinvar.js` | Correct data directory via `PATHS.meatspace` | VERIFIED | Line 9: `const GENOME_DIR = PATHS.meatspace;` |
| `server/services/epigenetic.js` | Correct data directory via `PATHS.meatspace` | VERIFIED | Line 6: `const DATA_DIR = PATHS.meatspace;` |
| `client/src/components/digital-twin/tabs/IdentityTab.jsx` | Working genome navigation to `/meatspace/genome` | VERIFIED | Line 190: `navigate('/meatspace/genome')` |
| `data/meatspace/genome.json` | Migrated genome metadata | VERIFIED | 82KB file, parses as valid JSON: `uploaded: true`, `savedMarkers` is an object with 117 entries |
| `data/meatspace/genome-raw.txt` | Migrated raw genome file | VERIFIED | 16MB file present on disk |
| `data/meatspace/clinvar-index.json` | Migrated ClinVar index | VERIFIED | 44MB file present on disk |
| `data/meatspace/clinvar-meta.json` | Migrated ClinVar metadata | VERIFIED | 142B file present on disk |

### Key Link Verification

| From | To | Via | Status | Details |
|------|----|-----|--------|---------|
| `server/services/genome.js` | `data/meatspace/genome.json` | `GENOME_DIR = PATHS.meatspace` | WIRED | Pattern `PATHS\.meatspace` found at line 7; data file confirmed on disk |
| `server/services/clinvar.js` | `data/meatspace/clinvar-index.json` | `GENOME_DIR = PATHS.meatspace` | WIRED | Pattern `PATHS\.meatspace` found at line 9; data file confirmed on disk |
| `client/src/components/digital-twin/tabs/IdentityTab.jsx` | `MeatSpace.jsx` genome tab | `navigate('/meatspace/genome')` | WIRED | Pattern `navigate\('/meatspace/genome'\)` found at line 190; `MeatSpace.jsx` confirms live `case 'genome'` route |

### Requirements Coverage

| Requirement | Source Plan | Description | Status | Evidence |
|-------------|------------|-------------|--------|----------|
| GEN-01 | 01-01-PLAN.md | Route comments updated from `/api/digital-twin/genome/` to `/api/meatspace/genome/` | SATISFIED | 19 meatspace route comment references in `server/routes/genome.js`, 0 digital-twin references remain |
| GEN-02 | 01-01-PLAN.md | IdentityTab Genome card removed or redirected to `/meatspace/genome` | SATISFIED | `IdentityTab.jsx` line 190 navigates to `/meatspace/genome`; destination route is live |
| GEN-03 | 01-01-PLAN.md | genome.js data paths verified to read from correct directory | SATISFIED | All three services (genome.js, clinvar.js, epigenetic.js) use `PATHS.meatspace`; data files confirmed in `data/meatspace/` |

All three GEN requirements fully satisfied. No orphaned requirements — REQUIREMENTS.md maps only GEN-01, GEN-02, GEN-03 to Phase 1, and all three are covered by plan 01-01.

### Anti-Patterns Found

No anti-patterns found. Scan of all modified files (`server/routes/genome.js`, `server/services/genome.js`, `server/services/clinvar.js`, `server/services/epigenetic.js`, `client/src/components/digital-twin/tabs/IdentityTab.jsx`) returned zero matches for TODO, FIXME, placeholder patterns, empty implementations, or console.log-only stubs.

**Note on `docs/features/identity-system.md`:** The file contains references to `data/digital-twin/chronotype.json` and `data/digital-twin/identity.json` (lines 260-262). These are for a future identity orchestrator feature (not genome), are unrelated to this phase's scope, and do not constitute stale genome references. Not a concern.

**Note on `data/meatspace/genome.json` `savedMarkers` structure:** The SUMMARY described `savedMarkers` as having `length: 117`, but it is an object keyed by UUID (not an array), so `.length` is `undefined`. The actual data is correct — 117 saved markers exist as keys in the object. This is a minor SUMMARY inaccuracy, not a code defect.

### Human Verification Required

None. All must-haves are programmatically verifiable and confirmed.

The one item that would benefit from a manual smoke test is runtime behavior — confirming the genome API actually serves data successfully when hit over HTTP. This is a confidence check rather than a gap; the code paths are correctly wired.

### Commits Verified

| Hash | Task | Files |
|------|------|-------|
| 6503b70 | Task 1: service paths + route comments | genome.js, clinvar.js, epigenetic.js, routes/genome.js |
| 912946f | Task 2: client navigation + docs | IdentityTab.jsx, docs/API.md, docs/features/identity-system.md |
| Task 3 | Data file migration (disk only — gitignored) | data/meatspace/{genome.json,genome-raw.txt,clinvar-index.json,clinvar-meta.json} |

Both code commits confirmed present in git history.

### Gaps Summary

No gaps. All five observable truths verified, all nine artifacts confirmed (exists, substantive, wired), all three key links confirmed wired, and all three requirements (GEN-01, GEN-02, GEN-03) are satisfied with implementation evidence.

---

_Verified: 2026-02-26_
_Verifier: Claude (gsd-verifier)_
