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missing stdout before subprocess.Popen crash [duplicate]

I am using a 3rd-party python module which is normally called through terminal commands. When called through terminal commands it has a verbose option which prints to terminal in real time.
I then have another python program which calls the 3rd-party program through subprocess. Unfortunately, when called through subprocess the terminal output no longer flushes, and is only returned on completion (the process takes many hours so I would like real-time progress).
I can see the source code of the 3rd-party module and it does not set printing to be flushed such as print('example', flush=True). Is there a way to force the flushing through my module without editing the 3rd-party source code? Furthermore, can I send this output to a log file (again in real time)?
Thanks for any help.

The issue is most likely that many programs work differently if run interactively in a terminal or as part of a pipe line (i.e. called using subprocess). It has very little to do with Python itself, but more with the Unix/Linux architecture.
As you have noted, it is possible to force a program to flush stdout even when run in a pipe line, but it requires changes to the source code, by manually applying stdout.flush calls.
Another way to print to screen, is to "trick" the program to think it is working with an interactive terminal, using a so called pseudo-terminal. There is a supporting module for this in the Python standard library, namely pty. Using, that, you will not explicitly call subprocess.run (or Popen or ...). Instead you have to use the pty.spawn call:
def prout(fd):
data = os.read(fd, 1024)
while(data):
print(data.decode(), end="")
data = os.read(fd, 1024)
pty.spawn("./callee.py", prout)
As can be seen, this requires a special function for handling stdout. Here above, I just print it to the terminal, but of course it is possible to do other thing with the text as well (such as log or parse...)
Another way to trick the program, is to use an external program, called unbuffer. Unbuffer will take your script as input, and make the program think (as for the pty call) that is called from a terminal. This is arguably simpler if unbuffer is installed or you are allowed to install it on your system (it is part of the expect package). All you have to do then, is to change your subprocess call as
p=subprocess.Popen(["unbuffer", "./callee.py"], stdout=subprocess.PIPE)
and then of course handle the output as usual, e.g. with some code like
for line in p.stdout:
print(line.decode(), end="")
print(p.communicate()[0].decode(), end="")
or similar. But this last part I think you have already covered, as you seem to be doing something with the output.

run bash script from windows pc on linux machine in python [duplicate]

I am using the python paramiko module to run a built in parmiko function SSH.execute on a remote server. I want to run a script on the server which will require 4 prompts. I was planning to do a more complex version of this:
ExpectedString = 'ExpectedOutput'
Output = SSH.execute('./runScript')
if Output == ExpectedString:
SSH.execute('Enter this')
else:
raise SomeException
The problem is nothing comes back for output as the server was waiting for a number to entered and the script gets stuck at this SSH.execute command. So even if another SSH.execute command is run after it never gets run! Should I be looking to use something other than paramiko?

You need to interact with the remote script. Actually, SSH.execute doesn't exist, I assume you're talking about exec_command. Instead of just returning the output, it actually gives you wrappers for stdout, stdin and stderr streams. You can directly use these in order to communicate with the remote script.
Basically, this is how you run a command and pass data over stdin (and receive output using stdout):
ssh.connect('127.0.0.1', username='foo', password='bar')
stdin, stdout, stderr = ssh.exec_command("some_script")
stdin.write('expected_input\n')
stdin.flush()
data = stdout.read.splitlines()
You should check for the prompts, of course, instead of relying on good timing.

#leoluk - yep, I understand your problem, both those recommended solutions won't work. The problem, as you said, with exec_command is that you can only read the output once the command completes. So, if you wanted to remotely run the command rm -i *, you won't be able to read which file is to be deleted before you can respond with a "yes" or a "no". The key here is to use invoke_shell. See this youtube link - https://www.youtube.com/watch?v=lLKdxIu3-A4 - this helped and got me going.

Is it possible to launch and record only the input of a bash session?

I am trying to achieve the following:
Have a python script launch a shell. User uses that shell for whatever purposes he needs. After having closed the shell, a log of only the input commands is available to the python script for parsing.
All I have gotten are ways to invoke the shell through popen and similar, but that's not quite what I need.

The easiest way to do this is with pexpect. Moreover, the examples it ships with include a script.py, which
out-of-the-box acts like the UNIX script command (recording both stdin and stdout), but requires only a one-line change to do what you intend:
Change p.logfile = fout to p.logfile_send = fout, and you'll be logging only data sent to the remote process; alternately, you could make it p.logfile_recv = fout and you would log only data received by that process.

Accessing an ALREADY running process, with Python

Question: Is there a way, using Python, to access the stdout of a running process? This process has not been started by Python.
Context: There is a program called mayabatch, that renders out images from 3D Maya scene files. If I were to run the program from the command line I would see progress messages from mayabatch. Sometimes, artists close these windows, leaving the progress untracable until the program finishes. That led me along this route of trying to read its stdout after it's been spawned by a foreign process.
Background:
OS: Windows 7 64-bit
My research so far: I have only found questions and answers of how to do this if it was a subprocess, using the subprocess module. I also looked briefly into psutil, but I could not find any way to read a process' stdout.
Any help would be really appreciated. Thank you.

I don't think you can get to the stdout of a process outside of the code that created it
The lazy way to is just to pipe the output of mayabatch to a text file, and then poll the text file periodically in your own code so it's under your control, rather than forcing you to wait on the pipe (which is especially hard on Windows, since Windows select doesn't work with the pipes used by subprocess.
I think this is what maya does internally too: by default mayaBatch logs its results to a file called mayaRenderLog.txt in the user's Maya directory.
If you're running mayabatch from the command line or a bat file, you can funnel stdout to a file with a > character:
mayabatch.exe "file.ma" > log.txt
You should be able to poll that text file from the outside using standard python as long as you only open it for reading. The advantage of doing it this way is that you control the frequency at which you check the file.
OTOH If you're doing it from python, it's a little tougher unless you don't mind having your python script idled until the mayabatch completes. The usual subprocess recipe, which uses popen.communicate() is going to wait for an end-of-process return code:
test = subprocess.Popen(["mayabatch.exe","filename.mb"], stdout=subprocess.PIPE)
print test.communicate()[0]
works but won't report until the process dies. But you calling readlines on the process's stdout will trigger the process and report it one line at a time:
test = subprocess.Popen(["mayabatch.exe","filename.mb"], stdout=subprocess.PIPE)
reader = iter(test.subprocess.readlines, "")
for line in reader:
print line
More discussion here

Read remote output and respond using paramiko (SSH.execute)

I am using the python paramiko module to run a built in parmiko function SSH.execute on a remote server. I want to run a script on the server which will require 4 prompts. I was planning to do a more complex version of this:
ExpectedString = 'ExpectedOutput'
Output = SSH.execute('./runScript')
if Output == ExpectedString:
SSH.execute('Enter this')
else:
raise SomeException
The problem is nothing comes back for output as the server was waiting for a number to entered and the script gets stuck at this SSH.execute command. So even if another SSH.execute command is run after it never gets run! Should I be looking to use something other than paramiko?

You need to interact with the remote script. Actually, SSH.execute doesn't exist, I assume you're talking about exec_command. Instead of just returning the output, it actually gives you wrappers for stdout, stdin and stderr streams. You can directly use these in order to communicate with the remote script.
Basically, this is how you run a command and pass data over stdin (and receive output using stdout):
ssh.connect('127.0.0.1', username='foo', password='bar')
stdin, stdout, stderr = ssh.exec_command("some_script")
stdin.write('expected_input\n')
stdin.flush()
data = stdout.read.splitlines()
You should check for the prompts, of course, instead of relying on good timing.

#leoluk - yep, I understand your problem, both those recommended solutions won't work. The problem, as you said, with exec_command is that you can only read the output once the command completes. So, if you wanted to remotely run the command rm -i *, you won't be able to read which file is to be deleted before you can respond with a "yes" or a "no". The key here is to use invoke_shell. See this youtube link - https://www.youtube.com/watch?v=lLKdxIu3-A4 - this helped and got me going.