Add read-only mode and query execution capabilities

[kevingatera]

This PR introduces read-only mode as a default security feature to prevent accidental write operations, adds the run_sql_query tool for executing SELECT statements, and implements a wrap_untrusted function to mitigate prompt injection risks. Changes update the DatabaseContext and DatabaseConnector classes to enforce read-only checks.

Please see: README documentation for configuration and usage.

This resolves #19 and is also a more flexible implementation of #17

[danielmeppiel]

Great base, let's iterate - I've left my comments

[kevingatera]

@danielmeppiel The PR is now ready. All concerns were addressed.

[danielmeppiel]

Thanks for your latest changes @kevingatera !
Let's security-harden this with sqlparse library and we will be ready to merge

[kevingatera]

@danielmeppiel The requested changes have been made. But, there are two items of note:

1. I ran uv lock and it included the new sqlparse but I think in the newer versions of uv it appends an upload time that resulted in a larger than expected line changes. From the cursory glance I made nothing important appears to have been disturbed other than bumping the revision, adding an unavoidable upload time per package, and adding sqlparse.
2. The _assert_query_executable method only validates SQL when in read-only mode. When read-only mode is disabled, it doesn't check for stacked statements at all. I chose to keep it that way for non-read mode so the user/llm will have freedom of arbitrary commands.

[kevingatera]

Fixed and ran tests for it. Ready.

[kevingatera]

@danielmeppiel is there anything else you'd like me to add/modify?

[danielmeppiel]

Sorry for the delay, currently on a summer break, but will have a look at merging this ASAP

[Copilot]

Pull Request Overview

This PR introduces comprehensive read-only mode and SQL query execution capabilities to enhance database security and functionality. The default read-only mode prevents accidental write operations while still allowing full read access, and the new query execution tool enables users to run SELECT statements directly through the MCP server.

• Adds read-only mode as a default security feature with environment variable configuration
• Implements run_sql_query tool for executing SELECT statements with formatted output
• Introduces wrap_untrusted function to mitigate prompt injection risks in returned data

Reviewed Changes

Copilot reviewed 6 out of 7 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
pyproject.toml	Adds sqlparse dependency for SQL statement parsing
main.py	Implements wrap_untrusted function, adds run_sql_query tool, and enables read-only mode configuration
db_context/schema/formatter.py	Adds format_sql_query_result function for creating markdown tables from query results
db_context/database.py	Refactors DatabaseConnector with read-only checks, SQL parsing, and query execution capabilities
db_context/init.py	Updates DatabaseContext to support read-only mode and expose run_sql_query method
README.md	Documents read-only mode configuration and usage instructions

Comments suppressed due to low confidence (1)

db_context/database.py:1

• The _close_connection method implementation was removed but the method is still being called throughout the code. This will cause AttributeError exceptions when the method is invoked.

import sys

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