diff --git a/.env.example.mcp b/.env.example.mcp
deleted file mode 100644
index 09321a68..00000000
--- a/.env.example.mcp
+++ /dev/null
@@ -1,17 +0,0 @@
-# SmartEM Decisions - MCP Server Configuration
-# Optional environment variables for the MCP (Model Context Protocol) server
-# Copy this file to .env.mcp and configure for your MCP deployment
-# See: docs/how-to/use-mcp-interface.md for usage documentation
-
-# Data source configuration
-# For filesystem adapter: path to EPU sessions directory
-#SMARTEM_MCP_DATA_PATH=/path/to/epu/sessions
-
-# For API adapter: URL of SmartEM backend API
-#SMARTEM_MCP_API_URL=http://localhost:8000
-
-# Adapter selection (filesystem or api)
-#SMARTEM_MCP_ADAPTER=filesystem
-
-# Logging configuration
-#SMARTEM_MCP_LOG_LEVEL=INFO
diff --git a/README.md b/README.md
index 8b5b690a..cbd9c550 100644
--- a/README.md
+++ b/README.md
@@ -196,7 +196,6 @@ After installation with `pip install -e .[all]`, the following command-line util
### Development and Integration Tools
- **`smartem_agent_tools`** - Agent development and debugging utilities
-- **`smartem-mcp`** - Model Context Protocol (MCP) integration tools
### Data Retention Policies
diff --git a/docs/explanations/backend-agent-communication-system-design.md b/docs/explanations/backend-agent-communication-system-design.md
index 76a06f7e..2f8a961e 100644
--- a/docs/explanations/backend-agent-communication-system-design.md
+++ b/docs/explanations/backend-agent-communication-system-design.md
@@ -35,10 +35,6 @@ graph TB
subgraph athena["athena_api"]
athena_client["client.py
External API Integration"]
end
-
- subgraph mcp["smartem_mcp"]
- mcp_server["server.py
Model Context Protocol"]
- end
end
subgraph infra["Infrastructure Services"]
@@ -119,7 +115,7 @@ graph TB
classDef equipment fill:#e8f5e8,stroke:#2e7d32,stroke-width:2px
classDef communication fill:#fff8e1,stroke:#f57f17,stroke-width:2px
- class k8s,packages,backend,common,athena,mcp,infra k8s
+ class k8s,packages,backend,common,athena,infra k8s
class boundary,agents,agent_pkg,equipment boundary
class db,mq database
class scope1,scope2,scopeN,epu1,epu2,epuN,em1,em2,emN,gpfs1,gpfs2,gpfsN equipment
diff --git a/docs/how-to/configure-environment-variables.md b/docs/how-to/configure-environment-variables.md
index b9c7e448..e043ebaf 100644
--- a/docs/how-to/configure-environment-variables.md
+++ b/docs/how-to/configure-environment-variables.md
@@ -16,8 +16,6 @@ The project uses multiple environment configuration patterns for different deplo
| `.env.k8s.staging` | K8s staging cluster config | Yes | Copy from `.env.example.k8s.staging` |
| `.env.example.k8s.production` | Template for K8s production | No (committed) | N/A |
| `.env.k8s.production` | K8s production cluster config | Yes | Copy from `.env.example.k8s.production` |
-| `.env.example.mcp` | Template for MCP configuration | No (committed) | N/A |
-| `.env.mcp` | MCP server configuration | Yes | Copy from `.env.example.mcp` |
## Environment File Types
@@ -131,28 +129,6 @@ cp .env.example.k8s.production .env.k8s.production
- Production CI/CD pipelines
- Production deployment automation
-### 5. MCP Configuration: `.env.mcp`
-
-**Use Case**: Configuring Model Context Protocol (MCP) server for Claude Code integration.
-
-**Setup**:
-```bash
-cp .env.example.mcp .env.mcp
-# Configure paths and adapter settings
-```
-
-**Key Configuration**:
-```bash
-SMARTEM_MCP_DATA_PATH=/path/to/epu/sessions # Filesystem adapter
-SMARTEM_MCP_API_URL=http://backend:8000 # API adapter
-SMARTEM_MCP_ADAPTER=filesystem # Adapter selection
-SMARTEM_MCP_LOG_LEVEL=INFO
-```
-
-**Used By**:
-- MCP server when run via Claude Code
-- See [Use MCP Interface](use-mcp-interface.md) for details
-
## Quick Start: First-Time Setup
For local development on a new machine:
@@ -344,4 +320,3 @@ env | grep POSTGRES
- [Deploy to Kubernetes](deploy-kubernetes.md) - K8s deployment guide
- [Manage Kubernetes Secrets](manage-kubernetes-secrets.md) - Sealed Secrets and security
- [Database Migrations](database-migrations.md) - Alembic migration workflow
-- [Use MCP Interface](use-mcp-interface.md) - Claude Code MCP integration
diff --git a/docs/how-to/use-mcp-interface.md b/docs/how-to/use-mcp-interface.md
deleted file mode 100644
index a0f11bbd..00000000
--- a/docs/how-to/use-mcp-interface.md
+++ /dev/null
@@ -1,507 +0,0 @@
-# Using SmartEM MCP Interface
-
-The SmartEM MCP (Model Context Protocol) interface provides natural language querying capabilities for microscopy session data. Built with FastMCP 2.0, it supports both filesystem-based parsing and API-based queries for comprehensive data access.
-
-## Overview
-
-The MCP interface consists of:
-- **FastMCP Server**: Provides natural language query capabilities via MCP protocol using FastMCP framework
-- **MCP Client**: Python client for programmatic access with simplified FastMCP patterns
-- **CLI Interface**: Command-line tools for interactive usage
-
-## Installation
-
-Install with MCP dependencies (includes FastMCP 2.0 framework):
-
-```bash
-pip install -e .[mcp]
-```
-
-This installs the required FastMCP 2.0 framework and SmartEM MCP components.
-
-## Configuration
-
-The MCP server can be configured using environment variables. A template configuration file is provided:
-
-```bash
-# Copy the example configuration
-cp .env.example.mcp .env.mcp
-
-# Edit .env.mcp with your settings
-```
-
-Available configuration options (see `.env.example.mcp` for details):
-- `SMARTEM_MCP_DATA_PATH`: Path to EPU sessions directory (for filesystem adapter)
-- `SMARTEM_MCP_API_URL`: SmartEM backend API URL (for API adapter)
-- `SMARTEM_MCP_ADAPTER`: Data adapter selection (`filesystem` or `api`)
-- `SMARTEM_MCP_LOG_LEVEL`: Logging level (`DEBUG`, `INFO`, `WARNING`, `ERROR`)
-
-## Quick Start
-
-### 1. Interactive Query Mode
-
-Start interactive mode for natural language questions:
-
-```bash
-python -m smartem_mcp interactive
-```
-
-Example questions:
-- "Show me a summary of session /path/to/epu/directory"
-- "Find low quality items in /path/to/epu with threshold 0.3"
-- "What are the recent acquisitions?"
-
-### 2. Command Line Usage
-
-Parse EPU directory:
-```bash
-python -m smartem_mcp client parse --path /path/to/epu/session
-```
-
-Find low quality items:
-```bash
-python -m smartem_mcp client quality --path /path/to/epu --threshold 0.3
-```
-
-Query recent acquisitions (requires API):
-```bash
-python -m smartem_mcp client acquisitions --limit 10
-```
-
-### 3. Programmatic Usage
-
-```python
-from smartem_mcp.client import SmartEMMCPClient
-
-async with SmartEMMCPClient() as client:
- # Parse EPU directory
- result = await client.parse_epu_directory("/path/to/epu")
- if result.get("success"):
- print(f"Found {result['grid_count']} grids")
-
- # Find low quality items
- quality_result = await client.find_low_quality_items(
- "/path/to/epu",
- threshold=0.3
- )
-
- # Query API data
- acquisitions = await client.query_recent_acquisitions(limit=5)
-```
-
-## Data Sources
-
-### Filesystem Queries
-
-Direct parsing of EPU XML files using existing `smartem_agent` tools:
-
-- **Use case**: Ad-hoc analysis, debugging, development
-- **Capabilities**: Full EPU directory parsing, quality analysis
-- **Requirements**: Direct filesystem access to EPU data
-
-### API Queries
-
-Query historical and in-flight sessions via SmartEM API:
-
-- **Use case**: Historical analysis, live session monitoring
-- **Capabilities**: Acquisition status, grid processing, real-time data
-- **Requirements**: Running SmartEM backend service
-
-## Claude Code Integration
-
-The SmartEM MCP server integrates seamlessly with Claude Code, allowing natural language queries about microscopy data directly within your development environment.
-
-### Prerequisites
-
-Ensure MCP dependencies are installed (includes FastMCP 2.0):
-
-```bash
-pip install -e .[mcp]
-```
-
-Verify the installation:
-
-```bash
-python -m smartem_mcp --version
-```
-
-### Registration with Claude Code
-
-#### Option 1: Using Claude CLI (Recommended)
-
-Register the SmartEM MCP server using the Claude CLI:
-
-```bash
-# Basic registration (user-wide scope)
-claude mcp add smartem -- python -m smartem_mcp server
-
-# With custom API URL
-claude mcp add smartem -- python -m smartem_mcp server --api-url http://localhost:30080
-
-# Project-scoped registration
-claude mcp add smartem --scope project -- python -m smartem_mcp server --api-url http://localhost:30080
-```
-
-#### Option 2: Manual Configuration
-
-If you prefer manual configuration, add the server to your Claude Code settings:
-
-**For user-wide registration:**
-Edit `~/.config/claude-code/mcp.json`:
-
-```json
-{
- "mcpServers": {
- "smartem": {
- "command": "python",
- "args": ["-m", "smartem_mcp", "server", "--api-url", "http://localhost:30080"],
- "env": {
- "SMARTEM_API_URL": "http://localhost:30080",
- "SMARTEM_MCP_LOG_LEVEL": "INFO"
- }
- }
- }
-}
-```
-
-**For project-scoped registration:**
-Create `.claude/mcp.json` in your project root:
-
-```json
-{
- "mcpServers": {
- "smartem": {
- "command": "python",
- "args": ["-m", "smartem_mcp", "server"],
- "env": {
- "SMARTEM_API_URL": "http://localhost:30080"
- }
- }
- }
-}
-```
-
-### Registration Options
-
-#### Environment Variables
-
-Configure the MCP server behaviour through environment variables:
-
-- `SMARTEM_API_URL`: Base URL for SmartEM API (default: `http://localhost:30080`)
-- `SMARTEM_MCP_LOG_LEVEL`: Logging level (`DEBUG`, `INFO`, `WARNING`, `ERROR`)
-- `PYTHON_PATH`: Python executable path if not in system PATH
-
-Example with custom environment:
-
-```bash
-claude mcp add smartem --env SMARTEM_API_URL=http://production.server:8080 --env SMARTEM_MCP_LOG_LEVEL=DEBUG -- python -m smartem_mcp server
-```
-
-#### Scope Options
-
-- **User scope** (default): Available across all Claude Code projects
-- **Project scope**: Only available within the current project directory
-
-```bash
-# User-wide (default)
-claude mcp add smartem -- python -m smartem_mcp server
-
-# Project-specific
-claude mcp add smartem --scope project -- python -m smartem_mcp server
-```
-
-### Verification
-
-#### 1. Check Registration Status
-
-```bash
-# List all registered MCP servers
-claude mcp list
-
-# Check SmartEM server status
-claude mcp status smartem
-```
-
-#### 2. Test Connection
-
-Start a new Claude Code session and verify the SmartEM tools are available:
-
-```bash
-# In Claude Code, type a natural language query:
-# "List all available SmartEM tools"
-```
-
-You should see the following tools available:
-- `parse_epu_directory` - Parse EPU microscopy directories
-- `query_quality_metrics` - Find low-quality images and foil holes
-- `query_acquisitions` - Query recent acquisition sessions
-- `query_grid_status` - Get grid processing status
-
-**Note**: The client provides high-level methods such as `find_low_quality_items()` which internally call the corresponding MCP tools.
-
-#### 3. Test Basic Functionality
-
-Try a simple query in Claude Code:
-
-> "Parse the EPU directory at /path/to/your/epu/session"
-
-### Usage in Claude Code
-
-Once registered, you can interact with SmartEM data using natural language within Claude Code:
-
-#### Directory Analysis
-
-> "Show me a comprehensive analysis of the EPU session at /data/microscopy/session_001"
-
-> "What grids and grid squares are available in /path/to/epu/directory?"
-
-#### Quality Assessment
-
-> "Find all images with quality scores below 0.4 in the EPU directory /data/session_001"
-
-> "Show me foil holes that need attention from /path/to/epu with quality threshold 0.3"
-
-#### Session Monitoring
-
-> "What are the 5 most recent microscopy acquisitions?"
-
-> "Check the processing status of grid uuid-12345"
-
-#### Advanced Queries
-
-> "Compare quality metrics between /data/session_001 and /data/session_002"
-
-> "Generate a report for all low-quality items found today"
-
-### Server Mode (Standalone)
-
-For advanced users or debugging, run the MCP server in standalone mode:
-
-```bash
-python -m smartem_mcp server --api-url http://localhost:30080 --log-level DEBUG
-```
-
-This starts the server with stdio communication, primarily useful for:
-- Debugging MCP protocol issues
-- Custom client integrations
-- Development and testing
-
-## Available Tools
-
-### `parse_epu_directory`
-Parse EPU microscopy directory and extract comprehensive session data.
-
-**Parameters:**
-- `path` (required): Path to EPU output directory containing EpuSession.dm
-
-**Returns:** Acquisition data, grids, grid squares, and statistics
-
-### `query_quality_metrics`
-Find foil holes and micrographs with quality scores below threshold.
-
-**Parameters:**
-- `path` (required): Path to EPU directory
-- `threshold` (optional): Quality threshold (default: 0.5)
-- `source` (optional): "filesystem" or "api" (default: filesystem)
-
-**Returns:** List of low-quality items with metadata
-
-### `query_acquisitions`
-Query recent microscopy acquisition sessions from API.
-
-**Parameters:**
-- `limit` (optional): Number of acquisitions to return (default: 10)
-
-**Returns:** List of acquisitions with status and metadata
-
-### `query_grid_status`
-Get detailed status and processing state for specific grid.
-
-**Parameters:**
-- `grid_id` (required): Grid UUID or identifier
-
-**Returns:** Grid details and processing status
-
-## Future Enhancements
-
-The following capabilities are scaffolded for future implementation:
-
-### Real-time Event Streaming
-```python
-# Future capability - real-time updates via RabbitMQ
-events = await client.subscribe_to_events("acquisition.*.quality_updated")
-```
-
-### Direct Database Querying
-```python
-# Future capability - direct read-only database access
-result = await client.query_database("SELECT * FROM micrographs WHERE quality < 0.3")
-```
-
-## Error Handling
-
-All operations return structured results with success indicators:
-
-```python
-result = await client.parse_epu_directory("/path/to/epu")
-if result.get("success"):
- # Process result data
- data = result.get("data", {})
- pass
-else:
- print(f"Error: {result.get('error')}")
-```
-
-## Configuration
-
-### Environment Variables
-
-- `SMARTEM_API_URL`: Base URL for SmartEM API (default: http://localhost:30080)
-- `SMARTEM_MCP_LOG_LEVEL`: Logging level (default: INFO)
-
-### API Authentication
-
-For authenticated API access (future):
-```python
-client = SmartEMMCPClient(api_token="your_token_here")
-```
-
-## Troubleshooting
-
-### Common Issues
-
-#### 1. MCP Server Registration Problems
-
-**"SmartEM MCP server not found"**
-- Ensure MCP dependencies are installed: `pip install -e .[mcp]` (includes FastMCP 2.0)
-- Verify Python path includes smartem_mcp module: `python -c "import smartem_mcp; print('OK')"`
-- Check registration with `claude mcp list`
-
-**"Failed to start MCP server"**
-- Verify Python executable is accessible: `which python`
-- Test server manually: `python -m smartem_mcp server --api-url http://localhost:30080`
-- Check environment variables are properly set
-
-**"MCP server registered but not responding"**
-- Remove and re-add the server: `claude mcp remove smartem && claude mcp add smartem -- python -m smartem_mcp server`
-- Restart Claude Code completely
-- Check server logs: `claude mcp logs smartem`
-
-#### 2. Directory and Data Issues
-
-**"Invalid EPU directory"**
-- Verify directory contains EpuSession.dm file
-- Check Metadata/ and Images-Disc*/ subdirectories exist
-- Ensure proper file permissions for reading EPU data
-
-**"Permission denied accessing EPU files"**
-- Check file permissions: `ls -la /path/to/epu/directory`
-- Ensure user has read access to all EPU subdirectories
-- For network mounts, verify mount permissions
-
-#### 3. API Connection Issues
-
-**"API connection failed"**
-- Verify SmartEM backend is running: `curl http://localhost:30080/health`
-- Check API URL is correct in registration command
-- Test network connectivity to API endpoint
-
-**"Authentication failed"** (Future feature)
-- Verify API tokens are properly configured
-- Check token expiration and renewal
-
-#### 4. Claude Code Integration Issues
-
-**"Tools not available in Claude Code"**
-- Restart Claude Code after registration
-- Check MCP server status: `claude mcp status smartem`
-- Verify registration scope (user vs project)
-
-**"Queries return empty results"**
-- Test with standalone client: `python -m smartem_mcp client parse --path /path/to/epu`
-- Check EPU directory structure and data validity
-- Verify API connectivity for acquisition queries
-
-### Debug Mode
-
-#### Enable Debug Logging
-
-For MCP server debugging:
-```bash
-claude mcp add smartem --env SMARTEM_MCP_LOG_LEVEL=DEBUG -- python -m smartem_mcp server --api-url http://localhost:30080 --log-level DEBUG
-```
-
-For client debugging:
-```bash
-python -m smartem_mcp --log-level DEBUG client parse --path /path/to/epu
-```
-
-#### Check Server Logs
-
-View MCP server logs in Claude Code:
-```bash
-claude mcp logs smartem
-```
-
-#### Manual Server Testing
-
-Test the server independently of Claude Code:
-```bash
-# Start server in stdio mode for testing
-python -m smartem_mcp server --log-level DEBUG
-
-# The server uses FastMCP stdio communication protocol
-# For testing, use interactive mode or programmatic client instead:
-python -m smartem_mcp interactive
-```
-
-### Environment-Specific Troubleshooting
-
-#### Development Environment
-- Ensure virtual environment is activated when registering
-- Use absolute Python paths: `claude mcp add smartem -- /path/to/.venv/bin/python -m smartem_mcp server`
-
-#### Production Environment
-- Verify all dependencies are installed in production Python environment
-- Check firewall rules for API connectivity
-- Ensure proper logging configuration for production
-
-#### Container Environments
-- Mount EPU directories properly in container
-- Expose API ports correctly
-- Set environment variables in container runtime
-
-### Getting Help
-
-If issues persist:
-
-1. **Gather diagnostic information:**
- ```bash
- # System info
- python --version
- pip list | grep -E "(smartem|mcp)"
- claude mcp list
- claude mcp status smartem
-
- # Test basic functionality
- python -m smartem_mcp --version
- python -c "import smartem_mcp; print('Import successful')"
- ```
-
-2. **Check project documentation:** [SmartEM Decisions README](/README.md)
-
-3. **Review MCP protocol documentation:** [Model Context Protocol Specification](https://modelcontextprotocol.io/)
-
-4. **Submit issue:** Include diagnostic information and specific error messages
-
-## Integration with Claude Code
-
-When properly configured, you can ask Claude Code natural language questions:
-
-> "Show me all grid squares with quality scores below 0.5 from the EPU session at /data/session1"
-
-> "What's the current status of acquisition abc-123?"
-
-> "List micrographs acquired in the last hour with defocus values"
-
-The MCP server will automatically route these queries to the appropriate data sources and return formatted results.
diff --git a/docs/tutorials/installation.md b/docs/tutorials/installation.md
index 77eda4bd..bb4e0d4f 100644
--- a/docs/tutorials/installation.md
+++ b/docs/tutorials/installation.md
@@ -47,18 +47,6 @@ cd smartem-decisions
pip install -e .[all]
```
-### Installation with Optional Dependencies
-
-Install with specific feature sets:
-
-```bash
-# Install with MCP (Model Context Protocol) support
-pip install -e .[mcp]
-
-# Install with all optional dependencies (recommended for development)
-pip install -e .[all]
-```
-
## Verify Installation
The library should now be installed with the command-line interface available on your system path. Verify the installation by checking the installed version:
@@ -72,9 +60,6 @@ You can also verify that all components are correctly installed by running:
```bash
# Test core functionality
python -c "import smartem_backend, smartem_agent, smartem_common; print('Core components imported successfully')"
-
-# Test MCP functionality (if installed with MCP support)
-python -c "import smartem_mcp; print('MCP components available')"
```
## Next Steps
diff --git a/pyproject.toml b/pyproject.toml
index 7a927327..87c2e3de 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -107,15 +107,9 @@ mock = [
"uvicorn[standard]>=0.30.0,<1.0.0",
]
-# MCP server and client dependencies (optional)
-mcp = [
- "smartem-decisions[common,client,cli,agent]",
- "fastmcp>=2.0.0",
-]
-
# Combined dependencies (for convenience)
all = [
- "smartem-decisions[dev,common,client,cli,backend,agent,fsrecorder,mock,mcp,images]",
+ "smartem-decisions[dev,common,client,cli,backend,agent,fsrecorder,mock,images]",
]
[project.scripts]
@@ -129,9 +123,6 @@ smartem_agent_tools = "smartem_agent.__main__:main"
"smartem.random-model-predictions" = "smartem_backend.cli.random_model_predictions:run"
"smartem.random-prior-updates" = "smartem_backend.cli.random_prior_updates:run"
-# Additional services
-"smartem-mcp" = "smartem_mcp.__main__:main"
-
[project.urls]
GitHub = "https://github.com/DiamondLightSource/smartem-decisions"
@@ -149,7 +140,6 @@ packages = [
"smartem_agent",
"smartem_common",
"athena_api",
- "smartem_mcp"
]
package-dir = {"" = "src"}
diff --git a/setup.py b/setup.py
index b2783655..a9182aba 100644
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,6 @@ def copy_version_files():
Path("src/smartem_agent/_version.py"),
Path("src/smartem_common/_version.py"),
Path("src/smartem_api/_version.py"),
- Path("src/smartem_mcp/_version.py"),
]
# Make sure target directories exist
diff --git a/src/smartem_mcp/__init__.py b/src/smartem_mcp/__init__.py
deleted file mode 100644
index 2d16c402..00000000
--- a/src/smartem_mcp/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-"""
-SmartEM MCP (Model Context Protocol) Server and Client
-
-Provides natural language interface to SmartEM microscopy data through MCP protocol.
-Supports both filesystem-based parsing and API-based querying for comprehensive
-microscopy session data access.
-"""
diff --git a/src/smartem_mcp/__main__.py b/src/smartem_mcp/__main__.py
deleted file mode 100644
index 46671d89..00000000
--- a/src/smartem_mcp/__main__.py
+++ /dev/null
@@ -1,281 +0,0 @@
-"""
-SmartEM MCP Command Line Interface using FastMCP
-
-Provides command-line access to SmartEM MCP server and client functionality.
-"""
-
-import argparse
-import asyncio
-import json
-import logging
-import sys
-
-from smartem_mcp._version import __version__
-from smartem_mcp.client import SmartEMMCPClient
-
-
-async def run_client(args):
- """Run client commands"""
- logging.basicConfig(level=getattr(logging, args.log_level))
-
- async with SmartEMMCPClient() as client:
- if args.client_command == "parse":
- if not args.path:
- print("Error: --path required for parse command")
- return 1
-
- try:
- result = await client.parse_epu_directory(args.path)
- if args.json:
- print(json.dumps(result, indent=2, default=str))
- else:
- print(f"Successfully parsed EPU directory: {args.path}")
- print(f" Grids: {result.get('grid_count', 0)}")
- print(f" Grid squares: {result.get('total_gridsquares', 0)}")
- if result.get("acquisition"):
- print(f" Acquisition: {result['acquisition'].get('name', 'Unknown')}")
- except Exception as e:
- print(f"Failed to parse directory: {str(e)}")
- return 1
-
- elif args.client_command == "quality":
- if not args.path:
- print("Error: --path required for quality command")
- return 1
-
- try:
- result = await client.find_low_quality_items(args.path, args.threshold, args.source)
- if args.json:
- print(json.dumps(result, indent=2, default=str))
- else:
- items = result.get("low_quality_items", [])
- print(f"Quality analysis complete (threshold: {args.threshold})")
- print(f" Found {len(items)} low-quality items")
- if items:
- for item in items[:5]: # Show first 5
- print(f" - {item}")
- if len(items) > 5:
- print(f" ... and {len(items) - 5} more")
- except Exception as e:
- print(f"Quality analysis failed: {str(e)}")
- return 1
-
- elif args.client_command == "acquisitions":
- try:
- result = await client.query_recent_acquisitions(args.limit)
- if args.json:
- print(json.dumps(result, indent=2, default=str))
- else:
- acquisitions = result.get("acquisitions", [])
- print(f"Found {len(acquisitions)} recent acquisitions")
- for acq in acquisitions:
- print(f" - {acq.get('name', 'Unknown')} (ID: {acq.get('id', 'N/A')})")
- except Exception as e:
- print(f"Failed to query acquisitions: {str(e)}")
- return 1
-
- elif args.client_command == "grid":
- if not args.grid_id:
- print("Error: --grid-id required for grid command")
- return 1
-
- try:
- result = await client.get_grid_status(args.grid_id)
- if args.json:
- print(json.dumps(result, indent=2, default=str))
- else:
- grid = result.get("grid", {})
- print(f"Grid {args.grid_id} status:")
- print(f" Status: {grid.get('status', 'Unknown')}")
- print(f" Created: {grid.get('created_at', 'Unknown')}")
- except Exception as e:
- print(f"Failed to get grid status: {str(e)}")
- return 1
-
- else:
- print(f"Unknown client command: {args.client_command}")
- return 1
-
- return 0
-
-
-async def run_interactive(args):
- """Run interactive query mode"""
- logging.basicConfig(level=getattr(logging, args.log_level))
-
- print(f"SmartEM Interactive Query Interface v{__version__}")
- print("Execute direct tool calls against the MCP server!")
- print("Available tools: parse_epu_directory, query_quality_metrics, query_acquisitions, query_grid_status")
- print("Examples:")
- print(" parse /path/to/epu")
- print(" quality /path/to/epu 0.3")
- print(" acquisitions 10")
- print(" grid ")
- print()
-
- client = SmartEMMCPClient()
-
- try:
- while True:
- command = input("ā Tool command: ").strip()
- if command.lower() in ["exit", "quit", "q"]:
- break
-
- if not command:
- continue
-
- parts = command.split()
- tool_cmd = parts[0].lower()
-
- try:
- if tool_cmd == "parse" and len(parts) >= 2:
- path = parts[1]
- result = await client.parse_epu_directory(path)
- grid_count = result.get("grid_count", 0)
- total_squares = result.get("total_gridsquares", 0)
- print(f" Parsed {grid_count} grids, {total_squares} grid squares")
-
- elif tool_cmd == "quality" and len(parts) >= 2:
- path = parts[1]
- threshold = float(parts[2]) if len(parts) > 2 else 0.5
- result = await client.find_low_quality_items(path, threshold)
- items = result.get("low_quality_items", [])
- print(f" Found {len(items)} low-quality items (threshold: {threshold})")
-
- elif tool_cmd == "acquisitions":
- limit = int(parts[1]) if len(parts) > 1 else 10
- result = await client.query_recent_acquisitions(limit)
- acquisitions = result.get("acquisitions", [])
- print(f" Found {len(acquisitions)} recent acquisitions")
-
- elif tool_cmd == "grid" and len(parts) >= 2:
- grid_id = parts[1]
- result = await client.get_grid_status(grid_id)
- grid = result.get("grid", {})
- print(f" Grid {grid_id}: {grid.get('status', 'Unknown')}")
-
- else:
- print("Invalid command format")
- print("Use: parse | quality [threshold] | acquisitions [limit] | grid ")
-
- except Exception as e:
- print(f"Error: {str(e)}")
-
- print()
-
- except KeyboardInterrupt:
- print("\nš Goodbye!")
- finally:
- await client.disconnect()
-
- return 0
-
-
-def main():
- """Main CLI entry point"""
- parser = argparse.ArgumentParser(
- description="SmartEM MCP - Natural language interface to microscopy data",
- formatter_class=argparse.RawDescriptionHelpFormatter,
- epilog="""
-Examples:
- # Start MCP server
- python -m smartem_mcp server --api-url http://localhost:30080
-
- # Parse EPU directory
- python -m smartem_mcp client parse --path /path/to/epu/session
-
- # Find low quality items
- python -m smartem_mcp client quality --path /path/to/epu --threshold 0.3
-
- # Query recent acquisitions
- python -m smartem_mcp client acquisitions --limit 10
-
- # Interactive mode
- python -m smartem_mcp interactive
- """,
- )
-
- parser.add_argument("--version", action="version", version=f"SmartEM MCP v{__version__}")
- parser.add_argument(
- "--log-level", choices=["DEBUG", "INFO", "WARNING", "ERROR"], default="INFO", help="Logging level"
- )
-
- subparsers = parser.add_subparsers(dest="mode", help="Mode to run")
-
- # Server mode
- server_parser = subparsers.add_parser("server", help="Run MCP server")
- server_parser.add_argument("--api-url", default="http://localhost:30080", help="SmartEM API base URL")
-
- # Client mode
- client_parser = subparsers.add_parser("client", help="Run client commands")
- client_subparsers = client_parser.add_subparsers(dest="client_command", help="Client command")
-
- # Parse command
- parse_parser = client_subparsers.add_parser("parse", help="Parse EPU directory")
- parse_parser.add_argument("--path", required=True, help="Path to EPU directory")
- parse_parser.add_argument("--json", action="store_true", help="Output raw JSON")
-
- # Quality command
- quality_parser = client_subparsers.add_parser("quality", help="Analyze quality metrics")
- quality_parser.add_argument("--path", required=True, help="Path to EPU directory")
- quality_parser.add_argument("--threshold", type=float, default=0.5, help="Quality threshold")
- quality_parser.add_argument("--source", choices=["filesystem", "api"], default="filesystem", help="Data source")
- quality_parser.add_argument("--json", action="store_true", help="Output raw JSON")
-
- # Acquisitions command
- acq_parser = client_subparsers.add_parser("acquisitions", help="Query acquisitions")
- acq_parser.add_argument("--limit", type=int, default=10, help="Number of acquisitions")
- acq_parser.add_argument("--json", action="store_true", help="Output raw JSON")
-
- # Grid command
- grid_parser = client_subparsers.add_parser("grid", help="Get grid status")
- grid_parser.add_argument("--grid-id", required=True, help="Grid UUID")
- grid_parser.add_argument("--json", action="store_true", help="Output raw JSON")
-
- # Interactive mode
- subparsers.add_parser("interactive", help="Interactive query mode")
-
- args = parser.parse_args()
-
- if not args.mode:
- parser.print_help()
- return 1
-
- try:
- if args.mode == "server":
- # Run server with proper argument passing
- from smartem_mcp.server import init_api_client
-
- logging.basicConfig(level=getattr(logging, args.log_level))
-
- # Initialize API client
- api_connected = init_api_client(args.api_url)
- if api_connected:
- logger = logging.getLogger(__name__)
- logger.info("Initialized SmartEM API client")
- else:
- logger = logging.getLogger(__name__)
- logger.warning("Could not initialize SmartEM API client - some features may be limited")
-
- # Import the mcp instance and run it
- from smartem_mcp.server import mcp
-
- return asyncio.run(mcp.run())
- elif args.mode == "client":
- return asyncio.run(run_client(args))
- elif args.mode == "interactive":
- return asyncio.run(run_interactive(args))
- else:
- parser.print_help()
- return 1
-
- except KeyboardInterrupt:
- print("\nInterrupted by user")
- return 130
- except Exception as e:
- print(f"Unexpected error: {str(e)}")
- return 1
-
-
-if __name__ == "__main__":
- sys.exit(main())
diff --git a/src/smartem_mcp/client.py b/src/smartem_mcp/client.py
deleted file mode 100644
index ac3229af..00000000
--- a/src/smartem_mcp/client.py
+++ /dev/null
@@ -1,179 +0,0 @@
-"""
-SmartEM MCP Client using FastMCP
-
-Provides client interface for connecting to SmartEM MCP server and executing
-natural language queries against microscopy data.
-
-Usage Examples:
- # Filesystem queries
- client = SmartEMMCPClient()
- result = await client.parse_epu_directory("/path/to/epu/session")
-
- # API queries
- result = await client.query_recent_acquisitions(limit=5)
-
- # Quality analysis
- low_quality = await client.find_low_quality_items("/path/to/epu", threshold=0.3)
-"""
-
-import asyncio
-import json
-import logging
-from typing import Any
-
-from fastmcp.client import Client
-
-logger = logging.getLogger(__name__)
-
-
-class SmartEMMCPClient:
- """Client for interacting with SmartEM MCP Server using FastMCP"""
-
- def __init__(self, server_command: list[str] | None = None):
- """
- Initialize MCP client
-
- Args:
- server_command: Command to start MCP server. Defaults to local server.
- """
- self.server_command = server_command or ["python", "-m", "smartem_mcp.server"]
- self.client = None
- self.logger = logging.getLogger(__name__)
-
- async def connect(self) -> bool:
- """Connect to SmartEM MCP server"""
- try:
- self.logger.info(f"Connecting to SmartEM MCP server: {' '.join(self.server_command)}")
- self.client = Client(self.server_command)
- self.logger.info("Connected to SmartEM MCP server")
- return True
-
- except Exception as e:
- self.logger.error(f"Failed to connect to MCP server: {str(e)}")
- self.client = None
- return False
-
- async def disconnect(self):
- """Disconnect from MCP server"""
- if self.client:
- await self.client.close()
- self.client = None
- self.logger.info("Disconnected from MCP server")
-
- async def _call_tool(self, tool_name: str, arguments: dict[str, Any]) -> dict[str, Any]:
- """Execute MCP tool with error handling"""
- if not self.client:
- await self.connect()
-
- try:
- async with self.client:
- result = await self.client.call_tool(tool_name, arguments)
- return result
-
- except Exception as e:
- self.logger.error(f"Error calling tool {tool_name}: {str(e)}")
- raise RuntimeError(f"Tool call failed: {str(e)}") from e
-
- # High-level query methods
-
- async def parse_epu_directory(self, path: str) -> dict[str, Any]:
- """
- Parse EPU microscopy directory and extract comprehensive session data
-
- Args:
- path: Path to EPU output directory containing EpuSession.dm
-
- Returns:
- Parsed acquisition data, grids, and statistics
- """
- return await self._call_tool("parse_epu_directory", {"path": path})
-
- async def find_low_quality_items(
- self, path: str, threshold: float = 0.5, source: str = "filesystem"
- ) -> dict[str, Any]:
- """
- Find foil holes and micrographs with quality scores below threshold
-
- Args:
- path: Path to EPU directory (for filesystem) or ignored (for API)
- threshold: Quality threshold (0.0 to 1.0)
- source: Data source - "filesystem" or "api"
-
- Returns:
- Low quality items and statistics
- """
- return await self._call_tool("query_quality_metrics", {"path": path, "threshold": threshold, "source": source})
-
- async def query_recent_acquisitions(self, limit: int = 10) -> dict[str, Any]:
- """
- Query recent microscopy acquisition sessions from API
-
- Args:
- limit: Number of acquisitions to return
-
- Returns:
- Acquisition list and metadata
- """
- return await self._call_tool("query_acquisitions", {"limit": limit})
-
- async def get_grid_status(self, grid_id: str) -> dict[str, Any]:
- """
- Get detailed status and processing state for a specific grid
-
- Args:
- grid_id: Grid UUID or identifier
-
- Returns:
- Grid details and processing status
- """
- return await self._call_tool("query_grid_status", {"grid_id": grid_id})
-
- # Context manager support
-
- async def __aenter__(self):
- """Async context manager entry"""
- if not self.client:
- await self.connect()
- return self
-
- async def __aexit__(self, exc_type, exc_val, exc_tb):
- """Async context manager exit"""
- await self.disconnect()
-
-
-# Utility functions for CLI usage
-
-
-async def main():
- """Example usage of SmartEM MCP Client"""
- import argparse
-
- parser = argparse.ArgumentParser(description="SmartEM MCP Client")
- parser.add_argument("--path", help="Path to EPU directory")
- parser.add_argument("--command", help="Command to execute")
- parser.add_argument("--threshold", type=float, default=0.5, help="Quality threshold")
-
- args = parser.parse_args()
-
- async with SmartEMMCPClient() as client:
- if args.command == "parse" and args.path:
- result = await client.parse_epu_directory(args.path)
- print(json.dumps(result, indent=2, default=str))
-
- elif args.command == "quality" and args.path:
- result = await client.find_low_quality_items(args.path, args.threshold)
- print(json.dumps(result, indent=2, default=str))
-
- elif args.command == "acquisitions":
- result = await client.query_recent_acquisitions()
- print(json.dumps(result, indent=2, default=str))
-
- else:
- print("Usage examples:")
- print(" python -m smartem_mcp.client --command parse --path /path/to/epu")
- print(" python -m smartem_mcp.client --command quality --path /path/to/epu --threshold 0.3")
- print(" python -m smartem_mcp.client --command acquisitions")
-
-
-if __name__ == "__main__":
- asyncio.run(main())
diff --git a/src/smartem_mcp/server.py b/src/smartem_mcp/server.py
deleted file mode 100644
index 1ebbbdeb..00000000
--- a/src/smartem_mcp/server.py
+++ /dev/null
@@ -1,249 +0,0 @@
-"""
-SmartEM MCP Server using FastMCP
-
-Provides MCP (Model Context Protocol) server for natural language querying of
-microscopy session data. Supports both filesystem-based parsing and API-based
-querying with read-only access to scientific data.
-
-Architecture:
-- Direct filesystem parsing using smartem_agent tools
-- API querying via SmartEM API client
-- FastMCP decorators for simplified tool and resource registration
-"""
-
-import asyncio
-import json
-import logging
-from pathlib import Path
-from typing import Any
-
-from fastmcp import FastMCP
-
-from smartem_agent.fs_parser import EpuParser
-from smartem_agent.model.store import InMemoryDataStore
-from smartem_backend.api_client import SmartEMAPIClient
-from smartem_mcp._version import __version__
-
-logger = logging.getLogger(__name__)
-
-# Initialize FastMCP server
-mcp = FastMCP("smartem-mcp")
-
-# Global API client instance
-api_client: SmartEMAPIClient | None = None
-
-
-def init_api_client(api_base_url: str = "http://localhost:30080") -> bool:
- """Initialize global API client"""
- global api_client
- try:
- api_client = SmartEMAPIClient(base_url=api_base_url)
- return True
- except Exception as e:
- logger.error(f"Failed to initialize API client: {e}")
- return False
-
-
-@mcp.tool()
-async def parse_epu_directory(path: str) -> dict[str, Any]:
- """
- Parse EPU microscopy directory and extract comprehensive session data
-
- Args:
- path: Path to EPU output directory containing EpuSession.dm
-
- Returns:
- Comprehensive acquisition data including grids and statistics
- """
- try:
- epu_path = Path(path)
- if not epu_path.exists():
- raise ValueError(f"Path does not exist: {path}")
-
- # Validate EPU directory structure
- is_valid, errors = EpuParser.validate_project_dir(epu_path)
- if not is_valid:
- raise ValueError(f"Invalid EPU directory: {'; '.join(errors)}")
-
- # Parse the directory
- datastore = InMemoryDataStore(root_dir=epu_path)
- datastore = EpuParser.parse_epu_output_dir(datastore)
-
- # Convert to serializable format
- return {
- "acquisition": datastore.acquisition.model_dump() if datastore.acquisition else None,
- "grids": [grid.model_dump() for grid in datastore.grids.values()],
- "grid_count": len(datastore.grids),
- "total_gridsquares": sum(
- len(grid_data.gridsquares)
- for grid_data in datastore.grids.values()
- if hasattr(grid_data, "gridsquares")
- ),
- "source": "filesystem",
- }
-
- except Exception as e:
- logger.error(f"Error parsing EPU directory {path}: {str(e)}")
- raise RuntimeError(f"Failed to parse EPU directory: {str(e)}") from e
-
-
-@mcp.tool()
-async def query_quality_metrics(path: str, threshold: float = 0.5, source: str = "filesystem") -> dict[str, Any]:
- """
- Find foil holes and micrographs with quality scores below threshold
-
- Args:
- path: Path to EPU directory (for filesystem queries)
- threshold: Quality threshold (0.0 to 1.0)
- source: Data source - "filesystem" or "api"
-
- Returns:
- Low quality items and statistics
- """
- if source == "api":
- raise NotImplementedError("API-based quality queries not yet implemented")
-
- try:
- # Get parsed directory data
- directory_data = await parse_epu_directory(path)
-
- # This is a simplified example - would need proper quality metric extraction
- # from the parsed EPU data structures
- low_quality_items = []
- for _grid in directory_data.get("grids", []):
- # Future implementation: extract actual quality metrics
- pass
-
- return {
- "low_quality_items": low_quality_items,
- "threshold": threshold,
- "source": source,
- }
-
- except Exception as e:
- logger.error(f"Error querying quality metrics: {str(e)}")
- raise RuntimeError(f"Failed to query quality metrics: {str(e)}") from e
-
-
-@mcp.tool()
-async def query_acquisitions(limit: int = 10) -> dict[str, Any]:
- """
- Query recent microscopy acquisition sessions from API
-
- Args:
- limit: Number of acquisitions to return
-
- Returns:
- List of recent acquisitions with metadata
- """
- global api_client
-
- if not api_client:
- raise RuntimeError("API client not initialized")
-
- try:
- # Test connection first
- health = await api_client.get_health()
- if health.get("status") != "healthy":
- raise RuntimeError("API is not healthy")
-
- acquisitions = await api_client.get_acquisitions(limit=limit)
-
- return {
- "acquisitions": acquisitions,
- "count": len(acquisitions),
- "source": "api",
- }
-
- except Exception as e:
- logger.error(f"Error querying acquisitions: {str(e)}")
- raise RuntimeError(f"Failed to query acquisitions: {str(e)}") from e
-
-
-@mcp.tool()
-async def query_grid_status(grid_id: str) -> dict[str, Any]:
- """
- Get detailed status and processing state for a specific grid
-
- Args:
- grid_id: Grid UUID or identifier
-
- Returns:
- Grid details and processing status
- """
- global api_client
-
- if not api_client:
- raise RuntimeError("API client not initialized")
-
- try:
- grid = await api_client.get_grid(grid_id)
- if not grid:
- raise ValueError(f"Grid {grid_id} not found")
-
- return {
- "grid": grid,
- "source": "api",
- }
-
- except Exception as e:
- logger.error(f"Error querying grid {grid_id}: {str(e)}")
- raise RuntimeError(f"Failed to query grid status: {str(e)}") from e
-
-
-@mcp.resource("smartem://acquisitions")
-async def get_acquisitions_resource() -> str:
- """Current and recent microscopy acquisition sessions"""
- try:
- result = await query_acquisitions(limit=5)
- return json.dumps(result, indent=2, default=str)
- except Exception:
- return json.dumps({"error": "Failed to fetch acquisitions"})
-
-
-@mcp.resource("smartem://quality-metrics")
-async def get_quality_metrics_resource() -> str:
- """Image and foil hole quality assessment data"""
- return json.dumps({"message": "Quality metrics resource - requires specific query parameters"})
-
-
-@mcp.resource("smartem://events")
-async def get_events_resource() -> str:
- """Live event stream from microscopy sessions (Future)"""
- return json.dumps({"message": "Resource not yet implemented - planned for future release"})
-
-
-@mcp.resource("smartem://database")
-async def get_database_resource() -> str:
- """Direct read-only database queries (Future)"""
- return json.dumps({"message": "Resource not yet implemented - planned for future release"})
-
-
-async def main():
- """Main entry point for SmartEM MCP Server"""
- import argparse
-
- parser = argparse.ArgumentParser(description="SmartEM MCP Server")
- parser.add_argument("--api-url", default="http://localhost:30080", help="SmartEM API base URL")
- parser.add_argument(
- "--log-level", choices=["DEBUG", "INFO", "WARNING", "ERROR"], default="INFO", help="Logging level"
- )
-
- args = parser.parse_args()
-
- logging.basicConfig(level=getattr(logging, args.log_level))
- logger.info(f"Starting SmartEM MCP Server v{__version__}")
-
- # Initialize API client
- api_connected = init_api_client(args.api_url)
- if api_connected:
- logger.info("Initialized SmartEM API client")
- else:
- logger.warning("Could not initialize SmartEM API client - some features may be limited")
-
- # Run FastMCP server
- await mcp.run()
-
-
-if __name__ == "__main__":
- asyncio.run(main())
diff --git a/tests/smartem_mcp/__init__.py b/tests/smartem_mcp/__init__.py
deleted file mode 100644
index 3579641b..00000000
--- a/tests/smartem_mcp/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-"""Tests for SmartEM MCP functionality"""
diff --git a/tools/mcp_demo.py b/tools/mcp_demo.py
deleted file mode 100644
index 9014d1f7..00000000
--- a/tools/mcp_demo.py
+++ /dev/null
@@ -1,195 +0,0 @@
-#!/usr/bin/env python
-"""
-SmartEM MCP Demo - Show off the natural language interface
-
-This is a demonstration script showcasing MCP capabilities.
-Run with: python tools/mcp_demo.py
-
-For actual testing, see tests/smartem_mcp/
-"""
-
-import asyncio
-
-from smartem_mcp.client import SmartEMQueryInterface
-from smartem_mcp.server import FilesystemAdapter
-
-
-class MockMCPClient:
- """Mock client that bypasses MCP protocol for demo purposes"""
-
- async def session_summary(self, path):
- adapter = FilesystemAdapter()
- result = await adapter.parse_epu_directory(path)
-
- if result.success and result.data:
- data = result.data
- return {
- "session_path": path,
- "acquisition_name": data.get("acquisition", {}).get("name", "Unknown"),
- "grid_count": data.get("grid_count", 0),
- "total_gridsquares": data.get("total_gridsquares", 0),
- "success": True,
- }
- else:
- return {"error": result.error, "success": False}
-
- async def quality_report(self, path, threshold):
- adapter = FilesystemAdapter()
- result = await adapter.query_quality_metrics(path, threshold)
-
- if result.success and result.data:
- data = result.data
- return {
- "quality_threshold": threshold,
- "low_quality_count": len(data.get("low_quality_items", [])),
- "items": data.get("low_quality_items", []),
- "success": True,
- }
- else:
- return {"error": result.error, "success": False}
-
- async def query_recent_acquisitions(self, limit):
- return {"success": False, "error": "API not available in demo mode - would normally query SmartEM API"}
-
-
-async def demo_natural_language_queries():
- """Demonstrate natural language querying capabilities"""
-
- print("š SmartEM MCP Natural Language Interface Demo")
- print("=" * 60)
-
- # Use test dataset
- test_path = (
- "/home/vredchenko/dev/DLS/smartem-decisions-test-datasets/bi37708-28-copy/"
- "Supervisor_20250129_134723_36_bi37708-28_grid7_EPU"
- )
-
- interface = SmartEMQueryInterface(client=MockMCPClient())
-
- # Demo queries
- queries = [
- {
- "question": "Show me a session summary",
- "context": {"path": test_path},
- "description": "Get high-level overview of microscopy session",
- },
- {
- "question": "Find low quality items with threshold 0.5",
- "context": {"path": test_path, "threshold": 0.5},
- "description": "Analyze quality metrics for troubleshooting",
- },
- {
- "question": "What are the recent acquisitions?",
- "context": {},
- "description": "Query recent microscopy sessions (would use API)",
- },
- ]
-
- for i, query in enumerate(queries, 1):
- print(f"\nExample {i}: {query['description']}")
- print(f' Question: "{query["question"]}"')
-
- try:
- answer = await interface.ask(query["question"], query["context"])
- print(f" Answer: {answer}")
- except Exception as e:
- print(f" Error: {str(e)}")
-
- print("-" * 40)
-
-
-async def demo_direct_queries():
- """Show direct filesystem adapter queries"""
-
- print("\n Direct SmartEM Data Queries")
- print("=" * 60)
-
- adapter = FilesystemAdapter()
- test_path = (
- "/home/vredchenko/dev/DLS/smartem-decisions-test-datasets/bi37708-28-copy/"
- "Supervisor_20250129_134723_36_bi37708-28_grid7_EPU"
- )
-
- # 1. Parse EPU directory
- print("\n Parsing EPU Directory Structure...")
- result = await adapter.parse_epu_directory(test_path)
-
- if result.success:
- data = result.data or {}
- print(" Success!")
- print(f" Grids: {data.get('grid_count', 0)}")
- print(f" Grid squares: {data.get('total_gridsquares', 0)}")
-
- if data.get("grids"):
- grid = data["grids"][0]
- print(f" Grid UUID: {grid.get('uuid', 'N/A')}")
- print(f" Data directory: {grid.get('data_dir', 'N/A')}")
- else:
- print(f" Failed: {result.error}")
-
- # 2. Quality analysis
- print("\n Quality Metrics Analysis...")
- for threshold in [0.3, 0.5, 0.8]:
- quality_result = await adapter.query_quality_metrics(test_path, threshold)
- if quality_result.success:
- quality_data = quality_result.data or {}
- count = len(quality_data.get("low_quality_items", []))
- print(f" Threshold {threshold}: {count} low-quality items")
-
-
-def show_mcp_capabilities():
- """Show what the MCP interface can do"""
-
- print("\n SmartEM MCP Capabilities")
- print("=" * 60)
-
- capabilities = [
- " Parse EPU microscopy directories",
- " Natural language querying of session data",
- " Quality metrics analysis and filtering",
- " Grid square and foil hole enumeration",
- " Integration with SmartEM API (when available)",
- " Interactive command-line interface",
- " Claude Code MCP protocol integration",
- " Both filesystem and API data sources",
- ]
-
- for capability in capabilities:
- print(f" {capability}")
-
- print("\n Available Tools:")
- tools = [
- "parse_epu_directory - Extract comprehensive session data",
- "query_quality_metrics - Find low-quality items",
- "query_acquisitions - Get recent microscopy sessions (API)",
- "query_grid_status - Check specific grid processing state (API)",
- ]
-
- for tool in tools:
- print(f" ā¢ {tool}")
-
- print("\n Usage Examples:")
- examples = [
- 'smartem-mcp client parse --path "/path/to/epu"',
- 'smartem-mcp client quality --path "/path/to/epu" --threshold 0.3',
- "smartem-mcp interactive # Natural language mode",
- "python -m smartem_mcp server # Start MCP server for Claude Code",
- ]
-
- for example in examples:
- print(f" $ {example}")
-
-
-async def main():
- """Main demo function"""
-
- show_mcp_capabilities()
- await demo_direct_queries()
- await demo_natural_language_queries()
-
- print("\nš SmartEM MCP Demo Complete!")
- print("š” Try: 'smartem-mcp interactive' for hands-on natural language queries")
-
-
-if __name__ == "__main__":
- asyncio.run(main())
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