fw-curation

fw-curation is a python package maintained by Flywheel It provides a set of utilities for writing SDK scripts to perform curation.

Features

• Validation and Curation: Perform highly configurable curation tasks on a given container or file
• Traversal Control: Walk the Flywheel Hierarchy depth-first or breadth-first, with configurable stop levels, custom callback functions, and the ability to exclude analyses and/or files
• Multiprocessing Support: Parallel processing with configurable worker count and shared data between workers
• Aggregated Logging: Customizable output logging in CSV or JSON format

Installation

Basic Installation

pip install fw-curation

With Optional Dependencies

Install specific extras for additional functionality:

# Install with SDK support
pip install fw-curation[sdk]

Available extras:

• sdk: Flywheel SDK integration

Quick Start

Create a simple HierarchyCurator script:

from fw_curation.curator import HierarchyCurator
from fw_curation.walker import Walker
import flywheel
import logging

log = logging.getLogger(__name__)

class Curator(HierarchyCurator):
    def curate_acquisition(self, acq):
        log.info(f'Processing acquisition: {acq.label}')

if __name__ == '__main__':
    # Connect to Flywheel
    fw = flywheel.Client(<YOUR_API_KEY>)

    # Get your project
    project = fw.lookup('example/test')

    # Create a walker starting from the project
    walker = Walker.from_container(project)

    # Create and run the curator
    curator = Curator()
    curator.curate(walker)

Documentation

Comprehensive documentation is available at: https://flywheel-io.gitlab.io/scientific-solutions/lib/fw-curation/

• Getting Started - Tutorial with practical examples
• Curator - Curating Flywheel containers and files
• Walker - Traversing the Flywheel Hierarchy
• Reporters - Logging to CSV or JSON output
• Config - Configuring the Curator, Walker, and Reporters
• Multiprocessing - Running in multi-processing mode
• Examples - Additional practical examples
• API Reference - Complete API documentation
• Migration Guide - Migrating from flywheel-gear-toolkit

Contributing

We welcome contributions! Please see CONTRIBUTING.md for guidelines on contributing.

License

fw-curation is released under the MIT License.

Support

• Documentation: https://flywheel-io.gitlab.io/scientific-solutions/lib/fw-curation/
• Issues: GitLab Issue Tracker
• Flywheel Docs: https://docs.flywheel.io/