feat: add SeekDB MCP server with vector search capabilities (issue #34) #41

YixinZ-NUS · 2026-01-29T17:28:12Z

Implements a Rust-based Model Context Protocol (MCP) server for SeekDB vector database, located at examples/mcp/seekdb/ . Built with rmcp 0.14.0 and features client-side embeddings via fastembed (all-MiniLM-L6-v2 model) to reduce the need for api keys and ensure consistency with pyseekdb.

MCP Tools Provided:
create_collection: Create tables with 384-dim HNSW vector index
add_documents: Insert documents with auto-generated embeddings
search_collection: Perform vector similarity search
list_collections: List all tables with vector indexes
collection_info: Get schema, row count, and embedding info

Includes usage guide under examples/mcp/seekdb/README.md and unit testing for validation.

Closes #34

Implements Issue second-state#34: SeekDB Rust MCP Server with: - rmcp 0.14.0 from crates.io for MCP server - fastembed for client-side embeddings (all-MiniLM-L6-v2, 384 dims) - mysql_async for SeekDB connectivity - Three tools: search_collection, list_collections, collection_info - Local .gitignore for build artifacts

- README.md: concise usage guide, test instructions (--test-threads=1) - config.toml: example EchoKit MCP integration - .env.template: environment variable reference - Cargo.toml: add repository URL, rust-version, updated description - Documents alternative AI_EMBED() for DB-side embeddings

- Add Docker lifecycle commands (start, status, logs, stop) - Document MCP session management with notifications/initialized - Add step-by-step curl examples with actual responses - Clarify EchoKit config.toml location - Explain --test-threads=1 requirement for unit tests - Update all example outputs from live testing

Environment variables are already documented in README.md. The .env.template file is redundant since this implementation uses client-side embeddings without requiring API keys.

Copilot

Pull request overview

Implements a Rust-based MCP server for SeekDB that provides vector-search tools backed by client-side embeddings via fastembed, and wires it into the existing EchoKit MCP integration. The PR adds the SeekDB MCP binary/library, embedding service, DB/config helpers, example EchoKit config, and documentation plus lockfile.

Changes:

Add seekdb-mcp-server crate with MCP tool implementations for create_collection, add_documents, search_collection, list_collections, and collection_info, served over rmcp’s streamable HTTP transport.
Introduce a client-side EmbeddingService using fastembed (all-MiniLM-L6-v2, 384-dim) with unit tests validating embedding shape, normalization, and semantic similarity.
Provide SeekDB MCP-specific configuration (config.toml), README usage guide (including curl-based MCP interaction walkthrough), and standard Rust project scaffolding (Cargo.toml, Cargo.lock, .gitignore).

Reviewed changes

Copilot reviewed 9 out of 10 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
`examples/mcp/seekdb/src/main.rs`	Defines the `SeekDbServer` MCP handler, all five tools (search, add, create, list, info), error mapping, and the axum-based HTTP server bootstrapping with rmcp’s `StreamableHttpService`.
`examples/mcp/seekdb/src/lib.rs`	Exposes the `config`, `db`, and `embeddings` modules for reuse by the binary and tests.
`examples/mcp/seekdb/src/embeddings.rs`	Implements `EmbeddingService` around `fastembed` for single/batch embedding, formatting for SQL, and includes unit tests confirming embedding dimension, normalization, semantic similarity, and SQL formatting.
`examples/mcp/seekdb/src/db.rs`	Adds a small helper to construct a `mysql_async::Pool` from `ServerConfig` for connecting to SeekDB via the MySQL protocol.
`examples/mcp/seekdb/src/config.rs`	Introduces `ServerConfig` loaded from environment variables (`SEEKDB_*`), including sensible defaults and required `SEEKDB_DATABASE` validation.
`examples/mcp/seekdb/config.toml`	Example EchoKit server configuration showing how to register the SeekDB MCP server and wire it into TTS/ASR/LLM, plus a system prompt for using the search tools (currently references some non-existent tool names).
`examples/mcp/seekdb/README.md`	Documents SeekDB MCP server setup (Dockerized SeekDB, building & running the server), MCP usage via curl (session initialization, tool calls), testing strategy, environment variables, architecture, and notes on client-side vs DB-side embeddings.
`examples/mcp/seekdb/Cargo.toml`	Declares the new `seekdb-mcp-server` crate (edition 2024), its binary target, and dependencies on rmcp, fastembed, mysql_async, axum, tokio, tracing, dotenvy, etc.
`examples/mcp/seekdb/Cargo.lock`	Lockfile capturing the full dependency graph for the new crate (including rmcp, fastembed/ORT, mysql_async, reqwest/ureq, rustls, etc.).
`examples/mcp/seekdb/.gitignore`	Ignores standard Rust build artifacts and the local `.fastembed_cache/` directory used for model downloads.

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Copilot · 2026-01-31T02:39:23Z

examples/mcp/seekdb/src/main.rs

+        let sql = format!(
+            r#"SELECT id, document, metadata, 
+                      COSINE_DISTANCE(embedding, '{}') as distance
+               FROM {}
+               ORDER BY distance ASC


collection_name from tool input is interpolated directly into the SQL string in the FROM {} clause (and into the log), which allows a malicious or malformed collection name to break the query or perform SQL injection. Please either validate collection names against a strict identifier pattern and/or quote+escape them as identifiers instead of concatenating raw user input into the query string.

Copilot · 2026-01-31T02:39:24Z

examples/mcp/seekdb/src/main.rs

+            let sql = format!(
+                r#"INSERT INTO {} (id, document, embedding, metadata) 
+                   VALUES (?, ?, '{}', ?)
+                   ON DUPLICATE KEY UPDATE 
+                   document = VALUES(document),


collection_name is concatenated directly into the INSERT INTO {} statement, so a crafted collection name could inject additional SQL or reference unintended tables. This should be hardened by validating the collection name and/or properly quoting and escaping it as an identifier rather than embedding raw user input in the SQL template.

Copilot · 2026-01-31T02:39:24Z

examples/mcp/seekdb/src/main.rs

+        let sql = format!(
+            r#"CREATE TABLE IF NOT EXISTS {} (
+                id VARCHAR(255) PRIMARY KEY,
+                document TEXT NOT NULL,
+                embedding VECTOR({}) NOT NULL,


collection_name is directly interpolated into the CREATE TABLE IF NOT EXISTS {} DDL, which makes it possible to inject arbitrary SQL via the tool argument or to fail on unusual table names. Consider enforcing an allowed-character whitelist for collection names and/or quoting+escaping them as identifiers instead of concatenating the raw string.

Copilot · 2026-01-31T02:39:24Z

examples/mcp/seekdb/src/main.rs

+        // Get row count
+        let count_sql = format!("SELECT COUNT(*) FROM {}", collection_name);
+        let rows: Vec<Row> = conn.query(&count_sql).await.map_err(|e| {
+            error!("Failed to get row count: {}", e);
+            McpError::internal_error(format!("Query failed: {}", e), None)
+        })?;
+        let count: i64 = rows.first().and_then(|r| r.get(0)).unwrap_or(0);
+
+        // Get column info
+        let schema_sql = format!(
+            "SELECT COLUMN_NAME, DATA_TYPE FROM INFORMATION_SCHEMA.COLUMNS WHERE TABLE_NAME = '{}' AND TABLE_SCHEMA = DATABASE()",


In collection_info, collection_name is interpolated directly into both SELECT COUNT(*) FROM {} and the TABLE_NAME = '{}' filter, which allows SQL injection or malformed queries if a caller passes a crafted name. As with the other tools, this should instead validate and safely quote/escape the identifier, or otherwise ensure only valid collection names can reach these format strings.

Copilot · 2026-01-31T02:39:24Z

examples/mcp/seekdb/config.toml

+You are a helpful voice assistant with access to a knowledge base through the SeekDB search tools.
+
+When users ask questions that might be answered by the knowledge base:
+1. Use the `query_collection` tool to search for relevant information
+2. Use the `hybrid_search` tool for complex queries that need both keyword and semantic matching


The system prompt mentions query_collection and hybrid_search tools, but this MCP server only exposes create_collection, add_documents, search_collection, list_collections, and collection_info. This mismatch can confuse clients and LLM behavior; please update the prompt text to reference the actual tool names and behaviors provided by this server.

YixinZ-NUS added 4 commits January 30, 2026 00:07

chore: remove .env.template from seekdb MCP server

a67a18d

Environment variables are already documented in README.md. The .env.template file is redundant since this implementation uses client-side embeddings without requiring API keys.

YixinZ-NUS mentioned this pull request Jan 29, 2026

[Feature Request] Implement SeekDB Search MCP Server #34

Open

zhanghuidinah mentioned this pull request Jan 30, 2026

Developer Activities: Call for Participation! oceanbase/seekdb#123

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alabulei1 requested a review from Copilot January 31, 2026 02:33

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feat: add SeekDB MCP server with vector search capabilities (issue #34) #41

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