pediatric-ai-scribe-v3/TODO.md

TODO

Live state as of 2026-09-11. Everything not listed under Open is deployed and green (674 tests, three consecutive clean runs).

Open

Needs your decision

• Replace Cloudflare Turnstile. Used on registration and password reset only (src/routes/auth.js); login is not gated, it relies on a 10-per-15-min limit and a constant-time credential check. Recommended replacement: ALTCHA — open source, self-hosted, proof-of-work, no third-party calls and no tracking, which also lets three CSP entries and frameSrc go away. Alternatives: mCaptcha (open source, self-hosted, heavier to run) and Cap (newer, smaller). hCaptcha is neither Google nor open source, so it trades one third party for another.
• Kubernetes / CI-CD hardening. Details under Deployment readiness.
• Audio backups are in MinIO. Same server, its own audio-backups bucket. The app key carries a second policy covering only that bucket, so the mounted credentials serve both. Verified: storage=object, round trip byte-identical, objects removed with their rows.
• Basic index has no reader. MilvusVectorStore.search() exists, but no tool calls it. Decide where the query path lives: pymilvus inside the deliberately-lean nextcloud-basic-mcp image, or a query API from the indexer container. Nothing can read that index until this is settled. Source: /home/danvics/docker/nextcloud-basic-mcp
• Apply the restored clinical vector-store compose. Written, committed and validated at /home/danvics/docker/clinical-storage-milvus, deliberately NOT applied — up -d recreates the live clinical Milvus.

Known gaps

• Multi-collection, ped-ai half. The MCP side is deployed (clinical_semantic_search(collection=…) + clinical_list_collections, allowlisted by MILVUS_COLLECTIONS). ped-ai still searches one collection per request. Needs an admin setting for which collections to search, then fan-out and merge — dedupeSources in src/utils/clinicalRetrieval.js already merges and renumbers. See clinical-assist/COLLECTIONS.md.
• Mail indexing works. It was never reached: mail ran last, after nine other sources, and Tables alone is thousands of rows at about a second each. Mail leads now — it is the only bounded source (identities only, capped by BASIC_INDEXING_MAIL_MAX_MESSAGES, bodies left to the processor), so it cannot starve the others the way they starved it. Messages are indexing.
• Mail attachments were never indexed. An attachment's id is its index within its message, so /api/attachments/{id} meant nothing and answered 500 every time. Fixed to /api/messages/{id}/attachment/{id}, verified live against a real message.
• The basic collection is renamed personal_assistant_bge_m3_1024 (was basic_bge_m3_1024_v2), matching mcp_bge_m3_1024 on the clinical side. Milvus grants name the collection, so the rename revoked basic_reader/basic_writer; bootstrap_basic.py restored them, but it must be bind-mounted because the operator image ships an older copy.
• The indexed folder is Personal assistant, and the setting now takes a comma-separated list (Personal assistant,Clinical Notes), each walked recursively. Note the file reconciliation removed the chunks of the 68 Documents files, since a complete listing is the deletion authority and they are no longer under an indexed root. Entities went 27,930 -> ~9,700. Re-add those files under an indexed folder if they are still wanted.

Deployment readiness (CI/CD and Kubernetes)

What already exists: ci.yml (tests on PR and main), security.yml (weekly audit), docker-publish.yml and Android/versioning workflows, a Dockerfile HEALTHCHECK, and /api/health.

Worth doing before Kubernetes, roughly in order:

• Fail CI on vulnerabilities. security.yml runs weekly and does not gate merges. npm audit --audit-level=high in ci.yml would have caught the nodemailer advisories at the PR.
• Build the image on PRs too. docker-publish.yml only runs on tags, so a Dockerfile break is found at release time.
• Run the e2e suite in CI. scripts/e2e.sh and docker-compose.e2e.yml exist but nothing calls them.
• Separate liveness from readiness. /api/health is one endpoint; Kubernetes wants liveness (process up) apart from readiness (database, gateway and MinIO reachable), or rollouts take traffic too early.
• Graceful shutdown. No SIGTERM handler, so a rolling update can cut off an in-flight transcription or image job.
• Externalise state. Uploads and audio backups assume local paths and a single instance; more than one replica needs them all in MinIO/Postgres.
• Config as secrets. Everything is env vars in compose today, which maps to ConfigMap/Secret cleanly, but JWT_SECRET, gateway keys and database credentials should be a Secret from the start.
• Pin the base image by digest and keep the SBOM the build already has.

Done since this file was written

2026-09-11

• Live transcription: proved working end to end against the live gateway — local-kokoro-tts produced 92KB of speech and mistral-voxtral-mini-transcribe returned the sentence back verbatim. The Settings picker offered six hardcoded ids that do not exist on this gateway (local-whisper-large-v3-turbo → 400 Invalid model name); it now lists the nine the gateway advertises, cached, with the admin default marked.

• Assistant voice mode is wired end to end: record → browser recognition, falling back to server transcription → send → spoken answer. All four helpers it needs exist.

• Recordings can be exported (server and local copies) and a recorder that dies — an error, or the microphone taken by another app, unplugged or revoked — now says so instead of appearing to record silence. No wake lock, deliberately: stopping on sleep or sign-out is the behaviour you want.

• nodemailer 9.0.1 → 9.1.1, clearing four high advisories, two of them delivery bugs that can route mail to an attacker-controlled domain.

• Admin routers state their own authentication. adminMilestones relied on adminConfig being mounted first on /api/admin; it failed closed, but on mount order rather than intent.

• Test suite made deterministic. A file failed about one run in four with "Unable to deserialize cloned data": node:test parses each child's stdout, and page/server logging was landing inside those frames. Every test child's stdout is now pure TAP.

• iOS: text fields are 16px on phones, so Safari no longer zooms the page on focus — which was also why fixed chrome (the menu button) scrolled away.

• Settings claim corrected: there is no "use my normal physical exam" trigger, and the prompt forbids copying template content.

• Storage stack is under version control (/home/danvics/docker/personal-assistant-storage-milvus), secrets verified excluded, with a README recording the misleading project names and the MinIO/separate-etcd requirements.

• Both Milvus stores keep objects in MinIO; verified end to end on the basic side (16 objects in the bucket, rows queryable, collection Loaded).

• The operator image is built from source (Dockerfile.operator), so the drifted check.py that broke image generation can no longer be run by accident.

Worth knowing

• Four repos were rescued from container images today: nextcloud-basic-mcp, clinical-assist, the deleted clinical-storage compose file, and the operator's check.py drift. Prefer building from a repo over a live container.
• Two Milvus instances, historically misleading names. Clinical index = nextcloud-mcp-server-milvus-1 in clinical-storage-milvus (MinIO-backed, collection mcp_bge_m3_1024). Personal assistant index = personal-assistant-storage-milvus-basic-milvus-1 (db basic, collection personal_assistant_bge_m3_1024).
• Embedded etcd is unusable with authorization on. Every non-root Milvus user failed etcdserver: invalid auth token. Both stores now run a separate etcd container, matching the profile that always worked.
• Both Milvus stores now keep objects in MinIO, matching what clinical always did. COMMON_STORAGETYPE=local wrote segment files relative to the working directory, so a recreate destroyed them while etcd kept referencing them and the collection hung at Loading forever. S3 semantics also mean either store can be pointed at a managed bucket without touching Milvus — which is what makes a Terraform-managed deployment straightforward.
• Milvus object-store credentials live in milvus-user.yaml in the protected secrets dir, not in the compose, because Milvus has no file-based option for them and the compose should stay reviewable.

Co-Authored-By: Claude Opus 5 noreply@anthropic.com

Sign-in by one-time code, alongside passwords

An option, not a replacement. An account keeps its password; the sign-in screen offers "email me a code" as a second way in, and an account can use either.

• Reuse the invite machinery rather than inventing a second one: codes are hashed at rest, single-use, short-lived, and claimed by one atomic UPDATE carrying every condition, so two attempts at the same code cannot both win.
• Much shorter TTL than an invite — minutes, not days — and rate limited per account and per IP, because a login code is a credential and an attacker can ask for one without knowing the password.
• A code must never reveal whether the address has an account. The response is the same either way.
• 2FA still applies on top where enabled: a code replaces the password step, not the second factor.

The signed-out preview, as it should behave

The preview works now, but it is currently all-or-nothing. Intended shape:

• Signed out with preview on, the assistant chat is visible and usable.
• Anything else — saved chats, images, settings — prompts sign-in rather than failing. Today those simply 401.
• A cap of three questions per visitor, then an invitation to sign in. The cap has to be enforced on the server: a preview visitor has no identity, so it cannot be per-account, and a purely client-side count is worth nothing.
• Nothing is persisted for a preview visitor. That is already true and must stay true — PREVIEW_USER has id: null precisely so nothing can be owned.
• If the visitor then signs in in the same browser, the preview conversation is adopted into the new account and saved. This is the interesting part: because preview deliberately has no identity, the transcript has to be held client-side and replayed on the first authenticated request, not looked up server-side. Size-cap it and drop it on sign-out.

PubMed as a search source of its own

Web search reaches the open web through Tavily, Serper, Brave or a self-hosted SearXNG. PubMed is a different kind of source and deserves its own tool rather than being a site: filter on a search engine.

• E-utilities (esearch then efetch) needs no key for modest use, and an NCBI_API_KEY raises the rate limit. No commercial third party either way.
• It returns structured records — title, journal, year, PMID, abstract — so a citation can be exact rather than reconstructed from a page title. That is the real argument for a separate tool: the References section could carry a PMID.
• A separate tool, not a provider option, because the model should be able to reach for "the literature" distinctly from "the web": one search per resource each, and a resource may legitimately want both.
• Same guardrails as web search: admin-enabled, opt-in per generation, only the query leaves, and hidden entirely when unavailable.