fairly 2.0.0

A package to create, publish, and download research datasets

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Anaconda package

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 from PYPI or Conda-Forge.

# Using pip
pip install fairly

# using anaconda or miniconda
conda install conda-forge::fairly

Installing from source

1. Clone or download the source code:

   git clone https://github.com/ITC-CRIB/fairly.git

2. Go to the root directory:

   cd fairly/

3. Compile and install using pip:

   pip install .

Usage

Python API

Basic example to create a local research dataset and deposit it to a repository using the Python API:

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')

Command Line

fairly --help

You should see the following:

Usage: fairly [OPTIONS] [COMMAND] [ARGS]...

fairly command-line tool.

Options:
-v, --version  Show the version and exit.
-h, --help     Show this message and exit.

Commands:
client      Client commands.
dataset     Dataset commands.
repository  Repository commands.

Currently, the package supports the following research data management platforms:

• Invenio

• Figshare

• Djehuty (experimental)

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 (Version 2.0.0) [Computer software]

Acknowledgements

This research is funded by the Dutch Research Council (NWO) Open Science Fund, File No. 203.001.114.

Project members:

• Center of Expertise in Big Geodata Science, University of Twente, Faculty ITC

• Digital Competence Centre, TU Delft

• 4TU.ResearchData