Brocoli: Browse Collections for iRODS

Brocoli application allows users to browse iRODS catalog collections in a simple Tkinter GUI.

Install Brocoli

Pre-requisites

Brocoli runs on Linux platforms. Windows and MacOS support is experimental.

Brocoli needs a Python installation with Tkinter. Under Ubuntu <http://www.ubuntu.com>, you may have to install a specific package to get Tkinter.

Python 2.7+ and 3.5+ are expected to work.

Dependencies

Brocoli depends on the following packages:

• six: https://pypi.python.org/pypi/six
• python-irodsclient >= 0.8.0: https://pypi.python.org/pypi/python-irodsclient

Installing with pip

From a command shell, run:

pip install brocoli [--user]

If you don't have administrative privileges, you may need to use the --user optional argument, in order to install Brocoli in your user account.

Installing from source

1. Download Brocoli from https://github.com/mesocentre-mcia/brocoli
2. from distribution directory, run python setup.py install [--user]

If you don't have administrative privileges, you may need to use the --user optional argument, in order to install Brocoli in your user account.

Using Brocoli

Run brocoli from a command shell:

$ brocoli

Connections

At first run, Brocoli will appear empty. You will want to create a more useful connection with an iRODS catalog. Just configure it following the menus:

Settings -> New Connection

This will open a dialog where you can set the connection configuration. The configuration fields are:

• Connection name - choose a name to identify the connection
• Catalog type - choose os, irods3 or irods4. Currently, irods* are the only useful catalogs available (os is used for testing purposes only)
• Root path - enter the catalog path you want to base your display from
• Make default connection - check if you want Brocoli to open this connection at startup
• Perform local checksum - configures brocoli to verify checksum of downloaded/uploaded files against catalog registered checksum (if available)

irods3 specific configuration fields:

• Use irods environment file - check if you want to use iRODS iCommands configuration file (usually ~/.irods/.irodsEnv fr v3 instances and ~/.irods/irods_environment.json for v4)
• iRODS host - the iRODS server DNS name you want to connect to (usually your iCAT Enabled Server)
• iRODS port - depending on your iRODS instance (1247 is the default)
• iRODS zone - the name of your iRODS zone
• iRODS user name - your iRODS account name
• iRODS default resource - the iRODS resource to use (optional)
• Remember password - check if you want Brocoli to store your iRODS password (dangerous: although Brocoli scrambles the stored password, it may be easy to unscramble for someone who gained access to that value)
• iRODS password

irods4 connections have a few extra configuration fields:

• Default hash scheme - choose checksum hash method among available algorithms
• irods_client_server_policy - iRODS client/server negociation behaviour
• Use irods SSL transfer - check if you need SSL communication with your catalog
• irods_encryption_algorithm - SSL specific setting depending on your catalog configuration
• irods_encryption_key_size - SSL specific setting depending on your catalog configuration
• irods_encryption_num_hash_rounds - SSL specific setting depending on your catalog configuration
• irods_encryption_salt_size - SSL specific setting depending on your catalog configuration
• irods_ssl_ca_certificate_file - SSL specific setting depending on your catalog configuration

Now, you should be able to switch to the newly created connection by following:

Settings -> Switch connection -> Your new connection name

Navigating

Sub-directories can be opened by clicking on the triangle icon before their name.

You can base the display from a sub-directory by choosing Go to in the popup menu or entering its path directly in the navigation bar.

The . special entry refers to the currently displayed directory (the path displayed in the navigation bar).

The .. special entry appears when visiting a subdirectory of the connection root path. It refers to the current path parent directory.

File operations

Operations on files and directories are accessible in a popup menu shown when right clicking on the target.

File/directory operations

• Download to local disk - download selected entry (recursively) to your local computer
• Delete - delete selected entry (recursively) from the catalog
• Properties - displays catalog specific properties of the selected entry

Directory only operations

• New directory - creates a subdirectory of the selected directory
• Upload local files - uploads local files into the catalog under the selected directory
• Recursive upload - recursively uploads the contents of a local directory to the catalog
• Go to - rebase Brocoli navigation bar to the selected directory