Python subprocess stdout iterator always blocks - python

I want to capture the output while printing it, but I'm blocking forever without reading even a single line. What's going on? I'm using Python2.
Generator script:
#!/usr/bin/env python2.7
import random
import time
while True:
print(random.random())
time.sleep(1)
Sample generator output:
$ ./generator.py
0.334835137212
0.896609571236
0.833267988558
0.55456332113
^CTraceback (most recent call last):
Reader script:
import subprocess
cmd = ['./generator.py']
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
for line in p.stdout:
print(line)
print('Looping')
p.wait()
I've also tried:
import subprocess
import sys
cmd = ['./generator.py']
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
while True:
line = p.stdout.readline()
print(line)
print('Looping')
p.wait()
...and:
import sys
import subprocess
import select
import time
cmd = ['./generator.py']
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
s = select.poll()
s.register(p.stdout, select.POLLIN)
while True:
if s.poll(1):
line = p.stdout.read()
else:
p.poll()
if p.returncode is not None:
break
print('Looping')
time.sleep(1)
p.wait()

As #dhke mentioned, one of the issues is implicit output-buffering in the producer. If you have the ability to change the producer, and you're willing to, and the production is done by calls to the print-function then just add "flush=True" as an argument to the print function. You can also fall-back to doing a sys.stdout.flush() at key points in the producer.
The second problem appears to be iterating over sys.stdout. This never seems to work for a long-running process. The second and third methods

I'm dealing with a similar problem. This is the workaround im currently using to prevent buffering.
proc = subprocess.Popen(['stdbuf', '-o0'] + cmd, stdout=subprocess.PIPE)
The disadvantage of this methood is that it relys on an external Linux command to solve the problem. Have a look in the comments here for a different and native python approach to get rid of the PIPE buffering. Many thanks to #9000 for suggesting both solutions to me.

Related

python subprocess.Popen output during execution [duplicate]

I'm using a python script as a driver for a hydrodynamics code. When it comes time to run the simulation, I use subprocess.Popen to run the code, collect the output from stdout and stderr into a subprocess.PIPE --- then I can print (and save to a log-file) the output information, and check for any errors. The problem is, I have no idea how the code is progressing. If I run it directly from the command line, it gives me output about what iteration its at, what time, what the next time-step is, etc.
Is there a way to both store the output (for logging and error checking), and also produce a live-streaming output?
The relevant section of my code:
ret_val = subprocess.Popen( run_command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True )
output, errors = ret_val.communicate()
log_file.write(output)
print output
if( ret_val.returncode ):
print "RUN failed\n\n%s\n\n" % (errors)
success = False
if( errors ): log_file.write("\n\n%s\n\n" % errors)
Originally I was piping the run_command through tee so that a copy went directly to the log-file, and the stream still output directly to the terminal -- but that way I can't store any errors (to my knowlege).
My temporary solution so far:
ret_val = subprocess.Popen( run_command, stdout=log_file, stderr=subprocess.PIPE, shell=True )
while not ret_val.poll():
log_file.flush()
then, in another terminal, run tail -f log.txt (s.t. log_file = 'log.txt').
TLDR for Python 3:
import subprocess
import sys
with open("test.log", "wb") as f:
process = subprocess.Popen(your_command, stdout=subprocess.PIPE)
for c in iter(lambda: process.stdout.read(1), b""):
sys.stdout.buffer.write(c)
f.buffer.write(c)
You have two ways of doing this, either by creating an iterator from the read or readline functions and do:
import subprocess
import sys
# replace "w" with "wb" for Python 3
with open("test.log", "w") as f:
process = subprocess.Popen(your_command, stdout=subprocess.PIPE)
# replace "" with b'' for Python 3
for c in iter(lambda: process.stdout.read(1), ""):
sys.stdout.write(c)
f.write(c)
or
import subprocess
import sys
# replace "w" with "wb" for Python 3
with open("test.log", "w") as f:
process = subprocess.Popen(your_command, stdout=subprocess.PIPE)
# replace "" with b"" for Python 3
for line in iter(process.stdout.readline, ""):
sys.stdout.write(line)
f.write(line)
Or you can create a reader and a writer file. Pass the writer to the Popen and read from the reader
import io
import time
import subprocess
import sys
filename = "test.log"
with io.open(filename, "wb") as writer, io.open(filename, "rb", 1) as reader:
process = subprocess.Popen(command, stdout=writer)
while process.poll() is None:
sys.stdout.write(reader.read())
time.sleep(0.5)
# Read the remaining
sys.stdout.write(reader.read())
This way you will have the data written in the test.log as well as on the standard output.
The only advantage of the file approach is that your code doesn't block. So you can do whatever you want in the meantime and read whenever you want from the reader in a non-blocking way. When you use PIPE, read and readline functions will block until either one character is written to the pipe or a line is written to the pipe respectively.
Executive Summary (or "tl;dr" version): it's easy when there's at most one subprocess.PIPE, otherwise it's hard.
It may be time to explain a bit about how subprocess.Popen does its thing.
(Caveat: this is for Python 2.x, although 3.x is similar; and I'm quite fuzzy on the Windows variant. I understand the POSIX stuff much better.)
The Popen function needs to deal with zero-to-three I/O streams, somewhat simultaneously. These are denoted stdin, stdout, and stderr as usual.
You can provide:
None, indicating that you don't want to redirect the stream. It will inherit these as usual instead. Note that on POSIX systems, at least, this does not mean it will use Python's sys.stdout, just Python's actual stdout; see demo at end.
An int value. This is a "raw" file descriptor (in POSIX at least). (Side note: PIPE and STDOUT are actually ints internally, but are "impossible" descriptors, -1 and -2.)
A stream—really, any object with a fileno method. Popen will find the descriptor for that stream, using stream.fileno(), and then proceed as for an int value.
subprocess.PIPE, indicating that Python should create a pipe.
subprocess.STDOUT (for stderr only): tell Python to use the same descriptor as for stdout. This only makes sense if you provided a (non-None) value for stdout, and even then, it is only needed if you set stdout=subprocess.PIPE. (Otherwise you can just provide the same argument you provided for stdout, e.g., Popen(..., stdout=stream, stderr=stream).)
The easiest cases (no pipes)
If you redirect nothing (leave all three as the default None value or supply explicit None), Pipe has it quite easy. It just needs to spin off the subprocess and let it run. Or, if you redirect to a non-PIPE—an int or a stream's fileno()—it's still easy, as the OS does all the work. Python just needs to spin off the subprocess, connecting its stdin, stdout, and/or stderr to the provided file descriptors.
The still-easy case: one pipe
If you redirect only one stream, Pipe still has things pretty easy. Let's pick one stream at a time and watch.
Suppose you want to supply some stdin, but let stdout and stderr go un-redirected, or go to a file descriptor. As the parent process, your Python program simply needs to use write() to send data down the pipe. You can do this yourself, e.g.:
proc = subprocess.Popen(cmd, stdin=subprocess.PIPE)
proc.stdin.write('here, have some data\n') # etc
or you can pass the stdin data to proc.communicate(), which then does the stdin.write shown above. There is no output coming back so communicate() has only one other real job: it also closes the pipe for you. (If you don't call proc.communicate() you must call proc.stdin.close() to close the pipe, so that the subprocess knows there is no more data coming through.)
Suppose you want to capture stdout but leave stdin and stderr alone. Again, it's easy: just call proc.stdout.read() (or equivalent) until there is no more output. Since proc.stdout() is a normal Python I/O stream you can use all the normal constructs on it, like:
for line in proc.stdout:
or, again, you can use proc.communicate(), which simply does the read() for you.
If you want to capture only stderr, it works the same as with stdout.
There's one more trick before things get hard. Suppose you want to capture stdout, and also capture stderr but on the same pipe as stdout:
proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
In this case, subprocess "cheats"! Well, it has to do this, so it's not really cheating: it starts the subprocess with both its stdout and its stderr directed into the (single) pipe-descriptor that feeds back to its parent (Python) process. On the parent side, there's again only a single pipe-descriptor for reading the output. All the "stderr" output shows up in proc.stdout, and if you call proc.communicate(), the stderr result (second value in the tuple) will be None, not a string.
The hard cases: two or more pipes
The problems all come about when you want to use at least two pipes. In fact, the subprocess code itself has this bit:
def communicate(self, input=None):
...
# Optimization: If we are only using one pipe, or no pipe at
# all, using select() or threads is unnecessary.
if [self.stdin, self.stdout, self.stderr].count(None) >= 2:
But, alas, here we've made at least two, and maybe three, different pipes, so the count(None) returns either 1 or 0. We must do things the hard way.
On Windows, this uses threading.Thread to accumulate results for self.stdout and self.stderr, and has the parent thread deliver self.stdin input data (and then close the pipe).
On POSIX, this uses poll if available, otherwise select, to accumulate output and deliver stdin input. All this runs in the (single) parent process/thread.
Threads or poll/select are needed here to avoid deadlock. Suppose, for instance, that we've redirected all three streams to three separate pipes. Suppose further that there's a small limit on how much data can be stuffed into to a pipe before the writing process is suspended, waiting for the reading process to "clean out" the pipe from the other end. Let's set that small limit to a single byte, just for illustration. (This is in fact how things work, except that the limit is much bigger than one byte.)
If the parent (Python) process tries to write several bytes—say, 'go\n'to proc.stdin, the first byte goes in and then the second causes the Python process to suspend, waiting for the subprocess to read the first byte, emptying the pipe.
Meanwhile, suppose the subprocess decides to print a friendly "Hello! Don't Panic!" greeting. The H goes into its stdout pipe, but the e causes it to suspend, waiting for its parent to read that H, emptying the stdout pipe.
Now we're stuck: the Python process is asleep, waiting to finish saying "go", and the subprocess is also asleep, waiting to finish saying "Hello! Don't Panic!".
The subprocess.Popen code avoids this problem with threading-or-select/poll. When bytes can go over the pipes, they go. When they can't, only a thread (not the whole process) has to sleep—or, in the case of select/poll, the Python process waits simultaneously for "can write" or "data available", writes to the process's stdin only when there is room, and reads its stdout and/or stderr only when data are ready. The proc.communicate() code (actually _communicate where the hairy cases are handled) returns once all stdin data (if any) have been sent and all stdout and/or stderr data have been accumulated.
If you want to read both stdout and stderr on two different pipes (regardless of any stdin redirection), you will need to avoid deadlock too. The deadlock scenario here is different—it occurs when the subprocess writes something long to stderr while you're pulling data from stdout, or vice versa—but it's still there.
The Demo
I promised to demonstrate that, un-redirected, Python subprocesses write to the underlying stdout, not sys.stdout. So, here is some code:
from cStringIO import StringIO
import os
import subprocess
import sys
def show1():
print 'start show1'
save = sys.stdout
sys.stdout = StringIO()
print 'sys.stdout being buffered'
proc = subprocess.Popen(['echo', 'hello'])
proc.wait()
in_stdout = sys.stdout.getvalue()
sys.stdout = save
print 'in buffer:', in_stdout
def show2():
print 'start show2'
save = sys.stdout
sys.stdout = open(os.devnull, 'w')
print 'after redirect sys.stdout'
proc = subprocess.Popen(['echo', 'hello'])
proc.wait()
sys.stdout = save
show1()
show2()
When run:
$ python out.py
start show1
hello
in buffer: sys.stdout being buffered
start show2
hello
Note that the first routine will fail if you add stdout=sys.stdout, as a StringIO object has no fileno. The second will omit the hello if you add stdout=sys.stdout since sys.stdout has been redirected to os.devnull.
(If you redirect Python's file-descriptor-1, the subprocess will follow that redirection. The open(os.devnull, 'w') call produces a stream whose fileno() is greater than 2.)
We can also use the default file iterator for reading stdout instead of using iter construct with readline().
import subprocess
import sys
process = subprocess.Popen(
your_command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
)
for line in process.stdout:
sys.stdout.write(line)
In addition to all these answer, one simple approach could also be as follows:
process = subprocess.Popen(your_command, stdout=subprocess.PIPE)
while process.stdout.readable():
line = process.stdout.readline()
if not line:
break
print(line.strip())
Loop through the readable stream as long as it's readable and if it gets an empty result, stop.
The key here is that readline() returns a line (with \n at the end) as long as there's an output and empty if it's really at the end.
Hope this helps someone.
If you're able to use third-party libraries, You might be able to use something like sarge (disclosure: I'm its maintainer). This library allows non-blocking access to output streams from subprocesses - it's layered over the subprocess module.
If all you need is that the output will be visible on the console the easiest solution for me was to pass the following arguments to Popen
with Popen(cmd, stdout=sys.stdout, stderr=sys.stderr) as proc:
which will use your python scripts stdio file handles
Solution 1: Log stdout AND stderr concurrently in realtime
A simple solution which logs both stdout AND stderr concurrently, line-by-line in realtime into a log file.
import subprocess as sp
from concurrent.futures import ThreadPoolExecutor
def log_popen_pipe(p, stdfile):
with open("mylog.txt", "w") as f:
while p.poll() is None:
f.write(stdfile.readline())
f.flush()
# Write the rest from the buffer
f.write(stdfile.read())
with sp.Popen(["ls"], stdout=sp.PIPE, stderr=sp.PIPE, text=True) as p:
with ThreadPoolExecutor(2) as pool:
r1 = pool.submit(log_popen_pipe, p, p.stdout)
r2 = pool.submit(log_popen_pipe, p, p.stderr)
r1.result()
r2.result()
Solution 2: A function read_popen_pipes() that allows you to iterate over both pipes (stdout/stderr), concurrently in realtime
import subprocess as sp
from queue import Queue, Empty
from concurrent.futures import ThreadPoolExecutor
def enqueue_output(file, queue):
for line in iter(file.readline, ''):
queue.put(line)
file.close()
def read_popen_pipes(p):
with ThreadPoolExecutor(2) as pool:
q_stdout, q_stderr = Queue(), Queue()
pool.submit(enqueue_output, p.stdout, q_stdout)
pool.submit(enqueue_output, p.stderr, q_stderr)
while True:
if p.poll() is not None and q_stdout.empty() and q_stderr.empty():
break
out_line = err_line = ''
try:
out_line = q_stdout.get_nowait()
err_line = q_stderr.get_nowait()
except Empty:
pass
yield (out_line, err_line)
# The function in use:
with sp.Popen(["ls"], stdout=sp.PIPE, stderr=sp.PIPE, text=True) as p:
for out_line, err_line in read_popen_pipes(p):
print(out_line, end='')
print(err_line, end='')
p.poll()
Similar to previous answers but the following solution worked for me on windows using Python3 to provide a common method to print and log in realtime (source)
def print_and_log(command, logFile):
with open(logFile, 'wb') as f:
command = subprocess.Popen(command, stdout=subprocess.PIPE, shell=True)
while True:
output = command.stdout.readline()
if not output and command.poll() is not None:
f.close()
break
if output:
f.write(output)
print(str(output.strip(), 'utf-8'), flush=True)
return command.poll()
A good but "heavyweight" solution is to use Twisted - see the bottom.
If you're willing to live with only stdout something along those lines should work:
import subprocess
import sys
popenobj = subprocess.Popen(["ls", "-Rl"], stdout=subprocess.PIPE)
while not popenobj.poll():
stdoutdata = popenobj.stdout.readline()
if stdoutdata:
sys.stdout.write(stdoutdata)
else:
break
print "Return code", popenobj.returncode
(If you use read() it tries to read the entire "file" which isn't useful, what we really could use here is something that reads all the data that's in the pipe right now)
One might also try to approach this with threading, e.g.:
import subprocess
import sys
import threading
popenobj = subprocess.Popen("ls", stdout=subprocess.PIPE, shell=True)
def stdoutprocess(o):
while True:
stdoutdata = o.stdout.readline()
if stdoutdata:
sys.stdout.write(stdoutdata)
else:
break
t = threading.Thread(target=stdoutprocess, args=(popenobj,))
t.start()
popenobj.wait()
t.join()
print "Return code", popenobj.returncode
Now we could potentially add stderr as well by having two threads.
Note however the subprocess docs discourage using these files directly and recommends to use communicate() (mostly concerned with deadlocks which I think isn't an issue above) and the solutions are a little klunky so it really seems like the subprocess module isn't quite up to the job (also see: http://www.python.org/dev/peps/pep-3145/ ) and we need to look at something else.
A more involved solution is to use Twisted as shown here: https://twistedmatrix.com/documents/11.1.0/core/howto/process.html
The way you do this with Twisted is to create your process using reactor.spawnprocess() and providing a ProcessProtocol that then processes output asynchronously. The Twisted sample Python code is here: https://twistedmatrix.com/documents/11.1.0/core/howto/listings/process/process.py
Based on all the above I suggest a slightly modified version (python3):
while loop calling readline (The iter solution suggested seemed to block forever for me - Python 3, Windows 7)
structered so handling of read data does not need to be duplicated after poll returns not-None
stderr piped into stdout so both output outputs are read
Added code to get exit value of cmd.
Code:
import subprocess
proc = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE,
stderr=subprocess.STDOUT, universal_newlines=True)
while True:
rd = proc.stdout.readline()
print(rd, end='') # and whatever you want to do...
if not rd: # EOF
returncode = proc.poll()
if returncode is not None:
break
time.sleep(0.1) # cmd closed stdout, but not exited yet
# You may want to check on ReturnCode here
I found a simple solution to a much complicated problem.
Both stdout and stderr need to be streamed.
Both of them need to be non-blocking: when there is no output and when there are too much output.
Do not want to use Threading or multiprocessing, also not willing to use pexpect.
This solution uses a gist I found here
import subprocess as sbp
import fcntl
import os
def non_block_read(output):
fd = output.fileno()
fl = fcntl.fcntl(fd, fcntl.F_GETFL)
fcntl.fcntl(fd, fcntl.F_SETFL, fl | os.O_NONBLOCK)
try:
return output.readline()
except:
return ""
with sbp.Popen('find / -name fdsfjdlsjf',
shell=True,
universal_newlines=True,
encoding='utf-8',
bufsize=1,
stdout=sbp.PIPE,
stderr=sbp.PIPE) as p:
while True:
out = non_block_read(p.stdout)
err = non_block_read(p.stderr)
if out:
print(out, end='')
if err:
print('E: ' + err, end='')
if p.poll() is not None:
break
It looks like line-buffered output will work for you, in which case something like the following might suit. (Caveat: it's untested.) This will only give the subprocess's stdout in real time. If you want to have both stderr and stdout in real time, you'll have to do something more complex with select.
proc = subprocess.Popen(run_command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
while proc.poll() is None:
line = proc.stdout.readline()
print line
log_file.write(line + '\n')
# Might still be data on stdout at this point. Grab any
# remainder.
for line in proc.stdout.read().split('\n'):
print line
log_file.write(line + '\n')
# Do whatever you want with proc.stderr here...
Why not set stdout directly to sys.stdout? And if you need to output to a log as well, then you can simply override the write method of f.
import sys
import subprocess
class SuperFile(open.__class__):
def write(self, data):
sys.stdout.write(data)
super(SuperFile, self).write(data)
f = SuperFile("log.txt","w+")
process = subprocess.Popen(command, stdout=f, stderr=f)
All of the above solutions I tried failed either to separate stderr and stdout output, (multiple pipes) or blocked forever when the OS pipe buffer was full which happens when the command you are running outputs too fast (there is a warning for this on python poll() manual of subprocess). The only reliable way I found was through select, but this is a posix-only solution:
import subprocess
import sys
import os
import select
# returns command exit status, stdout text, stderr text
# rtoutput: show realtime output while running
def run_script(cmd,rtoutput=0):
p = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
poller = select.poll()
poller.register(p.stdout, select.POLLIN)
poller.register(p.stderr, select.POLLIN)
coutput=''
cerror=''
fdhup={}
fdhup[p.stdout.fileno()]=0
fdhup[p.stderr.fileno()]=0
while sum(fdhup.values()) < len(fdhup):
try:
r = poller.poll(1)
except select.error, err:
if err.args[0] != EINTR:
raise
r=[]
for fd, flags in r:
if flags & (select.POLLIN | select.POLLPRI):
c = os.read(fd, 1024)
if rtoutput:
sys.stdout.write(c)
sys.stdout.flush()
if fd == p.stderr.fileno():
cerror+=c
else:
coutput+=c
else:
fdhup[fd]=1
return p.poll(), coutput.strip(), cerror.strip()
None of the Pythonic solutions worked for me.
It turned out that proc.stdout.read() or similar may block forever.
Therefore, I use tee like this:
subprocess.run('./my_long_running_binary 2>&1 | tee -a my_log_file.txt && exit ${PIPESTATUS}', shell=True, check=True, executable='/bin/bash')
This solution is convenient if you are already using shell=True.
${PIPESTATUS} captures the success status of the entire command chain (only available in Bash).
If I omitted the && exit ${PIPESTATUS}, then this would always return zero since tee never fails.
unbuffer might be necessary for printing each line immediately into the terminal, instead of waiting way too long until the "pipe buffer" gets filled.
However, unbuffer swallows the exit status of assert (SIG Abort)...
2>&1 also logs stderror to the file.
I think that the subprocess.communicate method is a bit misleading: it actually fills the stdout and stderr that you specify in the subprocess.Popen.
Yet, reading from the subprocess.PIPE that you can provide to the subprocess.Popen's stdout and stderr parameters will eventually fill up OS pipe buffers and deadlock your app (especially if you've multiple processes/threads that must use subprocess).
My proposed solution is to provide the stdout and stderr with files - and read the files' content instead of reading from the deadlocking PIPE. These files can be tempfile.NamedTemporaryFile() - which can also be accessed for reading while they're being written into by subprocess.communicate.
Below is a sample usage:
try:
with ProcessRunner(
("python", "task.py"), env=os.environ.copy(), seconds_to_wait=0.01
) as process_runner:
for out in process_runner:
print(out)
except ProcessError as e:
print(e.error_message)
raise
And this is the source code which is ready to be used with as many comments as I could provide to explain what it does:
If you're using python 2, please make sure to first install the latest version of the subprocess32 package from pypi.
import os
import sys
import threading
import time
import tempfile
import logging
if os.name == 'posix' and sys.version_info[0] < 3:
# Support python 2
import subprocess32 as subprocess
else:
# Get latest and greatest from python 3
import subprocess
logger = logging.getLogger(__name__)
class ProcessError(Exception):
"""Base exception for errors related to running the process"""
class ProcessTimeout(ProcessError):
"""Error that will be raised when the process execution will exceed a timeout"""
class ProcessRunner(object):
def __init__(self, args, env=None, timeout=None, bufsize=-1, seconds_to_wait=0.25, **kwargs):
"""
Constructor facade to subprocess.Popen that receives parameters which are more specifically required for the
Process Runner. This is a class that should be used as a context manager - and that provides an iterator
for reading captured output from subprocess.communicate in near realtime.
Example usage:
try:
with ProcessRunner(('python', task_file_path), env=os.environ.copy(), seconds_to_wait=0.01) as process_runner:
for out in process_runner:
print(out)
except ProcessError as e:
print(e.error_message)
raise
:param args: same as subprocess.Popen
:param env: same as subprocess.Popen
:param timeout: same as subprocess.communicate
:param bufsize: same as subprocess.Popen
:param seconds_to_wait: time to wait between each readline from the temporary file
:param kwargs: same as subprocess.Popen
"""
self._seconds_to_wait = seconds_to_wait
self._process_has_timed_out = False
self._timeout = timeout
self._process_done = False
self._std_file_handle = tempfile.NamedTemporaryFile()
self._process = subprocess.Popen(args, env=env, bufsize=bufsize,
stdout=self._std_file_handle, stderr=self._std_file_handle, **kwargs)
self._thread = threading.Thread(target=self._run_process)
self._thread.daemon = True
def __enter__(self):
self._thread.start()
return self
def __exit__(self, exc_type, exc_val, exc_tb):
self._thread.join()
self._std_file_handle.close()
def __iter__(self):
# read all output from stdout file that subprocess.communicate fills
with open(self._std_file_handle.name, 'r') as stdout:
# while process is alive, keep reading data
while not self._process_done:
out = stdout.readline()
out_without_trailing_whitespaces = out.rstrip()
if out_without_trailing_whitespaces:
# yield stdout data without trailing \n
yield out_without_trailing_whitespaces
else:
# if there is nothing to read, then please wait a tiny little bit
time.sleep(self._seconds_to_wait)
# this is a hack: terraform seems to write to buffer after process has finished
out = stdout.read()
if out:
yield out
if self._process_has_timed_out:
raise ProcessTimeout('Process has timed out')
if self._process.returncode != 0:
raise ProcessError('Process has failed')
def _run_process(self):
try:
# Start gathering information (stdout and stderr) from the opened process
self._process.communicate(timeout=self._timeout)
# Graceful termination of the opened process
self._process.terminate()
except subprocess.TimeoutExpired:
self._process_has_timed_out = True
# Force termination of the opened process
self._process.kill()
self._process_done = True
#property
def return_code(self):
return self._process.returncode
Here is a class which I'm using in one of my projects. It redirects output of a subprocess to the log. At first I tried simply overwriting the write-method but that doesn't work as the subprocess will never call it (redirection happens on filedescriptor level). So I'm using my own pipe, similar to how it's done in the subprocess-module. This has the advantage of encapsulating all logging/printing logic in the adapter and you can simply pass instances of the logger to Popen: subprocess.Popen("/path/to/binary", stderr = LogAdapter("foo"))
class LogAdapter(threading.Thread):
def __init__(self, logname, level = logging.INFO):
super().__init__()
self.log = logging.getLogger(logname)
self.readpipe, self.writepipe = os.pipe()
logFunctions = {
logging.DEBUG: self.log.debug,
logging.INFO: self.log.info,
logging.WARN: self.log.warn,
logging.ERROR: self.log.warn,
}
try:
self.logFunction = logFunctions[level]
except KeyError:
self.logFunction = self.log.info
def fileno(self):
#when fileno is called this indicates the subprocess is about to fork => start thread
self.start()
return self.writepipe
def finished(self):
"""If the write-filedescriptor is not closed this thread will
prevent the whole program from exiting. You can use this method
to clean up after the subprocess has terminated."""
os.close(self.writepipe)
def run(self):
inputFile = os.fdopen(self.readpipe)
while True:
line = inputFile.readline()
if len(line) == 0:
#no new data was added
break
self.logFunction(line.strip())
If you don't need logging but simply want to use print() you can obviously remove large portions of the code and keep the class shorter. You could also expand it by an __enter__ and __exit__ method and call finished in __exit__ so that you could easily use it as context.
import os
def execute(cmd, callback):
for line in iter(os.popen(cmd).readline, ''):
callback(line[:-1])
execute('ls -a', print)
Had the same problem and worked out a simple and clean solution using process.sdtout.read1() which works perfectly for my needs in python3.
Here is a demo using the ping command (requires internet connection):
from subprocess import Popen, PIPE
cmd = "ping 8.8.8.8"
proc = Popen([cmd], shell=True, stdout=PIPE)
while True:
print(proc.stdout.read1())
Every second or so a new line is printed in the python console as the ping command reports its data in real time.
In my view "live output from subprocess command" means that both stdout and stderr should be live. And stdin should also be delivered to the subprocess.
The fragment below produces live output on stdout and stderr and also captures them as bytes in outcome.{stdout,stderr}.
The trick involves proper use of select and poll.
Works well for me on Python 3.9.
if self.log == 1:
print(f"** cmnd= {fullCmndStr}")
self.outcome.stdcmnd = fullCmndStr
try:
process = subprocess.Popen(
fullCmndStr,
shell=True,
encoding='utf8',
executable="/bin/bash",
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
except OSError:
self.outcome.error = OSError
else:
process.stdin.write(stdin)
process.stdin.close() # type: ignore
stdoutStrFile = io.StringIO("")
stderrStrFile = io.StringIO("")
pollStdout = select.poll()
pollStderr = select.poll()
pollStdout.register(process.stdout, select.POLLIN)
pollStderr.register(process.stderr, select.POLLIN)
stdoutEOF = False
stderrEOF = False
while True:
stdoutActivity = pollStdout.poll(0)
if stdoutActivity:
c= process.stdout.read(1)
if c:
stdoutStrFile.write(c)
if self.log == 1:
sys.stdout.write(c)
else:
stdoutEOF = True
stderrActivity = pollStderr.poll(0)
if stderrActivity:
c= process.stderr.read(1)
if c:
stderrStrFile.write(c)
if self.log == 1:
sys.stderr.write(c)
else:
stderrEOF = True
if stdoutEOF and stderrEOF:
break
if self.log == 1:
print(f"** cmnd={fullCmndStr}")
process.wait() # type: ignore
self.outcome.stdout = stdoutStrFile.getvalue()
self.outcome.stderr = stderrStrFile.getvalue()
self.outcome.error = process.returncode # type: ignore
The only way i've found how to read a subprocess' output in a streaming fashion (while also capturing it in a variable) in Python (for multiple output streams, i.e. both stdout and stderr) is by passing the subprocess a named temporary file to write to and then opening the same temporary file in a separate reading handle.
Note: this is for Python 3
stdout_write = tempfile.NamedTemporaryFile()
stdout_read = io.open(stdout_write.name, "r")
stderr_write = tempfile.NamedTemporaryFile()
stderr_read = io.open(stderr_write.name, "r")
stdout_captured = ""
stderr_captured = ""
proc = subprocess.Popen(["command"], stdout=stdout_write, stderr=stderr_write)
while True:
proc_done: bool = cli_process.poll() is not None
while True:
content = stdout_read.read(1024)
sys.stdout.write(content)
stdout_captured += content
if len(content) < 1024:
break
while True:
content = stderr_read.read(1024)
sys.stderr.write(content)
stdout_captured += content
if len(content) < 1024:
break
if proc_done:
break
time.sleep(0.1)
stdout_write.close()
stdout_read.close()
stderr_write.close()
stderr_read.close()
However, if you don't need to capture the output, then you can simply pass sys.stdout and sys.stderr streams from your Python script to the called subprocess, as xaav suggested in his answer :
subprocess.Popen(["command"], stdout=sys.stdout, stderr=sys.stderr)

Getting output from and giving commands to a python subprocess

I am trying to get output from a subprocess and then give commands to that process based on the preceding output. I need to do this a variable number of times, when the program needs further input. (I also need to be able to hide the subprocess command prompt if possible).
I figured this would be an easy task given that I have seen this problem being discussed in posts from 2003 and it is nearly 2012 and it appears to be a pretty common need and really seems like it should be a basic part of any programming language. Apparently I was wrong and somehow almost 9 years later there is still no standard way of accomplishing this task in a stable, non-destructive, platform independent way!
I don't really understand much about file i/o and buffering or threading so I would prefer a solution that is as simple as possible. If there is a module that accomplishes this that is compatible with python 3.x, I would be very willing to download it. I realize that there are multiple questions that ask basically the same thing, but I have yet to find an answer that addresses the simple task that I am trying to accomplish.
Here is the code I have so far based on a variety of sources; however I have absolutely no idea what to do next. All my attempts ended in failure and some managed to use 100% of my CPU (to do basically nothing) and would not quit.
import subprocess
from subprocess import Popen, PIPE
p = Popen(r'C:\postgis_testing\shellcomm.bat',stdin=PIPE,stdout=PIPE,stderr=subprocess.STDOUT shell=True)
stdout,stdin = p.communicate(b'command string')
In case my question is unclear I am posting the text of the sample batch file that I demonstrates a situation in which it is necessary to send multiple commands to the subprocess (if you type an incorrect command string the program loops).
#echo off
:looper
set INPUT=
set /P INPUT=Type the correct command string:
if "%INPUT%" == "command string" (echo you are correct) else (goto looper)
If anyone can help me I would very much appreciate it, and I'm sure many others would as well!
EDIT here is the functional code using eryksun's code (next post) :
import subprocess
import threading
import time
import sys
try:
import queue
except ImportError:
import Queue as queue
def read_stdout(stdout, q, p):
it = iter(lambda: stdout.read(1), b'')
for c in it:
q.put(c)
if stdout.closed:
break
_encoding = getattr(sys.stdout, 'encoding', 'latin-1')
def get_stdout(q, encoding=_encoding):
out = []
while 1:
try:
out.append(q.get(timeout=0.2))
except queue.Empty:
break
return b''.join(out).rstrip().decode(encoding)
def printout(q):
outdata = get_stdout(q)
if outdata:
print('Output: %s' % outdata)
if __name__ == '__main__':
#setup
p = subprocess.Popen(['shellcomm.bat'], stdin=subprocess.PIPE,
stdout=subprocess.PIPE, stderr=subprocess.PIPE,
bufsize=0, shell=True) # I put shell=True to hide prompt
q = queue.Queue()
encoding = getattr(sys.stdin, 'encoding', 'utf-8')
#for reading stdout
t = threading.Thread(target=read_stdout, args=(p.stdout, q, p))
t.daemon = True
t.start()
#command loop
while p.poll() is None:
printout(q)
cmd = input('Input: ')
cmd = (cmd + '\n').encode(encoding)
p.stdin.write(cmd)
time.sleep(0.1) # I added this to give some time to check for closure (otherwise it doesn't work)
#tear down
for n in range(4):
rc = p.poll()
if rc is not None:
break
time.sleep(0.25)
else:
p.terminate()
rc = p.poll()
if rc is None:
rc = 1
printout(q)
print('Return Code: %d' % rc)
However when the script is run from a command prompt the following happens:
C:\Users\username>python C:\postgis_testing\shellcomm7.py
Input: sth
Traceback (most recent call last):
File "C:\postgis_testing\shellcomm7.py", line 51, in <module>
p.stdin.write(cmd)
IOError: [Errno 22] Invalid argument
It seems that the program closes out when run from command prompt. any ideas?
This demo uses a dedicated thread to read from stdout. If you search around, I'm sure you can find a more complete implementation written up in an object oriented interface. At least I can say this is working for me with your provided batch file in both Python 2.7.2 and 3.2.2.
shellcomm.bat:
#echo off
echo Command Loop Test
echo.
:looper
set INPUT=
set /P INPUT=Type the correct command string:
if "%INPUT%" == "command string" (echo you are correct) else (goto looper)
Here's what I get for output based on the sequence of commands "wrong", "still wrong", and "command string":
Output:
Command Loop Test
Type the correct command string:
Input: wrong
Output:
Type the correct command string:
Input: still wrong
Output:
Type the correct command string:
Input: command string
Output:
you are correct
Return Code: 0
For reading the piped output, readline might work sometimes, but set /P INPUT in the batch file naturally isn't writing a line ending. So instead I used lambda: stdout.read(1) to read a byte at a time (not so efficient, but it works). The reading function puts the data on a queue. The main thread gets the output from the queue after it writes a a command. Using a timeout on the get call here makes it wait a small amount of time to ensure the program is waiting for input. Instead you could check the output for prompts to know when the program is expecting input.
All that said, you can't expect a setup like this to work universally because the console program you're trying to interact with might buffer its output when piped. In Unix systems there are some utility commands available that you can insert into a pipe to modify the buffering to be non-buffered, line-buffered, or a given size -- such as stdbuf. There are also ways to trick the program into thinking it's connected to a pty (see pexpect). However, I don't know a way around this problem on Windows if you don't have access to the program's source code to explicitly set the buffering using setvbuf.
import subprocess
import threading
import time
import sys
if sys.version_info.major >= 3:
import queue
else:
import Queue as queue
input = raw_input
def read_stdout(stdout, q):
it = iter(lambda: stdout.read(1), b'')
for c in it:
q.put(c)
if stdout.closed:
break
_encoding = getattr(sys.stdout, 'encoding', 'latin-1')
def get_stdout(q, encoding=_encoding):
out = []
while 1:
try:
out.append(q.get(timeout=0.2))
except queue.Empty:
break
return b''.join(out).rstrip().decode(encoding)
def printout(q):
outdata = get_stdout(q)
if outdata:
print('Output:\n%s' % outdata)
if __name__ == '__main__':
ARGS = ["shellcomm.bat"] ### Modify this
#setup
p = subprocess.Popen(ARGS, bufsize=0, stdin=subprocess.PIPE,
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
q = queue.Queue()
encoding = getattr(sys.stdin, 'encoding', 'utf-8')
#for reading stdout
t = threading.Thread(target=read_stdout, args=(p.stdout, q))
t.daemon = True
t.start()
#command loop
while 1:
printout(q)
if p.poll() is not None or p.stdin.closed:
break
cmd = input('Input: ')
cmd = (cmd + '\n').encode(encoding)
p.stdin.write(cmd)
#tear down
for n in range(4):
rc = p.poll()
if rc is not None:
break
time.sleep(0.25)
else:
p.terminate()
rc = p.poll()
if rc is None:
rc = 1
printout(q)
print('\nReturn Code: %d' % rc)

Merging a Python script's subprocess' stdout and stderr while keeping them distinguishable

I would like to direct a python script's subprocess' stdout and stdin into the same file. What I don't know is how to make the lines from the two sources distinguishable? (For example prefix the lines from stderr with an exclamation mark.)
In my particular case there is no need for live monitoring of the subprocess, the executing Python script can wait for the end of its execution.
tsk = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.STDOUT)
subprocess.STDOUT is a special flag that tells subprocess to route all stderr output to stdout, thus combining your two streams.
btw, select doesn't have a poll() in windows. subprocess only uses the file handle number, and doesn't call your file output object's write method.
to capture the output, do something like:
logfile = open(logfilename, 'w')
while tsk.poll() is None:
line = tsk.stdout.readline()
logfile.write(line)
I found myself having to tackle this problem recently, and it took a while to get something I felt worked correctly in most cases, so here it is! (It also has the nice side effect of processing the output via a python logger, which I've noticed is another common question here on Stackoverflow).
Here is the code:
import sys
import logging
import subprocess
from threading import Thread
logging.basicConfig(stream=sys.stdout,level=logging.INFO)
logging.addLevelName(logging.INFO+2,'STDERR')
logging.addLevelName(logging.INFO+1,'STDOUT')
logger = logging.getLogger('root')
pobj = subprocess.Popen(['python','-c','print 42;bargle'],
stdout=subprocess.PIPE, stderr=subprocess.PIPE)
def logstream(stream,loggercb):
while True:
out = stream.readline()
if out:
loggercb(out.rstrip())
else:
break
stdout_thread = Thread(target=logstream,
args=(pobj.stdout,lambda s: logger.log(logging.INFO+1,s)))
stderr_thread = Thread(target=logstream,
args=(pobj.stderr,lambda s: logger.log(logging.INFO+2,s)))
stdout_thread.start()
stderr_thread.start()
while stdout_thread.isAlive() and stderr_thread.isAlive():
pass
Here is the output:
STDOUT:root:42
STDERR:root:Traceback (most recent call last):
STDERR:root: File "<string>", line 1, in <module>
STDERR:root:NameError: name 'bargle' is not defined
You can replace the subprocess call to do whatever you want, I just chose running python with a command that I knew would print to both stdout and stderr. The key bit is reading stderr and stdout each in a separate thread. Otherwise you may be blocking on reading one while there is data ready to be read on the other.
If you want to interleave to get roughly the same order that you would if you ran the process interactively then you need to do what the shell does and poll stdin/stdout and write in the order that they poll.
Here's some code that does something along the lines of what you want - in this case sending the stdout/stderr to a logger info/error streams.
tsk = subprocess.Popen(args,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
poll = select.poll()
poll.register(tsk.stdout,select.POLLIN | select.POLLHUP)
poll.register(tsk.stderr,select.POLLIN | select.POLLHUP)
pollc = 2
events = poll.poll()
while pollc > 0 and len(events) > 0:
for event in events:
(rfd,event) = event
if event & select.POLLIN:
if rfd == tsk.stdout.fileno():
line = tsk.stdout.readline()
if len(line) > 0:
logger.info(line[:-1])
if rfd == tsk.stderr.fileno():
line = tsk.stderr.readline()
if len(line) > 0:
logger.error(line[:-1])
if event & select.POLLHUP:
poll.unregister(rfd)
pollc = pollc - 1
if pollc > 0: events = poll.poll()
tsk.wait()
At the moment all other answers don't handle buffering on the child subprocess' side if the subprocess is not a Python script that accepts -u flag. See "Q: Why not just use a pipe (popen())?" in the pexpect documentation.
To simulate -u flag for some of C stdio-based (FILE*) programs you could try stdbuf.
If you ignore this then your output won't be properly interleaved and might look like:
stderr
stderr
...large block of stdout including parts that are printed before stderr...
You could try it with the following client program, notice the difference with/without -u flag (['stdbuf', '-o', 'L', 'child_program'] also fixes the output):
#!/usr/bin/env python
from __future__ import print_function
import random
import sys
import time
from datetime import datetime
def tprint(msg, file=sys.stdout):
time.sleep(.1*random.random())
print("%s %s" % (datetime.utcnow().strftime('%S.%f'), msg), file=file)
tprint("stdout1 before stderr")
tprint("stdout2 before stderr")
for x in range(5):
tprint('stderr%d' % x, file=sys.stderr)
tprint("stdout3 after stderr")
On Linux you could use pty to get the same behavior as when the subprocess runs interactively e.g., here's a modified #T.Rojan's answer:
import logging, os, select, subprocess, sys, pty
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)
master_fd, slave_fd = pty.openpty()
p = subprocess.Popen(args,stdout=slave_fd, stderr=subprocess.PIPE, close_fds=True)
with os.fdopen(master_fd) as stdout:
poll = select.poll()
poll.register(stdout, select.POLLIN)
poll.register(p.stderr,select.POLLIN | select.POLLHUP)
def cleanup(_done=[]):
if _done: return
_done.append(1)
poll.unregister(p.stderr)
p.stderr.close()
poll.unregister(stdout)
assert p.poll() is not None
read_write = {stdout.fileno(): (stdout.readline, logger.info),
p.stderr.fileno(): (p.stderr.readline, logger.error)}
while True:
events = poll.poll(40) # poll with a small timeout to avoid both
# blocking forever and a busy loop
if not events and p.poll() is not None:
# no IO events and the subprocess exited
cleanup()
break
for fd, event in events:
if event & select.POLLIN: # there is something to read
read, write = read_write[fd]
line = read()
if line:
write(line.rstrip())
elif event & select.POLLHUP: # free resources if stderr hung up
cleanup()
else: # something unexpected happened
assert 0
sys.exit(p.wait()) # return child's exit code
It assumes that stderr is always unbuffered/line-buffered and stdout is line-buffered in an interactive mode. Only full lines are read. The program might block if there are non-terminated lines in the output.
I suggest you write your own handlers, something like (not tested, I hope you catch the idea):
class my_buffer(object):
def __init__(self, fileobject, prefix):
self._fileobject = fileobject
self.prefix = prefix
def write(self, text):
return self._fileobject.write('%s %s' % (self.prefix, text))
# delegate other methods to fileobject if necessary
log_file = open('log.log', 'w')
my_out = my_buffer(log_file, 'OK:')
my_err = my_buffer(log_file, '!!!ERROR:')
p = subprocess.Popen(command, stdout=my_out, stderr=my_err, shell=True)
You may write the stdout/err to a file after the command execution.
In the example below I use pickling so I am sure I will be able to read without any particular parsing to differentiate between the stdout/err and at some point I could dumo the exitcode and the command itself.
import subprocess
import cPickle
command = 'ls -altrh'
outfile = 'log.errout'
pipe = subprocess.Popen(command, stdout = subprocess.PIPE,
stderr = subprocess.PIPE, shell = True)
stdout, stderr = pipe.communicate()
f = open(outfile, 'w')
cPickle.dump({'out': stdout, 'err': stderr},f)
f.close()

Python: How to read stdout non blocking from another process?

During the runtime of a process I would like to read its stdout and write it to a file. Any attempt of mine however failed because no matter what I tried as soon as I tried reading from the stdout it blocked until the process finished.
Here is a snippet of what I am trying to do. (The first part is simply a python script that writes something to stdout.)
import subprocess
p = subprocess.Popen('python -c \'\
from time import sleep\n\
for i in range(3):\n\
sleep(1)\n\
print "Hello", i\
\'', shell = True, stdout = subprocess.PIPE)
while p.poll() == None:
#read the stdout continuously
pass
print "Done"
I know that there are multiple questions out there that deal with the same subject. However, none of the ones I found was able to answer my question.
What is happening is buffering on the writer side. Since you are writing such small chunks from the little code snippet the underlying FILE object is buffering the output until the end. The following works as you expect.
#!/usr/bin/python
import sys
import subprocess
p = subprocess.Popen("""python -c '
from time import sleep ; import sys
for i in range(3):
sleep(1)
print "Hello", i
sys.stdout.flush()
'""", shell = True, stdout = subprocess.PIPE)
while True:
inline = p.stdout.readline()
if not inline:
break
sys.stdout.write(inline)
sys.stdout.flush()
print "Done"
However, you may not be expecting the right thing. The buffering is there to reduce the number of system calls in order to make the system more efficient. Does it really matter to you that the whole text is buffered until the end before you write it to a file? Don't you still get all the output in the file?
the following code would print stdout line by line as the subprocess runs until the readline() method returns an empty string:
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
for line in iter(p.stdout.readline, ''):
print line
p.stdout.close()
print 'Done'
update relating to your question better:
import subprocess
p = subprocess.Popen(['python'], stdout=subprocess.PIPE, stdin=subprocess.PIPE)
p.stdin.write("""
from time import sleep ; import sys
for i in range(3):
sleep(1)
print "Hello", i
sys.stdout.flush()
""")
p.stdin.close()
for line in iter(p.stdout.readline, ''):
print line
p.stdout.close()
print 'Done'
You can use subprocess.communicate() to get the output from stdout. Something like:
while(p.poll() == None):
#read the stdout continuously
print(p.communicate()[0])
pass
More info available at: http://docs.python.org/library/subprocess.html

read subprocess stdout line by line

My python script uses subprocess to call a linux utility that is very noisy. I want to store all of the output to a log file and show some of it to the user. I thought the following would work, but the output doesn't show up in my application until the utility has produced a significant amount of output.
#fake_utility.py, just generates lots of output over time
import time
i = 0
while True:
print hex(i)*512
i += 1
time.sleep(0.5)
#filters output
import subprocess
proc = subprocess.Popen(['python','fake_utility.py'],stdout=subprocess.PIPE)
for line in proc.stdout:
#the real code does filtering here
print "test:", line.rstrip()
The behavior I really want is for the filter script to print each line as it is received from the subprocess. Sorta like what tee does but with python code.
What am I missing? Is this even possible?
Update:
If a sys.stdout.flush() is added to fake_utility.py, the code has the desired behavior in python 3.1. I'm using python 2.6. You would think that using proc.stdout.xreadlines() would work the same as py3k, but it doesn't.
Update 2:
Here is the minimal working code.
#fake_utility.py, just generates lots of output over time
import sys, time
for i in range(10):
print i
sys.stdout.flush()
time.sleep(0.5)
#display out put line by line
import subprocess
proc = subprocess.Popen(['python','fake_utility.py'],stdout=subprocess.PIPE)
#works in python 3.0+
#for line in proc.stdout:
for line in iter(proc.stdout.readline,''):
print line.rstrip()
I think the problem is with the statement for line in proc.stdout, which reads the entire input before iterating over it. The solution is to use readline() instead:
#filters output
import subprocess
proc = subprocess.Popen(['python','fake_utility.py'],stdout=subprocess.PIPE)
while True:
line = proc.stdout.readline()
if not line:
break
#the real code does filtering here
print "test:", line.rstrip()
Of course you still have to deal with the subprocess' buffering.
Note: according to the documentation the solution with an iterator should be equivalent to using readline(), except for the read-ahead buffer, but (or exactly because of this) the proposed change did produce different results for me (Python 2.5 on Windows XP).
Bit late to the party, but was surprised not to see what I think is the simplest solution here:
import io
import subprocess
proc = subprocess.Popen(["prog", "arg"], stdout=subprocess.PIPE)
for line in io.TextIOWrapper(proc.stdout, encoding="utf-8"): # or another encoding
# do something with line
(This requires Python 3.)
Indeed, if you sorted out the iterator then buffering could now be your problem. You could tell the python in the sub-process not to buffer its output.
proc = subprocess.Popen(['python','fake_utility.py'],stdout=subprocess.PIPE)
becomes
proc = subprocess.Popen(['python','-u', 'fake_utility.py'],stdout=subprocess.PIPE)
I have needed this when calling python from within python.
You want to pass these extra parameters to subprocess.Popen:
bufsize=1, universal_newlines=True
Then you can iterate as in your example. (Tested with Python 3.5)
A function that allows iterating over both stdout and stderr concurrently, in realtime, line by line
In case you need to get the output stream for both stdout and stderr at the same time, you can use the following function.
The function uses Queues to merge both Popen pipes into a single iterator.
Here we create the function read_popen_pipes():
from queue import Queue, Empty
from concurrent.futures import ThreadPoolExecutor
def enqueue_output(file, queue):
for line in iter(file.readline, ''):
queue.put(line)
file.close()
def read_popen_pipes(p):
with ThreadPoolExecutor(2) as pool:
q_stdout, q_stderr = Queue(), Queue()
pool.submit(enqueue_output, p.stdout, q_stdout)
pool.submit(enqueue_output, p.stderr, q_stderr)
while True:
if p.poll() is not None and q_stdout.empty() and q_stderr.empty():
break
out_line = err_line = ''
try:
out_line = q_stdout.get_nowait()
except Empty:
pass
try:
err_line = q_stderr.get_nowait()
except Empty:
pass
yield (out_line, err_line)
read_popen_pipes() in use:
import subprocess as sp
with sp.Popen(my_cmd, stdout=sp.PIPE, stderr=sp.PIPE, text=True) as p:
for out_line, err_line in read_popen_pipes(p):
# Do stuff with each line, e.g.:
print(out_line, end='')
print(err_line, end='')
return p.poll() # return status-code
You can also read lines w/o loop. Works in python3.6.
import os
import subprocess
process = subprocess.Popen(command, stdout=subprocess.PIPE)
list_of_byte_strings = process.stdout.readlines()
Pythont 3.5 added the methods run() and call() to the subprocess module, both returning a CompletedProcess object. With this you are fine using proc.stdout.splitlines():
proc = subprocess.run( comman, shell=True, capture_output=True, text=True, check=True )
for line in proc.stdout.splitlines():
print "stdout:", line
See also How to Execute Shell Commands in Python Using the Subprocess Run Method
I tried this with python3 and it worked, source
When you use popen to spawn the new thread, you tell the operating system to PIPE the stdout of the child processes so the parent process can read it and here, stderr is copied to the stderr of the parent process.
in output_reader we read each line of stdout of the child process by wrapping it in an iterator that populates line by line output from the child process whenever a new line is ready.
def output_reader(proc):
for line in iter(proc.stdout.readline, b''):
print('got line: {0}'.format(line.decode('utf-8')), end='')
def main():
proc = subprocess.Popen(['python', 'fake_utility.py'],
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
t = threading.Thread(target=output_reader, args=(proc,))
t.start()
try:
time.sleep(0.2)
import time
i = 0
while True:
print (hex(i)*512)
i += 1
time.sleep(0.5)
finally:
proc.terminate()
try:
proc.wait(timeout=0.2)
print('== subprocess exited with rc =', proc.returncode)
except subprocess.TimeoutExpired:
print('subprocess did not terminate in time')
t.join()
The following modification of Rômulo's answer works for me on Python 2 and 3 (2.7.12 and 3.6.1):
import os
import subprocess
process = subprocess.Popen(command, stdout=subprocess.PIPE)
while True:
line = process.stdout.readline()
if line != '':
os.write(1, line)
else:
break
I was having a problem with the arg list of Popen to update servers, the following code resolves this a bit.
import getpass
from subprocess import Popen, PIPE
username = 'user1'
ip = '127.0.0.1'
print ('What is the password?')
password = getpass.getpass()
cmd1 = f"""sshpass -p {password} ssh {username}#{ip}"""
cmd2 = f"""echo {password} | sudo -S apt update"""
cmd3 = " && "
cmd4 = f"""echo {password} | sudo -S apt upgrade -y"""
cmd5 = " && "
cmd6 = "exit"
commands = [cmd1, cmd2, cmd3, cmd4, cmd5, cmd6]
command = " ".join(commands)
cmd = command.split()
with Popen(cmd, stdout=PIPE, bufsize=1, universal_newlines=True) as p:
for line in p.stdout:
print(line, end='')
And to run the update on a local computer, the following code example does this.
import getpass
from subprocess import Popen, PIPE
print ('What is the password?')
password = getpass.getpass()
cmd1_local = f"""apt update"""
cmd2_local = f"""apt upgrade -y"""
commands = [cmd1_local, cmd2_local]
with Popen(['echo', password], stdout=PIPE) as auth:
for cmd in commands:
cmd = cmd.split()
with Popen(['sudo','-S'] + cmd, stdin=auth.stdout, stdout=PIPE, bufsize=1, universal_newlines=True) as p:
for line in p.stdout:
print(line, end='')

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