@djmima/pubmed-mcp 1.0.2 → 1.2.0

package/CHANGELOG.md

@@ -5,6 +5,36 @@
 
 ## [Unreleased]
 
+## [1.2.0] - 2026-11-04
+
+### 追加
+
+- CLI に `-v` / `--version` を追加しました。インストールされている `pubmed` のバージョンを表示します。
+
+### 修正
+
+- MCP サーバーが `initialize` の応答（`serverInfo.version`）でバージョンを常に `1.0.0` と返していたのを、`package.json` のバージョンを返すようにしました。
+
+## [1.1.0] - 2026-11-04
+
+### 変更
+
+- **HTTP モードで `ALLOWED_SUBJECTS` を必須にしました。** 未設定または空のときは起動時に終了します。これまでは空のとき、認可サーバー（WorkOS AuthKit）で有効なトークンを取得できるユーザー全員が `/mcp` を使えました。
+- HTTP モードで、`/mcp` への GET と DELETE に 405 を返すようにしました。ステートレスなサーバーには GET で開く SSE ストリームに送るものがなく、開いたままのストリームがサーバーインスタンスと Cloud Run のリクエストを占有していました。
+
+### セキュリティ
+
+- MCP サーバーが `.env` を起動時のカレントディレクトリから読み込んでいたのをやめ、パッケージ自身のルート（ソースからビルドした場合はリポジトリ直下）からだけ読み込むようにしました（CLI はもともとこの動作です）。MCP クライアントは開いているプロジェクトのディレクトリでサーバーを起動するため、そのプロジェクトの `.env` に `PORT` があると HTTP モードで起動し、`HTTPS_PROXY` と `NODE_TLS_REJECT_UNAUTHORIZED=0` があると NCBI への通信（API キーを含む）を第三者のプロキシが読み書きできました。
+- ID を受け取るツール（`get_article_metadata`、`find_related_articles`、`get_copyright_status`、`get_full_text_article`、`convert_article_ids`）で、1 つの値に 1 つの ID だけを受け付けるようにしました。NCBI はカンマを ID の区切りとして扱うため、`"1,2,3"` のような値で 1 回あたりの上限を超える件数を取得できました。上限のなかった `find_related_articles` の `pmids` も 200 件までにしました。
+- `lookup_article_by_citation` で、引用の各項目に含まれる `|` と改行を空白に置き換えるようにしました。どちらも ECitMatch の区切り文字なので、項目がずれたり別の引用として送られたりして、結果が別の引用に対応づけられるおそれがありました。
+- NCBI へのリクエストに 60 秒のタイムアウトを設けました。応答のない接続で、ツールの呼び出し（HTTP モードではクライアントのリクエスト）が止まったままになることがなくなります。
+- NCBI へのリクエストがリダイレクトされたときは、HTTPS で `*.ncbi.nlm.nih.gov` に向かうものだけをたどるようにしました。API キーはクエリ文字列に含まれ、リダイレクト先にも引き継がれます。
+- エラーメッセージの中の API キーは、NCBI が返した本文のどこに現れても伏せるようにしました。ネットワークエラーには、API キーを含む axios のエラーオブジェクトを付けないようにしました。
+- HTTP モードで、`exp` と `sub` のないアクセストークンを拒否するようにしました。
+- HTTP モードで、リクエスト本文の JSON をトークンの検証後に解析するようにしました。不正な形式や大きすぎる本文などのエラーには、スタックトレースを含む HTML ではなく JSON を返し、`X-Powered-By` ヘッダーも送らないようにしました。Docker イメージでは `NODE_ENV=production` を設定し、依存パッケージのインストールスクリプトを実行しないようにしました。
+- `@modelcontextprotocol/sdk`、`axios`、`express` の最低バージョンを、既知の脆弱性の修正を含むバージョンに上げました。
+- GitHub Actions のアクションをコミット SHA で固定し、`actions/checkout` が認証情報を `.git` に残さないようにしました。
+
 ## [1.0.2] - 2026-11-03
 
 ### 変更
@@ -29,7 +59,9 @@ npm パッケージ [`@djmima/pubmed-mcp`](https://www.npmjs.com/package/@djmima
 - 同じツールをシェルから実行する `pubmed` CLI と、エージェント向けの Skill（`skills/pubmed-cli`）
 - MIT License
 
-[Unreleased]: https://github.com/DJMIMA/PubMed_MCP/compare/v1.0.2...HEAD
+[Unreleased]: https://github.com/DJMIMA/PubMed_MCP/compare/v1.2.0...HEAD
+[1.2.0]: https://github.com/DJMIMA/PubMed_MCP/compare/v1.1.0...v1.2.0
+[1.1.0]: https://github.com/DJMIMA/PubMed_MCP/compare/v1.0.2...v1.1.0
 [1.0.2]: https://github.com/DJMIMA/PubMed_MCP/compare/v1.0.1...v1.0.2
 [1.0.1]: https://github.com/DJMIMA/PubMed_MCP/compare/v1.0.0...v1.0.1
 [1.0.0]: https://github.com/DJMIMA/PubMed_MCP/releases/tag/v1.0.0

package/README.md

@@ -119,8 +119,8 @@ With an API key, the rate limit goes from 3 to 8 req/s.
 2. Set it in the `NCBI_API_KEY` environment variable (see the client-specific settings below)
 
 When an MCP client starts the server locally, pass the key in the `env` section of the client configuration.
-`.env` is read from the current directory at startup, so when a client starts the server, the `.env` in
-the project root may not be read.
+The server reads `.env` only from its own package root (the repository root if you [built from source](#building-from-source)),
+never from the directory it is started in, so a `.env` in a project open in your MCP client cannot change its settings.
 
 Use an API key owned and managed by the person or organization running this server.
 The repository does not ship an API key. When a response includes the `echo` from the NCBI API,
@@ -279,14 +279,14 @@ PORT=8080 npm run dev
 # → http://localhost:8080/health Health check
 ```
 
-HTTP mode reads `OAUTH_ISSUER`, `OAUTH_JWKS_URL`, and `MCP_RESOURCE_URL` at startup, and exits with the following error if any of them is missing:
+HTTP mode reads `OAUTH_ISSUER`, `OAUTH_JWKS_URL`, `MCP_RESOURCE_URL`, and `ALLOWED_SUBJECTS` at startup, and exits with the following error if any of them is missing:
 
 ```
 Fatal error: Error: Missing required environment variable: OAUTH_ISSUER
 ```
 
 Set these values in `.env` before starting (see [Environment variables](#environment-variables) for what each one means).
-To check `/health` or the 401 response, placeholder values in URL form are enough to start the server, but to actually call `/mcp`
+To check `/health` or the 401 response, placeholder values (in URL form for the URLs) are enough to start the server, but to actually call `/mcp`
 you need an access token issued with `MCP_RESOURCE_URL` as its `aud`. To try the tools without authentication, use stdio mode.
 
 ---
@@ -306,7 +306,7 @@ but extracting only the PMID, year, and title brings it down to 3.2 KB (about 1/
 npm install -g @djmima/pubmed-mcp
 ```
 
-You're done when `pubmed --help` prints the help.
+You're done when `pubmed --help` prints the help. `pubmed --version` (or `-v`) prints the installed version.
 
 The NCBI API key is read from the `NCBI_API_KEY` environment variable. Add
 `export NCBI_API_KEY=your_api_key_here` to your shell configuration file (`~/.bashrc`, `~/.zshrc`, etc.), or on Windows run
@@ -543,9 +543,9 @@ gcloud run deploy pubmed-mcp \
 | `OAUTH_ISSUER` | The `issuer` from the authorization server metadata. It is compared with the token's `iss` exactly, so copy it as-is, including whether it has a trailing `/` |
 | `OAUTH_JWKS_URL` | The `jwks_uri` from the same metadata: the URL of the public keys used to verify token signatures |
 | `MCP_RESOURCE_URL` | The MCP endpoint URL you decided in step 5. It is compared with the token's `aud`, and published as `resource` in `/.well-known/oauth-protected-resource` |
-| `ALLOWED_SUBJECTS` | A comma-separated list of user IDs (the token's `sub`) allowed to connect. If empty, every user who can get a valid token from AuthKit can connect |
+| `ALLOWED_SUBJECTS` | A comma-separated list of user IDs (the token's `sub`) allowed to connect. Required: without it, every user who can get a valid token from AuthKit could connect |
 
-If any of `OAUTH_ISSUER`, `OAUTH_JWKS_URL`, or `MCP_RESOURCE_URL` is missing, the server exits at startup with
+If any of `OAUTH_ISSUER`, `OAUTH_JWKS_URL`, `MCP_RESOURCE_URL`, or `ALLOWED_SUBJECTS` is missing, the server exits at startup with
 `Missing required environment variable: ...` and the deployment fails. If it fails, look for this message in the Cloud Run logs
 (if you set the variables in Cloud Console, also check for spaces around the variable names).
 
@@ -620,11 +620,11 @@ curl.exe -i "$CLOUD_RUN_URL/mcp" -X POST -H "Content-Type: application/json" `
 
 ### Step 8 — Add your user ID to ALLOWED_SUBJECTS
 
-With Dynamic Client Registration, anyone can register an OAuth client, so use `ALLOWED_SUBJECTS` to limit which users can connect
-(if it is empty, every user who can log in to AuthKit can use `/mcp`; if AuthKit allows sign-ups, that includes third parties).
+With Dynamic Client Registration, anyone can register an OAuth client, so `ALLOWED_SUBJECTS` limits which users can connect
+(without it, every user who can log in to AuthKit could use `/mcp`, including third parties if AuthKit allows sign-ups, so the server does not start without it).
 The value is the access token's `sub` (the WorkOS user ID, starting with `user_`).
 
-When `ALLOWED_SUBJECTS` is empty, `sub` is not logged. So connect once with the placeholder value in place, and find your `sub` in the log entry for the rejected request.
+The server logs the `sub` of users it rejects. So connect once with the placeholder value in place, and find your `sub` in the log entry for the rejected request.
 
 1. Connect from claude.ai or another client following [Client connection settings](#client-connection-settings) below, and log in with WorkOS AuthKit.
    Because your `sub` is not in `ALLOWED_SUBJECTS`, the connection fails with 403, and the server logs `[auth] forbidden subject: ...`.
@@ -796,7 +796,7 @@ The first release is published by hand, because Trusted Publishing can't be conf
 | `OAUTH_ISSUER` | Required in HTTP mode | The authorization server's issuer (`issuer` in its metadata). Compared with the token's `iss` |
 | `OAUTH_JWKS_URL` | Required in HTTP mode | The URL of the authorization server's JWKS (`jwks_uri` in the same metadata). Used to verify token signatures |
 | `MCP_RESOURCE_URL` | Required in HTTP mode | The public URL of the MCP endpoint. Compared with the token's `aud`, and published as `resource` in the Protected Resource Metadata |
-| `ALLOWED_SUBJECTS` | No (recommended) | A comma-separated list of token `sub` values allowed to connect. If empty, every user with a valid token is allowed |
+| `ALLOWED_SUBJECTS` | Required in HTTP mode | A comma-separated list of token `sub` values allowed to connect |
 
 `OAUTH_ISSUER`, `OAUTH_JWKS_URL`, `MCP_RESOURCE_URL`, and `ALLOWED_SUBJECTS` are used only in HTTP mode and are not needed in stdio mode.
 See steps 5–8 of [Deploying to Google Cloud Run](#deploying-to-google-cloud-run) for how to choose their values.

package/dist/auth.d.ts

@@ -12,7 +12,8 @@
  *      JWKS (signature, issuer, audience, expiry).
  *   3. Restricts access to an allowlist of token subjects — since DCR lets
  *      anyone register a client, this is what makes the server *yours only*.
- *      With the allowlist empty, any valid token is accepted.
+ *      The allowlist is required, so a missing value cannot open the server
+ *      to everyone who can sign in to the authorization server.
  *
  * Required environment variables (copy issuer/jwks from the provider's
  *   https://<your-authkit-domain>/.well-known/oauth-authorization-server ):
@@ -23,13 +24,10 @@
  *                       https://pubmed-mcp-PROJECT_NUMBER.asia-northeast1.run.app/mcp);
  *                       used as the expected token `aud` and as the resource
  *                       identifier
- *
- * Optional:
  *   ALLOWED_SUBJECTS  — comma-separated token `sub` values (user IDs) permitted
- *                       to connect. When empty, nothing is logged, so to find
- *                       your own id deploy with a placeholder value first:
- *                       rejected subjects are logged as
- *                       "[auth] forbidden subject: <sub>". Then set the real
+ *                       to connect. To find your own id, deploy with a
+ *                       placeholder value first: rejected subjects are logged
+ *                       as "[auth] forbidden subject: <sub>". Then set the real
  *                       value with `gcloud run services update --update-env-vars`.
  */
 import type { Request, Response, NextFunction } from 'express';

package/dist/auth.d.ts.map

@@ -1 +1 @@
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package/dist/auth.js

@@ -12,7 +12,8 @@
  *      JWKS (signature, issuer, audience, expiry).
  *   3. Restricts access to an allowlist of token subjects — since DCR lets
  *      anyone register a client, this is what makes the server *yours only*.
- *      With the allowlist empty, any valid token is accepted.
+ *      The allowlist is required, so a missing value cannot open the server
+ *      to everyone who can sign in to the authorization server.
  *
  * Required environment variables (copy issuer/jwks from the provider's
  *   https://<your-authkit-domain>/.well-known/oauth-authorization-server ):
@@ -23,23 +24,23 @@
  *                       https://pubmed-mcp-PROJECT_NUMBER.asia-northeast1.run.app/mcp);
  *                       used as the expected token `aud` and as the resource
  *                       identifier
- *
- * Optional:
  *   ALLOWED_SUBJECTS  — comma-separated token `sub` values (user IDs) permitted
- *                       to connect. When empty, nothing is logged, so to find
- *                       your own id deploy with a placeholder value first:
- *                       rejected subjects are logged as
- *                       "[auth] forbidden subject: <sub>". Then set the real
+ *                       to connect. To find your own id, deploy with a
+ *                       placeholder value first: rejected subjects are logged
+ *                       as "[auth] forbidden subject: <sub>". Then set the real
  *                       value with `gcloud run services update --update-env-vars`.
  */
 import { createRemoteJWKSet, jwtVerify } from 'jose';
 const ISSUER = requireEnv('OAUTH_ISSUER');
 const JWKS_URL = requireEnv('OAUTH_JWKS_URL');
 const RESOURCE = requireEnv('MCP_RESOURCE_URL');
-const ALLOWED_SUBJECTS = (process.env.ALLOWED_SUBJECTS ?? '')
+const ALLOWED_SUBJECTS = requireEnv('ALLOWED_SUBJECTS')
     .split(',')
     .map((s) => s.trim())
     .filter(Boolean);
+if (ALLOWED_SUBJECTS.length === 0) {
+    throw new Error('ALLOWED_SUBJECTS must list at least one token subject');
+}
 // Metadata lives at the well-known path on the same origin as the resource.
 const RESOURCE_METADATA_URL = `${originOf(RESOURCE)}/.well-known/oauth-protected-resource`;
 const jwks = createRemoteJWKSet(new URL(JWKS_URL));
@@ -60,23 +61,28 @@ export async function requireAuth(req, res, next) {
         return;
     }
     const token = header.slice('Bearer '.length).trim();
+    let subject;
     try {
         const { payload } = await jwtVerify(token, jwks, {
             issuer: ISSUER,
             audience: RESOURCE,
+            // jose checks exp only when present; a token without it would never expire.
+            requiredClaims: ['exp', 'sub'],
         });
-        if (ALLOWED_SUBJECTS.length > 0 && !ALLOWED_SUBJECTS.includes(payload.sub ?? '')) {
-            // Valid token, but not you. Log the subject so you can allowlist yourself.
-            process.stderr.write(`[auth] forbidden subject: ${payload.sub ?? '(none)'}\n`);
-            res.status(403).json({ error: 'forbidden' });
-            return;
-        }
-        next();
+        subject = String(payload.sub);
     }
     catch (err) {
         process.stderr.write(`[auth] token rejected: ${String(err)}\n`);
         unauthorized(res, 'invalid_token');
+        return;
+    }
+    if (!ALLOWED_SUBJECTS.includes(subject)) {
+        // Valid token, but not you. Log the subject so you can allowlist yourself.
+        process.stderr.write(`[auth] forbidden subject: ${subject}\n`);
+        res.status(403).json({ error: 'forbidden' });
+        return;
     }
+    next();
 }
 // ── Helpers ─────────────────────────────────────────────────────────────────
 /** 401 with the RFC 9728 pointer so the client can discover how to authorize. */

package/dist/auth.js.map

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+{"version":3,"file":"auth.js","sourceRoot":"","sources":["../src/auth.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAGH,OAAO,EAAE,kBAAkB,EAAE,SAAS,EAAE,MAAM,MAAM,CAAC;AAErD,MAAM,MAAM,GAAG,UAAU,CAAC,cAAc,CAAC,CAAC;AAC1C,MAAM,QAAQ,GAAG,UAAU,CAAC,gBAAgB,CAAC,CAAC;AAC9C,MAAM,QAAQ,GAAG,UAAU,CAAC,kBAAkB,CAAC,CAAC;AAEhD,MAAM,gBAAgB,GAAG,UAAU,CAAC,kBAAkB,CAAC;KACpD,KAAK,CAAC,GAAG,CAAC;KACV,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;KACpB,MAAM,CAAC,OAAO,CAAC,CAAC;AACnB,IAAI,gBAAgB,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;IAClC,MAAM,IAAI,KAAK,CAAC,uDAAuD,CAAC,CAAC;AAC3E,CAAC;AAED,4EAA4E;AAC5E,MAAM,qBAAqB,GAAG,GAAG,QAAQ,CAAC,QAAQ,CAAC,uCAAuC,CAAC;AAE3F,MAAM,IAAI,GAAG,kBAAkB,CAAC,IAAI,GAAG,CAAC,QAAQ,CAAC,CAAC,CAAC;AAEnD,+EAA+E;AAE/E,4EAA4E;AAC5E,MAAM,UAAU,yBAAyB,CAAC,IAAa,EAAE,GAAa;IACpE,GAAG,CAAC,IAAI,CAAC;QACP,QAAQ,EAAE,QAAQ;QAClB,qBAAqB,EAAE,CAAC,MAAM,CAAC;QAC/B,wBAAwB,EAAE,CAAC,QAAQ,CAAC;KACrC,CAAC,CAAC;AACL,CAAC;AAED,+EAA+E;AAE/E,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,GAAY,EACZ,GAAa,EACb,IAAkB;IAElB,MAAM,MAAM,GAAG,GAAG,CAAC,OAAO,CAAC,aAAa,CAAC;IACzC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,SAAS,CAAC,EAAE,CAAC;QACnC,YAAY,CAAC,GAAG,EAAE,eAAe,CAAC,CAAC;QACnC,OAAO;IACT,CAAC;IAED,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,CAAC;IACpD,IAAI,OAAe,CAAC;IACpB,IAAI,CAAC;QACH,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,SAAS,CAAC,KAAK,EAAE,IAAI,EAAE;YAC/C,MAAM,EAAE,MAAM;YACd,QAAQ,EAAE,QAAQ;YAClB,4EAA4E;YAC5E,cAAc,EAAE,CAAC,KAAK,EAAE,KAAK,CAAC;SAC/B,CAAC,CAAC;QACH,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;IAChC,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,0BAA0B,MAAM,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAChE,YAAY,CAAC,GAAG,EAAE,eAAe,CAAC,CAAC;QACnC,OAAO;IACT,CAAC;IAED,IAAI,CAAC,gBAAgB,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE,CAAC;QACxC,2EAA2E;QAC3E,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,6BAA6B,OAAO,IAAI,CAAC,CAAC;QAC/D,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,WAAW,EAAE,CAAC,CAAC;QAC7C,OAAO;IACT,CAAC;IAED,IAAI,EAAE,CAAC;AACT,CAAC;AAED,+EAA+E;AAE/E,iFAAiF;AACjF,SAAS,YAAY,CAAC,GAAa,EAAE,KAAa;IAChD,GAAG,CAAC,SAAS,CACX,kBAAkB,EAClB,6BAA6B,qBAAqB,aAAa,KAAK,GAAG,CACxE,CAAC;IACF,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC;AAClC,CAAC;AAED,SAAS,QAAQ,CAAC,GAAW;IAC3B,OAAO,IAAI,GAAG,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC;AAC7B,CAAC;AAED,SAAS,UAAU,CAAC,IAAY;IAC9B,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;IAChC,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,MAAM,IAAI,KAAK,CAAC,0CAA0C,IAAI,EAAE,CAAC,CAAC;IACpE,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}

package/dist/cli/commands.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"commands.d.ts","sourceRoot":"","sources":["../../src/cli/commands.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAGH,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAgCtD,4EAA4E;AAC5E,qBAAa,UAAW,SAAQ,KAAK;gBACvB,OAAO,EAAE,MAAM;CAI5B;AAED,MAAM,WAAW,YAAY;IAC3B,oFAAoF;IACpF,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAAC,CAAC;IAC3C,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,8CAA8C;IAC9C,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC;CACzC;AAED,MAAM,WAAW,aAAa;IAC5B,MAAM,EAAE,OAAO,CAAC;IAChB,2DAA2D;IAC3D,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,OAAO;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,sCAAsC;IACtC,IAAI,EAAE,MAAM,CAAC;IACb,wDAAwD;IACxD,WAAW,EAAE,MAAM,CAAC;IACpB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE;QAAE,IAAI,EAAE,QAAQ,CAAA;KAAE,CAAC,CAAC;IAC5C,OAAO,CAAC,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,UAAU,GAAG,OAAO,CAAC,aAAa,CAAC,CAAC;CAC1E;AAmbD,eAAO,MAAM,QAAQ,EAAE,OAAO,EAQ7B,CAAC;AAsGF,wBAAgB,YAAY,CAAC,GAAG,EAAE,OAAO,GAAG,MAAM,CAEjD"}
+{"version":3,"file":"commands.d.ts","sourceRoot":"","sources":["../../src/cli/commands.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAGH,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAiCtD,4EAA4E;AAC5E,qBAAa,UAAW,SAAQ,KAAK;gBACvB,OAAO,EAAE,MAAM;CAI5B;AAED,MAAM,WAAW,YAAY;IAC3B,oFAAoF;IACpF,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAAC,CAAC;IAC3C,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,8CAA8C;IAC9C,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC;CACzC;AAED,MAAM,WAAW,aAAa;IAC5B,MAAM,EAAE,OAAO,CAAC;IAChB,2DAA2D;IAC3D,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,OAAO;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,sCAAsC;IACtC,IAAI,EAAE,MAAM,CAAC;IACb,wDAAwD;IACxD,WAAW,EAAE,MAAM,CAAC;IACpB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE;QAAE,IAAI,EAAE,QAAQ,CAAA;KAAE,CAAC,CAAC;IAC5C,OAAO,CAAC,KAAK,EAAE,YAAY,EAAE,MAAM,EAAE,UAAU,GAAG,OAAO,CAAC,aAAa,CAAC,CAAC;CAC1E;AAgbD,eAAO,MAAM,QAAQ,EAAE,OAAO,EAQ7B,CAAC;AAsGF,wBAAgB,YAAY,CAAC,GAAG,EAAE,OAAO,GAAG,MAAM,CAEjD"}

package/dist/cli/commands.js

@@ -11,7 +11,7 @@
 import { z } from 'zod';
 import { searchArticles, searchArticlesSchema } from '../tools/searchArticles.js';
 import { getArticleMetadata, getArticleMetadataSchema, MAX_METADATA_PMIDS, } from '../tools/getArticleMetadata.js';
-import { findRelatedArticles, findRelatedArticlesSchema, } from '../tools/findRelatedArticles.js';
+import { findRelatedArticles, findRelatedArticlesSchema, MAX_RELATED_PMIDS, } from '../tools/findRelatedArticles.js';
 import { lookupArticleByCitation, lookupArticleByCitationSchema, MAX_CITATIONS, } from '../tools/lookupArticleByCitation.js';
 import { convertArticleIds, convertArticleIdsSchema, MAX_CONVERT_IDS, } from '../tools/convertArticleIds.js';
 import { getFullTextArticle, getFullTextArticleSchema, MAX_FULL_TEXT_IDS, } from '../tools/getFullTextArticle.js';
@@ -133,8 +133,6 @@ Example:
     },
 };
 // ─── related ────────────────────────────────────────────────────────────────
-/** ELink takes the IDs in the URL, so keep each request's list short. */
-const RELATED_BATCH_SIZE = 200;
 const related = {
     name: 'related',
     tool: 'find_related_articles',
@@ -146,7 +144,7 @@ const related = {
     help: `Usage: pubmed related <pmid>... | - [options]
 
 Find linked records for each PMID with NCBI ELink (same JSON as
-find_related_articles). Lists longer than ${RELATED_BATCH_SIZE} PMIDs are split into batches.
+find_related_articles). Lists longer than ${MAX_RELATED_PMIDS} PMIDs are split into batches.
 
 Options:
   --link-type <type>  similar_articles (default)  similar PubMed articles
@@ -167,7 +165,7 @@ Example:
         const pmids = await readIds(input, PMID);
         const linkType = input.values['link-type'];
         const maxResults = intOption(input, 'max-results');
-        const batches = chunk(pmids, RELATED_BATCH_SIZE).map((batch) => validate(findRelatedArticlesSchema, {
+        const batches = chunk(pmids, MAX_RELATED_PMIDS).map((batch) => validate(findRelatedArticlesSchema, {
             pmids: batch,
             link_type: linkType,
             max_results: maxResults,

package/dist/cli/commands.js.map

@@ -1 +1 @@
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package/dist/cli/run.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"run.d.ts","sourceRoot":"","sources":["../../src/cli/run.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAGH,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAUjD,MAAM,WAAW,KAAK;IACpB,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,8CAA8C;IAC9C,QAAQ,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC;IACxC,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC;CACtD;AAOD,yDAAyD;AACzD,wBAAsB,MAAM,CAC1B,IAAI,EAAE,MAAM,EAAE,EACd,EAAE,EAAE,KAAK,EACT,MAAM,CAAC,EAAE,UAAU,GAClB,OAAO,CAAC,MAAM,CAAC,CAmFjB"}

package/dist/cli/run.js

@@ -10,6 +10,7 @@
  */
 import { parseArgs } from 'node:util';
 import { NcbiClient } from '../pubmed/client.js';
+import { packageVersion } from '../version.js';
 import { COMMANDS, UsageError, errorMessage, } from './commands.js';
 const COMMON_OPTIONS = {
     output: { type: 'string', short: 'o' },
@@ -26,6 +27,10 @@ export async function runCli(argv, io, client) {
         io.stdout(globalHelp());
         return 0;
     }
+    if (name === '-v' || name === '--version') {
+        io.stdout(`${packageVersion()}\n`);
+        return 0;
+    }
     if (name === 'help') {
         if (args[0] === undefined) {
             io.stdout(globalHelp());
@@ -127,6 +132,7 @@ ${commandList}
 Options:
   -o, --output <file>  Write the JSON to <file> instead of stdout
   -h, --help           Show help; "pubmed <command> --help" for a command
+  -v, --version        Show the version
 
 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.

package/dist/cli/run.js.map

@@ -1 +1 @@
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package/dist/http.d.ts

@@ -0,0 +1,20 @@
+/**
+ * Express app for HTTP mode (Cloud Run / remote deployment).
+ *
+ * Kept apart from the entrypoint (src/index.ts) so tests can run it with a
+ * mocked NCBI client. Importing this module loads auth.ts, which reads the
+ * OAuth environment variables and throws if any of them is missing.
+ *
+ * Routes:
+ *   POST /mcp                                — MCP Streamable HTTP (Bearer token required)
+ *   GET  /.well-known/oauth-protected-resource — RFC 9728 metadata (public)
+ *   GET  /health                             — Cloud Run probes (public)
+ */
+import express from 'express';
+import type { NcbiClient } from './pubmed/client.js';
+/**
+ * @param ncbiClient Shared by every per-request MCP server, so that its rate
+ *   limiter spans concurrent requests.
+ */
+export declare function createHttpApp(ncbiClient: NcbiClient): express.Express;
+//# sourceMappingURL=http.d.ts.map

package/dist/http.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"http.d.ts","sourceRoot":"","sources":["../src/http.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,OAA2D,MAAM,SAAS,CAAC;AAIlF,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAC;AAErD;;;GAGG;AACH,wBAAgB,aAAa,CAAC,UAAU,EAAE,UAAU,GAAG,OAAO,CAAC,OAAO,CA6ErE"}

package/dist/http.js

@@ -0,0 +1,86 @@
+/**
+ * Express app for HTTP mode (Cloud Run / remote deployment).
+ *
+ * Kept apart from the entrypoint (src/index.ts) so tests can run it with a
+ * mocked NCBI client. Importing this module loads auth.ts, which reads the
+ * OAuth environment variables and throws if any of them is missing.
+ *
+ * Routes:
+ *   POST /mcp                                — MCP Streamable HTTP (Bearer token required)
+ *   GET  /.well-known/oauth-protected-resource — RFC 9728 metadata (public)
+ *   GET  /health                             — Cloud Run probes (public)
+ */
+import express from 'express';
+import { StreamableHTTPServerTransport } from '@modelcontextprotocol/sdk/server/streamableHttp.js';
+import { protectedResourceMetadata, requireAuth } from './auth.js';
+import { createServer } from './server.js';
+/**
+ * @param ncbiClient Shared by every per-request MCP server, so that its rate
+ *   limiter spans concurrent requests.
+ */
+export function createHttpApp(ncbiClient) {
+    const app = express();
+    app.disable('x-powered-by');
+    // 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);
+    // 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');
+    });
+    // MCP Streamable HTTP. The body is parsed only after the token is verified.
+    // SDK v1.x: stateless transports cannot be reused across requests.
+    // A new transport and server instance must be created for every request.
+    app.post('/mcp', requireAuth, express.json(), (req, res) => {
+        const transport = new StreamableHTTPServerTransport({
+            sessionIdGenerator: undefined, // stateless mode
+        });
+        const mcpServer = createServer(ncbiClient);
+        res.on('close', () => {
+            // Also closes the transport.
+            mcpServer.close().catch((err) => {
+                process.stderr.write(`[http] close error: ${String(err)}\n`);
+            });
+        });
+        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' });
+            }
+        });
+    });
+    // A stateless server sends no server-initiated messages and has no session,
+    // so there is no SSE stream to open with GET and nothing to end with DELETE.
+    // Answering 405, as the MCP spec allows, keeps clients from holding idle
+    // streams open (each one would keep a server instance and a Cloud Run
+    // request alive).
+    app.all('/mcp', requireAuth, (_req, res) => {
+        res.setHeader('Allow', 'POST');
+        res.status(405).json({ error: 'method_not_allowed' });
+    });
+    // Errors such as malformed or oversized request bodies get JSON, not
+    // Express's default HTML page, which includes the stack trace unless
+    // NODE_ENV is "production".
+    app.use((err, _req, res, next) => {
+        if (res.headersSent) {
+            next(err);
+            return;
+        }
+        if (err.type === 'entity.parse.failed') {
+            res.status(400).json({ error: 'Invalid JSON body' });
+            return;
+        }
+        if (err.status !== undefined && err.status >= 400 && err.status < 500) {
+            res.status(err.status).json({ error: err.expose ? err.message : 'Bad request' });
+            return;
+        }
+        process.stderr.write(`[http] unhandled error: ${String(err)}\n`);
+        res.status(500).json({ error: 'Internal server error' });
+    });
+    return app;
+}
+//# sourceMappingURL=http.js.map

package/dist/http.js.map

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

@@ -11,7 +11,8 @@
  *
  *   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.
+ *     Starts an Express server (see http.ts) 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
@@ -23,10 +24,9 @@
  *   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
+ *   OAUTH_ISSUER, OAUTH_JWKS_URL, MCP_RESOURCE_URL, ALLOWED_SUBJECTS
  *                    — Required in HTTP mode; startup fails without them.
- *   ALLOWED_SUBJECTS — Optional allowlist of token subjects (HTTP mode).
- *                      See auth.ts for all four.
+ *                      See auth.ts.
  */
 export {};
 //# sourceMappingURL=index.d.ts.map