iBridges

About

The git repository contains a generic iRODS graphical user interface and the corresponding command-line interface clients. The GUI and CLI work with any iRODS instance. However, for user and data security we depend on some iRODS event hooks that need to be installed on the iRODS server. Please refer to the documentation below.

Explore the documentation

Authors

Tim van Daalen, Christine Staiger

Wageningen University & Research 2021

Contributors

J.P. Mc Farland

University of Groningen, Center for Information Technology, 2022

Dependencies

Python

• Python 3 (>= 3.6)
  • Tested on versions up to 3.10 on multiple platforms
• pip-22.2.2
• Python packages (see install via requirements.txt below)

Install dependencies with, for example:

python3.10 -m pip install -r requirements.txt

Configuration

iRODS environment.json

• Please create a directory/folder named .irods in your home directory/folder (~/.irods/ in Linux shorthand).

  • Linux: /home/\<username\>/.irods/irods_environment.json
  • Mac: /Users/\<username\>/.irods/irods_environment.json
  • Windows: C:\\\\....\\\<username\>\\.irods\\irods_environment.json

• Your iRODS admin will provide an irods_environment.json file, its contents, or instructions on how to create it. Place that file into the .irods directory/folder. Here it an example that can be created with the iinit iCommand on Linux:

{
    "irods_host": "server.fqdn.nl", 
    "irods_port": 1247, 
    "irods_user_name": "username", 
    "irods_zone_name": "myZone", 
    "irods_default_resource": "myResc" 
}

iBridges config.json

iBridges will create its own configuration file in ~/.ibridges/ containing the name of the last iRODS environment file used. This config.json file can be updated to control other aspects of iBridges. For example:

{
    "last_ienv": "irods_environment.json", 
    "davrods_server": "https://server.fqdn.nl", 
    "ui_tabs": [ 
        "tabUpDownload", 
        "tabELNData", 
        "tabDataBundle", 
        "tabCreateTicket" 
    ], 
    "force_unknown_free_space": false 
}

Options:

• davrods_server: for annotation of eLabJournal data
• ui_tabs: configure which tabs are shown (Browser and Info tabs always are)
  • tabUpDownload: a two-pane upload/download tab
  • tabELNData: for the Electronic Lab Notebook, eLabJournal
  • tabDataBundle: (un)bundle datasets from/to four supported formats
  • tabCreateTicket: create iRODS tickets for anonymous access
• force_unknown_free_space: ignore if resources' free space is unannotated

The force_unknown_free_space option is REQUIRED to be set to true if your default resource does not yet have its free space annotated. It makes unannotated top-level resources visible in the drop-downs allowing selection of them. In addition, it sets the force flag for uploads overriding resource overflow protection.

The logs for both GUI and CLI clients can be found in the ~/.ibridges/ directory/folder.

Usage

export PYTHON_IRODSCLIENT_DEFAULT_XML=QUASI_XML
./irods-iBridgesGui.py

Contributing

Code

Instructions on how to extend the GUI or contribute to the code base can be found in the documentation.

License

This project is licensed under the GPL-v3 license. The full license can be found in LICENSE.