Develop Reference

Not able to run command via wsl.exe

I'm trying to run this commands from a python script:
def raw(path_avd_py, path_avd, snp_name, out_file):
if OS == 'Windows':
cmd_raw = f"wsl.exe -e sh -c 'python3 {path_avd_py} -a {path_avd}
-s {snp_name} -o {out_file}'"
else:
cmd_raw = f'python3 {path_avd_py} -a {path_avd} -s {snp_name} -o {out_file}'
subprocess.Popen(cmd_raw, shell=True)
time.sleep(25)
return None
def idiffer(i_path, raw_1, raw_2, path, state):
if OS == 'Windows':
cmd_idiff = f"wsl.exe -e sh -c 'python3 {i_path} {raw_1} {raw_2}'"
[...]
file = os.path.join(path, f'{state}.idiff')
with open(file, 'w') as f:
subprocess.Popen(cmd_idiff, stdout=f, text=True)
If im executing cmd_raw with subprocess.run from a python-shell (Powershell), things are working. If im try running this via script, this exception occurs, using different shells:
-e sh: avdecrypt-master\avdecrypt.py: 1: Syntax error: Unterminated quoted string
-e bash: avdecrypt-master\avdecrypt.py: -c: line 0: unexpected EOF while looking for matching `''
avdecrypt-master\avdecrypt.py: -c: line 1: syntax error: unexpected end of file
I already tried os.system, os.run([list]) no change.
Thanks for the help!

For those who have a similar question, I found a solution, which is working for me:
Apparently calling scripts with some argv has to be in one single quotation mark and can be executed via run (in my case important, because the process has to be terminated). This leads to a form like:
cmd = ['wsl.exe', '-e', 'bash', '-c', '-a foo -b bar [...]']
subprocess.run(cmd, shell=True)
Lib shlex is helping here and formatting the strings like subprocess is needing it:
cmd_finished = shlex.split(cmd)
https://docs.python.org/3/library/shlex.html

/bin/sh: -c: line 0: syntax error near unexpected token `('

arg2 = f'cat <(grep \'#\' temp2.vcf) <(sort <(grep -v \'#\' temp2.vcf) | sortBed -i - | uniq ) > out.vcf'
print(arg2)
try:
subprocess.call(arg2,shell=True)
except Exception as error:
print(f'{error}')
While I'm running this I get the following error:
/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `cat <(grep '#' temp2.vcf) <(sort <(grep -v '#' temp2.vcf) | sortBed -i - | uniq ) > Out.vcf'
but when I run in the command line it works.

Python's call() function invokes the command with sh by default. The process substitution syntax is supported by bash, but not by sh.
$ sh -c "cat <(date)"
sh: -c: line 0: syntax error near unexpected token `('
sh: -c: line 0: `cat <(date)'
$ bash -c "cat <(date)"
Mon Mar 14 11:12:48 PDT 2022
If you really need to use the bash-specific syntax, you should be able to specify the shell executable (but I have not tried this):
subprocess.call(arg2, shell=True, executable='/bin/bash')

The immediate error is that your attempt uses Bash-specific syntax. You can work around that with an executable="/bin/bash" keyword argument; but really, why are you using a complex external pipeline here at all? Python can do all these things except sortBed natively.
with open("temp2.vcf", "r"
) as vcfin, open("out.vcf", "w") as vcfout:
sub = subprocess.Popen(
["sortBed", "-i", "-"],
text=True,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE)
for line in vcfin:
if "#" in line:
vcfout.write(line)
else:
sub.stdin.write(line)
subout, suberr = sub.communicate()
if suberr is not None:
sys.stderr.write(suberr)
seen = set()
for line in subout.split("\n"):
if line not in seen:
vcfout.write(line + "\n")
seen.add(line)
The Python reimplementation is slightly clunkier (and untested, as I don't have sortBed or your input data) but that also means it's more obvious where to change something if you want to modify it.

Syntax error when trying to create and print out a series of command-line commands

I'm trying to write a Python 3 script that will print out a series of command-line commands using variables.
Here's an example of the commands I'm trying to replicate:
filemorph cp testBitmap_1 gs://mapper-bitmap/TestBitmaps
filemorph cp gs://mapper-bitmap/TestBitmaps/testBitmap_1.svs /mnt/pixels/bitmaps
mkdir -p /mnt/pixels/1024/testBitmap_1
image_rotate --image_rotate-progress bitsave "/mnt/pixels/bitmaps/testBitmap_1.svs" /mnt/pixels/1024/testBitmap_1/ --pixel-size 1024
filemorph -m rsync -d -r /mnt/pixels/1024/testBitmap_1 gs://mapper-pixels/1024/testBitmap_1
Whenever I run my script, I get this error:
G:\Projects\Python\BitmapBot
λ python bitmapbot.py
File "bitmapbot.py", line 26
commands = """\
^
SyntaxError: invalid syntax
I checked all my intentations and they all seem correct so I'm not sure why it's giving me an error.
I'm not quite sure what I'm doing wrong.
If anyone sees anything, please let me know.
Thanks!
Oh here's the script:
import os
# define variables
data = dict(
Bitmap_Name = 'testBitmap_1.svs',
Bitmap_Title = 'testBitmap_1',
Bitmap_Folder_Name = 'TestBitmaps',
Cloud_Bitmap_Directory = 'gs://mapper-bitmap/',
Pixel_Bitmap_Engine = '/mnt/pixels/bitmaps',
Local_Bitmap_Directory = '',
Local_Pixel_Directory = '/mnt/pixels/1024/',
Cloud_Pixel_Directory = 'gs://mapper-pixels/1024/'
# create commands with Python:
commands = """\
filemorph cp {Bitmap_Name} {Cloud_Bitmap_Directory}/{Bitmap_Folder_Name}
filemorph cp {Cloud_Bitmap_Directory}/{Bitmap_Folder_Name}/{Bitmap_Name} {Pixel_Bitmap_Engine}
mkdir -p {Local_Pixel_Directory}/{Bitmap_Title}
image_rotate --image_rotate-progress bitsave {Pixel_Bitmap_Engine}/{Bitmap_Name} {Local_Pixel_Directory}/{Bitmap_Title}/ --pixel-size 1024
filemorph -m rsync -d -r {Local_Pixel_Directory}/{Bitmap_Title} {Cloud_Pixel_Directory}/{Bitmap_Title}
"""
# loop through commands and print
for command in commands.splitlines():
command = command.format(**data) # populate command
# os.system(command) # execute command
print(command)

You never closed the bracket after data = dict(…

Run Powershell command in Python (SyntaxError: invalid syntax)

I'm trying to execute a code on the system that downloads a file from direct link to %appdata% dir on Windows.
My code:
def downloadfile():
mycommand = "powershell -command "$cli = New-Object System.Net.WebClient;$cli.Headers['User-Agent'] = {};$cli.DownloadFile('https://drive.google.com/uc?export=download&id=19LJ6Otr9p_stY5MLeEfRnA-jD8xXvK3m', '%appdata%\putty.exe')""
down = subprocess.call(mycommand)
downloadfile()
But I get this error:
File "searchmailfolder.py", line 4
mycommand = "powershell -command "$cli = New-Object System.Net.WebClient;$cli.Headers['User-Agent'] = 'myUserAgentString';$cli.DownloadFile('https://drive.google.com/uc?export=download&id=19LJ6Otr9p_stY5MLeEfRnA-jD8xXvK3m', '%appdata%\putty.exe')""
^
SyntaxError: invalid syntax

Hope this helps.Import subprocess and sys. And then try something like this
"command = subprocess.Popen(["powershell.exe","user_command.ps1"],stdout=sys.stdout)
command.communicate()"
Try putting your code into the .ps1 file

Failed to execute command line argument from python script

I am trying to run a command line argument through python script. Script triggers the .exe but it throws an error as System.IO.IOException: The handle is invalid..
Following is my code :
import os , sys , os.path
from subprocess import call
import subprocess, shlex
def execute(cmd):
"""
Purpose : To execute a command and return exit status
"""
process = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(result, error) = process.communicate()
rc = process.wait()
if rc != 0:
print "Error: failed to execute command:",cmd
print error
return result
found_alf = r"C:\AniteSAS\ResultData\20170515\Run01\1733200515.alf"
filter_alvf = r"C:\Users\sshaique\Desktop\ALF\AniteLogFilter.alvf"
command = str(r'ALVConsole.exe -e -t -i ' + '\"'+found_alf+'\"' + ' --ffile ' + '\"'+filter_alvf+'\"')
print command
os.chdir('C:\Program Files\Anite\LogViewer\ALV2')
print os.getcwd()
print "This process detail: \n", execute(command)
Output is as follows :
ALVConsole.exe -e -t -i "C:\AniteSAS\ResultData\20170515\Run01\1733200515.alf" --ffile "C:\Users\sshaique\Desktop\ALF\AniteLogFilter.alvf"
C:\Program Files\Anite\LogViewer\ALV2
This process detail:
Error: failed to execute command: ALVConsole.exe -e -t -i "C:\AniteSAS\ResultData\20170515\Run01\1733200515.alf" --ffile "C:\Users\sshaique\Desktop\ALF\AniteLogFilter.alvf"
Unhandled Exception: System.IO.IOException: The handle is invalid.
at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
at System.Console.GetBufferInfo(Boolean throwOnNoConsole, Boolean& succeeded)
at ALV.Console.CommandLineParametersHandler.ConsoleWriteLine(String message, Boolean isError)
at ALV.Console.CommandLineParametersHandler.InvokeActions()
at ALV.Console.Program.Main(String[] args)
When I copy the command line argument from the above output and run manually from cmd it works fine.
ALVConsole.exe -e -t -i "C:\AniteSAS\ResultData\20170515\Run01\1733200515.alf" --ffile "C:\Users\sshaique\Desktop\ALF\AniteLogFilter.alvf"
I am using Windows 7 and Python 2.7.13 for. Please suggest overcoming this issue.
EDIT:
I have also tried to pass command as a list s as per below code but the issue remains the same.
command = str(r'ALVConsole.exe -e --csv -i ' + '\"'+found_alf+'\"' + ' --ffile ' + '\"'+filter_alvf+'\"')
s=shlex.split(command)
print s
print "This process detail: \n", execute(s)

Based on your error messages I think that this problem is with ALVConsole.exe, not your Python script.
When you redirect the output, ALVConsole.exe tries to do something to the console (like setting cursor position, or getting the size of the terminal) but fails like this.
Is there a flag to ALVConsole.exe that modifies the output to a machine-readable version? I wasn't able to find the documentation for this program.