NeuroDataPub Assistant Guide¶
Introduction¶
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.
1. Start the Graphical User Interface¶
In a terminal, activate the neurodatapub-env
conda environment:
$ conda activate neurodatapub-env
Please check Creation of neurodatapub-env 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.
2. Configure input and outputs directories¶
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
.
3. Configure the siblings¶
You can configure or reconfigure the settings for the special git-annex and GitHub remote siblings.
3.1 Special remote sibling settings¶
"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
3.2 GitHub sibling settings¶
"github_login"
(mandatory): user login to GitHub."github_repo_name"
(mandatory): Dataset repository name on GitHub
3.3 Create the JSON sibling configuration files¶
Settings for each of the two siblings can be saved in a JSON file by clicking on their respective button.
4. Check the configuration and execute NeuroDataPub
¶
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)
[...]
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.