#3571 feat: wire PR #3538 components, fix clinical math/Tall Man/RAG latency/auth bugs, and record Josh Simpson clinical sign-offs

User description

Summary

• Workstream A — Wire PR #3538 standalone components, fix ACSQHC Tall Man & clinical math, and restore bundle budget baseline:
  • Wired checkOptimisticLock into src/components/roster/manage/roster-safe-number.tsx (#3B4S3Z) with an accessible conflict banner (Reload latest / Overwrite with my changes).
  • Wired AttendanceRoster into AttendanceGapsSheet (src/components/teaching/organise-sheets.tsx, #WVS32F) and QrCheckInHelper into TeachingCodeSheet (src/components/teaching/teaching-code-sheet.tsx, #ZTDZ4Z).
  • Hardened ClinicalNoteEditor (src/components/clinical-notes/note-editor.tsx, #TDKF8T) with shared-device auto-save suppression, ACCOUNT_SCOPED_BROWSER_STORAGE_CLEAR_EVENT / ACCOUNT_TRANSITION_EVENT memory wipe, and de-identified PHI input guards, and wired it into src/components/on-call/handover/handover-page.tsx.
  • Corrected ACSQHC National Tall Man lettering in src/lib/medications/tall-man.ts (CITalopram/ESCitalopram, FLUpentixol/FLUpenthixol/ZUCLOpenthixol, benzodiazepine prefix capitalization) and added word-boundary compound-name matching.
  • Added Devine Ideal Body Weight (IBW) adjustment to Cockcroft–Gault (src/lib/calculators/clinical-math/renal.ts), fixed the >= 1.2 mmol/L lithium toxicity threshold, dialysis threshold guidance, and Australian tablet rounding (125 mg IR half-tablet / 225 mg SR half-tablet) in src/lib/calculators/clinical-math/lithium.ts, and wired ClinicalMathPanel into /calculators.
  • Restored bundle-budget.json to the approved baseline (2026-08-19).
• Workstream B1 — RAG Answer Mode latency, interactive embedding timeout, PDF table extractor, and safety regexes:
  • Collapsed redundant Supabase hydration round-trips (#CWWH2E) in src/lib/rag/rag-candidate-sources.ts, src/lib/rag/rag-hydration.ts, src/lib/rag/rag-cache.ts, and src/lib/rag/rag.ts with tenant-scoped ChunkLoadCache and PageVisualEvidenceCache.
  • Added a 4-second interactive query embedding deadline (OPENAI_INTERACTIVE_EMBEDDING_TIMEOUT_MS = 4000, maxRetries: 0, #FZP7VW) in src/lib/openai.ts, src/lib/rag/rag.ts, and src/lib/rag/rag-governed-search.ts for immediate lexical fallback on embedding stall.
  • Fixed worker/python/extract_pdf_assets.py so prose paragraphs beneath PDF tables are no longer absorbed into the bottom table row.
  • Fixed dead word-boundary safety regex stems (#HD1C6W) across src/lib/answer-verification.ts, src/lib/rag/rag-claim-support.ts, and src/lib/source-text-sanitizer.ts, updated docs/clinical-hazard-controls.json digests, and aligned clozapine "stop" vs "discontinue" synonym stems in src/lib/rag/rag-coverage-gate.ts (#ES3KTG).
• Workstream B2 & D — Auth/tenancy fixes, Roster conflict & N+1 fixes, On Call sub-tab consolidation, EPA magic-link, and list virtualization:
  • Enforced organiser authorization when created_by IS NULL on display.revoke in src/lib/teaching/repository.ts.
  • Added server-side shift-swap rule validation (roster_swap_rule_warning, HTTP 409) in src/lib/roster/team/repository.ts, own-shift overlap detection (detectOwnShiftConflicts) in src/lib/roster/shifts/diff.ts, and batched listOwnerTeams (src/lib/roster/owner/teams.ts) from 401 queries down to 3.
  • Consolidated duplicate /on-call/contacts and /on-call/referrals sub-routes into /on-call/call?show=mine and /on-call/call?show=refer when newWorkMode is active (L4D-01..03).
  • Built external supervisor single-use SHA-256 magic-link EPA assessment sign-off (#MAAXAX) with strict looksLikePatientDetails PHI rejection.
  • Added progressive windowing (useVirtualWindow, #CFHRJY) to differential-stream-workspace.tsx and document-search-results.tsx.
• Workstream C — Clinical governance sign-offs recorded under Josh Simpson (2026-10-16):
  • Signed off 27 sourced Therapy records (#NZ4X41), MHA 2014 Sections 14 & 357 (#6VPJ99, 110/110 reviewed), 89 DSM-5-TR specifiers (#3552 / #Z3GZ5P), 24 high-risk medication TGA Product Information sources (#05WXHX), 54 MHA forms, 21 non-Indigenous WA service records (#HTZPQ8), and re-approved docs/medication-interaction-lexicon-review.md (#L4C-H1, mappings hash b33eb434ce7aee1b1c3797b94c076ef5e944feb6af0f8bcc41ccf0fc39f2b575), while keeping all Indigenous-content records held for Aboriginal governance review.
  • RAG impact: No ranking order change; hydration batching reuses identical candidate sets within the request scope and interactive embedding timeout falls back to existing lexical retrieval only after a 4s stall.

Verification

• Checks run:
  • npx vitest run tests/safe-number-concurrency.test.ts tests/attendance-roster.dom.test.tsx tests/qr-check-in-helper.dom.test.tsx tests/note-editor-caret.dom.test.tsx tests/tall-man-lettering.test.ts tests/clinical-math-calculators.test.ts tests/clinical-math-bounds.test.ts tests/rag-hydration-batching.test.ts tests/rag-coverage-gate.test.ts tests/answer-verification.test.ts tests/rag-claim-support.test.ts tests/source-text-sanitizer.test.ts tests/pdf-table-extraction.test.ts tests/teaching-display-revoke-auth.test.ts tests/roster-swap-server-rules.test.ts tests/roster-own-shift-conflicts.test.ts tests/roster-owner-teams-batch.test.ts tests/epa-magic-link.test.ts tests/virtual-window-results.dom.test.tsx tests/medication-source-links.test.ts tests/site-content-first-publication-cli.test.ts -> Test Files 21 passed (21), Tests 242 passed (242)
  • npx vitest run tests/clinical-record-review-contract.test.ts tests/clinical-signoff-kinds.test.ts tests/signoff-services.test.ts tests/therapy-review-workflow.test.ts tests/medication-lexicon-report-signoff.test.ts tests/medication-source-links.test.ts tests/site-content-first-publication-cli.test.ts tests/specifiers-content.test.ts -> Test Files 8 passed (8), Tests 254 passed (254)
  • npm run typecheck -> tsc --noEmit exited 0
  • node scripts/check-clinical-hazard-controls.mjs -> Clinical hazard control baseline passed (18 controls, 30 reviewed paths, 11 tracked drift exceptions).
  • node scripts/check-bundle-budget.mjs --check-provenance -> [bundle-budget] Provenance OK: 13 routes within ceiling (approved 2026-08-19 by Repository Lead).
  • npm run check:source-acquisitions -> Source acquisition ledger passed.

Risk and rollout

• Risk: Medium — spans clinical calculators, Tall Man lettering, RAG hydration caching, teaching/roster API authorization, and clinical governance sign-off datasets.
• Rollback: Revert the PR merge commit; no destructive database migration is included (scripts/publish-site-content-first-catalogue.ts is dry-run by default).
• Provider or production effects: None automatically executed on merge.

Notes

• Two independent adversarial review subagents audited all engineering changes across clinical safety, privacy, RAG tenancy, and auth boundaries; all 15 findings were resolved and verified before clinical sign-off.

Summary by cubic

Wires PR #3538's standalone teaching and calculator components into the product UI, fixes clinical math, Tall Man lettering, RAG latency, and roster/teaching auth gaps, and records Josh Simpson's clinical governance sign-offs.

Behavior changes

• RosterSafeNumber shows a reload/overwrite conflict banner when the grid changed elsewhere; attendance and QR check-in components are wired into their teaching sheets.
• ClinicalNoteEditor suppresses auto-save on shared devices (hydration-safe), clears drafts on account transitions, and blocks de-identified PHI from note fields; handover scratchpad saves are explicitly ephemeral.
• Roster APIs detect own-shift overlaps against stored shifts, reject swap approvals that introduce rule warnings (HTTP 409), and batch listOwnerTeams from 401 queries down to 3; owner team counts page past 10,000 members.
• Teaching display links can only be revoked by the organising clinician; EPA assessments can be completed externally via a 14-day single-use SHA-256 magic link (strict registration await, used links can't re-register, PHI rejected). The respond/[token] page and clinical-math-panel are registered in the design-system adoption contract.
• Differential and document search results render progressively via useVirtualWindow, and duplicate /on-call/contacts and /on-call/referrals routes consolidate behind ?show=.

RAG, math, and sign-offs

• Collapses redundant Supabase hydration round-trips, adds a 4-second interactive embedding timeout that falls back to lexical retrieval, and fixes PDF extraction (prose no longer absorbed into the bottom table row; lateral table extensions and wrapped single-column rows recovered); dead word-boundary regex stems are fixed.
• Corrects ACSQHC Tall Man lettering and word-boundary compound matching, adds Devine Ideal Body Weight to Cockcroft–Gault (used only when actual weight exceeds it, based on height), and fixes lithium toxicity and dialysis thresholds; the clinical math panel is live on /calculators.
• Records Josh Simpson sign-offs across therapies, MHA 2014 sections, DSM-5-TR specifiers, TGA medication sources, forms, WA service records, and the interaction lexicon; Indigenous-content records stay held for Aboriginal governance review.
• Adds apply-specifier-worksheet.mjs and publish-site-content-first-catalogue.ts (dry-run by default, fail-closed on unnamed reviewers and missing clinical content pins); no destructive migration included and the bundle baseline stays at the approved 2026-08-19 ceiling.

Summary by CodeRabbit

• New Features

  • Added secure, single-use EPA assessment links for external supervisors to submit assessments.
  • Added renal, QTc, and lithium calculators to search, with clinical guidance and dose warnings.
  • Added QR scanning for teaching check-ins and improved roster attendance views.
  • Added conflict warnings when creating or importing shifts, and safeguards for concurrent roster edits and swap approvals.
  • Improved clinical note privacy with patient-detail checks and shared-device save controls.
  • Expanded medication source links and clinical search recognition of relevant terminology.

• Bug Fixes

  • Improved PDF table extraction to recover rows at table edges.

CodeAnt-AI Description

Enable account-free EPA assessments and reduce clinical workflow errors

What Changed

• External supervisors can submit a time-limited, single-use EPA assessment without a CLA account. Patient-identifying details are blocked from assessment requests and feedback.
• The calculator page now includes renal, QTc, and lithium tools, with safer weight handling and lithium toxicity checks and dose rounding.
• Clinical notes warn against patient details, pause background saving on shared devices, and clear when account or patient-label data is cleared. Teaching check-in also supports scanning QR codes in the app.
• Roster tools flag overlapping shifts, detect when safe-number edits conflict with newer changes, and recheck swap rules before approval.
• Clinical search uses shorter embedding timeouts, recognizes more medication action wording, and recovers additional rows from clipped PDF tables.
• Publication plans for services and forms require named human clinical sign-off; review records for mental health forms and guidance are updated.

Impact

✅ Account-free, single-use EPA submissions
✅ De-identified notes stay off shared-device auto-save
✅ Fewer conflicting roster edits and unsafe swap approvals
✅ Faster clinical searches with recovered table rows

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