BaseMCPManager Reference

The BaseMCPManager is the foundational class for creating MCP (Model Context Protocol) servers in the scmcphub ecosystem. It provides a standardized way to manage and organize multiple MCP modules, with built-in filtering capabilities for both modules and tools.

Overview

BaseMCPManager serves as an abstract base class that handles:

Module registration and management
Tool filtering (include/exclude)
Module filtering (include/exclude)
Backend integration
FastMCP lifecycle management

Class Definition

class BaseMCPManager:
    """Base class for MCP module management."""

Constructor

`init(name, instructions=None, include_modules=None, exclude_modules=None, include_tools=None, exclude_tools=None, include_tags=None, exclude_tags=None, backend=None)`

Initializes a new BaseMCPManager instance.

Parameters

Parameter	Type	Default	Description
`name`	`str`	Required	Name of the MCP server
`instructions`	`Optional[str]`	`None`	Instructions for the MCP server
`include_modules`	`Optional[List[str]]`	`None`	List of module names to include. If `None`, all modules are included
`exclude_modules`	`Optional[List[str]]`	`None`	List of module names to exclude. If `None`, no modules are excluded
`include_tools`	`Optional[List[str]]`	`None`	Dictionary mapping module names to lists of tool names to include
`exclude_tools`	`Optional[List[str]]`	`None`	Dictionary mapping module names to lists of tool names to exclude
`include_tags`	`Optional[List[str]]`	`None`	List of tags to include
`exclude_tags`	`Optional[List[str]]`	`None`	List of tags to exclude
`backend`	`Optional[NotebookManager]`	`None`	Backend manager class (e.g., `AdataManager`, `NotebookManager`)

Instance Attributes

Attribute	Type	Description
`exec_backend`	`NotebookManager`	Backend instance for execution
`mcp`	`FastMCP`	The main FastMCP instance
`include_modules`	`Optional[List[str]]`	Modules to include
`exclude_modules`	`Optional[List[str]]`	Modules to exclude
`include_tools`	`Optional[List[str]]`	Tools to include per module
`exclude_tools`	`Optional[List[str]]`	Tools to exclude per module
`available_modules`	`Dict[str, Any]`	Dictionary of available modules

Methods

`init_mcp()`

Abstract method - Must be implemented by subclasses. Initializes the available_modules dictionary with module instances.

def init_mcp(self):
    """Initialize available modules. To be implemented by subclasses."""
    raise NotImplementedError("Subclasses must implement init_mcp")

`register_mcp()`

Registers modules based on include/exclude filters and imports them into the main MCP server.

def register_mcp(self):
    """Register modules based on include/exclude filters."""

`exec_lifespan(server)`

Async context manager that provides the execution backend during the server’s lifespan.

@asynccontextmanager
async def exec_lifespan(self, server: FastMCP) -> AsyncIterator[Any]:
    yield self.exec_backend

Usage Examples

Basic Implementation

from scmcp_shared.mcp_base import BaseMCPManager
from scmcp_shared.backend import AdataManager

class MyMCPManager(BaseMCPManager):
    """Manager class for My MCP modules."""
    
    def init_mcp(self):
        """Initialize available MCP modules."""
        self.available_modules = {
            "io": io_mcp,
            "pp": pp_mcp,
            "tl": tl_mcp,
            "pl": pl_mcp,
        }

# Usage
manager = MyMCPManager(
    name="my-mcp",
    backend=AdataManager
)
mcp = manager.mcp

With Module Filtering

# Include only specific modules
manager = MyMCPManager(
    name="my-mcp",
    include_modules=["io", "pp"],
    backend=AdataManager
)

# Exclude specific modules
manager = MyMCPManager(
    name="my-mcp",
    exclude_modules=["auto"],
    backend=AdataManager
)

With Tool Filtering

# Include specific tools from specific modules
manager = MyMCPManager(
    name="my-mcp",
    include_tools={
        "io": ["read_h5ad", "write_h5ad"],
        "pp": ["normalize_total", "log1p"],
    },
    backend=AdataManager
)

# Exclude specific tools from specific modules
manager = MyMCPManager(
    name="my-mcp",
    exclude_tools={
        "auto": ["search_tool", "run_tool"],
    },
    backend=AdataManager
)

With Tag Filtering

# Include only tools with specific tags
manager = MyMCPManager(
    name="my-mcp",
    include_tags=["nb", "rag"],
    backend=AdataManager
)

# Exclude tools with specific tags
manager = MyMCPManager(
    name="my-mcp",
    exclude_tags=["experimental"],
    backend=AdataManager
)

Complete Example

from scmcp_shared.mcp_base import BaseMCPManager
from scmcp_shared.backend import AdataManager
from .preset import io_mcp, pp_mcp, tl_mcp, pl_mcp

class ScanpyMCPManager(BaseMCPManager):
    """Manager class for Scanpy MCP modules."""
    
    def init_mcp(self):
        """Initialize available Scanpy MCP modules."""
        self.available_modules = {
            "io": io_mcp,
            "pp": pp_mcp,
            "tl": tl_mcp,
            "pl": pl_mcp,
        }

# Create manager with comprehensive filtering
manager = ScanpyMCPManager(
    name="scanpy-mcp",
    instructions="Scanpy MCP server for single-cell analysis",
    include_modules=["io", "pp", "tl"],
    exclude_modules=["auto"],
    include_tools={
        "io": ["read_h5ad", "write_h5ad"],
        "pp": ["normalize_total", "log1p", "highly_variable_genes"],
    },
    exclude_tools={
        "auto": ["search_tool", "run_tool"],
    },
    backend=AdataManager
)

# Get the MCP instance
mcp = manager.mcp

Real-World Examples

ScanpyMCPManager

class ScanpyMCPManager(BaseMCPManager):
    """Manager class for Scanpy MCP modules."""
    
    def init_mcp(self):
        """Initialize available Scanpy MCP modules."""
        self.available_modules = {
            "io": ScanpyIOMCP().mcp,
            "pp": ScanpyPreprocessingMCP().mcp,
            "tl": ScanpyToolsMCP().mcp,
            "pl": ScanpyPlottingMCP().mcp,
            "ul": ul_mcp,
            "auto": auto_mcp,
            "nb": nb_mcp
        }

CellrankMCPManager

class CellrankMCPManager(BaseMCPManager):
    """Manager class for Cellrank MCP modules."""
    
    def init_mcp(self):
        """Initialize available Cellrank MCP modules."""
        self.available_modules = {
            "io": io_mcp,
            "pp": pp_mcp,
            "kernel": kernel_mcp,
            "estimator": estimator_mcp,
            "pl": pl_mcp,
            "tl": tl_mcp,
            "ul": ul_mcp,
            "nb": nb_mcp,
        }

Best Practices

1. Module Naming Convention

Use consistent module names across your MCP server:

io - Input/Output operations
pp - Preprocessing
tl - Tools
pl - Plotting
ul - Utilities
auto - Auto-completion tools
nb - Notebook integration

2. Backend Selection

Choose the appropriate backend based on your use case:

AdataManager - For AnnData-based operations/tool-mode
NotebookManager - For notebook-based execution/code-mode

3. Filtering Strategy

Use include_modules when you want to limit to specific modules
Use exclude_modules when you want to exclude specific modules from a larger set
Use include_tools for fine-grained control over which tools are available
Use exclude_tools to remove specific tools from modules

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BaseMCPManager Reference

BaseMCPManager Reference

Overview

Class Definition

Constructor

`init(name, instructions=None, include_modules=None, exclude_modules=None, include_tools=None, exclude_tools=None, include_tags=None, exclude_tags=None, backend=None)`

Parameters

Instance Attributes

Methods

`init_mcp()`

`register_mcp()`

`exec_lifespan(server)`

Usage Examples

Basic Implementation

With Module Filtering

With Tool Filtering

With Tag Filtering

Complete Example

Real-World Examples

ScanpyMCPManager

CellrankMCPManager

Best Practices

1. Module Naming Convention

2. Backend Selection

3. Filtering Strategy

Get Started

Chat with single cell

Bioinformatic agent

Intelligent Tool Selection

Development Guide

Servers

​BaseMCPManager Reference

​Overview

​Class Definition

​Constructor

​__init__(name, instructions=None, include_modules=None, exclude_modules=None, include_tools=None, exclude_tools=None, include_tags=None, exclude_tags=None, backend=None)

​Parameters

​Instance Attributes

​Methods

​init_mcp()

​register_mcp()

​exec_lifespan(server)

​Usage Examples

​Basic Implementation

​With Module Filtering

​With Tool Filtering

​With Tag Filtering

​Complete Example

​Real-World Examples

​ScanpyMCPManager

​CellrankMCPManager

​Best Practices

​1. Module Naming Convention

​2. Backend Selection

​3. Filtering Strategy

BaseMCPManager Reference

Overview

Class Definition

Constructor

`init(name, instructions=None, include_modules=None, exclude_modules=None, include_tools=None, exclude_tools=None, include_tags=None, exclude_tags=None, backend=None)`

Parameters

Instance Attributes

Methods

`init_mcp()`

`register_mcp()`

`exec_lifespan(server)`

Usage Examples

Basic Implementation

With Module Filtering

With Tool Filtering

With Tag Filtering

Complete Example

Real-World Examples

ScanpyMCPManager

CellrankMCPManager

Best Practices

1. Module Naming Convention

2. Backend Selection

3. Filtering Strategy