agent-bober 0.18.0 → 0.19.0

package/dist/medical/analysis/trends.d.ts

@@ -0,0 +1,36 @@
+/**
+ * Lab trend analyzer — deterministic reference-range and slope rules.
+ *
+ * PURE / NO network / NO LLM / NO Date.now() / NO async / NO fs.
+ * Identical input => identical output.
+ *
+ * ADR-3: The LLM NEVER performs arithmetic. All trend math is delegated exclusively to
+ * NumericsQueryLayer.getLabTrend (slope + latestValue). No hand-rolled slope arithmetic.
+ *
+ * Rules:
+ *   A. Reference-range crossing: latestValue outside [referenceLow, referenceHigh]
+ *      → kind 'watch' (severity 3, urgency 3);
+ *        >20% beyond the edge → kind 'risk' (severity 4, urgency 4).
+ *   B. Slope-toward-edge: slope != null, value is in range, trending toward the nearer
+ *      reference edge with a projected crossing → kind 'watch' (severity 2, urgency 2).
+ *
+ * Abstains (empty findings) when sampleCount === 0 for a biomarker.
+ * Reference range is read from store.getLabSeries (LabTrend does not carry it).
+ */
+import type { HealthDataStore } from "../health-store.js";
+import type { MedicalFinding } from "./finding.js";
+/**
+ * Analyze lab trends for a set of biomarkers and return detected findings.
+ *
+ * PURE, synchronous, deterministic. No async, no fs, no network, no LLM.
+ * Delegates ALL trend math to NumericsQueryLayer.getLabTrend (ADR-3).
+ * Reference ranges are read from store.getLabSeries (LabTrend does not carry them).
+ *
+ * @param store       HealthDataStore (caller is responsible for lifecycle)
+ * @param biomarkers  List of biomarker names to analyze
+ * @param opts        { now: ISO 8601 injected timestamp }
+ */
+export declare function analyzeTrends(store: HealthDataStore, biomarkers: string[], opts: {
+    now: string;
+}): MedicalFinding[];
+//# sourceMappingURL=trends.d.ts.map

package/dist/medical/analysis/trends.d.ts.map

@@ -0,0 +1 @@
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package/dist/medical/analysis/trends.js

@@ -0,0 +1,157 @@
+/**
+ * Lab trend analyzer — deterministic reference-range and slope rules.
+ *
+ * PURE / NO network / NO LLM / NO Date.now() / NO async / NO fs.
+ * Identical input => identical output.
+ *
+ * ADR-3: The LLM NEVER performs arithmetic. All trend math is delegated exclusively to
+ * NumericsQueryLayer.getLabTrend (slope + latestValue). No hand-rolled slope arithmetic.
+ *
+ * Rules:
+ *   A. Reference-range crossing: latestValue outside [referenceLow, referenceHigh]
+ *      → kind 'watch' (severity 3, urgency 3);
+ *        >20% beyond the edge → kind 'risk' (severity 4, urgency 4).
+ *   B. Slope-toward-edge: slope != null, value is in range, trending toward the nearer
+ *      reference edge with a projected crossing → kind 'watch' (severity 2, urgency 2).
+ *
+ * Abstains (empty findings) when sampleCount === 0 for a biomarker.
+ * Reference range is read from store.getLabSeries (LabTrend does not carry it).
+ */
+import { NumericsQueryLayer } from "../numerics.js";
+import { findingId } from "./finding.js";
+// -- Internal helpers -----------------------------------------------------
+/**
+ * Build a MedicalFinding for a detected trend condition.
+ * Uses findingId with domain|biomarker|ruleKey (NOT now) for idempotency.
+ */
+function makeFinding(biomarker, ruleKey, title, kind, urgency, severity, evidence, now) {
+    return {
+        id: findingId("medical", biomarker, ruleKey),
+        domain: "medical",
+        title,
+        kind,
+        urgency,
+        severity,
+        evidence,
+        surfacedAt: now,
+        tags: ["lab-trend", biomarker],
+        status: "open",
+    };
+}
+// -- Rule A ---------------------------------------------------------------
+/**
+ * Apply Rule A: latestValue outside [referenceLow, referenceHigh].
+ *   - >20% beyond edge → 'risk', severity 4, urgency 4
+ *   - ≤20% beyond edge → 'watch', severity 3, urgency 3
+ *
+ * Returns a finding or undefined when in range.
+ */
+function applyRuleA(biomarker, latestValue, latestUnit, referenceLow, referenceHigh, now) {
+    // Above referenceHigh
+    if (referenceHigh !== undefined && latestValue > referenceHigh) {
+        const pctBeyond = referenceHigh !== 0 ? (latestValue - referenceHigh) / referenceHigh : 0;
+        const isRisk = pctBeyond > 0.2;
+        const kind = isRisk ? "risk" : "watch";
+        const severity = isRisk ? 4 : 3;
+        const urgency = isRisk ? 4 : 3;
+        const ruleKey = isRisk ? "rule-a-high-risk" : "rule-a-high";
+        const evidence = [
+            `${biomarker} = ${latestValue} ${latestUnit} (reference: ≤${referenceHigh} ${latestUnit})`,
+            `${(pctBeyond * 100).toFixed(1)}% above upper reference limit`,
+        ];
+        return makeFinding(biomarker, ruleKey, `${biomarker}: above reference range`, kind, urgency, severity, evidence, now);
+    }
+    // Below referenceLow
+    if (referenceLow !== undefined && latestValue < referenceLow) {
+        const divisor = Math.abs(referenceLow) > 0 ? referenceLow : 1;
+        const pctBeyond = (referenceLow - latestValue) / divisor;
+        const isRisk = pctBeyond > 0.2;
+        const kind = isRisk ? "risk" : "watch";
+        const severity = isRisk ? 4 : 3;
+        const urgency = isRisk ? 4 : 3;
+        const ruleKey = isRisk ? "rule-a-low-risk" : "rule-a-low";
+        const evidence = [
+            `${biomarker} = ${latestValue} ${latestUnit} (reference: ≥${referenceLow} ${latestUnit})`,
+            `${(pctBeyond * 100).toFixed(1)}% below lower reference limit`,
+        ];
+        return makeFinding(biomarker, ruleKey, `${biomarker}: below reference range`, kind, urgency, severity, evidence, now);
+    }
+    return undefined;
+}
+// -- Rule B ---------------------------------------------------------------
+/**
+ * Apply Rule B: value is in range, slope != null, trending toward the nearer reference edge.
+ * The slope direction (positive toward high edge, negative toward low edge) combined with
+ * which edge is nearer determines whether there is a projected crossing.
+ *
+ * Returns a finding or undefined when no projected crossing is detected.
+ */
+function applyRuleB(biomarker, latestValue, latestUnit, slope, referenceLow, referenceHigh, now) {
+    if (referenceLow === undefined && referenceHigh === undefined)
+        return undefined;
+    const distToHigh = referenceHigh !== undefined ? referenceHigh - latestValue : Infinity;
+    const distToLow = referenceLow !== undefined ? latestValue - referenceLow : Infinity;
+    // Trending upward toward referenceHigh and high edge is nearer (or the only bound)
+    if (slope > 0 && referenceHigh !== undefined && distToHigh <= distToLow && distToHigh > 0) {
+        const evidence = [
+            `${biomarker} = ${latestValue} ${latestUnit}, rising trend (slope > 0)`,
+            `Upper reference limit: ${referenceHigh} ${latestUnit} (${distToHigh.toFixed(2)} ${latestUnit} away)`,
+        ];
+        return makeFinding(biomarker, "rule-b-high", `${biomarker}: rising trend toward upper reference limit`, "watch", 2, 2, evidence, now);
+    }
+    // Trending downward toward referenceLow and low edge is nearer (or the only bound)
+    if (slope < 0 && referenceLow !== undefined && distToLow <= distToHigh && distToLow > 0) {
+        const evidence = [
+            `${biomarker} = ${latestValue} ${latestUnit}, falling trend (slope < 0)`,
+            `Lower reference limit: ${referenceLow} ${latestUnit} (${distToLow.toFixed(2)} ${latestUnit} away)`,
+        ];
+        return makeFinding(biomarker, "rule-b-low", `${biomarker}: falling trend toward lower reference limit`, "watch", 2, 2, evidence, now);
+    }
+    return undefined;
+}
+// -- Public API -----------------------------------------------------------
+/**
+ * Analyze lab trends for a set of biomarkers and return detected findings.
+ *
+ * PURE, synchronous, deterministic. No async, no fs, no network, no LLM.
+ * Delegates ALL trend math to NumericsQueryLayer.getLabTrend (ADR-3).
+ * Reference ranges are read from store.getLabSeries (LabTrend does not carry them).
+ *
+ * @param store       HealthDataStore (caller is responsible for lifecycle)
+ * @param biomarkers  List of biomarker names to analyze
+ * @param opts        { now: ISO 8601 injected timestamp }
+ */
+export function analyzeTrends(store, biomarkers, opts) {
+    const numerics = new NumericsQueryLayer(store);
+    const findings = [];
+    for (const biomarker of biomarkers) {
+        const trend = numerics.getLabTrend(biomarker);
+        // Abstain when no data (sc-1-2, sc-1-3)
+        if (trend.sampleCount === 0)
+            continue;
+        if (trend.latestValue === null)
+            continue;
+        // Read reference range from the latest LabResult (LabTrend does not carry it)
+        const series = store.getLabSeries(biomarker);
+        const latestResult = series[series.length - 1];
+        if (!latestResult)
+            continue;
+        const { referenceLow, referenceHigh } = latestResult;
+        const { latestValue, latestUnit } = trend;
+        // Rule A: reference-range crossing (takes precedence over Rule B)
+        const ruleAFinding = applyRuleA(biomarker, latestValue, latestUnit, referenceLow, referenceHigh, opts.now);
+        if (ruleAFinding !== undefined) {
+            findings.push(ruleAFinding);
+            continue; // Rule A takes precedence; Rule B not evaluated for this biomarker
+        }
+        // Rule B: slope-toward-edge (only when in range and sampleCount >= 2 for valid slope)
+        if (trend.slope !== null && trend.sampleCount >= 2) {
+            const ruleBFinding = applyRuleB(biomarker, latestValue, latestUnit, trend.slope, referenceLow, referenceHigh, opts.now);
+            if (ruleBFinding !== undefined) {
+                findings.push(ruleBFinding);
+            }
+        }
+    }
+    return findings;
+}
+//# sourceMappingURL=trends.js.map

package/dist/medical/analysis/trends.js.map

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package/dist/medical/health-store.d.ts

@@ -74,6 +74,11 @@ export declare class HealthDataStore {
      * Returns undefined if the key is not set.
      */
     getPreference(key: string): string | undefined;
+    /**
+     * Return all distinct biomarker names present in the lab_results table, ordered alphabetically.
+     * Returns an empty array when no lab results have been loaded.
+     */
+    listBiomarkers(): string[];
     /** Close the underlying database connection. */
     close(): void;
 }

package/dist/medical/health-store.d.ts.map

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package/dist/medical/health-store.js

@@ -196,6 +196,16 @@ export class HealthDataStore {
             .get(`pref:${key}`);
         return row?.v;
     }
+    /**
+     * Return all distinct biomarker names present in the lab_results table, ordered alphabetically.
+     * Returns an empty array when no lab results have been loaded.
+     */
+    listBiomarkers() {
+        const rows = this.db
+            .prepare(`SELECT DISTINCT biomarker FROM lab_results ORDER BY biomarker ASC`)
+            .all();
+        return rows.map((r) => r.biomarker);
+    }
     /** Close the underlying database connection. */
     close() {
         this.db.close();

package/dist/medical/health-store.js.map

@@ -1 +1 @@
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package/dist/medical/lab-note.d.ts

@@ -0,0 +1,72 @@
+/**
+ * Lab-note vault writer — serializes parsed lab markers to YAML-frontmatter markdown notes.
+ *
+ * Status classification is deterministic JS: value vs reference range (ADR-3 spirit).
+ *
+ * PURE file I/O + deterministic helpers only.
+ * NO network. NO LLM. NO Date.now(). All timestamps are injected parameters.
+ *
+ * bober: hand-rolled YAML-frontmatter subset (flat scalars only, no arrays/nested objects).
+ *        Mirror of src/vault/frontmatter.ts approach — never import that module.
+ *        Swap for a vetted YAML library if quoted strings or nested objects are required.
+ */
+import type { ParsedLabMarker } from "./lab-types.js";
+/** Deterministic lab status — derived in pure JS, never by an LLM (ADR-3 spirit). */
+export type LabStatus = "low" | "normal" | "high" | "critical";
+/** Report-level metadata supplied alongside a ParsedLabMarker at write time. */
+export interface LabNoteMeta {
+    panel: string;
+    /** ISO 8601 collection timestamp — INJECTED, never Date.now(). */
+    collectedAtIso: string;
+    source: string;
+}
+/**
+ * Structured contents of a lab note's YAML frontmatter.
+ * All 10 keys are always present; ref_low / ref_high are undefined when absent.
+ */
+export interface LabNoteFrontmatter {
+    marker: string;
+    value: number;
+    unit: string;
+    ref_low: number | undefined;
+    ref_high: number | undefined;
+    /** Human-readable range string, e.g. "70-100", or "" when bounds are absent. */
+    ref_range: string;
+    /** ISO 8601 collection date (stored verbatim from collectedAtIso). */
+    date: string;
+    status: LabStatus;
+    panel: string;
+    source: string;
+}
+/**
+ * Produce a URL-safe slug from an arbitrary string.
+ * Precedent: src/incident/timeline.ts:117.
+ */
+export declare function slugify(s: string): string;
+/**
+ * Derive a deterministic lab status from value vs reference range.
+ * Pure sync — no LLM, no network, no Date.now() (ADR-3 spirit).
+ *
+ * Priority: critical flag wins; else compare to bounds; missing bounds → "normal".
+ */
+export declare function deriveLabStatus(value: number, refLow?: number, refHigh?: number, critical?: boolean): LabStatus;
+/**
+ * Parse the YAML frontmatter from a raw lab-note markdown string.
+ * Numeric fields (value, ref_low, ref_high) are coerced from their string representation.
+ * ref_low / ref_high are undefined when the value is absent or empty.
+ *
+ * Throws if the opening or closing `---` fence is missing.
+ *
+ * Mirror of src/vault/frontmatter.ts:53-135 — DO NOT import that module.
+ */
+export declare function parseLabNote(raw: string): LabNoteFrontmatter;
+/**
+ * Write one parsed lab marker to a YAML-frontmatter markdown note.
+ *
+ * Note path: `<vaultDir>/labs/<panel-slug>/<marker-slug>-<date>.md`
+ * The date segment is the YYYY-MM-DD portion of collectedAtIso (colons stripped).
+ *
+ * Parent directories are created automatically. Returns the absolute path written.
+ */
+export declare function writeLabNote(vaultDir: string, marker: ParsedLabMarker, meta: LabNoteMeta): Promise<string>;
+//# sourceMappingURL=lab-note.d.ts.map

package/dist/medical/lab-note.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"lab-note.d.ts","sourceRoot":"","sources":["../../src/medical/lab-note.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAKH,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAC;AAKtD,qFAAqF;AACrF,MAAM,MAAM,SAAS,GAAG,KAAK,GAAG,QAAQ,GAAG,MAAM,GAAG,UAAU,CAAC;AAE/D,gFAAgF;AAChF,MAAM,WAAW,WAAW;IAC1B,KAAK,EAAE,MAAM,CAAC;IACd,kEAAkE;IAClE,cAAc,EAAE,MAAM,CAAC;IACvB,MAAM,EAAE,MAAM,CAAC;CAChB;AAED;;;GAGG;AACH,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,GAAG,SAAS,CAAC;IAC5B,QAAQ,EAAE,MAAM,GAAG,SAAS,CAAC;IAC7B,gFAAgF;IAChF,SAAS,EAAE,MAAM,CAAC;IAClB,sEAAsE;IACtE,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,SAAS,CAAC;IAClB,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,CAAC;CAChB;AAID;;;GAGG;AACH,wBAAgB,OAAO,CAAC,CAAC,EAAE,MAAM,GAAG,MAAM,CAKzC;AAED;;;;;GAKG;AACH,wBAAgB,eAAe,CAC7B,KAAK,EAAE,MAAM,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,MAAM,EAChB,QAAQ,CAAC,EAAE,OAAO,GACjB,SAAS,CAKX;AA8BD;;;;;;;;GAQG;AACH,wBAAgB,YAAY,CAAC,GAAG,EAAE,MAAM,GAAG,kBAAkB,CA2D5D;AAID;;;;;;;GAOG;AACH,wBAAsB,YAAY,CAChC,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,eAAe,EACvB,IAAI,EAAE,WAAW,GAChB,OAAO,CAAC,MAAM,CAAC,CAyCjB"}

package/dist/medical/lab-note.js

@@ -0,0 +1,161 @@
+/**
+ * Lab-note vault writer — serializes parsed lab markers to YAML-frontmatter markdown notes.
+ *
+ * Status classification is deterministic JS: value vs reference range (ADR-3 spirit).
+ *
+ * PURE file I/O + deterministic helpers only.
+ * NO network. NO LLM. NO Date.now(). All timestamps are injected parameters.
+ *
+ * bober: hand-rolled YAML-frontmatter subset (flat scalars only, no arrays/nested objects).
+ *        Mirror of src/vault/frontmatter.ts approach — never import that module.
+ *        Swap for a vetted YAML library if quoted strings or nested objects are required.
+ */
+import { writeFile } from "node:fs/promises";
+import { join, dirname } from "node:path";
+import { ensureDir } from "../utils/fs.js";
+// -- Pure helpers --------------------------------------------------------
+/**
+ * Produce a URL-safe slug from an arbitrary string.
+ * Precedent: src/incident/timeline.ts:117.
+ */
+export function slugify(s) {
+    return s
+        .toLowerCase()
+        .replace(/[^a-z0-9]+/g, "-")
+        .replace(/^-+|-+$/g, "");
+}
+/**
+ * Derive a deterministic lab status from value vs reference range.
+ * Pure sync — no LLM, no network, no Date.now() (ADR-3 spirit).
+ *
+ * Priority: critical flag wins; else compare to bounds; missing bounds → "normal".
+ */
+export function deriveLabStatus(value, refLow, refHigh, critical) {
+    if (critical === true)
+        return "critical";
+    if (refLow !== undefined && value < refLow)
+        return "low";
+    if (refHigh !== undefined && value > refHigh)
+        return "high";
+    return "normal";
+}
+// -- Hand-rolled YAML frontmatter ----------------------------------------
+/** Matches an integer or float (with optional leading minus). */
+const NUM_REGEX = /^-?\d+(\.\d+)?$/;
+/**
+ * Serialize a LabNoteFrontmatter to a YAML-frontmatter markdown string.
+ * Produces `---\n<key: value lines>\n---\n`.
+ * Flat scalar keys only; undefined numeric values are serialized as empty strings.
+ *
+ * Mirror of src/vault/frontmatter.ts:145-164 — DO NOT import that module.
+ */
+function serializeLabFrontmatter(fm) {
+    const lines = ["---"];
+    lines.push(`marker: ${fm.marker}`);
+    lines.push(`value: ${String(fm.value)}`);
+    lines.push(`unit: ${fm.unit}`);
+    lines.push(`ref_low: ${fm.ref_low !== undefined ? String(fm.ref_low) : ""}`);
+    lines.push(`ref_high: ${fm.ref_high !== undefined ? String(fm.ref_high) : ""}`);
+    lines.push(`ref_range: ${fm.ref_range}`);
+    lines.push(`date: ${fm.date}`);
+    lines.push(`status: ${fm.status}`);
+    lines.push(`panel: ${fm.panel}`);
+    lines.push(`source: ${fm.source}`);
+    lines.push("---");
+    return lines.join("\n") + "\n";
+}
+/**
+ * Parse the YAML frontmatter from a raw lab-note markdown string.
+ * Numeric fields (value, ref_low, ref_high) are coerced from their string representation.
+ * ref_low / ref_high are undefined when the value is absent or empty.
+ *
+ * Throws if the opening or closing `---` fence is missing.
+ *
+ * Mirror of src/vault/frontmatter.ts:53-135 — DO NOT import that module.
+ */
+export function parseLabNote(raw) {
+    const lines = raw.split("\n");
+    if (lines[0]?.trim() !== "---") {
+        throw new Error("parseLabNote: missing opening '---' fence");
+    }
+    let closingIdx = -1;
+    for (let i = 1; i < lines.length; i++) {
+        if (lines[i].trim() === "---") {
+            closingIdx = i;
+            break;
+        }
+    }
+    if (closingIdx === -1) {
+        throw new Error("parseLabNote: missing closing '---' fence");
+    }
+    const yamlLines = lines.slice(1, closingIdx);
+    const record = {};
+    for (const line of yamlLines) {
+        const colonIdx = line.indexOf(":");
+        if (colonIdx < 0)
+            continue;
+        const key = line.slice(0, colonIdx).trim();
+        if (key === "")
+            continue;
+        const rawVal = line.slice(colonIdx + 1).trim();
+        record[key] = NUM_REGEX.test(rawVal) ? Number(rawVal) : rawVal;
+    }
+    // -- Coerce and extract fields --
+    const marker = String(record["marker"] ?? "");
+    const valueRaw = record["value"];
+    const value = typeof valueRaw === "number" ? valueRaw : Number(valueRaw ?? 0);
+    const unit = String(record["unit"] ?? "");
+    const refLowRaw = record["ref_low"];
+    const ref_low = typeof refLowRaw === "number"
+        ? refLowRaw
+        : refLowRaw === "" || refLowRaw === undefined
+            ? undefined
+            : Number(refLowRaw);
+    const refHighRaw = record["ref_high"];
+    const ref_high = typeof refHighRaw === "number"
+        ? refHighRaw
+        : refHighRaw === "" || refHighRaw === undefined
+            ? undefined
+            : Number(refHighRaw);
+    const ref_range = String(record["ref_range"] ?? "");
+    const date = String(record["date"] ?? "");
+    const status = String(record["status"] ?? "normal");
+    const panel = String(record["panel"] ?? "");
+    const source = String(record["source"] ?? "");
+    return { marker, value, unit, ref_low, ref_high, ref_range, date, status, panel, source };
+}
+// -- Note writer ---------------------------------------------------------
+/**
+ * Write one parsed lab marker to a YAML-frontmatter markdown note.
+ *
+ * Note path: `<vaultDir>/labs/<panel-slug>/<marker-slug>-<date>.md`
+ * The date segment is the YYYY-MM-DD portion of collectedAtIso (colons stripped).
+ *
+ * Parent directories are created automatically. Returns the absolute path written.
+ */
+export async function writeLabNote(vaultDir, marker, meta) {
+    const status = deriveLabStatus(marker.value, marker.referenceLow, marker.referenceHigh, marker.critical);
+    const refRange = marker.referenceLow !== undefined && marker.referenceHigh !== undefined
+        ? `${marker.referenceLow}-${marker.referenceHigh}`
+        : "";
+    const fm = {
+        marker: marker.name,
+        value: marker.value,
+        unit: marker.unit,
+        ref_low: marker.referenceLow,
+        ref_high: marker.referenceHigh,
+        ref_range: refRange,
+        date: meta.collectedAtIso,
+        status,
+        panel: meta.panel,
+        source: meta.source,
+    };
+    // Use only the YYYY-MM-DD portion so the filename contains no colons.
+    const datePortion = meta.collectedAtIso.split("T")[0] ?? meta.collectedAtIso;
+    const notePath = join(vaultDir, "labs", slugify(meta.panel), `${slugify(marker.name)}-${datePortion}.md`);
+    const serialized = serializeLabFrontmatter(fm);
+    await ensureDir(dirname(notePath));
+    await writeFile(notePath, serialized, "utf-8");
+    return notePath;
+}
+//# sourceMappingURL=lab-note.js.map

package/dist/medical/lab-note.js.map

@@ -0,0 +1 @@
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package/dist/medical/lab-pdf-parser.d.ts

@@ -0,0 +1,19 @@
+import type { LLMClient } from "../providers/types.js";
+import { type ParsedLabReport } from "./lab-types.js";
+export interface ParseLabPdfDeps {
+    /** Injectable LLMClient; tests inject a fake, production uses buildMedicalInferenceClient (Sprint 3). */
+    client: LLMClient;
+    /** Model identifier to pass to the client. */
+    model: string;
+}
+/**
+ * Base64-encodes `pdfBytes`, sends it as an Anthropic document content block
+ * via an injectable `LLMClient` with schema-constrained output, and returns a
+ * Zod-validated `ParsedLabReport`. Throws a `ZodError` on malformed model output
+ * — never returns an unvalidated object.
+ *
+ * @param pdfBytes  Raw bytes of a native-text PDF lab report.
+ * @param deps      Injectable `{ client, model }` seam for testing and egress gating.
+ */
+export declare function parseLabPdf(pdfBytes: Uint8Array, deps: ParseLabPdfDeps): Promise<ParsedLabReport>;
+//# sourceMappingURL=lab-pdf-parser.d.ts.map

package/dist/medical/lab-pdf-parser.d.ts.map

@@ -0,0 +1 @@
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package/dist/medical/lab-pdf-parser.js

@@ -0,0 +1,57 @@
+/** parseLabPdf — native-text lab PDF -> Zod-validated ParsedLabReport via injectable LLMClient. */
+import { Buffer } from "node:buffer";
+import { ParsedLabReportSchema } from "./lab-types.js";
+// -- Response schema (hand-written JsonSchemaObject literal) ----------
+const LAB_REPORT_JSON_SCHEMA = {
+    type: "object",
+    properties: {
+        panel: { type: "string" },
+        collectedAtIso: { type: "string" },
+        markers: {
+            type: "array",
+            items: {
+                type: "object",
+                properties: {
+                    name: { type: "string" },
+                    value: { type: "number" },
+                    unit: { type: "string" },
+                    referenceLow: { type: "number" },
+                    referenceHigh: { type: "number" },
+                    critical: { type: "boolean" },
+                },
+                required: ["name", "value", "unit"],
+            },
+        },
+    },
+    required: ["panel", "collectedAtIso", "markers"],
+};
+// -- parseLabPdf ------------------------------------------------------
+/**
+ * Base64-encodes `pdfBytes`, sends it as an Anthropic document content block
+ * via an injectable `LLMClient` with schema-constrained output, and returns a
+ * Zod-validated `ParsedLabReport`. Throws a `ZodError` on malformed model output
+ * — never returns an unvalidated object.
+ *
+ * @param pdfBytes  Raw bytes of a native-text PDF lab report.
+ * @param deps      Injectable `{ client, model }` seam for testing and egress gating.
+ */
+export async function parseLabPdf(pdfBytes, deps) {
+    const base64 = Buffer.from(pdfBytes).toString("base64");
+    const response = await deps.client.chat({
+        model: deps.model,
+        system: "You are a medical data extraction assistant. Extract structured lab results from the provided PDF document. Return ONLY a JSON object matching the requested schema — no prose, no markdown.",
+        messages: [
+            {
+                role: "user",
+                content: "Extract all lab markers from the attached PDF. Return a JSON object with panel name, ISO collection date, and a markers array (name, numeric value, unit, optional referenceLow/referenceHigh/critical).",
+            },
+        ],
+        documents: [{ base64, mediaType: "application/pdf" }],
+        responseSchema: LAB_REPORT_JSON_SCHEMA,
+    });
+    // With responseSchema set, the adapter guarantees response.text holds the JSON document.
+    const parsed = JSON.parse(response.text);
+    // Throws ZodError on malformed output — never coerce (sc-1-4).
+    return ParsedLabReportSchema.parse(parsed);
+}
+//# sourceMappingURL=lab-pdf-parser.js.map

package/dist/medical/lab-pdf-parser.js.map

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package/dist/medical/lab-reindex.d.ts

@@ -0,0 +1,24 @@
+/**
+ * Lab-note reindexer — globs lab vault notes and upserts each result into HealthDataStore.
+ *
+ * Pure file + SQLite. NO network. NO LLM. NO Date.now().
+ *
+ * Architecture: vault is canonical; SQLite store is a derived, rebuildable index.
+ * Dedup runs at ingest time via the deterministic labResultId (INSERT OR IGNORE).
+ * Re-running over unchanged notes returns 0 new rows (idempotent).
+ */
+import type { HealthDataStore } from "./health-store.js";
+/**
+ * Glob all markdown notes under `<vaultDir>/labs/`, parse each note's YAML frontmatter,
+ * map the fields to a LabResult, and upsert into the store.
+ *
+ * Returns the total count of NEW rows inserted (sum of upsertLabResult return values).
+ * Duplicate notes produce 0 new rows — dedup is automatic via the deterministic
+ * labResultId (biomarker|collectedAtIso|value) under INSERT OR IGNORE.
+ *
+ * @param vaultDir  Root of the vault directory tree (contains the `labs/` subdirectory).
+ * @param store     An open HealthDataStore instance to upsert into.
+ * @returns         Number of genuinely new rows inserted in this run.
+ */
+export declare function reindexLabNotes(vaultDir: string, store: HealthDataStore): Promise<number>;
+//# sourceMappingURL=lab-reindex.d.ts.map

package/dist/medical/lab-reindex.d.ts.map

@@ -0,0 +1 @@
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