OpenNeuro CLI for Deno

Command line tools for OpenNeuro implemented in Deno. Deno eliminates the need to install the CLI and allows for more code reuse with OpenNeuro’s web frontend.

Install

Download deno via any supported installation method.

Usage

OpenNeuro CLI will validate your dataset with the bids-validator and then allow you to upload to OpenNeuro. If you wish to make changes to a dataset, the CLI can download, allow you to make local changes, and reupload only the changes to OpenNeuro.

Login

To upload or download data from OpenNeuro, login with your account.

# Run login and follow the prompts
deno run -A cli/openneuto.ts login

You can also create an API key on OpenNeuro and specify this as an option or environment variable.

# For scripts
export OPENNEURO_API_KEY=<api_key>
deno run -A cli/openneuro.ts login --error-reporting true

Uploading

# Path to the dataset root (directory containing dataset_description.json)
deno run -A cli/openneuro.ts upload --affirmDefaced path/to/dataset

# To debug issues - enable logging and provide this log to support or open a GitHub issue
export OPENNEURO_LOG=INFO
deno run -A cli/openneuro.ts upload --affirmDefaced path/to/dataset

Implementation Notes

This tool uses isomorphic git to download, modify, and push datasets using OpenNeuro’s git interface. Other tools that support git and git-annex repositories such as DataLad can also be used with the local copy.