This package provides code examples for the file iterator package.

The circles_file_iterator package provides classes and utility functions for handling file interactions with CIRCLES CyVerse.

It allows:

(version 1.0.4)

• Communication with CyVerse's fileshare (ls, cd, pwd)
• I/O Commands through IRODS
• Iterating over files from CyVerse
• Cache handling

(version 1.1.1)

• Detect event in a CAN file
• Build an analysis of all the events in the files listed in a file iteration

Installation

Python dependancies

To install the packages needed, simply run:

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

Configure the file iterator

Then, you can configure the file iterator by runnning the following command:

python3 -m circles_file_iterator

It will ask for some information, fill it out and it should be fine.

WARNING: If you use a different name for your virtual environment, the __main__.py script from circles_file_iterator might not work. WARNING 2: Run those commands from the folder's base (here, from /file_iterator_code_examples/).

Configure IRODS CLI

Then, you may need to install IRODS CLI (if not already installed on your system) on your computer by running:

(On linux)

wget https://files.renci.org/pub/irods/releases/4.1.10/ubuntu14/irods-icommands-4.1.10-ubuntu14-x86_64.deb
sudo apt-get install -y ./irods-icommands-4.1.10-ubuntu14-x86_64.deb
iinit

Then answer the required prompts.

(On Mac)

Download the installer from: https://cyverse.atlassian.net/wiki/download/attachments/241869823/cyverse-icommands-4.1.9.pkg?version=3&modificationDate=1472820029000&cacheVersion=1&api=v2

Then follow the instructions of the installer.

Note: If you need more information on this, visit: https://cyverse.atlassian.net/wiki/spaces/DS/pages/241869823/Setting+Up+iCommands

Code examples

Several file examples are available for you to try the functionnalities provided by this package.

The commands' usage is describe in the comments of the code examples files.

The output of those file when you run them shows the results of the different actions launched.

To run a code example, simply run the following command in a terminal (from the folder root, with the virtual environment activated):

python3 example_name.py

Useful Links

GitHub repository of the circles_file_iterator package: https://github.com/codingrosquick

PyPI page of the circles_file_iterator package: https://pypi.org/project/circles-file-iterator/