ibridges 0.1.4

Package for accessing data and metadata on iRods servers.

iBridges

iBridges is 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.
• Synchronize 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.

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/UtrechtUniversity/iBridges.git@develop

Usage

Below are some basic examples of the features in iBridges.

# Create an iRODS session
from ibridges import Session

session = Session(irods_env_path="~/.irods/irods_environment.json", password="mypassword")

# 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")

Commandline interface

To simply upload or download data you do not need to write full python program, we offer a Commandline interface

• Establish a connection

  ibridges init
  

• List a colletion

  # 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

• QuickStart
• iRODS Paths
• Data synchronisation

Beginners tutorials

• Setup client configuration
• Working with data
• iRODS and local Paths
• Metadata
• Sharing data

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.