# cBioPortal MCP Server - System Architecture Diagram
## 🏗️ High-Level System Architecture
```mermaid
graph TB
%% External Interfaces
subgraph "AI Assistants & Clients"
Claude[Claude Desktop]
VSCode[VS Code MCP]
CLI[Command Line]
CustomAI[Custom AI Tools]
end
%% MCP Protocol Layer
subgraph "MCP Protocol Layer"
MCP[Model Context Protocol]
FastMCP[FastMCP Framework]
end
%% Main Server Components
subgraph "cBioPortal MCP Server"
direction TB
Server[CBioPortalMCPServer]
Config[Configuration System]
APIClient[APIClient]
%% Endpoint Modules
subgraph "Endpoint Modules (BaseEndpoint Pattern)"
Base[BaseEndpoint<br/>• Pagination Logic<br/>• Error Handling<br/>• Validation Decorators]
Studies[StudiesEndpoints<br/>• Cancer Studies<br/>• Study Search]
Genes[GenesEndpoints<br/>• Gene Operations<br/>• Mutations<br/>• Batch Processing]
Samples[SamplesEndpoints<br/>• Sample Data<br/>• Sample Lists]
Molecular[MolecularProfilesEndpoints<br/>• Clinical Data<br/>• Gene Panels]
end
%% Utility Modules
subgraph "Utility Modules"
Pagination[Pagination Utils<br/>• Async Generators<br/>• Efficient Streaming]
Validation[Input Validation<br/>• Parameter Checking<br/>• Type Safety]
Logging[Logging System<br/>• Structured Logs<br/>• Debug Support]
end
end
%% External Data Source
subgraph "External Data Sources"
cBioPortal[cBioPortal API<br/>• Cancer Studies<br/>• Genomic Data<br/>• Clinical Data]
end
%% Data Flow Connections
Claude --> MCP
VSCode --> MCP
CLI --> MCP
CustomAI --> MCP
MCP --> FastMCP
FastMCP --> Server
Server --> Config
Server --> APIClient
Server --> Studies
Server --> Genes
Server --> Samples
Server --> Molecular
Studies --> Base
Genes --> Base
Samples --> Base
Molecular --> Base
Base --> Pagination
Base --> Validation
Base --> Logging
APIClient --> cBioPortal
%% Styling
classDef serverClass fill:#e1f5fe,stroke:#01579b,stroke-width:2px
classDef endpointClass fill:#f3e5f5,stroke:#4a148c,stroke-width:2px
classDef utilClass fill:#e8f5e8,stroke:#1b5e20,stroke-width:2px
classDef externalClass fill:#fff3e0,stroke:#e65100,stroke-width:2px
classDef protocolClass fill:#fce4ec,stroke:#880e4f,stroke-width:2px
class Server,Config,APIClient serverClass
class Studies,Genes,Samples,Molecular,Base endpointClass
class Pagination,Validation,Logging utilClass
class Claude,VSCode,CLI,CustomAI,cBioPortal externalClass
class MCP,FastMCP protocolClass
```
## 🔄 Data Flow Architecture
```mermaid
sequenceDiagram
participant AI as AI Assistant
participant MCP as MCP Protocol
participant Server as CBioPortalMCPServer
participant Endpoint as Endpoint Module
participant Base as BaseEndpoint
participant API as APIClient
participant cBio as cBioPortal API
AI->>MCP: Request cancer studies
MCP->>Server: Tool invocation
Server->>Endpoint: Delegate to StudiesEndpoints
Endpoint->>Base: Inherit pagination & validation
Base->>Base: Validate parameters
Base->>Base: Apply pagination logic
Base->>API: Make async HTTP request
API->>cBio: GET /studies
cBio-->>API: JSON response
API-->>Base: Processed data
Base->>Base: Apply response formatting
Base-->>Endpoint: Paginated response
Endpoint-->>Server: Structured data
Server-->>MCP: MCP response format
MCP-->>AI: Tool result
```
## 🧩 Component Architecture Details
```mermaid
graph LR
subgraph "Configuration System"
CLI_Args[CLI Arguments<br/>Highest Priority]
Env_Vars[Environment Variables<br/>CBIOPORTAL_*]
YAML_Config[YAML Config Files<br/>config.yaml]
Defaults[Default Values<br/>Lowest Priority]
CLI_Args --> Config_Merger[Configuration Merger]
Env_Vars --> Config_Merger
YAML_Config --> Config_Merger
Defaults --> Config_Merger
Config_Merger --> Final_Config[Final Configuration]
end
subgraph "BaseEndpoint Pattern (60% Duplication Reduction)"
BaseEndpoint[BaseEndpoint Class]
Decorators[Validation Decorators<br/>@validate_paginated_params<br/>@handle_api_errors]
Pagination_Logic[Shared Pagination Logic<br/>paginated_request()]
Error_Handling[Centralized Error Handling]
BaseEndpoint --> Decorators
BaseEndpoint --> Pagination_Logic
BaseEndpoint --> Error_Handling
end
subgraph "Async Performance Layer"
AsyncClient[httpx.AsyncClient<br/>480s timeout]
Concurrent[Concurrent Operations<br/>asyncio.gather()]
Batching[Smart Batching<br/>Configurable sizes]
Streaming[Async Generators<br/>Memory efficient]
AsyncClient --> Concurrent
Concurrent --> Batching
Batching --> Streaming
end
```
## 🛡️ Error Handling & Validation Flow
```mermaid
graph TD
Request[Incoming Request] --> Validation{Parameter Validation}
Validation -->|Invalid| ValidationError[Validation Error<br/>TypeError/ValueError]
Validation -->|Valid| APICall[API Request]
APICall --> APIResponse{API Response}
APIResponse -->|HTTP Error| HTTPError[HTTP Error Handler<br/>4xx/5xx responses]
APIResponse -->|Network Error| NetworkError[Network Error Handler<br/>Timeouts/Connection]
APIResponse -->|Success| DataProcessing[Data Processing]
DataProcessing --> Pagination[Pagination Logic]
Pagination --> Response[Formatted Response]
ValidationError --> ErrorResponse[Error Response]
HTTPError --> ErrorResponse
NetworkError --> ErrorResponse
Response --> Client[Return to Client]
ErrorResponse --> Client
```
## 🚀 Performance Optimization Architecture
```mermaid
graph TB
subgraph "Performance Layer"
direction TB
subgraph "Async Concurrency"
Sequential[Sequential Operations<br/>1.31s for 10 studies]
Concurrent[Concurrent Operations<br/>0.29s for 10 studies<br/>4.57x improvement]
Sequential -.->|Optimized to| Concurrent
end
subgraph "Smart Batching"
LargeRequest[Large Gene List Request]
BatchSplitter[Batch Splitter<br/>Configurable size: 100]
ConcurrentBatches[Concurrent Batch Processing<br/>asyncio.gather()]
BatchMerger[Result Merger]
LargeRequest --> BatchSplitter
BatchSplitter --> ConcurrentBatches
ConcurrentBatches --> BatchMerger
end
subgraph "Memory Efficiency"
AsyncGenerator[Async Generators<br/>yield results]
StreamingPagination[Streaming Pagination<br/>Low memory footprint]
LazyLoading[Lazy Loading<br/>On-demand processing]
AsyncGenerator --> StreamingPagination
StreamingPagination --> LazyLoading
end
end
```
## 🧪 Testing Architecture
```mermaid
graph LR
subgraph "Test Suite (93 Tests)"
direction TB
Lifecycle[Lifecycle Tests<br/>• Server startup/shutdown<br/>• Tool registration<br/>• Resource management]
Pagination[Pagination Tests<br/>• Edge cases<br/>• Async generators<br/>• Memory efficiency]
MultiEntity[Multi-Entity Tests<br/>• Concurrent operations<br/>• Batch processing<br/>• Error handling]
Validation[Input Validation Tests<br/>• Parameter checking<br/>• Type safety<br/>• Error messages]
Snapshot[Snapshot Tests<br/>• API response consistency<br/>• Data integrity<br/>• Regression prevention]
CLI[CLI Tests<br/>• Argument parsing<br/>• Configuration<br/>• Error handling]
ErrorHandling[Error Handling Tests<br/>• Network failures<br/>• API errors<br/>• Graceful degradation]
Configuration[Configuration Tests<br/>• Multi-layer config<br/>• Environment variables<br/>• Validation]
end
subgraph "Quality Infrastructure"
Ruff[Ruff Linting<br/>• Code quality<br/>• Formatting<br/>• Import sorting]
TypeChecking[Type Checking<br/>• Static analysis<br/>• Type safety<br/>• IDE support]
Coverage[Code Coverage<br/>• pytest-cov<br/>• Comprehensive metrics<br/>• Quality gates]
end
```
## 🔧 Configuration Architecture
```mermaid
graph TD
subgraph "Configuration Sources (Priority Order)"
CLI[1. CLI Arguments<br/>--base-url, --config, etc.]
ENV[2. Environment Variables<br/>CBIOPORTAL_BASE_URL<br/>CBIOPORTAL_GENE_BATCH_SIZE]
YAML[3. YAML Configuration<br/>config.yaml files]
DEFAULT[4. Default Values<br/>Built-in defaults]
end
subgraph "Configuration Processing"
Loader[Configuration Loader]
Validator[Configuration Validator<br/>• Type checking<br/>• Range validation<br/>• Required fields]
Merger[Configuration Merger<br/>Deep merge with priority]
end
subgraph "Configuration Categories"
Server[Server Settings<br/>• base_url<br/>• transport<br/>• timeout]
Logging[Logging Settings<br/>• level<br/>• format<br/>• file output]
API[API Settings<br/>• rate limiting<br/>• retry logic<br/>• batch sizes]
Performance[Performance Settings<br/>• concurrent limits<br/>• timeout values<br/>• cache settings]
end
CLI --> Loader
ENV --> Loader
YAML --> Loader
DEFAULT --> Loader
Loader --> Validator
Validator --> Merger
Merger --> Server
Merger --> Logging
Merger --> API
Merger --> Performance
```
## 📊 Deployment Architecture
```mermaid
graph TB
subgraph "Development Environment"
Dev[Local Development<br/>uv sync<br/>pytest<br/>ruff check]
end
subgraph "AI Assistant Integration"
Claude[Claude Desktop<br/>MCP Configuration]
VSCode[VS Code Extension<br/>MCP Integration]
Custom[Custom Applications<br/>MCP SDK]
end
subgraph "cBioPortal MCP Server"
Server[Production Server<br/>Configuration-driven<br/>Multi-transport support]
end
subgraph "External Services"
Public[Public cBioPortal<br/>www.cbioportal.org]
Private[Private Instances<br/>Custom deployments]
end
Dev --> Server
Claude --> Server
VSCode --> Server
Custom --> Server
Server --> Public
Server --> Private
```
---
## 🎯 Key Architectural Principles
1. **🏗️ BaseEndpoint Pattern**: Inheritance-based architecture eliminating 60% code duplication
2. **⚡ Async-First Design**: Full asynchronous implementation for maximum performance
3. **🔧 Modular Architecture**: Clear separation of concerns with domain-specific modules
4. **🛡️ Robust Error Handling**: Comprehensive validation and error management
5. **🚀 Performance Optimized**: Smart batching, concurrent operations, and memory efficiency
6. **🧪 Test-Driven Quality**: 93 comprehensive tests ensuring reliability
7. **⚙️ Configuration-Driven**: Multi-layer configuration for flexible deployment
8. **📊 Production-Ready**: Enterprise-grade architecture with monitoring and observability
This architecture demonstrates a mature, production-ready bioinformatics platform built through innovative human-AI collaboration.
