Commit Graph
4462 Commits
Author SHA1 Message Date
Marc-André Bombeck 7cb67c2e75 Merge branch 'fix/v147-nightly' into release/v1.47.0 2026-11-03 22:30:50 +01:00
Marc-André Bombeck a598b00081 test(coach): start every snapshot case with no readings
The query-shape case read the measurement mock without setting it and
passed only after a case that left rows behind.
2026-11-03 22:25:43 +01:00
Marc-André Bombeck 9a3140a4d3 test(backup): hold the record-shaped slices at their edges
The health score day, the intraday curve, a medication with its
composition and custom category, an intake row and the cycle's own
symptoms had fields and defaults no slice test met, added since the
floor was set; the backup-validation score had drifted to 40.2 % under
its 41 % floor. It is 54.1 % with these cases, and the floor follows
to 53 %.
2026-11-03 22:15:05 +01:00
Marc-André Bombeck b1cb387062 Merge branch 'fix/v147-pdf-unrenderable' into release/v1.47.0
# Conflicts:
#	.env.production.example
2026-11-03 22:10:14 +01:00
Marc-André Bombeck df6d20b696 fix(documents): read a PDF the server cannot render by its text layer
On a host whose CPU cannot run the page renderer (x64 without AVX2, arm64
musl without LSE/RCpc), every AI read of a PDF for a provider that only
takes images failed with "Scanning PDFs needs a Claude vision provider",
which says nothing about the cause. Most medical PDFs are produced
digitally and carry every word in their text layer, which pdf.js reads
without rendering.

`prepareVisionInput` now answers a text read (`mode: "text"`) when the
renderer is unavailable on this host, the provider cannot take the PDF
whole and the PDF has a usable text layer. Summary, suggest and the
background summary send that text through their existing text mode;
"Read with AI" and the index backfill write it as the local text index it
is, with no provider call; the automatic index leaves it to its local path.
`planVisionReads` does the same for the extraction and the lab scan: text
reads by page group, with anchored provenance, and the pages without a text
layer reported as `extractionIncomplete` on a document and as `unreadPages`
on a lab scan. A supplement label PDF is read from its text layer too.

A scan on such a host now answers `documents.inbound.pdfRendererUnavailable`
and `labs.ocr.pdfRendererUnavailable` (422): this server's processor cannot
run the page renderer, so a scanned PDF can only be read by a provider that
takes PDF files directly, or as photos. The `pdfNeedsAnthropic` codes are no
longer emitted, since with a working renderer every provider reads a PDF;
the recorded index outcome keeps its `pdf-needs-anthropic` value with
corrected copy.

The extraction path no longer folds a render failure of one document into
the capability error: like `prepareVisionInput` since #776 it reports
"The PDF pages couldn't be rendered for scanning." (`extractFailed`), and
the lab scan answers `labs.ocr.extractFailed`.

Hosts that render, and providers that take PDFs whole, are unchanged.

Refs #1311
2026-11-03 22:07:22 +01:00
Marc-André Bombeck c47f61f02a feat(documents): read a PDF's text layer page by page without rendering
The reader child gains a `page-texts` request: the first pages' text
layers, each read the way a rendered page's is (cut and marked past the
per-page cap), plus the document's page count. Nothing is rendered, so it
works where the page renderer cannot run.

`readPdfTextLayer` judges what that read is worth: a page counts only with
at least 40 characters of its own besides white space, so a scanner's
stamped page number or fax header does not pass for a page of text; a PDF
with no such page is a scan and is reported as one.
2026-11-03 22:07:11 +01:00
Marc-André Bombeck a503c8855d Merge branch 'feat/v147-wolfi' into release/v1.47.0 2026-11-03 21:56:23 +01:00
Marc-André Bombeck 5d36afb487 build: run the image on a Wolfi runner
The dependency and build stages stay on node:22-trixie-slim, where pnpm
picks the glibc native packages. The runner moves to wolfi-base, pinned
by its index digest: glibc, about fifty packages, and every one of them
known to the image scan, Node and the PostgreSQL client included.

nodejs-22, tzdata and postgresql-18-client come from apk, so the pgclient
stage and its pin guard go. The builder writes its Node module ABI and
glibc version out and the runner refuses to build on another ABI or an
older glibc. Wolfi's npm is major 12 and runs no install scripts unless
package.json allows them, so the Prisma CLI install names the three
packages that have one, and the build checks that the schema engine file
is there before asking the CLI about it. npm is installed for that step
and removed in the same layer; the check that nothing is left asks a
fresh shell, whose command cache cannot remember the deleted binary.
2026-11-03 21:55:30 +01:00
Marc-André Bombeck 899a054e64 Merge branch 'feat/v147-mcp-reading-id' into release/v1.47.0 2026-11-03 21:33:50 +01:00
Marc-André Bombeck ba27e728cf feat(mcp): fetch one lab reading by its own id
A link to a lab result named its analyte, and fetch lab:<analyte> answers
with the latest reading of that marker. Following a link from a report that
holds an earlier draw therefore landed on a later reading, whose links named
a different report and visit.

fetch labresult:<id> now returns that one reading (value or text result,
unit, reference range, status, date) with its own links, behind the labs
module and narrowed to the caller's live rows. Every link to a lab result
uses this id, each reading in get_labs carries it, and fetch lab:<analyte>
names the reading it quotes in metadata.readingId. The analyte view and
search are unchanged.

Refs #1323
2026-11-03 21:33:16 +01:00
Marc-André Bombeck 691c2e7301 refactor(labs): shape one reading from one shared select
The labs block and a single-reading read now build a reading from the same
select and the same shaping, so one reading fetched by its id renders exactly
like the latest reading of a marker.
2026-11-03 21:33:14 +01:00
Marc-André Bombeck cd344125d5 fix(labs): let a text-only marker take the unit of its first number
A marker minted from a text result ("SEE NOTE") has an empty unit, and a
marker with a reading has its unit locked, so the first number to arrive,
a unitless ratio included, was refused against a unit nothing had chosen.
While every reading is text the unit has nothing to contradict, so the
first number sets it. A marker that already holds a number keeps its unit.

Refs #1313
2026-11-03 21:19:28 +01:00
Marc-André Bombeck cf7905dc92 refactor(medications): hold recurrence.ts at its size baseline 2026-11-03 20:58:46 +01:00
Marc-André Bombeck 227c80878c test: give every case its own mock state under a shuffled order
Cases leaned on what an earlier case set up or left behind: a once-value
the code under test never consumed, an implementation swapped in and
kept by clearAllMocks, a payload only another block's setup provided,
the zone resolver's per-user cache, module state in a hoisted object,
and a scope set one case discovered for the next. Each now resets or
states what it reads.
2026-11-03 20:58:38 +01:00
Marc-André Bombeck 54d0647a6d fix(stats): keep r² within [0, 1] when y sits far from zero
The centred sums lose their last digits when every y is close to one
large value, and a two-point fit came out at r² 1.00000004. Clamp the
ratio to 1 and the y sum of squares at 0, and pin the two shrunk
counterexamples the nightly property run found.
2026-11-03 20:58:37 +01:00
Marc-André Bombeck 270c6ca619 refactor(medications): keep the rrule start alignment in its own module
recurrence.ts sits on the source-size ratchet; the helper and its reasoning
read on their own.
2026-11-03 20:57:46 +01:00
Marc-André Bombeck 3d0ae05192 docs: say the published image renders documents on a Raspberry Pi 4
The image runs the glibc canvas build now, which needs no ARMv8.2
features, so the Pi 4 gets thumbnails and scanned-PDF rendering back
without a code change: the gate only ever closed for musl on arm64. The
gate's comment, the env example and the getting-started prerequisites
say so, and keep NATIVE_CANVAS as the override. The x64 AVX2 gate stays:
the glibc x64 build rendered a PDF page under an emulated core without
AVX2, but it still carries AVX2 code and that one run does not cover
every path.
2026-11-03 20:53:28 +01:00
Marc-André Bombeck 775933b7d5 Merge branch 'feat/v147-dbroles' into release/v1.47.0 2026-11-03 20:52:17 +01:00
Marc-André Bombeck 95525a0259 fix(jobs): let pg-boss create its schema only when it is missing
Postgres checks the database's CREATE privilege before it checks
whether the schema exists, so CREATE SCHEMA IF NOT EXISTS fails for a
role that may not create schemas even when the schema is there. The
worker now asks first and passes createSchema: false when it exists.
2026-11-03 20:32:53 +01:00
Marc-André Bombeck f05a112c61 feat(jobs): leave index drops to the owner when maintenance runs without it
DROP INDEX belongs to the table's owner; the MAINTAIN privilege covers
VACUUM and REINDEX but not the drops of retired indexes and invalid
rebuild copies. A run that does not own measurements now skips those
drops and names what is left, for the boot to drop as the owner. The
retired-index list moves to a plain module the boot script can read.
2026-11-03 20:32:53 +01:00
Marc-André Bombeck b6da360856 refactor(db): drop the runtime schema mirror
ensureDbCompatibility ran ALTER TABLE / CREATE TABLE IF NOT EXISTS on the
login, register, token and session paths, mirroring columns every
migration under prisma/migrations already creates. The entrypoint applies
those migrations before the server listens and stops the boot when one
fails, so the mirror never had work to do, and DDL on a request path
needs the table's owner: a connection that may only read and write rows
fails every login on it. Drop the module, its call sites and the mocks
that stubbed it out.
2026-11-03 20:32:35 +01:00
Marc-André Bombeck 381726f471 perf(medications): start the rrule walk just before the window
between() iterates from DTSTART, so every compliance read walked a daily
schedule from the day the medication was created: about 4 ms per rate,
growing with the medication's age, and enough under a loaded test run to
push a compliance property past its timeout. DAILY and WEEKLY rules repeat
with a fixed period, so the start moves forward by whole periods to just
before the window. A property test holds the occurrences in the window
equal to the walk from the real anchor.
2026-11-03 20:23:31 +01:00
Marc-André Bombeck 49a0eb92ff fix(labs): word a value without a unit the same on every remaining surface
The briefing's lab input passed the stored "1" to the model, the unit
mismatch refusal read "is in 1", and the trend card left a gap where a
language puts the unit before a particle. get_labs says that a value
without a unit has an empty unit, and a lab link id is scrubbed like its
label. The review row is back at its baseline length.
2026-11-02 20:52:18 +01:00
Marc-André Bombeck 70cc753c49 Merge branch 'fix/pdf-unicode-font' into release/v1.46.6 2026-11-02 20:38:27 +01:00
Marc-André Bombeck ee0adae99c test(doctor-report): read the font guard's files through readSource 2026-11-02 20:36:16 +01:00
Marc-André Bombeck 0115a02d22 fix(doctor-report): draw the PDF in an embedded Unicode font
Helvetica's WinAnsi encoding turned every glyph outside Latin-1 into an
empty box: a Polish report lost its diacritics, a Korean report was
unreadable, and free text in any other script broke in every locale.

The renderer now registers the embedded ReportSans family on each
document, names it in every setFont, and makes it the autoTable default.
The Hangul variant is read only when the report is Korean or its data
contains Hangul. Font files are cached per process; streams are
compressed so the subset fonts add about 30 KB to a report.

The arrows, superscripts and comparison signs now print as themselves,
so the WinAnsi sanitiser and its ASCII fallbacks are gone. Tests render
Polish, Russian and Korean strings and arrows and read them back out of
the text layer.
2026-11-02 20:32:17 +01:00
Marc-André Bombeck 80a62afbbf build(pdf): add Unicode fonts for the doctor report
The report's built-in Helvetica is WinAnsi-only. These fonts cover what
the report can carry: ReportSans (Noto Sans plus the arrows and
mathematical operators of Noto Sans Math; Latin incl. Extended-A/B,
Greek, Cyrillic) in regular, bold and italic, and ReportSansKR, the same
plus Hangul from Noto Sans KR, in regular and bold.

scripts/build-pdf-fonts.py rebuilds them from the upstream sources. All
are SIL OFL 1.1; the licence sits beside the files. The directory is
named in outputFileTracingIncludes because the renderer reads the files
by a path the tracer cannot follow.
2026-11-02 20:32:11 +01:00
Marc-André Bombeck a822aa5a0e fix(documents): send a read that states no unit itself to review
A unit of "1" is the explicit no-unit choice a person makes. When a
document read returns it on its own, the value is staged for review
instead of passing straight through, so a unit the read dropped never
lands as a dimensionless value.
2026-11-02 20:31:33 +01:00
Marc-André Bombeck 2c6fb82326 Merge branch 'feat/unitless' into release/v1.46.6 2026-11-02 20:30:41 +01:00
Marc-André Bombeck e605fe0ae8 docs(api): describe the dimensionless lab unit on every lab unit field
The unit on lab results, biomarkers, the scanned-report commit and the
document fact edit now states that "1" means the value has no unit, that
it matches only itself, and that an empty unit stays refused. The lab CSV
import description names the 1 in the unit column.

Refs #1313
2026-11-02 20:28:35 +01:00
Marc-André Bombeck f9431da64f feat(labs): show a value without a unit as the number alone
Every place a lab unit is printed beside a value now goes through one
helper, so a reading stored in "1" reads "3.6" and not "3.6 1": the
list, history and detail, the chart and its tooltips, the reference bar
and range notes, the trend card, the timeline, the day view, the
clinician page, the doctor-report PDF and the changes card. Where the
unit stands alone (a marker's subtitle, a picker row, the merge preview)
it reads "No unit".

The Coach's lab block, the get_labs history and the visit-prep summary
hand the model an empty unit for such a value, so it never quotes the
"1" either.

Refs #1313
2026-11-02 20:28:34 +01:00
Marc-André Bombeck 5405ce053d feat(fhir): code a lab value without a unit as the UCUM unity
A value stored with unit "1" carries system and code on its quantity
even when the analyte map knows no coding for it: the unity is UCUM by
definition.

Refs #1313
2026-11-02 20:28:34 +01:00
Marc-André Bombeck 79ac5670c7 feat(labs): offer an explicit no-unit choice for ratios and indices
A ratio (cholesterol/HDL, albumin/globulin) or an index such as INR has
no unit, and every lab write path refuses a numeric value without one.
That refusal stays: an empty unit usually means the extraction dropped
it. Instead the value is stored as the UCUM unity "1", chosen on purpose.

The unit field when a marker is defined, on a scanned report's row and
in the document review edit now carries a "No unit" checkbox that sets
"1". The CSV import takes 1 in the unit column, as the template and the
import sheet say; an empty cell is still refused, and other spellings
such as "ratio" or "-" stay the literal unit they always were.

"1" compares as a unit of its own: it matches only itself, so it is
refused under a marker kept in mg/dL and the other way round.

Refs #1313
2026-11-02 20:28:23 +01:00
Marc-André Bombeck cae6edec64 Merge branch 'feat/mcp-links' into release/v1.46.6 2026-11-02 20:25:04 +01:00
Marc-André Bombeck 34302867aa feat(mcp): list links on lab and medication reads, ids on visit and condition rows
get_labs readings (the latest, earlier values in full, trajectory readings)
carry the fetch ids of what they link to, with linksTruncated; each linked
record is described once per answer in linkedRecords, because one report
usually holds a whole panel and would otherwise repeat on every reading.
fetch lab: and fetch med: list their links like the other record kinds, and
get_medication_schedule rows carry their id and links inline. get_visits and
get_illness_recovery rows carry visit: and condition: ids, so a row's links
are one fetch away. The labs and illness blocks gain an opt-in to carry row
ids; the Coach never asks for them.
2026-11-02 20:24:28 +01:00
Marc-André Bombeck ea7c6c860e feat(mcp): share one record-link builder and list labs and medications on a document
The links fetch lists beside a visit, condition, document or vaccination move
out of record-search into record-links, so the lab and medication reads can
list theirs through the same builder. A linked document imported from
Paperless-ngx or Papra now names its source system and its id there, never
the instance address. fetch document: also lists the lab results read from
it and the medications filed against it, each behind its own module.
2026-11-02 20:24:27 +01:00
Marc-André Bombeck 0810285061 fix(series): keep the repeated hour of a fall-back night apart
The hour grain of the dense series read truncated the local wall clock,
so the hour a fall-back night runs twice folded both instances into one
bucket: on that day a sensor stream showed one mean for two hours of
readings. An hour bucket now starts at the reading's instant less its
local minutes and seconds, which keeps the two hours apart and still
starts a half-hour zone's buckets on the half hour.

The new integration test pins a New York fall-back night and a
half-hour zone to fixed dates, so the case runs every day instead of
only when the rolling window of the existing tests covers one.
2026-11-02 20:06:15 +01:00
Marc-André Bombeck 773b943bde fix(documents): keep PDF reading alive on CPUs the canvas build skips
The arm64 musl build of the native canvas uses LSE atomics and RCpc
loads throughout, so loading it on an ARMv8.0 core such as the
Raspberry Pi 4 ends the process with SIGILL. The CPU gate only knew
the x64 AVX2 case, and pdf.js loads the canvas as soon as it starts,
so on such a host every PDF read died in the child: no text layer, no
index, and the manual read reported a busy reader.

The gate now also closes on linux/arm64 under musl when the CPU lacks
the atomics or lrcpc feature. A closed gate travels to the PDF child,
which refuses to resolve the canvas module, so pdf.js carries on
without it and the text layer reads; rendering and thumbnails keep
their existing fail-soft path. A child that ends without an answer
now logs its exit code and signal.

Refs #1311
2026-11-01 01:24:37 +01:00
Marc-André Bombeck 1c4bcce6c7 fix(ui): name the account by its display name
The dashboard greeting, the Insights greeting, the top bar and the
sidebar read the username, so a display name set on the profile card
reached the reports but none of the surfaces that address the account.
They now read one helper that returns the display name when set and
falls back to the username otherwise.

Refs #1309
2026-11-01 00:56:24 +01:00
Marc-André Bombeck 3d5d5fc4ff fix(rollups): count a type as covered only when its buckets reach its oldest reading
The coverage probe called a type covered as soon as one DAY bucket existed.
A write hook folds the day it writes, so a type whose history was not yet
folded (an account before its backfill, or a read racing the detached
refresh) had one fresh bucket, took the bucket-composed path, and its
summary counted that one day: three weight readings read as one.

A type is now covered when its oldest DAY bucket starts no later than its
oldest live reading inside the fold window. The bucket holding a reading
starts at or before it in any time zone, so the comparison holds without
knowing the account's day boundaries. Both sides are one index descent per
type; anything not covered falls back to the live aggregate as before.
2026-10-31 11:25:04 +01:00
Marc-André Bombeck 087c8868cf test: type the off-spec WHOOP profile and drop a version-stamped comment
The realism ratchet counts as-never casts and the version-stamp ratchet
refuses comment lines that open with a release; both caught the previous
commits.
2026-10-31 10:00:39 +01:00
Marc-André Bombeck 5306ba7614 fix(google-health): read the account id back for connections that lost it
Migration 0491 cleared the shared "profile" placeholder to null. Those
connections sync normally, but the one-account-per-record check cannot see
them, so the same Google account could still be connected to a second
record until the first one reconnected.

After a clean sync cycle, a connection without an id now reads it the way
the callback does (profile, then identity) and stores it, guarded on the id
still being null so a reconnect landing meanwhile wins. An id another
record already holds is not written, and a failed read leaves the id for
the next cycle without touching the cycle's verdict. The outcome is on the
wide event as googleHealth.accountId.heal.
2026-10-31 09:34:25 +01:00
Marc-André Bombeck 685cb2fa01 fix(ai): learn the max_tokens refusal from the field the request carried
A call that ran beside the one that learned the lesson read today's
selection instead and failed with the 400. The matcher now also wants the
refusal to name max_tokens, so a refusal of another field that echoes the
request does not switch the token field.

Refs #1304
2026-10-30 17:13:09 +01:00
Marc-André Bombeck 21af344054 fix(ai): send max_completion_tokens to Azure OpenAI reasoning deployments
An OpenAI-compatible gateway entry pointed at an Azure OpenAI v1 endpoint
was treated as a generic gateway and sent max_tokens and temperature, which
a reasoning deployment refuses with a 400. An Azure v1 endpoint now takes
the api.openai.com contract for a reasoning model, and any gateway that
refuses max_tokens for a model is asked again with max_completion_tokens
and remembers it, which covers deployments named something of their own.

Refs #1304
2026-10-30 17:08:43 +01:00
Marc-André Bombeck cd6cbc06f5 fix(google-health): store the account's id, not the word "profile"
The profile's resource name is `users/{user}/profile`, and the connect
stored its last segment, the same constant for every account. Since the
one-account-per-record check, a second record on an instance could not
connect or reconnect Google Health: it was refused as `already_linked`.

The connect now stores the `{user}` segment, reads `users/me/identity`
when the profile answers through the `me` alias, and stores the id as
unknown when neither names the account. A migration makes the column
nullable and clears the placeholder, so the next connect stores the
real id.
2026-10-30 13:17:54 +01:00
Marc-André Bombeck cd98db82eb test(insights): date the comparison's sleep readings by calendar day
The readings sat at now minus n times 24 hours, which keeps the wall-clock
hour only between two clock changes. Run late in the evening after the
October change, two of them fell into the same night and the average read
525 minutes instead of 420.
2026-10-29 23:16:00 +01:00
Marc-André Bombeck eed83befa3 fix(google-health): protect only a night's own segments in the sleep sweep
Every night's replace-by-window clean-up carried every fresh segment id of
the fetch. On a first sync that reads years of sleep that is one query per
night with tens of thousands of bound values, over Postgres's limit, and
the process spent minutes building them before each one failed. The sweep
can only reach rows inside the window, so each window now protects the
fresh rows inside it, from whichever session reported them.

Refs #1195
2026-10-29 23:13:43 +01:00
Marc-André Bombeck 3674c1757d fix(timeline): leave hidden lab markers out of the values menu
Hiding a marker takes it out of the labs catalogue and the entry
pickers, but the timeline still offered it among the lab values.

The timeline now offers only markers that are not hidden. A hidden
marker that was chosen before keeps drawing its line and stays in the
menu as a ticked entry, named from that line, so it can be unticked,
the way the entry form keeps a hidden marker that is already selected.
Once unticked it is no longer offered.
2026-10-29 22:01:43 +01:00
Marc-André Bombeck 5dec158c9d fix(ai): keep the reasoning-field day for what a 400 taught
The dialect cache gave a day to every value that says the reasoning
field is refused, and that includes the combined "field refused, reasons
regardless" value, which one answerless reply writes. One reply could
therefore stretch a lesson to a full fresh day, against the rule that a
lesson read from a single reply keeps the hour.

A lesson now says what taught it. A 400 refusal gives a refused field
its day. A reply that upgrades a refused field to the combined value
keeps the refusal's remaining lifetime rather than a new day or the
hour, so the refused request does not come back early either.
2026-10-29 21:58:40 +01:00
Marc-André Bombeck c920266f32 fix(backup): explain a second restore of one file into another account
Restored rows keep the ids they had in the file. Once an erased
account's copy had gone into one account, the same file uploaded into a
second account restored into a primary-key conflict, reported only as
the generic "the database rejected a record" failure.

For a copy put into a chosen account, a primary-key conflict now ends
the restore with backup.restore.rows_exist_elsewhere and a sentence that
says the file was most likely restored into another account already.
The transaction still rolls back, so neither account changes. The code
is in the catalogue, the console names it, and the runbook says a file
goes into one account only.
2026-10-29 21:50:34 +01:00