agent-bober 0.18.0 → 0.19.0

package/dist/medical/lab-reindex.js

@@ -0,0 +1,45 @@
+/**
+ * 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 { readFile } from "node:fs/promises";
+import { join } from "node:path";
+import { glob } from "glob";
+import { parseLabNote } from "./lab-note.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 async function reindexLabNotes(vaultDir, store) {
+    const labsDir = join(vaultDir, "labs");
+    const paths = await glob("**/*.md", { cwd: labsDir, absolute: true, nodir: true });
+    let newRows = 0;
+    for (const notePath of paths) {
+        const raw = await readFile(notePath, "utf-8");
+        const fm = parseLabNote(raw);
+        const result = {
+            biomarker: fm.marker,
+            value: fm.value,
+            unit: fm.unit,
+            collectedAtIso: fm.date,
+            referenceLow: fm.ref_low,
+            referenceHigh: fm.ref_high,
+        };
+        newRows += store.upsertLabResult(result);
+    }
+    return newRows;
+}
+//# sourceMappingURL=lab-reindex.js.map

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

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

@@ -0,0 +1,75 @@
+/** Zod schemas for parsed lab reports (medical-ingest Sprint 1). */
+import { z } from "zod";
+export declare const ParsedLabMarkerSchema: z.ZodObject<{
+    name: z.ZodString;
+    value: z.ZodNumber;
+    unit: z.ZodString;
+    referenceLow: z.ZodOptional<z.ZodNumber>;
+    referenceHigh: z.ZodOptional<z.ZodNumber>;
+    critical: z.ZodOptional<z.ZodBoolean>;
+}, "strip", z.ZodTypeAny, {
+    name: string;
+    value: number;
+    unit: string;
+    referenceLow?: number | undefined;
+    referenceHigh?: number | undefined;
+    critical?: boolean | undefined;
+}, {
+    name: string;
+    value: number;
+    unit: string;
+    referenceLow?: number | undefined;
+    referenceHigh?: number | undefined;
+    critical?: boolean | undefined;
+}>;
+export declare const ParsedLabReportSchema: z.ZodObject<{
+    panel: z.ZodString;
+    collectedAtIso: z.ZodString;
+    markers: z.ZodArray<z.ZodObject<{
+        name: z.ZodString;
+        value: z.ZodNumber;
+        unit: z.ZodString;
+        referenceLow: z.ZodOptional<z.ZodNumber>;
+        referenceHigh: z.ZodOptional<z.ZodNumber>;
+        critical: z.ZodOptional<z.ZodBoolean>;
+    }, "strip", z.ZodTypeAny, {
+        name: string;
+        value: number;
+        unit: string;
+        referenceLow?: number | undefined;
+        referenceHigh?: number | undefined;
+        critical?: boolean | undefined;
+    }, {
+        name: string;
+        value: number;
+        unit: string;
+        referenceLow?: number | undefined;
+        referenceHigh?: number | undefined;
+        critical?: boolean | undefined;
+    }>, "many">;
+}, "strip", z.ZodTypeAny, {
+    panel: string;
+    collectedAtIso: string;
+    markers: {
+        name: string;
+        value: number;
+        unit: string;
+        referenceLow?: number | undefined;
+        referenceHigh?: number | undefined;
+        critical?: boolean | undefined;
+    }[];
+}, {
+    panel: string;
+    collectedAtIso: string;
+    markers: {
+        name: string;
+        value: number;
+        unit: string;
+        referenceLow?: number | undefined;
+        referenceHigh?: number | undefined;
+        critical?: boolean | undefined;
+    }[];
+}>;
+export type ParsedLabMarker = z.infer<typeof ParsedLabMarkerSchema>;
+export type ParsedLabReport = z.infer<typeof ParsedLabReportSchema>;
+//# sourceMappingURL=lab-types.d.ts.map

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

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

@@ -0,0 +1,17 @@
+/** Zod schemas for parsed lab reports (medical-ingest Sprint 1). */
+import { z } from "zod";
+// -- Schemas ----------------------------------------------------------
+export const ParsedLabMarkerSchema = z.object({
+    name: z.string(),
+    value: z.number(),
+    unit: z.string(),
+    referenceLow: z.number().optional(),
+    referenceHigh: z.number().optional(),
+    critical: z.boolean().optional(),
+});
+export const ParsedLabReportSchema = z.object({
+    panel: z.string(),
+    collectedAtIso: z.string(),
+    markers: z.array(ParsedLabMarkerSchema),
+});
+//# sourceMappingURL=lab-types.js.map

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

@@ -0,0 +1 @@
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package/dist/medical/profile.d.ts

@@ -0,0 +1,96 @@
+/**
+ * Personalization profile -> SOPS-encrypted <vaultDir>/profile.yaml (Sprint 5).
+ * Encryption is behind an injectable cipher seam; tests inject a reversible fake.
+ * When the cipher is unavailable BOTH paths refuse and write NO plaintext PHI.
+ * Hand-rolled flat YAML emit/parse (string[] arrays) — NEVER import src/vault.
+ */
+import { z } from "zod";
+export declare const ProfileSchema: z.ZodObject<{
+    age: z.ZodNumber;
+    sex: z.ZodEnum<["male", "female", "other"]>;
+    conditions: z.ZodDefault<z.ZodArray<z.ZodString, "many">>;
+    medications: z.ZodDefault<z.ZodArray<z.ZodString, "many">>;
+    supplements: z.ZodDefault<z.ZodArray<z.ZodString, "many">>;
+    allergies: z.ZodDefault<z.ZodArray<z.ZodString, "many">>;
+    goals: z.ZodDefault<z.ZodArray<z.ZodString, "many">>;
+}, "strip", z.ZodTypeAny, {
+    age: number;
+    sex: "male" | "female" | "other";
+    conditions: string[];
+    medications: string[];
+    supplements: string[];
+    allergies: string[];
+    goals: string[];
+}, {
+    age: number;
+    sex: "male" | "female" | "other";
+    conditions?: string[] | undefined;
+    medications?: string[] | undefined;
+    supplements?: string[] | undefined;
+    allergies?: string[] | undefined;
+    goals?: string[] | undefined;
+}>;
+export type Profile = z.infer<typeof ProfileSchema>;
+/**
+ * Encryption seam for profile.yaml (SOPS age key by default).
+ * Tests inject a reversible fake; production uses the sops-via-execa default.
+ * available() MUST be synchronous — the caller gates IO on its return value.
+ */
+export interface ProfileCipher {
+    /** Returns true synchronously when the underlying binary is available. */
+    available(): boolean;
+    /** Encrypt plaintext to ciphertext (may return a Promise). */
+    encrypt(plaintext: string): string | Promise<string>;
+    /** Decrypt ciphertext to plaintext (may return a Promise). */
+    decrypt(ciphertext: string): string | Promise<string>;
+}
+/**
+ * Emit a Profile as a minimal YAML string.
+ * Scalars (age, sex) first; array fields follow.
+ * Empty arrays are emitted as `key: []`; non-empty as `key:\n  - item\n`.
+ */
+export declare function emitProfileYaml(p: Profile): string;
+/**
+ * Parse a minimal profile YAML string into a plain object (for ProfileSchema.parse).
+ * Handles flat scalars (age: 42, sex: male) and string arrays (key:\n  - item).
+ * Returns unknown — callers must validate through ProfileSchema.parse.
+ */
+export declare function parseProfileYaml(raw: string): unknown;
+/** Injectable dependencies for writeProfile / readProfile — production callers omit. */
+export interface ProfileDeps {
+    /** Override the encryption cipher (e.g. reversible fake in tests). */
+    cipher?: ProfileCipher;
+}
+/**
+ * Validate, serialize, encrypt and write the profile to <vaultDir>/profile.yaml.
+ *
+ * SAFETY: throws with a clear message (and writes NOTHING to disk) when
+ * cipher.available() returns false. The only bytes written to disk are ciphertext.
+ */
+export declare function writeProfile(vaultDir: string, profile: Profile, deps?: ProfileDeps): Promise<void>;
+/**
+ * Read, decrypt, parse and validate the profile from <vaultDir>/profile.yaml.
+ *
+ * SAFETY: throws with a clear message when cipher.available() returns false
+ * (no disk reads are attempted).
+ */
+export declare function readProfile(vaultDir: string, deps?: ProfileDeps): Promise<Profile>;
+/**
+ * Core logic for `bober medical profile show`.
+ * Reads and prints the profile to stdout.
+ * Errors are caught, written to stderr, process.exitCode set to 1 — never throws.
+ */
+export declare function runProfileShow(projectRoot: string, opts: {
+    vault?: string;
+}, deps?: ProfileDeps): Promise<void>;
+/**
+ * Core logic for `bober medical profile set <key> <value>`.
+ * Reads the existing profile (or starts from a safe default on ENOENT),
+ * updates one field, re-validates via ProfileSchema, and writes back.
+ * For array keys, value is parsed as a comma-separated list.
+ * Errors are caught, written to stderr, process.exitCode set to 1 — never throws.
+ */
+export declare function runProfileSet(projectRoot: string, key: string, value: string, opts: {
+    vault?: string;
+}, deps?: ProfileDeps): Promise<void>;
+//# sourceMappingURL=profile.d.ts.map

package/dist/medical/profile.d.ts.map

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

@@ -0,0 +1,273 @@
+/**
+ * Personalization profile -> SOPS-encrypted <vaultDir>/profile.yaml (Sprint 5).
+ * Encryption is behind an injectable cipher seam; tests inject a reversible fake.
+ * When the cipher is unavailable BOTH paths refuse and write NO plaintext PHI.
+ * Hand-rolled flat YAML emit/parse (string[] arrays) — NEVER import src/vault.
+ */
+import { writeFile, readFile } from "node:fs/promises";
+import { join } from "node:path";
+import { execa, execaSync } from "execa";
+import { z } from "zod";
+import { ensureDir } from "../utils/fs.js";
+// -- Schema --------------------------------------------------------------
+export const ProfileSchema = z.object({
+    age: z.number().int().min(0),
+    sex: z.enum(["male", "female", "other"]),
+    conditions: z.array(z.string()).default([]),
+    medications: z.array(z.string()).default([]),
+    supplements: z.array(z.string()).default([]),
+    allergies: z.array(z.string()).default([]),
+    goals: z.array(z.string()).default([]),
+});
+/**
+ * Default cipher: shells out to `sops` via execa with --age recipient.
+ * available() probes the binary synchronously via execaSync.
+ *
+ * bober: sops --age key path is not parameterised here; callers supply an age
+ *        recipient once key-distribution is solved out-of-band (contract assumption 3).
+ *        Swap for a KMS-backed cipher when distributed key management is added.
+ */
+function createSopsCipher() {
+    return {
+        available() {
+            try {
+                const r = execaSync("sops", ["--version"], {
+                    reject: false,
+                    timeout: 5_000,
+                });
+                return r.exitCode === 0;
+            }
+            catch {
+                return false;
+            }
+        },
+        async encrypt(plaintext) {
+            const r = await execa("sops", ["--encrypt", "--input-type", "yaml", "--output-type", "yaml", "/dev/stdin"], { input: plaintext, reject: false });
+            if (r.exitCode !== 0) {
+                throw new Error(`sops encrypt failed (exit ${String(r.exitCode)}): ${r.stderr || r.stdout || "no output"}`);
+            }
+            return r.stdout;
+        },
+        async decrypt(ciphertext) {
+            const r = await execa("sops", ["--decrypt", "--input-type", "yaml", "--output-type", "yaml", "/dev/stdin"], { input: ciphertext, reject: false });
+            if (r.exitCode !== 0) {
+                throw new Error(`sops decrypt failed (exit ${String(r.exitCode)}): ${r.stderr || r.stdout || "no output"}`);
+            }
+            return r.stdout;
+        },
+    };
+}
+// -- YAML emit/parse (flat scalars + string[] arrays) --------------------
+/** Array fields in the profile (serialized after the scalar fields). */
+const ARRAY_KEYS = [
+    "conditions",
+    "medications",
+    "supplements",
+    "allergies",
+    "goals",
+];
+/**
+ * Emit a Profile as a minimal YAML string.
+ * Scalars (age, sex) first; array fields follow.
+ * Empty arrays are emitted as `key: []`; non-empty as `key:\n  - item\n`.
+ */
+export function emitProfileYaml(p) {
+    const lines = [];
+    lines.push(`age: ${String(p.age)}`);
+    lines.push(`sex: ${p.sex}`);
+    for (const key of ARRAY_KEYS) {
+        const arr = p[key];
+        if (arr.length === 0) {
+            lines.push(`${key}: []`);
+        }
+        else {
+            lines.push(`${key}:`);
+            for (const item of arr) {
+                lines.push(`  - ${item}`);
+            }
+        }
+    }
+    return lines.join("\n") + "\n";
+}
+/**
+ * Parse a minimal profile YAML string into a plain object (for ProfileSchema.parse).
+ * Handles flat scalars (age: 42, sex: male) and string arrays (key:\n  - item).
+ * Returns unknown — callers must validate through ProfileSchema.parse.
+ */
+export function parseProfileYaml(raw) {
+    const result = {};
+    const lines = raw.split("\n");
+    let currentArrayKey = null;
+    let currentArray = [];
+    const flushArray = () => {
+        if (currentArrayKey !== null) {
+            result[currentArrayKey] = currentArray;
+            currentArrayKey = null;
+            currentArray = [];
+        }
+    };
+    for (const line of lines) {
+        if (line.trim() === "")
+            continue;
+        // List item: "  - value"
+        const listMatch = /^\s+-\s+(.+)$/.exec(line);
+        if (listMatch !== null) {
+            if (currentArrayKey !== null) {
+                currentArray.push((listMatch[1] ?? "").trim());
+            }
+            continue;
+        }
+        // Non-list line: flush any in-progress array
+        flushArray();
+        const colonIdx = line.indexOf(":");
+        if (colonIdx < 0)
+            continue;
+        const key = line.slice(0, colonIdx).trim();
+        if (key === "")
+            continue;
+        const rest = line.slice(colonIdx + 1).trim();
+        if (rest === "[]") {
+            // Explicit empty array shorthand
+            result[key] = [];
+        }
+        else if (rest === "") {
+            // Start of an indented array block
+            currentArrayKey = key;
+            currentArray = [];
+        }
+        else {
+            // Scalar: coerce to number when the value parses as a finite number
+            const n = Number(rest);
+            result[key] = Number.isFinite(n) && rest.trim() !== "" ? n : rest;
+        }
+    }
+    // Flush any trailing array (file may not end with a blank line)
+    flushArray();
+    return result;
+}
+// -- read / write --------------------------------------------------------
+/**
+ * Validate, serialize, encrypt and write the profile to <vaultDir>/profile.yaml.
+ *
+ * SAFETY: throws with a clear message (and writes NOTHING to disk) when
+ * cipher.available() returns false. The only bytes written to disk are ciphertext.
+ */
+export async function writeProfile(vaultDir, profile, deps = {}) {
+    const validated = ProfileSchema.parse(profile);
+    const cipher = deps.cipher ?? createSopsCipher();
+    if (!cipher.available()) {
+        throw new Error("writeProfile: sops cipher unavailable — install sops with an age key configured before writing the profile");
+    }
+    const yaml = emitProfileYaml(validated);
+    const encrypted = await cipher.encrypt(yaml);
+    await ensureDir(vaultDir);
+    await writeFile(join(vaultDir, "profile.yaml"), encrypted, "utf-8");
+}
+/**
+ * Read, decrypt, parse and validate the profile from <vaultDir>/profile.yaml.
+ *
+ * SAFETY: throws with a clear message when cipher.available() returns false
+ * (no disk reads are attempted).
+ */
+export async function readProfile(vaultDir, deps = {}) {
+    const cipher = deps.cipher ?? createSopsCipher();
+    if (!cipher.available()) {
+        throw new Error("readProfile: sops cipher unavailable — install sops with an age key configured before reading the profile");
+    }
+    const encrypted = await readFile(join(vaultDir, "profile.yaml"), "utf-8");
+    const yaml = await cipher.decrypt(encrypted);
+    const parsed = parseProfileYaml(yaml);
+    return ProfileSchema.parse(parsed);
+}
+// -- CLI cores -----------------------------------------------------------
+/** Profile scalar keys. */
+const SCALAR_KEYS = ["age", "sex"];
+/** All profile field keys (scalars + arrays). */
+const ALL_KEYS = [...SCALAR_KEYS, ...ARRAY_KEYS];
+/**
+ * Core logic for `bober medical profile show`.
+ * Reads and prints the profile to stdout.
+ * Errors are caught, written to stderr, process.exitCode set to 1 — never throws.
+ */
+export async function runProfileShow(projectRoot, opts, deps = {}) {
+    try {
+        const vaultDir = opts.vault ?? join(projectRoot, ".bober", "medical");
+        const profile = await readProfile(vaultDir, deps);
+        process.stdout.write(`age: ${String(profile.age)}\n`);
+        process.stdout.write(`sex: ${profile.sex}\n`);
+        for (const key of ARRAY_KEYS) {
+            const arr = profile[key];
+            if (arr.length === 0) {
+                process.stdout.write(`${key}: []\n`);
+            }
+            else {
+                process.stdout.write(`${key}:\n`);
+                for (const item of arr) {
+                    process.stdout.write(`  - ${item}\n`);
+                }
+            }
+        }
+    }
+    catch (err) {
+        process.stderr.write(`Failed to show profile: ${err instanceof Error ? err.message : String(err)}\n`);
+        process.exitCode = 1;
+    }
+}
+/**
+ * Core logic for `bober medical profile set <key> <value>`.
+ * Reads the existing profile (or starts from a safe default on ENOENT),
+ * updates one field, re-validates via ProfileSchema, and writes back.
+ * For array keys, value is parsed as a comma-separated list.
+ * Errors are caught, written to stderr, process.exitCode set to 1 — never throws.
+ */
+export async function runProfileSet(projectRoot, key, value, opts, deps = {}) {
+    try {
+        const vaultDir = opts.vault ?? join(projectRoot, ".bober", "medical");
+        if (!ALL_KEYS.includes(key)) {
+            throw new Error(`Unknown profile key: "${key}". Valid keys: ${ALL_KEYS.join(", ")}`);
+        }
+        const typedKey = key;
+        // Read existing profile; fall back to safe default when the file is absent
+        let current;
+        try {
+            current = await readProfile(vaultDir, deps);
+        }
+        catch (readErr) {
+            const msg = readErr instanceof Error ? readErr.message : String(readErr);
+            if (msg.includes("ENOENT") || msg.includes("no such file")) {
+                current = ProfileSchema.parse({ age: 0, sex: "other" });
+            }
+            else {
+                throw readErr;
+            }
+        }
+        // Coerce the string value to the right type per key
+        let coerced;
+        if (typedKey === "age") {
+            const n = Number(value);
+            if (!Number.isFinite(n)) {
+                throw new Error(`age must be a finite number, got: "${value}"`);
+            }
+            coerced = n;
+        }
+        else if (typedKey === "sex") {
+            coerced = value;
+        }
+        else {
+            // Array key: comma-separated items -> string[]
+            coerced = value
+                .split(",")
+                .map((s) => s.trim())
+                .filter((s) => s.length > 0);
+        }
+        const next = { ...current, [typedKey]: coerced };
+        const validated = ProfileSchema.parse(next);
+        await writeProfile(vaultDir, validated, deps);
+        process.stdout.write(`Profile updated: ${key} = ${value}\n`);
+    }
+    catch (err) {
+        process.stderr.write(`Failed to set profile field: ${err instanceof Error ? err.message : String(err)}\n`);
+        process.exitCode = 1;
+    }
+}
+//# sourceMappingURL=profile.js.map

package/dist/medical/profile.js.map

@@ -0,0 +1 @@
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package/dist/medical/recommend/context.d.ts

@@ -0,0 +1,48 @@
+/**
+ * Recommendation context assembler — reads meds/supplements from FactStore
+ * and conditions/allergies/goals from the medical profile reader.
+ *
+ * NO network / NO LLM. All fs uses node:fs/promises (principles).
+ *
+ * FactStore lifecycle: injected store (tests) — caller owns; else open and close in finally.
+ * Profile: wrapped in try/catch — degraded but functional when SOPS is unavailable or file absent.
+ *
+ * Most similar: src/medical/analysis/review-pass.ts (open-store / try / finally-close / inject-store).
+ * supplement predicate is "dose" (not "takes-supplement") — see supplements.ts:106-121.
+ */
+import type { BoberConfig } from "../../config/schema.js";
+import { FactStore } from "../../state/facts.js";
+import type { FactRecord } from "../../state/facts.js";
+import type { ProfileCipher } from "../profile.js";
+export interface RecommendationContext {
+    meds: FactRecord[];
+    supplements: Array<{
+        name: string;
+        dose: string;
+    }>;
+    conditions: string[];
+    allergies: string[];
+    goal?: string;
+}
+export interface ContextDeps {
+    /** Injected FactStore (tests pass :memory:); caller owns lifecycle. */
+    facts?: FactStore;
+    /** Injected ProfileCipher for tests (avoids real SOPS binary). */
+    profileCipher?: ProfileCipher;
+}
+/**
+ * Assemble the recommendation context from FactStore and the medical profile.
+ *
+ * Meds: scope="medical", subject="patient", predicate="takes-medication".
+ * Supplements: scope="medical", predicate="dose" (subject = supplement name).
+ * Profile: conditions/allergies/goals from profile.yaml; defaults to [] on any error.
+ */
+export declare function assembleRecommendationContext(projectRoot: string, _config: BoberConfig, opts: {
+    goal?: string;
+}, deps?: ContextDeps): Promise<RecommendationContext>;
+/**
+ * Serialize a RecommendationContext to a plain string for runJudgeLoop.
+ * runJudgeLoop.context must be a STRING — this bridges the object to that contract.
+ */
+export declare function contextToString(ctx: RecommendationContext): string;
+//# sourceMappingURL=context.d.ts.map

package/dist/medical/recommend/context.d.ts.map

@@ -0,0 +1 @@
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