Adding MySQL Support/Tools (#15)

- **MySQL ML and AI Tools**
  - Similarity search and RAG on existing vector stores
  - Create vector store from objects in Object Store
  - Create vector store from objects in file system

- **Additional Features**
  - OCI Object Store list buckets and objects
  - MySQL AI secure file system list

Signed-off-by: Gregory Howe <[email protected]>

Author: GregorySHowe

src/mysql-mcp-server/README.md

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+# MySQL MCP Server (mysql_mcp_server.py)
+
+A Python-based MCP (Model Context Protocol) server that provides a suite of tools for managing and interacting with MySQL AI and MySQL HeatWave database resources. This MCP server is not intended for production use but as a proof of concept for exploring models using MCP Servers.
+
+## Overview
+
+`mysql_mcp_server.py` is a FastMCP-based server that provides tools for managing MySQL connections, executing SQL, using MySQL AI ML/AI features, and working with OCI Object Storage.
+
+## Features
+
+- **Database Connection Management**
+  - Load connection configs from JSON or environment variables
+  - List all configured database connections
+  - Validate connectivity and resolve provider mode (MySQL AI vs. OCI)
+
+- **Database Operations**
+  - Execute SQL queries
+
+- **MySQL AI ML and AI Tools**
+  - `ml_generate`: Text generation with MySQL AI GenAI
+  - `ragify_column`: Create/populate vector columns for embeddings
+  - `ask_ml_rag`: Retrieval-augmented generation from vector stores
+
+- **Vector Store Management**
+  - List files in `secure_file_priv` (local mode)
+  - Load documents into vector stores from local file system
+  - Load documents from OCI Object Storage into vector stores
+
+- **OCI Object Store Tools**
+  - List all compartments
+  - Get compartment by name
+  - List buckets in a compartment
+  - List objects in a bucket
+
+## Prerequisites
+
+- Python 3.x
+- `fastmcp`
+- `oci` SDK
+- `mysql-connector-python` SDK
+- Valid database connection file. Resolution order:
+  1) Path specified by environment variable `MYSQL_MCP_CONFIG` (absolute or relative to this module)
+  2) `src/mysql-mcp-server/local_config.json` (default)
+- Valid OCI configuration file (`~/.oci/config`) or environment variables
+
+## Installation
+
+1. Clone this repository.
+2. Install required dependencies using pip:
+   ```
+   pip install -r requirements.txt
+   ```
+   This will install `oci`, `fastmcp`, `mysql-connector-python`, and all other dependencies.
+3. Set up your OCI config file at ~/.oci/config
+
+## OCI Configuration
+
+The server requires a valid OCI config file with proper credentials.
+The default location is ~/.oci/config. For instructions on setting up this file,
+see the [OCI SDK documentation](https://docs.oracle.com/en-us/iaas/Content/API/Concepts/sdkconfig.htm).
+
+## Required Python Packages
+
+- `oci`
+- `requests`
+- `fastmcp`
+- `mysql-connector-python`
+
+## Supported Database Modes
+
+- **MYSQL_AI** (local MySQL AI AI mode)
+- **OCI** (Oracle Cloud Infrastructure-managed databases)
+
+## MCP Server Configuration
+
+Installation is dependent on the MCP Client being used, it usually consists of adding the MCP Server invocation in a json config file, for example with Claude UI on windows it looks like this:
+```json
+{
+  "mcpServers": {
+    "mysqltools": {
+      "command": "C:\\Python\\python.exe",
+      "args": [
+        "C:\\Users\\user1\\mysql-mcp-server\\mysql_mcp_server.py"
+      ]
+    }
+  }
+}
+```
+
+
+
+Example with TENANCY_ID_OVERRIDE::
+```json
+{
+  "mcpServers": {
+    "mysqltools": {
+      "command": "C:\\Python\\python.exe",
+      "args": [
+        "C:\\Users\\user1\\mysql-mcp-server\\mysql_mcp_server.py"
+      ],
+      "env": {
+        "TENANCY_ID_OVERRIDE": "ocid1.tenancy.oc1..deadbeef"
+      }
+    }
+  }
+}
+```
+
+## Environment Variables
+
+The server supports the following environment variables:
+
+- `PROFILE_NAME`: OCI configuration profile name (default: "DEFAULT")
+- `TENANCY_ID_OVERRIDE`: Overrides the tenancy ID from the config file
+
+## Configuration (utils.fill_config_defaults and utils.load_mysql_config)
+
+The server loads and validates connection configuration using two helpers in utils.py.
+
+- utils.load_mysql_config:
+  - Search order (first existing file wins):
+    1) Path from env `MYSQL_MCP_CONFIG` (if set). If relative, also tries `<module_dir>/<value>`.
+    2) `<module_dir>/local_config.json` (default when env not set)
+    3) `<module_dir>/config.json`
+    4) `<cwd>/config.json`
+  - Returns a validated dict after passing the loaded JSON through fill_config_defaults.
+
+- utils.fill_config_defaults:
+  - Validates the schema and applies defaults for the optional bastion section.
+  - Expected JSON shape:
+    {
+      "server_infos": {
+        "<connection_id>": {
+          "host": "<hostname or IP>",
+          "user": "<username>",
+          "password": "<password>",
+          "database": "<default_schema>",
+          "port": 3306
+        }
+      },
+      "bastion": {                         // optional; for SSH tunneling
+        "bastion_host": "<host>",
+        "bastion_username": "<user>",
+        "private_key_path": "<path to private key>",
+        "db_host": "<remote DB host>",
+        "db_port": 3306,                   // default 3306
+        "bastion_port": 22,                // default 22
+        "local_bind_host": "127.0.0.1",    // default 127.0.0.1
+        "local_bind_port": 3306            // default 3306
+      }
+    }
+  - Required server entry keys are exactly: {"host","user","password","database","port"}.
+  - If a bastion block is present, only the allowed keys above are permitted; defaults are applied when omitted.
+
+Example minimal config (local file):
+{
+  "server_infos": {
+    "local_server": {
+      "host": "localhost",
+      "user": "root",
+      "password": "",
+      "database": "mysql_mcp",
+      "port": 3306
+    }
+  }
+}
+
+Example with bastion:
+{
+  "server_infos": {
+    "remote_via_bastion": {
+      "host": "127.0.0.1",
+      "user": "dbuser",
+      "password": "secret",
+      "database": "appdb",
+      "port": 3306
+    }
+  },
+  "bastion": {
+    "bastion_host": "bastion.example.com",
+    "bastion_username": "ubuntu",
+    "private_key_path": "/home/user/.ssh/id_rsa",
+    "db_host": "mysql.internal",
+    "db_port": 3306
+    // optional keys (with defaults if omitted): bastion_port, local_bind_host, local_bind_port
+  }
+}
+
+Note:
+- Set `MYSQL_MCP_CONFIG` to point at a specific JSON file if you don't want to use `local_config.json`.
+- The defaults and schema enforcement are performed at startup; invalid or incomplete entries raise clear exceptions.
+
+## Usage
+
+The server runs using stdio transport and can be started by running:
+
+```bash
+python mysql_mcp_server.py
+```
+
+## API Tools
+
+1. `list_all_connections()`: List configured database connections and modes
+2. `execute_sql_tool_by_connection_id(connection_id, sql, params)`: Execute SQL on a database connection
+3. `ml_generate(connection_id, question)`: Generate text via MySQL AI ML
+4. `ragify_column(connection_id, table, input_col, embedding_col)`: Embed text into a VECTOR column
+5. `list_vector_store_files_local(connection_id)`: List available files in `secure_file_priv`
+6. `load_vector_store_local(connection_id, file_path)`: Load documents from local filesystem
+7. `load_vector_store_oci(connection_id, namespace, bucket, prefix, schema, table)`: Load documents from OCI Object Storage
+8. `ask_ml_rag_vector_store(connection_id, question)`: RAG query on default vector store
+9. `ask_ml_rag_innodb(connection_id, question, segment_col, embedding_col)`: RAG query restricted to InnoDB tables
+10. `list_all_compartments()`: List OCI compartments
+11. `object_storage_list_buckets(compartment_name | compartment_id)`: List buckets in a compartment
+12. `object_storage_list_objects(namespace, bucket_name)`: List objects in a bucket
+
+## Security
+
+- Uses OCI’s config-based authentication
+- MySQL connection parameters may be stored in JSON config or environment variables
+
+## Example Prompts
+
+Here are example prompts you can use to interact with the MCP server, note that depending on the model being used you might need to be more specific, for example: "list all employees using myConnection1 mysql connection".
+
+### 1. Database Operations
+
+```
+"List all configured database connections"
+"Execute 'SELECT * FROM employees' on my connection"
+"Add embeddings for 'body' column into 'embedding' column in docs table"
+```
+
+### 2. MySQL AI AI
+
+```
+"Generate a summary of error logs using MySQL AI ML"
+"Ask ml_rag: Show me refund policy from the vector store"
+```
+
+### 3. Object Storage
+
+```
+"List all compartments in my tenancy"
+"Show all buckets in the development compartment"
+"List objects in my 'docs-bucket'"
+```
+
+### 4. Vector Store
+
+```
+"Load all documents with prefix 'manuals/' into schema hr, table product_docs"
+"List local files for vector store ingestion"
+```

src/mysql-mcp-server/example_config.json

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+{
+  "server_infos": {
+    "example_local_server": {
+      "host": "<local-db-hostname-or-ip>",
+      "user": "<local-db-username>",
+      "password": "<local-db-password>",
+      "database": "<local-default-schema>",
+      "port": 3306
+    },
+    "example_remote_server": {
+      "host": "<remote-db-hostname-or-ip-or-tunnel-endpoint>",
+      "user": "<remote-db-username>",
+      "password": "<remote-db-password>",
+      "database": "<remote-default-schema>",
+      "port": 3306
+    }
+  },
+  "bastion": {
+    "bastion_host": "<bastion-hostname-or-ip>",
+    "bastion_username": "<bastion-ssh-username>",
+    "private_key_path": "<absolute-path-to-private-key>",
+    "db_host": "<remote-db-hostname-or-ip>",
+    "db_port": 3306,
+    "bastion_port": 22,
+    "local_bind_host": "127.0.0.1",
+    "local_bind_port": 3306
+  }
+}

src/mysql-mcp-server/local_config.json

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+{
+  "server_infos": {
+    "local_server": {
+      "host": "localhost",
+      "user": "root",
+      "password": "",
+      "database": "mysql_mcp",
+      "port": 3306
+    }
+  }
+}