mirror of
https://github.com/MBombeck/HealthLog.git
synced 2026-11-12 14:16:12 +00:00
Merge branch 'feat/v144-report' into release/v1.44.0
This commit is contained in:
Marc-André Bombeck committed
commit
4e71cf4dc2
58 files changed
+5703
-91
No files matched your search
@@ -0,0 +1,362 @@
|
||||
/**
|
||||
* v1.44 against a real Postgres: the FHIR Observation time series (the UNION
|
||||
* page query, its count, the BP pairing, the glucose-context filter, owner and
|
||||
* soft-delete scoping), the segmented medication effect read end to end, and
|
||||
* the doctor report's workout and effect blocks.
|
||||
*
|
||||
* The effect fixture: an ACE inhibitor started on 2026-03-01 with systolic
|
||||
* readings of exactly 140 for 60 days before and 130 − 0.1·t after, so the
|
||||
* fit must recover a level change of −10 mmHg and a slope change of
|
||||
* −0.7 mmHg/week, and a second medication starting inside the window must be
|
||||
* listed as a confounder.
|
||||
*/
|
||||
import { beforeAll, describe, expect, it } from "vitest";
|
||||
|
||||
import type { Prisma } from "@/generated/prisma/client";
|
||||
import {
|
||||
emitSeriesPage,
|
||||
querySeriesPage,
|
||||
resolveSeriesScope,
|
||||
} from "@/lib/fhir/series";
|
||||
import {
|
||||
EFFECT_MEDICATION_INCLUDE,
|
||||
loadSegmentedEffects,
|
||||
} from "@/lib/medications/efficacy/load-segmented-effects";
|
||||
import { collectDoctorReportData } from "@/lib/doctor-report-data";
|
||||
import { selectionFromLeaves } from "@/lib/report-selection/selection";
|
||||
import type { ReportLeafId } from "@/lib/report-selection/catalogue";
|
||||
|
||||
import { getPrismaClient, truncateAllTables } from "./setup";
|
||||
|
||||
const DAY = 86_400_000;
|
||||
const PIVOT = Date.parse("2026-03-01T00:00:00.000Z");
|
||||
|
||||
let userId = "";
|
||||
let otherId = "";
|
||||
let medId = "";
|
||||
|
||||
const MODULES = {
|
||||
cycle: false,
|
||||
mood: false,
|
||||
sleep: true,
|
||||
glucose: true,
|
||||
workouts: true,
|
||||
recovery: true,
|
||||
labs: true,
|
||||
illness: true,
|
||||
achievements: true,
|
||||
coach: true,
|
||||
insights: true,
|
||||
medications: true,
|
||||
doctorReport: true,
|
||||
environment: true,
|
||||
mcp: true,
|
||||
inboundDocuments: true,
|
||||
mentalHealth: true,
|
||||
nutrients: true,
|
||||
vaccinations: true,
|
||||
timeline: true,
|
||||
} as const;
|
||||
|
||||
const gateOf = (leaves: ReportLeafId[]) => ({
|
||||
admits: (leaf: ReportLeafId) => leaves.includes(leaf),
|
||||
});
|
||||
|
||||
beforeAll(async () => {
|
||||
const prisma = getPrismaClient();
|
||||
await truncateAllTables(prisma);
|
||||
const user = await prisma.user.create({
|
||||
data: {
|
||||
username: "fhir-series-effect",
|
||||
email: "fhir-series-effect@example.test",
|
||||
timezone: "UTC",
|
||||
},
|
||||
});
|
||||
userId = user.id;
|
||||
const other = await prisma.user.create({
|
||||
data: {
|
||||
username: "fhir-series-other",
|
||||
email: "fhir-series-other@example.test",
|
||||
timezone: "UTC",
|
||||
},
|
||||
});
|
||||
otherId = other.id;
|
||||
|
||||
const rows: Prisma.MeasurementCreateManyInput[] = [];
|
||||
// Systolic: 140 before, 130 − 0.1·t after (one reading a day at 08:00).
|
||||
for (let t = -60; t < 60; t++) {
|
||||
rows.push({
|
||||
userId,
|
||||
type: "BLOOD_PRESSURE_SYS",
|
||||
value: t < 0 ? 140 : 130 - 0.1 * t,
|
||||
unit: "mmHg",
|
||||
source: "MANUAL",
|
||||
measuredAt: new Date(PIVOT + t * DAY + 8 * 3_600_000),
|
||||
});
|
||||
}
|
||||
// Two paired diastolic readings and one lone diastolic.
|
||||
rows.push(
|
||||
{
|
||||
userId,
|
||||
type: "BLOOD_PRESSURE_DIA",
|
||||
value: 85,
|
||||
unit: "mmHg",
|
||||
source: "MANUAL",
|
||||
measuredAt: new Date(PIVOT + 10 * DAY + 8 * 3_600_000),
|
||||
},
|
||||
{
|
||||
userId,
|
||||
type: "BLOOD_PRESSURE_DIA",
|
||||
value: 84,
|
||||
unit: "mmHg",
|
||||
source: "MANUAL",
|
||||
measuredAt: new Date(PIVOT + 11 * DAY + 8 * 3_600_000),
|
||||
},
|
||||
{
|
||||
userId,
|
||||
type: "BLOOD_PRESSURE_DIA",
|
||||
value: 80,
|
||||
unit: "mmHg",
|
||||
source: "MANUAL",
|
||||
measuredAt: new Date(PIVOT + 11 * DAY + 20 * 3_600_000),
|
||||
},
|
||||
);
|
||||
rows.push(
|
||||
{
|
||||
userId,
|
||||
type: "BLOOD_GLUCOSE",
|
||||
value: 95,
|
||||
unit: "mg/dL",
|
||||
source: "MANUAL",
|
||||
glucoseContext: "FASTING",
|
||||
measuredAt: new Date(PIVOT + 12 * DAY),
|
||||
},
|
||||
{
|
||||
userId,
|
||||
type: "BLOOD_GLUCOSE",
|
||||
value: 130,
|
||||
unit: "mg/dL",
|
||||
source: "MANUAL",
|
||||
glucoseContext: null,
|
||||
measuredAt: new Date(PIVOT + 12 * DAY + 3_600_000),
|
||||
},
|
||||
{
|
||||
userId,
|
||||
type: "WEIGHT",
|
||||
value: 80,
|
||||
unit: "kg",
|
||||
source: "MANUAL",
|
||||
measuredAt: new Date(PIVOT + 13 * DAY),
|
||||
deletedAt: new Date(PIVOT + 14 * DAY),
|
||||
},
|
||||
{
|
||||
userId: otherId,
|
||||
type: "WEIGHT",
|
||||
value: 70,
|
||||
unit: "kg",
|
||||
source: "MANUAL",
|
||||
measuredAt: new Date(PIVOT + 13 * DAY),
|
||||
},
|
||||
);
|
||||
await prisma.measurement.createMany({ data: rows });
|
||||
|
||||
await prisma.workout.createMany({
|
||||
data: [
|
||||
{
|
||||
userId,
|
||||
source: "MANUAL",
|
||||
sportType: "running",
|
||||
externalId: "run-1",
|
||||
startedAt: new Date(PIVOT + 11 * DAY + 12 * 3_600_000),
|
||||
endedAt: new Date(PIVOT + 11 * DAY + 13 * 3_600_000),
|
||||
durationSec: 3600,
|
||||
totalDistanceM: 10_000,
|
||||
totalEnergyKcal: 700,
|
||||
avgHeartRate: 150,
|
||||
},
|
||||
{
|
||||
userId,
|
||||
source: "MANUAL",
|
||||
sportType: "running",
|
||||
externalId: "run-2",
|
||||
startedAt: new Date(PIVOT + 20 * DAY),
|
||||
endedAt: new Date(PIVOT + 20 * DAY + 1_800_000),
|
||||
durationSec: 1800,
|
||||
},
|
||||
],
|
||||
});
|
||||
|
||||
const med = await prisma.medication.create({
|
||||
data: {
|
||||
userId,
|
||||
name: "Ramipril",
|
||||
dose: "5 mg",
|
||||
treatmentClass: "GENERIC",
|
||||
atcCode: "C09AA05",
|
||||
trackIntake: false,
|
||||
startsOn: new Date(PIVOT),
|
||||
},
|
||||
});
|
||||
medId = med.id;
|
||||
await prisma.medication.create({
|
||||
data: {
|
||||
userId,
|
||||
name: "Second drug",
|
||||
dose: "1 mg",
|
||||
treatmentClass: "GENERIC",
|
||||
startsOn: new Date(PIVOT + 20 * DAY),
|
||||
},
|
||||
});
|
||||
});
|
||||
|
||||
describe("FHIR Observation series in Postgres", () => {
|
||||
const range = {
|
||||
from: new Date(PIVOT + 10 * DAY),
|
||||
to: new Date(PIVOT + 21 * DAY),
|
||||
};
|
||||
|
||||
it("pages newest first, pairs BP, scopes to the owner and drops soft-deleted rows", async () => {
|
||||
const scope = resolveSeriesScope(
|
||||
gateOf([
|
||||
"BLOOD_PRESSURE_SYS",
|
||||
"BLOOD_PRESSURE_DIA",
|
||||
"BLOOD_GLUCOSE",
|
||||
"WEIGHT",
|
||||
"WORKOUTS",
|
||||
]),
|
||||
null,
|
||||
);
|
||||
const { total, refs } = await querySeriesPage({
|
||||
userId,
|
||||
scope,
|
||||
range,
|
||||
count: 200,
|
||||
offset: 0,
|
||||
});
|
||||
// 11 systolic (days 10..20), 1 lone diastolic, 2 glucose, 2 workouts.
|
||||
// The two paired diastolic rows ride inside their systolic panels; the
|
||||
// deleted weight and the other account's weight never appear.
|
||||
expect(total).toBe(16);
|
||||
expect(refs).toHaveLength(16);
|
||||
const page = await emitSeriesPage({
|
||||
userId,
|
||||
refs,
|
||||
scope,
|
||||
glucoseUnit: "mg/dL",
|
||||
});
|
||||
expect(page).toHaveLength(16);
|
||||
// Newest first: the day-20 systolic (08:00, no diastolic partner, so a
|
||||
// lone 8480-6 reading), then the day-20 run (00:00).
|
||||
expect(page[0].code.coding?.[0]?.code).toBe("8480-6");
|
||||
expect(page[1].id.startsWith("w-")).toBe(true);
|
||||
const panels = page.filter(
|
||||
(o) =>
|
||||
o.code.coding?.[0]?.code === "85354-9" && o.component?.length === 2,
|
||||
);
|
||||
expect(
|
||||
panels.map((p) => p.component?.[1]?.valueQuantity?.value).sort(),
|
||||
).toEqual([84, 85]);
|
||||
expect(page.some((o) => o.code.coding?.[0]?.code === "8462-4")).toBe(true);
|
||||
expect(page.some((o) => o.code.coding?.[0]?.code === "29463-7")).toBe(
|
||||
false,
|
||||
);
|
||||
});
|
||||
|
||||
it("pages with offset and agrees with the count", async () => {
|
||||
const scope = resolveSeriesScope(gateOf(["BLOOD_PRESSURE_SYS"]), null);
|
||||
const first = await querySeriesPage({
|
||||
userId,
|
||||
scope,
|
||||
range,
|
||||
count: 5,
|
||||
offset: 0,
|
||||
});
|
||||
const second = await querySeriesPage({
|
||||
userId,
|
||||
scope,
|
||||
range,
|
||||
count: 5,
|
||||
offset: 5,
|
||||
});
|
||||
expect(first.total).toBe(11);
|
||||
expect(first.refs).toHaveLength(5);
|
||||
expect(second.refs).toHaveLength(5);
|
||||
const ids = new Set([...first.refs, ...second.refs].map((r) => r.id));
|
||||
expect(ids.size).toBe(10);
|
||||
});
|
||||
|
||||
it("narrows glucose to a code's contexts", async () => {
|
||||
const scope = resolveSeriesScope(gateOf(["BLOOD_GLUCOSE"]), {
|
||||
types: new Set(["BLOOD_GLUCOSE"]),
|
||||
glucoseContexts: new Set(["FASTING"]),
|
||||
workouts: false,
|
||||
});
|
||||
const { total } = await querySeriesPage({
|
||||
userId,
|
||||
scope,
|
||||
range,
|
||||
count: 50,
|
||||
offset: 0,
|
||||
});
|
||||
expect(total).toBe(1);
|
||||
});
|
||||
});
|
||||
|
||||
describe("segmented medication effect in Postgres", () => {
|
||||
it("recovers the known level and slope change and lists the confounder", async () => {
|
||||
const prisma = getPrismaClient();
|
||||
const med = await prisma.medication.findFirstOrThrow({
|
||||
where: { id: medId },
|
||||
include: EFFECT_MEDICATION_INCLUDE,
|
||||
});
|
||||
const effects = await loadSegmentedEffects({
|
||||
userId,
|
||||
med,
|
||||
targets: ["BLOOD_PRESSURE_SYS"],
|
||||
timezone: "UTC",
|
||||
now: new Date(PIVOT + 59 * DAY + 12 * 3_600_000),
|
||||
});
|
||||
const e = effects.get("BLOOD_PRESSURE_SYS")!;
|
||||
expect(e.present).toBe(true);
|
||||
expect(e.levelChange!.estimate).toBeCloseTo(-10, 6);
|
||||
expect(e.slopeChangePerWeek!.estimate).toBeCloseTo(-0.7, 6);
|
||||
expect(e.days.before).toBe(60);
|
||||
expect(e.days.after).toBe(60);
|
||||
expect(e.adherence.status).toBe("not_tracked");
|
||||
expect(e.confounders).toEqual([
|
||||
{ medicationName: "Second drug", event: "started", date: "2026-03-21" },
|
||||
]);
|
||||
});
|
||||
|
||||
it("reaches the doctor report with its workout block", async () => {
|
||||
const data = await collectDoctorReportData(
|
||||
userId,
|
||||
{
|
||||
start: new Date(PIVOT),
|
||||
end: new Date(PIVOT + 59 * DAY + 12 * 3_600_000),
|
||||
days: 60,
|
||||
},
|
||||
selectionFromLeaves([
|
||||
"MEDICATION_LIST",
|
||||
"MEDICATION_EFFECT",
|
||||
"BLOOD_PRESSURE_SYS",
|
||||
"WORKOUTS",
|
||||
]),
|
||||
{ moduleMap: MODULES as never },
|
||||
);
|
||||
const effect = data.medicationEffects?.find(
|
||||
(m) => m.medicationName === "Ramipril",
|
||||
);
|
||||
// Diastolic was not selected, so only the systolic target rides.
|
||||
expect(effect?.targets.map((t) => t.type)).toEqual(["BLOOD_PRESSURE_SYS"]);
|
||||
expect(effect?.targets[0].effect.present).toBe(true);
|
||||
expect(data.workouts?.sessions).toBe(2);
|
||||
expect(data.workouts?.bySport[0]).toMatchObject({
|
||||
sportType: "running",
|
||||
sessions: 2,
|
||||
durationSec: 5400,
|
||||
distanceM: 10_000,
|
||||
distanceSessions: 1,
|
||||
});
|
||||
});
|
||||
});
|
||||
Reference in new issue
Block a user