We Keep Coding

Running Command from Python. Works with os.system but not subprocces.run

I have been on this problem for quite a while now. I have this command line that I want run trough python:
Users\name.lastname\Desktop\TESTER\Latitude 5431\Latitude-5431-46KCM_Win10_1.0_A01.exe /s /e=C:Users\name.lastname\Desktop\TESTER\Latitude 5431
this should run the .exe and then extract the files to the specified folder. I tried this with os.system and it worked but when I run it with
import subprocess
x = '"' + "\\Users\\name.lastname\\Desktop\\TESTER\\Latitude 5431\\Latitude-5431-46KCM_Win10_1.0_A01.exe" + '" ' + "/s /e=C:Users\\name.lastname\\Desktop\\TESTER\\Latitude 5431"
p1 = subprocess.run(x, shell=True)
it only shows me 'tips' like these but no error message and the .exe is not executed.
Pass command line arguments directly to vendor installer.
Turn the return code to success if required
Latitude-5431-46KCM_Win10_1.0_A01.exe /factoryinstall /passthrough D:\Sample.xml C:\log\FI.log
Change from the default log location to C:\my path with spaces\log.txt
Latitude-5431-46KCM_Win10_1.0_A01.exe /l="C:\my path with spaces\log.txt"
Force update to continue, even on "soft" qualification errors
Latitude-5431-46KCM_Win10_1.0_A01.exe /s /f

Try running without shell=True as it makes things more complicated than it helps:
import subprocess
prog = r"C:\Users\name.lastname\Desktop\TESTER\Latitude 5431\Latitude-5431-46KCM_Win10_1.0_A01.exe"
args = ["/s", r"/e=C:\Users\name.lastname\Desktop\TESTER\Latitude 5431"]
subprocess.run([prog]+args)

Structuring python code to run a message through subprocess.Popen

I am in a process of building a simple remote shell tool to communicate with Windows 10. Server sends a "message" through its own shell to the client who runs the message. I need this received message to be run by other process other that default cmd (shell=True) - a specified app.exe. Here is the code that runs on the client:
1)
def work( storage, message ) :
import subprocess
process = subprocess.Popen([message], stdout=subprocess.PIPE, stderr=None, shell=True)
#Launch the shell command:
output = process.communicate()
print output[0]
I tried including "app.exe" or "cmd" to execute the message but with that I get error: TypeError: bufsize must be an integer.
I have also tried pinpointing the issue locally and I can run:
2)
import subprocess
import sys
subprocess.Popen(["C:\\Users\\User\\Desktop\\app.exe", "-switch"] + sys.argv[1:], shell=False)
and pass arguments from a command terminal and it works as it should. Now I am trying to apply the same logic to a remote execution with my program and use either solution 1 or 2.
Update:
3) Trying to implement what I did locally to a remote solution:
def work( storage, message ) :
import subprocess
import sys
process = subprocess.Popen(["C:\\Users\\User\\Desktop\\app.exe", "-switch"] + sys.argv[1:], shell=False)
#Launch the shell command:
output = process.communicate()
print output[0]
I tried replacing sys.argv[1:] with message but I get:
TypeError: can only concatenate list (not "str") to list

shell=True doesn't mean the first argument to Popen is a list of arguments to the shell; it just means the first argument is processed by the shell, rather than being arguments to whatever system call your system would use to execute a new process.
In this case, you appear to want to run app.exe with a given argument; that's simply
cmd = r"C:\Users\User\Desktop\app.exe"
subprocess.Popen([cmd, "-switch", message], stdout=subprocess.PIPE)

#chepner sir, you are a very helpful. That was it! I am so happy, thanks for your help.
Your solution:
Popen(["...\\app.exe", "-switch", message], stdout=subprocess.PIPE, stderr=None)
That was the badger!

subprocess.call to run mafft

I wrote a script to run mafft module from the terminal:
import subprocess
def linsi_MSA(sequnces_file_path):
cmd = ' mafft --maxiterate 1000 --localpair {seqs} > {out}'.format(seqs=sequnces_file_path, out=sequnces_file_path)
subprocess.call(cmd.split(), shell=True)
if __name__ == '__main__':
import logging
logger = logging.getLogger('main')
from sys import argv
if len(argv) < 2:
logger.error('Usage: MSA <sequnces_file_path> ')
exit()
else:
linsi_MSA(*argv[1:])
for some reason when trying to run the script from the terminal using:
python ./MSA.py ./sample.fa
I get the mafft interactive version opening directly in the trminal (asking for input ..output etc..)
when i'm trying to write the cmd directly in the terminal using:
mafft --maxiterate 1000 --localpair sample.fa > sample.fa
its working as expected and perfoming the command line version as without opening the interactive version.
I want my script to be able to perform the cmd line version on the terminal. what seems to be the problem?
thanks!

If you use shell=True you should pass one string as argument, not a list, e.g.:
subprocess.call("ls > outfile", shell=True)
It's not explained in the docs, but I suspect it has to do with what low-level library function is ultimately called:
call(["ls", "-l"]) --> execlp("ls", "-l")
^^^^^^^^^^ ^^^^^^^^^^
call("ls -l", shell=True) --> execlp("sh", "-c", "ls -l")
^^^^^^^ ^^^^^^^
call(["ls", "-l"], shell=True) --> execlp("sh", "-c", "ls", "-l")
# which can be tried from command line:
sh -c ls -l
# result is a list of files without details, -l was ignored.
# see sh(1) man page for -c string syntax and what happens to further arguments.

subprocess.run simple scenario fails

I am trying to run python subprocess.run function to execute following command:
pdftoppm -jpeg -f 1 -scale-to 200 data/andromeda.pdf and-page
pdftoppm - is part of poppler utility and it generates images from pdf files.
File data/andromeda.pdf exists. Folder data is on same level with python script and/or where I run command from.
Command basically will generate a jpeg file, from page 1 (-f 1) 200px wide (-scale-to) from given file of and-page-1.jpeg format (so called ppmtroot).
Long story short: from command line it works as expected i.e. if I call the above command either from zsh or bash shell, manually - it generates thumbnail as expected. However if I run it from python subprocess module - it fails it returns 99 error code!
Following is python code (file name is sc_02_thumbnails.py):
import subprocess
import sys
def main(filename, ppmroot):
cmd = [
'pdftoppm',
'-f 1',
'-scale-to 200',
'-jpeg',
filename,
ppmroot
]
result = subprocess.run(
cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE
)
if result.returncode:
print("Failed to generate thumbnail. Return code: {}. stderr: {}".format(
result.returncode,
result.stderr
))
print("Used cmd: {}".format(' '.join(cmd)))
sys.exit(1)
else:
print("Success!")
if __name__ == "__main__":
if len(sys.argv) > 2:
filename = sys.argv[1]
ppmroot = sys.argv[2]
else:
print("Usage: {} <pdffile> <ppmroot>".format(sys.argv[0]))
sys.exit(1)
main(filename, ppmroot)
And here is repo which includes data/andromeda.pdf file as well.
I call my script with as (from zsh):
$ chmod +x ./sc_02_thumbnauils.py
$ ./sc_02_thumbnails.py data/andromeda.pdf and-page
and ... thumbnail generating fails!
I have tried executing python script from both, from zsh and bash shells :(
What I am doing wrong?

The quoting is wrong, you should have '-f', '1', etc

How can I use an executable jar file with a mainClass in python? [duplicate]

I have been looking for an answer for how to execute a java jar file through python and after looking at:
Execute .jar from Python
How can I get my python (version 2.5) script to run a jar file inside a folder instead of from command line?
How to run Python egg files directly without installing them?
I tried to do the following (both my jar and python file are in the same directory):
import os
if __name__ == "__main__":
os.system("java -jar Blender.jar")
and
import subprocess
subprocess.call(['(path)Blender.jar'])
Neither have worked. So, I was thinking that I should use Jython instead, but I think there must a be an easier way to execute jar files through python.
Do you have any idea what I may do wrong? Or, is there any other site that I study more about my problem?

I would use subprocess this way:
import subprocess
subprocess.call(['java', '-jar', 'Blender.jar'])
But, if you have a properly configured /proc/sys/fs/binfmt_misc/jar you should be able to run the jar directly, as you wrote.
So, which is exactly the error you are getting?
Please post somewhere all the output you are getting from the failed execution.

This always works for me:
from subprocess import *
def jarWrapper(*args):
process = Popen(['java', '-jar']+list(args), stdout=PIPE, stderr=PIPE)
ret = []
while process.poll() is None:
line = process.stdout.readline()
if line != '' and line.endswith('\n'):
ret.append(line[:-1])
stdout, stderr = process.communicate()
ret += stdout.split('\n')
if stderr != '':
ret += stderr.split('\n')
ret.remove('')
return ret
args = ['myJarFile.jar', 'arg1', 'arg2', 'argN'] # Any number of args to be passed to the jar file
result = jarWrapper(*args)
print result

I used the following way to execute tika jar to extract the content of a word document. It worked and I got the output also. The command I'm trying to run is "java -jar tika-app-1.24.1.jar -t 42250_EN_Upload.docx"
from subprocess import PIPE, Popen
process = Popen(['java', '-jar', 'tika-app-1.24.1.jar', '-t', '42250_EN_Upload.docx'], stdout=PIPE, stderr=PIPE)
result = process.communicate()
print(result[0].decode('utf-8'))
Here I got result as tuple, hence "result[0]". Also the string was in binary format (b-string). To convert it into normal string we need to decode with 'utf-8'.

With args: concrete example using Closure Compiler (https://developers.google.com/closure/) from python
import os
import re
src = test.js
os.execlp("java", 'blablabla', "-jar", './closure_compiler.jar', '--js', src, '--js_output_file', '{}'.format(re.sub('.js$', '.comp.js', src)))
(also see here When using os.execlp, why `python` needs `python` as argv[0])

How about using os.system() like:
os.system('java -jar blabla...')
os.system(command)
Execute the command (a string) in a subshell. This is implemented by calling the Standard C function system(), and has the same limitations. Changes to sys.stdin, etc. are not reflected in the environment of the executed command.