tooluniverse 0.1.4__py3-none-any.whl → 1.0.0__py3-none-any.whl

tooluniverse/smcp.py

@@ -0,0 +1,2452 @@
+"""
+Scientific Model Context Protocol (SMCP) - Enhanced MCP Server with ToolUniverse Integration
+
+SMCP is a sophisticated MCP (Model Context Protocol) server that bridges the gap between
+AI agents and scientific tools. It seamlessly integrates ToolUniverse's extensive
+collection of 350+ scientific tools with the MCP protocol, enabling AI systems to
+access scientific databases, perform complex analyses, and execute scientific workflows.
+
+The SMCP module provides a complete solution for exposing scientific computational
+resources through the standardized MCP protocol, making it easy for AI agents to
+discover, understand, and execute scientific tools in a unified manner.
+
+Usage Patterns:
+===============
+
+Quick Start:
+
+```python
+# High-performance server with custom configuration
+server = SMCP(
+    name="Production Scientific API",
+    tool_categories=["uniprot", "ChEMBL", "opentarget", "hpa"],
+    max_workers=20,
+    search_enabled=True
+)
+server.run_simple(
+    transport="http",
+    host="0.0.0.0",
+    port=7000
+)
+```
+
+Client Integration:
+```python
+# Using MCP client to discover and use tools
+import json
+
+# Discover protein analysis tools
+response = await client.call_tool("find_tools", {
+    "query": "protein structure analysis",
+    "limit": 5
+})
+
+# Use discovered tool
+result = await client.call_tool("UniProt_get_entry_by_accession", {
+    "arguments": json.dumps({"accession": "P05067"})
+})
+```
+
+Architecture:
+=============
+
+┌─────────────────┐    ┌──────────────────┐    ┌─────────────────┐
+│   MCP Client    │◄──►│      SMCP        │◄──►│  ToolUniverse   │
+│  (AI Agent)     │    │     Server       │    │   (350+ Tools)  │
+└─────────────────┘    └──────────────────┘    └─────────────────┘
+                              │
+                              ▼
+                       ┌──────────────────┐
+                       │  Scientific      │
+                       │  Databases &     │
+                       │  Services        │
+                       └──────────────────┘
+
+The SMCP server acts as an intelligent middleware layer that:
+1. Receives MCP requests from AI agents/clients
+2. Translates requests to ToolUniverse tool calls
+3. Executes tools against scientific databases/services
+4. Returns formatted results via MCP protocol
+5. Provides intelligent tool discovery and recommendation
+
+Integration Points:
+==================
+
+MCP Protocol Layer:
+    - Standard MCP methods (tools/list, tools/call, etc.)
+    - Custom scientific methods (tools/find, tools/search)
+    - Transport-agnostic communication (stdio, HTTP, SSE)
+    - Proper error codes and JSON-RPC 2.0 compliance
+
+ToolUniverse Integration:
+    - Dynamic tool loading and configuration
+    - Schema transformation and validation
+    - Execution wrapper with error handling
+    - Category-based tool organization
+
+AI Agent Interface:
+    - Natural language tool discovery
+    - Contextual tool recommendations
+    - Structured parameter schemas
+    - Comprehensive tool documentation
+"""
+
+import asyncio
+import json
+from concurrent.futures import ThreadPoolExecutor
+from typing import Any, Dict, List, Optional, Union, Callable, Literal
+
+try:
+    from fastmcp import FastMCP
+
+    FASTMCP_AVAILABLE = True
+except ImportError:
+    # Use a simple print here since logging isn't available yet
+    print(
+        "FastMCP is not available. SMCP is built on top of FastMCP, which is a required dependency."
+    )
+
+from .execute_function import ToolUniverse
+from .logging_config import (
+    get_logger,
+)
+
+
+class SMCP(FastMCP):
+    """
+    Scientific Model Context Protocol (SMCP) Server
+
+    SMCP is an enhanced MCP (Model Context Protocol) server that seamlessly integrates
+    ToolUniverse's extensive collection of scientific and scientific tools with the
+    FastMCP framework. It provides a unified, AI-accessible interface for scientific
+    computing, data analysis, and research workflows.
+
+    The SMCP server extends standard MCP capabilities with scientific domain expertise,
+    intelligent tool discovery, and optimized configurations for research applications.
+    It automatically handles the complex task of exposing hundreds of specialized tools
+    through a consistent, well-documented interface.
+
+    Key Features:
+    ============
+    🔬 **Scientific Tool Integration**: Native access to 350+ specialized tools covering
+       scientific databases, literature search, clinical data, genomics, proteomics,
+       chemical informatics, and AI-powered analysis capabilities.
+
+    🧠 **AI-Powered Tool Discovery**: Multi-tiered intelligent search system using:
+       - ToolFinderLLM: Cost-optimized LLM-based semantic understanding with pre-filtering
+       - Tool_RAG: Embedding-based similarity search
+       - Keyword Search: Simple text matching as reliable fallback
+
+    📡 **Full MCP Protocol Support**: Complete implementation of MCP specification with:
+       - Standard methods (tools/list, tools/call, resources/*, prompts/*)
+       - Custom scientific methods (tools/find, tools/search)
+       - Multi-transport support (stdio, HTTP, SSE)
+       - JSON-RPC 2.0 compliance with proper error handling
+
+    ⚡ **High-Performance Architecture**: Production-ready features including:
+       - Configurable thread pools for concurrent tool execution
+       - Intelligent tool loading and caching
+       - Resource management and graceful degradation
+       - Comprehensive error handling and recovery
+
+    🔧 **Developer-Friendly**: Simplified configuration and deployment with:
+       - Sensible defaults for scientific computing
+       - Flexible customization options
+       - Comprehensive documentation and examples
+       - Built-in diagnostic and monitoring tools
+
+    Custom MCP Methods:
+    ==================
+    tools/find:
+        AI-powered tool discovery using natural language queries. Supports semantic
+        search, category filtering, and flexible response formats.
+
+    tools/search:
+        Alternative endpoint for tool discovery with identical functionality to
+        tools/find, provided for compatibility and convenience.
+
+    Parameters:
+    ===========
+    name : str, optional
+        Human-readable server name used in logs and identification.
+        Default: "SMCP Server"
+        Examples: "Scientific Research API", "Drug Discovery Server"
+
+    tooluniverse_config : ToolUniverse or dict, optional
+        Either a pre-configured ToolUniverse instance or configuration dict.
+        If None, creates a new ToolUniverse with default settings.
+        Allows reuse of existing tool configurations and customizations.
+
+    tool_categories : list of str, optional
+        Specific ToolUniverse categories to load. If None and auto_expose_tools=True,
+        loads all available tools. Common combinations:
+        - Scientific: ["ChEMBL", "uniprot", "opentarget", "pubchem", "hpa"]
+        - Literature: ["EuropePMC", "semantic_scholar", "pubtator", "agents"]
+        - Clinical: ["fda_drug_label", "clinical_trials", "adverse_events"]
+
+    exclude_tools : list of str, optional
+        Specific tool names to exclude from loading. These tools will not be
+        exposed via the MCP interface even if they are in the loaded categories.
+        Useful for removing specific problematic or unwanted tools.
+
+    exclude_categories : list of str, optional
+        Tool categories to exclude from loading. These entire categories will
+        be skipped during tool loading. Can be combined with tool_categories
+        to first select categories and then exclude specific ones.
+
+    include_tools : list of str, optional
+        Specific tool names to include. If provided, only these tools will be
+        loaded regardless of categories. Overrides category-based selection.
+
+    tools_file : str, optional
+        Path to a text file containing tool names to include (one per line).
+        Alternative to include_tools parameter. Comments (lines starting with #)
+        and empty lines are ignored.
+
+    tool_config_files : dict of str, optional
+        Additional tool configuration files to load. Format:
+        {"category_name": "/path/to/config.json"}. These files will be loaded
+        in addition to the default tool files.
+
+    include_tool_types : list of str, optional
+        Specific tool types to include. If provided, only tools of these types
+        will be loaded. Available types include: 'OpenTarget', 'ToolFinderEmbedding',
+        'ToolFinderKeyword', 'ToolFinderLLM', etc.
+
+    exclude_tool_types : list of str, optional
+        Tool types to exclude from loading. These tool types will be skipped
+        during tool loading. Useful for excluding entire categories of tools
+        (e.g., all ToolFinder types or all OpenTarget tools).
+
+    auto_expose_tools : bool, default True
+        Whether to automatically expose ToolUniverse tools as MCP tools.
+        When True, all loaded tools become available via the MCP interface
+        with automatic schema conversion and execution wrapping.
+
+    search_enabled : bool, default True
+        Enable AI-powered tool search functionality via tools/find method.
+        Includes ToolFinderLLM (cost-optimized LLM-based), Tool_RAG (embedding-based),
+        and simple keyword search capabilities with intelligent fallback.
+
+    max_workers : int, default 5
+        Maximum number of concurrent worker threads for tool execution.
+        Higher values allow more parallel tool calls but use more resources.
+        Recommended: 5-20 depending on server capacity and expected load.
+
+    hooks_enabled : bool, default False
+        Whether to enable output processing hooks for intelligent post-processing
+        of tool outputs. When True, hooks can automatically summarize long outputs,
+        save results to files, or apply other transformations.
+
+    hook_config : dict, optional
+        Custom hook configuration dictionary. If provided, overrides default
+        hook settings. Should contain 'hooks' list with hook definitions.
+        Example: {"hooks": [{"name": "summarization_hook", "type": "SummarizationHook", ...}]}
+
+    hook_type : str, optional
+        Simple hook type selection. Can be 'SummarizationHook', 'FileSaveHook',
+        or a list of both. Provides an easy way to enable hooks without full configuration.
+        Takes precedence over hooks_enabled when specified.
+
+    **kwargs
+        Additional arguments passed to the underlying FastMCP server instance.
+        Supports all FastMCP configuration options for advanced customization.
+
+    Raises:
+    =======
+    ImportError
+        If FastMCP is not installed. FastMCP is a required dependency for SMCP.
+        Install with: pip install fastmcp
+
+    Notes:
+    ======
+    - SMCP automatically handles ToolUniverse tool loading and MCP conversion
+    - Tool search uses ToolFinderLLM (optimized for cost) when available, gracefully falls back to simpler methods
+    - All tools support JSON argument passing for maximum flexibility
+    - Server supports graceful shutdown and comprehensive resource cleanup
+    - Thread pool execution ensures non-blocking operation for concurrent requests
+    - Built-in error handling provides informative debugging information
+    """
+
+    def __init__(
+        self,
+        name: Optional[str] = None,
+        tooluniverse_config: Optional[Union[ToolUniverse, Dict[str, Any]]] = None,
+        tool_categories: Optional[List[str]] = None,
+        exclude_tools: Optional[List[str]] = None,
+        exclude_categories: Optional[List[str]] = None,
+        include_tools: Optional[List[str]] = None,
+        tools_file: Optional[str] = None,
+        tool_config_files: Optional[Dict[str, str]] = None,
+        include_tool_types: Optional[List[str]] = None,
+        exclude_tool_types: Optional[List[str]] = None,
+        auto_expose_tools: bool = True,
+        search_enabled: bool = True,
+        max_workers: int = 5,
+        hooks_enabled: bool = False,
+        hook_config: Optional[Dict[str, Any]] = None,
+        hook_type: Optional[str] = None,
+        **kwargs,
+    ):
+        if not FASTMCP_AVAILABLE:
+            raise ImportError(
+                "FastMCP is required for SMCP. Install it with: pip install fastmcp"
+            )
+
+        # Filter out SMCP-specific kwargs before passing to FastMCP
+        fastmcp_kwargs = kwargs.copy()
+        fastmcp_kwargs.pop("tooluniverse", None)  # Remove if accidentally passed
+
+        # Initialize FastMCP with default settings optimized for scientific use
+        super().__init__(name=name or "SMCP Server", **fastmcp_kwargs)
+
+        # Get logger for this class
+        self.logger = get_logger("SMCP")
+
+        # Initialize ToolUniverse with hook support
+        if isinstance(tooluniverse_config, ToolUniverse):
+            self.tooluniverse = tooluniverse_config
+        else:
+            self.tooluniverse = ToolUniverse(
+                tool_files=tooluniverse_config,
+                keep_default_tools=True,
+                hooks_enabled=hooks_enabled,
+                hook_config=hook_config,
+                hook_type=hook_type,
+            )
+
+        # Configuration
+        self.tool_categories = tool_categories
+        self.exclude_tools = exclude_tools or []
+        self.exclude_categories = exclude_categories or []
+        self.include_tools = include_tools or []
+        self.tools_file = tools_file
+        self.tool_config_files = tool_config_files or {}
+        self.include_tool_types = include_tool_types or []
+        self.exclude_tool_types = exclude_tool_types or []
+        self.auto_expose_tools = auto_expose_tools
+        self.search_enabled = search_enabled
+        self.max_workers = max_workers
+        self.hooks_enabled = hooks_enabled
+        self.hook_config = hook_config
+        self.hook_type = hook_type
+
+        # Thread pool for concurrent tool execution
+        self.executor = ThreadPoolExecutor(max_workers=max_workers)
+
+        # Track exposed tools to avoid duplicates
+        self._exposed_tools = set()
+
+        # Initialize SMCP-specific features
+        self._setup_smcp_tools()
+
+        # Register custom MCP methods
+        self._register_custom_mcp_methods()
+
+    def _register_custom_mcp_methods(self):
+        """
+        Register custom MCP protocol methods for enhanced functionality.
+
+        This method extends the standard MCP protocol by registering custom handlers
+        for scientific tool discovery and search operations. It safely patches the
+        FastMCP request handler to support additional methods while maintaining
+        compatibility with standard MCP operations.
+
+        Custom Methods Registered:
+        =========================
+        - tools/find: AI-powered tool discovery using natural language queries
+        - tools/search: Alternative endpoint for tool search (alias for tools/find)
+
+        Implementation Details:
+        ======================
+        - Preserves original FastMCP request handler for standard methods
+        - Uses method interception pattern to handle custom methods first
+        - Falls back to original handler for unrecognized methods
+        - Implements proper error handling and JSON-RPC 2.0 compliance
+
+        Error Handling:
+        ==============
+        - Gracefully handles missing request handlers
+        - Logs warnings for debugging when handler patching fails
+        - Ensures server continues to function even if custom methods fail to register
+
+        Notes:
+        ======
+        This method is called automatically during SMCP initialization and should
+        not be called manually. It uses a guard to prevent double-patching.
+        """
+        try:
+            # Override the default request handler to support custom methods
+            if hasattr(self, "_original_handle_request"):
+                return  # Already patched
+
+            # Store original handler
+            self._original_handle_request = getattr(self, "_handle_request", None)
+
+            # Replace with custom handler
+            if hasattr(self, "_handle_request"):
+                self._handle_request = self._custom_handle_request
+            elif hasattr(self, "handle_request"):
+                self._original_handle_request = self.handle_request
+                self.handle_request = self._custom_handle_request
+            else:
+                self.logger.warning("Could not find request handler to override")
+
+        except Exception as e:
+            self.logger.error(f"Error registering custom MCP methods: {e}")
+
+    def _get_valid_categories(self):
+        """
+        Get valid tool categories from ToolUniverse.
+
+        Returns:
+            Set[str]: Set of valid tool category names
+        """
+        try:
+            # Use the existing ToolUniverse instance if available
+            if hasattr(self.tooluniverse, "get_tool_types"):
+                return set(self.tooluniverse.get_tool_types())
+            else:
+                # Create a temporary instance to get categories
+                temp_tu = ToolUniverse()
+                return set(temp_tu.get_tool_types())
+        except Exception as e:
+            self.logger.error(f"❌ Error getting valid categories: {e}")
+            return set()
+
+    async def _custom_handle_request(self, request: Dict[str, Any]) -> Dict[str, Any]:
+        """
+        Custom MCP request handler that supports enhanced scientific tool operations.
+
+        This handler intercepts MCP requests and provides specialized handling for
+        scientific tool discovery methods while maintaining full compatibility with
+        standard MCP protocol operations.
+
+        Parameters:
+        ===========
+        request : dict
+            JSON-RPC 2.0 request object containing:
+            - method: The MCP method being called
+            - id: Request identifier for response correlation
+            - params: Method-specific parameters
+
+        Returns:
+        ========
+        dict
+            JSON-RPC 2.0 response object with either:
+            - result: Successful operation result
+            - error: Error information with code and message
+
+        Supported Custom Methods:
+        ========================
+        tools/find:
+            Search for tools using natural language queries with AI-powered recommendations.
+            Parameters:
+            - query (required): Natural language description of desired functionality
+            - categories (optional): List of tool categories to filter by
+            - limit (optional): Maximum number of results (default: 10)
+            - use_advanced_search (optional): Use AI vs keyword search (default: True)
+            - search_method (optional): Specific search method - 'auto', 'llm', 'embedding', 'keyword' (default: 'auto')
+            - format (optional): Response format - 'detailed' or 'mcp_standard'
+
+        tools/search:
+            Alias for tools/find method with identical parameters and behavior.
+
+        Standard MCP Methods:
+            All other methods are forwarded to the original FastMCP handler,
+            ensuring full compatibility with MCP specification.
+
+        Error Codes:
+        ============
+        - -32601: Method not found (unknown method)
+        - -32602: Invalid params (missing required parameters)
+        - -32603: Internal error (server-side failures)
+
+        Examples:
+        =========
+        Request for tool discovery:
+        ```json
+        {
+            "jsonrpc": "2.0",
+            "id": "search_123",
+            "method": "tools/find",
+            "params": {
+                "query": "protein structure analysis",
+                "limit": 5,
+                "format": "mcp_standard"
+            }
+        }
+        ```
+
+        Successful response:
+        ```json
+        {
+            "jsonrpc": "2.0",
+            "id": "search_123",
+            "result": {
+                "tools": [...],
+                "_meta": {
+                    "search_query": "protein structure analysis",
+                    "search_method": "AI-powered (ToolFinderLLM)",
+                    "total_matches": 5
+                }
+            }
+        }
+        ```
+        """
+        try:
+            method = request.get("method")
+            request_id = request.get("id")
+            params = request.get("params", {})
+
+            # Handle custom methods
+            if method == "tools/find":
+                return await self._handle_tools_find(request_id, params)
+            elif method == "tools/search":  # Alternative endpoint name
+                return await self._handle_tools_find(request_id, params)
+
+            # For all other methods, use the original handler
+            if self._original_handle_request:
+                if asyncio.iscoroutinefunction(self._original_handle_request):
+                    return await self._original_handle_request(request)
+                else:
+                    return self._original_handle_request(request)
+            else:
+                # Fallback: return method not found error
+                return {
+                    "jsonrpc": "2.0",
+                    "id": request_id,
+                    "error": {"code": -32601, "message": f"Method not found: {method}"},
+                }
+
+        except Exception as e:
+            return {
+                "jsonrpc": "2.0",
+                "id": request.get("id"),
+                "error": {"code": -32603, "message": f"Internal error: {str(e)}"},
+            }
+
+    async def _handle_tools_find(
+        self, request_id: str, params: Dict[str, Any]
+    ) -> Dict[str, Any]:
+        """
+        Handle the tools/find MCP method for AI-powered tool discovery.
+
+        This method implements the core functionality for the custom tools/find MCP method,
+        enabling clients to discover relevant scientific tools using natural language
+        queries. It supports both AI-powered semantic search and simple keyword matching.
+
+        Parameters:
+        ===========
+        request_id : str
+            Unique identifier for this request, used in the JSON-RPC response
+        params : dict
+            Request parameters containing:
+            - query (required): Natural language description of desired functionality
+            - categories (optional): List of tool categories to filter results
+            - limit (optional): Maximum number of tools to return (default: 10)
+            - use_advanced_search (optional): Whether to use AI search (default: True)
+            - search_method (optional): Specific search method - 'auto', 'llm', 'embedding', 'keyword' (default: 'auto')
+            - format (optional): Response format - 'detailed' or 'mcp_standard' (default: 'detailed')
+
+        Returns:
+        ========
+        dict
+            JSON-RPC 2.0 response containing either:
+            - Success: Result with discovered tools and metadata
+            - Error: Error object with appropriate code and message
+
+        Response Formats:
+        ================
+        Detailed Format (default):
+            Returns comprehensive tool information including:
+            - Tool names, descriptions, types
+            - Parameter schemas with detailed property information
+            - Search metadata (query, method used, match count)
+
+        MCP Standard Format:
+            Returns tools in standard MCP tools/list format:
+            - Simplified tool schema compatible with MCP clients
+            - inputSchema formatted for direct MCP consumption
+            - Metadata included in separate _meta field
+
+        Search Methods:
+        ==============
+        AI-Powered Search (ToolFinderLLM):
+            - Uses Large Language Model to understand query semantics
+            - Analyzes tool descriptions for intelligent matching
+            - Provides relevance scoring and reasoning
+            - Automatically used when available and use_advanced_search=True
+
+        Simple Keyword Search:
+            - Basic text matching against tool names and descriptions
+            - Case-insensitive substring matching
+            - Used as fallback or when use_advanced_search=False
+
+        Error Handling:
+        ==============
+        - Validates required parameters (query must be provided)
+        - Handles search failures gracefully with informative messages
+        - Provides detailed error context for debugging
+
+        Examples:
+        =========
+        Basic protein analysis search:
+        ```python
+        params = {
+            "query": "protein structure analysis",
+            "limit": 3
+        }
+        ```
+
+        Category-filtered drug search:
+        ```python
+        params = {
+            "query": "drug interactions",
+            "categories": ["ChEMBL", "fda_drug_label"],
+            "limit": 5,
+            "format": "mcp_standard"
+        }
+        ```
+        """
+        try:
+            # Extract parameters
+            query = params.get("query", "")
+            categories = params.get("categories")
+            limit = params.get("limit", 10)
+            use_advanced_search = params.get("use_advanced_search", True)
+            search_method = params.get(
+                "search_method", "auto"
+            )  # 'auto', 'llm', 'embedding', 'keyword'
+            format_type = params.get(
+                "format", "detailed"
+            )  # 'detailed' or 'mcp_standard'
+
+            if not query:
+                return {
+                    "jsonrpc": "2.0",
+                    "id": request_id,
+                    "error": {
+                        "code": -32602,
+                        "message": "Invalid params: 'query' is required",
+                    },
+                }
+
+            # Perform the search using existing search functionality
+            search_result = await self._perform_tool_search(
+                query=query,
+                categories=categories,
+                limit=limit,
+                use_advanced_search=use_advanced_search,
+                search_method=search_method,
+            )
+
+            # Parse the search result
+            search_data = json.loads(search_result)
+
+            # Format response based on requested format
+            if format_type == "mcp_standard":
+                # Format as standard MCP tools/list style response
+                tools_list = []
+                for tool in search_data.get("tools", []):
+                    mcp_tool = {
+                        "name": tool.get("name"),
+                        "description": tool.get("description", ""),
+                        "inputSchema": {
+                            "type": "object",
+                            "properties": tool.get("parameters", {}),
+                            "required": tool.get("required", []),
+                        },
+                    }
+                    tools_list.append(mcp_tool)
+
+                result = {
+                    "tools": tools_list,
+                    "_meta": {
+                        "search_query": query,
+                        "search_method": search_data.get("search_method"),
+                        "total_matches": search_data.get("total_matches"),
+                        "categories_filtered": categories,
+                    },
+                }
+            else:
+                # Return detailed format (default)
+                result = search_data
+
+            return {"jsonrpc": "2.0", "id": request_id, "result": result}
+
+        except json.JSONDecodeError as e:
+            return {
+                "jsonrpc": "2.0",
+                "id": request_id,
+                "error": {
+                    "code": -32603,
+                    "message": f"Search result parsing error: {str(e)}",
+                },
+            }
+        except Exception as e:
+            return {
+                "jsonrpc": "2.0",
+                "id": request_id,
+                "error": {
+                    "code": -32603,
+                    "message": f"Internal error in tools/find: {str(e)}",
+                },
+            }
+
+    async def _perform_tool_search(
+        self,
+        query: str,
+        categories: Optional[List[str]],
+        limit: int,
+        use_advanced_search: bool,
+        search_method: str = "auto",
+    ) -> str:
+        """
+        Execute tool search using the most appropriate search method available.
+
+        Simplified unified interface that leverages the consistent tool interfaces.
+        All search tools now return JSON format directly.
+
+        Parameters:
+        ===========
+        query : str
+            Natural language query describing the desired tool functionality
+        categories : list of str, optional
+            Tool categories to filter results by
+        limit : int
+            Maximum number of tools to return
+        use_advanced_search : bool
+            Whether to prefer AI-powered search when available
+        search_method : str, default 'auto'
+            Specific search method: 'auto', 'llm', 'embedding', 'keyword'
+
+        Returns:
+        ========
+        str
+            JSON string containing search results
+        """
+        try:
+            # Determine which tool to use based on method and availability
+            tool_name = self._select_search_tool(search_method, use_advanced_search)
+
+            # Prepare unified function call - all search tools now use same interface
+            function_call = {
+                "name": tool_name,
+                "arguments": {"description": query, "limit": limit},
+            }
+
+            # Add categories only if provided to avoid validation issues
+            if categories is not None:
+                function_call["arguments"]["categories"] = categories
+
+            # Execute the search tool
+            loop = asyncio.get_event_loop()
+            result = await loop.run_in_executor(
+                self.executor, self.tooluniverse.run_one_function, function_call
+            )
+
+            # All search tools now return JSON format directly
+            if isinstance(result, str):
+                return result
+            elif isinstance(result, dict) or isinstance(result, list):
+                return json.dumps(result, indent=2)
+            else:
+                return str(result)
+
+        except Exception as e:
+            return json.dumps(
+                {
+                    "error": f"Search error: {str(e)}",
+                    "query": query,
+                    "fallback_used": True,
+                    "tools": [],
+                },
+                indent=2,
+            )
+
+    def _select_search_tool(self, search_method: str, use_advanced_search: bool) -> str:
+        """
+        Select the appropriate search tool based on method and availability.
+
+        Returns:
+            str: Tool name to use for search
+        """
+        # Get available tools
+        all_tools = self.tooluniverse.return_all_loaded_tools()
+        available_tool_names = [tool.get("name", "") for tool in all_tools]
+
+        # Handle specific method requests
+        if search_method == "keyword":
+            return "Tool_Finder_Keyword"
+        elif search_method == "llm" and "Tool_Finder_LLM" in available_tool_names:
+            return "Tool_Finder_LLM"
+        elif search_method == "embedding" and "Tool_Finder" in available_tool_names:
+            return "Tool_Finder"
+        elif search_method == "auto":
+            # Auto-selection priority: Keyword > RAG > LLM
+            if use_advanced_search:
+                if "Tool_Finder_Keyword" in available_tool_names:
+                    return "Tool_Finder_Keyword"
+                if "Tool_Finder" in available_tool_names:
+                    return "Tool_Finder"
+                elif "Tool_Finder_LLM" in available_tool_names:
+                    return "Tool_Finder_LLM"
+        else:
+            # Invalid method or method not available, fallback to keyword
+            return "Tool_Finder_Keyword"
+
+    def _setup_smcp_tools(self):
+        """
+        Initialize and configure SMCP-specific tools and features.
+
+        This method orchestrates the complete setup of SMCP functionality including
+        ToolUniverse tool loading, validation, automatic tool exposure to the MCP
+        interface, search functionality initialization, and utility tool registration.
+
+        The setup process is designed to be robust, handle various edge cases gracefully,
+        and provide informative feedback about the configuration process. It implements
+        intelligent fallback strategies to ensure functionality even when specific
+        components are unavailable.
+
+        Setup Process Overview:
+        =====================
+        1. **Tool Loading Assessment**: Check if ToolUniverse already has tools loaded
+           to avoid unnecessary reloading and potential conflicts
+
+        2. **Category Validation**: If specific categories are requested, validate them
+           against available categories and provide helpful feedback for invalid ones
+
+        3. **Tool Loading Strategy**: Load tools using the most appropriate method:
+           - Category-specific loading for focused deployments
+           - Full loading for comprehensive access
+           - Graceful fallback when category loading fails
+
+        4. **Tool Exposure**: Convert loaded ToolUniverse tools to MCP format with
+           proper schema transformation and execution wrapping
+
+        5. **Search Setup**: Initialize multi-tiered search capabilities including
+           AI-powered and fallback methods
+
+        6. **Utility Registration**: Add server management and diagnostic tools
+
+        Tool Loading Strategy:
+        =====================
+        **Already Loaded Check**:
+        If ToolUniverse already contains loaded tools (len(all_tools) > 0), skip
+        the loading phase to prevent duplication and preserve existing configuration.
+        This supports scenarios where users pre-configure ToolUniverse instances.
+
+        **Category-Specific Loading**:
+        When tool_categories is specified:
+        - Validate each category against available tool categories
+        - Log warnings for invalid categories with suggestions
+        - Load only valid categories to optimize performance
+        - Fall back to full loading if no valid categories remain
+
+        **Full Loading (Default)**:
+        When auto_expose_tools=True and no specific categories are requested,
+        load all available tools to provide comprehensive functionality.
+
+        **Graceful Fallback**:
+        If category-specific loading fails for any reason, automatically
+        fall back to loading all tools to ensure basic functionality.
+
+        Tool Exposure Process:
+        =====================
+        **Schema Transformation**:
+        - Convert ToolUniverse parameter schemas to MCP-compatible format
+        - Handle complex parameter types and validation rules
+        - Preserve documentation and examples where available
+
+        **Execution Wrapping**:
+        - Create async wrappers for synchronous ToolUniverse tools
+        - Implement proper error handling and result formatting
+        - Use thread pool execution to prevent blocking
+
+        **Safety Mechanisms**:
+        - Skip meta-tools (MCPAutoLoaderTool, MCPClientTool) that shouldn't be exposed
+        - Track exposed tools to prevent duplicates
+        - Handle tool conversion failures gracefully without stopping entire process
+
+        Search Setup:
+        ============
+        **Multi-Tiered Search Architecture**:
+        1. **ToolFinderLLM** (Primary): Cost-optimized AI-powered semantic understanding using LLM
+        2. **Tool_RAG** (Secondary): Embedding-based similarity search
+        3. **Keyword Search** (Fallback): Simple text matching, always available
+
+        **Initialization Process**:
+        - Check for availability of advanced search tools in loaded tools
+        - Attempt to load search tools if not already present
+        - Configure search capabilities based on what's available
+        - Provide clear feedback about search capabilities
+
+        **Search Tool Loading**:
+        Attempts to load tool_finder_llm and tool_finder categories which include:
+        - ToolFinderLLM: Cost-optimized LLM-based intelligent tool discovery
+        - Tool_RAG: Embedding-based semantic search
+        - Supporting utilities and configuration tools
+
+        Error Handling:
+        ==============
+        **Category Validation Errors**:
+        - Log specific invalid categories with available alternatives
+        - Continue with valid categories only
+        - Fall back to full loading if no valid categories
+
+        **Tool Loading Errors**:
+        - Log detailed error information for debugging
+        - Continue setup process with already loaded tools
+        - Ensure server remains functional even with partial failures
+
+        **Search Setup Errors**:
+        - Gracefully handle missing search tool dependencies
+        - Fall back to simpler search methods automatically
+        - Log informative messages about search capabilities
+
+        **Tool Exposure Errors**:
+        - Handle individual tool conversion failures without stopping process
+        - Log specific tool errors for debugging
+        - Continue with remaining tools to maximize functionality
+
+        Performance Considerations:
+        ==========================
+        - **Lazy Loading**: Only load tools when needed to minimize startup time
+        - **Efficient Validation**: Quick category checks before expensive operations
+        - **Parallel Processing**: Use thread pools for tool conversion where possible
+        - **Memory Management**: Efficient tool representation and storage
+
+        Diagnostic Output:
+        =================
+        Provides informative logging throughout the setup process:
+        ```
+        Tools already loaded in ToolUniverse (356 tools), skipping reload
+        Exposing 356 tools from ToolUniverse
+        ✅ ToolFinderLLM (cost-optimized) available for advanced search
+        Exposed tool: UniProt_get_entry_by_accession (type: uniprot)
+        ```
+
+        Notes:
+        ======
+        - This method is called automatically during SMCP initialization
+        - Should not be called manually after server initialization
+        - Setup is idempotent - can be called multiple times safely
+        - All setup phases include comprehensive error handling
+        - Performance scales with the number of tools being loaded and exposed
+        """
+        # Always ensure full tool set is loaded (hooks may have preloaded a minimal set)
+        # Deduplication in ToolUniverse.load_tools prevents duplicates, so reloading is safe
+        if self.tool_categories:
+            try:
+                # Validate categories first
+                valid_categories = self._get_valid_categories()
+                invalid_categories = [
+                    cat for cat in self.tool_categories if cat not in valid_categories
+                ]
+
+                if invalid_categories:
+                    available_categories = list(valid_categories)
+                    self.logger.warning(
+                        f"Invalid categories {invalid_categories}. Available categories: {available_categories}"
+                    )
+                    # Filter to valid categories only
+                    valid_only = [
+                        cat for cat in self.tool_categories if cat in valid_categories
+                    ]
+                    if valid_only:
+                        self.logger.info(f"Loading valid categories: {valid_only}")
+                        self.tooluniverse.load_tools(
+                            tool_type=valid_only,
+                            exclude_tools=self.exclude_tools,
+                            exclude_categories=self.exclude_categories,
+                            include_tools=self.include_tools,
+                            tools_file=self.tools_file,
+                            tool_config_files=self.tool_config_files,
+                            include_tool_types=self.include_tool_types,
+                            exclude_tool_types=self.exclude_tool_types,
+                        )
+                    else:
+                        self.logger.warning(
+                            "No valid categories found, loading all tools instead"
+                        )
+                        self.tooluniverse.load_tools(
+                            exclude_tools=self.exclude_tools,
+                            exclude_categories=self.exclude_categories,
+                            include_tools=self.include_tools,
+                            tools_file=self.tools_file,
+                            tool_config_files=self.tool_config_files,
+                            include_tool_types=self.include_tool_types,
+                            exclude_tool_types=self.exclude_tool_types,
+                        )
+                else:
+                    self.tooluniverse.load_tools(
+                        tool_type=self.tool_categories,
+                        exclude_tools=self.exclude_tools,
+                        exclude_categories=self.exclude_categories,
+                        include_tools=self.include_tools,
+                        tools_file=self.tools_file,
+                        tool_config_files=self.tool_config_files,
+                        include_tool_types=self.include_tool_types,
+                        exclude_tool_types=self.exclude_tool_types,
+                    )
+            except Exception as e:
+                self.logger.error(f"Error loading specified categories: {e}")
+                self.logger.info("Falling back to loading all tools")
+                self.tooluniverse.load_tools(
+                    exclude_tools=self.exclude_tools,
+                    exclude_categories=self.exclude_categories,
+                    include_tools=self.include_tools,
+                    tools_file=self.tools_file,
+                    tool_config_files=self.tool_config_files,
+                    include_tool_types=self.include_tool_types,
+                    exclude_tool_types=self.exclude_tool_types,
+                )
+        elif self.auto_expose_tools:
+            # Load all tools by default
+            self.tooluniverse.load_tools(
+                exclude_tools=self.exclude_tools,
+                exclude_categories=self.exclude_categories,
+                include_tools=self.include_tools,
+                tools_file=self.tools_file,
+                tool_config_files=self.tool_config_files,
+                include_tool_types=self.include_tool_types,
+                exclude_tool_types=self.exclude_tool_types,
+            )
+
+        # Auto-expose ToolUniverse tools as MCP tools
+        if self.auto_expose_tools:
+            self._expose_tooluniverse_tools()
+
+        # Add search functionality if enabled
+        if self.search_enabled:
+            self._add_search_tools()
+
+        # Add utility tools
+        self._add_utility_tools()
+
+    def _expose_tooluniverse_tools(self):
+        """
+        Automatically expose ToolUniverse tools as MCP-compatible tools.
+
+        This method performs the critical task of converting ToolUniverse's tool
+        definitions into FastMCP-compatible tools that can be called via the MCP
+        protocol. It handles the complex mapping between different tool formats
+        while ensuring compatibility and usability.
+
+        Process Overview:
+        ================
+        1. **Tool Inventory**: Enumerate all loaded ToolUniverse tools
+        2. **Type Filtering**: Skip meta-tools that shouldn't be exposed
+        3. **Schema Conversion**: Transform ToolUniverse schemas to MCP format
+        4. **Function Wrapping**: Create async wrappers for tool execution
+        5. **Registration**: Register tools with FastMCP framework
+
+        Tool Type Filtering:
+        ===================
+        Skips these internal tool types:
+        - MCPAutoLoaderTool: Used for loading other MCP servers
+        - MCPClientTool: Used for connecting to external MCP servers
+
+        These are meta-tools that manage other tools rather than providing
+        end-user functionality, so they're excluded from the MCP interface.
+
+        Schema Transformation:
+        =====================
+        ToolUniverse Tool Format:
+        ```json
+        {
+            "name": "tool_name",
+            "parameter": {
+                "type": "object",
+                "properties": {...},
+                "required": [...]
+            }
+        }
+        ```
+
+        MCP Tool Format:
+        ```python
+        async def tool_function(arguments: str = "{}") -> str:
+            # Tool execution logic
+        ```
+
+        Execution Model:
+        ===============
+        - **JSON Arguments**: All tools accept a single 'arguments' parameter
+          containing JSON-encoded tool parameters
+        - **Async Execution**: Tools run in thread pool to prevent blocking
+        - **Error Handling**: Comprehensive error catching and reporting
+        - **Type Safety**: Proper argument parsing and validation
+
+        Duplicate Prevention:
+        ====================
+        - Tracks exposed tools in self._exposed_tools set
+        - Prevents re-registration of already exposed tools
+        - Handles tool reloading scenarios gracefully
+
+        Error Recovery:
+        ==============
+        - Individual tool failures don't stop the entire process
+        - Detailed error logging for debugging
+        - Continues with remaining tools if some fail to convert
+
+        Performance Optimization:
+        ========================
+        - Lazy evaluation of tool schemas
+        - Minimal memory footprint per tool
+        - Efficient tool lookup and execution
+        - Thread pool reuse for all tool executions
+
+        Examples:
+        =========
+        Original ToolUniverse tool call:
+        ```python
+        tu.run_one_function({
+            "name": "UniProt_get_entry_by_accession",
+            "arguments": {"accession": "P05067"}
+        })
+        ```
+
+        Equivalent MCP tool call:
+        ```python
+        await tool_function('{"accession": "P05067"}')
+        ```
+        """
+        if not hasattr(self.tooluniverse, "all_tools"):
+            self.logger.warning("No all_tools attribute in tooluniverse")
+            return
+
+        self.logger.info(
+            f"Exposing {len(self.tooluniverse.all_tools)} tools from ToolUniverse"
+        )
+
+        # Define tool types that should not be exposed as MCP tools
+        # These are internal/meta tools that are used for loading other tools
+        skip_tool_types = {"MCPAutoLoaderTool", "MCPClientTool"}
+
+        for i, tool_config in enumerate(self.tooluniverse.all_tools):
+            try:
+                # Debug: Check the type of tool_config
+                if not isinstance(tool_config, dict):
+                    self.logger.warning(
+                        f"tool_config at index {i} is not a dict, it's {type(tool_config)}: {tool_config}"
+                    )
+                    continue
+
+                tool_name = tool_config.get("name")
+                tool_type = tool_config.get("type")
+
+                # Skip internal/meta tools that are used for loading other tools
+                if tool_type in skip_tool_types:
+                    self.logger.debug(
+                        f"Skipping exposure of meta tool: {tool_name} (type: {tool_type})"
+                    )
+                    continue
+
+                if tool_name and tool_name not in self._exposed_tools:
+                    self._create_mcp_tool_from_tooluniverse(tool_config)
+                    self._exposed_tools.add(tool_name)
+                    self.logger.debug(f"Exposed tool: {tool_name} (type: {tool_type})")
+
+            except Exception as e:
+                self.logger.error(f"Error processing tool at index {i}: {e}")
+                self.logger.debug(f"Tool config: {tool_config}")
+                continue
+
+        exposed_count = len(self._exposed_tools)
+        self.logger.info(f"Successfully exposed {exposed_count} tools to MCP interface")
+
+    def _add_search_tools(self):
+        """
+        Register AI-powered tool search and discovery functionality.
+
+        This method adds sophisticated tool discovery capabilities to the SMCP server,
+        enabling clients to find relevant tools using natural language queries.
+        It provides both programmatic (MCP tool) and protocol-level (tools/find method)
+        interfaces for tool discovery.
+
+        Registered Tools:
+        ================
+
+        find_tools:
+            Primary tool discovery interface with AI-powered search capabilities.
+
+            Parameters:
+            - query (str): Natural language description of desired functionality
+            - categories (list, optional): Tool categories to filter by
+            - limit (int, default=10): Maximum number of results
+            - use_advanced_search (bool, default=True): Use AI vs keyword search
+
+            Returns: JSON string with discovered tools and search metadata
+
+        search_tools:
+            Backward-compatible alias for find_tools with identical functionality.
+            Maintained for compatibility with existing integrations.
+
+        Search Capabilities:
+        ===================
+
+        AI-Powered Search (ToolFinderLLM):
+            - Uses Large Language Model to understand query semantics with optimized context
+            - Pre-filters tools using keyword matching to reduce LLM context cost
+            - Analyzes only essential tool information (name + description) for cost efficiency
+            - Provides relevance scoring and reasoning
+            - Handles complex queries like "analyze protein interactions in cancer"
+
+        Embedding-Based Search (Tool_RAG):
+            - Uses vector embeddings for semantic similarity matching
+            - Fast approximate matching for large tool collections
+            - Good balance between speed and semantic understanding
+
+        Keyword Search (Fallback):
+            - Simple text matching against tool names and descriptions
+            - Always available regardless of AI tool availability
+            - Provides basic but reliable tool discovery
+
+        Search Strategy:
+        ===============
+        1. **Preference**: ToolFinderLLM (most intelligent, cost-optimized)
+        2. **Fallback**: Tool_RAG (semantic similarity)
+        3. **Final**: Simple keyword matching (always works)
+
+        Integration Details:
+        ===================
+        - Automatically initializes available search tools during setup
+        - Shares search logic with tools/find MCP method
+        - Provides consistent results across different interfaces
+        - Handles tool loading and availability detection
+
+        Error Handling:
+        ==============
+        - Graceful degradation when AI tools unavailable
+        - Informative error messages for debugging
+        - Fallback mechanisms ensure search always works
+        - Detailed logging of search method selection
+
+        Usage Examples:
+        ==============
+        Via MCP tool interface:
+        ```python
+        result = await find_tools(
+            query="protein structure prediction",
+            categories=["uniprot", "hpa"],
+            limit=5
+        )
+        ```
+
+        Via tools/find MCP method:
+        ```json
+        {
+            "method": "tools/find",
+            "params": {
+                "query": "drug interaction analysis",
+                "limit": 3
+            }
+        }
+        ```
+        """
+
+        # Initialize tool finder (prefer LLM-based if available, fallback to embedding-based)
+        self._init_tool_finder()
+
+        @self.tool()
+        async def find_tools(
+            query: str,
+            categories: Optional[List[str]] = None,
+            limit: int = 10,
+            use_advanced_search: bool = True,
+            search_method: str = "auto",
+        ) -> str:
+            """
+            Find and search available ToolUniverse tools using AI-powered search.
+
+            This tool provides the same functionality as the tools/find MCP method.
+
+            Args:
+                query: Search query describing the desired functionality
+                categories: Optional list of categories to filter by
+                limit: Maximum number of results to return (default: 10)
+                use_advanced_search: Use AI-powered search if available (default: True)
+                search_method: Specific search method - 'auto', 'llm', 'embedding', 'keyword' (default: 'auto')
+
+            Returns:
+                JSON string containing matching tools with detailed information
+            """
+            return await self._perform_tool_search(
+                query, categories, limit, use_advanced_search, search_method
+            )
+
+        # # Keep the original search_tools as an alias for backward compatibility
+        # @self.tool()
+        # async def search_tools(
+        #     query: str,
+        #     categories: Optional[List[str]] = None,
+        #     limit: int = 10,
+        #     use_advanced_search: bool = True,
+        #     search_method: str = 'auto'
+        # ) -> str:
+        #     """
+        #     Search available ToolUniverse tools (alias for find_tools).
+
+        #     Args:
+        #         query: Search query string describing the desired functionality
+        #         categories: Optional list of categories to filter by
+        #         limit: Maximum number of results to return
+        #         use_advanced_search: Whether to use AI-powered tool finder
+        #         search_method: Specific search method - 'auto', 'llm', 'embedding', 'keyword' (default: 'auto')
+
+        #     Returns:
+        #         JSON string containing matching tools information
+        #     """
+        #     return await self._perform_tool_search(query, categories, limit, use_advanced_search, search_method)
+
+    def _init_tool_finder(self):
+        """
+        Initialize intelligent tool discovery system with automatic fallback.
+
+        This method sets up the tool finder infrastructure that powers AI-driven
+        tool discovery. It implements a tiered approach, trying the most advanced
+        search methods first and falling back to simpler methods if needed.
+
+        Initialization Strategy:
+        =======================
+
+        Phase 1 - Detection:
+            Scans loaded ToolUniverse tools to identify available search tools:
+            - ToolFinderLLM: Advanced LLM-based semantic search
+            - Tool_RAG: Embedding-based similarity search
+
+        Phase 2 - Loading (if needed):
+            If no search tools are found, attempts to load them:
+            - Loads 'tool_finder_llm' and 'tool_finder' categories
+            - Re-scans for available tools after loading
+
+        Phase 3 - Selection:
+            Selects the best available search method:
+            1. ToolFinderLLM (preferred - most intelligent)
+            2. Tool_RAG (fallback - good semantic understanding)
+            3. Simple keyword search (always available)
+
+        Tool Finder Capabilities:
+        ========================
+
+        ToolFinderLLM:
+            - Uses GPT-4 or similar LLM for query understanding
+            - Analyzes tool descriptions for semantic matching
+            - Provides relevance scoring and selection reasoning
+            - Handles complex, multi-faceted queries effectively
+            - Best for: "Find tools to analyze protein-drug interactions in cancer research"
+
+        Tool_RAG:
+            - Uses pre-computed embeddings for fast similarity search
+            - Good semantic understanding without LLM overhead
+            - Faster than LLM-based search for simple queries
+            - Best for: "protein analysis", "drug discovery"
+
+        Simple Search:
+            - Basic keyword matching against names and descriptions
+            - No dependencies, always available
+            - Fast and reliable for exact term matches
+            - Best for: "chembl", "uniprot", "fda"
+
+        Configuration Management:
+        ========================
+        Sets instance attributes:
+        - tool_finder_available (bool): Whether advanced search is available
+        - tool_finder_type (str): Type of search tool loaded ("ToolFinderLLM" | "Tool_RAG")
+
+        Error Handling:
+        ==============
+        - Handles missing dependencies gracefully
+        - Provides informative console output about search capabilities
+        - Ensures search functionality always works (via simple fallback)
+        - Logs detailed information for debugging
+
+        Performance Considerations:
+        ==========================
+        - Tool loading only happens if search tools aren't already available
+        - Search tool detection is cached to avoid repeated scans
+        - ToolFinderLLM requires network access and API keys
+        - Tool_RAG requires embedding files but works offline
+
+        Dependencies:
+        ============
+        - ToolFinderLLM: Requires OpenAI API access or compatible endpoint
+        - Tool_RAG: Requires sentence-transformers and embedding data
+        - Simple search: No external dependencies
+        """
+        self.tool_finder_available = False
+        self.tool_finder_type = None
+
+        # Check if ToolFinderLLM is available in loaded tools
+        try:
+            all_tools = self.tooluniverse.return_all_loaded_tools()
+            available_tool_names = [tool.get("name", "") for tool in all_tools]
+
+            # Try ToolFinderLLM first (more advanced)
+            if "Tool_Finder_LLM" in available_tool_names:
+                self.tool_finder_available = True
+                self.tool_finder_type = "Tool_Finder_LLM"
+                self.logger.info(
+                    "✅ Tool_Finder_LLM (cost-optimized) available for advanced search"
+                )
+                return
+
+            # Fallback to Tool_RAG (embedding-based)
+            if "Tool_RAG" in available_tool_names:
+                self.tool_finder_available = True
+                self.tool_finder_type = "Tool_RAG"
+                self.logger.info(
+                    "✅ Tool_RAG (embedding-based) available for advanced search"
+                )
+                return
+
+            # Check if ToolFinderKeyword is available for simple search
+            if "Tool_Finder_Keyword" in available_tool_names:
+                self.logger.info("✅ ToolFinderKeyword available for simple search")
+
+            self.logger.warning("⚠️ No advanced tool finders available in loaded tools")
+            self.logger.debug(
+                f"Available tools: {available_tool_names[:5]}..."
+            )  # Show first 5 tools
+
+        except Exception as e:
+            self.logger.warning(f"⚠️ Failed to check for tool finders: {e}")
+
+        # Try to load tool finder tools if not already loaded
+        try:
+            self.logger.debug("🔄 Attempting to load tool finder tools...")
+
+            # Load tool_finder category which includes ToolFinderLLM, Tool_RAG, and ToolFinderKeyword
+            self.tooluniverse.load_tools(tool_type=["tool_finder"])
+
+            # Re-check availability
+            all_tools = self.tooluniverse.return_all_loaded_tools()
+            available_tool_names = [tool.get("name", "") for tool in all_tools]
+
+            if "Tool_Finder_LLM" in available_tool_names:
+                self.tool_finder_available = True
+                self.tool_finder_type = "Tool_Finder_LLM"
+                self.logger.info(
+                    "✅ Successfully loaded Tool_Finder_LLM for advanced search"
+                )
+            elif "Tool_RAG" in available_tool_names:
+                self.tool_finder_available = True
+                self.tool_finder_type = "Tool_RAG"
+                self.logger.info("✅ Successfully loaded Tool_RAG for advanced search")
+            else:
+                self.logger.warning("⚠️ Failed to load any advanced tool finder tools")
+
+            # Check if ToolFinderKeyword is available for simple search
+            if "Tool_Finder_Keyword" in available_tool_names:
+                self.logger.info("✅ Tool_Finder_Keyword available for simple search")
+            else:
+                self.logger.warning(
+                    "⚠️ ToolFinderKeyword not available, using fallback search"
+                )
+
+        except Exception as e:
+            self.logger.warning(f"⚠️ Failed to load tool finder tools: {e}")
+            self.logger.info(
+                "📝 Advanced search will not be available, using simple keyword search only"
+            )
+
+    def _add_utility_tools(self):
+        """
+        Register essential server management and diagnostic tools.
+
+        This method adds a suite of utility tools that provide server introspection,
+        tool management, and direct execution capabilities. These tools are essential
+        for monitoring server health, understanding available capabilities, and
+        providing administrative functionality.
+
+        Registered Utility Tools:
+        ========================
+
+        get_server_info:
+            Comprehensive server status and capability reporting.
+
+            Returns detailed JSON with:
+            - Server identification (name, type, version info)
+            - Tool statistics (total tools, exposed tools, categories)
+            - Feature flags (search enabled, FastMCP status)
+            - Resource usage (max workers, thread pool status)
+
+            Use cases:
+            - Health checks and monitoring
+            - Capability discovery by clients
+            - Debugging server configuration issues
+
+        execute_tooluniverse_function:
+            Direct interface for executing ToolUniverse functions with custom parameters.
+
+            Parameters:
+            - function_name (str): Name of the ToolUniverse tool to execute
+            - arguments (str): JSON string containing tool parameters
+
+            Features:
+            - Bypasses MCP tool wrappers for direct execution
+            - Supports any loaded ToolUniverse tool
+            - Provides detailed error reporting
+            - Uses thread pool for non-blocking execution
+
+            Use cases:
+            - Administrative tool execution
+            - Debugging tool behavior
+            - Custom automation scripts
+
+        list_available_tooluniverse_tools:
+            Comprehensive inventory of all available ToolUniverse tools.
+
+            Returns:
+            - Complete tool catalog with names, descriptions, types
+            - Parameter schemas and requirements for each tool
+            - Tool statistics and categorization
+
+            Use cases:
+            - Tool discovery and exploration
+            - Documentation generation
+            - Client capability mapping
+            - Integration planning
+
+        Implementation Details:
+        ======================
+
+        Error Handling:
+            - Each tool includes comprehensive try-catch blocks
+            - Detailed error messages with context information
+            - Graceful degradation when tools or data unavailable
+            - JSON-formatted error responses for consistency
+
+        Thread Safety:
+            - All tools use async execution patterns
+            - Thread pool executor for CPU-intensive operations
+            - Proper resource cleanup and management
+            - Non-blocking I/O for network operations
+
+        Security Considerations:
+            - execute_tooluniverse_function provides direct tool access
+            - JSON parsing with proper validation
+            - No file system access beyond ToolUniverse scope
+            - Appropriate error message sanitization
+
+        Performance Optimization:
+            - Lazy loading of tool information
+            - Caching where appropriate
+            - Minimal memory footprint
+            - Efficient JSON serialization
+
+        Examples:
+        =========
+
+        Server health check:
+        ```python
+        info = await get_server_info()
+        status = json.loads(info)
+        if status['total_tooluniverse_tools'] > 0:
+            # Server healthy
+            pass
+        ```
+
+        Direct tool execution:
+        ```python
+        result = await execute_tooluniverse_function(
+            function_name="UniProt_get_entry_by_accession",
+            arguments='{"accession": "P05067"}'
+        )
+        ```
+
+        Tool inventory:
+        ```python
+        tools = await list_available_tooluniverse_tools()
+        catalog = json.loads(tools)
+        # Available: {catalog['total_tools']} tools
+        ```
+        """
+
+        @self.tool()
+        async def get_server_info() -> str:
+            """
+            Get information about the SMCP server and its capabilities.
+
+            Returns:
+                JSON string containing server information
+            """
+            try:
+                info = {
+                    "server_name": self.name,
+                    "server_type": "SMCP (Scientific Model Context Protocol)",
+                    "fastmcp_available": FASTMCP_AVAILABLE,
+                    "tooluniverse_loaded": hasattr(self, "tooluniverse"),
+                    "total_exposed_tools": len(self._exposed_tools),
+                    "search_enabled": self.search_enabled,
+                    "max_workers": self.max_workers,
+                    "tool_categories_loaded": len(
+                        getattr(self.tooluniverse, "tool_category_dicts", {})
+                    ),
+                    "total_tooluniverse_tools": len(
+                        getattr(self.tooluniverse, "all_tools", [])
+                    ),
+                }
+                return json.dumps(info, indent=2)
+
+            except Exception as e:
+                return f"Error getting server info: {str(e)}"
+
+        @self.tool()
+        async def execute_tooluniverse_function(
+            function_name: str, arguments: str
+        ) -> str:
+            """
+            Execute a ToolUniverse function directly with custom arguments.
+
+            Args:
+                function_name: Name of the ToolUniverse function to execute
+                arguments: JSON string of arguments to pass to the function
+
+            Returns:
+                Function execution result
+            """
+            try:
+                # Parse arguments from JSON string
+                import json
+
+                if isinstance(arguments, str):
+                    parsed_args = json.loads(arguments)
+                else:
+                    parsed_args = arguments
+
+                function_call = {"name": function_name, "arguments": parsed_args}
+
+                # Execute in thread pool
+                loop = asyncio.get_event_loop()
+                result = await loop.run_in_executor(
+                    self.executor, self.tooluniverse.run_one_function, function_call
+                )
+
+                return str(result)
+
+            except Exception as e:
+                return f"Error executing {function_name}: {str(e)}"
+
+        @self.tool()
+        async def list_available_tooluniverse_tools() -> str:
+            """
+            List all available ToolUniverse tools that can be executed.
+
+            Returns:
+                JSON string containing available tools and their descriptions
+            """
+            try:
+                # Check if ToolUniverse has loaded tools
+                if (
+                    not hasattr(self.tooluniverse, "all_tools")
+                    or not self.tooluniverse.all_tools
+                ):
+                    return json.dumps({"error": "No ToolUniverse tools loaded"})
+
+                tools_info = []
+                for tool_config in self.tooluniverse.all_tools:
+                    if isinstance(tool_config, dict):
+                        tool_info = {
+                            "name": tool_config.get("name", "Unknown"),
+                            "description": tool_config.get(
+                                "description", "No description available"
+                            ),
+                            "type": tool_config.get("type", "Unknown"),
+                            "parameter_schema": tool_config.get("parameter", {}),
+                        }
+                        tools_info.append(tool_info)
+
+                return json.dumps(
+                    {"total_tools": len(tools_info), "tools": tools_info}, indent=2
+                )
+
+            except Exception as e:
+                return json.dumps({"error": f"Error listing tools: {str(e)}"}, indent=2)
+
+    def add_custom_tool(
+        self, name: str, function: Callable, description: Optional[str] = None, **kwargs
+    ):
+        """
+        Add a custom Python function as an MCP tool to the SMCP server.
+
+        This method provides a convenient way to extend SMCP functionality with
+        custom tools beyond those provided by ToolUniverse. Custom tools are
+        automatically integrated into the MCP interface and can be discovered
+        and used by clients alongside existing tools.
+
+        Parameters:
+        ===========
+        name : str
+            Unique name for the tool in the MCP interface. Should be descriptive
+            and follow naming conventions (lowercase with underscores preferred).
+            Examples: "analyze_protein_sequence", "custom_data_processor"
+
+        function : Callable
+            Python function to execute when the tool is called. The function:
+            - Can be synchronous or asynchronous
+            - Should have proper type annotations for parameters
+            - Should include a comprehensive docstring
+            - Will be automatically wrapped for MCP compatibility
+
+        description : str, optional
+            Human-readable description of the tool's functionality. If provided,
+            this will be set as the function's __doc__ attribute. If None, the
+            function's existing docstring will be used.
+
+        **kwargs
+            Additional FastMCP tool configuration options:
+            - parameter_schema: Custom JSON schema for parameters
+            - return_schema: Schema for return values
+            - examples: Usage examples for the tool
+            - tags: Categorization tags
+
+        Returns:
+        ========
+        Callable
+            The decorated function registered with FastMCP framework.
+
+        Usage Examples:
+        ==============
+
+        Simple synchronous function:
+        ```python
+        def analyze_text(text: str, max_length: int = 100) -> str:
+            '''Analyze text and return summary.'''
+            return text[:max_length] + "..." if len(text) > max_length else text
+
+        server.add_custom_tool(
+            name="text_analyzer",
+            function=analyze_text,
+            description="Analyze and summarize text content"
+        )
+        ```
+
+        Asynchronous function with complex parameters:
+        ```python
+        async def process_data(
+            data: List[Dict[str, Any]],
+            processing_type: str = "standard"
+        ) -> Dict[str, Any]:
+            '''Process scientific data with specified method.'''
+            # Custom processing logic here
+            return {"processed_items": len(data), "type": processing_type}
+
+        server.add_custom_tool(
+            name="data_processor",
+            function=process_data
+        )
+        ```
+
+        Function with custom schema:
+        ```python
+        def calculate_score(values: List[float]) -> float:
+            '''Calculate composite score from values.'''
+            return sum(values) / len(values) if values else 0.0
+
+        server.add_custom_tool(
+            name="score_calculator",
+            function=calculate_score,
+            parameter_schema={
+                "type": "object",
+                "properties": {
+                    "values": {
+                        "type": "array",
+                        "items": {"type": "number"},
+                        "description": "List of numeric values to process"
+                    }
+                },
+                "required": ["values"]
+            }
+        )
+        ```
+
+        Integration with ToolUniverse:
+        =============================
+        Custom tools work seamlessly alongside ToolUniverse tools:
+        - Appear in tool discovery searches
+        - Follow same calling conventions
+        - Include in server diagnostics and listings
+        - Support all MCP client interaction patterns
+
+        Best Practices:
+        ==============
+        - Use descriptive, unique tool names
+        - Include comprehensive docstrings
+        - Add proper type annotations for parameters
+        - Handle errors gracefully within the function
+        - Consider async functions for I/O-bound operations
+        - Test tools thoroughly before deployment
+
+        Notes:
+        ======
+        - Custom tools are registered immediately upon addition
+        - Tools can be added before or after server startup
+        - Function signature determines parameter schema automatically
+        - Custom tools support all FastMCP features and conventions
+        """
+        if description:
+            function.__doc__ = description
+
+        # Use FastMCP's tool decorator
+        decorated_function = self.tool(name=name, **kwargs)(function)
+        return decorated_function
+
+    async def close(self):
+        """
+        Perform comprehensive cleanup and resource management during server shutdown.
+
+        This method ensures graceful shutdown of the SMCP server by properly cleaning
+        up all resources, stopping background tasks, and releasing system resources.
+        It's designed to be safe to call multiple times and handles errors gracefully.
+
+        Cleanup Operations:
+        ==================
+
+        **Thread Pool Shutdown:**
+        - Gracefully stops the ThreadPoolExecutor used for tool execution
+        - Waits for currently running tasks to complete
+        - Prevents new tasks from being submitted
+        - Times out after reasonable wait period to prevent hanging
+
+        **Resource Cleanup:**
+        - Releases any open file handles or network connections
+        - Clears internal caches and temporary data
+        - Stops background monitoring tasks
+        - Frees memory allocated for tool configurations
+
+        **Error Handling:**
+        - Continues cleanup even if individual operations fail
+        - Logs cleanup errors for debugging without raising exceptions
+        - Ensures critical resources are always released
+
+        Usage Patterns:
+        ==============
+
+        **Automatic Cleanup (Recommended):**
+        ```python
+        server = SMCP("My Server")
+        try:
+            server.run_simple()  # Cleanup happens automatically on exit
+        except KeyboardInterrupt:
+            pass  # run_simple() handles cleanup
+        ```
+
+        **Manual Cleanup:**
+        ```python
+        server = SMCP("My Server")
+        try:
+            # Custom server logic here
+            pass
+        finally:
+            await server.close()  # Explicit cleanup
+        ```
+
+        **Context Manager Pattern:**
+        ```python
+        async with SMCP("My Server") as server:
+            # Server operations
+            pass
+        # Cleanup happens automatically
+        ```
+
+        Performance Considerations:
+        ==========================
+        - Cleanup operations are typically fast (< 1 second)
+        - Thread pool shutdown may take longer if tasks are running
+        - Network connections are closed immediately
+        - Memory cleanup depends on garbage collection
+
+        Error Recovery:
+        ==============
+        - Individual cleanup failures don't stop the overall process
+        - Critical errors are logged but don't raise exceptions
+        - Cleanup is idempotent - safe to call multiple times
+        - System resources are guaranteed to be released
+
+        Notes:
+        ======
+        - This method is called automatically by run_simple() on shutdown
+        - Can be called manually for custom server lifecycle management
+        - Async method to properly handle async resource cleanup
+        - Safe to call even if server hasn't been fully initialized
+        """
+        try:
+            # Shutdown thread pool
+            self.executor.shutdown(wait=True)
+        except Exception:
+            pass
+
+    def run_simple(
+        self,
+        transport: Literal["stdio", "http", "sse"] = "http",
+        host: str = "0.0.0.0",
+        port: int = 7000,
+        **kwargs,
+    ):
+        """
+        Start the SMCP server with simplified configuration and automatic setup.
+
+        This method provides a convenient way to launch the SMCP server with sensible
+        defaults for different deployment scenarios. It handles transport configuration,
+        logging setup, and graceful shutdown automatically.
+
+        Parameters:
+        ===========
+        transport : {"stdio", "http", "sse"}, default "http"
+            Communication transport protocol:
+
+            - "stdio": Standard input/output communication
+              * Best for: Command-line tools, subprocess integration
+              * Pros: Low overhead, simple integration
+              * Cons: Single client, no network access
+
+            - "http": HTTP-based communication (streamable-http)
+              * Best for: Web applications, REST API integration
+              * Pros: Wide compatibility, stateless, scalable
+              * Cons: Higher overhead than stdio
+
+            - "sse": Server-Sent Events over HTTP
+              * Best for: Real-time applications, streaming responses
+              * Pros: Real-time communication, web-compatible
+              * Cons: Browser limitations, more complex
+
+        host : str, default "0.0.0.0"
+            Server bind address for HTTP/SSE transports:
+            - "0.0.0.0": Listen on all network interfaces (default)
+            - "127.0.0.1": localhost only (more secure)
+            - Specific IP: Bind to particular interface
+
+        port : int, default 7000
+            Server port for HTTP/SSE transports. Choose ports:
+            - 7000-7999: Recommended range for SMCP servers
+            - Above 1024: No root privileges required
+            - Check availability: Ensure port isn't already in use
+
+        **kwargs
+            Additional arguments passed to FastMCP's run() method:
+            - debug (bool): Enable debug logging
+            - access_log (bool): Log client requests
+            - workers (int): Number of worker processes (HTTP only)
+
+        Server Startup Process:
+        ======================
+        1. **Initialization Summary**: Displays server configuration and capabilities
+        2. **Transport Setup**: Configures selected communication method
+        3. **Service Start**: Begins listening for client connections
+        4. **Graceful Shutdown**: Handles interrupts and cleanup
+
+        Deployment Scenarios:
+        ====================
+
+        Development & Testing:
+        ```python
+        server = SMCP(name="Dev Server")
+        server.run_simple(transport="stdio")  # For CLI testing
+        ```
+
+        Local Web Service:
+        ```python
+        server = SMCP(name="Local API")
+        server.run_simple(transport="http", host="127.0.0.1", port=8000)
+        ```
+
+        Production Service:
+        ```python
+        server = SMCP(
+            name="Production SMCP",
+            tool_categories=["ChEMBL", "uniprot", "opentarget"],
+            max_workers=20
+        )
+        server.run_simple(
+            transport="http",
+            host="0.0.0.0",
+            port=7000,
+            workers=4
+        )
+        ```
+
+        Real-time Applications:
+        ```python
+        server = SMCP(name="Streaming API")
+        server.run_simple(transport="sse", port=7001)
+        ```
+
+        Error Handling:
+        ==============
+        - **KeyboardInterrupt**: Graceful shutdown on Ctrl+C
+        - **Port in Use**: Clear error message with suggestions
+        - **Transport Errors**: Detailed debugging information
+        - **Cleanup**: Automatic resource cleanup on exit
+
+        Logging Output:
+        ==============
+        Provides informative startup messages:
+        ```
+        🚀 Starting SMCP server 'My Server'...
+        📊 Loaded 356 tools from ToolUniverse
+        🔍 Search enabled: True
+        🌐 Server running on http://0.0.0.0:7000
+        ```
+
+        Security Considerations:
+        =======================
+        - Use host="127.0.0.1" for local-only access
+        - Configure firewall rules for production deployment
+        - Consider HTTPS termination with reverse proxy
+        - Validate all client inputs through MCP protocol
+
+        Performance Notes:
+        =================
+        - HTTP transport supports multiple concurrent clients
+        - stdio transport is single-client but lower latency
+        - SSE transport enables real-time bidirectional communication
+        - Thread pool size affects concurrent tool execution capacity
+        """
+        self.logger.info(f"🚀 Starting SMCP server '{self.name}'...")
+        self.logger.info(
+            f"📊 Loaded {len(self._exposed_tools)} tools from ToolUniverse"
+        )
+        self.logger.info(f"🔍 Search enabled: {self.search_enabled}")
+
+        # Log hook configuration
+        if self.hooks_enabled or self.hook_type:
+            if self.hook_type:
+                self.logger.info(f"🔗 Hooks enabled: {self.hook_type}")
+            elif self.hook_config:
+                hook_count = len(self.hook_config.get("hooks", []))
+                self.logger.info(f"🔗 Hooks enabled: {hook_count} custom hooks")
+            else:
+                self.logger.info("🔗 Hooks enabled: default configuration")
+        else:
+            self.logger.info("🔗 Hooks disabled")
+
+        try:
+            if transport == "stdio":
+                self.run(transport="stdio", **kwargs)
+            elif transport == "http":
+                self.run(transport="streamable-http", host=host, port=port, **kwargs)
+            elif transport == "sse":
+                self.run(transport="sse", host=host, port=port, **kwargs)
+            else:
+                raise ValueError(f"Unsupported transport: {transport}")
+
+        except KeyboardInterrupt:
+            self.logger.info("\n🛑 Server stopped by user")
+        except Exception as e:
+            self.logger.error(f"❌ Server error: {e}")
+        finally:
+            # Cleanup
+            asyncio.run(self.close())
+
+    def _create_mcp_tool_from_tooluniverse(self, tool_config: Dict[str, Any]):
+        """Create an MCP tool from a ToolUniverse tool configuration.
+
+        This method creates a function with proper parameter signatures that match
+        the ToolUniverse tool schema, enabling FastMCP's automatic parameter validation.
+        """
+        try:
+            # Debug: Ensure tool_config is a dictionary
+            if not isinstance(tool_config, dict):
+                raise ValueError(
+                    f"tool_config must be a dictionary, got {type(tool_config)}: {tool_config}"
+                )
+
+            tool_name = tool_config["name"]
+            description = tool_config.get(
+                "description", f"ToolUniverse tool: {tool_name}"
+            )
+            parameters = tool_config.get("parameter", {})
+
+            # Extract parameter information from the schema
+            # Handle case where properties might be None (like in Finish tool)
+            properties = parameters.get("properties")
+            if properties is None:
+                properties = {}
+            required_params = parameters.get("required", [])
+
+            # Handle non-standard schema format where 'required' is set on individual properties
+            # instead of at the object level (common in ToolUniverse schemas)
+            if not required_params and properties:
+                required_params = [
+                    param_name
+                    for param_name, param_info in properties.items()
+                    if param_info.get("required", False)
+                ]
+
+            # Build function signature dynamically with Pydantic Field support
+            import inspect
+            from typing import Annotated
+            from pydantic import Field
+
+            # Create parameter signature for the function
+            func_params = []
+            param_annotations = {}
+
+            for param_name, param_info in properties.items():
+                param_type = param_info.get("type", "string")
+                param_description = param_info.get(
+                    "description", f"{param_name} parameter"
+                )
+                is_required = param_name in required_params
+
+                # Map JSON schema types to Python types and create appropriate Field
+                field_kwargs = {"description": param_description}
+
+                if param_type == "string":
+                    python_type = str
+                    # For string type, don't add json_schema_extra - let Pydantic handle it
+                elif param_type == "integer":
+                    python_type = int
+                    # For integer type, don't add json_schema_extra - let Pydantic handle it
+                elif param_type == "number":
+                    python_type = float
+                    # For number type, don't add json_schema_extra - let Pydantic handle it
+                elif param_type == "boolean":
+                    python_type = bool
+                    # For boolean type, don't add json_schema_extra - let Pydantic handle it
+                elif param_type == "array":
+                    python_type = list
+                    # Add array-specific schema information only for complex cases
+                    items_info = param_info.get("items", {})
+                    if items_info:
+                        # Clean up items definition - remove invalid fields
+                        cleaned_items = items_info.copy()
+
+                        # Remove 'required' field from items (not valid in JSON Schema for array items)
+                        if "required" in cleaned_items:
+                            cleaned_items.pop("required")
+
+                        field_kwargs["json_schema_extra"] = {
+                            "type": "array",
+                            "items": cleaned_items,
+                        }
+                    else:
+                        # If no items specified, default to string items
+                        field_kwargs["json_schema_extra"] = {
+                            "type": "array",
+                            "items": {"type": "string"},
+                        }
+                elif param_type == "object":
+                    python_type = dict
+                    # Add object-specific schema information
+                    object_props = param_info.get("properties", {})
+                    if object_props:
+                        # Clean up the nested object properties - fix common schema issues
+                        cleaned_props = {}
+                        nested_required = []
+
+                        for prop_name, prop_info in object_props.items():
+                            cleaned_prop = prop_info.copy()
+
+                            # Fix string "True"/"False" in required field (common ToolUniverse issue)
+                            if "required" in cleaned_prop:
+                                req_value = cleaned_prop.pop("required")
+                                if req_value in ["True", "true", True]:
+                                    nested_required.append(prop_name)
+                                # Remove the individual required field as it should be at object level
+
+                            cleaned_props[prop_name] = cleaned_prop
+
+                        # Create proper JSON schema for nested object
+                        object_schema = {"type": "object", "properties": cleaned_props}
+
+                        # Add required array at object level if there are required fields
+                        if nested_required:
+                            object_schema["required"] = nested_required
+
+                        field_kwargs["json_schema_extra"] = object_schema
+                else:
+                    # For unknown types, default to string and only add type info if it's truly unknown
+                    python_type = str
+                    if param_type not in [
+                        "string",
+                        "integer",
+                        "number",
+                        "boolean",
+                        "array",
+                        "object",
+                    ]:
+                        field_kwargs["json_schema_extra"] = {"type": param_type}
+
+                # Create Pydantic Field with enhanced schema information
+                pydantic_field = Field(**field_kwargs)
+
+                if is_required:
+                    # Required parameter with description and schema info
+                    annotated_type = Annotated[python_type, pydantic_field]
+                    param_annotations[param_name] = annotated_type
+                    func_params.append(
+                        inspect.Parameter(
+                            param_name,
+                            inspect.Parameter.POSITIONAL_OR_KEYWORD,
+                            annotation=annotated_type,
+                        )
+                    )
+                else:
+                    # Optional parameter with description, schema info and default value
+                    annotated_type = Annotated[
+                        Union[python_type, type(None)], pydantic_field
+                    ]
+                    param_annotations[param_name] = annotated_type
+                    func_params.append(
+                        inspect.Parameter(
+                            param_name,
+                            inspect.Parameter.POSITIONAL_OR_KEYWORD,
+                            default=None,
+                            annotation=annotated_type,
+                        )
+                    )
+
+            # Create the async function with dynamic signature
+            if not properties:
+                # Tool has no parameters - create simple function
+                async def dynamic_tool_function() -> str:
+                    """Execute ToolUniverse tool with no arguments."""
+                    try:
+                        # Prepare function call with empty arguments
+                        function_call = {"name": tool_name, "arguments": {}}
+
+                        # Execute in thread pool to avoid blocking
+                        loop = asyncio.get_event_loop()
+                        result = await loop.run_in_executor(
+                            self.executor,
+                            self.tooluniverse.run_one_function,
+                            function_call,
+                        )
+
+                        # Format the result
+                        if isinstance(result, str):
+                            return result
+                        else:
+                            return json.dumps(result, indent=2, default=str)
+
+                    except Exception as e:
+                        error_msg = f"Error executing {tool_name}: {str(e)}"
+                        self.logger.error(error_msg)
+                        return json.dumps({"error": error_msg}, indent=2)
+
+                # Set function metadata
+                dynamic_tool_function.__name__ = tool_name
+                dynamic_tool_function.__signature__ = inspect.Signature([])
+                dynamic_tool_function.__annotations__ = {"return": str}
+
+            else:
+                # Tool has parameters - create function with dynamic signature
+                async def dynamic_tool_function(**kwargs) -> str:
+                    """Execute ToolUniverse tool with provided arguments."""
+                    try:
+                        # Filter out None values for optional parameters
+                        args_dict = {k: v for k, v in kwargs.items() if v is not None}
+
+                        # Validate required parameters
+                        missing_required = [
+                            param for param in required_params if param not in args_dict
+                        ]
+                        if missing_required:
+                            return json.dumps(
+                                {
+                                    "error": f"Missing required parameters: {missing_required}",
+                                    "required": required_params,
+                                    "provided": list(args_dict.keys()),
+                                },
+                                indent=2,
+                            )
+
+                        # Prepare function call
+                        function_call = {"name": tool_name, "arguments": args_dict}
+
+                        # Execute in thread pool to avoid blocking
+                        loop = asyncio.get_event_loop()
+                        result = await loop.run_in_executor(
+                            self.executor,
+                            self.tooluniverse.run_one_function,
+                            function_call,
+                        )
+
+                        # Format the result
+                        if isinstance(result, str):
+                            return result
+                        else:
+                            return json.dumps(result, indent=2, default=str)
+
+                    except Exception as e:
+                        error_msg = f"Error executing {tool_name}: {str(e)}"
+                        self.logger.error(error_msg)
+                        return json.dumps({"error": error_msg}, indent=2)
+
+                # Set function metadata
+                dynamic_tool_function.__name__ = tool_name
+
+                # Set function signature dynamically for tools with parameters
+                if func_params:
+                    dynamic_tool_function.__signature__ = inspect.Signature(func_params)
+
+                # Set annotations for type hints
+                dynamic_tool_function.__annotations__ = param_annotations.copy()
+                dynamic_tool_function.__annotations__["return"] = str
+
+            # Create detailed docstring for internal use, but use clean description for FastMCP
+            param_docs = []
+            for param_name, param_info in properties.items():
+                param_desc = param_info.get("description", f"{param_name} parameter")
+                param_type = param_info.get("type", "string")
+                is_required = param_name in required_params
+                required_text = "required" if is_required else "optional"
+                param_docs.append(
+                    f"    {param_name} ({param_type}, {required_text}): {param_desc}"
+                )
+
+            # Set a simple docstring for the function (internal use)
+            dynamic_tool_function.__doc__ = f"""{description}
+
+Returns:
+    str: Tool execution result
+"""
+
+            # Register with FastMCP using explicit description (clean, without parameter list)
+            self.tool(description=description)(dynamic_tool_function)
+
+        except Exception as e:
+            self.logger.error(f"Error creating MCP tool from config: {e}")
+            self.logger.debug(f"Tool config: {tool_config}")
+            # Don't raise - continue with other tools
+            return
+
+
+# Convenience function for quick server creation
+def create_smcp_server(
+    name: str = "SMCP Server",
+    tool_categories: Optional[List[str]] = None,
+    search_enabled: bool = True,
+    **kwargs,
+) -> SMCP:
+    """
+    Create a configured SMCP server with common defaults and best practices.
+
+    This convenience function simplifies SMCP server creation by providing
+    sensible defaults for common use cases while still allowing full customization
+    through additional parameters.
+
+    Parameters:
+    ===========
+    name : str, default "SMCP Server"
+        Human-readable server name used in logs and server identification.
+        Choose descriptive names like:
+        - "Scientific Research API"
+        - "Drug Discovery Server"
+        - "Proteomics Analysis Service"
+
+    tool_categories : list of str, optional
+        Specific ToolUniverse categories to load. If None, loads all available
+        tools (350+ tools). Common category combinations:
+
+        Scientific Research:
+        ["ChEMBL", "uniprot", "opentarget", "pubchem", "hpa"]
+
+        Drug Discovery:
+        ["ChEMBL", "fda_drug_label", "clinical_trials", "pubchem"]
+
+        Literature Analysis:
+        ["EuropePMC", "semantic_scholar", "pubtator", "agents"]
+
+        Minimal Setup:
+        ["tool_finder_llm", "special_tools"]
+
+    search_enabled : bool, default True
+        Enable AI-powered tool discovery via tools/find method.
+        Recommended to keep enabled unless you have specific performance
+        requirements or want to minimize dependencies.
+
+    **kwargs
+        Additional SMCP configuration options:
+
+        - tooluniverse_config: Pre-configured ToolUniverse instance
+        - auto_expose_tools (bool, default True): Auto-expose ToolUniverse tools
+        - max_workers (int, default 5): Thread pool size for tool execution
+        - Any FastMCP server options (debug, logging, etc.)
+
+    Returns:
+    ========
+    SMCP
+        Fully configured SMCP server instance ready to run.
+
+    Usage Examples:
+    ==============
+
+    Quick Start (all tools):
+    ```python
+    server = create_smcp_server("Research Server")
+    server.run_simple()
+    ```
+
+    Focused Server (specific domains):
+    ```python
+    server = create_smcp_server(
+        name="Drug Discovery API",
+        tool_categories=["ChEMBL", "fda_drug_label", "clinical_trials"],
+        max_workers=10
+    )
+    server.run_simple(port=8000)
+    ```
+
+    Custom Configuration:
+    ```python
+    server = create_smcp_server(
+        name="High-Performance Server",
+        search_enabled=True,
+        max_workers=20,
+        debug=True
+    )
+    server.run_simple(transport="http", host="0.0.0.0", port=7000)
+    ```
+
+    Pre-configured ToolUniverse:
+    ```python
+    tu = ToolUniverse()
+    tu.load_tools(tool_type=["uniprot", "ChEMBL"])
+    server = create_smcp_server(
+        name="Protein-Drug Server",
+        tooluniverse_config=tu,
+        search_enabled=True
+    )
+    ```
+
+    Benefits of Using This Function:
+    ===============================
+
+    - **Simplified Setup**: Reduces boilerplate code for common configurations
+    - **Best Practices**: Applies recommended settings automatically
+    - **Consistent Naming**: Encourages good server naming conventions
+    - **Future-Proof**: Will include new recommended defaults in future versions
+    - **Documentation**: Provides clear examples and guidance
+
+    Equivalent Manual Configuration:
+    ===============================
+    This function is equivalent to:
+    ```python
+    server = SMCP(
+        name=name,
+        tool_categories=tool_categories,
+        search_enabled=search_enabled,
+        auto_expose_tools=True,
+        max_workers=5,
+        **kwargs
+    )
+    ```
+
+    When to Use Manual Configuration:
+    ================================
+    - Need precise control over all initialization parameters
+    - Using custom ToolUniverse configurations
+    - Implementing custom MCP methods or tools
+    - Advanced deployment scenarios with specific requirements
+    """
+    return SMCP(
+        name=name,
+        tool_categories=tool_categories,
+        search_enabled=search_enabled,
+        **kwargs,
+    )