garrettmflynn/dandi-cli

DANDI command line client to facilitate common operations

DANDI Client

The DANDI Python client allows you to:

• Download Dandisets and individual subject folders or files
• Validate data to locally conform to standards
• Organize your data locally before upload
• Upload Dandisets
• Interact with the DANDI archive's web API from Python
• Delete data in the DANDI archive
• Perform other auxiliary operations with data or the DANDI archive

Note: This project is under heavy development. See the issues log or Work-in-Progress (WiP).

Installation

DANDI Client releases are available from PyPI and conda-forge. Install them in your Python (native, virtualenv, or conda) environment via

pip install dandi

or

conda install -c conda-forge dandi

CLI Tool

This package provides a command line utility with a basic interface to help you prepare and upload your data to, or obtain data from, the DANDI archive.

$> dandi
Usage: dandi [OPTIONS] COMMAND [ARGS]...

  A client to support interactions with DANDI archive
  (http://dandiarchive.org).

  To see help for a specific command, run

      dandi COMMAND --help

  e.g. dandi upload --help

Options:
  --version
  -l, --log-level [DEBUG|INFO|WARNING|ERROR|CRITICAL]
                                  Log level (case insensitive).  May be
                                  specified as an integer.  [default: INFO]
  --pdb                           Fall into pdb if errors out
  --help                          Show this message and exit.

Commands:
  delete            Delete dandisets and assets from the server.
  digest            Calculate file digests
  download          Download a file or entire folder from DANDI.
  instances         List known Dandi Archive instances that the CLI can...
  ls                List .nwb files and dandisets metadata.
  move              Move or rename assets in a local Dandiset and/or on...
  organize          (Re)organize files according to the metadata.
  shell-completion  Emit shell script for enabling command completion.
  upload            Upload Dandiset files to DANDI Archive.
  validate          Validate files for NWB and DANDI compliance.
  validate-bids     Validate BIDS paths.

Run dandi --help or dandi <subcommand> --help (e.g. dandi upload --help) to see manual pages.

Resources

• To learn how to interact with the DANDI archive and for examples on how to use the DANDI Client in various use cases, see the handbook (specifically the sections on using the CLI to download and upload Dandisets).

• To get help:

  • ask a question: https://github.com/dandi/helpdesk/discussions
  • file a feature request or bug report: https://github.com/dandi/helpdesk/issues/new/choose
  • contact the DANDI team: help@dandiarchive.org

• To understand how to contribute to the dandi-cli repository, see the DEVELOPMENT.md file.