A package to create, publish, and download research datasets
Project description
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fairly
A package to create, publish and clone research datasets.
Installation
fairly requires Python 3.8 or later, and ruamel.yaml version 0.17.26 or later. It can be installed directly using pip.
pip install fairly
Installing from source
Clone or download the source code:
git clone https://github.com/ITC-CRIB/fairly.git
Go to the root directory:
cd fairly/
Compile and install using pip:
pip install .
Usage
Basic example to create a local research dataset and deposit it to a repository:
import fairly
# Initialize a local dataset
dataset = fairly.init_dataset('/path/dataset')
# Set metadata
dataset.metadata['license'] = 'MIT'
dataset.set_metadata(
title='My dataset',
keywords=['FAIR', 'research', 'data'],
authors=[
'0000-0002-0156-185X',
{'name': 'John', 'surname': 'Doe'}
]
)
# Add data files
dataset.includes.extend([
'README.txt',
'*.csv',
'train/*.jpg'
])
# Save dataset
dataset.save()
# Upload to a data repository
remote_dataset = dataset.upload('zenodo')
Basic example to access a remote dataset and store it locally:
import fairly
# Open a remote dataset
dataset = fairly.dataset('doi:10.4121/21588096.v1')
# Get dataset information
dataset.id
>>> {'id': '21588096', 'version': '1'}
dataset.url
>>> 'https://data.4tu.nl/articles/dataset/.../21588096/1'
dataset.size
>>> 33339
len(dataset.files)
>>> 6
dataset.metadata
>>> Metadata({'keywords': ['Earthquakes', 'precursor', ...], ...})
# Update metadata
dataset.metadata['keywords'] = ['Landslides', 'precursor']
dataset.save_metadata()
# Store dataset to a local directory (i.e. clone dataset)
local_dataset = dataset.store('/path/dataset')
Currently, the package supports the following research data management platforms:
All research data repositories based on the listed platforms are supported.
For more details and examples, consult the package documentation.
Testing
Unit tests can be run by using pytest command in the root directory.
Contributions
Read the guidelines to know how you can be part of this open source project.
JupyterLab Extension
An extension for JupyerLab is being developed in a different repository.
Citation
Please cite this software using as follows:
Girgin, S., Garcia Alvarez, M., & Urra Llanusa, J., fairly: a package to create, publish and clone research datasets [Computer software]
Acknowledgements
This research is funded by the Dutch Research Council (NWO) Open Science Fund, File No. 203.001.114.
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