mcp-server-mysql

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A security-first MySQL MCP server. Every SQL statement must survive a full AST parse by an industrial-grade SQL parser (TiDB parser) before it can touch your database — backed by a read-only transaction fallback and a driver-level multi-statement lockout. Three independent layers of defense-in-depth: let AI query your database, without letting it walk off with your database.

Why this one?

Most MySQL MCP servers enforce "read-only" with regex/keyword matching, or by wrapping queries in a read-only transaction. Both are broken:

• Regex checks are defeated by SQL comments and creative rewriting.

• A read-only transaction alone is defeated by COMMIT; DROP TABLE ... stacked-statement injection — the exact attack Datadog demonstrated against the official Postgres reference server, which has since been archived.

This project puts the security boundary on real SQL semantic parsing instead. Every statement is parsed into an AST by the TiDB parser (MySQL 8.0-grammar compatible); anything the parser cannot understand is rejected — fail-closed, so incomplete grammar coverage can only over-block, never under-block. And because the parser sees real MySQL semantics, tricks like hiding a JOIN mysql.user inside a versioned comment /*!80000 ... */ are extracted and checked like any other table reference.

Related MCP server: DatabaseMCP

Highlights

• Statement-class gating — SELECT / INSERT / UPDATE / DELETE / DDL are individually switchable; the default is read-only. SET, GRANT, CALL, USE, LOAD DATA, LOCK TABLES, and transaction control (BEGIN/COMMIT/ROLLBACK) are rejected unconditionally — classification itself is an allowlist, so unknown statement types land on the deny side by construction.

• Default-deny table whitelist — nothing is visible until whitelisted; patterns like db.*, db.table, app_*.logs (glob per side, case-insensitive). Every table reference is extracted from the AST: JOINs, subqueries, derived tables, CTEs (scope-aware — a CTE name can't shadow a real table to smuggle it past the check), multi-table DML, INSERT ... SELECT, and versioned comments.

• Execution guardrails — hard row cap, per-query timeout, single-statement enforcement, and a tripwire for UPDATE/DELETE without WHERE.

• Built-in observability — per-query latency and row counts, slow-query flagging, and a mysql_stats tool so you can ask "which query was slowest?" right in the conversation.

• Structured audit, opt-in — JSONL with daily rotation; denied SQL is recorded with the exact rule that fired. Off by default: no log files unless you enable it.

• Atomic scripts — mysql_script runs a multi-statement script in a single transaction with every statement individually re-validated; any failure rolls back everything. DDL is banned inside scripts because MySQL's implicit commit would break atomicity.

• Query-plan analysis — mysql_explain with traditional / json / tree formats and EXPLAIN ANALYZE support.

• Easy to run, small to trust — a single static Go binary over stdio, built on the official MCP Go SDK; the Docker image is distroless and runs as a non-root user.

Tools

Quick start

1. Get the binary

Prebuilt — download the tarball for your platform (linux_amd64 / linux_arm64 / darwin_arm64) from Releases (checksums included), or install with Go:

go install github.com/Kurok1/mcp-server-mysql/cmd/mcp-server-mysql@latest

Docker — multi-arch images are published to GitHub Container Registry:

docker pull ghcr.io/kurok1/mcp-server-mysql:latest

2. Configure

Copy config.example.yaml and adjust:

mkdir -p ~/.mcp-server-mysql
cp config.example.yaml ~/.mcp-server-mysql/config.yaml

A minimal config:

mysql:
  host: 127.0.0.1
  port: 3306
  user: mcp_dev                  # use a dedicated least-privilege account, not root
  password: ${MYSQL_MCP_PASSWORD}
  database: myapp

security:
  allowed_statements: [select]   # add insert/update/delete/ddl only if you need them
  table_whitelist:
    - "myapp.*"

3. Wire up your MCP client

Claude Code:

claude mcp add mysql --env MYSQL_MCP_PASSWORD=your-password -- \
  ~/go/bin/mcp-server-mysql --config ~/.mcp-server-mysql/config.yaml

Claude Desktop or any JSON-configured client:

{
  "mcpServers": {
    "mysql": {
      "command": "/usr/local/bin/mcp-server-mysql",
      "args": ["--config", "/Users/me/.mcp-server-mysql/config.yaml"],
      "env": { "MYSQL_MCP_PASSWORD": "..." }
    }
  }
}

Docker:

{
  "mcpServers": {
    "mysql": {
      "command": "docker",
      "args": [
        "run", "-i", "--rm",
        "-v", "/Users/me/.mcp-server-mysql:/data",
        "-e", "MYSQL_MCP_PASSWORD",
        "ghcr.io/kurok1/mcp-server-mysql:latest",
        "--config", "/data/config.yaml"
      ],
      "env": { "MYSQL_MCP_PASSWORD": "..." }
    }
  }
}

Docker note 1 — audit logs must live on a mounted volume. The container is destroyed with the session; if you enable audit logging, point audit.log_dir at the mounted volume (e.g. /data/logs) or the logs vanish with the container.

Docker note 2 — reaching MySQL on the host. On macOS/Windows set mysql.host: host.docker.internal; on Linux also append "--add-host=host.docker.internal:host-gateway" to args.

Security model

            MCP client  (Claude Code / Claude Desktop / …)
                               │  stdio
                               ▼
┌───────────────────────  mcp-server-mysql  ───────────────────────┐
│                                                                  │
│  mysql_query · mysql_execute · mysql_script · mysql_explain      │
│  mysql_list_tables · mysql_describe_table · mysql_stats          │
│                             │                                    │
│                             ▼                                    │
│  ┌ Layer 1 · AST main gate (TiDB parser) ───────────────────┐    │
│  │ unparseable ⇒ denied (fail-closed) → single statement    │    │
│  │ → statement-class allowlist + read/write tool check      │    │
│  │ → per-class switches (default: select only)              │    │
│  │ → dangerous constructs (INTO OUTFILE / LOAD_FILE)        │    │
│  │ → missing-WHERE tripwire                                 │    │
│  │ → default-deny table whitelist (JOIN / subquery /        │    │
│  │   CTE scope-aware / versioned comments)                  │    │
│  └────────────┬───────────────────────────────┬─────────────┘    │
│               │ allowed                       │ denied           │
│               ▼                               ▼                  │
│  ┌ Layer 2 · executor ─────────────┐    DENIED [rule]: reason    │
│  │ single-stmt reads: READ ONLY tx │    is returned to the model │
│  │ row cap · query timeout         │    with the rule name       │
│  └────────────┬────────────────────┘                             │
│               ▼                                                  │
│  ┌ Layer 3 · driver ───────────────┐                             │
│  │ multiStatements=false: stacked  │                             │
│  │ injection impossible            │                             │
│  └────────────┬────────────────────┘                             │
│               │   guard decisions — allowed & denied — go to     │
│               │   audit: ring buffer (+ optional JSONL files)    │
└───────────────┬──────────────────────────────────────────────────┘
                ▼
      MySQL  —  Layer 0: dedicated least-privilege account

Layer 0 — your MySQL account (strongly recommended). Run the server with a dedicated account that has only the privileges you intend to use (read-only workloads get SELECT only). Never root. This is the containment layer everything below reinforces.

Layer 1 — the AST main gate. Every statement is parsed by the TiDB parser (parse failure ⇒ denied), then must pass, in order: single-statement enforcement → statement-class allowlist (with a read/write tool cross-check: a write sent through mysql_query is denied even if writes are enabled) → per-class enable switches → dangerous-construct scan (SELECT ... INTO OUTFILE/DUMPFILE, LOAD_FILE() at any nesting depth) → missing-WHERE tripwire → full table-reference extraction checked against the default-deny whitelist.

Layer 2 — read-only transaction fallback. Reads executed through the single-statement read path (mysql_query, mysql_explain, mysql_list_tables, mysql_describe_table) run inside START TRANSACTION READ ONLY — if the parser ever misclassified a write as a read, MySQL itself rejects it. (Write statements you explicitly enabled, and everything inside mysql_script — reads included — run outside this backstop; there, Layer 1 and Layer 0 are the controls.)

Layer 3 — driver-level lockout. The connection sets multiStatements=false, so COMMIT; DROP TABLE ...-style stacked injection is impossible at the protocol level even if every layer above failed.

Every denial comes back as machine-readable text — DENIED [rule_name]: reason — and the rule names are stable:

mysql_script denials prefix the reason with the position of the offending statement: DENIED [rule]: statement N: reason.

The guard is the test suite's center of gravity: ~100 table-driven cases cover stacked-statement injection, versioned-comment smuggling, CTE-shadowing whitelist bypasses, INSERT ... SELECT table extraction, and more; end-to-end tests — whitelist enforcement, the READ ONLY backstop rejecting writes, script rollback, EXPLAIN-tree denials — run against a real MySQL 8.0 in testcontainers.

The fine print

Security documentation you can't verify is marketing. The precise boundaries:

• The read-only transaction backstop covers the single-statement read path. Write types you explicitly enable — and every statement inside mysql_script, reads included, since they share the script's read-write transaction — execute without it; there, the AST gate plus your database account privileges (Layer 0) are the controls.

• unfiltered_write is a missing-WHERE tripwire, not full-table-write prevention: UPDATE t SET a=1 WHERE 1=1 passes it. It catches mistakes, not malice.

• Two utility paths execute fixed, non-user SQL by design: mysql_list_tables queries information_schema directly (results filtered row-by-row through the whitelist), and EXPLAIN FORMAT=TREE executes a hardcoded constant prefix + the inner SELECT — the inner statement passes the full guard pipeline first (the TiDB parser cannot parse FORMAT=TREE as a whole statement).

• Audit records cover SQL that reaches the guard pipeline, allowed and denied. Not audited: mysql_stats calls, mysql_describe_table pre-check denials (invalid_identifier and its table_whitelist name check), and mysql_explain parameter denials (invalid_query, not_select, invalid_format). Script auditing follows actual execution: a guard-denied script yields one record for the whole script, and statements after a failed one — validated but never executed — are not recorded.

• The MySQL connection is plain TCP — no TLS option and no Unix socket yet. Keep the server and the database on a trusted network, or tunnel the connection.

Configuration

Full annotated example: config.example.yaml. The governing principle is secure by default: omit allowed_statements and you're read-only; omit table_whitelist and everything is denied; leave block_unfiltered_writes unset and it's on.

And it fails closed at startup: an unreadable file, an unknown/misspelled key, an invalid duration, a malformed whitelist pattern, an unknown statement type, a negative script cap, or a missing mysql.user/mysql.database all abort the process — it refuses to run sick rather than degrade silently.

Secrets never need to live in the file: the whole config is passed through environment-variable expansion before parsing, so ${ENV_VAR} works in any field. The config path itself can come from the MYSQL_MCP_CONFIG environment variable instead of --config.

Audit log

Disk logging is controlled by audit.enabled — default false: no log files, no log directory created. Session statistics (mysql_stats) are backed by an in-memory ring buffer and work either way (reset on restart).

When enabled, JSONL files rotate daily (audit-2026-07-02.jsonl), one JSON object per line:

Claude Code skill

skills/mysql-mcp is a companion skill that teaches Claude to use these tools well: pick the right tool, respect the security boundaries (single statement, whitelist, WHERE tripwire), and read DENIED [rule] messages correctly instead of blindly retrying. Install:

cp -r skills/mysql-mcp ~/.claude/skills/

Compatibility

• MySQL 8.x — the E2E suite runs against MySQL 8.0 (8.0.45) via testcontainers. MySQL 5.7 and MariaDB are untested.

• Transport — stdio; server identity mcp-server-mysql. Exposes 7 tools (no MCP resources or prompts).

Development

go test ./... -short           # unit tests (no Docker needed)
go test ./... -timeout 600s    # full suite incl. testcontainers integration/E2E (needs Docker)

Design docs live in docs/superpowers — each feature ships with a spec and an implementation plan.

License

Apache-2.0