aind-metadata-manager

AIND Metadata Manager

AIND Metadata Manager is a Python package for managing, upgrading, and validating metadata files used in the Allen Institute for Neural Dynamics (AIND) data pipelines. It provides tools to upgrade metadata schemas, process and validate metadata, and support reproducible data workflows.

Features

• Upgrade metadata files to the latest schema versions
• Validate and process metadata for AIND data pipelines
• Utilities for handling data descriptions, procedures, and processing metadata
• Command-line and programmatic interfaces

Installation

1. Clone the repository:

   git clone https://github.com/AllenNeuralDynamics/aind-metadata-manager.git
   cd aind-metadata-manager
   

2. Create and activate a virtual environment (recommended):

   python -m venv venv
   venv\Scripts\activate  # On Windows
   # or
   source venv/bin/activate  # On macOS/Linux
   

3. Install dependencies:

   pip install -e .
   pip install aind-data-schema aind-metadata-upgrader
   

Usage

As a Python package

from aind_metadata_manager.metadata_manager import MetadataManager, MetadataSettings
settings = MetadataSettings(input_dir='path/to/input', output_dir='path/to/output')
manager = MetadataManager(settings)
manager.create_processing_metadata()

Command Line Interface

A CLI may be available (see src/aind_metadata_manager/metadata_manager.py for details):

python -m aind_metadata_manager.metadata_manager --help

Development & Testing

• Tests are located in the tests/ directory.
• To run tests:

  venv\Scripts\python -m unittest discover -s tests -p "test_*.py" -v
  

Project Structure

• src/aind_metadata_manager/ — Main package code
• tests/ — Unit tests and test resources
• docs/ — Documentation

Requirements

• Python 3.10+
• aind-data-schema
• aind-metadata-upgrader
• pydantic, pydantic-settings

License

This project is licensed under the terms of the MIT license. See the LICENSE file for details.

Citation

If you use this package, please cite as described in CITATION.cff.

Contributing

See CONTRIBUTING.md for guidelines.

Contact

For questions or support, please open an issue on GitHub or contact the Allen Institute for Neural Dynamics.