mycelium-hq/ai-brain-starter/backfill-journal-body-context

backfill-journal-body-context

Reads existing daily journals, pulls health-mcp data for each entry's date, and appends a "Body track" section BELOW the original verbatim content. The original entry text is NEVER modified — the rule from feedback_journal_verbatim_words.md is non-negotiable.

When to use

• User says /backfill-journal-body-context
• User wants their existing journals enriched with body data (HRV, sleep, recovery, cycle phase) retroactively
• User wants to see what /weekly and /monthly would surface if they had been pulling body data all along
• After running /health-setup for the first time and importing a backfill window of biometric data

Do NOT use for:

• Brand-new journal entries (daily-journal already pulls body context via health-context skill)
• Editing journal content beyond appending the body section
• Anything that touches the original verbatim journal body

How it works

1. Determine the date range. Default: --year <current-year> (Jan 1 to today).
2. Find journal entries in that range using [VAULT_PATH]/⚙️ Meta/journal-index.json (or Meta/journal-index.json on non-emoji vaults; rebuild if stale).
3. For each entry:

• Read the file
• Check if it already has a ## Body track (health-mcp, backfilled YYYY-MM-DD) section — if yes, skip (idempotent)
• Call health_journal_context(date, voice_profile="warm") for the data + rendered prose
• Call health_cycle_context(date) if cycle data exists (for women's cycle awareness)
• Call health_recovery_score(date) + health_sleep_score(date) for the scores
• Call health_lab_panel(date, lookback_days=180) for any out-of-range markers active that period
• Pair the body data with the entry's floor tag (from frontmatter floor_level + floor)
• Render the body-track section using the template below
• Append BELOW the original content with a clear divider

1. Print summary: N entries processed, M backfilled, K skipped.

Body track template

Append below the original journal content, after a blank line + horizontal rule:

 
---
 
## Body track (health-mcp, backfilled {{today_iso}})
 
*Auto-generated context. Original journal entry above is preserved verbatim.*
 
**Floor that day:** {{floor_name}} ({{floor_level}})
 
**Cycle phase** (if cycle data exists): {{phase}}, cycle day {{cycle_day}}{{ — irregularity flag if any}}
 
**The body that day:**
-HRV: {{hrv_ms}} ms ({{hrv_delta_pct}}% vs 30-day baseline)
-RHR: {{rhr_bpm}} bpm
-Sleep: {{sleep_asleep_min}} min ({{sleep_efficiency}}% efficiency, REM {{rem_min}}min, deep {{deep_min}}min)
-Steps: {{steps_total}}
-Workouts: {{workout_count}} ({{workout_min}}min)
-Mindful: {{mindful_min}}min
 
**Scores:**
-Recovery: {{recovery_score}}/100 ({{confidence}} confidence)
-Sleep: {{sleep_score}}/100
 
**Floor-paired interpretation** (1-3 sentences, see synthesis rule below): {{interpretation}}
 
**Lab markers** (if any out-of-range result from the prior 180 days, paired with today): {{lab_flags}}

Synthesis rule (the helpful-not-just-cool part)

The interpretation line must follow the same shape as the /weekly section 0d synthesis. Each line:

• Names the pattern (cycle phase explaining HRV, under-fueling masking recovery, anniversary coupling, etc.)
• Hypothesizes what it might mean
• Suggests a specific next-action when applicable

Examples (template SHAPES, not for verbatim use):

Floor was Fear and HRV ran 22% below baseline on a luteal day. The body and the mind both registered the threat. Without the journal entry the recovery score would have called this "rest more"; pairing with Fear shows the actual signal was "the worry is doing work the rest can't fix."

Floor was Joy after a strong gym week. HRV at baseline, sleep efficiency 94%. This is the high-water mark — note what conditions produced it.

Floor was Apathy and Vitamin D 25-OH came back at 26 ng/mL (below range) the month before. The mood floor may have had a metabolic floor under it. Worth a re-test after 3 months of supplementation.

Banned shapes (from /weekly section 0d, same rules apply):

• Listing body numbers without an interpretation
• Generic "rest more / eat better / hydrate" advice
• Treating recovery score as ground truth when cycle phase or under-fuel explains the dip
• Pretending in-range labs cause symptoms

Model routing

The interpretation line is grunt-work prose. Use the cheapest model that produces a helpful sentence. Order of preference:

1. Python template (zero cost) — for high-confidence cases (HRV in normal range during follicular, no out-of-range labs, no anniversary signal). The script scripts/backfill-journal-body-context.py covers this.
2. MiniMax (~$0.06/M tokens, very cheap) — for cases where the data shows a real pattern that deserves a synthesized sentence. Invoke via "⚙️ Meta/scripts/minimax.sh" if the vault has it, otherwise skip the LLM step and use a fallback template.
3. Haiku (cheap, fast, reliable) — for cases where MiniMax is unavailable.
4. Sonnet — only if explicit --high-quality flag passed and the user accepts the cost.

The default is Python template + MiniMax fallback. Do NOT default to Sonnet for hundreds of journal entries.

Invocation

The actual work runs in scripts/backfill-journal-body-context.py. The skill assembles arguments and hands off to the script.

When invoked:

1. Parse arguments:

• --year YYYY (default: current year)
• --start YYYY-MM-DD and --end YYYY-MM-DD (override year)
• --vault-root PATH (default: $VAULT_ROOT or autodetect from cwd)
• --llm-model {python,minimax,haiku,sonnet} (default: python with minimax fallback)
• --dry-run (print what would change without writing)
• --force (overwrite an existing body-track section)

1. Sanity checks:

• health-mcp must be registered. If not, abort with setup instructions.
• Run health_status() to confirm there's biometric data in the DuckDB. If the count is zero, abort and suggest /health-setup first.
• The vault must have a ⚙️ Meta/journal-index.json (or Meta/journal-index.json on non-emoji vaults) and a journal folder. Rebuild the index if stale.

1. Run the script:

`` /usr/bin/python3 "[REPO_ROOT]/scripts/backfill-journal-body-context.py" --year 2026 --vault-root "$VAULT_ROOT" ``

1. Surface the summary: N entries processed, M backfilled, K skipped, plus the date range covered.

Output

The skill does NOT write to the vault itself — the Python script does the file mutations. The skill only:

• Validates inputs
• Calls health-mcp tools to verify data exists
• Invokes the Python script
• Reports the result

Idempotency

The Python script checks each journal file for an existing ## Body track (health-mcp, backfilled line. If present, skip unless --force. Re-running the skill on the same range is safe.

Ongoing daily run

After the initial backfill, the same script runs daily for yesterday's entry via a scheduled task (use the /schedule skill). Suggested cadence: 7am local, after Apple Watch has uploaded the previous night's sleep data.

Scheduled-task body:

/usr/bin/python3 "[REPO_ROOT]/scripts/backfill-journal-body-context.py" --start "$(date -v-1d +%F)" --end "$(date -v-1d +%F)" --vault-root "$VAULT_ROOT"

That's "backfill yesterday, every morning, forever." Set it up after the initial backfill completes successfully.

Voice rules

• The auto-generated body-track section is in warm register (narrative sentences, not clinical exact-number dumps)
• For Spanish journals, render the section in Spanish (the script detects via the journal's frontmatter language: field if present)
• Floor names use the appropriate language alias ([[Joy]] in English / [[Alegría]] in Spanish)
• Never modify the original entry's content. Only append.

Privacy

The script reads journal files + the local DuckDB. It writes only to journal files (appending body-track sections). No data leaves the machine. The interpretation step (if LLM-backed) sends ONLY the structured body data + floor tag to the chosen model — never the journal body content.