iBridges

iBridges is a library for scientific programmers who are working with data in iRODS. We provide a wrapper around the python-irodsclient to facilitate easy interaction with the iRODS server. iBridges is currently still in very active development.

Highlights

• Works on Windows, Mac OS and Linux
• Runs on Python 3.8 or higher.
• Supported iRODS server versions: 4.2.11 or higher and 4.3.0 or higher.
• Interactive connection to your iRODS server.
• Upload and Download your data.
• Manipulate the metadata on the iRODS server.
• Synchronise your data between your local computer and the iRODS server.
• Create and manipulate Tickets to temporarily grant access to outside users.
• Search through all metadata for your dataset or collection.
• Small number of dependencies (python-irodsclient and tqdm)
• Safe default options when working with your data.

iBridges also has a graphical user interface, which you can install here.

Report Bug . Request Feature . Share an idea . Leave some feedback . Ask a question

Installation

There are two main ways to install iBridges. The recommended way is to use the stable version that is available on PyPi:

pip install ibridges

If you want to install the unstable version to test out new features, you can install the development branch:

pip install git+https://github.com/iBridges-for-iRods/iBridges.git@develop

Configuration

You will need to have a so-called irods_environment.json. Please follow the documentation how to set it up.

Usage

Below are some basic examples of the features in iBridges.

# Create an iRODS session
from ibridges.interactive import interactive_auth

session = interactive_auth()

# Upload data
from ibridges import upload

upload(session, "/your/local/path", "/irods/path")

# Download data
from ibridges import download

download(session, "/irods/path", "/other/local/path")

Command line interface

To simply upload or download data you do not need to write full python program, we offer a command line interface (see also the documentation).

• Establish a connection

  ibridges init

• List a collection

  # list your home collection
  ibridges list
  
  # list a different collection in your home
  ibridges list "irods:~/<collection>"
  
  # list a collection on a different path than your home
  
  ibridges list "irods:/full/irods/path"

• Upload data

  ibridges upload my_file.json "irods:~/some_collection"

• Download data

  ibridges download "irods:~/some_collection/some_object" download_dir

• Synchronise data

  ibridges sync some_local_directory "irods:~/some_collection"
  
  

Tutorials

Documentation

• ReadTheDocs

Guides

• Manual with examples

Beginners tutorials

• Setup client configuration
• iRODS Paths
• Working with data
• Metadata
• Sharing data
• Synchronising data

Do I have to choose between the python-irodsclient and iBridges?

No. iBridges itself is based on the python-irodsclient. When you connect to iRODS a python-irodsclient irods.iRODSSession is automatically created with which you can access all functionality of the python-irodsclient.

Authors

Christine Staiger (Maintainer) ORCID

• Wageningen University & Research 2021 - 2022
• Utrecht University 2022

Tim van Daalen, Wageningen University & Research 2021

Maarten Schermer (Maintainer) ORCID, Utrecht University 2023

Raoul Schram (Maintainer) ORCID. Utrecht University 2023

Contributors

J.P. Mc Farland, University of Groningen, Center for Information Technology, 2022

License

This project is licensed under the MIT license. The full license can be found in LICENSE.