sanuann/dandi-cli

DANDI command line client to facilitate common operations

DANDI Client

This project is under heavy development. Beware of hidden and disclosed issues, or Work-in-Progress (WiP).

Installation

At the moment DANDI client releases are available from PyPI and conda-forge. You could install them in your Python (native, virtualenv, or conda) environment via

pip install dandi

or

conda install -c conda-forge dandi

if you are in a conda environment.

dandi tool

This package provides a dandi command line utility with a basic interface which should assist you in preparing and uploading your data to and/or obtaining data from the http://dandiarchive.org:

$> 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 name  [default: INFO]
  --pdb                           Fall into pdb if errors out
  --help                          Show this message and exit.

Commands:
  download  Download a file or entire folder from DANDI
  ls        List .nwb files and dandisets metadata.
  organize  (Re)organize files according to the metadata.
  register  Register a new dandiset in the DANDI archive
  upload    Upload dandiset (files) to DANDI archive.
  validate  Validate files for NWB (and DANDI) compliance.

Each of the commands has a set of options to alter their behavior. Please run dandi COMMAND --help to get more information, e.g.

$> dandi ls --help
Usage: dandi ls [OPTIONS] [PATHS]...

  List .nwb files metadata

Options:
  -F, --fields TEXT               Comma-separated list of fields to display.
                                  An empty value to trigger a list of
                                  available fields to be printed out
  -f, --format [auto|pyout|json|json_pp|yaml]
                                  Choose the format/frontend for output. If
                                  'auto', 'pyout' will be used in case of
                                  multiple files, and 'yaml' for a single
                                  file.
  --help                          Show this message and exit.

See DANDI Handbook for examples on how to use this client in various use cases.

Development/contributing

Please see DEVELOPMENT.md file.

3rd party components included

dandi/core/digests/dandietag.py

From https://github.com/girder/django-s3-file-field as of v0.1.1-10-g829b9b0 Copyright (c) 2019-2021 Kitware, Inc., Apache 2.0 license

dandi/support/generatorify.py

From https://github.com/eric-wieser/generatorify, as of 7bd759ecf88f836ece6cdbcf7ce1074260c0c5ef Copyright (c) 2019 Eric Wieser, MIT/Expat licensed.

dandi/tests/skip.py

From https://github.com/ReproNim/reproman, as of v0.2.1-40-gf4f026d Copyright (c) 2016-2020 ReproMan Team