@djmima/pubmed-mcp 0.0.0-stage → 1.0.0

package/dist/cli/run.js

@@ -0,0 +1,154 @@
+/**
+ * Argument parsing, dispatch, and output for the pubmed CLI.
+ *
+ * Kept apart from the entrypoint (src/cli.ts) so tests can run commands with
+ * in-memory I/O and a mocked NCBI client.
+ *
+ * Output contract: the command's JSON goes to stdout (or to the -o file) and
+ * nothing else does; messages go to stderr. Exit status is 0 on success, 1
+ * when NCBI or a file operation fails, and 2 for invalid usage.
+ */
+import { parseArgs } from 'node:util';
+import { NcbiClient } from '../pubmed/client.js';
+import { COMMANDS, UsageError, errorMessage, } from './commands.js';
+const COMMON_OPTIONS = {
+    output: { type: 'string', short: 'o' },
+    help: { type: 'boolean', short: 'h' },
+};
+/** Run one CLI invocation and return its exit status. */
+export async function runCli(argv, io, client) {
+    const [name, ...args] = argv;
+    if (name === undefined) {
+        io.stderr(globalHelp());
+        return 2;
+    }
+    if (name === '-h' || name === '--help') {
+        io.stdout(globalHelp());
+        return 0;
+    }
+    if (name === 'help') {
+        if (args[0] === undefined) {
+            io.stdout(globalHelp());
+            return 0;
+        }
+        const target = findCommand(args[0]);
+        if (!target)
+            return unknownCommand(io, args[0]);
+        io.stdout(commandHelp(target));
+        return 0;
+    }
+    if (name.startsWith('-')) {
+        io.stderr(`pubmed: options go after the command, e.g. pubmed search <query> ${name} ...\n` +
+            'Run "pubmed --help" to list the commands.\n');
+        return 2;
+    }
+    const command = findCommand(name);
+    if (!command)
+        return unknownCommand(io, name);
+    let values;
+    let positionals;
+    try {
+        ({ values, positionals } = parseArgs({
+            args,
+            options: { ...COMMON_OPTIONS, ...command.options },
+            allowPositionals: true,
+            strict: true,
+        }));
+    }
+    catch (err) {
+        // parseArgs appends advice about "--" that does not apply here.
+        return usageFailure(io, command, errorMessage(err).split(/\.\s|\n/)[0]);
+    }
+    if (values.help) {
+        io.stdout(commandHelp(command));
+        return 0;
+    }
+    const { output: outFile, help: _help, ...options } = values;
+    let stdin;
+    const input = {
+        values: options,
+        positionals,
+        // Several "-" arguments share one read of stdin.
+        readText: (path) => (path === '-' ? (stdin ??= io.readText('-')) : io.readText(path)),
+    };
+    try {
+        const { output, summary } = await command.execute(input, client ?? new NcbiClient());
+        const json = `${JSON.stringify(output)}\n`;
+        if (typeof outFile === 'string' && outFile !== '-') {
+            await io.writeText(outFile, json);
+            // The size tells an agent whether the file is safe to read whole.
+            io.stderr(`pubmed ${command.name}: ${summary}; wrote ${formatBytes(Buffer.byteLength(json))} to ${outFile}\n`);
+        }
+        else {
+            io.stdout(json);
+        }
+        return 0;
+    }
+    catch (err) {
+        if (err instanceof UsageError)
+            return usageFailure(io, command, err.message);
+        io.stderr(`pubmed ${command.name}: ${errorMessage(err)}\n`);
+        return 1;
+    }
+}
+// ─── Help and messages ───────────────────────────────────────────────────────
+function findCommand(name) {
+    return COMMANDS.find((c) => c.name === name);
+}
+function unknownCommand(io, name) {
+    io.stderr(`pubmed: unknown command ${JSON.stringify(name)}\nRun "pubmed --help" to list the commands.\n`);
+    return 2;
+}
+function usageFailure(io, command, message) {
+    io.stderr(`pubmed ${command.name}: ${message}\nRun "pubmed ${command.name} --help" for usage.\n`);
+    return 2;
+}
+const COMMON_OPTIONS_HELP = `
+Common options:
+  -o, --output <file>  Write the JSON to <file> instead of stdout ("-" = stdout)
+  -h, --help           Show this help
+`;
+function commandHelp(command) {
+    return command.help + COMMON_OPTIONS_HELP;
+}
+function globalHelp() {
+    const nameWidth = Math.max(...COMMANDS.map((c) => c.name.length));
+    const descriptionWidth = Math.max(...COMMANDS.map((c) => c.description.length));
+    const commandList = COMMANDS.map((c) => `  ${c.name.padEnd(nameWidth)}  ${c.description.padEnd(descriptionWidth)}  (${c.tool})`).join('\n');
+    return `Usage: pubmed <command> [options] [arguments]
+
+Query PubMed and PubMed Central through NCBI E-utilities. Each command runs
+the matching PubMed MCP tool and prints the same JSON, so results can be
+saved to a file and filtered with jq instead of being read in full.
+
+Commands:
+${commandList}
+
+Options:
+  -o, --output <file>  Write the JSON to <file> instead of stdout
+  -h, --help           Show help; "pubmed <command> --help" for a command
+
+IDs are given as arguments separated by spaces or commas, or read from stdin
+with "-". Long lists are split into batches and sent one at a time.
+
+Environment:
+  NCBI_API_KEY  NCBI API key; raises the rate limit from 3 to 8 requests/s.
+                In a source checkout, also read from its .env file.
+
+Exit status: 0 on success, 1 when NCBI or a file operation fails, 2 on
+invalid usage.
+
+Example:
+  pubmed search "TP53 AND myelodysplastic syndromes[mh]" --max-results 100 -o search.json
+  jq -r '.pmids[]' search.json | pubmed metadata - -o meta.json
+  jq -c '.articles[] | {pmid: .identifiers.pmid, title}' meta.json
+`;
+}
+function formatBytes(bytes) {
+    if (bytes < 1024)
+        return `${bytes} bytes`;
+    if (bytes < 1024 * 1024)
+        return `${(bytes / 1024).toFixed(1)} KB`;
+    return `${(bytes / 1024 / 1024).toFixed(1)} MB`;
+}
+//# sourceMappingURL=run.js.map

package/dist/cli/run.js.map

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package/dist/cli.d.ts

@@ -0,0 +1,16 @@
+#!/usr/bin/env node
+/**
+ * PubMed CLI — entrypoint.
+ *
+ * Runs the same tool functions as the MCP server and prints their JSON to
+ * stdout, or to a file with -o, so large results can be saved and filtered
+ * with jq instead of being loaded into an LLM's context. See `pubmed --help`.
+ *
+ * Environment variables:
+ *   NCBI_API_KEY — NCBI API key; raises rate limit from 3 → 8 req/s.
+ *                  Falls back to the .env file in the package root, so in a
+ *                  source checkout the key is found whichever directory the
+ *                  command runs in.
+ */
+export {};
+//# sourceMappingURL=cli.d.ts.map

package/dist/cli.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"cli.d.ts","sourceRoot":"","sources":["../src/cli.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;GAYG"}

package/dist/cli.js

@@ -0,0 +1,52 @@
+#!/usr/bin/env node
+/**
+ * PubMed CLI — entrypoint.
+ *
+ * Runs the same tool functions as the MCP server and prints their JSON to
+ * stdout, or to a file with -o, so large results can be saved and filtered
+ * with jq instead of being loaded into an LLM's context. See `pubmed --help`.
+ *
+ * Environment variables:
+ *   NCBI_API_KEY — NCBI API key; raises rate limit from 3 → 8 req/s.
+ *                  Falls back to the .env file in the package root, so in a
+ *                  source checkout the key is found whichever directory the
+ *                  command runs in.
+ */
+import { readFile, writeFile } from 'node:fs/promises';
+import path from 'node:path';
+import { fileURLToPath } from 'node:url';
+import { config as loadDotenv } from 'dotenv';
+import { runCli } from './cli/run.js';
+// quiet: dotenv >=17 logs to stdout by default, which would corrupt the JSON
+// output. Variables already set in the environment take precedence.
+loadDotenv({
+    path: path.join(path.dirname(fileURLToPath(import.meta.url)), '..', '.env'),
+    quiet: true,
+});
+// A reader that stops early (e.g. `pubmed ... | head`) is not an error.
+process.stdout.on('error', (err) => {
+    if (err.code !== 'EPIPE')
+        process.stderr.write(`pubmed: ${err.message}\n`);
+    process.exit(err.code === 'EPIPE' ? 0 : 1);
+});
+async function readStdin() {
+    const chunks = [];
+    for await (const chunk of process.stdin) {
+        chunks.push(chunk);
+    }
+    return Buffer.concat(chunks).toString('utf8');
+}
+runCli(process.argv.slice(2), {
+    stdout: (text) => process.stdout.write(text),
+    stderr: (text) => process.stderr.write(text),
+    readText: (file) => (file === '-' ? readStdin() : readFile(file, 'utf8')),
+    writeText: (file, text) => writeFile(file, text, 'utf8'),
+}).then(
+// Set exitCode rather than calling process.exit() so stdout can drain.
+(code) => {
+    process.exitCode = code;
+}, (err) => {
+    process.stderr.write(`pubmed: ${String(err)}\n`);
+    process.exitCode = 1;
+});
+//# sourceMappingURL=cli.js.map

package/dist/cli.js.map

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

@@ -0,0 +1,32 @@
+#!/usr/bin/env node
+/**
+ * PubMed MCP Server — entrypoint.
+ *
+ * Transport is selected at startup based on environment:
+ *
+ *   STDIO mode (default):
+ *     Used by local MCP clients that launch the server as a subprocess
+ *     (Claude Desktop, Claude Code, Codex).
+ *     Start with:  node dist/index.js
+ *
+ *   HTTP mode (Cloud Run / remote deployment):
+ *     Activated when the PORT environment variable is set.
+ *     Starts an Express server that handles Streamable HTTP transport at /mcp.
+ *     Used by remote clients: Claude custom connectors and the Anthropic API
+ *     MCP connector, which can only reach servers over HTTP.
+ *     /mcp requires an OAuth 2.0 Bearer token (see auth.ts); /health and
+ *     /.well-known/oauth-protected-resource are public.
+ *     Cloud Run injects PORT=8080 automatically.
+ *     Start with:  PORT=8080 node dist/index.js  (plus the OAuth variables)
+ *
+ * Environment variables:
+ *   NCBI_API_KEY     — NCBI API key; raises rate limit from 3 → 8 req/s
+ *                      Register free at https://www.ncbi.nlm.nih.gov/account/
+ *   PORT             — When set, enables HTTP mode on the specified port.
+ *   OAUTH_ISSUER, OAUTH_JWKS_URL, MCP_RESOURCE_URL
+ *                    — Required in HTTP mode; startup fails without them.
+ *   ALLOWED_SUBJECTS — Optional allowlist of token subjects (HTTP mode).
+ *                      See auth.ts for all four.
+ */
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG"}

package/dist/index.js

@@ -0,0 +1,126 @@
+#!/usr/bin/env node
+/**
+ * PubMed MCP Server — entrypoint.
+ *
+ * Transport is selected at startup based on environment:
+ *
+ *   STDIO mode (default):
+ *     Used by local MCP clients that launch the server as a subprocess
+ *     (Claude Desktop, Claude Code, Codex).
+ *     Start with:  node dist/index.js
+ *
+ *   HTTP mode (Cloud Run / remote deployment):
+ *     Activated when the PORT environment variable is set.
+ *     Starts an Express server that handles Streamable HTTP transport at /mcp.
+ *     Used by remote clients: Claude custom connectors and the Anthropic API
+ *     MCP connector, which can only reach servers over HTTP.
+ *     /mcp requires an OAuth 2.0 Bearer token (see auth.ts); /health and
+ *     /.well-known/oauth-protected-resource are public.
+ *     Cloud Run injects PORT=8080 automatically.
+ *     Start with:  PORT=8080 node dist/index.js  (plus the OAuth variables)
+ *
+ * Environment variables:
+ *   NCBI_API_KEY     — NCBI API key; raises rate limit from 3 → 8 req/s
+ *                      Register free at https://www.ncbi.nlm.nih.gov/account/
+ *   PORT             — When set, enables HTTP mode on the specified port.
+ *   OAUTH_ISSUER, OAUTH_JWKS_URL, MCP_RESOURCE_URL
+ *                    — Required in HTTP mode; startup fails without them.
+ *   ALLOWED_SUBJECTS — Optional allowlist of token subjects (HTTP mode).
+ *                      See auth.ts for all four.
+ */
+// Load .env file if present. Silently skipped in production where env vars
+// are injected by the runtime (Cloud Run, Docker --env, etc.).
+// quiet: dotenv >=17 logs to stdout by default, which corrupts the stdio
+// JSON-RPC stream.
+import { config as loadDotenv } from 'dotenv';
+loadDotenv({ quiet: true });
+import { createServer } from './server.js';
+import { NcbiClient } from './pubmed/client.js';
+async function main() {
+    const port = process.env.PORT ? parseInt(process.env.PORT, 10) : undefined;
+    if (port !== undefined) {
+        await startHttpServer(port);
+    }
+    else {
+        await startStdioServer();
+    }
+}
+// ── HTTP mode (Cloud Run) ──────────────────────────────────────────────────
+// One NCBI client for the whole process. HTTP mode creates an MCP server per
+// request, and passing them all this client makes its rate limiter span
+// concurrent requests instead of restarting with each one. Must be created
+// after loadDotenv() so that it reads NCBI_API_KEY from .env.
+const sharedNcbiClient = new NcbiClient();
+async function startHttpServer(port) {
+    const { default: express } = await import('express');
+    const { StreamableHTTPServerTransport } = await import('@modelcontextprotocol/sdk/server/streamableHttp.js');
+    const { protectedResourceMetadata, requireAuth } = await import('./auth.js');
+    const app = express();
+    app.use(express.json());
+    // OAuth 2.0 Protected Resource Metadata (RFC 9728) — public so the client can
+    // discover the authorization server. No token required.
+    app.get('/.well-known/oauth-protected-resource', protectedResourceMetadata);
+    // Return JSON (not HTML) for malformed request bodies.
+    app.use((err, _req, res, next) => {
+        if (err.type === 'entity.parse.failed') {
+            res.status(400).json({ error: 'Invalid JSON body' });
+            return;
+        }
+        next(err);
+    });
+    // MCP Streamable HTTP — handles both POST (client→server) and GET (SSE stream).
+    // SDK v1.x: stateless transports cannot be reused across requests.
+    // A new transport and server instance must be created for every request.
+    app.all('/mcp', requireAuth, (req, res) => {
+        const transport = new StreamableHTTPServerTransport({
+            sessionIdGenerator: undefined, // stateless mode
+        });
+        const mcpServer = createServer(sharedNcbiClient);
+        mcpServer
+            .connect(transport)
+            .then(() => transport.handleRequest(req, res, req.body))
+            .catch((err) => {
+            process.stderr.write(`[http] handleRequest error: ${String(err)}\n`);
+            if (!res.headersSent) {
+                res.status(500).json({ error: 'Internal server error' });
+            }
+        });
+    });
+    // Health check endpoint — used by Cloud Run readiness/liveness probes.
+    // No auth required so Cloud Run can always reach it.
+    app.get('/health', (_req, res) => {
+        res.send('ok');
+    });
+    const httpServer = app.listen(port, () => {
+        process.stderr.write(`PubMed MCP server running on HTTP port ${port}\n`);
+        process.stderr.write(`  MCP endpoint : http://localhost:${port}/mcp\n`);
+        process.stderr.write(`  Health check : http://localhost:${port}/health\n`);
+        process.stderr.write('  Auth         : OAuth 2.0 (WorkOS AuthKit) — Bearer required on /mcp\n');
+    });
+    const shutdown = () => {
+        process.stderr.write('Shutting down PubMed MCP server\n');
+        httpServer.close(() => process.exit(0));
+    };
+    process.on('SIGINT', shutdown);
+    process.on('SIGTERM', shutdown);
+}
+// ── Stdio mode (local / Claude Desktop) ───────────────────────────────────
+async function startStdioServer() {
+    const { StdioServerTransport } = await import('@modelcontextprotocol/sdk/server/stdio.js');
+    const server = createServer();
+    const transport = new StdioServerTransport();
+    await server.connect(transport);
+    process.stderr.write('PubMed MCP server running on stdio\n');
+    const shutdown = () => {
+        process.stderr.write('Shutting down PubMed MCP server\n');
+        process.exit(0);
+    };
+    process.on('SIGINT', shutdown);
+    process.on('SIGTERM', shutdown);
+}
+// ──────────────────────────────────────────────────────────────────────────
+main().catch((err) => {
+    process.stderr.write(`Fatal error: ${String(err)}\n`);
+    process.exit(1);
+});
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/dist/pubmed/client.d.ts

@@ -0,0 +1,150 @@
+/**
+ * NCBI E-utilities HTTP client.
+ * Handles rate limiting, API key injection, and request construction.
+ *
+ * Base URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/
+ * Rate limits:
+ *   - Without API key: 3 requests/sec
+ *   - With API key:   10 requests/sec
+ * NCBI counts requests by arrival time, so we send at 8 req/s with a key to
+ * absorb network jitter, and retry briefly on HTTP 429.
+ */
+export declare class NcbiNetworkError extends Error {
+    readonly cause?: unknown | undefined;
+    constructor(message: string, cause?: unknown | undefined);
+}
+export declare class NcbiApiError extends Error {
+    readonly statusCode?: number | undefined;
+    constructor(message: string, statusCode?: number | undefined);
+}
+export declare class NcbiParseError extends Error {
+    readonly cause?: unknown | undefined;
+    constructor(message: string, cause?: unknown | undefined);
+}
+export declare class NcbiClient {
+    private readonly apiKey;
+    private readonly rateLimiter;
+    constructor(apiKey?: string);
+    private commonParams;
+    /**
+     * Throttle, send, and retry on HTTP 429. Every NCBI call goes through here
+     * so each attempt (including retries) takes its own rate-limiter slot.
+     */
+    private request;
+    /**
+     * ESearch — search PubMed for article IDs.
+     * Returns the raw JSON response from NCBI.
+     */
+    esearch(params: {
+        term: string;
+        retmax?: number;
+        retstart?: number;
+        sort?: string;
+        field?: string;
+        datetype?: string;
+        mindate?: string;
+        maxdate?: string;
+    }): Promise<EsearchResult>;
+    /**
+     * EFetch — retrieve full records from PubMed or PMC.
+     * Returns raw XML text.
+     */
+    efetch(params: {
+        db: string;
+        id: string | string[];
+        retmode?: string;
+        rettype?: string;
+    }): Promise<string>;
+    /**
+     * ELink — find related articles or cross-database links.
+     * Accepts multiple IDs and returns the raw JSON response.
+     */
+    elink(params: {
+        dbfrom: string;
+        id: string[];
+        linkname: string;
+        cmd?: string;
+    }): Promise<ElinkResponse>;
+    /**
+     * ECitmatch — look up PubMed IDs from structured citation data.
+     * Returns raw text with pipe-delimited fields.
+     */
+    ecitmatch(citations: CitationInput[]): Promise<string>;
+    /**
+     * PMC ID Converter — convert between PMID, PMCID, and DOI.
+     */
+    idConvert(params: {
+        ids: string[];
+        idtype?: string;
+    }): Promise<IdConvResponse>;
+}
+export interface EsearchResult {
+    count: string;
+    retmax: string;
+    retstart: string;
+    idlist: string[];
+    translationset: unknown[];
+    querytranslation: string;
+    errorlist?: {
+        phrasesnotfound?: string[];
+        fieldsnotfound?: string[];
+    };
+    warninglist?: {
+        phrasesignored?: string[];
+        quotedphrasesnotfound?: string[];
+        outputmessages?: string[];
+    };
+}
+export interface ElinkResponse {
+    header?: {
+        type: string;
+        version: string;
+    };
+    linksets: ElinkLinkset[];
+}
+export interface ElinkLinkset {
+    dbfrom: string;
+    ids: string[];
+    linksetdbs?: ElinkLinksetDb[];
+    idurllist?: unknown[];
+}
+export interface ElinkLinksetDb {
+    dbto: string;
+    linkname: string;
+    links: Array<{
+        id: string;
+        score?: string;
+    } | string>;
+}
+export interface CitationInput {
+    journal: string;
+    year: number;
+    volume: string;
+    first_page: string;
+    author: string;
+    key: string;
+}
+export interface IdConvResponse {
+    status: string;
+    'response-date': string;
+    request: {
+        warnings: string[];
+        format: string;
+        idtype: string;
+        ids: string[];
+        email: string;
+        tool: string;
+        echo: string;
+        versions: string;
+        showaiid: string;
+    };
+    records: Array<{
+        pmid?: string;
+        pmcid?: string;
+        doi?: string;
+        'requested-id': string;
+        errmsg?: string;
+        [key: string]: string | undefined;
+    }>;
+}
+//# sourceMappingURL=client.d.ts.map

package/dist/pubmed/client.d.ts.map

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