ewels / dds_cli

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SciLifeLab Data Delivery System - Command line interface

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

This will be used for data delivery within larger projects and/or projects resulting in the production of large amounts of data, for example next-generation sequencing data and imaging.

This tool is written and maintained by the SciLifeLab Data Centre.

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 1.0.0
          ︶

 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.

╭─ 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.                          │
│  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.