SQLAlchemy DatabaseMixin for Multi-Database Support

[itomek]

Add SQLAlchemy DatabaseMixin for Multi-Database Support

Implements a production-ready database mixin using SQLAlchemy Core, enabling multi-database support (SQLite, PostgreSQL, MySQL) with connection pooling and thread safety.

Overview

Replaces the sqlite3-based DatabaseMixin with SQLAlchemy Core to support the Medical Intake PoC with production-grade database capabilities.

Key Features

• Multi-database support via SQLAlchemy connection URLs
• Thread-safe connection pooling (QueuePool with configurable pool_size)
• Transaction management with context managers
• SQL injection prevention via parameterized queries
• Backward compatibility - existing code continues working via method aliases

Implementation Approach

Test-Driven Development:

1. Wrote 35 comprehensive tests FIRST (730 lines)
2. Implemented DatabaseMixin to pass all tests (489 lines)
3. Migrated MedicalIntakeAgent to use new mixin
4. Added backward compatibility aliases for dashboard server

Thread Safety:

• Per-operation connections (no shared state)
• Validated with concurrent tests (20 threads on pool_size=5)
• QueuePool handles connection management

API Example

class MyAgent(Agent, DatabaseMixin):
    def __init__(self, **kwargs):
        super().__init__(**kwargs)
        
        # Multi-database support
        self.init_database("postgresql://localhost/mydb", pool_size=10)
        
        # Parameterized queries
        results = self.execute_query(
            "SELECT * FROM items WHERE name = :name",
            {"name": user_input}  # Safe from SQL injection
        )

[Copilot]

Pull request overview

This PR replaces the sqlite3-based DatabaseMixin with a SQLAlchemy Core implementation, enabling multi-database support (SQLite, PostgreSQL, MySQL) with connection pooling for the Medical Intake PoC. The implementation follows a test-driven development approach with 35 comprehensive tests written before the implementation.

Key Changes:

• Implements SQLAlchemy-based DatabaseMixin with connection pooling and thread-safe operations
• Migrates MedicalIntakeAgent to use new database methods with named parameters
• Adds backward compatibility aliases for existing code using old method names

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
tests/unit/test_database_mixin_sqlalchemy.py	Comprehensive test suite with 35 tests covering initialization, CRUD operations, transactions, security, and thread safety
src/gaia/agents/base/database_mixin.py	New SQLAlchemy-based DatabaseMixin with multi-database support, connection pooling, and backward compatibility aliases
src/gaia/agents/emr/agent.py	Updated MedicalIntakeAgent to use new database methods (execute_query, execute_insert, etc.) and SQLAlchemy URLs
src/gaia/agents/base/init.py	Exports DatabaseMixin from base module
setup.py	Adds sqlalchemy>=2.0 dependency

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