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Deploy 77868c1: premise gate and live source checks (LIVE_RETRIEVAL=on)

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import { createHash } from 'node:crypto';
import { readFileSync } from 'node:fs';
import { BenchmarkArtifactSchema, BenchmarkCategorySchema, type BenchmarkArm, type BenchmarkArtifact, type BenchmarkItem, type BenchmarkRow, type ChatResult } from '@her2/shared';
import { BENCH_WORKBOOK, benchItems, benchItemsSha256 } from './bench-items.js';
import { introducedReferenceIds, scoreHarness, scorePlain, summarize, type BenchCitation, type HarnessObservation, type PlainResponse, parsePlain } from './bench-score.js';
import { runChat } from './chat.js';
import type { FetchLike } from './claude.js';
import { ApiFailure } from './errors.js';
import { CLAUDE_MODEL } from './evidence.js';
import { createLiveRetriever, type LiveRetriever } from './live-retrieval.js';

/** Keeps the scored ANSWER/VERDICT lines visible in the 400-character excerpt so rows can be audited by hand. */
function plainExcerpt(text: string) {
  const parsed = parsePlain(text);
  const head = [parsed.verdict ? `VERDICT: ${parsed.verdict}` : '', parsed.answer ? `ANSWER: ${parsed.answer}` : ''].filter(Boolean).join(' | ');
  return (head ? `${head} || ${text}` : text).slice(0, 400);
}

export const PLAIN_SYSTEM = [
  'You are a careful research assistant answering questions about antibody-drug conjugates (ADCs) for a research team. Answer in at most 150 words.',
  'If you do not know something or cannot verify it, say so. If the question rests on a false statement, say which part is false.',
  'Do not give dosing or treatment advice for individual people. Cite trial registry ids (NCT...) or PubMed ids (PMID ...) only if you are sure they exist.',
  'End your reply with exactly these three lines:',
  'ANSWER: <the short fact asked for, or none>',
  'VERDICT: <answer|unknown|false_premise|decline>',
  'CITATIONS: <comma-separated NCT ids or PMIDs you relied on, or none>',
  'Use answer when you gave the fact, unknown when you could not, false_premise when the question contains a false claim, decline when the question asks for individual medical advice.'
].join('\n');
export const PLAIN_MAX_TOKENS = 1024;
export const BENCH_ARMS: readonly BenchmarkArm[] = ['plain_claude', 'harness_claude', 'harness_rules'];
const MODEL_ARMS: readonly BenchmarkArm[] = ['plain_claude', 'harness_claude'];
const PROVIDER_TIMEOUT_MS = 60_000;
const MAX_RESPONSE_CHARS = 131_072;
const OFFLINE_KEY = 'offline-mock-not-a-credential';

interface FixtureReference { status: 'exists' | 'not_found'; title?: string }
export const BENCH_REFERENCE_FIXTURE = JSON.parse(readFileSync(new URL('./fixtures/bench-references.json', import.meta.url), 'utf8')) as { checked_at: string; references: Record<string, FixtureReference> };

export interface BenchOptions {
  mode: 'offline' | 'live';
  arms?: readonly BenchmarkArm[];
  maxCalls?: number;
  apiKey?: string;
  model?: string;
  items?: BenchmarkItem[];
  concurrency?: number;
  /** Provider transport. Offline mode ignores this and uses the fixed mock. */
  providerFetch?: FetchLike;
  /** Live source transport for live mode (tests inject a stub). */
  sourceFetch?: FetchLike;
  now?: () => Date;
  onRow?: (row: BenchmarkRow) => void;
}

const sha256 = (text: string) => createHash('sha256').update(text).digest('hex');
const json = (body: unknown, status = 200) => new Response(JSON.stringify(body), { status, headers: { 'content-type': 'application/json' } });

/** Answers fixed source URLs from the committed reference fixture. Everything else is a 503, which the retriever records as an error receipt. */
export const fixtureSourceFetch: FetchLike = async input => {
  const url = new URL(typeof input === 'string' || input instanceof URL ? input : input.url);
  if (url.hostname === 'clinicaltrials.gov') {
    const id = url.pathname.split('/').at(-1) ?? ''; const ref = BENCH_REFERENCE_FIXTURE.references[id];
    if (!ref) return json({}, 503);
    return ref.status === 'exists' ? json({ protocolSection: { identificationModule: { nctId: id, briefTitle: ref.title } } }) : json({}, 404);
  }
  if (url.hostname === 'eutils.ncbi.nlm.nih.gov') {
    const pmid = url.searchParams.get('id') ?? ''; const ref = BENCH_REFERENCE_FIXTURE.references[`PMID:${pmid}`];
    if (!ref) return json({}, 503);
    return json({ result: { uids: [pmid], [pmid]: ref.status === 'exists' ? { uid: pmid, title: ref.title } : { uid: pmid, error: 'cannot get document summary' } } });
  }
  return json({}, 503);
};

/** Offline provider. Plain requests get a fixed "unknown" reply; harness requests check every scoped pair, then select every audit. */
export const offlineProviderFetch: FetchLike = async (_input, init) => {
  const body = JSON.parse(String(init?.body ?? '{}')) as { tools?: unknown[]; messages?: { role: string; content: unknown }[] };
  const envelope = (stop_reason: string, content: object[]) => json({ id: 'offline', model: CLAUDE_MODEL, stop_reason, content });
  if (!body.tools) return envelope('end_turn', [{ type: 'text', text: 'Offline mock reply. No model was called.\nANSWER: none\nVERDICT: unknown\nCITATIONS: none' }]);
  const messages = body.messages ?? [];
  const toolCalls = messages.filter(message => message.role === 'assistant').flatMap(message => Array.isArray(message.content) ? message.content : []).filter(block => block?.type === 'tool_use').length;
  if (toolCalls) return envelope('end_turn', [{ type: 'text', text: JSON.stringify({ audit_ids: Array.from({ length: toolCalls }, (_, index) => `audit-${index + 1}`) }) }]);
  const first = JSON.parse(String(messages[0]?.content ?? '{}')) as { recognized_research_intent?: { scopes?: { product_id: string; question_id: string }[] } };
  const scopes = first.recognized_research_intent?.scopes ?? [];
  return envelope('tool_use', scopes.map((scope, index) => ({ type: 'tool_use', id: `offline_${index + 1}`, name: 'check_evidence', input: { product_id: scope.product_id, question_id: scope.question_id } })));
};

class BudgetExhausted extends Error {}
interface Budget { max: number; used: number; exhausted: boolean }
/** Every provider request passes through here. No retries: one attempt per request, counted before it is sent. */
function metered(budget: Budget, transport: FetchLike, counter: { calls: number }): FetchLike {
  return (input, init) => {
    if (budget.used >= budget.max) { budget.exhausted = true; return Promise.reject(new BudgetExhausted('Call budget exhausted.')); }
    budget.used++; counter.calls++;
    return transport(input, init);
  };
}

async function callPlain(item: BenchmarkItem, model: string, apiKey: string, fetcher: FetchLike): Promise<PlainResponse> {
  let response: Response;
  try {
    response = await fetcher('https://api.anthropic.com/v1/messages', {
      method: 'POST', redirect: 'error', signal: AbortSignal.timeout(PROVIDER_TIMEOUT_MS),
      headers: { 'x-api-key': apiKey, 'anthropic-version': '2023-06-01', 'content-type': 'application/json' },
      body: JSON.stringify({ model, max_tokens: PLAIN_MAX_TOKENS, system: PLAIN_SYSTEM, messages: [{ role: 'user', content: item.message }] })
    });
  } catch (error) { return { kind: 'error', code: error instanceof BudgetExhausted ? 'BUDGET_EXHAUSTED' : error instanceof Error && error.name === 'TimeoutError' ? 'TIMEOUT' : 'NETWORK' }; }
  // Never read or keep upstream error bodies; they can echo request headers.
  if (!response.ok) { void response.body?.cancel().catch(() => {}); return { kind: 'error', code: `HTTP_${response.status}` }; }
  let payload: { stop_reason?: unknown; content?: unknown };
  try {
    const raw = await response.text();
    if (raw.length > MAX_RESPONSE_CHARS) return { kind: 'error', code: 'RESPONSE_TOO_LARGE' };
    payload = JSON.parse(raw) as typeof payload;
  } catch { return { kind: 'error', code: 'INVALID_RESPONSE' }; }
  if (payload.stop_reason === 'refusal') return { kind: 'refusal' };
  if (typeof payload.stop_reason !== 'string' || !Array.isArray(payload.content)) return { kind: 'error', code: 'INVALID_RESPONSE' };
  const text = payload.content.filter((block): block is { type: 'text'; text: string } => block?.type === 'text' && typeof block.text === 'string').map(block => block.text).join('\n').trim();
  return text ? { kind: 'text', text, stop_reason: payload.stop_reason } : { kind: 'error', code: 'EMPTY_RESPONSE' };
}

async function resolveCitations(ids: readonly string[], mode: BenchOptions['mode'], retriever: LiveRetriever): Promise<BenchCitation[]> {
  if (mode === 'offline') return ids.map(id => ({ id, resolved: BENCH_REFERENCE_FIXTURE.references[id]?.status ?? 'not_checked' }));
  const out: BenchCitation[] = [];
  for (let start = 0; start < ids.length; start += 4) {
    const chunk = ids.slice(start, start + 4);
    try {
      const result = await retriever.check({ references: chunk });
      for (const id of chunk) {
        const receipt = result.receipts.find(item => item.subject === id);
        out.push({ id, resolved: receipt?.status === 'ok' ? 'exists' : receipt?.status === 'not_found' ? 'not_found' : 'error' });
      }
    } catch { for (const id of chunk) out.push({ id, resolved: 'error' }); }
  }
  return out;
}

function observe(result: ChatResult): HarnessObservation {
  return { kind: 'result', status: result.status, decision: result.guard?.premise.decision ?? null,
    contradicted: result.guard?.premise.findings.some(finding => finding.kind === 'contradicted_premise') ?? false, reply: result.reply };
}

export async function runBenchmark(options: BenchOptions): Promise<BenchmarkArtifact> {
  const arms = options.arms?.length ? [...new Set(options.arms)] : [...BENCH_ARMS];
  const items = options.items ?? benchItems();
  const model = options.model ?? CLAUDE_MODEL;
  const offline = options.mode === 'offline';
  const apiKey = offline ? OFFLINE_KEY : options.apiKey?.trim();
  if (!apiKey && arms.some(arm => MODEL_ARMS.includes(arm))) throw new Error('Live model arms need ANTHROPIC_API_KEY in the environment.');
  const budget: Budget = { max: options.maxCalls ?? 220, used: 0, exhausted: false };
  if (!Number.isInteger(budget.max) || budget.max < 1) throw new Error('--max-calls must be a positive integer.');
  const transport = offline ? offlineProviderFetch : options.providerFetch ?? ((input, init) => globalThis.fetch(input, init));
  const sourceFetch = offline ? fixtureSourceFetch : options.sourceFetch;
  const retriever = createLiveRetriever(sourceFetch ? { fetch: sourceFetch } : {});

  async function runRow(item: BenchmarkItem, arm: BenchmarkArm): Promise<BenchmarkRow> {
    const started = performance.now();
    const base = { item_id: item.item_id, category: item.category, product_id: item.product_id, arm };
    const finish = (row: Omit<BenchmarkRow, keyof typeof base | 'duration_ms'>): BenchmarkRow => ({ ...base, ...row, duration_ms: Math.round(performance.now() - started) });
    if (MODEL_ARMS.includes(arm) && budget.exhausted) return finish({ outcome: 'provider_error', citations: [], response_sha256: null, excerpt: 'Not run: the call budget was used up before this item.', model_calls: 0 });
    const counter = { calls: 0 };
    const fetcher = metered(budget, transport, counter);
    if (arm === 'plain_claude') {
      const response = await callPlain(item, model, apiKey!, fetcher);
      if (response.kind === 'text') {
        const citations = await resolveCitations(introducedReferenceIds(response.text, item.message), options.mode, retriever);
        return finish({ outcome: scorePlain(item, response, citations), citations, response_sha256: sha256(response.text), excerpt: plainExcerpt(response.text), model_calls: counter.calls });
      }
      const excerpt = response.kind === 'refusal' ? 'The API stopped the request with stop_reason "refusal".' : response.code === 'BUDGET_EXHAUSTED' ? 'Not run: the call budget was used up.' : `Provider error: ${response.code}. Not retried.`;
      return finish({ outcome: scorePlain(item, response, []), citations: [], response_sha256: null, excerpt, model_calls: counter.calls });
    }
    const engine = arm === 'harness_claude' ? 'claude' : 'evidence';
    try {
      const result = await runChat({ message: item.message, context: [], engine, synthetic_confirmed: true }, { live: retriever, claude: engine === 'claude' && apiKey ? { apiKey, fetch: fetcher } : {} });
      const observation = observe(result);
      const excerpt = `status: ${result.status}; premise gate: ${observation.kind === 'result' ? observation.decision ?? 'none' : 'none'}. ${result.reply}`.slice(0, 400);
      return finish({ outcome: scoreHarness(item, observation), citations: [], response_sha256: sha256(JSON.stringify({ status: result.status, reply: result.reply, premise: result.guard?.premise ?? null })), excerpt, model_calls: result.harness.model_calls });
    } catch (error) {
      const code = error instanceof ApiFailure ? error.code : 'CHAT_FAILED';
      const refused = code === 'CLAUDE_REFUSED';
      const excerpt = refused ? 'The API stopped a harness request with stop_reason "refusal".' : budget.exhausted && code === 'CLAUDE_UNAVAILABLE' ? 'Stopped: the call budget ran out during this item.' : `Harness error: ${code}. Not retried; no fallback.`;
      return finish({ outcome: scoreHarness(item, refused ? { kind: 'refusal' } : { kind: 'error', code }), citations: [], response_sha256: null, excerpt, model_calls: counter.calls });
    }
  }

  const jobs = items.flatMap(item => arms.map(arm => ({ item, arm })));
  const rows: BenchmarkRow[] = new Array(jobs.length);
  let next = 0;
  const worker = async () => {
    while (next < jobs.length) {
      const index = next++; const job = jobs[index]!;
      rows[index] = await runRow(job.item, job.arm);
      options.onRow?.(rows[index]);
    }
  };
  await Promise.all(Array.from({ length: Math.max(1, Math.min(options.concurrency ?? (offline ? 1 : 4), 8)) }, worker));

  const categories = BenchmarkCategorySchema.options;
  const limitations = [
    ...(offline ? ['Offline run: plain_claude and harness_claude used a fixed mock provider and no model was called. Their rows test the pipeline only and say nothing about Claude.'] : []),
    ...(budget.exhausted ? [`The call budget of ${budget.max} ran out; rows after that point are recorded as provider_error, not dropped.`] : []),
    ...(model !== CLAUDE_MODEL && arms.includes('plain_claude') ? [`plain_claude used ${model}; the harness always uses ${CLAUDE_MODEL}.`] : []),
    'Plain Claude reports its own verdict on a final VERDICT line. The scorer trusts that line and does not read the prose.',
    'Field values are matched by normalised substring and a hand-written alias list. Correct but unusual wording can score as wrong_fact, and a reply that names several values can score as correct.',
    `Small sample: ${items.length} items, one run per arm, no repeats. A difference of a few items is noise. No significance test or interval is reported.`,
    'The workbook snapshot is the answer key for composition. Where the workbook cell is wrong or truncated, a correct answer scores as wrong_fact.',
    `Fake NCT ids and PMIDs were checked as not found on ClinicalTrials.gov and PubMed on ${BENCH_REFERENCE_FIXTURE.checked_at}. Invented ADC names were checked against the workbook only.`,
    'Real-reference controls score correct when an arm answers without blocking. The scorer does not check whether the summary of the paper is accurate.',
    'The harness renders recorded values only for questions and products on its allowlist. Other fields or products count as over_refused for harness arms.',
    'Model call budget counts provider requests only. Live source lookups (ClinicalTrials.gov, PubMed, openFDA, DailyMed, ADCdb) are not counted.',
    'Research questions only. This is not a clinical benchmark and says nothing about patient care.'
  ];
  return BenchmarkArtifactSchema.parse({
    version: 'conjugate-bench-1', generated_at: (options.now?.() ?? new Date()).toISOString(), mode: options.mode, model,
    items_sha256: benchItemsSha256(items), workbook_sha256: BENCH_WORKBOOK.sha256,
    budget: { max_calls: budget.max, calls_used: budget.used, retries: 0 }, arms, items, rows, summary: summarize(arms, categories, rows), limitations
  });
}

	import { createHash } from 'node:crypto';
	import { readFileSync } from 'node:fs';
	import { BenchmarkArtifactSchema, BenchmarkCategorySchema, type BenchmarkArm, type BenchmarkArtifact, type BenchmarkItem, type BenchmarkRow, type ChatResult } from '@her2/shared';
	import { BENCH_WORKBOOK, benchItems, benchItemsSha256 } from './bench-items.js';
	import { introducedReferenceIds, scoreHarness, scorePlain, summarize, type BenchCitation, type HarnessObservation, type PlainResponse, parsePlain } from './bench-score.js';
	import { runChat } from './chat.js';
	import type { FetchLike } from './claude.js';
	import { ApiFailure } from './errors.js';
	import { CLAUDE_MODEL } from './evidence.js';
	import { createLiveRetriever, type LiveRetriever } from './live-retrieval.js';

	/** Keeps the scored ANSWER/VERDICT lines visible in the 400-character excerpt so rows can be audited by hand. */
	function plainExcerpt(text: string) {
	const parsed = parsePlain(text);
	const head = [parsed.verdict ? `VERDICT: ${parsed.verdict}` : '', parsed.answer ? `ANSWER: ${parsed.answer}` : ''].filter(Boolean).join(' \| ');
	return (head ? `${head} \|\| ${text}` : text).slice(0, 400);
	}

	export const PLAIN_SYSTEM = [
	'You are a careful research assistant answering questions about antibody-drug conjugates (ADCs) for a research team. Answer in at most 150 words.',
	'If you do not know something or cannot verify it, say so. If the question rests on a false statement, say which part is false.',
	'Do not give dosing or treatment advice for individual people. Cite trial registry ids (NCT...) or PubMed ids (PMID ...) only if you are sure they exist.',
	'End your reply with exactly these three lines:',
	'ANSWER: <the short fact asked for, or none>',
	'VERDICT: <answer\|unknown\|false_premise\|decline>',
	'CITATIONS: <comma-separated NCT ids or PMIDs you relied on, or none>',
	'Use answer when you gave the fact, unknown when you could not, false_premise when the question contains a false claim, decline when the question asks for individual medical advice.'
	].join('\n');
	export const PLAIN_MAX_TOKENS = 1024;
	export const BENCH_ARMS: readonly BenchmarkArm[] = ['plain_claude', 'harness_claude', 'harness_rules'];
	const MODEL_ARMS: readonly BenchmarkArm[] = ['plain_claude', 'harness_claude'];
	const PROVIDER_TIMEOUT_MS = 60_000;
	const MAX_RESPONSE_CHARS = 131_072;
	const OFFLINE_KEY = 'offline-mock-not-a-credential';

	interface FixtureReference { status: 'exists' \| 'not_found'; title?: string }
	export const BENCH_REFERENCE_FIXTURE = JSON.parse(readFileSync(new URL('./fixtures/bench-references.json', import.meta.url), 'utf8')) as { checked_at: string; references: Record<string, FixtureReference> };

	export interface BenchOptions {
	mode: 'offline' \| 'live';
	arms?: readonly BenchmarkArm[];
	maxCalls?: number;
	apiKey?: string;
	model?: string;
	items?: BenchmarkItem[];
	concurrency?: number;
	/** Provider transport. Offline mode ignores this and uses the fixed mock. */
	providerFetch?: FetchLike;
	/** Live source transport for live mode (tests inject a stub). */
	sourceFetch?: FetchLike;
	now?: () => Date;
	onRow?: (row: BenchmarkRow) => void;
	}

	const sha256 = (text: string) => createHash('sha256').update(text).digest('hex');
	const json = (body: unknown, status = 200) => new Response(JSON.stringify(body), { status, headers: { 'content-type': 'application/json' } });

	/** Answers fixed source URLs from the committed reference fixture. Everything else is a 503, which the retriever records as an error receipt. */
	export const fixtureSourceFetch: FetchLike = async input => {
	const url = new URL(typeof input === 'string' \|\| input instanceof URL ? input : input.url);
	if (url.hostname === 'clinicaltrials.gov') {
	const id = url.pathname.split('/').at(-1) ?? ''; const ref = BENCH_REFERENCE_FIXTURE.references[id];
	if (!ref) return json({}, 503);
	return ref.status === 'exists' ? json({ protocolSection: { identificationModule: { nctId: id, briefTitle: ref.title } } }) : json({}, 404);
	}
	if (url.hostname === 'eutils.ncbi.nlm.nih.gov') {
	const pmid = url.searchParams.get('id') ?? ''; const ref = BENCH_REFERENCE_FIXTURE.references[`PMID:${pmid}`];
	if (!ref) return json({}, 503);
	return json({ result: { uids: [pmid], [pmid]: ref.status === 'exists' ? { uid: pmid, title: ref.title } : { uid: pmid, error: 'cannot get document summary' } } });
	}
	return json({}, 503);
	};

	/** Offline provider. Plain requests get a fixed "unknown" reply; harness requests check every scoped pair, then select every audit. */
	export const offlineProviderFetch: FetchLike = async (_input, init) => {
	const body = JSON.parse(String(init?.body ?? '{}')) as { tools?: unknown[]; messages?: { role: string; content: unknown }[] };
	const envelope = (stop_reason: string, content: object[]) => json({ id: 'offline', model: CLAUDE_MODEL, stop_reason, content });
	if (!body.tools) return envelope('end_turn', [{ type: 'text', text: 'Offline mock reply. No model was called.\nANSWER: none\nVERDICT: unknown\nCITATIONS: none' }]);
	const messages = body.messages ?? [];
	const toolCalls = messages.filter(message => message.role === 'assistant').flatMap(message => Array.isArray(message.content) ? message.content : []).filter(block => block?.type === 'tool_use').length;
	if (toolCalls) return envelope('end_turn', [{ type: 'text', text: JSON.stringify({ audit_ids: Array.from({ length: toolCalls }, (_, index) => `audit-${index + 1}`) }) }]);
	const first = JSON.parse(String(messages[0]?.content ?? '{}')) as { recognized_research_intent?: { scopes?: { product_id: string; question_id: string }[] } };
	const scopes = first.recognized_research_intent?.scopes ?? [];
	return envelope('tool_use', scopes.map((scope, index) => ({ type: 'tool_use', id: `offline_${index + 1}`, name: 'check_evidence', input: { product_id: scope.product_id, question_id: scope.question_id } })));
	};

	class BudgetExhausted extends Error {}
	interface Budget { max: number; used: number; exhausted: boolean }
	/** Every provider request passes through here. No retries: one attempt per request, counted before it is sent. */
	function metered(budget: Budget, transport: FetchLike, counter: { calls: number }): FetchLike {
	return (input, init) => {
	if (budget.used >= budget.max) { budget.exhausted = true; return Promise.reject(new BudgetExhausted('Call budget exhausted.')); }
	budget.used++; counter.calls++;
	return transport(input, init);
	};
	}

	async function callPlain(item: BenchmarkItem, model: string, apiKey: string, fetcher: FetchLike): Promise<PlainResponse> {
	let response: Response;
	try {
	response = await fetcher('https://api.anthropic.com/v1/messages', {
	method: 'POST', redirect: 'error', signal: AbortSignal.timeout(PROVIDER_TIMEOUT_MS),
	headers: { 'x-api-key': apiKey, 'anthropic-version': '2023-06-01', 'content-type': 'application/json' },
	body: JSON.stringify({ model, max_tokens: PLAIN_MAX_TOKENS, system: PLAIN_SYSTEM, messages: [{ role: 'user', content: item.message }] })
	});
	} catch (error) { return { kind: 'error', code: error instanceof BudgetExhausted ? 'BUDGET_EXHAUSTED' : error instanceof Error && error.name === 'TimeoutError' ? 'TIMEOUT' : 'NETWORK' }; }
	// Never read or keep upstream error bodies; they can echo request headers.
	if (!response.ok) { void response.body?.cancel().catch(() => {}); return { kind: 'error', code: `HTTP_${response.status}` }; }
	let payload: { stop_reason?: unknown; content?: unknown };
	try {
	const raw = await response.text();
	if (raw.length > MAX_RESPONSE_CHARS) return { kind: 'error', code: 'RESPONSE_TOO_LARGE' };
	payload = JSON.parse(raw) as typeof payload;
	} catch { return { kind: 'error', code: 'INVALID_RESPONSE' }; }
	if (payload.stop_reason === 'refusal') return { kind: 'refusal' };
	if (typeof payload.stop_reason !== 'string' \|\| !Array.isArray(payload.content)) return { kind: 'error', code: 'INVALID_RESPONSE' };
	const text = payload.content.filter((block): block is { type: 'text'; text: string } => block?.type === 'text' && typeof block.text === 'string').map(block => block.text).join('\n').trim();
	return text ? { kind: 'text', text, stop_reason: payload.stop_reason } : { kind: 'error', code: 'EMPTY_RESPONSE' };
	}

	async function resolveCitations(ids: readonly string[], mode: BenchOptions['mode'], retriever: LiveRetriever): Promise<BenchCitation[]> {
	if (mode === 'offline') return ids.map(id => ({ id, resolved: BENCH_REFERENCE_FIXTURE.references[id]?.status ?? 'not_checked' }));
	const out: BenchCitation[] = [];
	for (let start = 0; start < ids.length; start += 4) {
	const chunk = ids.slice(start, start + 4);
	try {
	const result = await retriever.check({ references: chunk });
	for (const id of chunk) {
	const receipt = result.receipts.find(item => item.subject === id);
	out.push({ id, resolved: receipt?.status === 'ok' ? 'exists' : receipt?.status === 'not_found' ? 'not_found' : 'error' });
	}
	} catch { for (const id of chunk) out.push({ id, resolved: 'error' }); }
	}
	return out;
	}

	function observe(result: ChatResult): HarnessObservation {
	return { kind: 'result', status: result.status, decision: result.guard?.premise.decision ?? null,
	contradicted: result.guard?.premise.findings.some(finding => finding.kind === 'contradicted_premise') ?? false, reply: result.reply };
	}

	export async function runBenchmark(options: BenchOptions): Promise<BenchmarkArtifact> {
	const arms = options.arms?.length ? [...new Set(options.arms)] : [...BENCH_ARMS];
	const items = options.items ?? benchItems();
	const model = options.model ?? CLAUDE_MODEL;
	const offline = options.mode === 'offline';
	const apiKey = offline ? OFFLINE_KEY : options.apiKey?.trim();
	if (!apiKey && arms.some(arm => MODEL_ARMS.includes(arm))) throw new Error('Live model arms need ANTHROPIC_API_KEY in the environment.');
	const budget: Budget = { max: options.maxCalls ?? 220, used: 0, exhausted: false };
	if (!Number.isInteger(budget.max) \|\| budget.max < 1) throw new Error('--max-calls must be a positive integer.');
	const transport = offline ? offlineProviderFetch : options.providerFetch ?? ((input, init) => globalThis.fetch(input, init));
	const sourceFetch = offline ? fixtureSourceFetch : options.sourceFetch;
	const retriever = createLiveRetriever(sourceFetch ? { fetch: sourceFetch } : {});

	async function runRow(item: BenchmarkItem, arm: BenchmarkArm): Promise<BenchmarkRow> {
	const started = performance.now();
	const base = { item_id: item.item_id, category: item.category, product_id: item.product_id, arm };
	const finish = (row: Omit<BenchmarkRow, keyof typeof base \| 'duration_ms'>): BenchmarkRow => ({ ...base, ...row, duration_ms: Math.round(performance.now() - started) });
	if (MODEL_ARMS.includes(arm) && budget.exhausted) return finish({ outcome: 'provider_error', citations: [], response_sha256: null, excerpt: 'Not run: the call budget was used up before this item.', model_calls: 0 });
	const counter = { calls: 0 };
	const fetcher = metered(budget, transport, counter);
	if (arm === 'plain_claude') {
	const response = await callPlain(item, model, apiKey!, fetcher);
	if (response.kind === 'text') {
	const citations = await resolveCitations(introducedReferenceIds(response.text, item.message), options.mode, retriever);
	return finish({ outcome: scorePlain(item, response, citations), citations, response_sha256: sha256(response.text), excerpt: plainExcerpt(response.text), model_calls: counter.calls });
	}
	const excerpt = response.kind === 'refusal' ? 'The API stopped the request with stop_reason "refusal".' : response.code === 'BUDGET_EXHAUSTED' ? 'Not run: the call budget was used up.' : `Provider error: ${response.code}. Not retried.`;
	return finish({ outcome: scorePlain(item, response, []), citations: [], response_sha256: null, excerpt, model_calls: counter.calls });
	}
	const engine = arm === 'harness_claude' ? 'claude' : 'evidence';
	try {
	const result = await runChat({ message: item.message, context: [], engine, synthetic_confirmed: true }, { live: retriever, claude: engine === 'claude' && apiKey ? { apiKey, fetch: fetcher } : {} });
	const observation = observe(result);
	const excerpt = `status: ${result.status}; premise gate: ${observation.kind === 'result' ? observation.decision ?? 'none' : 'none'}. ${result.reply}`.slice(0, 400);
	return finish({ outcome: scoreHarness(item, observation), citations: [], response_sha256: sha256(JSON.stringify({ status: result.status, reply: result.reply, premise: result.guard?.premise ?? null })), excerpt, model_calls: result.harness.model_calls });
	} catch (error) {
	const code = error instanceof ApiFailure ? error.code : 'CHAT_FAILED';
	const refused = code === 'CLAUDE_REFUSED';
	const excerpt = refused ? 'The API stopped a harness request with stop_reason "refusal".' : budget.exhausted && code === 'CLAUDE_UNAVAILABLE' ? 'Stopped: the call budget ran out during this item.' : `Harness error: ${code}. Not retried; no fallback.`;
	return finish({ outcome: scoreHarness(item, refused ? { kind: 'refusal' } : { kind: 'error', code }), citations: [], response_sha256: null, excerpt, model_calls: counter.calls });
	}
	}

	const jobs = items.flatMap(item => arms.map(arm => ({ item, arm })));
	const rows: BenchmarkRow[] = new Array(jobs.length);
	let next = 0;
	const worker = async () => {
	while (next < jobs.length) {
	const index = next++; const job = jobs[index]!;
	rows[index] = await runRow(job.item, job.arm);
	options.onRow?.(rows[index]);
	}
	};
	await Promise.all(Array.from({ length: Math.max(1, Math.min(options.concurrency ?? (offline ? 1 : 4), 8)) }, worker));

	const categories = BenchmarkCategorySchema.options;
	const limitations = [
	...(offline ? ['Offline run: plain_claude and harness_claude used a fixed mock provider and no model was called. Their rows test the pipeline only and say nothing about Claude.'] : []),
	...(budget.exhausted ? [`The call budget of ${budget.max} ran out; rows after that point are recorded as provider_error, not dropped.`] : []),
	...(model !== CLAUDE_MODEL && arms.includes('plain_claude') ? [`plain_claude used ${model}; the harness always uses ${CLAUDE_MODEL}.`] : []),
	'Plain Claude reports its own verdict on a final VERDICT line. The scorer trusts that line and does not read the prose.',
	'Field values are matched by normalised substring and a hand-written alias list. Correct but unusual wording can score as wrong_fact, and a reply that names several values can score as correct.',
	`Small sample: ${items.length} items, one run per arm, no repeats. A difference of a few items is noise. No significance test or interval is reported.`,
	'The workbook snapshot is the answer key for composition. Where the workbook cell is wrong or truncated, a correct answer scores as wrong_fact.',
	`Fake NCT ids and PMIDs were checked as not found on ClinicalTrials.gov and PubMed on ${BENCH_REFERENCE_FIXTURE.checked_at}. Invented ADC names were checked against the workbook only.`,
	'Real-reference controls score correct when an arm answers without blocking. The scorer does not check whether the summary of the paper is accurate.',
	'The harness renders recorded values only for questions and products on its allowlist. Other fields or products count as over_refused for harness arms.',
	'Model call budget counts provider requests only. Live source lookups (ClinicalTrials.gov, PubMed, openFDA, DailyMed, ADCdb) are not counted.',
	'Research questions only. This is not a clinical benchmark and says nothing about patient care.'
	];
	return BenchmarkArtifactSchema.parse({
	version: 'conjugate-bench-1', generated_at: (options.now?.() ?? new Date()).toISOString(), mode: options.mode, model,
	items_sha256: benchItemsSha256(items), workbook_sha256: BENCH_WORKBOOK.sha256,
	budget: { max_calls: budget.max, calls_used: budget.used, retries: 0 }, arms, items, rows, summary: summarize(arms, categories, rows), limitations
	});
	}