psyclaw 0.25.1 → 0.26.0

package/dist/src/workflows/expert-review.js

@@ -0,0 +1,111 @@
+import { Type } from "typebox";
+import { Compile } from "typebox/compile";
+const Role = Type.Union([
+    Type.Literal("methodologist"),
+    Type.Literal("evidence-critic"),
+    Type.Literal("writing-editor"),
+    Type.Literal("devil-advocate"),
+    Type.Literal("ethics-reviewer"),
+    Type.Literal("reproducibility-reviewer"),
+]);
+const Finding = Type.Object({
+    id: Type.String({ minLength: 1 }),
+    severity: Type.Union([Type.Literal("block"), Type.Literal("major"), Type.Literal("minor"), Type.Literal("note")]),
+    rule: Type.String({ minLength: 1 }),
+    message: Type.String({ minLength: 1 }),
+    refs: Type.Array(Type.String()),
+    disposition: Type.Union([Type.Literal("accept"), Type.Literal("revise"), Type.Literal("reject"), Type.Literal("uncertain")]),
+}, { additionalProperties: false });
+export const ExpertReviewOpinionSchema = Type.Object({
+    schemaVersion: Type.Literal("psyclaw/expert-review-opinion/v1"),
+    runId: Type.String({ minLength: 1 }), taskId: Type.String({ minLength: 1 }), dispatchId: Type.String({ minLength: 1 }),
+    expertId: Type.String({ minLength: 1 }), role: Role,
+    outcome: Type.Union([Type.Literal("complete"), Type.Literal("blocked"), Type.Literal("uncertain")]),
+    summary: Type.String({ minLength: 1 }), findings: Type.Array(Finding), evidenceRefs: Type.Array(Type.String()),
+}, { additionalProperties: false });
+export const ExpertReviewContractSchema = Type.Object({
+    schemaVersion: Type.Literal("psyclaw/expert-review/v1"), runId: Type.String({ minLength: 1 }),
+    subject: Type.Object({ kind: Type.Union([Type.Literal("manuscript"), Type.Literal("artifact"), Type.Literal("workflow")]), ref: Type.String({ minLength: 1 }) }, { additionalProperties: false }),
+    inputRefs: Type.Array(Type.String()),
+    experts: Type.Array(Type.Object({ expertId: Type.String({ minLength: 1 }), role: Role, taskId: Type.String({ minLength: 1 }) }, { additionalProperties: false }), { minItems: 1 }),
+    requiredRoles: Type.Array(Role, { minItems: 1 }), minOpinions: Type.Integer({ minimum: 1 }), independent: Type.Literal(true),
+    output: Type.Object({ artifactPath: Type.String({ minLength: 1 }), verdictPath: Type.String({ minLength: 1 }) }, { additionalProperties: false }),
+}, { additionalProperties: false });
+export const ExpertReviewResultSchema = Type.Object({
+    schemaVersion: Type.Literal("psyclaw/expert-review-result/v1"), runId: Type.String({ minLength: 1 }),
+    verdict: Type.Union([Type.Literal("pass"), Type.Literal("blocked"), Type.Literal("uncertain")]),
+    opinions: Type.Array(ExpertReviewOpinionSchema), findings: Type.Array(Finding), unresolvedRoles: Type.Array(Role), blockReasons: Type.Array(Type.String()),
+}, { additionalProperties: false });
+const contractValidator = Compile(ExpertReviewContractSchema);
+const opinionValidator = Compile(ExpertReviewOpinionSchema);
+const resultValidator = Compile(ExpertReviewResultSchema);
+export function validateExpertReviewContract(value) {
+    if (!contractValidator.Check(value))
+        throw new Error("invalid psyclaw/expert-review/v1 contract");
+    const contract = value;
+    const expertRoles = new Set(contract.experts.map((expert) => expert.role));
+    if (contract.minOpinions > contract.experts.length)
+        throw new Error("minOpinions exceeds configured experts");
+    if (contract.requiredRoles.some((role) => !expertRoles.has(role)))
+        throw new Error("required role has no configured expert");
+    if (new Set(contract.requiredRoles).size !== contract.requiredRoles.length)
+        throw new Error("duplicate required role");
+    if (new Set(contract.experts.map((expert) => expert.expertId)).size !== contract.experts.length)
+        throw new Error("duplicate expertId");
+    return contract;
+}
+export function validateExpertReviewOpinion(value) {
+    if (!opinionValidator.Check(value))
+        throw new Error("invalid psyclaw/expert-review-opinion/v1 opinion");
+    return value;
+}
+export function validateExpertReviewResult(value) {
+    if (!resultValidator.Check(value))
+        throw new Error("invalid psyclaw/expert-review-result/v1 result");
+    return value;
+}
+/**
+ * Deterministically combines independent opinions. It does not infer a
+ * finding from a vote and never upgrades an uncertain or blocked opinion.
+ */
+export function aggregateExpertReview(contractValue, opinionValues) {
+    const contract = validateExpertReviewContract(contractValue);
+    const opinions = opinionValues.map(validateExpertReviewOpinion);
+    const blockReasons = [];
+    const configured = new Map(contract.experts.map((expert) => [expert.expertId, expert]));
+    const seen = new Set();
+    for (const opinion of opinions) {
+        if (opinion.runId !== contract.runId)
+            blockReasons.push(`opinion ${opinion.expertId} belongs to another run`);
+        const expert = configured.get(opinion.expertId);
+        if (!expert)
+            blockReasons.push(`unconfigured expert: ${opinion.expertId}`);
+        else if (expert.role !== opinion.role || expert.taskId !== opinion.taskId)
+            blockReasons.push(`opinion identity mismatch: ${opinion.expertId}`);
+        if (seen.has(opinion.expertId))
+            blockReasons.push(`duplicate opinion: ${opinion.expertId}`);
+        seen.add(opinion.expertId);
+        if (opinion.outcome === "blocked")
+            blockReasons.push(`expert blocked: ${opinion.expertId}`);
+    }
+    const roles = new Set(opinions.map((opinion) => opinion.role));
+    const unresolvedRoles = contract.requiredRoles.filter((role) => !roles.has(role));
+    if (opinions.length < contract.minOpinions)
+        blockReasons.push("minimum opinion count not met");
+    if (unresolvedRoles.length > 0)
+        blockReasons.push(`missing required roles: ${unresolvedRoles.join(", ")}`);
+    const findings = opinions.flatMap((opinion) => opinion.findings);
+    if (findings.some((finding) => finding.severity === "block"))
+        blockReasons.push("blocking finding reported");
+    const uncertain = opinions.some((opinion) => opinion.outcome === "uncertain") || findings.some((finding) => finding.disposition === "uncertain");
+    return {
+        schemaVersion: "psyclaw/expert-review-result/v1",
+        runId: contract.runId,
+        verdict: blockReasons.length > 0 ? "blocked" : uncertain ? "uncertain" : "pass",
+        opinions,
+        findings,
+        unresolvedRoles,
+        blockReasons,
+    };
+}
+//# sourceMappingURL=expert-review.js.map

package/dist/src/workflows/expert-review.js.map

@@ -0,0 +1 @@
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package/dist/src/workflows/institutional-fulltext.d.ts

@@ -0,0 +1,16 @@
+import type { InstitutionalRequestPlan, LiteratureRequestMode, MetadataCandidate, VerifiedFulltextRecord } from "../literature/contracts.js";
+import { type WorkflowResult, type WorkflowSpec } from "./spec.js";
+export declare const institutionalFulltextSpec: WorkflowSpec;
+export declare function runInstitutionalFulltext(root: string, identifier?: string): Promise<WorkflowResult>;
+export declare function recordVerifiedInstitutionalFulltext(root: string, options: {
+    path: string;
+    expected: MetadataCandidate;
+    observed: MetadataCandidate;
+    approved: boolean;
+    retrievedAt?: string;
+}): Promise<VerifiedFulltextRecord>;
+export declare function makeInstitutionalRequestPlan(target: string, options?: {
+    mode?: LiteratureRequestMode;
+    apiUrl?: string;
+    allowedDomains?: string[];
+}): InstitutionalRequestPlan;

package/dist/src/workflows/institutional-fulltext.js

@@ -0,0 +1,110 @@
+import { readFile } from "node:fs/promises";
+import { basename, resolve } from "node:path";
+import { appendEvidence, readProject } from "../research/ledger.js";
+import { assertSafeProjectPath } from "../project/paths.js";
+import { crossCheckMetadata, detectFulltext, sha256Bytes } from "../literature/metadata.js";
+import { allParadigms, finalizeWorkflow } from "./spec.js";
+export const institutionalFulltextSpec = {
+    id: "institutional-fulltext",
+    version: "1.0.0",
+    description: "Prepare an auditable, human-approved browser workflow for retrieving institutionally authorized full text.",
+    paradigms: allParadigms,
+    steps: [
+        { id: "identify", role: "researcher", effect: "read", description: "normalize the DOI, publisher URL, or title supplied by the researcher" },
+        { id: "browse", role: "researcher", effect: "read", description: "use the user's already authenticated browser session" },
+        { id: "approve-download", role: "verifier", effect: "write", description: "ask for confirmation before downloading a licensed full text" },
+        { id: "validate", role: "verifier", effect: "read", description: "verify PDF signature, title/DOI, size, and SHA-256" },
+        { id: "ledger", role: "writer", effect: "write", description: "import the verified local PDF as evidence" },
+    ],
+    requiredArtifacts: ["institutional-fulltext-plan.json", "institutional-fulltext-plan.md"],
+};
+export async function runInstitutionalFulltext(root, identifier = "") {
+    const project = await readProject(root);
+    const target = identifier.trim() || project.goal;
+    const isUrl = /^https?:\/\//i.test(target);
+    const isDoi = /^10\.\d{4,9}\//i.test(target);
+    const plan = {
+        schemaVersion: "psyclaw/institutional-fulltext-plan/v1",
+        documentVersion: "1.0.0",
+        target: { value: target, kind: isUrl ? "publisher-url" : isDoi ? "doi" : "title-or-query" },
+        bridge: {
+            adapter: "playwright-mcp",
+            mode: "existing-chrome-tab",
+            credentialPolicy: "user-authenticated-session-only",
+            network: "publisher-domain-only",
+        },
+        steps: [
+            { id: "identify", action: "resolve DOI/title and verify publisher page" },
+            { id: "authenticate", action: "user completes institutional login, VPN, or proxy in the visible browser" },
+            { id: "confirm", action: "human confirms the exact article and download action" },
+            { id: "download", action: "save PDF under data/clean or an approved evidence staging path" },
+            { id: "validate", action: "check PDF magic bytes, non-HTML content, title/DOI match, size, and SHA-256" },
+            { id: "record", action: "import verified file with psyclaw evidence add and retain source receipt" },
+        ],
+        stopConditions: [
+            "login page, CAPTCHA, or access denied",
+            "publisher page does not match the requested work",
+            "download is HTML, truncated, or hash changes",
+            "the action would bypass access controls or violate the user's authorization",
+        ],
+        approval: { requiredBefore: ["download", "record"], actor: "human", status: "pending" },
+    };
+    const markdown = [
+        "# Institutional Full Text Plan",
+        "",
+        `Target: ${target}`,
+        `Bridge: ${plan.bridge.adapter} (${plan.bridge.mode})`,
+        "",
+        "## Human Gate",
+        "",
+        "The user must complete institutional authentication in the visible browser and confirm the exact article before download.",
+        "",
+        "## Steps",
+        "",
+        ...plan.steps.map((step, index) => `${index + 1}. **${step.id}** — ${step.action}`),
+        "",
+        "## Stop Conditions",
+        "",
+        ...plan.stopConditions.map((item) => `- ${item}`),
+        "",
+        "## Next Action",
+        "",
+        "Open the plan in the workbench, connect the approved browser bridge, and request human confirmation before the download step.",
+        "",
+    ].join("\n");
+    return finalizeWorkflow(root, institutionalFulltextSpec, {
+        gates: [{ gateId: "institutional-fulltext:human-approval", ok: false, severity: "block", reason: "human must confirm the authenticated article and download" }],
+        outputs: [
+            { path: "institutional-fulltext-plan.json", contents: `${JSON.stringify(plan, null, 2)}\n` },
+            { path: "institutional-fulltext-plan.md", contents: markdown },
+        ],
+        completed: ["target normalized", "browser bridge and validation plan prepared"],
+    });
+}
+export async function recordVerifiedInstitutionalFulltext(root, options) {
+    if (!options.approved)
+        throw new Error("human approval is required before ledger record");
+    const safe = await assertSafeProjectPath(root, options.path);
+    const bytes = await readFile(safe);
+    const contentType = detectFulltext(bytes);
+    if (contentType === "unknown")
+        throw new Error("full text is neither PDF nor HTML");
+    const crossCheck = crossCheckMetadata(options.expected, options.observed);
+    if (!crossCheck.match)
+        throw new Error(`metadata cross-check failed: ${crossCheck.reasons.join("; ")}`);
+    const hash = sha256Bytes(bytes);
+    const evidence = { id: `institutional:${hash.slice(0, 16)}`, source: { kind: "file", locator: resolve(root, options.path), title: options.observed.title ?? basename(options.path) }, level: "fulltext", retrievedAt: options.retrievedAt ?? new Date().toISOString(), sha256: hash, accessStatus: "verified", locators: [{ kind: "file", value: options.path }, ...(crossCheck.normalizedDoi ? [{ kind: "doi", value: crossCheck.normalizedDoi }] : [])] };
+    await appendEvidence(root, evidence);
+    return { evidence, crossCheck, contentType, sha256: hash, approval: "approved" };
+}
+export function makeInstitutionalRequestPlan(target, options = {}) {
+    const value = target.trim();
+    const doi = /^10\.\d{4,9}\//i.test(value);
+    const url = /^https?:\/\//i.test(value);
+    const mode = options.mode ?? "browser";
+    const plan = { schemaVersion: "psyclaw/institutional-request-plan/v1", mode, target: { value, kind: url ? "publisher-url" : doi ? "doi" : "title-or-query" }, allowedDomains: options.allowedDomains ?? [], approval: { required: true, before: ["network", "download", "ledger-record"], status: "pending" }, stopConditions: ["authentication, CAPTCHA, or access denied", "domain is not allowlisted", "request would bypass access controls", "response is HTML login page or metadata does not match"] };
+    if (mode === "api")
+        plan.api = { method: "GET", url: options.apiUrl ?? value, headers: { Accept: "application/pdf, text/html, application/json" }, response: "pdf-or-html" };
+    return plan;
+}
+//# sourceMappingURL=institutional-fulltext.js.map

package/dist/src/workflows/institutional-fulltext.js.map

@@ -0,0 +1 @@
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package/dist/src/workflows/literature-review.d.ts

@@ -0,0 +1,3 @@
+import { type WorkflowResult, type WorkflowSpec } from "./spec.js";
+export declare const literatureReviewSpec: WorkflowSpec;
+export declare function runLiteratureReview(root: string): Promise<WorkflowResult>;

package/dist/src/workflows/literature-review.js

@@ -0,0 +1,76 @@
+import { checkEvidenceSufficiency } from "../core/evidence-policy.js";
+import { loadLedger, readProject } from "../research/ledger.js";
+import { buildKnowledgeMap } from "../knowledge-map/index.js";
+import { allParadigms, finalizeWorkflow } from "./spec.js";
+export const literatureReviewSpec = {
+    id: "literature-review",
+    version: "1.0.0",
+    description: "Aggregate the evidence ledger into a review matrix with conflicts and gaps.",
+    paradigms: allParadigms,
+    steps: [
+        { id: "capture", role: "researcher", effect: "read", description: "load sources and claims" },
+        { id: "audit", role: "critic", effect: "read", description: "evidence sufficiency and conflict disclosure" },
+        { id: "write", role: "writer", effect: "write", description: "write review matrix and markdown" },
+    ],
+    requiredArtifacts: ["literature-review.md", "review-matrix.json", "knowledge-map.json"],
+};
+export async function runLiteratureReview(root) {
+    const project = await readProject(root);
+    const ledger = await loadLedger(root);
+    const gates = checkEvidenceSufficiency({ ...ledger, paradigm: project.paradigm });
+    if (ledger.evidence.length === 0) {
+        gates.push({ gateId: "review:sources", ok: false, severity: "block", reason: "no sources recorded" });
+    }
+    const matrix = {
+        schemaVersion: "psyclaw/review-matrix/v1",
+        sources: ledger.evidence.map((item) => ({
+            id: item.id,
+            locator: item.source.locator,
+            level: item.level,
+            accessStatus: item.accessStatus,
+        })),
+        claims: ledger.claims.map((item) => ({
+            id: item.id,
+            kind: item.kind,
+            status: item.status,
+            evidenceIds: item.evidenceIds,
+        })),
+        conflicts: ledger.links
+            .filter((link) => link.relation === "contradicts")
+            .map((link) => ({ claimId: link.claimId, evidenceId: link.evidenceId })),
+        gaps: gates.filter((gate) => !gate.ok).map((gate) => gate.reason),
+    };
+    const knowledgeMap = buildKnowledgeMap(ledger.evidence, ledger.claims);
+    const markdown = [
+        "# Literature Review",
+        "",
+        `Research goal: ${project.goal}`,
+        "",
+        "## Sources",
+        "",
+        ...(matrix.sources.length ? matrix.sources.map((item) => `- [${item.level}] ${item.locator}`) : ["- None"]),
+        "",
+        "## Claims",
+        "",
+        ...(matrix.claims.length ? matrix.claims.map((item) => `- (${item.kind}) ${item.status}: ${item.id}`) : ["- None"]),
+        "",
+        "## Conflicts",
+        "",
+        ...(matrix.conflicts.length ? matrix.conflicts.map((item) => `- ${item.claimId} vs ${item.evidenceId}`) : ["- None"]),
+        "",
+        "## Gaps",
+        "",
+        ...(matrix.gaps.length ? matrix.gaps.map((item) => `- ${item}`) : ["- None"]),
+        "",
+    ].join("\n");
+    return finalizeWorkflow(root, literatureReviewSpec, {
+        gates,
+        outputs: [
+            { path: "literature-review.md", contents: markdown },
+            { path: "review-matrix.json", contents: `${JSON.stringify(matrix, null, 2)}\n` },
+            { path: "knowledge-map.json", contents: `${JSON.stringify(knowledgeMap, null, 2)}\n` },
+        ],
+        completed: ["sources loaded", "claims aggregated", "conflicts and gaps disclosed"],
+    });
+}
+//# sourceMappingURL=literature-review.js.map

package/dist/src/workflows/literature-review.js.map

@@ -0,0 +1 @@
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package/dist/src/workflows/meta-analysis.d.ts

@@ -0,0 +1,38 @@
+import { type StageRunner } from "../run.js";
+import { type WorkflowResult, type WorkflowSpec } from "./spec.js";
+export declare const metaAnalysisSpec: WorkflowSpec;
+export interface MetaStudy {
+    id: string;
+    title: string;
+    authors: string[];
+    year?: number;
+    venue?: string;
+    doi?: string;
+    citations?: number;
+}
+/** Search OpenAlex for studies matching the target (real network; injectable for tests). */
+export declare function searchOpenAlex(target: string, nStudies: number, fetchFn?: typeof fetch): Promise<MetaStudy[]>;
+export interface EffectRow {
+    studyId: string;
+    effectSize: number;
+    standardError: number;
+    n?: number;
+}
+/** Parse a CSV with at least `study_id,effect_size,standard_error`. */
+export declare function parseEffectCsv(text: string): EffectRow[];
+export declare function loadEffectDataset(root: string): Promise<EffectRow[] | undefined>;
+/** R metafor script that computes the random-effects model, I², Egger's test, and the forest plot. */
+export declare function metaforScript(datasetPath: string): string;
+export interface MetaAnalysisOptions {
+    target: string;
+    nStudies: number;
+    fetchFn?: typeof fetch;
+    runner?: StageRunner;
+}
+/**
+ * Real meta-analysis pipeline. Statistics are never computed in core: the
+ * audit stage writes an R (metafor) script and the brief records what was
+ * found and what must run externally. Effect sizes come from the project's
+ * dataset; without one the workflow blocks honestly instead of faking numbers.
+ */
+export declare function runMetaAnalysis(root: string, options: MetaAnalysisOptions): Promise<WorkflowResult>;

package/dist/src/workflows/meta-analysis.js

@@ -0,0 +1,185 @@
+import { readFile } from "node:fs/promises";
+import { join } from "node:path";
+import { sha256Text } from "../core/hash.js";
+import { appendJsonlIfMissing, atomicWriteFile } from "../project/jsonl.js";
+import { projectPaths } from "../project/paths.js";
+import { readProject } from "../research/ledger.js";
+import { createStageRunner } from "../run.js";
+import { finalizeWorkflow } from "./spec.js";
+export const metaAnalysisSpec = {
+    id: "meta-analysis",
+    version: "1.0.0",
+    description: "Systematic meta-analysis: literature intake, effect-size dataset contract, R metafor audit, brief.",
+    paradigms: ["meta-analysis"],
+    steps: [
+        { id: "intake", role: "researcher", effect: "read", description: "search OpenAlex for studies" },
+        { id: "capture", role: "analyst", effect: "read", description: "bind the effect-size dataset contract" },
+        { id: "audit", role: "analyst", effect: "write", description: "delegate metafor audit (I², Egger funnel)" },
+        { id: "brief", role: "writer", effect: "write", description: "write the report and ledger entry" },
+    ],
+    requiredArtifacts: ["meta-analysis.json", "meta-analysis.md"],
+};
+/** Search OpenAlex for studies matching the target (real network; injectable for tests). */
+export async function searchOpenAlex(target, nStudies, fetchFn = fetch) {
+    const perPage = Math.min(50, Math.max(1, nStudies));
+    const url = `https://api.openalex.org/works?search=${encodeURIComponent(target)}&per-page=${perPage}&mailto=psyclaw@example.org`;
+    const response = await fetchFn(url, { signal: AbortSignal.timeout(15_000) });
+    if (!response.ok)
+        throw new Error(`OpenAlex 检索失败 (${response.status})`);
+    const body = await response.json();
+    return (body.results ?? []).slice(0, nStudies).map((item, index) => ({
+        id: `study_${index + 1}`,
+        title: item.title ?? "untitled",
+        authors: (item.authorships ?? []).map((entry) => entry.author?.display_name ?? "?").slice(0, 10),
+        ...(item.publication_year === undefined ? {} : { year: item.publication_year }),
+        ...(item.host_venue?.display_name ? { venue: item.host_venue.display_name } : {}),
+        ...(item.doi ? { doi: item.doi } : {}),
+        ...(item.cited_by_count === undefined ? {} : { citations: item.cited_by_count }),
+    }));
+}
+/** Parse a CSV with at least `study_id,effect_size,standard_error`. */
+export function parseEffectCsv(text) {
+    const rows = [];
+    const lines = text.split(/\r?\n/).filter((line) => line.trim());
+    if (lines.length === 0)
+        return rows;
+    const header = lines[0].split(",").map((cell) => cell.trim().toLowerCase());
+    // Accept the canonical names plus common shorthand (study, effect, se/g/d).
+    const ALIASES = {
+        study_id: ["study_id", "study", "id"],
+        effect_size: ["effect_size", "effect", "es", "g", "d"],
+        standard_error: ["standard_error", "se", "std_error", "std_err"],
+    };
+    const indexOf = (name) => {
+        const aliases = ALIASES[name] ?? [name];
+        return header.findIndex((cell) => aliases.includes(cell) || cell.endsWith(name));
+    };
+    const studyIdx = indexOf("study_id");
+    const effectIdx = indexOf("effect_size");
+    const seIdx = indexOf("standard_error");
+    if (studyIdx < 0 || effectIdx < 0 || seIdx < 0)
+        return rows;
+    for (const line of lines.slice(1)) {
+        const cells = line.split(",").map((cell) => cell.trim());
+        const effectSize = Number(cells[effectIdx]);
+        const standardError = Number(cells[seIdx]);
+        if (!Number.isFinite(effectSize) || !Number.isFinite(standardError) || standardError <= 0)
+            continue;
+        const n = Number(cells[header.indexOf("n")]);
+        rows.push({
+            studyId: cells[studyIdx] ?? `study_${rows.length + 1}`,
+            effectSize,
+            standardError,
+            ...(Number.isFinite(n) && n > 0 ? { n } : {}),
+        });
+    }
+    return rows;
+}
+export async function loadEffectDataset(root) {
+    const candidates = ["data/clean/effects.csv", "analysis/outputs/effects.csv", "outputs/effects.csv"];
+    for (const candidate of candidates) {
+        try {
+            const rows = parseEffectCsv(await readFile(join(root, candidate), "utf8"));
+            if (rows.length > 0)
+                return rows;
+        }
+        catch { /* try next */ }
+    }
+    return undefined;
+}
+/** R metafor script that computes the random-effects model, I², Egger's test, and the forest plot. */
+export function metaforScript(datasetPath) {
+    return [
+        "# metafor.R — 随机效应元分析（委托 R 执行；psyclaw 不在核心计算统计量）",
+        "suppressMessages(library(metafor))",
+        `d <- read.csv("${datasetPath.replaceAll("\\", "/")}", stringsAsFactors = FALSE)`,
+        "fit <- rma(yi = d$effect_size, vi = d$standard_error^2, method = \"REML\")",
+        'cat(sprintf("I2=%.1f%%\\n", fit$I2))',
+        'cat(sprintf("k=%d\\n", fit$k))',
+        'res <- regtest(fit, predictor = "sei")',
+        'cat(sprintf("egger_p=%.3f\\n", res$pval))',
+        'dir.create("outputs/figures", recursive = TRUE, showWarnings = FALSE)',
+        'png("outputs/figures/forest.png", width = 800, height = 480, res = 110)',
+        "forest(fit)",
+        "dev.off()",
+        'dir.create("analysis/outputs", recursive = TRUE, showWarnings = FALSE)',
+        'saveRDS(fit, "analysis/outputs/meta_fit.rds")',
+        "",
+    ].join("\n");
+}
+/**
+ * Real meta-analysis pipeline. Statistics are never computed in core: the
+ * audit stage writes an R (metafor) script and the brief records what was
+ * found and what must run externally. Effect sizes come from the project's
+ * dataset; without one the workflow blocks honestly instead of faking numbers.
+ */
+export async function runMetaAnalysis(root, options) {
+    const runner = options.runner ?? createStageRunner();
+    const project = await readProject(root);
+    const gates = [];
+    const studies = await runner.stage("intake", `检索 OpenAlex 数据库并提取 "${options.target}" 的实证研究`, async () => searchOpenAlex(options.target, options.nStudies, options.fetchFn ?? fetch), (found) => `命中 ${found.length} 项研究，登记为证据账本条目`);
+    if (studies.length < 2) {
+        gates.push({ gateId: "meta:insufficient-studies", ok: false, severity: "block", reason: `需要至少 2 项研究，实际 ${studies.length}` });
+    }
+    const dataset = await runner.stage("capture", "绑定效应量数据集（Hedges' g / SE）", async () => loadEffectDataset(root), (rows) => rows === undefined ? "未找到数据集，进入数据契约状态" : `解析 ${rows.length} 条效应量记录`);
+    if (dataset === undefined) {
+        gates.push({ gateId: "meta:effect-data-missing", ok: false, severity: "block", reason: "缺少效应量数据集（data/clean/effects.csv：study_id,effect_size,standard_error）" });
+    }
+    const datasetPath = dataset === undefined ? null : `data/clean/effects.csv`;
+    await runner.stage("audit", "委托 R (metafor) 生成随机效应模型、I² 与 Egger 检验", async () => {
+        const scriptPath = join(root, "analysis", "scripts", "metafor.R");
+        await atomicWriteFile(scriptPath, metaforScript(datasetPath ?? "data/clean/effects.csv"));
+        return scriptPath;
+    }, (path) => `已写入 ${path}；统计由 R 执行，psyclaw 不伪造 I²/Egger 数值`);
+    const auditNote = dataset === undefined
+        ? "数据集缺失：I² 与 Egger 检验待 R 在有数据后执行"
+        : `数据集就绪（${dataset.length} 条）：运行 analysis/scripts/metafor.R 得到 I² 与 Egger p 值`;
+    await runner.stage("brief", "生成元分析报告与账本条目", async () => {
+        for (const study of studies) {
+            await appendJsonlIfMissing(projectPaths(root).evidence, {
+                id: `meta:${sha256Text(study.title).slice(0, 16)}`,
+                source: { kind: "url", locator: study.doi ?? study.id, title: study.title },
+                level: "metadata",
+                retrievedAt: new Date().toISOString(),
+                accessStatus: "partial",
+                locators: [{ kind: "url", value: study.doi ?? "" }],
+            }, (item) => item.id);
+        }
+        const summary = {
+            schemaVersion: "psyclaw/meta-analysis/v1",
+            target: options.target,
+            nStudiesRequested: options.nStudies,
+            studiesFound: studies.length,
+            effectRows: dataset?.length ?? 0,
+            audit: { delegatedTo: "R metafor", script: "analysis/scripts/metafor.R", note: auditNote },
+            generatedAt: new Date().toISOString(),
+        };
+        const markdown = [
+            `# Meta-Analysis: ${options.target}`,
+            "",
+            `- 检索：OpenAlex，目标 "${options.target}"，${studies.length} 项研究`,
+            `- 效应量数据集：${dataset === undefined ? "缺失（需 data/clean/effects.csv）" : `${dataset.length} 条`}`,
+            `- 统计：委托 R metafor（REML 随机效应、I²、Egger 漏斗回归、森林图）`,
+            `- 审计：${auditNote}`,
+            "",
+            "## 研究清单",
+            "",
+            ...studies.map((study) => `- ${study.title}${study.year ? ` (${study.year})` : ""}${study.doi ? ` · ${study.doi}` : ""}`),
+            "",
+            "> 统计数值由 R (metafor) 在数据集就绪后计算，本文件不伪造任何效应量或检验结果。",
+            "",
+        ].join("\n");
+        await atomicWriteFile(join(root, "analysis", "outputs", "meta-analysis.json"), `${JSON.stringify(summary, null, 2)}\n`);
+        await atomicWriteFile(join(root, "analysis", "outputs", "meta-analysis.md"), markdown);
+        return { studies: studies.length, rows: dataset?.length ?? 0 };
+    }, (result) => `签发 ${result.studies} 条研究账本条目，报告落盘`);
+    return finalizeWorkflow(root, metaAnalysisSpec, {
+        gates,
+        outputs: [
+            { path: "meta-analysis.md", contents: `# Meta-Analysis: ${options.target}\n\n见 analysis/outputs/meta-analysis.md\n` },
+            { path: "meta-analysis.json", contents: `${JSON.stringify({ target: options.target, studies: studies.length, effectRows: dataset?.length ?? 0 }, null, 2)}\n` },
+        ],
+        completed: ["literature intake", "effect-size contract", "metafor delegation", "report written"],
+    });
+}
+//# sourceMappingURL=meta-analysis.js.map

package/dist/src/workflows/meta-analysis.js.map

@@ -0,0 +1 @@
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