fix: Address critical PR review issues

- Fix KuzuDB compatibility: Replace verify_connectivity() with universal query
- Fix boolean env var expansion: Properly convert "true"/"false" strings to booleans
- Fix Docker command paths: Update all docker-compose files to use src/graphiti_mcp_server.py

These fixes address the critical runtime issues identified in PR review:
1. KuzuDB crash when calling non-existent verify_connectivity() method
2. Boolean environment variables being treated as truthy strings
3. Docker containers failing to start due to incorrect script path

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

mcp_server/docker/docker-compose-falkordb.yml

@@ -51,7 +51,7 @@ services:
       - ../config/config-docker-falkordb.yaml:/app/config/config.yaml:ro
     ports:
       - "8000:8000" # Expose the MCP server via HTTP for SSE transport
-    command: ["uv", "run", "graphiti_mcp_server.py", "--transport", "sse", "--config", "/app/config/config.yaml"]
+    command: ["uv", "run", "src/graphiti_mcp_server.py", "--transport", "sse", "--config", "/app/config/config.yaml"]
 
 volumes:
   falkordb_data:

mcp_server/docker/docker-compose-neo4j.yml

@@ -57,7 +57,7 @@ services:
       - ../config/config-docker-neo4j.yaml:/app/config/config.yaml:ro
     ports:
       - "8000:8000" # Expose the MCP server via HTTP for SSE transport
-    command: ["uv", "run", "graphiti_mcp_server.py", "--transport", "sse", "--config", "/app/config/config.yaml"]
+    command: ["uv", "run", "src/graphiti_mcp_server.py", "--transport", "sse", "--config", "/app/config/config.yaml"]
 
 volumes:
   neo4j_data:

mcp_server/docker/docker-compose.yml

@@ -34,7 +34,7 @@ services:
       - kuzu_data:/data
     ports:
       - "8000:8000" # Expose the MCP server via HTTP for SSE transport
-    command: ["uv", "run", "graphiti_mcp_server.py", "--transport", "sse", "--config", "/app/config/config.yaml"]
+    command: ["uv", "run", "src/graphiti_mcp_server.py", "--transport", "sse", "--config", "/app/config/config.yaml"]
 
 # Volume for persistent KuzuDB storage
 volumes:

mcp_server/src/config/schema.py

@@ -29,10 +29,31 @@ class YamlSettingsSource(PydanticBaseSettingsSource):
             def replacer(match):
                 var_name = match.group(1)
                 default_value = match.group(3) if match.group(3) is not None else ''
-                return os.environ.get(var_name, default_value)
+                result = os.environ.get(var_name, default_value)
+
+                # Convert string booleans to actual booleans
+                if result.lower() == 'true':
+                    return 'true'  # Keep as string, let Pydantic handle conversion
+                elif result.lower() == 'false':
+                    return 'false'  # Keep as string, let Pydantic handle conversion
+                return result
 
             pattern = r'\$\{([^:}]+)(:([^}]*))?\}'
-            return re.sub(pattern, replacer, value)
+
+            # Check if the entire value is a single env var expression with boolean default
+            full_match = re.fullmatch(pattern, value)
+            if full_match:
+                result = replacer(full_match)
+                # If the result is a boolean string and the whole value was the env var,
+                # return the actual boolean
+                if result == 'true':
+                    return True
+                elif result == 'false':
+                    return False
+                return result
+            else:
+                # Otherwise, do string substitution
+                return re.sub(pattern, replacer, value)
         elif isinstance(value, dict):
             return {k: self._expand_env_vars(v) for k, v in value.items()}
         elif isinstance(value, list):

mcp_server/src/graphiti_mcp_server.py

@@ -641,8 +641,12 @@ async def get_status() -> StatusResponse:
     try:
         client = await graphiti_service.get_client()
 
-        # Test database connection
+        # Test database connection with a simple query
-        await client.driver.client.verify_connectivity()  # type: ignore
+        # This works for all supported databases (Neo4j, FalkorDB, KuzuDB)
+        async with client.driver.session() as session:
+            result = await session.run('MATCH (n) RETURN count(n) as count')
+            # Consume the result to verify query execution
+            _ = [record async for record in result]
 
         provider_info = f'{config.database.provider} database'
         return StatusResponse(