Running Bash commands in Python


Question

On my local machine, I run a python script which contains this line

bashCommand = "cwm --rdf test.rdf --ntriples > test.nt"
os.system(bashCommand)

This works fine.

Then I run the same code on a server and I get the following error message

'import site' failed; use -v for traceback
Traceback (most recent call last):
File "/usr/bin/cwm", line 48, in <module>
from swap import  diag
ImportError: No module named swap

So what I did then is I inserted a print bashCommand which prints me than the command in the terminal before it runs it with os.system().

Of course, I get again the error (caused by os.system(bashCommand)) but before that error it prints the command in the terminal. Then I just copied that output and did a copy paste into the terminal and hit enter and it works...

Does anyone have a clue what's going on?

1
234
5/30/2019 8:43:33 PM

Don't use os.system. It has been deprecated in favor of subprocess. From the docs: "This module intends to replace several older modules and functions: os.system, os.spawn".

Like in your case:

bashCommand = "cwm --rdf test.rdf --ntriples > test.nt"
import subprocess
process = subprocess.Popen(bashCommand.split(), stdout=subprocess.PIPE)
output, error = process.communicate()
265
1/12/2018 8:54:47 AM

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