fandanGO-cryoem-dls

Diamond Light Source FandanGO Plugin for Cryo-EM Metadata Deposition

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Source of Truth: This repository (DiamondLightSource/fandanGO-cryoem-dls) is the authoritative source maintained by Diamond Light Source. A mirror exists at FragmentScreen/fandanGO-cryoem-dls for ecosystem visibility.

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Overview

FandanGO plugin for integrating Diamond Light Source cryo-EM metadata from the SmartEM decision system into the ARIA data deposition platform.

This plugin enables the extraction, management, and deposition of cryo-EM experimental metadata from DLS's SmartEM system into ARIA for centralised tracking and sharing within the Fragment Screen / WP4 ecosystem.

Key Features

• SmartEM Integration: Extracts complete hierarchical metadata from DLS's SmartEM API
• ARIA Deposition: Submits structured metadata to ARIA with embargo controls
• Extract -> Transform -> Load: Clean architecture for metadata pipeline
• Facility-Specific: DLS-maintained plugin following FandanGO facility pattern

Architecture

smartem-decisions     fandanGO-cryoem-dls          ARIA
   (DLS server)    ->    (this plugin)    ->    (remote)
     HTTP API              ETL pipeline         HTTP API

Quick Start

# Clone and install
git clone https://github.com/DiamondLightSource/fandanGO-cryoem-dls.git
cd fandanGO-cryoem-dls
pip install -e .

# Extract metadata from SmartEM
fandango generate-metadata my_project --acquisition-id <uuid>

# Send to ARIA
fandango send-metadata my_project --visit-id <aria_visit_id>

Documentation

Full documentation: https://DiamondLightSource.github.io/smartem-devtools

Related Repositories

FandanGO Ecosystem

• fandanGO-core - Plugin framework
• fandanGO-aria - ARIA API client

SmartEM

• smartem-decisions - Source system for metadata

Development

pip install pre-commit
pre-commit install

This enables local hooks for secrets scanning and code quality checks.

Contributing

Contributions are welcome. This is an open-source project maintained by Diamond Light Source for the Fragment Screen community.

1. Fork the repository
2. Create a feature branch
3. Make your changes and add tests
4. Submit a Pull Request

Contact: scientificsoftware@diamond.ac.uk

Acknowledgments

• FandanGO Framework: Fragment Screen consortium
• SmartEM System: Diamond Light Source Electron Microscopy team
• ARIA Platform: Structural biology data repository
• Fragment Screen: European structural biology infrastructure project