science-ai-mcp-server 0.1.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2026 Science AI Journal
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# science-ai-mcp-server
+
+[Model Context Protocol](https://modelcontextprotocol.io/) server for [Science AI Journal](https://scienceaijournal.com) tools. Use Pre-Check, AI Review, Research Gaps, Journal Recommender, Duplicate Publication Checker, and the Article Writer from inside Claude Desktop, Cursor, Cline, or any MCP-enabled client — without leaving your assistant.
+
+Full docs and screenshots: **<https://scienceaijournal.com/developers/mcp>**
+
+## Quick start (≈ 2 minutes)
+
+1. Generate an API key at <https://scienceaijournal.com/settings?section=api-keys> (free account required). Copy the `saij_…` token — you only see it once.
+2. Add this block to your Claude Desktop config file:
+
+   ```json
+   {
+     "mcpServers": {
+       "science-ai-journal": {
+         "command": "npx",
+         "args": ["-y", "science-ai-mcp-server"],
+         "env": {
+           "SCIENCE_AI_API_KEY": "saij_…paste your key…"
+         }
+       }
+     }
+   }
+   ```
+
+   Config file locations:
+   - **macOS:** `~/Library/Application Support/Claude/claude_desktop_config.json`
+   - **Windows:** `%APPDATA%\Claude\claude_desktop_config.json`
+   - **Linux:** `~/.config/Claude/claude_desktop_config.json`
+
+3. Restart Claude Desktop. The `science-ai-journal` server appears in the 🔌 tool list.
+
+The same config works in **Cursor** (`~/.cursor/mcp.json`), **Cline** (via the VS Code extension panel), and **Continue** (anywhere that supports an `mcpServers` object).
+
+## Tools
+
+| Tool | What it does | Cost |
+| --- | --- | --- |
+| `pre_check_paper` | Tier 1-5 acceptance probability from title + abstract (local FTS5, no LLM) | Free |
+| `check_duplicate_publication` | Cross-reference against CrossRef + arXiv + medRxiv + bioRxiv + Unpaywall + a 900k-paper library | Free |
+| `recommend_journals` | Ranked target journals from a 1,214-venue index, with predatory-journal flags | Free |
+| `find_research_gaps` | Synthesised gaps + most-cited + most-recent papers around your query | Credits |
+| `hakem_review_paper` | Single-agent HAKEM peer-review pass on a prepared prompt | Credits |
+| `start_writer_pipeline` / `get_writer_pipeline_status` | Drive the Article Writer pipeline from outside the wizard | Credits |
+
+## Configuration
+
+| Env var | Default | Purpose |
+| --- | --- | --- |
+| `SCIENCE_AI_API_KEY` | _required_ | Your `saij_…` token |
+| `SCIENCE_AI_BASE_URL` | `https://scienceaijournal.com` | Override for self-hosted or staging environments |
+
+## Troubleshooting
+
+- **Tools don't appear after editing config:** fully quit the host app (not just close the window) and reopen.
+- **401 unauthorized when calling a tool:** the key was wrong, revoked, or expired. Mint a fresh one at Settings → API Keys.
+- **429 rate limit on `find_research_gaps`:** you hit the 10-per-hour IP quota. Wait an hour.
+- **`npx` can't resolve the package:** ensure Node ≥ 20 and that your npm registry isn't set to a private mirror without this package yet (`npm config set registry https://registry.npmjs.org/`).
+
+## License
+
+MIT

package/dist/config.d.ts

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+/**
+ * Runtime configuration — read once at process start.
+ *
+ * stdio MCP servers run as long-lived subprocesses spawned by the host
+ * client (Claude Desktop, Cursor, …). Env vars are baked in at spawn
+ * time from the client's config file; we don't watch for changes.
+ */
+export interface ServerConfig {
+    apiKey: string;
+    baseUrl: string;
+    userAgent: string;
+    /** Default request timeout in ms; per-tool overrides allowed. */
+    requestTimeoutMs: number;
+}
+export declare function getConfig(): ServerConfig;

package/dist/config.js

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+/**
+ * Runtime configuration — read once at process start.
+ *
+ * stdio MCP servers run as long-lived subprocesses spawned by the host
+ * client (Claude Desktop, Cursor, …). Env vars are baked in at spawn
+ * time from the client's config file; we don't watch for changes.
+ */
+const DEFAULT_BASE_URL = "https://scienceaijournal.com";
+let cached = null;
+export function getConfig() {
+    if (cached)
+        return cached;
+    const apiKey = (process.env.SCIENCE_AI_API_KEY || "").trim();
+    if (!apiKey) {
+        // Fail loudly on stdout so the MCP host surfaces a useful error to the
+        // user. Without an API key every tool call would just 401, which the
+        // host UI tends to render as a generic "tool failed".
+        throw new Error("SCIENCE_AI_API_KEY is required.\n" +
+            "Generate a key at https://scienceaijournal.com/settings?section=api-keys\n" +
+            "and add it to your MCP client config under the `env` block:\n\n" +
+            '  "env": { "SCIENCE_AI_API_KEY": "saij_…" }');
+    }
+    if (!apiKey.startsWith("saij_")) {
+        throw new Error(`SCIENCE_AI_API_KEY looks malformed (expected "saij_…" prefix). Got ${apiKey.slice(0, 8)}…`);
+    }
+    const baseUrl = (process.env.SCIENCE_AI_BASE_URL || DEFAULT_BASE_URL).replace(/\/$/, "") ||
+        DEFAULT_BASE_URL;
+    const requestTimeoutMs = (() => {
+        const raw = process.env.SCIENCE_AI_REQUEST_TIMEOUT_MS;
+        if (!raw)
+            return 120_000; // 2 min — covers HAKEM agent calls
+        const n = Number(raw);
+        return Number.isFinite(n) && n > 0 ? Math.min(n, 600_000) : 120_000;
+    })();
+    cached = {
+        apiKey,
+        baseUrl,
+        userAgent: `science-ai-mcp-server/0.1.0 (+${DEFAULT_BASE_URL}/developers/mcp)`,
+        requestTimeoutMs,
+    };
+    return cached;
+}
+//# sourceMappingURL=config.js.map

package/dist/config.js.map

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package/dist/http.d.ts

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+/**
+ * Minimal HTTP client for talking to the Science AI Journal app.
+ *
+ * Adds the Bearer auth header on every request, applies a generous-but-
+ * bounded timeout, normalises non-2xx responses into thrown Errors with
+ * useful messages, and parses JSON responses.
+ *
+ * Kept dependency-free — Node 20+ ships a global fetch + AbortController,
+ * which is everything we need.
+ */
+export interface RequestOpts {
+    method?: "GET" | "POST" | "DELETE";
+    path: string;
+    query?: Record<string, string | number | boolean | undefined>;
+    body?: unknown;
+    /** Override the per-process default. */
+    timeoutMs?: number;
+}
+export declare function request<T = unknown>(opts: RequestOpts): Promise<T>;

package/dist/http.js

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+/**
+ * Minimal HTTP client for talking to the Science AI Journal app.
+ *
+ * Adds the Bearer auth header on every request, applies a generous-but-
+ * bounded timeout, normalises non-2xx responses into thrown Errors with
+ * useful messages, and parses JSON responses.
+ *
+ * Kept dependency-free — Node 20+ ships a global fetch + AbortController,
+ * which is everything we need.
+ */
+import { getConfig } from "./config.js";
+export async function request(opts) {
+    const cfg = getConfig();
+    const url = new URL(opts.path, cfg.baseUrl);
+    if (opts.query) {
+        for (const [k, v] of Object.entries(opts.query)) {
+            if (v === undefined)
+                continue;
+            url.searchParams.set(k, String(v));
+        }
+    }
+    const controller = new AbortController();
+    const timeoutMs = opts.timeoutMs ?? cfg.requestTimeoutMs;
+    const t = setTimeout(() => controller.abort(), timeoutMs);
+    let res;
+    try {
+        res = await fetch(url, {
+            method: opts.method ?? (opts.body ? "POST" : "GET"),
+            headers: {
+                "Authorization": `Bearer ${cfg.apiKey}`,
+                "Accept": "application/json",
+                "User-Agent": cfg.userAgent,
+                ...(opts.body !== undefined
+                    ? { "Content-Type": "application/json" }
+                    : {}),
+            },
+            body: opts.body !== undefined ? JSON.stringify(opts.body) : undefined,
+            signal: controller.signal,
+        });
+    }
+    catch (err) {
+        clearTimeout(t);
+        if (err instanceof Error && err.name === "AbortError") {
+            throw new Error(`Request to ${url.pathname} timed out after ${timeoutMs}ms.`);
+        }
+        const msg = err instanceof Error ? err.message : String(err);
+        throw new Error(`Network error calling ${url.pathname}: ${msg}`);
+    }
+    finally {
+        clearTimeout(t);
+    }
+    if (!res.ok) {
+        let detail = "";
+        try {
+            detail = (await res.text()).slice(0, 500);
+        }
+        catch {
+            /* ignore */
+        }
+        if (res.status === 401) {
+            throw new Error(`401 Unauthorized — your SCIENCE_AI_API_KEY is missing, revoked, or expired. ` +
+                `Generate a fresh key at ${cfg.baseUrl}/settings?section=api-keys`);
+        }
+        if (res.status === 429) {
+            const retryAfter = res.headers.get("retry-after");
+            throw new Error(`429 Rate Limit — too many requests. ${retryAfter ? `Retry after ${retryAfter}s.` : "Wait a minute and try again."}`);
+        }
+        throw new Error(`HTTP ${res.status} from ${url.pathname}${detail ? `: ${detail}` : ""}`);
+    }
+    // Some routes return text/event-stream or plain text; we only do JSON here.
+    const ct = res.headers.get("content-type") || "";
+    if (!ct.includes("application/json")) {
+        const text = await res.text();
+        // Best-effort JSON parse; if it isn't JSON, surface as text.
+        try {
+            return JSON.parse(text);
+        }
+        catch {
+            return text;
+        }
+    }
+    return (await res.json());
+}
+//# sourceMappingURL=http.js.map

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package/dist/index.d.ts

@@ -0,0 +1,13 @@
+#!/usr/bin/env node
+/**
+ * science-ai-mcp-server — stdio entrypoint.
+ *
+ * Spawned as a subprocess by Claude Desktop / Cursor / Cline. Communicates
+ * over JSON-RPC on stdin/stdout (the stdio transport). One process per
+ * MCP host; configuration comes from env vars set in the host's
+ * mcp config file (see /developers/mcp on scienceaijournal.com).
+ *
+ * Failures during config load print to stderr so the host surfaces them
+ * to the user; the process exits 1 so the host knows the server is dead.
+ */
+export {};

package/dist/index.js

@@ -0,0 +1,43 @@
+#!/usr/bin/env node
+/**
+ * science-ai-mcp-server — stdio entrypoint.
+ *
+ * Spawned as a subprocess by Claude Desktop / Cursor / Cline. Communicates
+ * over JSON-RPC on stdin/stdout (the stdio transport). One process per
+ * MCP host; configuration comes from env vars set in the host's
+ * mcp config file (see /developers/mcp on scienceaijournal.com).
+ *
+ * Failures during config load print to stderr so the host surfaces them
+ * to the user; the process exits 1 so the host knows the server is dead.
+ */
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { getConfig } from "./config.js";
+import { registerAllTools } from "./tools/index.js";
+async function main() {
+    // Validate config first. Throws with a helpful message if SCIENCE_AI_API_KEY
+    // is missing or malformed — the host surfaces stderr to the user.
+    try {
+        getConfig();
+    }
+    catch (err) {
+        const msg = err instanceof Error ? err.message : String(err);
+        process.stderr.write(`[science-ai-mcp-server] startup failed:\n${msg}\n`);
+        process.exit(1);
+    }
+    const server = new McpServer({
+        name: "science-ai-journal",
+        version: "0.1.0",
+    });
+    registerAllTools(server);
+    const transport = new StdioServerTransport();
+    await server.connect(transport);
+    // Stdio servers run until the host disconnects. The SDK handles SIGINT
+    // / pipe-close cleanly, so no extra signal wiring needed here.
+}
+main().catch((err) => {
+    const msg = err instanceof Error ? err.stack || err.message : String(err);
+    process.stderr.write(`[science-ai-mcp-server] crashed:\n${msg}\n`);
+    process.exit(1);
+});
+//# sourceMappingURL=index.js.map

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package/dist/tools/article-writer.d.ts

@@ -0,0 +1,15 @@
+/**
+ * start_writer_pipeline + get_writer_pipeline_status — /api/writer/pipeline
+ *
+ * The Article Writer pipeline is long-running (minutes per step), so we
+ * expose it as TWO MCP tools — the LLM-host orchestrates polling. Same
+ * route, different HTTP methods:
+ *
+ *   POST  /api/writer/pipeline             → enqueues a job, returns jobId
+ *   GET   /api/writer/pipeline?sessionId=…&section=… → latest job for the (session, section)
+ *
+ * The MCP wrapper exposes status under a different name so callers can
+ * tell start vs poll apart.
+ */
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerArticleWriter(server: McpServer): void;

package/dist/tools/article-writer.js

@@ -0,0 +1,156 @@
+/**
+ * start_writer_pipeline + get_writer_pipeline_status — /api/writer/pipeline
+ *
+ * The Article Writer pipeline is long-running (minutes per step), so we
+ * expose it as TWO MCP tools — the LLM-host orchestrates polling. Same
+ * route, different HTTP methods:
+ *
+ *   POST  /api/writer/pipeline             → enqueues a job, returns jobId
+ *   GET   /api/writer/pipeline?sessionId=…&section=… → latest job for the (session, section)
+ *
+ * The MCP wrapper exposes status under a different name so callers can
+ * tell start vs poll apart.
+ */
+import { z } from "zod";
+import { request } from "../http.js";
+const SECTIONS = [
+    "step_7_5",
+    "introduction",
+    "methodology",
+    "results",
+    "discussion",
+    "references",
+    "abstract",
+];
+const startShape = {
+    sessionId: z
+        .string()
+        .min(1)
+        .max(200)
+        .describe("WriterSession id you already own. Create one via the web UI at /writer first; the MCP server does not own the session-creation flow today."),
+    section: z
+        .enum(SECTIONS)
+        .optional()
+        .describe("Which section to run. Default 'step_7_5' (the code-search → adapt → verify → simulate chain)."),
+    language: z
+        .string()
+        .max(40)
+        .optional()
+        .describe("Simulation language override (python | r | matlab | ...)."),
+    force: z
+        .boolean()
+        .optional()
+        .describe("If true, abort any existing queued/running job for this (sessionId, section) and enqueue fresh."),
+};
+const statusShape = {
+    sessionId: z.string().min(1).max(200),
+    section: z.enum(SECTIONS).optional(),
+};
+export function registerArticleWriter(server) {
+    server.registerTool("start_writer_pipeline", {
+        title: "Start Article Writer Pipeline",
+        description: "Enqueue a writer-pipeline job for an existing WriterSession. " +
+            "Returns immediately with a jobId; the orchestrator-worker claims " +
+            "it within ~5 seconds. Default section is step_7_5 — the auto-chain " +
+            "that replaces the three buttons in Step 7.5. Use " +
+            "`get_writer_pipeline_status` to poll until status is 'done', 'failed', " +
+            "or 'aborted'. Uses Science AI Journal credits.",
+        inputSchema: startShape,
+    }, async (args) => {
+        const body = {
+            sessionId: args.sessionId,
+            section: args.section ?? "step_7_5",
+            force: args.force ?? false,
+        };
+        if (args.language) {
+            body.config = { language: args.language };
+        }
+        const r = await request({
+            method: "POST",
+            path: "/api/writer/pipeline",
+            body,
+        });
+        if (!r.ok) {
+            return {
+                content: [
+                    {
+                        type: "text",
+                        text: `Failed to enqueue: ${r.error ?? "(no error message)"}`,
+                    },
+                ],
+                isError: true,
+            };
+        }
+        const tail = r.alreadyQueued
+            ? " (already queued; pass force=true to supersede)"
+            : "";
+        return {
+            content: [
+                {
+                    type: "text",
+                    text: `Writer job enqueued: jobId=${r.jobId}${tail}\nPoll with get_writer_pipeline_status({ sessionId: "${args.sessionId}", section: "${args.section ?? "step_7_5"}" }).`,
+                },
+            ],
+        };
+    });
+    server.registerTool("get_writer_pipeline_status", {
+        title: "Get Article Writer Pipeline Status",
+        description: "Return the latest writer-pipeline job for a (sessionId, section). " +
+            "Use after `start_writer_pipeline` and poll every 5-10 seconds. " +
+            "Terminal statuses: 'done', 'failed', 'aborted'.",
+        inputSchema: statusShape,
+    }, async (args) => {
+        const r = await request({
+            method: "GET",
+            path: "/api/writer/pipeline",
+            query: {
+                sessionId: args.sessionId,
+                section: args.section ?? "step_7_5",
+            },
+        });
+        if (!r.ok) {
+            return {
+                content: [
+                    {
+                        type: "text",
+                        text: `Status fetch failed: ${r.error ?? "(no error message)"}`,
+                    },
+                ],
+                isError: true,
+            };
+        }
+        if (!r.job) {
+            return {
+                content: [
+                    {
+                        type: "text",
+                        text: "No job found for this (sessionId, section). Did you call start_writer_pipeline first?",
+                    },
+                ],
+            };
+        }
+        const j = r.job;
+        const lines = [];
+        lines.push(`Writer pipeline job ${j.id}`);
+        lines.push(`  Section: ${j.section}`);
+        lines.push(`  Status:  ${j.status}${j.stage ? ` (stage: ${j.stage})` : ""}`);
+        if (typeof j.progressPct === "number") {
+            const stageProgress = j.stageIdx != null && j.totalStages != null
+                ? ` — stage ${j.stageIdx}/${j.totalStages}`
+                : "";
+            lines.push(`  Progress: ${j.progressPct}%${stageProgress}`);
+        }
+        if (j.progressNote)
+            lines.push(`  Note: ${j.progressNote}`);
+        if (j.hallucination)
+            lines.push(`  Hallucination flag: ${j.hallucination}`);
+        if (j.error)
+            lines.push(`  Error: ${j.error}`);
+        if (j.queuedAt)
+            lines.push(`  Queued: ${j.queuedAt}`);
+        if (j.finishedAt)
+            lines.push(`  Finished: ${j.finishedAt}`);
+        return { content: [{ type: "text", text: lines.join("\n") }] };
+    });
+}
+//# sourceMappingURL=article-writer.js.map

package/dist/tools/article-writer.js.map

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package/dist/tools/duplicate-publication.d.ts

@@ -0,0 +1,9 @@
+/**
+ * check_duplicate_publication — POST /api/prior-publication
+ *
+ * Cross-references title + abstract (and optionally DOI) against
+ * CrossRef + arXiv + medRxiv + bioRxiv + Unpaywall + the institutional
+ * library. Returns a status, confidence, and a human-readable message.
+ */
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerDuplicatePublication(server: McpServer): void;

package/dist/tools/duplicate-publication.js

@@ -0,0 +1,62 @@
+/**
+ * check_duplicate_publication — POST /api/prior-publication
+ *
+ * Cross-references title + abstract (and optionally DOI) against
+ * CrossRef + arXiv + medRxiv + bioRxiv + Unpaywall + the institutional
+ * library. Returns a status, confidence, and a human-readable message.
+ */
+import { z } from "zod";
+import { request } from "../http.js";
+const inputShape = {
+    title: z
+        .string()
+        .min(1)
+        .max(600)
+        .describe("Paper title (required)."),
+    abstract: z
+        .string()
+        .max(20_000)
+        .optional()
+        .describe("Paper abstract — improves match accuracy."),
+    doi: z
+        .string()
+        .max(200)
+        .optional()
+        .describe("Known DOI for the paper, if any."),
+};
+export function registerDuplicatePublication(server) {
+    server.registerTool("check_duplicate_publication", {
+        title: "Check Duplicate Publication",
+        description: "Pre-submission duplicate-publication and salami-slicing check. " +
+            "Cross-references the title + abstract against CrossRef, arXiv, " +
+            "medRxiv, bioRxiv, Unpaywall, and a 900k-paper institutional " +
+            "library in ~30 seconds. Returns a status (likely_published, " +
+            "uncertain, or not_found) with a confidence score and message. " +
+            "Free. Use before submission to catch accidental duplicates or " +
+            "to confirm a preprint hasn't been formally published yet.",
+        inputSchema: inputShape,
+    }, async (args) => {
+        const result = await request({
+            method: "POST",
+            path: "/api/prior-publication",
+            body: {
+                title: args.title,
+                abstract: args.abstract,
+                doi: args.doi,
+            },
+        });
+        const lines = ["Duplicate publication check"];
+        lines.push(`  Status: ${result.status ?? "(unknown)"}`);
+        if (typeof result.confidence === "number") {
+            lines.push(`  Confidence: ${Math.round(result.confidence * 100)}%`);
+        }
+        if (result.message) {
+            lines.push(`  Detail: ${result.message}`);
+        }
+        if (result.link) {
+            lines.push(`  Link: ${result.link}`);
+        }
+        return { content: [{ type: "text", text: lines.join("\n") }] };
+    });
+}
+//# sourceMappingURL=duplicate-publication.js.map

package/dist/tools/duplicate-publication.js.map

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package/dist/tools/hakem-review.d.ts

@@ -0,0 +1,9 @@
+/**
+ * hakem_review_paper — POST /api/review/claude
+ *
+ * Single HAKEM-agent peer-review call. Text-only for MVP (vision /
+ * figure-image review deferred). The MCP boundary doesn't stream — we
+ * return the final normalised review JSON in one chunk.
+ */
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerHakemReview(server: McpServer): void;

package/dist/tools/hakem-review.js

@@ -0,0 +1,76 @@
+/**
+ * hakem_review_paper — POST /api/review/claude
+ *
+ * Single HAKEM-agent peer-review call. Text-only for MVP (vision /
+ * figure-image review deferred). The MCP boundary doesn't stream — we
+ * return the final normalised review JSON in one chunk.
+ */
+import { z } from "zod";
+import { request } from "../http.js";
+const inputShape = {
+    prompt: z
+        .string()
+        .min(100)
+        .max(100_000)
+        .describe("Prepared agent prompt — usually the manuscript text plus any agent-specific framing. " +
+        "The server wraps it in <manuscript> tags to defuse injection, prepends RAG examples " +
+        "if agentType is supplied, and runs the chosen Claude model."),
+    agentType: z
+        .enum(["methodology", "language", "figures", "plagiarism", "literature"])
+        .optional()
+        .describe("Which HAKEM specialist agent to run. Drives the calibration RAG corpus " +
+        "and the system prompt; defaults to a generic reviewer when omitted."),
+};
+export function registerHakemReview(server) {
+    server.registerTool("hakem_review_paper", {
+        title: "HAKEM Single-Agent Review",
+        description: "Run one of the HAKEM specialist agents (methodology, language, figures, " +
+            "plagiarism, or literature) on a prepared agent prompt and return the " +
+            "structured editorial decision: score (1-10), verdict (Accept / Minor " +
+            "Revision / Major Revision / Reject), summary, strengths, concerns, " +
+            "detailed multi-section review, confidence band, and questions for the " +
+            "authors. Uses Science AI Journal credits. For the full 5-agent + " +
+            "synthesis flow, prefer the web UI at scienceaijournal.com/ai-review.",
+        inputSchema: inputShape,
+    }, async (args) => {
+        const result = await request({
+            method: "POST",
+            path: "/api/review/claude",
+            body: { prompt: args.prompt, agentType: args.agentType },
+            // 90s server-side max + 30s margin for slow upstream proxies.
+            timeoutMs: 120_000,
+        });
+        const lines = [];
+        lines.push(`HAKEM review (${args.agentType ?? "generic"})`);
+        lines.push(`  Score: ${result.score ?? "?"}/10   Verdict: ${result.verdict ?? "?"}   Confidence: ${result.confidence ?? "?"}`);
+        if (result.summary) {
+            lines.push("");
+            lines.push(`Summary:\n  ${result.summary}`);
+        }
+        if (result.strengths?.length) {
+            lines.push("");
+            lines.push("Strengths:");
+            for (const s of result.strengths)
+                lines.push(`  + ${s}`);
+        }
+        if (result.concerns?.length) {
+            lines.push("");
+            lines.push("Concerns:");
+            for (const c of result.concerns)
+                lines.push(`  - ${c}`);
+        }
+        if (result.detailed_review) {
+            lines.push("");
+            lines.push("Detailed review:");
+            lines.push(result.detailed_review);
+        }
+        if (result.questions_for_authors?.length) {
+            lines.push("");
+            lines.push("Questions for authors:");
+            for (const q of result.questions_for_authors)
+                lines.push(`  ? ${q}`);
+        }
+        return { content: [{ type: "text", text: lines.join("\n") }] };
+    });
+}
+//# sourceMappingURL=hakem-review.js.map

package/dist/tools/hakem-review.js.map

@@ -0,0 +1 @@
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package/dist/tools/index.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Barrel: register every tool against an McpServer.
+ *
+ * Adding a tool? Drop a new file alongside, export a `registerXxx(server)`
+ * function, and import + call it here. Keep the call list alphabetised by
+ * tool slug so it's easy to scan against the /developers/mcp catalogue.
+ */
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerAllTools(server: McpServer): void;

package/dist/tools/index.js

@@ -0,0 +1,22 @@
+/**
+ * Barrel: register every tool against an McpServer.
+ *
+ * Adding a tool? Drop a new file alongside, export a `registerXxx(server)`
+ * function, and import + call it here. Keep the call list alphabetised by
+ * tool slug so it's easy to scan against the /developers/mcp catalogue.
+ */
+import { registerArticleWriter } from "./article-writer.js";
+import { registerDuplicatePublication } from "./duplicate-publication.js";
+import { registerHakemReview } from "./hakem-review.js";
+import { registerJournalRecommender } from "./journal-recommender.js";
+import { registerPreCheck } from "./pre-check.js";
+import { registerResearchGaps } from "./research-gaps.js";
+export function registerAllTools(server) {
+    registerArticleWriter(server); // exposes start_ + get_writer_pipeline_status
+    registerDuplicatePublication(server);
+    registerHakemReview(server);
+    registerJournalRecommender(server);
+    registerPreCheck(server);
+    registerResearchGaps(server);
+}
+//# sourceMappingURL=index.js.map

package/dist/tools/index.js.map

@@ -0,0 +1 @@
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package/dist/tools/journal-recommender.d.ts

@@ -0,0 +1,9 @@
+/**
+ * recommend_journals — POST /api/journal-recommender
+ *
+ * Returns ranked target journals from a ~1,200-venue index with tier,
+ * publisher, OA status, impact factor proxy, predatory flag, and
+ * example similar papers per recommendation.
+ */
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerJournalRecommender(server: McpServer): void;

package/dist/tools/journal-recommender.js

@@ -0,0 +1,115 @@
+/**
+ * recommend_journals — POST /api/journal-recommender
+ *
+ * Returns ranked target journals from a ~1,200-venue index with tier,
+ * publisher, OA status, impact factor proxy, predatory flag, and
+ * example similar papers per recommendation.
+ */
+import { z } from "zod";
+import { request } from "../http.js";
+const filtersShape = z
+    .object({
+    excludePredatory: z.boolean().optional(),
+    openAccessOnly: z.boolean().optional(),
+    minTier: z.union([z.literal(1), z.literal(2), z.literal(3)]).optional(),
+    excludePreprints: z.boolean().optional(),
+})
+    .optional()
+    .describe("Optional filter object. excludePredatory drops Beall's-archive matches; " +
+    "openAccessOnly keeps only OA journals; minTier sets a Tier 1/2/3 floor.");
+const inputShape = {
+    title: z
+        .string()
+        .min(1)
+        .max(600)
+        .describe("Paper title (required)."),
+    abstract: z
+        .string()
+        .max(20_000)
+        .describe("Paper abstract (required, can be empty string)."),
+    fullText: z
+        .string()
+        .max(200_000)
+        .optional()
+        .describe("Optional full manuscript text for higher-signal matching."),
+    keywords: z
+        .string()
+        .max(600)
+        .optional()
+        .describe("Optional author keywords; comma-separated. High-signal topic input."),
+    field: z
+        .string()
+        .max(200)
+        .optional()
+        .describe("Detected research field for a topical boost (optional)."),
+    filters: filtersShape,
+    sort: z
+        .enum(["best", "fastest", "highestIf", "mostAccepting"])
+        .optional()
+        .describe('Sort mode. "best" (default) maximises relevance; "fastest" prefers fast-decision venues; ' +
+        '"highestIf" sorts by 2-year mean citedness; "mostAccepting" prefers higher published-volume venues.'),
+    maxResults: z
+        .number()
+        .int()
+        .min(1)
+        .max(25)
+        .optional()
+        .describe("How many recommendations to return. Default 10, cap 25."),
+};
+export function registerJournalRecommender(server) {
+    server.registerTool("recommend_journals", {
+        title: "Recommend Target Journals",
+        description: "Recommend ranked target journals for a paper from a ~1,200-venue " +
+            "index. Each result includes a letter grade (A-F), a match percentage, " +
+            "tier (1-3), publisher, open-access status, 2-year mean citedness, " +
+            "predatory-journal flag, and 2-3 example similar papers that landed " +
+            "at that venue. Free — runs locally via FTS5 + topic-RAG, no LLM call. " +
+            "Use when the user asks 'where should I submit this paper' or wants " +
+            "to compare target venues before deciding.",
+        inputSchema: inputShape,
+    }, async (args) => {
+        const result = await request({
+            method: "POST",
+            path: "/api/journal-recommender",
+            body: {
+                title: args.title,
+                abstract: args.abstract,
+                fullText: args.fullText,
+                keywords: args.keywords,
+                field: args.field,
+                filters: args.filters,
+                sort: args.sort,
+                maxResults: args.maxResults,
+            },
+        });
+        const lines = [];
+        lines.push(`Journal recommendations (${result.recommendations.length} of ${result.indexJournalCount} indexed, ${result.executionMs}ms)`);
+        if (result.ftsErrored) {
+            lines.push("  [warning] full-text-search index errored — results are degraded.");
+        }
+        lines.push("");
+        for (let i = 0; i < result.recommendations.length; i++) {
+            const r = result.recommendations[i];
+            const m = r.metadata;
+            const tier = m.tier ? `T${m.tier}` : "T?";
+            const oa = m.openAccess ? "OA" : "—";
+            const ifv = typeof m.citedness2yr === "number"
+                ? `IF≈${m.citedness2yr.toFixed(1)}`
+                : "IF—";
+            const predatory = m.isPredatory ? " ⚠ predatory" : "";
+            const overlap = r.topicOverlapTerms && r.topicOverlapTerms.length > 0
+                ? `\n      topic overlap: ${r.topicOverlapTerms.slice(0, 5).join(", ")}`
+                : "";
+            lines.push(`  ${i + 1}. ${r.canonical}  —  ${r.scorePct}% (${r.letterGrade}) · ${tier} · ${oa} · ${ifv} · ${m.publisher ?? "?"}${predatory}${overlap}`);
+            if (r.examplePapers && r.examplePapers.length > 0) {
+                for (const p of r.examplePapers.slice(0, 2)) {
+                    const y = p.year ? ` (${p.year})` : "";
+                    const doi = p.doi ? `  doi:${p.doi}` : "";
+                    lines.push(`        e.g. ${p.title}${y}${doi}`);
+                }
+            }
+        }
+        return { content: [{ type: "text", text: lines.join("\n") }] };
+    });
+}
+//# sourceMappingURL=journal-recommender.js.map

package/dist/tools/journal-recommender.js.map

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package/dist/tools/pre-check.d.ts

@@ -0,0 +1,13 @@
+/**
+ * pre_check_paper — POST /api/scorer
+ *
+ * Tier 1-5 acceptance probability from title + abstract. Local FTS5
+ * BM25 against the 33k-paper library + tier-density aggregation. Zero
+ * LLM cost, sub-second response.
+ *
+ * The route is anonymous on the server side, but we still attach the
+ * Bearer token so the activity log can attribute the call to the
+ * user's account (and so future per-account rate limits work).
+ */
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerPreCheck(server: McpServer): void;

package/dist/tools/pre-check.js

@@ -0,0 +1,84 @@
+/**
+ * pre_check_paper — POST /api/scorer
+ *
+ * Tier 1-5 acceptance probability from title + abstract. Local FTS5
+ * BM25 against the 33k-paper library + tier-density aggregation. Zero
+ * LLM cost, sub-second response.
+ *
+ * The route is anonymous on the server side, but we still attach the
+ * Bearer token so the activity log can attribute the call to the
+ * user's account (and so future per-account rate limits work).
+ */
+import { z } from "zod";
+import { request } from "../http.js";
+const inputShape = {
+    title: z.string().min(1).max(600).describe("Paper title (required)."),
+    abstract: z
+        .string()
+        .min(1)
+        .max(20_000)
+        .describe("Paper abstract (required)."),
+    keywords: z
+        .string()
+        .max(600)
+        .optional()
+        .describe("Optional author-supplied keywords; comma-separated."),
+    fullText: z
+        .string()
+        .max(200_000)
+        .optional()
+        .describe("Optional full manuscript text. Pass when available; results are more accurate."),
+    abstractOnly: z
+        .boolean()
+        .optional()
+        .describe("Set to false to score against fullText. Default true. Ignored when fullText is absent."),
+};
+export function registerPreCheck(server) {
+    server.registerTool("pre_check_paper", {
+        title: "Pre-Check Paper",
+        description: "Run a free, zero-LLM-cost pre-submission scoring of an academic paper. " +
+            "Returns predicted publication tier (Tier 1, 2, or 3 probability), the " +
+            "detected research field, and a confidence band. Backed by a local 33,000-paper " +
+            "library via FTS5 BM25. Use this when the user wants a fast sanity-check on " +
+            "whether a paper is ready to submit, or which tier of journal to target. " +
+            "Sub-second response. Free.",
+        inputSchema: inputShape,
+    }, async (args) => {
+        const result = await request({
+            method: "POST",
+            path: "/api/scorer",
+            body: {
+                title: args.title,
+                abstract: args.abstract,
+                keywords: args.keywords,
+                fullText: args.fullText,
+                abstractOnly: args.abstractOnly,
+            },
+        });
+        return {
+            content: [
+                {
+                    type: "text",
+                    text: formatScorerResult(result),
+                },
+            ],
+        };
+    });
+}
+function formatScorerResult(r) {
+    const field = r.field ?? "(unknown)";
+    const pct = (v) => typeof v === "number" ? `${Math.round(v * 100)}%` : "—";
+    const tier1 = pct(r.tier1);
+    const tier2 = pct(r.tier2);
+    const tier3 = pct(r.tier3);
+    const conf = typeof r.confidence === "number"
+        ? `${Math.round(r.confidence * 100)}%`
+        : "—";
+    return (`Pre-Check result\n` +
+        `  Detected field: ${field}\n` +
+        `  Tier 1 probability: ${tier1}\n` +
+        `  Tier 2 probability: ${tier2}\n` +
+        `  Tier 3 probability: ${tier3}\n` +
+        `  Confidence: ${conf}\n`);
+}
+//# sourceMappingURL=pre-check.js.map

package/dist/tools/pre-check.js.map

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package/dist/tools/research-gaps.d.ts

@@ -0,0 +1,9 @@
+/**
+ * find_research_gaps — POST /api/research-gaps
+ *
+ * Returns synthesised research gaps + a field overview + most-cited +
+ * most-recent papers around a query. Auth required (consumes credits;
+ * rate-limited to 10/hr per IP).
+ */
+import type { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerResearchGaps(server: McpServer): void;

package/dist/tools/research-gaps.js

@@ -0,0 +1,82 @@
+/**
+ * find_research_gaps — POST /api/research-gaps
+ *
+ * Returns synthesised research gaps + a field overview + most-cited +
+ * most-recent papers around a query. Auth required (consumes credits;
+ * rate-limited to 10/hr per IP).
+ */
+import { z } from "zod";
+import { request } from "../http.js";
+const inputShape = {
+    query: z
+        .string()
+        .min(10)
+        .max(2000)
+        .describe("Research query (≥ 10 chars). Free-form prose or a title + abstract joined by newline."),
+    field: z
+        .string()
+        .max(80)
+        .optional()
+        .describe("Optional field bias (e.g. 'computer_science', 'biology')."),
+    departmentId: z
+        .string()
+        .max(60)
+        .optional()
+        .describe("Optional departmentId to enable methodology-alignment hints (boosts gaps whose text matches your discipline's KPI / question vocabulary)."),
+};
+export function registerResearchGaps(server) {
+    server.registerTool("find_research_gaps", {
+        title: "Find Research Gaps",
+        description: "Surface research gaps + the most-cited and most-recent papers around " +
+            "a query. Returns cross-paper synthesis gaps first (LLM-derived, grounded " +
+            "in ≥ 2 papers), then catalogue-level single-paper gaps. Plus a field " +
+            "overview and ≤ 50 top-cited and ≤ 50 most-recent papers. Uses " +
+            "Science AI Journal credits; rate-limited to 10 requests/hour per IP. " +
+            "Use for early-stage research discovery, literature gap identification, " +
+            "and proposal scoping.",
+        inputSchema: inputShape,
+    }, async (args) => {
+        const result = await request({
+            method: "POST",
+            path: "/api/research-gaps",
+            body: {
+                query: args.query,
+                field: args.field,
+                departmentId: args.departmentId,
+            },
+        });
+        const lines = [];
+        const fo = result.fieldOverview;
+        if (fo?.name) {
+            lines.push(`Field: ${fo.name}`);
+            if (fo.description)
+                lines.push(`  ${fo.description}`);
+            lines.push("");
+        }
+        lines.push(`## Research gaps (${result.gaps.length})`);
+        for (let i = 0; i < result.gaps.length; i++) {
+            const g = result.gaps[i];
+            const prov = g.provenance ? ` [${g.provenance}]` : "";
+            const topic = g.topic ? ` (topic: ${g.topic})` : "";
+            const paper = g.paper ? ` — anchor: ${g.paper}` : "";
+            lines.push(`  ${i + 1}. ${g.text}${prov}${topic}${paper}`);
+        }
+        lines.push("");
+        lines.push(`## Most-cited (${result.mostCited.length})`);
+        for (const p of result.mostCited.slice(0, 10)) {
+            const yr = p.year ? ` (${p.year})` : "";
+            const cit = typeof p.citations === "number" ? ` · ${p.citations} cit` : "";
+            const venue = p.venue ? ` · ${p.venue}` : "";
+            lines.push(`  - ${p.title}${yr}${cit}${venue}`);
+        }
+        lines.push("");
+        lines.push(`## Most-recent (${result.mostRecent.length})`);
+        for (const p of result.mostRecent.slice(0, 10)) {
+            const yr = p.year ? ` (${p.year})` : "";
+            const venue = p.venue ? ` · ${p.venue}` : "";
+            lines.push(`  - ${p.title}${yr}${venue}`);
+        }
+        return { content: [{ type: "text", text: lines.join("\n") }] };
+    });
+}
+//# sourceMappingURL=research-gaps.js.map

package/dist/tools/research-gaps.js.map

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package/package.json

@@ -0,0 +1,49 @@
+{
+  "name": "science-ai-mcp-server",
+  "version": "0.1.0",
+  "description": "MCP (Model Context Protocol) server for Science AI Journal tools — Pre-Check, AI Review, Research Gaps, Journal Recommender, Duplicate Publication Checker, Article Writer. Use them inside Claude Desktop, Cursor, Cline, or any MCP-enabled client.",
+  "keywords": [
+    "mcp",
+    "model-context-protocol",
+    "claude",
+    "claude-desktop",
+    "cursor",
+    "cline",
+    "academic",
+    "peer-review",
+    "research",
+    "science-ai-journal"
+  ],
+  "homepage": "https://scienceaijournal.com/developers/mcp",
+  "bugs": {
+    "url": "https://github.com/science-ai-journal/science-ai-mcp-server/issues"
+  },
+  "license": "MIT",
+  "author": "Science AI Journal <support@scienceaijournal.com>",
+  "type": "module",
+  "main": "dist/index.js",
+  "bin": {
+    "science-ai-mcp-server": "dist/index.js"
+  },
+  "files": [
+    "dist",
+    "README.md",
+    "LICENSE"
+  ],
+  "scripts": {
+    "build": "tsc",
+    "prepublishOnly": "npm run build",
+    "start": "node dist/index.js"
+  },
+  "engines": {
+    "node": ">=20"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.29.0",
+    "zod": "^3.23.0"
+  },
+  "devDependencies": {
+    "@types/node": "^20.11.0",
+    "typescript": "^5.4.0"
+  }
+}