---
phase: 01-genome-migration-cleanup
plan: "01"
subsystem: genome
tags: [migration, data-paths, genome, meatspace]
dependency_graph:
  requires: []
  provides: [genome-meatspace-paths]
  affects: [genome-service, clinvar-service, epigenetic-service, identity-tab]
tech_stack:
  added: []
  patterns: [PATHS.meatspace]
key_files:
  created:
    - .changelog/v1.14.x.md
  modified:
    - server/services/genome.js
    - server/services/clinvar.js
    - server/services/epigenetic.js
    - server/routes/genome.js
    - client/src/components/digital-twin/tabs/IdentityTab.jsx
    - docs/API.md
    - docs/features/identity-system.md
decisions:
  - "Used PATHS.meatspace (existing constant) rather than creating a new one — avoids duplication"
  - "Moved data files with mv (not copy) to ensure no stale files remain in data/digital-twin/"
  - "Updated docs/API.md section header from 'Digital Twin Genome' to 'Meatspace Genome' for consistency"
metrics:
  duration: "108 seconds"
  completed: "2026-02-26"
  tasks_completed: 3
  files_modified: 8
---

# Phase 01 Plan 01: Genome Migration Cleanup Summary

Complete migration of genome data from digital-twin to meatspace — services now read from `data/meatspace/`, navigation links to live route, docs updated.

## Tasks Completed

| Task | Name | Commit | Files |
|------|------|--------|-------|
| 1 | Update service data paths and route comments | 6503b70 | genome.js, clinvar.js, epigenetic.js, routes/genome.js |
| 2 | Fix client navigation and update documentation | 912946f | IdentityTab.jsx, docs/API.md, docs/features/identity-system.md |
| 3 | Migrate genome data files from digital-twin to meatspace | (disk only — gitignored) | data/meatspace/{genome.json,genome-raw.txt,clinvar-index.json,clinvar-meta.json} |

## What Was Done

The genome API was partially migrated — the Express mount point (`/api/meatspace/genome`) and client API calls were already correct, but three service files still read from `data/digital-twin/`, route JSDoc comments were stale, IdentityTab had a dead navigation link pointing to `/digital-twin/genome`, and docs referenced old paths.

This plan completed the migration:

1. **Service paths:** All three services (`genome.js`, `clinvar.js`, `epigenetic.js`) now use `PATHS.meatspace` instead of `PATHS.digitalTwin` for their data directory constant. The `PATHS.meatspace` constant already existed in `server/lib/fileUtils.js`.

2. **Route comments:** All 18 JSDoc route comments in `server/routes/genome.js` updated from `/api/digital-twin/genome` to `/api/meatspace/genome` (comment-only changes, no functional code affected).

3. **Client navigation:** IdentityTab "View Full Genome" button now calls `navigate('/meatspace/genome')` instead of the broken `/digital-twin/genome`. The `/meatspace/genome` route was already live via `MeatSpace.jsx` case `'genome'`.

4. **Documentation:** `docs/API.md` section header and all 16 endpoint paths updated to `/meatspace/genome`. `docs/features/identity-system.md` updated two stale references (`data/digital-twin/genome.json` and `/digital-twin/genome` route).

5. **Data migration:** Four files moved from `data/digital-twin/` to `data/meatspace/` using `mv`. All files are gitignored (user data). Verified `genome.json` parses as valid JSON with `uploaded: true` and 117 saved markers.

## Verification Results

- Zero occurrences of `PATHS.digitalTwin` in genome.js, clinvar.js, epigenetic.js
- Zero occurrences of `/digital-twin/genome` anywhere in server routes, client src, or docs
- All four genome/clinvar files present in `data/meatspace/`, none remaining in `data/digital-twin/`
- `genome.json` valid: `uploaded: true`, 117 markers
- 1192 server tests pass (42 test files, no regressions)

## Deviations from Plan

### Auto-fixed Issues

**1. [Rule 2 - Missing] Updated docs/API.md section header**
- **Found during:** Task 2
- **Issue:** The `### Digital Twin Genome` section header was still stale after updating all endpoint paths
- **Fix:** Updated section header to `### Meatspace Genome` for consistency
- **Files modified:** `docs/API.md`
- **Commit:** 912946f

**2. [Rule 2 - Missing] Created v1.14.x.md changelog**
- **Found during:** Post-task
- **Issue:** CLAUDE.md requires updating changelog when making changes; no v1.14.x.md existed for the current version
- **Fix:** Created `.changelog/v1.14.x.md` with entries for all genome migration changes
- **Files modified:** `.changelog/v1.14.x.md`
- **Commit:** (in metadata commit)

## Self-Check: PASSED

Files verified:
- FOUND: server/services/genome.js (contains PATHS.meatspace)
- FOUND: server/services/clinvar.js (contains PATHS.meatspace)
- FOUND: server/services/epigenetic.js (contains PATHS.meatspace)
- FOUND: data/meatspace/genome.json
- FOUND: data/meatspace/genome-raw.txt
- FOUND: data/meatspace/clinvar-index.json
- FOUND: data/meatspace/clinvar-meta.json
- MISSING from digital-twin: genome.json, genome-raw.txt, clinvar-index.json, clinvar-meta.json (confirmed)

Commits verified:
- FOUND: 6503b70 (Task 1)
- FOUND: 912946f (Task 2)
