Allows to iterate over CyVerse CIRCLES files
Project description
File Iterator and IRODS Utility classes
Timeline
This repo gives utility classes for handling file interactions with CIRCLES CyVerse.
It allows:
- Communication with CyVerse's fileshare (ls, cd, pwd)
- I/O Commands through IRODS
- Iterating over files from CyVerse
- Cache handling
CONFIGURATION [if pulled repostory from PyPI]
To install everything properly, run the following command:
CONFIGURATION [if pulled repostory from GitHub]
Install the packages
To install the required packages, simply run in the terminal:
python3 -m venv venv
source venv/bin/activate
pip install requirements.txt
IRODS environment
To connect to CyVerse, you need your profile to be set.To retrieve this profile, the irods client tries: 1. Using the configuration file located in ~/.irods/irods_environment.json 2. If not located, the file given by the environment variable IRODS_ENVIRONMENT_FILE
To help in this configuration, a method, create_irods_env() can be used.
Check out the file code_examples/example_irods
for an example of such configuration.
WARNING: If your access to CyVerse through IRODS already works locally, there would be no need to do this step.
Once this has been done one time, there will be no need for using this method on local machines.
If you are working within Docker containers or VMs environment, you may need to call this at the beginning of each task.
Cache folders
To configure the cache, open the file /global_variables/global_variables.py
.
Then set the variable local_path
to the root of the folder you will be working into.
Check out the file code_examples/example_irods
for an example of such configuration.
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