Question

I am trying to write a python script that sends a string to a program and puts it in the background. On the command line, I can copy and paste the following code and have it successfully do what I want the python program to do:

printf "f\nil\ncs\n1.e-8 100.0 1.e-8\nn\n0.002\nb\n0.05\nz\n2.e-7\nx4\n5.e-7\n\n\nfort.13\nn\nn\n\n" | vpfit95

where: vpfit95 is an alias to an executable program in my PATH.

A few permutations of what I’ve tried (tried one at a time):

import subprocess
vpfitExecutable = 'vpfit95'

String1=r'f\nil\ncs\n1.e-8 100.0 1.e-8\nn\n0.002\nb\n0.05\nz\n2.e-7\nx4\n5.e-7\n\n\nfort.13\nn\nn\n\n'
String2=r"f\nil\ncs\n1.e-8 100.0 1.e-8\nn\n0.002\nb\n0.05\nz\n2.e-7\nx4\n5.e-7\n\n\nfort.13\nn\nn\n\n"
String3="f\nil\ncs\n1.e-8 100.0 1.e-8\nn\n0.002\nb\n0.05\nz\n2.e-7\nx4\n5.e-7\n\n\nfort.13\nn\nn\n\n"

cmd1 = "printf \"" + String1 + "\"" 
cmd2 = "printf \"" + String1 + "\" | " + vpfitExecutable 
cmd3 = "printf \"" + String2 + "\"" 
cmd4 = "printf \"" + String3 + "\"" 

print cmd2

p1 = subprocess.Popen([vpfitExecutable, cmd1])
p2 = subprocess.Popen([cmd2])
p3 = subprocess.Popen([vpfitExecutable, cmd3])
p4 = subprocess.Popen([vpfitExecutable, cmd4])
p4 = subprocess.Popen([vpfitExecutable, String1])
p5 = subprocess.Popen([vpfitExecutable, String2])
p6 = subprocess.Popen([vpfitExecutable, String3])

# check
p7 = subprocess.Popen([vpfitExecutable]) # works.

And all fail (except p7). Some fail with a “Fortran runtime error: End of file” (which is from the vpfit program). Others fail with a Traceback to the subprocess library and “OSError: [Errno 2] No such file or directory”.

Some checks: When I print cmd2 and copy and paste it into the terminal, it works perfectly. When I run p7, it correctly starts running the program as expected, just without the string fed to it. I’m obviously missing something fundamental here, and I just can’t figure out what. Any help appreciated!

Answer 1

Yes, you are missing something fundamental – pipes are handled by the shell. To do what you want with subprocess, you should run the vpfit95 as a subprocess, and then communicate with it. See section 17.1.4.2 of the docs, replacing a shell pipeline.

proc = subprocess.Popen([vpfitExecutable], stdin=subprocess.PIPE)
proc.communicate(input='your string') 

If you need to inspect the stdout and stderr of vpfit, then grab the handles from the output tuple of communicate.

A dirty alternative is to run your command with shell=True, which spawns it inside a shell and then you can use a pipe in your command, but it is cleaner to “cut out the middleman” and interact with the subprocess directly.