Using iBridges to access Yoda

iBridges is a fast and reliable way to work actively with data stored in Yoda. It offers many of the features that iCommands offers, but it is much more user-friendly and easier to set up.

You can use iBridges in three different ways: 

  • via the Graphical User Interface (GUI) 
  • as a Python package (Python API) 
  • via the Command Line Interface (CLI)

Installation

Configuration

To log into iBridges, you need a configuration file called ‘irods_environment.json’. This is a file that needs to be stored in a specific location on your computer, which contains settings used by iBridges to connect with Yoda.

Configuration through the GUI

1. If you work at Utrecht University, there are template configuration files available (if not, please continue to the next step). To use them, open a terminal, such as Anaconda prompt, Unix shell, Powershell, git bash, etc. and execute:
pip install ibridges-servers-uu
2. Start the GUI by typing in the terminal:
ibridges-gui
3. From the main menu click 'Configure' > ‘Add Configuration’.
4. If in the dropdown, there are templates available, select the relevant template and fill your email address in the field ‘irods_user_name’.

Using iBridges to access Yoda, configuration through the GUI
Select the relevant template

Click 'Save as', enter a file name and save it as .json file (e.g. irods_environment.json). When you have saved the file, click 'Check' and when you get no errors, 'Close'.

5. If in the dropdown menu, there are no templates available, select Create a new configuration, and fill in the fields. You can find the correct values of the to-be-filled fields for your Yoda instance by clicking the Yoda version number at the bottom of the Yoda web portal.

The Yoda version number at the bottom of the Yoda web portal

Configuration through the command line interface

  • If you work at Utrecht University, you can follow the steps outlined here to configure iBridges.  
  • If you do not work at Utrecht University, please follow the set-up instructions in this tutorial.

Using iBridges

You can use iBridges to: 

  • transfer data from and to Yoda; 
  • add self-defined metadata to single files and folders. For example, add an ‘author’ field, or ‘experimental condition’; 
  • synchronize data between your computer and Yoda; 
  • search data by name, metadata, checksum, or type.

All these functions can be done manually, but also in an automated way by integrating them in scripts.

Using the iBridges GUI

To start using the iBridges GUI, please follow the instructions to start a new session. Use your Data Access Password as the password to log in. Use the user documentation to see what you can do with the iBridges GUI.

Using the Command Line Interface

You can immediately start using the iBridges Command Line Interface (CLI). Simply try ibridges --help or ibridges <command> --help to get examples and help for the usage. For instructions on how to use the iBridges commands, please check the iBridges documentation.

Using the iBridges Python package

For use with Python, the iBridges documentation contains multiple notebooks to show you the capabilities of the iBridges python package.

Help with setting up or using iBridges

If you need help setting up or using iBridges, please do not hesitate to contact your data manager.