dds-cli 2.1.0

A command line tool to manage data and projects in the SciLifeLab Data Delivery System.

Data Delivery System CLI

A command line tool dds to manage data and projects in the SciLifeLab Data Delivery System.

The Data Delivery System (DDS) is a cloud-based system for all SciLifeLab platforms where data generated throughout each project can be delivered to the research groups in a fast, secure and simple way. The CLI makes requests to the API (see badge below for link) in order to use the API functionality.

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Table of contents

• Installation
• Overview of commands

Installation

Python Package Index

The dds-cli package can be installed from PyPI using pip as follows:

pip install dds-cli

After installing, run dds and verify that the output looks like this:

$ dds
     ︵
 ︵ (  )   ︵
(  ) ) (  (  )   SciLifeLab Data Delivery System
 ︶  (  ) ) (    https://delivery.scilifelab.se/
      ︶ (  )    Version 1.1.0
          ︶

 Usage: dds [OPTIONS] COMMAND [ARGS]...

 SciLifeLab Data Delivery System (DDS) command line interface.
 Access token is saved in a .dds_cli_token file in the home directory.
 The token is valid for 7 days. Make sure your token is valid long enough for the delivery to
 finish. To avoid that a delivery fails because of an expired token, we recommend reauthenticating
 yourself before each delivery ('dds data put' / 'get').

╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮
│ --verbose     -v               Print verbose output to the console.                              │
│ --log-file    -l   <filename>  Save a log to a file.                                             │
│ --no-prompt                    Run without any interactive features.                             │
│ --token-path  -tp  TEXT        The path where the authentication token will be stored. For a     │
│                                normal use-case, this should not be needed.                       │
│ --version                      Display the version of this software.                             │
│ --help                         List the options of any DDS subcommand and its default settings.  │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮
│ auth        Group command for creating and managing authenticated sessions.                      │
│ data        Group command for uploading, downloading and managing project data.                  │
│ ls          List the projects you have access to or the project contents.                        │
│ motd        Group command for managing Message of the Day within DDS.                            │
│ project     Group command for creating and managing projects within the DDS.                     │
│ unit        Group command for managing units.                                                    │
│ user        Group command for managing user accounts, including your own.                        │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯

Executables

Executables are available for Windows, MacOS and Linux. These allow you to run the CLI without needing to install it (and the pip / Python requirements) yourself. Download them from the (bottom of the) latest release page: Latest Release

Development version

If you would like the latest development version of tools, the command is:

pip install --upgrade --force-reinstall git+https://github.com/ScilifelabDataCentre/dds_cli.git@dev

If you intend to make edits to the code, first make a fork of the repository and then clone it locally. Go to the cloned directory and install with pip (also installs development requirements):

pip install --upgrade -r requirements-dev.txt -e .

Overview of commands

Once installed you can use the command dds in a terminal session. This has the following subcommands:

• auth: Create and manage authenticated sessions.
• user: Create and manage user accounts, including your own.
• project: Create and manage projects.
• data: Upload, download and manage project data.
• ls: List projects and project contents.
• motd: List and manage important messages displayed to the users ("Message of the Day")
• unit: Manage units using the DDS