Agent skill

API Auth

by cyanheads in cyanheads/pubmed-mcp-server

Authentication, authorization, and multi-tenancy patterns for @cyanheads/mcp-ts-core.

Apache-2.0Auto-check passedBackend & APIs

Install API Auth

skills CLI
$ npx skills add cyanheads/pubmed-mcp-server --skill api-auth -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install cyanheads/pubmed-mcp-server api-auth --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/cyanheads/pubmed-mcp-server.git skills-src && mkdir -p .claude/skills && cp -r skills-src/framework-skills/api-auth .claude/skills/api-auth && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
api-auth
GitHub stars
154
Token cost
~2.7k tokens
SKILL.md length
1,024 words
Files
1
Skills in repo
30
Repo updated
First seen
Licence
Apache-2.0

At a glance

Authentication, authorization, and multi-tenancy patterns for @cyanheads/mcp-ts-core.

  • Implementing auth scopes on tools/resources
  • SKILL.md covers Overview, Inline auth (primary pattern), Dynamic auth and Auth modes, plus 3 more sections
  • Needs MCP_AUTH_SECRET_KEY
  • Configuring auth modes (none/jwt/oauth)

What it does

API Auth is an agent skill from cyanheads/pubmed-mcp-server. Authentication, authorization, and multi-tenancy patterns for @cyanheads/mcp-ts-core. Use when implementing auth scopes on tools/resources, configuring auth modes (none/jwt/oauth), working with JWT/OAuth env vars, or understanding how tenantId flows through ctx.state.

Its SKILL.md is about 2.7k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Backend & APIs, covering Authentication, OAuth and OpenID Connect and MCP servers. It works with Model Context Protocol. The repository describes itself as: Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP. The licence is Apache-2.0.

When your agent uses it

  • Implementing auth scopes on tools/resources
  • Configuring auth modes (none/jwt/oauth)
  • Working with JWT/OAuth env vars
  • Understanding how tenantId flows through ctx.state

Example prompts

  • “/api-auth”

Requirements

  • A credential in MCP_AUTH_SECRET_KEY

What it can do on your machine

Read from SKILL.md and the folder at commit 5a417fb. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md (its code samples are typescript).

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names these keys or tokens, usually read from environment variables:

    • MCP_AUTH_SECRET_KEY

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

API Auth loads about 2.7k tokens when it runs. Until then it costs about 70 tokens; SKILL.md has 1,024 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~70
When it runs · the whole SKILL.md, loaded when a task matches
~2.7k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from cyanheads/pubmed-mcp-server at commit 5a417fb, republished under its Apache-2.0 licence (© cyanheads). 1,024 words, ~2,685 tokens.

Download SKILL.mdSave it as .claude/skills/api-auth/SKILL.md (or your agent's skills folder).
name
api-auth
description
Authentication, authorization, and multi-tenancy patterns for `@cyanheads/mcp-ts-core`. Use when implementing auth scopes on tools/resources, configuring auth modes (none/jwt/oauth), working with JWT/OAuth env vars, or understanding how tenantId flows through ctx.state.
metadata.author
cyanheads
metadata.version
1.5
metadata.audience
external
metadata.type
reference

Overview

The framework handles auth at the handler factory level — tools and resources declare required scopes declaratively, and the framework enforces them before calling the handler. No try/catch or manual scope checking required for the common case.


Inline auth (primary pattern)

Declare required scopes directly on the tool or resource definition via the auth property. The handler factory checks ctx.auth.scopes against these before calling handler.

ts
import { tool } from '@cyanheads/mcp-ts-core';

const myTool = tool('my_tool', {
  input: z.object({ query: z.string().describe('Search query') }),
  output: z.object({ result: z.string().describe('Search result') }),
  auth: ['tool:my_tool:read'],
  async handler(input, ctx) {
    // Only reached if caller has 'tool:my_tool:read' scope
  },
});

When MCP_AUTH_MODE=none, auth checks are skipped and defaults are allowed.

A failed check returns Forbidden (-32005, Insufficient permissions.) or, when auth is enabled but the request carries no auth context, Unauthorized (-32006). Neither carries data: the required, granted, and missing scope names stay in the server log, so a caller cannot enumerate scopes from the error.


Dynamic auth

For runtime-computed scopes (e.g., scopes that depend on input values like a team or resource ID), use checkScopes from @cyanheads/mcp-ts-core/auth inside the handler:

ts
import { checkScopes } from '@cyanheads/mcp-ts-core/auth';

handler: async (input, ctx) => {
  checkScopes(ctx, [`team:${input.teamId}:write`]);
  // Continues only if scope is satisfied
},

Signature: checkScopes(ctx: Context, requiredScopes: string[]): void

Throws:

  • McpError(Forbidden) — auth is active and one or more required scopes are missing
  • McpError(Unauthorized) — auth is enabled but no auth context exists on the request
  • No-ops when MCP_AUTH_MODE=none

Auth modes

Set via MCP_AUTH_MODE environment variable.

ModeValueBehavior
DisablednoneNo auth enforcement. All requests allowed.
JWTjwtLocal secret verification via MCP_AUTH_SECRET_KEY. Requires explicit DEV_MCP_AUTH_BYPASS=true to bypass in development.
OAuthoauthJWKS verification against an external issuer.
JWT config
VariableRequiredPurpose
MCP_AUTH_SECRET_KEYYes (unless bypass)Signing secret for HS256 JWT verification. Must be ≥ 32 characters.
DEV_MCP_AUTH_BYPASSNoSet to true to skip JWT verification in development. Blocked in NODE_ENV=production.
DEV_MCP_CLIENT_IDNoClient ID injected when bypass is active (default: 'dev-client-id').
DEV_MCP_SCOPESNoComma-separated scopes injected when bypass is active (default: ['dev-scope']).

Important: With MCP_AUTH_MODE=jwt, a missing MCP_AUTH_SECRET_KEY is a fatal startup error unless DEV_MCP_AUTH_BYPASS=true is explicitly set. Setting DEV_MCP_AUTH_BYPASS in production (NODE_ENV=production) is rejected at config parse time.

OAuth config
VariableRequiredPurpose
OAUTH_ISSUER_URLYesToken issuer URL (used for JWKS discovery)
OAUTH_AUDIENCEYesExpected aud claim value
OAUTH_JWKS_URINoOverride JWKS endpoint (defaults to {issuer}/.well-known/jwks.json)
MCP_SERVER_RESOURCE_IDENTIFIERNoRFC 8707 resource indicator URI. When set, the OAuth strategy validates that the token's resource or aud claim matches this value — throws Forbidden on mismatch.
JWT claims mapping
ClaimJWT FieldPurpose
clientIdcid / client_idIdentifies the calling client
scopesunion of scp, scope, mcp_tool_scopesGranted scope list (see below)
subsubSubject (user or service identity)
tenantIdtidTenant identifier — drives ctx.state scoping

scopes is the union of three claims, in this order:

ClaimFormSource
scparray of stringsOkta-style
scopespace-delimited stringOAuth 2.1 / OIDC standard
mcp_tool_scopesarray of strings or space-delimited stringCustom claim for OIDC providers that cannot inject scopes into scope during the authorization_code flow (Authentik, Keycloak < 26.5, Zitadel)

Auth0/Okta-style providers that already populate scp or scope need no migration. Other deployments add a property mapping returning {"mcp_tool_scopes": "tool:foo:read tool:bar:write"} — the framework unions it into ctx.auth.scopes alongside the standard claims. Hardcoded claim name; deployments whose IdP cannot emit mcp_tool_scopes use the bypass flag below.

OIDC operator setup (Authentik / Keycloak / Zitadel)

Standard OIDC providers compute the JWT scope claim from what the OAuth client requested at the authorization endpoint and ignore property mappings that try to override scope in the authorization_code flow. Property mappings that inject other claim names work fine. To grant per-tool scopes to a Claude.ai or ChatGPT custom connector that doesn't expose scope customization, configure your IdP to return the per-tool scopes under mcp_tool_scopes instead of overriding scope.

ProviderWhere to configure
AuthentikCustomization → Property Mappings → new "Scope Mapping" returning {"mcp_tool_scopes": "tool:foo:read tool:bar:write"}; bind to the OAuth2/OpenID provider
Keycloak (< 26.5)Client → Client Scopes → Mappers → new "Hardcoded claim" or "Script Mapper" emitting mcp_tool_scopes
ZitadelProject → Roles + Action returning {"mcp_tool_scopes": "..."} from a pre-token script

Keycloak ≥ 26.5 ships native MCP integration support; check its release notes before falling back to a custom claim.

Show full SKILL.md (394 more words)Show less
Bypass flag

For environments where no custom claim can be injected (managed services, restricted IdPs), set MCP_AUTH_DISABLE_SCOPE_CHECKS=true to bypass scope enforcement entirely.

VariableDefaultEffect
MCP_AUTH_DISABLE_SCOPE_CHECKSfalseWhen true, both withRequiredScopes (declared auth: [...]) and checkScopes (runtime-computed scopes inside handlers) early-return after the auth-context presence check. Token signature, audience, issuer, and expiry validation remain intact.

The flag bypasses both declared auth: [...] enforcement and runtime checkScopes calls — including tenant isolation patterns like team:${input.teamId}:write. Naming is deliberate: this disables all scope checks, not just per-tool ones. Applies to MCP_AUTH_MODE=jwt and MCP_AUTH_MODE=oauth (no effect under none).

A WARNING-level log is emitted at startup whenever the flag is active so operators don't lose track of it. Combine with server-side ACLs (path filters, allowlists, tenant rules) — without an in-handler ACL, every authenticated user effectively has every scope.


Endpoints

EndpointProtected
GET /healthzNo
GET /mcpNo
POST /mcpYes (when auth enabled)
DELETE /mcpYes (when auth enabled) — session termination
OPTIONS /mcpNo (handled by CORS middleware before auth)

CORS: Set MCP_ALLOWED_ORIGINS to a comma-separated list of allowed origins, or * for open access. Left unset, only loopback browser origins reach the endpoint. The preflight for an accepted origin allows every request header the server reads: Content-Type, Authorization, Mcp-Session-Id, MCP-Protocol-Version, the 2026-07-28 Mcp-Method and Mcp-Name, Last-Event-ID (SSE resume), and one Mcp-Param-<Name> per headerParam designation on a registered tool — derived from the tool definitions, nothing to configure. Any other origin gets the first four only, so it learns no designation names.

Stdio mode: No HTTP auth layer. Authorization is handled entirely by the host process.


Multi-tenancy

ctx.state is automatically scoped to the current tenant — no manual key prefixing needed.

tenantId sources
ModeSourceValue
Stdio (any auth mode)Hardcoded default'default'
HTTP + MCP_AUTH_MODE=noneHardcoded default'default' (single-tenant by design)
HTTP + MCP_AUTH_MODE=jwt/oauthJWT tid claimAuto-propagated from token; undefined if absent (fail-closed)
Tenant ID validation rules
  • Max 128 characters
  • Characters: alphanumeric, hyphens, underscores, dots
  • Must start and end with an alphanumeric character
  • No path traversal sequences (../)
  • No consecutive dots (..)
Using ctx.state
ts
handler: async (input, ctx) => {
  // Automatically scoped to ctx.tenantId — no manual prefixing
  await ctx.state.set('item/123', { name: 'Widget', count: 42 });
  const item = await ctx.state.get<Item>('item/123');
  await ctx.state.delete('item/123');

  const page = await ctx.state.list('item/', { cursor, limit: 20 });
  // page: { items: Array<{ key, value }>, cursor?: string }
},

ctx.state throws McpError(InvalidRequest) if tenantId is missing. Stdio (any auth mode) and HTTP+MCP_AUTH_MODE=none default tenantId to 'default' so ctx.state works without forcing operators to mint tokens. HTTP+jwt/oauth deliberately fails closed when the token lacks a tid claim — distinct authenticated callers must not silently share state.


Auth context shape

Available on ctx.auth inside handlers (when auth is enabled):

ts
interface AuthContext {
  clientId: string;        // Required — 'cid' or 'client_id' JWT claim
  scopes: string[];        // Required — union of 'scp', 'scope', and 'mcp_tool_scopes' claims
  sub: string;             // Required — 'sub' claim; falls back to clientId when absent
  token?: string;          // Optional — raw JWT or OAuth bearer token string (present when transport provides it)
  tenantId?: string;       // Optional — 'tid' claim; present only for multi-tenant tokens
}

Access directly for conditional logic:

ts
handler: async (input, ctx) => {
  const isAdmin = ctx.auth?.scopes.includes('admin:write') ?? false;
  // ...
},

© cyanheads, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in framework-skills/api-auth of cyanheads/pubmed-mcp-server.

Open the folder on GitHubat commit 5a417fb

Compare with similar skills

API Auth next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

API Auth compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
API Auth this skillcyanheads/pubmed-mcp-server154—~2.7kAutomated safety check: PassApache-2.0
Atlassiansanjay3290/ai-skills430—~1.6kAutomated safety check: PassApache-2.0
Spring Security ConfigurationAmplicode/spring-skills126—~4.3kAutomated safety check: PassNone
Cao MCP Appsawslabs/cli-agent-orchestrator1.4k—~1.9kAutomated safety check: PassApache-2.0
Review Security ReportPrefectHQ/fastmcp28k—~1.2kAutomated safety check: PassApache-2.0
Supercheck Security Authsupercheck-io/supercheck215—~1.2kAutomated safety check: PassAGPL-3.0

Similar skills

  • Atlassian

    sanjay3290/ai-skills

    Manage Jira issues and Confluence wiki pages in Atlassian Cloud.

    430 GitHub stars~1.6k tokensUpdated 27 days ago
    Backend & APIsAuto-check passed
  • Spring Security Configuration

    Amplicode/spring-skills

    Creates a Spring Security configuration class with authentication, authorization, and HTTP protection setup.

    126 GitHub stars~4.3k tokensUpdated 1 mo ago
    Backend & APIsAuto-check passed
  • Cao MCP Apps

    awslabs/cli-agent-orchestrator

    Official

    Enable, operate, and extend CAO's MCP Apps surface — the host-rendered fleet dashboard visible inside MCP App hosts (Claude Desktop, ChatGPT, VS Code Copilot, Goose, Postman).

    1.4k GitHub stars~1.9k tokensUpdated today
    Agent WorkflowsAuto-check passed
  • Review Security Report

    PrefectHQ/fastmcp

    Review FastMCP vulnerability reports before accepting, rejecting, patching, scoring, or publishing them.

    28k GitHub stars~1.2k tokensUpdated yesterday
    Backend & APIsAuto-check passed
  • Supercheck Security Auth

    supercheck-io/supercheck

    Work on Supercheck authentication, RBAC, tenant isolation, sessions, API and trigger keys, invitations, project membership, project variables, OAuth, super-admin behavior, SSRF, or…

    215 GitHub stars~1.2k tokensUpdated today
    Backend & APIsAuto-check passed
  • Xquik MCP

    Xquik-dev/x-twitter-scraper

    Connect, verify, and troubleshoot Xquik's remote MCP server.

    209 GitHub stars~997 tokensUpdated yesterday
    Backend & APIsAuto-check passed

More from cyanheads/pubmed-mcp-server

All 30 skills in this repo
  • Add App Tool

    cyanheads/pubmed-mcp-server

    Scaffold an MCP App tool + UI resource pair. An agent skill from cyanheads/pubmed-mcp-server.

    154 GitHub stars~3.2k tokensUpdated 3 days ago
    Auto-check passed
  • Add Prompt

    cyanheads/pubmed-mcp-server

    Scaffold a new MCP prompt template. An agent skill from cyanheads/pubmed-mcp-server.

    154 GitHub stars~1.6k tokensUpdated 3 days ago
    Auto-check passed
  • Add Resource

    cyanheads/pubmed-mcp-server

    Scaffold a new MCP resource definition. An agent skill from cyanheads/pubmed-mcp-server.

    154 GitHub stars~3k tokensUpdated 3 days ago
    Auto-check passed
  • Add Service

    cyanheads/pubmed-mcp-server

    Scaffold a new service integration. An agent skill from cyanheads/pubmed-mcp-server.

    154 GitHub stars~3.6k tokensUpdated 3 days ago
    Auto-check passed
  • Add Test

    cyanheads/pubmed-mcp-server

    Scaffold a test file for an existing tool, resource, or service.

    154 GitHub stars~4.1k tokensUpdated 3 days ago
    Auto-check passed
  • API Mirror

    cyanheads/pubmed-mcp-server

    Stand up a persistent, self-refreshing local mirror of a bulk upstream dataset with the MirrorService (@cyanheads/mcp-ts-core/mirror).

    154 GitHub stars~2.5k tokensUpdated 3 days ago
    Auto-check passed

Categories

Questions about API Auth

What does API Auth do?

Authentication, authorization, and multi-tenancy patterns for @cyanheads/mcp-ts-core. API Auth is an agent skill from cyanheads/pubmed-mcp-server. Authentication, authorization, and multi-tenancy patterns for @cyanheads/mcp-ts-core.

When should I use API Auth?

API Auth fits situations like: implementing auth scopes on tools/resources; configuring auth modes (none/jwt/oauth); working with JWT/OAuth env vars; understanding how tenantId flows through ctx.state.

How do I install API Auth in Claude Code?

Run `npx skills add cyanheads/pubmed-mcp-server --skill api-auth -a claude-code`. Or copy the skill folder (framework-skills/api-auth in cyanheads/pubmed-mcp-server) into .claude/skills/api-auth in your project. Claude Code loads it when a task matches its description.

How do I install API Auth in Codex?

Run `npx skills add cyanheads/pubmed-mcp-server --skill api-auth -a codex`. Or copy the skill folder (framework-skills/api-auth in cyanheads/pubmed-mcp-server) into .agents/skills/api-auth in your project. Codex loads it when a task matches its description.

Can I use API Auth in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add cyanheads/pubmed-mcp-server --skill api-auth -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/api-auth, .gemini/skills/api-auth, .github/skills/api-auth and .opencode/skills/api-auth in your project.

What does API Auth need to run?

Going by SKILL.md and its folder, API Auth needs credentials named MCP_AUTH_SECRET_KEY. Our summary lists: A credential in MCP_AUTH_SECRET_KEY.

Does API Auth access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is API Auth safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does API Auth use?

API Auth is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does API Auth use?

About 2.7k tokens (SKILL.md is roughly 11k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to API Auth?

Skills that share tags, products or a category with API Auth: Atlassian (sanjay3290/ai-skills, 430 stars), Spring Security Configuration (Amplicode/spring-skills, 126 stars), Cao MCP Apps (awslabs/cli-agent-orchestrator, 1.4k stars) and Review Security Report (PrefectHQ/fastmcp, 28k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains API Auth?

cyanheads (a GitHub user) maintains it in cyanheads/pubmed-mcp-server, which has 154 GitHub stars. The repository holds 30 skills in this directory. The repository was last updated on October 4, 2026.

Source: cyanheads/pubmed-mcp-server on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.