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Understanding subprocess module in python when running program from python script

I usually run a program from my OpenSuse linux terminal by typing ./run file_name. This will bring up a series of options that I can choose from by typing a numeric value 0-9 and hitting return on my keyboard. Now I want to do this from a python script automatically. My example below is not working, but I can't understand where I'm failing and how to debug:
import subprocess
p = subprocess.Popen(["/path/to/program/run", file_name], stdin = subprocess.PIPE,stdout=subprocess.PIPE,shell=False)
print "Hello"
out, err = p.communicate(input='0\r\n')
print out
print err
for line in p.stdout.readlines():
print line
The output of this program is just
>> Hello
>>
i.e. then it seems to freeze (I have no idea whats actually happening!) I would have expected to see what I see when I run ./run file_name
and hit 0 and then return directly in my terminal, but I assure you this is not the case.
What can I do to debug my code?
Edit 1: as suggested in comments
import subprocess
fileName = 'test_profile'
p = subprocess.Popen(["/path/to/program/run", fileName], stdin = subprocess.PIPE,stdout=subprocess.PIPE,shell=False)
print "Hello"
for line in iter(p.stdout.readline,""):
print line
will indeed return the stdout of my program!

communicate waits for the completion of the program. For example:
import subprocess
p = subprocess.Popen(["cut", "-c2"], stdin=subprocess.PIPE, stdout=subprocess.PIPE,shell=False)
out, err = p.communicate(input='abc')
print("Result: '{}'".format(out.strip()))
# Result: 'b'
It sounds like you have a more interactive script, in which case you probably should try out pexpect
import pexpect
child = pexpect.spawn('cut -c2')
child.sendline('abc')
child.readline() # repeat what was typed
print(child.readline()) # prints 'b'

How to check whether a shell command returned nothing or something

I am writing a script to extract something from a specified path. I am returning those values into a variable. How can i check whether the shell command has returned something or nothing.
My Code:
def any_HE():
global config, logger, status, file_size
config = ConfigParser.RawConfigParser()
config.read('config2.cfg')
for section in sorted(config.sections(), key=str.lower):
components = dict() #start with empty dictionary for each section
#Retrieving the username and password from config for each section
if not config.has_option(section, 'server.user_name'):
continue
env.user = config.get(section, 'server.user_name')
env.password = config.get(section, 'server.password')
host = config.get(section, 'server.ip')
print "Trying to connect to {} server.....".format(section)
with settings(hide('warnings', 'running', 'stdout', 'stderr'),warn_only=True, host_string=host):
try:
files = run('ls -ltr /opt/nds')
if files!=0:
print '{}--Something'.format(section)
else:
print '{} --Nothing'.format(section)
except Exception as e:
print e
I tried checking 1 or 0 and True or false but nothing seems to be working. In some servers, the path '/opt/nds/' does not exist. So in that case, nothing will be there on files. I wanted to differentiate between something returned to files and nothing returned to files.

First, you're hiding stdout.
If you get rid of that you'll get a string with the outcome of the command on the remote host. You can then split it by os.linesep (assuming same platform), but you should also take care of other things like SSH banners and colours from the retrieved outcome.

As perror commented already, the python subprocess module offers the right tools.
https://docs.python.org/2/library/subprocess.html
For your specific problem you can use the check_output function.
The documentation gives the following example:
import subprocess
subprocess.check_output(["echo", "Hello World!"])
gives "Hello World"

plumbum is a great library for running shell commands from a python script. E.g.:
from plumbum.local import ls
from plumbum import ProcessExecutionError
cmd = ls['-ltr']['/opt/nds'] # construct the command
try:
files = cmd().splitlines() # run the command
if ...:
print ...:
except ProcessExecutionError:
# command exited with a non-zero status code
...
On top of this basic usage (and unlike the subprocess module), it also supports things like output redirection and command pipelining, and more, with easy, intuitive syntax (by overloading python operators, such as '|' for piping).

In order to get more control of the process you run, you need to use the subprocess module.
Here is an example of code:
import subprocess
task = subprocess.Popen(['ls', '-ltr', '/opt/nds'], stdout=subprocess.PIPE)
print task.communicate()

running a python script on server

i have a python script on the server
#!/usr/bin/env python
import cgi
import cgitb; #cgitb.enable()
import sys, os
from subprocess import call
import time
import subprocess
form = cgi.FieldStorage()
component = form.getvalue('component')
command = form.getvalue('command')
success = True
print """Content-Type: text/html\n"""
if component=="Engine" and command=="Start":
try:
process = subprocess.Popen(['/usr/sbin/telepath','engine','start'], shell=False, stdout=subprocess.PIPE)
print "{ans:12}"
except Exception, e:
success = False
print "{ans:0}"
When I run this script and add the component and command parameters to be "Engine" and "Start" respectively - it starts the process and prints to the shell
"""Content-Type: text/html\n"""
{ans:12}
but most importantly - it starts the process!
however, when I run the script by POSTing to it, it returns {ans:12} but does not run the process which was the whole intention in the first place. Any logical explanation?

I suspect it's one of two things, firstly your process is probably running but your python code doesn't handle the output so do:
process = subprocess.Popen(['/usr/sbin/telepath','engine','start'], shell=False, stdout=subprocess.PIPE)
print process.stdout.read()
This is the most likely and explains why you see the output from the command line and not the browser, or secondly because the script is run through the browsers as the user apache and not with your userid check the permission for /usr/sbin/telepath.

How can I tell whether screen is running?

I am trying to run a Python program to see if the screen program is running. If it is, then the program should not run the rest of the code. This is what I have and it's not working:
#!/usr/bin/python
import os
var1 = os.system ('screen -r > /root/screenlog/screen.log')
fd = open("/root/screenlog/screen.log")
content = fd.readline()
while content:
if content == "There is no screen to be resumed.":
os.system ('/etc/init.d/tunnel.sh')
print "The tunnel is now active."
else:
print "The tunnel is running."
fd.close()
I know there are probably several things here that don't need to be and quite a few that I'm missing. I will be running this program in cron.

from subprocess import Popen, PIPE
def screen_is_running():
out = Popen("screen -list",shell=True,stdout=PIPE).communicate()[0]
return not out.startswith("This room is empty")

Maybe the error message that you redirect on the first os.system call is written on the standard error instead of the standard output. You should try replacing this line with:
var1 = os.system ('screen -r 2> /root/screenlog/screen.log')
Note the 2> to redirect standard error to your file.

How to redirect stderr in Python?

I would like to log all the output of a Python script. I tried:
import sys
log = []
class writer(object):
def write(self, data):
log.append(data)
sys.stdout = writer()
sys.stderr = writer()
Now, if I "print 'something' " it gets logged. But if I make for instance some syntax error, say "print 'something# ", it wont get logged - it will go into the console instead.
How do I capture also the errors from Python interpreter?
I saw a possible solution here:
http://www.velocityreviews.com/forums/showpost.php?p=1868822&postcount=3
but the second example logs into /dev/null - this is not what I want. I would like to log it into a list like my example above or StringIO or such...
Also, preferably I don't want to create a subprocess (and read its stdout and stderr in separate thread).

I have a piece of software I wrote for work that captures stderr to a file like so:
import sys
sys.stderr = open('C:\\err.txt', 'w')
so it's definitely possible.
I believe your problem is that you are creating two instances of writer.
Maybe something more like:
import sys
class writer(object):
log = []
def write(self, data):
self.log.append(data)
logger = writer()
sys.stdout = logger
sys.stderr = logger

You can't do anything in Python code that can capture errors during the compilation of that same code. How could it? If the compiler can't finish compiling the code, it won't run the code, so your redirection hasn't even taken effect yet.
That's where your (undesired) subprocess comes in. You can write Python code that redirects the stdout, then invokes the Python interpreter to compile some other piece of code.

I can't think of an easy way. The python process's standard error is living on a lower level than a python file object (C vs. python).
You could wrap the python script in a second python script and use subprocess.Popen. It's also possible you could pull some magic like this in a single script:
import os
import subprocess
import sys
cat = subprocess.Popen("/bin/cat", stdin=subprocess.PIPE, stdout=subprocess.PIPE)
os.close(sys.stderr.fileno())
os.dup2(cat.stdin.fileno(), sys.stderr.fileno())
And then use select.poll() to check cat.stdout regularly to find output.
Yes, that seems to work.
The problem I foresee is that most of the time, something printed to stderr by python indicates it's about to exit. The more usual way to handle this would be via exceptions.
---------Edit
Somehow I missed the os.pipe() function.
import os, sys
r, w = os.pipe()
os.close(sys.stderr.fileno())
os.dup2(w, sys.stderr.fileno())
Then read from r

To route the output and errors from Windows, you can use the following code outside of your Python file:
python a.py 1> a.out 2>&1
Source: https://support.microsoft.com/en-us/help/110930/redirecting-error-messages-from-command-prompt-stderr-stdout

Since python 3.5 you can use contextlib.redirect_stderr
with open('help.txt', 'w') as f:
with redirect_stdout(f):
help(pow)

For such a request, usually it would be much easier to do it in the OS instead of in Python.
For example, if you're going to run "a.py" and record all the messages it will generate into file "a.out", it would just be
python a.py 2>&1 > a.out
The first part 2>&1 redirects stderr to stdout (0: stdin, 1:stdout, 2:stderr), and the second redirects that to a file called a.out.
And as far as I know, this command works in Windows, Linux or MacOS! For other file redirection techniques, just search the os plus "file redirection"

I found this approach to redirecting stderr particularly helpful. Essentially, it is necessary to understand if your output is stdout or stderr. The difference? Stdout is any output posted by a shell command (think an 'ls' list) while sterr is any error output.
It may be that you want to take a shell commands output and redirect it to a log file only if it is normal output. Using ls as an example here, with an all files flag:
# Imports
import sys
import subprocess
# Open file
log = open("output.txt", "w+")
# Declare command
cmd = 'ls -a'
# Run shell command piping to stdout
result = subprocess.run(cmd, stdout=subprocess.PIPE, shell=True)
# Assuming utf-8 encoding
txt = result.stdout.decode('utf-8')
# Write and close file
log.write(txt)
log.close()
If you wanted to make this an error log, you could do the same with stderr. It's exactly the same code as stdout with stderr in its place. This pipes an error messages that get sent to the console to the log. Doing so actually keeps it from flooding your terminal window as well!
Saw this was a post from a while ago, but figured this could save someone some time :)

import sys
import tkinter
# ********************************************
def mklistenconsswitch(*printf: callable) -> callable:
def wrapper(*fcs: callable) -> callable:
def newf(data):
[prf(data) for prf in fcs]
return newf
stdoutw, stderrw = sys.stdout.write, sys.stderr.write
funcs = [(wrapper(sys.stdout.write, *printf), wrapper(sys.stderr.write, *printf)), (stdoutw, stderrw)]
def switch():
sys.stdout.write, sys.stderr.write = dummy = funcs[0]
funcs[0] = funcs[1]
funcs[1] = dummy
return switch
# ********************************************
def datasupplier():
i = 5.5
while i > 0:
yield i
i -= .5
def testloop():
print(supplier.__next__())
svvitch()
root.after(500, testloop)
root = tkinter.Tk()
cons = tkinter.Text(root)
cons.pack(fill='both', expand=True)
supplier = datasupplier()
svvitch = mklistenconsswitch(lambda text: cons.insert('end', text))
testloop()
root.mainloop()

Python will not execute your code if there is an error. But you can import your script in another script an catch exceptions. Example:
Script.py
print 'something#
FinalScript.py
from importlib.machinery import SourceFileLoader
try:
SourceFileLoader("main", "<SCRIPT PATH>").load_module()
except Exception as e:
# Handle the exception here

To add to Ned's answer, it is difficult to capture the errors on the fly during the compilation.
You can write several print statements in your script and you can stdout to a file, it will stop writing to the file when the error occurs. To debug the code you could check the last logged output and check your script after that point.
Something like this:
# Add to the beginning of the script execution(eg: if __name__ == "__main__":).
from datetime import datetime
dt = datetime.now()
script_dir = os.path.dirname(os.path.abspath(__file__)) # gets the path of the script
stdout_file = script_dir+r'\logs\log'+('').join(str(dt.date()).split("-"))+r'.log'
sys.stdout = open(stdout_file, 'w')
This will create a log file and stream the print statements to the file.
Note: Watch out for escape characters in your filepath while concatenating with script_dir in the second line from the last in the code. You might want something similar to raw string. You can check this thread for this.