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NeuroDataPub: Tool built for publication of BIDS datasets of the NCCR-Synapsy

Project description

NeuroDataPub: NCCR-SYNAPSY Neuroimaging Dataset Publishing Tool

This tool is developed by the Connectomics Lab at the University Hospital of Lausanne (CHUV) for use within the lab and within the National Centre of Competence in Research (NCCR) "SYNAPSY – Synaptic Bases of Mental Diseases" NCCR-SYNAPSY, as well as for open-source software distribution.

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Overview

NeuroDataPub is an open-source neuroimaging dataset publishing tool written in Python and built on top of Datalad and git-annex. It aims to lower the barriers, for the NCCR-SYNAPSY members, to manage and publish, privately or publicly, their dataset repositories on GitHub and the annexed files on their SSH data server, in order to fully fulfill the implemented Neuroimaging Data Management Plan.

Since v0.3, you can use either (1) a server accessible via ssh or (2) the Open Science Foundation (OSF) platform, as a git-annex special remote, to host your annexed files.

NeuroDataPub comes with its graphical user interface, aka the NeuroDataPub Assistant, created to facilitate:

  • the configuration of the siblings,

  • the creation of the JSON configuration files, as well as

  • the execution of NeuroDataPub in three different modes:

    1. creation and publication of a datalad dataset,
    2. creation of a datalad dataset only,
    3. publication of an existing datalad dataset only,

NeuroDataPub is a Python 3.8 package that can be easily installed with pip as follows:

pip install neurodatapub

Documentation

Usage

NeuroDataPub has the following commandline arguments:

usage: neurodatapub [-h] --mode {all,create-only,publish-only} --bids_dir
                    BIDS_DIR --datalad_dir DATALAD_DIR
                    --git_annex_ssh_special_sibling_config
                    GIT_ANNEX_SSH_SPECIAL_SIBLING_CONFIG
                    --github_sibling_config GITHUB_SIBLING_CONFIG [--gui] [-v]

Command-line argument parser of NeuroDataPub (v0.1)

optional arguments:
  -h, --help            show this help message and exit
  --mode {all,create-only,publish-only}
                        Mode in which ``neurodatapub`` is run: ``"create-
                        only"`` creates the datalad dataset only, ``"publish-
                        only"`` creates the datalad dataset only, ``"all"``
                        creates the datalad dataset only,
  --bids_dir BIDS_DIR   The directory with the input dataset formatted
                        according to the BIDS standard.
  --datalad_dir DATALAD_DIR
                        The local directory where the Datalad dataset should
                        be.
  --git_annex_ssh_special_sibling_config GIT_ANNEX_SSH_SPECIAL_SIBLING_CONFIG
                        Path to a JSON file containing configuration
                        parameters for the git-annex SSH special remote
                        dataset sibling
  --github_sibling_config GITHUB_SIBLING_CONFIG
                        Path to a JSON file containing configuration
                        parameters for the GitHub dataset repository sibling
  --gui                 Run NeuroDataPub in GUI mode
  -v, --version         show program's version number and exit

Acknowledgment

If your are using NeuroDataPub in your work, please acknowledge this software and its dependencies:

  • Tourbier S, Hagmann P., (2021). NCCR-SYNAPSY/neurodatapub: NCCR-SYNAPSY Neuroimaging Dataset Publishing Tool (Version 0.1). Zenodo.

  • Halchenko et al., (2021). DataLad: distributed system for joint management of code, data, and their relationship. Journal of Open Source Software, 6(63), 3262, https://doi.org/10.21105/joss.03262.

License information

This software is distributed under the open-source Apache 2.0 license. See license for more details.

All trademarks referenced herein are property of their respective holders.

Help/Questions

If you run into any problems or have any code bugs or questions, please create a new GitHub Issue.

Funding

Supported by the National Centre of Competence in Research (NCCR) "SYNAPSY – Synaptic Bases of Mental Diseases" (NCCR-SYNAPSY website / NCCR-SYNAPSY Swiss National Science Foundation page).

Contributors ✨

Thanks goes to these wonderful people (emoji key):


Sébastien Tourbier

💻 📖 🎨 🤔 🚇 🚧 🧑‍🏫 📆 💬 👀

Patric Hagmann

🔍

This project follows the all-contributors specification. Contributions of any kind welcome!

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