CODEWITHSUNDEEP
bashjupyter-notebookenvironment-variables
user2153903
user2153903

Reputation: 81

Setting Environmental Variables Through a BASH Script in Jupyter

I am attempting to execute a BASH script which sets needed environmental variables from within a Jupyter notebook. I understand that the magic command %env can accomplish this, but the BASH script is needed in this instance. Neither the use of !source or %system accomplishes the goal of making the environmental variables persist within the Jupyter notebook. Can this be done?

Upvotes: 4

Views: 2504

Answers (2)

Proteinologist
Proteinologist

Reputation: 53

To permanently set a variable (eg. a key) you can set a Bash environment variable for your Jupyter notebooks by creating or editing a startup config file in the IPython startup directory.

cd ~/.ipython/profile_default/startup/
vim my_startup_file.py

The file will be run on Jupyter startup (see the README in the same directory). Here is what the startup .py file should contain:

  1 import os
  2 os.environ['AWS_ACCESS_KEY_ID']='insert_your_key_here'
  3 os.environ['AWS_SECRET_ACCESS_KEY']='another_key'

Now inside a Jupyter notebook you can call these environment variables, eg.

#Inside a Jupyter Notebook cell
import os
session = boto3.session.Session( 
    aws_access_key_id=os.getenv('AWS_ACCESS_KEY_ID'), 
    aws_secret_access_key=os.getenv('AWS_SECRET_ACCESS_KEY'),
    region_name='us-east-1'
)

You will need to restart your kernel for the changes to be created.

Upvotes: 3

J.M. Robles
J.M. Robles

Reputation: 652

You could use python to update os variables:

Cell

! echo "export test1=\"This is the test 1\"" > test.sh
! echo "export test2=\"This is the test 2\"" >> test.sh
! cat test.sh

Result

export test1="This is the test 1"
export test2="This is the test 2"

Cell (taken from set environment variable in python script)

import os

with open('test.sh') as f:
    os.environ.update(
        line.replace('export ', '', 1).strip().split('=', 1) for line in f
        if 'export' in line
)

! echo $test1 
! echo $test2

Result

"This is the test 1"
"This is the test 2"

Upvotes: 2

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