agent-bober 0.17.1 → 0.19.0

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 @@
+{"version":3,"file":"context.d.ts","sourceRoot":"","sources":["../../../src/medical/recommend/context.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAIH,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,wBAAwB,CAAC;AAC1D,OAAO,EAAE,SAAS,EAAe,MAAM,sBAAsB,CAAC;AAC9D,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,sBAAsB,CAAC;AAEvD,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAInD,MAAM,WAAW,qBAAqB;IACpC,IAAI,EAAE,UAAU,EAAE,CAAC;IACnB,WAAW,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACnD,UAAU,EAAE,MAAM,EAAE,CAAC;IACrB,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,WAAW;IAC1B,uEAAuE;IACvE,KAAK,CAAC,EAAE,SAAS,CAAC;IAClB,kEAAkE;IAClE,aAAa,CAAC,EAAE,aAAa,CAAC;CAC/B;AAID;;;;;;GAMG;AACH,wBAAsB,6BAA6B,CACjD,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,WAAW,EACpB,IAAI,EAAE;IAAE,IAAI,CAAC,EAAE,MAAM,CAAA;CAAE,EACvB,IAAI,GAAE,WAAgB,GACrB,OAAO,CAAC,qBAAqB,CAAC,CAiDhC;AAID;;;GAGG;AACH,wBAAgB,eAAe,CAAC,GAAG,EAAE,qBAAqB,GAAG,MAAM,CAkClE"}

package/dist/medical/recommend/context.js

@@ -0,0 +1,109 @@
+/**
+ * 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 { join } from "node:path";
+import { FactStore, factsDbPath } from "../../state/facts.js";
+import { readProfile } from "../profile.js";
+// -- Public API ----------------------------------------------------------
+/**
+ * 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 async function assembleRecommendationContext(projectRoot, _config, opts, deps = {}) {
+    // -- Meds + supplements from FactStore --------------------------------
+    let meds = [];
+    let supplements = [];
+    if (deps.facts !== undefined) {
+        // Injected store (tests) — caller owns lifecycle; do NOT close
+        meds = deps.facts.getActiveFacts("medical", "patient", "takes-medication");
+        // PITFALL: supplements use predicate="dose" with subject=supplement name (supplements.ts:106-121)
+        const supplementFacts = deps.facts.getActiveFacts("medical", undefined, "dose");
+        supplements = supplementFacts.map((r) => ({ name: r.subject, dose: r.value }));
+    }
+    else {
+        // Production: open our own store; close in finally
+        const dbPath = factsDbPath(projectRoot, "medical");
+        let facts;
+        try {
+            facts = new FactStore(dbPath);
+            meds = facts.getActiveFacts("medical", "patient", "takes-medication");
+            const supplementFacts = facts.getActiveFacts("medical", undefined, "dose");
+            supplements = supplementFacts.map((r) => ({ name: r.subject, dose: r.value }));
+        }
+        catch {
+            // Dir not created yet → graceful empty (mirrors engine.ts:365-381)
+            // meds and supplements are already [] from initialization — nothing to reassign
+        }
+        finally {
+            facts?.close();
+        }
+    }
+    // -- Profile: conditions / allergies / goals --------------------------
+    let conditions = [];
+    let allergies = [];
+    let profileGoals = [];
+    // profile.yaml lives at <projectRoot>/.bober/medical (not in vaultDir)
+    const profileDir = join(projectRoot, ".bober", "medical");
+    try {
+        const profile = await readProfile(profileDir, { cipher: deps.profileCipher });
+        conditions = profile.conditions;
+        allergies = profile.allergies;
+        profileGoals = profile.goals;
+    }
+    catch {
+        // SOPS unavailable or profile file absent — degraded but functional (contract assumption 1)
+        // conditions, allergies, profileGoals are already [] from initialization — nothing to reassign
+    }
+    // Explicit goal wins; fall back to first profile goal
+    const goal = opts.goal ?? (profileGoals.length > 0 ? profileGoals[0] : undefined);
+    return { meds, supplements, conditions, allergies, goal };
+}
+// -- Context serializer --------------------------------------------------
+/**
+ * Serialize a RecommendationContext to a plain string for runJudgeLoop.
+ * runJudgeLoop.context must be a STRING — this bridges the object to that contract.
+ */
+export function contextToString(ctx) {
+    const parts = [];
+    if (ctx.meds.length > 0) {
+        parts.push(`Medications: ${ctx.meds.map((m) => m.value).join(", ")}`);
+    }
+    else {
+        parts.push("Medications: none");
+    }
+    if (ctx.supplements.length > 0) {
+        parts.push(`Supplements: ${ctx.supplements.map((s) => `${s.name} (${s.dose})`).join(", ")}`);
+    }
+    else {
+        parts.push("Supplements: none");
+    }
+    if (ctx.conditions.length > 0) {
+        parts.push(`Conditions: ${ctx.conditions.join(", ")}`);
+    }
+    else {
+        parts.push("Conditions: none");
+    }
+    if (ctx.allergies.length > 0) {
+        parts.push(`Allergies: ${ctx.allergies.join(", ")}`);
+    }
+    else {
+        parts.push("Allergies: none");
+    }
+    if (ctx.goal !== undefined) {
+        parts.push(`Goal: ${ctx.goal}`);
+    }
+    return parts.join("\n");
+}
+//# sourceMappingURL=context.js.map

package/dist/medical/recommend/context.js.map

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package/dist/medical/recommend/judge-panel.d.ts

@@ -0,0 +1,49 @@
+/**
+ * Judge panel loop for medical recommendation candidates.
+ *
+ * PURE orchestration over injected fns — NO fs / NO network / NO real provider / NO FactStore.
+ *
+ * Regenerate-on-reject loop structure adapted from runCritiqueLoop (src/fleet/critic-deep.ts:211-278),
+ * with the accept-best / fail-open tail REPLACED by fail-closed (mirror grounding-critic.ts:203-206).
+ *
+ * FAIL-CLOSED INVERSION: see getLensVerdict (lenses.ts) and the constant comment below.
+ * Red-flag guard fires FIRST — generateCandidate is NEVER called when the guard short-circuits.
+ */
+import type { GuardrailSet } from "../types.js";
+import { type LensClients, type LensName, type LensVerdict, type PanelDecision, type PanelOutcome } from "./types.js";
+/**
+ * Reconciles four lens verdicts into a panel decision.
+ *
+ * CRITICAL ORDERING:
+ * 1. Veto check FIRST — any veto:true from contraindication-checker forces accepted:false
+ *    with reason:'contraindication-veto' REGARDLESS of the approve count. A veto can NEVER
+ *    be overridden by a vote majority under any code path (NonGoal #4).
+ * 2. Strict majority — approveCount > rejectCount. A tie (2 approve / 2 reject) resolves
+ *    to accepted:false (fail-closed per lens-panel.md:80-84).
+ */
+export declare function reconcilePanel(verdicts: Record<LensName, LensVerdict>): PanelDecision;
+/**
+ * Runs the full multi-lens judge loop for a medical recommendation candidate.
+ *
+ * Execution order:
+ *  (1) Red-flag guard first — returns short-circuit/refuse BEFORE calling generateCandidate.
+ *  (2) For each round up to maxRounds: generate a candidate, run all four lenses, reconcile.
+ *  (3) On accept: return accepted outcome immediately.
+ *  (4) On reject: regenerate with collected dissent feedback for the next round.
+ *  (5) After maxRounds without consensus: return rejected outcome (fail-closed).
+ *
+ * NEVER throws — a thrown lens client is caught and counted as a reject verdict (fail-closed).
+ * NEVER exceeds MEDICAL_PANEL_MAX_TOTAL_CALLS.
+ *
+ * FAIL-CLOSED INVERSION: mirrors grounding-critic.ts:203-206, NOT critic-deep.ts:199-201.
+ */
+export declare function runJudgeLoop(input: {
+    question: string;
+    generateCandidate: (prevFeedback?: string) => Promise<string>;
+    lensClients: LensClients;
+    context: string;
+    redFlag: GuardrailSet;
+    maxRounds?: number;
+    now?: string;
+}): Promise<PanelOutcome>;
+//# sourceMappingURL=judge-panel.d.ts.map

package/dist/medical/recommend/judge-panel.d.ts.map

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