NeuroDataPub comes with a Graphical User Interface aka the NeuroDataPub Assistant to support not only the configuration of the siblings and the generation of the corresponding JSON configuration files, but also its execution in the three different modes.
In a terminal, activate the neurodatapub-env conda environment:
$ conda activate neurodatapub-env
Please check :ref:`creation-conda-environment` for more details about its creation.
After activation, the NeuroDataPub Assistant can be launched via the neurodatapub command-line interface with the --gui option flag:
$ neurodatapub --gui \ (--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 run the neurodatapub command-line interface with the --gui option, it is not required to specify the option flags required for a normal run from the commandline interface. However, if provided, the parameters will be used to initialize the configuration of the project.
You can select or reconfigure your input BIDS directory and the directory of the output Datalad dataset in the first tab of the NeuroDataPub Assistant.
You can configure or reconfigure the settings for the special git-annex and GitHub remote siblings.
"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_login"
(mandatory): user login to GitHub."github_repo_name"
(mandatory): Dataset repository name on GitHub
Settings for each of the two siblings can be saved in a JSON file by clicking on their respective button.
Before being able to initiate the processes of creation and/or publication of the datalad dataset, you will need to make the NeuroDataPub Assistant checking them out by clicking on the Check config button.
If the configuration is completely valid, this will enable the Create and Publish Dataset, Create Dataset, and Publish Dataset buttons.
Then, you can execute NeuroDataPub in one of the three execution modes by clicking on one of the buttons.
Note
You can always see the execution progress by checking the standard outputs in the terminal, such as the following:
$ neurodatapub --gui
[...]
############################################
# Check configuration
############################################
* PyBIDS summary:
BIDS Layout: ...localuser/Data/ds-sample | Subjects: 1 | Sessions: 1 | Runs: 0
* remote_ssh_login: user
* remote_ssh_url: ssh://stockage.server.ch
* remote_sibling_dir: /home/user/Data/ds-sample/.git
* github_login: user
* github_repo_name: ds-sample
Configuration is valid!
############################################
############################################
# Creation of Datalad Dataset
############################################
> Initialize the Datalad dataset /home/localuser/Data/ds-sample/derivative/neurodatapub-v0.1
[INFO ] Creating a new annex repo at /home/localuser/Data/ds-sample/derivative/neurodatapub-v0.1
[INFO ] Running procedure cfg_text2git
[INFO ] == Command start (output follows) =====
[INFO ] == Command exit (modification check follows) =====
[INFO ] Running procedure cfg_bids
[INFO ] == Command start (output follows) =====
[INFO ] Running procedure cfg_metadatatypes
[INFO ] == Command start (output follows) =====
[INFO ] == Command exit (modification check follows) =====
[INFO ] == Command exit (modification check follows) =====
Dataset(/home/localuser/Data/ds-sample/derivative/neurodatapub-v0.1)
[...]
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.