agent-bober 0.17.1 → 0.18.0

package/dist/medical/retrieval/literature.js

@@ -0,0 +1,292 @@
+import { MedlineSource } from "./medline-source.js";
+import { getGroundingVerdict, GROUNDING_MAX_LLM_CALLS } from "./grounding-critic.js";
+// ── LiteratureRetriever ──────────────────────────────────────────────
+/**
+ * Orchestrates literature retrieval behind the literature-retrieval egress gate.
+ *
+ * SYNCHRONOUS short-circuit: if the axis is off, return {disabled} — NO network
+ * attempt and NO MedlineSource method is called. This is the zero-egress proof.
+ */
+export class LiteratureRetriever {
+    egress;
+    source;
+    constructor(egress, source = new MedlineSource(egress)) {
+        this.egress = egress;
+        this.source = source;
+    }
+    /**
+     * Retrieve literature passages for the given query.
+     *
+     * When literature-retrieval is OFF: returns { kind: "disabled" } IMMEDIATELY,
+     * before MedlineSource is consulted — guarantees zero outbound bytes.
+     *
+     * When literature-retrieval is ON: delegates to MedlineSource.fetchPassages.
+     * Any throw from the source is caught and maps to abstain{source-error} (belt-and-braces;
+     * MedlineSource.fetchPassages itself is already fail-closed).
+     */
+    async retrieve(query) {
+        // isAllowed check MUST precede source call — proves zero-egress when axis is off.
+        if (!this.egress.isAllowed("literature-retrieval")) {
+            return { kind: "disabled" };
+        }
+        try {
+            return await this.source.fetchPassages(query);
+        }
+        catch {
+            return { kind: "abstain", reason: "source-error" };
+        }
+    }
+}
+// ── synthesize ───────────────────────────────────────────────────────
+const SYNTHESIS_MODEL = "ollama/llama3";
+const SYNTHESIS_MAX_TOKENS = 512;
+/**
+ * Build the system prompt that pins the model to the retrieved passages.
+ * The model is instructed to reply with exactly "ABSTAIN" if the passages
+ * do not support the query — synthesize treats that as an abstain signal.
+ */
+function buildSynthesisSystem(passages) {
+    const passageBlock = passages
+        .map((p, i) => `[${i + 1}] ${p.title}\n${p.text}\nSource: ${p.url}`)
+        .join("\n\n");
+    return ("You are a medical information assistant. Answer the user's question using ONLY " +
+        "the following retrieved passages from MedlinePlus. " +
+        "If the passages do not contain information that supports a specific answer, " +
+        "reply with exactly the single word: ABSTAIN\n\n" +
+        "Retrieved passages:\n" +
+        passageBlock);
+}
+/**
+ * Derive citations from grounded passages that were actually used in synthesis.
+ * For simplicity (all passages are pinned in the system prompt), all passages
+ * become citations when the model produces a non-abstained answer.
+ * This ensures citations.length >= 1 for every non-abstained answer.
+ */
+function passagesToCitations(passages) {
+    return passages.map((p) => ({
+        title: p.title,
+        url: p.url,
+        source: "medlineplus",
+    }));
+}
+/**
+ * synthesize — single LLM call that grounds the answer in retrieved passages.
+ *
+ * Rules (non-negotiable, enforced here):
+ * - disabled/abstain outcome => abstained MedicalAnswer, citations: [], no clinical assertion.
+ * - grounded outcome => one llm.chat call; if the model abstains or returns empty => abstained.
+ * - Every non-abstained answer carries >= 1 citation derived from the passages.
+ * - LLM error (e.g. Ollama unreachable) => abstained + "model unavailable" footer, NO cloud fallback.
+ * - Never emits an uncited clinical claim.
+ *
+ * @param query - The original user question.
+ * @param outcome - The RetrievalOutcome from LiteratureRetriever.retrieve.
+ * @param llm - Injectable LLMClient (tests pass {chat: vi.fn()}).
+ * @param footer - DisclaimerComposer footer string included in every answer.
+ * @param model - Model identifier to use for synthesis (default: SYNTHESIS_MODEL).
+ */
+export async function synthesize(query, outcome, llm, footer, model = SYNTHESIS_MODEL) {
+    // ── Abstain immediately on disabled / no-passages ────────────────
+    if (outcome.kind === "disabled" || outcome.kind === "abstain") {
+        return {
+            body: "I cannot ground an answer in retrieved literature. " +
+                "For evidence-based guidance, please consult a licensed healthcare professional.",
+            abstained: true,
+            citations: [],
+            disclaimerFooter: footer,
+            shortCircuit: false,
+        };
+    }
+    // outcome.kind === "grounded"
+    const passages = outcome.passages;
+    if (passages.length === 0) {
+        return {
+            body: "No supporting passages were retrieved. " +
+                "For evidence-based guidance, please consult a licensed healthcare professional.",
+            abstained: true,
+            citations: [],
+            disclaimerFooter: footer,
+            shortCircuit: false,
+        };
+    }
+    // ── Single LLM call ──────────────────────────────────────────────
+    let responseText;
+    try {
+        const response = await llm.chat({
+            model,
+            system: buildSynthesisSystem(passages),
+            messages: [{ role: "user", content: query }],
+            maxTokens: SYNTHESIS_MAX_TOKENS,
+        });
+        responseText = response.text.trim();
+    }
+    catch {
+        // Local model unavailable — abstain, NO cloud fallback.
+        return {
+            body: "I cannot ground an answer at this time (model unavailable). " +
+                "For evidence-based guidance, please consult a licensed healthcare professional.",
+            abstained: true,
+            citations: [],
+            disclaimerFooter: footer,
+            shortCircuit: false,
+        };
+    }
+    // ── Abstain if the model said so or returned empty ───────────────
+    if (!responseText || responseText.toUpperCase() === "ABSTAIN") {
+        return {
+            body: "The retrieved passages do not sufficiently support a specific answer to your question. " +
+                "For evidence-based guidance, please consult a licensed healthcare professional.",
+            abstained: true,
+            citations: [],
+            disclaimerFooter: footer,
+            shortCircuit: false,
+        };
+    }
+    // ── Non-abstained: attach citations (>= 1 guaranteed by passages.length > 0) ─
+    const citations = passagesToCitations(passages);
+    return {
+        body: responseText,
+        abstained: false,
+        citations,
+        disclaimerFooter: footer,
+        shortCircuit: false,
+    };
+}
+// ── synthesizeGrounded ────────────────────────────────────────────────
+/**
+ * Worst-case LLM call budget for the grounded gate:
+ *   1 synth + GROUNDING_MAX_LLM_CALLS critic + 1 re-synth + GROUNDING_MAX_LLM_CALLS re-critic
+ * Computed from the imported constant so it tracks future changes to the critic budget.
+ */
+export const GROUNDED_GATE_MAX_LLM_CALLS = 1 + GROUNDING_MAX_LLM_CALLS + 1 + GROUNDING_MAX_LLM_CALLS; // = 6 today (1+2+1+2)
+/**
+ * Canned abstain answer used throughout the gate when the answer cannot be
+ * sufficiently grounded in the retrieved literature.
+ */
+function abstainAnswer(footer) {
+    return {
+        body: "I cannot provide a sufficiently-supported answer grounded in the retrieved literature. " +
+            "For evidence-based guidance, please consult a licensed healthcare professional.",
+        abstained: true,
+        citations: [],
+        disclaimerFooter: footer,
+        shortCircuit: false,
+    };
+}
+/**
+ * Re-synthesize with critic feedback appended to the system prompt.
+ * A near-copy of the grounded branch inside synthesize, with one extra instruction line.
+ * Module-private — only synthesizeGrounded calls this.
+ */
+async function synthesizeWithFeedback(query, outcome, llm, footer, feedback, model = SYNTHESIS_MODEL) {
+    const passages = outcome.passages;
+    if (passages.length === 0)
+        return abstainAnswer(footer); // mirrors synthesize:120-130
+    const system = buildSynthesisSystem(passages) +
+        `\n\nAddress this reviewer feedback while staying grounded ONLY in the passages: ${feedback}`;
+    let responseText;
+    try {
+        const response = await llm.chat({
+            model,
+            system,
+            messages: [{ role: "user", content: query }],
+            maxTokens: SYNTHESIS_MAX_TOKENS,
+        });
+        responseText = response.text.trim();
+    }
+    catch {
+        return abstainAnswer(footer);
+    }
+    if (!responseText || responseText.toUpperCase() === "ABSTAIN")
+        return abstainAnswer(footer);
+    return {
+        body: responseText,
+        abstained: false,
+        citations: passagesToCitations(passages),
+        disclaimerFooter: footer,
+        shortCircuit: false,
+    };
+}
+/**
+ * synthesizeGrounded — fail-closed gate: synthesize → critic → one re-synth → abstain.
+ *
+ * For non-grounded outcomes, delegates to synthesize (disabled/abstain handled there).
+ * For grounded outcomes:
+ *   1. synthesize → if abstained, return it
+ *   2. getGroundingVerdict → if approve, return answer
+ *   3. synthesizeWithFeedback (one re-synth with critic feedback)
+ *   4. getGroundingVerdict again → if approve, return re-synth answer
+ *   5. else → return abstainAnswer (fail-closed)
+ *
+ * Any thrown error from synthesize or the critic maps to abstainAnswer (fail-closed).
+ * Bounded by GROUNDED_GATE_MAX_LLM_CALLS (= 6 worst case today).
+ *
+ * Returns { answer, verdict } where verdict is one of:
+ *   'approve'          — gate returned an approved answer
+ *   'reject-abstained' — gate abstained after a critic reject (second reject)
+ *   'error-abstained'  — gate abstained due to a thrown error or model unavailable
+ *
+ * @param model - Model identifier to use (default: SYNTHESIS_MODEL for back-compat).
+ */
+export async function synthesizeGrounded(query, outcome, llm, footer, model = SYNTHESIS_MODEL) {
+    // Non-grounded outcomes are already handled by synthesize (disabled/abstain → abstained).
+    if (outcome.kind !== "grounded") {
+        const answer = await synthesize(query, outcome, llm, footer, model);
+        return { answer, verdict: "error-abstained" };
+    }
+    // 1) First synthesis.
+    let answer;
+    try {
+        answer = await synthesize(query, outcome, llm, footer, model);
+    }
+    catch {
+        return { answer: abstainAnswer(footer), verdict: "error-abstained" };
+    }
+    if (answer.abstained)
+        return { answer, verdict: "error-abstained" }; // synthesize abstained (empty/ABSTAIN/no-passages/model-unavailable)
+    // 2) First critique. getGroundingVerdict PROPAGATES transport errors → wrap.
+    let verdict;
+    try {
+        verdict = await getGroundingVerdict({
+            llm,
+            model,
+            question: query,
+            answerBody: answer.body,
+            passages: outcome.passages,
+        });
+    }
+    catch {
+        return { answer: abstainAnswer(footer), verdict: "error-abstained" };
+    }
+    if (verdict.verdict === "approve")
+        return { answer, verdict: "approve" };
+    // 3) ONE re-synthesis with critic feedback appended to the system prompt.
+    let answer2;
+    try {
+        answer2 = await synthesizeWithFeedback(query, outcome, llm, footer, verdict.feedback, model);
+    }
+    catch {
+        return { answer: abstainAnswer(footer), verdict: "error-abstained" };
+    }
+    if (answer2.abstained)
+        return { answer: answer2, verdict: "error-abstained" };
+    // 4) Re-critique.
+    let verdict2;
+    try {
+        verdict2 = await getGroundingVerdict({
+            llm,
+            model,
+            question: query,
+            answerBody: answer2.body,
+            passages: outcome.passages,
+        });
+    }
+    catch {
+        return { answer: abstainAnswer(footer), verdict: "error-abstained" };
+    }
+    // Approved on re-critique => 'approve'. Not approved => 'reject-abstained' (critic ran and rejected).
+    return verdict2.verdict === "approve"
+        ? { answer: answer2, verdict: "approve" }
+        : { answer: abstainAnswer(footer), verdict: "reject-abstained" };
+}
+//# sourceMappingURL=literature.js.map

package/dist/medical/retrieval/literature.js.map

@@ -0,0 +1 @@
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package/dist/medical/retrieval/medline-source.d.ts

@@ -0,0 +1,72 @@
+/** MedlineSource — the ONLY medical file allowed network imports (ADR-6 exception). S7 adds the real call. */
+import type { EgressGuard } from "../egress.js";
+/**
+ * A single retrieved passage from MedlinePlus.
+ * title + url form the citation; text is the passage body for synthesis grounding.
+ */
+export interface Passage {
+    title: string;
+    url: string;
+    text: string;
+    source: "medlineplus";
+}
+/**
+ * Discriminated union for retrieval outcomes.
+ * disabled — the egress axis is off; no attempt was made.
+ * abstain  — the axis is on but the source could not produce passages (error or empty).
+ * grounded — passages retrieved from MedlinePlus (Sprint 7).
+ */
+export type RetrievalOutcome = {
+    kind: "disabled";
+} | {
+    kind: "abstain";
+    reason: string;
+} | {
+    kind: "grounded";
+    passages: Passage[];
+};
+/**
+ * Injectable transport type — a minimal fetch-like function.
+ * Tests pass a fake returning recorded fixture data; production defaults to the global fetch.
+ * Using a plain duck-typed return rather than the global Response to stay testable
+ * without the global fetch in test files (global fetch is banned in other medical files).
+ * No AbortSignal in the signature — tests inject synchronous fakes that don't need it.
+ */
+export type FetchLike = (url: string) => Promise<{
+    ok: boolean;
+    status: number;
+    json(): Promise<unknown>;
+}>;
+/**
+ * MedlinePlus retrieval source.
+ *
+ * This is the ONE file the ESLint no-restricted-imports exception permits to hold
+ * network imports (src/medical/retrieval/medline-source.ts — ADR-6).
+ *
+ * assertAllowed("literature-retrieval") is called BEFORE any fetch attempt — this
+ * is the runtime defense-in-depth that backs the static ESLint boundary.
+ *
+ * The injectable fetchImpl transport means tests NEVER reach the live MedlinePlus
+ * endpoint — they pass a fake FetchLike returning committed fixture data.
+ *
+ * bober: single source (MedlinePlus/NIH, no-auth); add PubMed in a future sprint
+ *        if multi-source support is needed — keep each source in its own file.
+ */
+export declare class MedlineSource {
+    private readonly egress;
+    private readonly fetchImpl;
+    constructor(egress: EgressGuard, fetchImpl?: FetchLike);
+    /**
+     * Fetch passages from MedlinePlus for the given query.
+     *
+     * Order:
+     * 1. assertAllowed — throws (and is caught below) if the axis is off.
+     * 2. fetchImpl(url) — injectable transport; default = global fetch.
+     * 3. Parse response into Passage[].
+     * 4. Return grounded | abstain{no-passages} | abstain{source-error}.
+     *
+     * NEVER throws out of this method — all errors map to abstain{source-error}.
+     */
+    fetchPassages(query: string): Promise<RetrievalOutcome>;
+}
+//# sourceMappingURL=medline-source.d.ts.map

package/dist/medical/retrieval/medline-source.d.ts.map

@@ -0,0 +1 @@
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package/dist/medical/retrieval/medline-source.js

@@ -0,0 +1,120 @@
+// ── MedlinePlus Web Service URL builder ─────────────────────────────
+// bober: MedlinePlus Web Service (health-topics JSON, no-auth) — https://wsearch.nlm.nih.gov/ws/query
+// Returns nlmSearchResult.list.document[] with content fields (title, FullSummary, link).
+// CI uses the committed fixture at __fixtures__/medlineplus-sample.json; live endpoint skipped by default.
+const MEDLINEPLUS_BASE = "https://wsearch.nlm.nih.gov/ws/query";
+function buildMedlineUrl(query) {
+    // Build query string manually — URLSearchParams is not declared as a global in the ESLint config.
+    const encodedTerm = encodeURIComponent(query);
+    return `${MEDLINEPLUS_BASE}?db=healthTopics&term=${encodedTerm}&rettype=brief&retmax=5&retformat=json`;
+}
+// ── MedlinePlus response parser ──────────────────────────────────────
+/**
+ * Parse the MedlinePlus Web Service JSON response into Passage[].
+ * Accepts unknown shape; returns [] on any structural mismatch (fail-closed).
+ */
+function parseMedline(raw) {
+    if (!raw || typeof raw !== "object")
+        return [];
+    const result = raw;
+    const nlmResult = result["nlmSearchResult"];
+    if (!nlmResult)
+        return [];
+    const list = nlmResult["list"];
+    if (!list)
+        return [];
+    const documents = list["document"];
+    if (!Array.isArray(documents))
+        return [];
+    const passages = [];
+    for (const doc of documents) {
+        if (!doc || typeof doc !== "object")
+            continue;
+        const d = doc;
+        // title: from content[] where name === "title"
+        let title = "";
+        let text = "";
+        let url = "";
+        const url_ = d["@url"];
+        if (typeof url_ === "string")
+            url = url_;
+        const contents = d["content"];
+        if (Array.isArray(contents)) {
+            for (const item of contents) {
+                if (!item || typeof item !== "object")
+                    continue;
+                const c = item;
+                const name = c["@name"];
+                const value = c["#text"];
+                if (name === "title" && typeof value === "string")
+                    title = value;
+                if (name === "FullSummary" && typeof value === "string")
+                    text = value;
+            }
+        }
+        if (title && url) {
+            passages.push({ title, url, text: text || title, source: "medlineplus" });
+        }
+    }
+    return passages;
+}
+// ── MedlineSource class ──────────────────────────────────────────────
+/**
+ * MedlinePlus retrieval source.
+ *
+ * This is the ONE file the ESLint no-restricted-imports exception permits to hold
+ * network imports (src/medical/retrieval/medline-source.ts — ADR-6).
+ *
+ * assertAllowed("literature-retrieval") is called BEFORE any fetch attempt — this
+ * is the runtime defense-in-depth that backs the static ESLint boundary.
+ *
+ * The injectable fetchImpl transport means tests NEVER reach the live MedlinePlus
+ * endpoint — they pass a fake FetchLike returning committed fixture data.
+ *
+ * bober: single source (MedlinePlus/NIH, no-auth); add PubMed in a future sprint
+ *        if multi-source support is needed — keep each source in its own file.
+ */
+export class MedlineSource {
+    egress;
+    fetchImpl;
+    constructor(egress, 
+    // bober: global fetch is the default ONLY in this file (ESLint exception);
+    //        tests inject a FetchLike returning fixture data so CI stays offline.
+    fetchImpl = fetch) {
+        this.egress = egress;
+        this.fetchImpl = fetchImpl;
+    }
+    /**
+     * Fetch passages from MedlinePlus for the given query.
+     *
+     * Order:
+     * 1. assertAllowed — throws (and is caught below) if the axis is off.
+     * 2. fetchImpl(url) — injectable transport; default = global fetch.
+     * 3. Parse response into Passage[].
+     * 4. Return grounded | abstain{no-passages} | abstain{source-error}.
+     *
+     * NEVER throws out of this method — all errors map to abstain{source-error}.
+     */
+    async fetchPassages(query) {
+        try {
+            // MUST be first — runtime defense-in-depth over the ESLint boundary.
+            this.egress.assertAllowed("literature-retrieval");
+            const url = buildMedlineUrl(query);
+            const res = await this.fetchImpl(url);
+            if (!res.ok) {
+                return { kind: "abstain", reason: "source-error" };
+            }
+            const json = await res.json();
+            const passages = parseMedline(json);
+            return passages.length > 0
+                ? { kind: "grounded", passages }
+                : { kind: "abstain", reason: "no-passages" };
+        }
+        catch {
+            // Includes: assertAllowed throws (axis off), network error, parse error.
+            // NEVER fail-open — abstain with source-error.
+            return { kind: "abstain", reason: "source-error" };
+        }
+    }
+}
+//# sourceMappingURL=medline-source.js.map

package/dist/medical/retrieval/medline-source.js.map

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

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+/**
+ * Medical team builder (Phase 6, Sprint 1).
+ *
+ * buildMedicalTeam returns the built-in 'medical' Team with pipelineShape
+ * 'medical-sop' and a concrete (stub) GuardrailSet in the guardrails slot.
+ * Real GuardrailSet.evaluate logic lands in S3.
+ */
+import type { BoberConfig } from "../config/schema.js";
+import type { Team } from "../teams/types.js";
+/**
+ * Builds the built-in 'medical' Team.
+ * Registered in loadTeam (registry.ts) before the config.teams lookup.
+ */
+export declare function buildMedicalTeam(config: BoberConfig): Team;
+//# sourceMappingURL=team.d.ts.map

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

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package/dist/medical/team.js

@@ -0,0 +1,44 @@
+import { resolveRoleProviders } from "../config/role-providers.js";
+import { MedicalGuardrails } from "./guardrails.js";
+// ── Role descriptors ────────────────────────────────────────────────
+/**
+ * The 7 role descriptors reused for the medical team.
+ * Mirrors DEFAULT_ROLES in registry.ts — kept separate to avoid a circular
+ * import (registry.ts → medical/team.ts → registry.ts).
+ * bober: inline copy; if roles diverge between teams, extract to a shared module.
+ */
+const MEDICAL_ROLES = [
+    { name: "planner", displayName: "Planner" },
+    { name: "researcher", displayName: "Researcher" },
+    { name: "chat", displayName: "Chat" },
+    { name: "curator", displayName: "Curator" },
+    { name: "generator", displayName: "Generator" },
+    { name: "evaluator", displayName: "Evaluator" },
+    { name: "codeReview", displayName: "Code Reviewer" },
+];
+// ── Built-in medical guardrails (real impl, Sprint 3) ───────────────
+/**
+ * Builds the real medical GuardrailSet (Sprint 3 and beyond).
+ * Wraps RedFlagDetector for emergency escalation; allows benign prompts.
+ * The stub allow-all from Sprint 1–2 is replaced by MedicalGuardrails.
+ */
+function buildMedicalGuardrails() {
+    return new MedicalGuardrails();
+}
+// ── buildMedicalTeam ────────────────────────────────────────────────
+/**
+ * Builds the built-in 'medical' Team.
+ * Registered in loadTeam (registry.ts) before the config.teams lookup.
+ */
+export function buildMedicalTeam(config) {
+    return {
+        id: "medical",
+        displayName: "Medical team",
+        memoryNamespace: "medical",
+        providers: resolveRoleProviders(config),
+        pipelineShape: "medical-sop",
+        roles: MEDICAL_ROLES,
+        guardrails: buildMedicalGuardrails(),
+    };
+}
+//# sourceMappingURL=team.js.map

package/dist/medical/team.js.map

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