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