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)


        

Answer 1

Also you can use 'os.popen'. Example:

import os

command = os.popen('ls -al')
print(command.read())
print(command.close())

Output:

total 16
drwxr-xr-x 2 root root 4096 ago 13 21:53 .
drwxr-xr-x 4 root root 4096 ago 13 01:50 ..
-rw-r--r-- 1 root root 1278 ago 13 21:12 bot.py
-rw-r--r-- 1 root root   77 ago 13 21:53 test.py

None

Answer 2

To run the command without a shell, pass the command as a list and implement the redirection in Python using [subprocess]:

#!/usr/bin/env python
import subprocess

with open('test.nt', 'wb', 0) as file:
    subprocess.check_call("cwm --rdf test.rdf --ntriples".split(),
                          stdout=file)

Note: no > test.nt at the end. stdout=file implements the redirection.

---

To run the command using the shell in Python, pass the command as a string and enable shell=True:

#!/usr/bin/env python
import subprocess

subprocess.check_call("cwm --rdf test.rdf --ntriples > test.nt",
                      shell=True)

Here's the shell is responsible for the output redirection (> test.nt is in the command).

---

To run a bash command that uses bashisms, specify the bash executable explicitly e.g., to emulate bash process substitution:

#!/usr/bin/env python
import subprocess

subprocess.check_call('program <(command) <(another-command)',
                      shell=True, executable='/bin/bash')

Answer 3

subprocess.Popen() is prefered over os.system() as it offers more control and visibility. However, If you find subprocess.Popen() too verbose or complex, peasyshell is a small wrapper I wrote above it, which makes it easy to interact with bash from Python.

https://github.com/davidohana/peasyshell

Answer 4

Call it with subprocess

import subprocess
subprocess.Popen("cwm --rdf test.rdf --ntriples > test.nt")

The error you are getting seems to be because there is no swap module on the server, you should install swap on the server then run the script again