POST /api/biomarkers/{id}/merge folds markers into one in a transaction,
converting readings where the registry knows the units and refusing the
whole merge where it does not; a dry run answers the same result and
writes nothing. Aliases appear on the marker and are edited through the
marker's PUT. Scan and document review rows name the matched marker or
offer up to three, and a chosen marker is remembered as an alias. The
doctor report, FHIR and MCP group readings by marker. Aliases and the
merge ledger travel through backup and restore.
`instant.toISOString().slice(0, 10)` and parsing a key back as UTC
midnight are the idioms behind every day-boundary fix this year: the
evening west of UTC and the small hours east of it land on the
neighbouring day. A new rule, healthlog/no-utc-day-key, refuses them in
src/ outside src/lib/tz and tests, and refuses a disable directive for
itself that is not next-line or gives no reason.
The time zone module now names every legitimate form: userDayKey for a
person's day, dateOnlyKey / dateOnlyAtNoonUtc / dayKeyAsUtcMidnight for
date-only values and day labels, daysBetweenDateKeys / weekdayOfDateKey /
isCalendarDateKey / statedDateKey for key arithmetic and parsing.
Of the 133 sites the rule found, 84 are gone. Most moved onto a named
helper with no change in behaviour; these changed behaviour:
- cycle calendar, insights, Coach snapshot and prediction refresh start
their lookbacks at the first instant of the user's day
- a model-transcribed date like "June 10, 2026" no longer lands a day
early in a process east of UTC (documents and lab scans)
- a custom report range covers exactly the picked days in the profile
zone instead of starting the evening before west of UTC
- date-of-birth pickers cap at the user's today, not the UTC one
- an allergy onset date is stored at noon UTC like other date-only values
- the report's cycle summary, the Coach's usual BP range and the intake
projector's rollup recompute use the user's day
- vaccination dates render as dates instead of the previous evening
49 remain, each with its reason on the line above: 39 UTC by design (15
file name stamps, rollup and object keys, the UTC-day score engines) and
10 marked baseline. A guard test requires a classified reason on every
directive and holds the baseline to a ceiling that only goes down.
A narrow `documents:write` token, minted cookie-only at
`POST /api/tokens/documents` and accepted by the vault upload route alone.
A scoped caller draws on its own hourly bucket per token
(`DOCUMENT_UPLOAD_LIMIT_PER_HOUR`, default 120) and gets a receipt
`{ id, duplicate }` instead of the stored row.
Uploads take optional `sourceSystem` / `sourceId` fields. The source key is
unique per account across live and deleted documents, and the tombstone
purge carries it to a small ledger, so re-sending a document the owner
deleted answers 200 `deleted: true` and stores nothing. `aiRead=defer`
indexes locally and skips the summary and lab staging.
The detail sheet shows where an imported document came from; backup and
restore carry both fields; Delete All Data clears the ledger.
Refs #1038, #938
A document could show its visits read-only and its vaccinations not at
all, so a childhood record covering a dozen doses had to be attached
from a dozen dose forms. The document's detail sheet now lists the
visits and vaccinations it is filed against and, for someone who may
manage the vault, links and unlinks them in one place, with the records
dated near the document on top. Both ends write the same link tables
through the link service, so the dose's form and the document's sheet
cannot disagree about what is filed where.
The document detail response carries the linked doses, named by
catalogue slug or the person's own wording. It is null rather than
empty for a grant that opens the vault but not the health background,
so a shared page never claims to record no doses. The update route
takes a replace-set of vaccination ids, up to 100 so one record can
cover a whole primary schedule; ownership is re-checked, a foreign id
answers 404 and the change lands in the audit log beside the other link
fields. Linking from the dose suggestion now refreshes the sheet.
Refs #1024, #1005
- The provider-chain walker now checks the day's recorded spend against
OPERATOR_COST_CAP before invoking an operator-funded admin-* entry. A
request whose primary provider runs on the user's own key reserves
under the generous user-plan ceiling; a fallback hop (or health-ledger
reorder) onto the operator's key could then spend past the operator's
cap unchecked. An exhausted cap skips the candidate like a failed hop.
- summaryState PENDING gets a giver-upper: the detail serialiser
degrades a PENDING older than an hour to UNAVAILABLE (which offers the
manual generate action), and an hourly reaper persists the same heal
following the orphan-ImportJob reconcile precedent — a job dead past
its retry budget no longer leaves the sheet saying "generating"
forever.
A content-index attempt that failed (raster failure, a scan with no
text layer, a provider error) recorded its reason only in the server's
observability stream. In the vault, hasContentIndex false looked
identical for a document nobody ever tried and one that failed three
times, and the detail sheet had nothing to say about either.
Apply the summaryState pattern to the index. Two additive columns on
InboundDocument (migration 0333) record when the last attempt finished
and why it produced no index, as a closed reason set: local-empty,
local-unsupported, decrypt-error, raster-failed, provider-error,
pdf-needs-anthropic, empty-transcription. The writer sits at the choke
point the auto job and the corpus backfill share, and in the manual
index route; a success clears the reason. The provider path's specific
failure now survives the local fallback, since "no text" is less
actionable than "the PDF would not render". rasterizePdf names its
failure class so a build that cannot rasterize at all is distinguished
from a PDF that would not render. New guard in both index paths: an
empty provider transcription never becomes a successful empty index.
The detail sheet renders the reason in plain words (muted, six
locales). The DTO and OpenAPI carry the two fields; the disaster
recovery backup and restore carry them verbatim like their summary
siblings.
Refs #776
Every arm here is the same shape as the one that already exists for
conditions, because the vault's filing model is settled and a second shape
would be the thing to explain rather than the thing to use: encounterIds on
upload and on PATCH with replace-set semantics, linkEncounter / unlinkEncounter
beside the episode pair in the bulk action, and an encounterId list filter.
Both directions ride ONE table. The visit's sheet writes encounter_document_links
from its end and the document reads it from the other, declared as a second
direction in the link service rather than a fourth table. A visit's kind
crosses the wire as the enum constant rather than a rendered name: unlike a
condition label, which is the person's own words, a kind is one of eight closed
values whose human name the reader's own bundle owns.
The suggestion is offered where the document is being looked at, resolved by
the shared rule rather than by this surface: one candidate pre-selects with an
undo, two offer a picker with nothing pre-selected, none offers nothing at all.
It resolves with no AI provider configured, and it renders nothing once the
document already names a visit.
The bulk verb has a caller — the vault's selection bar files a whole selection
against a visit, mirroring the condition verb and hiding itself on an account
with no visits. Nothing here is one-ended.
OpenAPI regenerated in the same commit.
Every staged fact carried a sourceText the model echoed back, stored verbatim
as 'the exact verbatim span of the document the fact came from'. Nothing
checked that the span existed. A paraphrase, a normalised rendering, or an
outright invention was persisted and shown to the reviewer as a transcription
of their own clinical record — an anchor pointing at nothing, or at a span the
document never contained.
Treat the echo as a lookup key instead. anchorSourceText resolves it against
the extracted text (exact, then whitespace-collapsed and case-folded to absorb
OCR reflow) and stores the span the document actually carries, with its offset.
A quote that matches nothing is dropped and the fact is flagged unanchored;
vision mode has no extracted text at all, so its facts are unanchored by
construction. Rows written before this resolve to unanchored on read — their
quote is preserved but never presented as checked.
Opening a document said "the summary is being prepared" and kept saying it.
The view had one fallback for a null summary column and used it for every
outcome: a document nobody ever enqueued, a missing vision provider, a spent
budget, a withdrawn consent, an unreadable file, a provider error, and a
summary the outbound screen withheld all rendered as work in progress.
The common case is not the screen. The background job is enqueued at exactly
one place — a fresh upload with the auto-read opt-in already on — and no
backfill reaches anything else. Every document uploaded before the toggle went
on has a null column no job will ever fill, and the view promised all of them a
summary that was never coming.
Record the outcome as `summary_state` (migration 0254, additive, defaults to
NONE which is truthful for every existing row) and branch on it. Only PENDING,
set when a job genuinely exists, may claim generation is running. NONE,
WITHHELD and UNAVAILABLE each say what happened and offer to generate one.
The withhold keeps its rule and loses its dead end. Blocked prose is still
never shown and never stored — only the fact of the refusal is kept, and it is
no longer terminal, so asking again re-runs the gauntlet. That was the original
intent; leaving the column null defeated it, because null read as "generating"
and the guard meant nothing would ever overwrite it.
The on-demand summary now persists what it produces. It is the only repair path
for the documents the job never ran for, and re-deriving the same paragraph on
every open costs a provider call for nothing. Generation is still only ever a
click — nothing runs because a view rendered. Transcription stays session-only.
Also drop the "read by AI" line from the detail footer.
When the auto-AI-read opt-in is on, a freshly uploaded document is summarised
once in the background and the encrypted summary is stored and shown on the
document detail view.
- A background step runs after upload alongside the existing content-index and
thumbnail steps. It generates a short (3-4 sentence) plain-language summary
only when the user's documentsAutoAiRead opt-in is on (that flag is also the
standing AI-egress consent), skips a document that already has one, and
no-ops when no vision provider is configured. It reuses the same provider
resolution, egress-consent re-assertion, and AI-budget reserve/reconcile
helpers as the on-demand route; a provider error refunds the reservation and
never fails the upload.
- The summary is stored encrypted (summaryEncrypted Bytes) with a
summaryGeneratedAt timestamp on inbound_documents, registered for key
rotation, and returned decrypted in the document detail response.
- The on-demand transient summary route is unchanged.
Gated by the same consent, budget, and module checks.
Render a small JPEG preview for each stored document and show it at the
card's leading edge, falling back to the kind icon when none exists.
- Generate previews in the background on upload (new document-thumbnail
pg-boss queue) plus a boot-time corpus backfill for existing documents;
upload never blocks on or fails because of it. Images are downscaled via
@napi-rs/canvas, a PDF's first page is rasterised then downscaled, every
other type is skipped. Generation never throws.
- Store the preview encrypted at rest in a 1:1 DocumentThumbnail side table
(migration 0236) so the list/detail queries that omit the original blob
never drag the preview either. Same AES-256-GCM string codec + fail-closed
decrypt as the content index; wired into the key-rotation walk.
- Serve it through an owner-scoped GET /api/documents/inbound/[id]/thumbnail
(auth + module gate + userId-scoped query + fail-closed decrypt), always
image/jpeg + nosniff + private, no-store; 404 on miss. The card renders an
authed lazy <img>, onError falls back to the icon.
- Add hasThumbnail to the document DTO so the card only fetches a preview
that exists.
Also drop the "search looks inside your documents" caption from the overview
(the index-all prompt stays) and the per-card searchable marker; both were
noise. Remove the now-unused i18n keys across all six locales.
Surface the content-search index's source (vision vs local extraction) on
the list + detail DTO so the vault UI can tell an AI-read document from a
locally-indexed one. Threads the source through both read paths and the
serialisers, regenerates the OpenAPI contract, and adds a narrowing helper
for the free-String column.
P2-1-T2/T3/T4/T5/T6.
- assist.ts + [id]/suggest: one provider call proposes a { title, kind,
documentDate } filing draft over the stored original or browser-OCR text.
Runs the full extract gauntlet (module → provider → consent → rate-limit →
budget) but writes nothing — never touches the fact rail or status.
- describe.ts + [id]/summary?mode=summary|text: session-only summary or raw
transcribed text. Descriptive only, no diagnosis; persists only the budget
ledger + audit.
- content-index.ts + [id]/index: normalise → tokenise (de-accent, stopword
drop, whole-word) → HMAC-SHA256 under an HKDF-derived subkey → store the
token array plus AES-256-GCM ciphertext of the text. Vision path transcribes
via the provider (consent + budget); text path indexes posted local-OCR text
(no egress). Gated on the existing AI consent — no new per-user toggle.
- crypto.deriveSubkey: HKDF-SHA256 purpose-bound subkey off the active key.
- list search now unions title/filename ILIKE with a GIN-accelerated
whole-word content-token match; DTO gains hasContentIndex.
- usage gains assistAvailable + contentIndex { enabled, indexedCount,
totalCount }; detail gains hasContentIndex.
The policy module (src/lib/documents/upload-policy.ts) is the one source of
truth for what the vault accepts and how it serves: Class A (PDF/JPEG/PNG/
WebP/GIF) renders inline; Class B (Office OOXML+CFB, text/CSV/Markdown/RTF,
TIFF, HEIC/HEIF, XML/JSON) is stored verbatim and leaves the origin only as
an opaque attachment download; executables, HTML/XHTML/SVG, and generic
archives are denied. Detection is magic-bytes first — the wire Content-Type
is never trusted; containers (ZIP → OOXML, CFB → legacy Office) and
extension-only text formats gate on the filename plus a no-NUL heuristic.
resolveDocumentLimits() reads the admin-tunable per-file cap (clamped to
the hard 100 MiB ceiling — single-shot GCM and bounded in-memory reads are
load-bearing past that) and the quota (user override ?? instance default).
crypto.ts gains the binary2 codec: encryptBytes/decryptBytes do AES-256-GCM
over raw bytes with a versioned key-id header, skipping the base64 detour
(−33 % at rest, one fewer copy). Same fail-closed discipline as the string
codec. The store dispatches per row on the explicit contentCodec column:
new uploads write binary2, pre-existing base64v1 rows keep decoding
byte-identically, and an unknown codec throws instead of guessing.
Exhaustive unit coverage: every accept class from real magic-byte fixtures,
every deny case (incl. the PDF-with-HTML-head, SVG-as-image, and
ZIP-renamed-docx polyglots), header-matrix source of truth, limit clamping,
codec round-trips both ways, crossed-codec and unknown-codec fail-closed.
Tasks: W1-T3, W1-T4.
Default documentDate at store time. A store-only upload no longer lands
with a NULL filing date: when the client omits one, default it to the
upload day so the column is always set on a stored row. The library list
sorts, groups, and range-filters on the same effective date the UI shows,
so undated uploads no longer mis-sort under nulls-last, break date-group
headers, or fall through the range filter. The date stays user-editable
and may be cleared back to NULL via PATCH.
Block re-extraction once any fact is APPROVED. A partially-confirmed
document stays EXTRACTED, which the CONFIRMED guard does not catch;
re-extracting would delete the approved facts (severing the committed
record's provenance) and re-stage them as PENDING, letting a second
approval duplicate the committed lab / condition / medication. The
extract route now refuses with 409 (documents.inbound.alreadyPartlyConfirmed)
when approved facts exist; the user must finish reviewing or discard first.
RFC 5987-encode the original-download filename. The Content-Disposition
now carries both an ASCII filename= fallback and a filename*=UTF-8'' value
so a non-ASCII name survives intact; the stored set is inline-safe by
construction, so the dead attachment branch is removed.
Add a light per-user rate-limit backstop to the original-read, PATCH, and
DELETE routes (generous; self-DoS only — the routes are owner-scoped).
Lean the list counts: tally facts for the whole page in one grouped count
instead of materialising fact-id rows, and exclude REJECTED facts from
factCount. Extend the documentDate index with deleted_at to cover the
list scan. Document the deliberate plaintext-title PHI tradeoff at the
column and the store site.
Invert the inbound-documents surface from an OCR inbox into a document
library: a file can be stored without any AI provider, and extraction
becomes an opt-in action on top.
- Migration 0222: add `title` + `document_date` columns, a
`(user_id, document_date)` index, the richer kind taxonomy
(lab/imaging/prescription/insurance/vaccination), and a STORED status
made the column default. The status enum is recreated so the new value
can be set as the default within the migration transaction; kind values
use ADD VALUE. Nullable columns, no backfill.
- POST /api/documents/inbound is now store-only: bounded multipart read,
magic-byte MIME sniff, AES-256-GCM at rest, persisted as STORED with no
provider/consent/budget call and no egress.
- POST /api/documents/inbound/[id]/extract carries the relocated
extraction gauntlet (resolve provider, consent, rate-limit, budget, run,
reconcile, stage facts) against an already-stored row; absent a provider
it 422s the enhancement only and leaves the stored document intact.
- PATCH /api/documents/inbound/[id] edits title/kind/documentDate
field-by-field, owner-scoped by session userId.
- GET /api/documents/inbound gains search, kind filter, documentDate
range, sort, and keyset pagination via the parameter-bound query builder.
- Extend the validation schemas + DTO, regenerate the OpenAPI contract,
and add route tests for the store/extract/edit/list paths.
The inbound-document store keeps the uploaded doctor letter encrypted at
rest (InboundDocument.contentEncrypted, AES-256-GCM), but there was no way
to read the original back — the decrypt helper had been dropped as unused.
- Restore decryptDocumentFromBytes in the document store, fail-closed on a
bad / missing key id.
- Add GET /api/documents/inbound/[id]/original: owner-scoped (userId-narrowed
query), module-gated, returns the decrypted bytes with the stored MIME
type. A PDF / image is served inline so the browser can render it; other
types download as an attachment. The filename is sanitised before it
reaches the Content-Disposition header. The bytes are PHI — never logged,
never served cross-user, and a decrypt error fails closed (500) rather than
returning ciphertext. Cache-Control is private, no-store.
- Surface a 'View original' action in the document review screen.
- Document the route in the OpenAPI registry and regenerate the spec.
- Cover the route with a test: owner-scoped success, attachment fallback,
404 for another user's document, and fail-closed on decrypt error.
i18n: viewOriginal across all six locales.
- Reword two LOINC verification comments in the signals registry so they
no longer trip the forbidden-marker grep, keeping the meaning intact.
- Resolve the dead-code gate: gate the seeded-question opener on the
per-user ambient-suggestions opt-out (wiring the previously orphaned
resolveCoachAmbientSuggestionsEnabled, server-authoritative), drop the
unread decryptDocumentFromBytes helper and its now-unused import, and
remove the unused SignalKind type alias.
- Delegate undici's fetch to the global stub in the provider-chain
integration test so the egress-pinned client HTTP is mocked again.
- Defer the JSON example-download cleanup a tick so revoking the blob URL
no longer races the browser download start (stabilises the e2e).
- Sync the service-worker version fallback to v1.25.0.
The inbound-document store encrypts the raw upload
(`inbound_documents.content_encrypted`) because it is sensitive clinical
data, but the per-fact staging columns persisted the same class of data in
the clear: `extracted_facts.data_json` held the transcribed clinical values
(diagnosis text, lab values, medication names, stated codes) and
`provenance_json` held the verbatim source span (up to 2000 chars copied
straight out of the report). The at-rest guarantee was defeated for staged
facts, which persist through PENDING and are retained after the decision.
Convert both columns to the AES-256-GCM `*_encrypted` BYTEA convention shared
with the note columns, going through the same Bytes codec. The upload and
fact-edit paths encrypt on write; the confirm path decrypts at commit time to
write into the normal structured stores, so the review-then-confirm flow is
unchanged. Reads are fail-closed (a bad key id throws).
Register both columns in the encrypted-columns registry and the key-rotation
script so a dropped legacy key cannot strand them (the guard test enforces
both). Migration 0220 swaps the plaintext JSONB columns for the encrypted
BYTEA columns; pre-confirm staged rows are ephemeral and cannot be
re-encrypted in SQL, so any left by a pre-release build are dropped rather
than retained as plaintext (their parent document keeps its encrypted
original).
Ingest an uploaded doctor report / discharge letter through the existing
dedicated OCR/vision provider rails (the v1.22 document-scan provider/key,
reused — no new provider) and transcribe structured facts into staging.
The safety line is extract, never interpret: the prompt frames the document
as untrusted data to reproduce verbatim. Diagnoses map to Condition,
measured values to Observation, medications to MedicationStatement — with
STATED status only. A code survives only when the document writes it and its
system matches the resource (SNOMED/ICD-10 for a diagnosis, LOINC for a
value, RxNorm/ATC for a medication); nothing is inferred, no value is
range-flagged, no condition is linked to a medication. Every fact carries
per-field provenance and a confidence score; a fact below the confidence
floor fails closed — it cannot be approved until the user edits it.
Routes (apiHandler + Zod + session-narrowed userId, opt-in module-gated):
- POST/GET /api/documents/inbound — upload+extract (vision or local-OCR
text), and list. The raw document is stored encrypted at rest.
- GET/DELETE /api/documents/inbound/[id] — review detail; soft-delete.
- PATCH .../facts/[factId] — correct a staged fact before approval.
- POST .../confirm — the only write path: approved facts flow into the
labs / conditions / medications stores through their normal create paths;
rejected facts are discarded; low-confidence facts are refused.
Marc-André Bombeck