Python - unable to call system command

Question

I have some python code, from which I want to call another program. This program will

Print some output to STDOUT
Write a file to disk

Using call I get the following behavior;

from subprocess import call
call(['./tango_x86_64_release', 'VTS1 ct="N" nt="N" ph="7.2" te="303" io="0.02" seq="MKHPYEEFPTGSKSPYNMSRGAHPGAV"'])
34, File not properly written, try writing it up again, 
1

This happens regardless if if the arguments are split into a list or not;

call(['./tango_x86_64_release', 'VTS1', 'ct="N"', 'nt="N"', 'ph="7.2"', 'te="303"', 'io="0.02"', 'seq="MKHPYEEFPTGSKSPYNMSRGAHPGAV"'])
34, File not properly written, try writing it up again, 
1

I can call this same command from the my terminal

./tango_x86_64_release VTS1 ct="N" nt="N" ph="7.2" te="303" io="0.02" seq="MKHPYEEFPTGSKSPYNMSRGAHPGAV"

Which works and gives an exit status of 0.

It seems like its the writing to disk which is causing issues, if I break the command then I get the appropriate warning message (i.e. remove an argument, it warns me that the argument is missing).

Using subprocess.Popen() gives an OSError;

import subprocess as sub
output = sub.Popen('./tango_x86_64_release VTS1 ct="N" nt="N" ph="7.2" te="303" io="0.02" seq="MKHPYEEFPTGSKSPYNMSRGAHPGAV"', stdout=sub.PIPE, stderr=sub.PIPE)

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib64/python2.7/subprocess.py", line 679, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.7/subprocess.py", line 1249, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

Any help greatly appreciated

Seems hard to reproduce outside your environment. Trying to create a small, reproducible use case probably will give you the answer (kind of [rubber-duck debugging](http://en.wikipedia.org/wiki/Rubber_duck_debugging)) — Paulo Scardine, Jun 28 '13 at 19:43
@alecxe - you're my hero. Bang on the money (post it as an answer - I can't believe that's all it took!!) — Alex, Jun 28 '13 at 19:44
@Alex no problems. All I did is just found two relevant threads that I've provided below - people there are your heroes! — alecxe, Jun 28 '13 at 19:47

score 3 · Accepted Answer · answered Jun 28 '13 at 19:44

Use shlex.split to split the command for you:

import shlex
call(shlex.split('./tango_x86_64_release VTS1 ct="N" nt="N" ph="7.2" te="303" io="0.02" seq="MKHPYEEFPTGSKSPYNMSRGAHPGAV"'))

Note that although you might be able to solve your problem by adding shell=True, you should avoid it if possible, since it can be a security risk (search for "shell injection").

score 1 · Answer 2 · edited May 23 '17 at 10:25

1

Try to add shell=True to the Popen call.

Also see:

Why does subprocess.Popen() with shell=True work differently on Linux vs Windows?
Popen error: [Errno 2] No such file or directory
Documentation (and why Passing shell=True can be a security hazard)

edited May 23 '17 at 10:25

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answered Jun 28 '13 at 19:46

alecxe

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Python - unable to call system command

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