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Commandline Usage

Important

NeuroDataPub takes as principal input the path of your dataset. The input dataset is required to be in valid BIDS format. See :ref:`BIDS standard <bids>` for more information about BIDS.

Before using NeuroDataPub, your dataset should be validated with the free, online BIDS Validator, or its standalone version.

Commandline Arguments

.. argparse::
        :ref: neurodatapub.parser.get_parser
        :prog: neurodatapub

Sibling configuration files

Git-annex special remote sibling configuration file

The Git-annex special remote sibling configuration file specified by the input flag --git_annex_ssh_special_sibling_config adopts the following JSON schema:

{
    "remote_ssh_login": "user",
    "remote_ssh_url": "ssh://neurodatapub.server.org",
    "remote_sibling_dir": "/remote/path/of/dataset/sibling/.git"
}
where:
  • "remote_ssh_login" (mandatory): user login to the remote
  • "remote_ssh_url" (mandatory): SSH-URL of the remote in the form "ssh://..."
  • "remote_sibling_dir" (mandatory): Remote .git/ directory of the sibling dataset

GitHub sibling configuration file

The GitHub sibling configuration file specified by the input flag --github_sibling_config adopts the following JSON schema:

{
    "github_login": "GitHubUserName",
    "github_repo_name": "DatasetName"
}
where:
  • "github_login" (mandatory): user login to GitHub.
  • "github_repo_name" (mandatory): Dataset repository name on GitHub

Note

You will be asked to enter a token for authentication to create and publish the repository on GitHub. Please see "Creating a personal access token" Github documentation for more details on how to get one. Make also sure that the write:org and read:org options are enabled.

Running neurodatapub

The neurodatapub command-line interface can be run in in the "create-only", "publish-only", and "all" modes with the --mode option flag (as described in :ref:`Commandline Arguments <cliparser>`). For example, an invocation of the interface to create and publish a dataset ("all" mode) would be as follows:

$ neurodatapub --mode "all" \
     --bids_dir '/local/path/to/input/bids/dataset' \
     --datalad_dir  '/local/path/to/output/datalad/dataset' \
     --git_annex_ssh_special_sibling_config '/local/path/to/special_annex_sibling_config.json' \
     --github_sibling_config '/local/path/to/github_sibling_config.json'

Note

When you use directly the command-line interface, you would need to provide the JSON files with the option flags --git_annex_ssh_special_sibling_config and --github_sibling_config to describe the configuration of the special remote and GitHub dataset siblings.

Support, bugs and new feature requests

All bugs, concerns and enhancement requests for this software are managed on GitHub and can be submitted at https://github.com/NCCR-SYNAPSY/neurodatapub/issues.