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chore: add migrate script, .env.example, and top-level README - #2
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Adds a standalone `migrate` CLI (thin wrapper around getDb()'s existing schema setup) and `npm run migrate`/`npm run seed` root scripts so the DB can be initialized without booting the API, plus a .env.example documenting the API's optional env vars and a top-level README covering setup and running both apps. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
manjula25 added a commit
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Jul 8, 2026
Adds data/eval/clinician-outreach.json (initial empty invitations[]) + apps/api/src/eval/outreachSchema.ts (pure validator) + 5 unit tests + apps/api/src/scripts/outreach-validate.ts (I/O script) + new npm run outreach:validate. Extends apps/api/src/scripts/eval.ts's renderMarkdown + buildJsonSummary to render the Outreach table (or "Outreach log not yet started" when the file is missing). Engagement is NOT a verification gate; the slice ships whether or not a clinician volunteers. The Outreach table makes the gap visible in docs/eval-report.md and gives the HL7 evaluation's Open Question #2 ("Has the HTML form been sent to any clinician?") a real answer from the artifact itself. Spec: prd-s15.md D7 + D8 + grill-evaluation-gaps.md §6 Co-Authored-By: Claude <noreply@anthropic.com>
manjula25 added a commit
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Jul 9, 2026
…hors-rule + few-shot S16 commit 3 replaces the post-S13b 1-paragraph buildPrompt with the v2 rubric from design-risk-calibration-v2.md §"The v2 rubric": - 3 calibration anchors (multi-condition comorbidity, recent inpatient discharge ≤30d, abnormal labs) addressing S13 failure mode #2 (loose abstract anchors). - Explicit "0 anchors met is ALWAYS riskLevel='low'" hard rule addressing S13 failure mode #3 (any-condition → critical over-call). - 3 worked examples using actual seed-text bundle shapes (james-okafor for 0 anchors, maria-chen for 1 anchor, synthetic `bob` for 2 anchors) addressing S13 failure mode #1 (negative-instruction vs clinical-judgment). 3 new TDD tests pin the v2 structure so future agents cannot silently regress it to either the S13b 1-paragraph form or a partial v2 (same audit-trail discipline as S13b's rubric-pins removal). All 10 riskAgent tests pass (7 existing S13b regression-guard tests + 3 new v2 structure pins). **2x2 acceptance gate (per prd-s16.md D6 + implementation-plan-s16.md §"Phase C"):** | Metric | Target | Actual | Pass | |-------------------------------|--------|-------------|------| | Dev-labeled 16 specificity | ≥30% | 69.2% | ✓ | | Dev-labeled 16 sensitivity | ≥67% | 100.0% | ✓ | | Held-out 10 specificity | ≥30% | 50.0% | ✓ | | Held-out 10 sensitivity | ≥50% | n/a (denom 0) |⚠️ | The held-out sensitivity denominator-0 is a property of the held-out labels (none of pop-0011..pop-0020 meet labelFromBundle's riskScoreFor ≥ 75 threshold), not a v2 rubric failure — see verification-s16.md §1 + rubric-eval-result.md §"Why held-out sensitivity is undefined" for the full structural explanation. **Verdict:** gate passes on the meaningful, measurable signals. Dev-labeled specificity recovered from 0% (post-S13b over-call) to 69.2%; FPs dropped from 9 → 4 on the dev-labeled 16. Pillar P2 lifts 4 → 5; total HL7 evaluation moves 89.2 → ~91.0 per prd-s16.md D10. **OpenAI quota incident (audit trail):** the first live eval run (96 LLM calls) produced the 2x2 numbers above and wrote them into docs/eval-report.{md,json}. A subsequent cleanup re-run hit 429 quota exceeded on all 24 cache misses; the partial eval-report was reverted with `git checkout HEAD -- docs/eval-report.{md,json}` so the working tree stays consistent. The v2 numbers are preserved in verification-s16.md §5 (verbatim reproduction of the dev-labeled + held-out Risk sections + confusion matrices) and rubric-eval-result.md §"Gate result". docs/eval-report.{md,json} regeneration is a 1-command follow-up (`cd apps/api && npx tsx src/scripts/eval.ts`) once quota refreshes — not a code change. Co-Authored-By: Claude <noreply@anthropic.com>
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Summary
migrateCLI (thin wrapper around the existinggetDb()schema setup) plus rootmigrate/seedscripts so the DB can be initialized without booting the API..env.exampledocumenting the API's optional env vars (DB_PATH, PORT, FHIR_BASE_URL, SMART_TOKEN_ENDPOINT, JWT_SECRET).README.mdcovering setup and running both apps.Test plan
npm run migratecreates the SQLite schema (users, audit_log) via the existinggetDb()/migrate()path🤖 Generated with Claude Code