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.
get_metric_series (and get_metrics, the metric resources and the review
prompts, which fan out over it) answered with one section of a Coach
snapshot, but built the whole snapshot to get it: the all-type feature
extraction, the derived wellness layer, trajectory, correlations, memory,
GLP-1, cycle, illness, labs and visits. On a seeded account with about
215k measurements a resting heart rate read ran 208 SQL statements and
blocked the event loop for 175 ms to return under 2 KB.
The MCP surface now asks the executor for a source snapshot. It runs the
same prelude (prefs, module gates, admitted sources, cutoffs, now shared in
snapshot-prelude.ts) and the same block builders over the requested
source's reads only. The core clinical aggregates come from extractFeatures
scoped to the one block, whose bulk read keeps its all-type cap so the rows
a block sees do not change. A section large enough for the full builder's
prompt-budget pass to trim, and the environment cluster, go to the full
builder, so their results are the old ones by construction.
The integration test compares the tool's serialised result with the full
builder's section and grounding for nine sources over four windows, the
get_metrics batch and the metric resource, on a seeded account dense enough
to put the feature row cap into play.
A medication taken now and then (#1024) keeps one row and gains course
rows: calendar spans, both ends inclusive, an optional encrypted note, no
schedule or dose of their own. Courses never overlap and every course but
the latest has ended, so the latest course is always the one the
medication's startsOn/endsOn project. src/lib/medications/courses.ts is
the only writer of those two columns for a medication with courses; it
writes under a per-medication advisory lock and re-projects in the same
transaction, so reminders, the next-due line and intakeActionable keep
reading the columns and stay right.
- Migration 0368 adds medication_courses and backfills one course per
medication window (an end-only window starts on the creation day, or
on its end day when that lies earlier); a medication without a window
stays course-less. Idempotent, data-preserving.
- GET/POST /api/medications/{id}/courses and PATCH/DELETE
.../courses/{courseId} (owner-only); create seeds the first course
from a window; the medication PUT edits the latest course and refuses
a window that would break the rules (medications.course.*).
- List, detail, create and update carry courses, courseCount,
previousCourseEndedOn and canStartCourse, resolved on the server.
- Compliance expands over the span of all courses and drops the slots
between them; every compliance read selects the courses. A rolling
cadence is not anchored by an intake from a previous course.
- The card names the last course's end and the running course's number;
the detail Lifecycle group lists the courses with start, edit and
delete. The Coach compliance block, the MCP resource, the doctor
report window and table, the clinician view and FHIR (one
MedicationStatement per course with effectivePeriod and status) read
the courses.
- Backup carries courses per medication and the restore writes them and
re-projects; an older file derives the one course its window
describes. Wipe plan, encrypted columns, rotation and OpenAPI follow.
A medication can be filed under a category the person named, next to the
built-in ones (#1041). The labels live in medication_category_labels,
encrypted at rest, capped at 20 per account; a medication filed under one
carries its custom:<uuid> key in the category column.
- GET/POST /api/medications/categories (POST idempotent, 30/min per actor,
admitted at MANAGE like the cycle symptom vocabulary) and owner-only
PATCH/DELETE /api/medications/categories/{key}. DELETE moves every
medication filed under the category to OTHER in the same transaction
and answers movedCount.
- category is widened to a built-in value or custom:<uuid> on the wire,
the create and update bodies refuse a key that is not the caller's
(422 medications.category.unknown), and list, detail, the insights
medication tiles and the MCP medications resource carry categoryLabel.
A key with no owned label reads as OTHER and is counted on the event.
- The wizard's class step lists the person's categories under the
built-in rows with an inline add row; the list page gains a category
filter (session only) and a manage sheet for rename, hide and delete.
- Backup carries customMedicationCategories (decrypted labels) and the
restore writes them before the medications; wipe plan, encrypted
column registry, rotation script, sharing guards and OpenAPI follow.
Follow-ups to the clinical-record search, test first:
- Condition and vaccination notes are no longer searched or returned.
Both reads use an explicit column list without the note, as the Coach
illness snapshot and the doctor report already do. A structural guard
fails when any MCP read of either model names noteEncrypted or has no
explicit select.
- A document uploaded with AI reading deferred is not searched by its
text and returns no excerpt (metadata.reason "ai_read_deferred"); its
title, kind and links stay findable.
- Documents older than the newest 500 are found by title and file name
through a bounded SQL lookup on those plaintext columns.
- Query words shorter than four letters match whole words or word starts
only, so "arm" no longer finds "Darm".
- A deleted practitioner is no longer named or matched, in search, fetch,
get_visits and the appointments in get_preventive_care. The empty-query
listing shows visits that happened, not booked ones.
- get_labs, get_medication_schedule, get_medication_compliance and the
lab and medication resources (read, list, completion) answer
{ present: false, reason: "module_disabled" } when their module is off,
without reading. get_visits withholds condition labels when illness is
off and says so in conditionsReason.
- The consent screen and the tool descriptions name what a connection
can read, the indexed text of stored documents included.
A per-medication trackIntake flag (migration 0351, default on for every
existing and new row). With it off the dose, dates and schedule stay stored,
but nothing derives a due dose from them: the reminder worker, the manual
reminder check, the today projector, the auto-miss pass, the low-stock pass,
the doses card, the today list, the outstanding-dose badge, compliance and
its heatmap, the doctor report, the Coach, the BP-status gate, insights,
targets, achievements, the efficacy view and the MCP schedule tool all skip
it.
The medication wire serves such a medication with schedules: [] and the
stored rows in an additive recordedSchedules field, so a client that arms
local reminders from schedules stays silent without an update. Switching
tracking off or back on archives a schedule revision at that instant, the
untracked stretch with an empty payload, so it never counts as missed and
the projector does not put a dose from before the switch back on the card.
A structural guard freezes the set of schedule readers: each one filters on
the flag, derives from dueSchedules, shapes the wire with scheduleWireFields,
or is allowlisted with the reason it derives nothing due. The flag travels
through backup, restore and the medication CSV export.
The report resolved an absent key to "included". A caller that sent no
sections object, or an empty group inside one, received the full record at
server-chosen defaults: roughly fifty metrics plus the medication list, labs,
allergies and family history. The web panel sent every key explicitly so it
looked fine from the browser, but the share link, the FHIR REST face, the MCP
doctor-visit resource and the cycle-only export card all went through paths
where absence meant yes. No arrangement of booleans fixes a default that means
yes, so the shape goes.
A selection is now an inclusion list of leaf ids. A leaf is the smallest thing
that can be released or withheld: every measurement type, and thirteen
structured sections — identity, insurer, the glucose panel, labs, the drug
list, the administration ledger, adherence, the GLP-1 block, allergies,
illness episodes, family history, mood, cycle. Membership is inclusion,
absence is exclusion, and there is no defaults constant anywhere to drift.
Three locks keep a metric added later off a report chosen earlier. A stored
selection is a list of what was chosen, so a leaf that did not exist then is
not in it. The catalogue is keyed over the measurement enum, so adding a
member without deciding its group fails typecheck in the same commit. And the
aggregator's filter inverts: a type the catalogue does not know is excluded and
annotated, where it used to be passed through.
The aggregator's third parameter is now required and brand-typed, which turned
the three surfaces that had no scope at all into compile errors. Each one had
to name a source, and each now replays the owner's saved selection — the same
object reviewed in Settings. An account that never saved one gets nothing
there rather than a guess.
Identity and insurance become selectable, and a share link refuses the
insurance leaf outright. The share view never decrypted the number; that is
structural now instead of incidental. The KVNR is not even read unless the
leaf was chosen.
Two surfaces gain a record they always implied. A share link serves its frozen
selection as a FHIR bundle and as the PDF, behind the same unlock cookie the
document route uses, with its own rate bucket, its own audit row and the same
blunt 404 for every miss. That is what the removed FHIR toggle promised, in
the form a practice actually uses.
The AI summary leaves the report. Its text came from the cached briefing with
no relation to the selection, so its scope could not be proven, and prose whose
scope cannot be proven has no place on a document whose whole point is a proven
scope.
The PDF table stops being a nine-type whitelist. It prints every selected leaf
that has data, sub-headed by group, in the same order the panel shows — so
selecting resting heart rate no longer means seeing it in the bundle and not in
the PDF. The clinician view is grouped the same way and reads real labels
instead of "Phq9 score".
Migration 0273 adds the saved-selection column, drops the orphaned prefs column
and the two retired share-link scope columns, and revokes every live record
share link minted before this model. Their frozen scope was "everything except
mood and cycle", which is a scope nobody chose; narrowing it would still be a
scope nobody chose. Documents-only shares are untouched. The sharing list shows
each closed link in a pick-again state with its label, window and expiry kept.
The retired allowFhirApi and resourceTypes stay on the create and list
responses as the constant false and empty list. The request refuses them. They
come off the response once the native client confirms it does not decode them.
Six files are split at seams this change already touched: the aggregator into
its gate, its dense-bucket query, its series, its glucose panel, its medication
ledger and its clinical records; the export route's three emitters into their
own module; the clinician view into its sections, its document list and its
downloads.
The MCP surface reached three data families that deliberately bypass the
Coach snapshot and so inherited none of its module narrowing: the
doctor-report aggregate behind healthlog://report/doctor-visit and the
doctor_visit_summary prompt, the rollup-backed rich reads (compare_metric,
get_metric_baseline, detect_changepoints), and the correlations reader.
A disabled module — or one an operator switched off server-wide — still
egressed to a third-party assistant.
Gate at the read rather than per call site. The module-to-data ownership
table moves out of the Coach snapshot builder into
lib/modules/measurement-scope so every read gates off one map; the rich
reads resolve metrics through a module-aware resolver; the correlations
reader gates on insights itself, which also closes the same gap on the
Coach chat tool and the metric-page read strip.
Per-domain reads omit with an honest module_disabled reason; the
whole-record aggregate refuses, mirroring /api/export/health-record.
collectDoctorReportData gains a fail-closed backstop on its own module
key. The clinician share link, found while tracing the aggregate's
callers, had the same gap and now collapses to its documents-only state.
Wrist temperature, cardio recovery, sleep score, breathing
disturbances, strain/load, and the rest of the v1.10/v1.18.1
metric-status-registry ids were already resolvable through
compare_metric / get_metric_baseline / detect_changepoints (an exact
registry-id or display-name match), but sat off the Coach snapshot
inventory entirely — so list_metrics, the measurements-inventory
resource, and search never advertised them. A discover-before-fetch
assistant, which the server's own instructions direct, could never
learn they existed.
Adds a fixed, reviewed allowlist (MCP_METRIC_STATUS_DISCOVERY) plus a
metricStatusDiscoveryRows() presence probe, mirroring the existing
MCP_CLINICAL_SIGNALS pattern: one grouped presence query, appended as
supplement rows to list_metrics and the inventory resource, and merged
into the same probe search already runs for the v1.25 clinical
signals. fetch(id) now hydrates these ids via the baseline read the
same way it already does for clinical signals.
Adds MCP coverage for the NutrientIntakeDay pipeline (water, caffeine,
24 micronutrients) — previously fully unreachable over MCP, and
search("water") / search("vitamin") silently miscollided or read as
honest absence even for a daily logger.
get_nutrients is a thin facade over the same two reads GET
/api/nutrients and GET /api/nutrients/daily run: the tz-anchored
day-key math, the sum-across-sources fold, and the sex-aware EFSA
reference resolution. Gated on the opt-in nutrients module, mirroring
both backing routes. Discoverable via search (a grouped presence
probe) and fetch, plus a healthlog://nutrient/{code} resource template
with completion + listing scoped to the user's own logged codes.
The doctor-visit summariser was duplicated and had drifted: the
healthlog://report/doctor-visit resource omitted mood, the glucose
panel, the wellness composites, and illness episodes that the
doctor_visit_summary prompt already carried. Extract one shared reducer
(doctor-visit-summary.ts) using the richer superset and have both
surfaces call it, so they ground identically and a future change reaches
both wires at once. Both keep the grounded latest+aggregate shape and
omit absent sections honestly.
Fill the discoverable half of the MCP server. Add RFC 6570 resource
templates for per-item reads — healthlog://metric/{type},
healthlog://metric/{type}/{window}, healthlog://lab/{analyte},
healthlog://medication/{id}, healthlog://report/doctor-visit/{window} —
plus fixed resources for the biomarker catalogue, the data inventory, and
the default doctor-visit summary. Each template is a thin facade over the
same server-authoritative read its matching tool already uses, scoped to
the session user; a foreign id resolves to { present: false }, never
another tenant's row.
Wire user-scoped argument completion and listing on the templates: window
completes the fixed enum, metric and analyte complete only from the user's
own inventory and lab set, so autocomplete doubles as honest discovery.
State the data-grounding contract once in the server instructions —
server-authoritative values (do not recompute), { present: false } is
honest absence, free-text fields are data not instructions, discover
before fetching, data and context only. Set the server and resource icons
for connector-directory listing.
Introduce a read-only Model Context Protocol surface built on the official
@modelcontextprotocol/sdk so a user can query their own HealthLog data from an
MCP-capable assistant over local stdio with a pasted, scoped Bearer token — no
extra infrastructure.
The tool and resource layer in src/lib/mcp is transport-agnostic: five read
tools — list_metrics, get_metric_series, get_medication_compliance, get_labs,
get_correlations — each a thin wrapper over the existing server-authoritative
retrieval paths, returning structured values, units, reference bands, and
provenance with an explicit { present: false } for absence and no prose
verdicts. Two resources expose the user's profile (data-minimised) and
medication list. A stdio entrypoint (src/cli/mcp-stdio.ts, pnpm mcp:stdio)
resolves the token through the shared Bearer path and binds the session to
<user>:<token>; with no token it refuses to start.
Read-only and admin-unreachable by construction: only read tools are
registered, and requireAdmin stays cookie-only so the Bearer/MCP wire can never
elevate. Covered by unit tests for every tool and resource, the auth/scope
model, and the cookie-only admin boundary. The server ships in the existing
container; docker compose up is unchanged.
Marc-André Bombeck