Here's my copy.py:
from subprocess import call
call("copy p2.txt p3.txt")
If in command prompt I use
copy p2.txt p3.txt it copies fine.
but when I use python copy.py it gives me:
Traceback (most recent call last):
File "copy.py", line 2, in <module>
call("copy p2.txt p3.txt")
File "C:\Python27\lib\subprocess.py", line 493, in call
return Popen(*popenargs, **kwargs).wait()
File "C:\Python27\lib\subprocess.py", line 679, in __init__
errread, errwrite)
File "C:\Python27\lib\subprocess.py", line 896, in _execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified
If I replace the python call to copy with xcopy, it works fine.
Why would this be?
When subprocess.call()ing a command like in a shell, you'll need to specify shell=True as well.
from subprocess import call
call("copy p2.txt p3.txt", shell=True)
The reason you need to use shell=True in this case is that the copy command in Windows is not actually an executable but a built-in command of the shell (if memory serves right). xcopy on the other hand is a real executable (in %WINDIR%\System32, which is usually in the %PATH%), so it can be called outside of a cmd.exe shell.
In this particular instance, shutil.copy or shutil.copy2 might be viable alternatives.
Please note that using shell=True can lead to security hazards, or as the docs put it:
Warning: Using shell=True can be a security hazard. See the warning under Frequently Used Arguments for details.
Related
I can't run the wonderful PypeR (r to python interface) anymore.
I can import it, but as I try to run it it crashes.
I suspect it is because I installed El Capitan OSX.
I tried to install update pypeR with no success.
when I run it with:
e.g.
r = R()
that's the error that I get.
Traceback (most recent call last):
File "<pyshell#3>", line 1, in <module>
a = R()
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pyper.py", line 600, in __init__
self.__dict__['prog'] = Popen(RCMD, stdin=PIPE, stdout=PIPE, stderr=return_err and _STDOUT or childstderr, startupinfo=info)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py", line 1335, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
does anyone have a clue on how to solve this problem?
update:
if I run it from a shell instead of Idle it works.
I really can't see why.
Python's version is exactly the same, built at the same time.
It looks like PypeR cannot find R to run. Most likely the R command is not in the search path for command ($PATH) when you are using idle. One way is to explicitly point out which R command to use, e.g., if the R command is located in /usr/local/bin, you may use
r = R(RCMD="/usr/local/bin/R")
Of course, it is best if you can add R's path for idle environment.
I have an executable file that I'd like to run from Python. I define a path variable pointing at it:
>>> path = '/root/Cognos/Cognos/linuxi38664h/issetupnx'
I verify that I am in fact pointing at a file and not a directory:
>>> from os.path import isdir, isfile
>>> isdir(path)
False
>>> isfile(path)
True
But as soon as I try to run the executable file via subprocess.call...
>>> from subprocess import call
>>> call([path])
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib64/python2.7/subprocess.py", line 524, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__
errread, errwrite)
File "/usr/lib64/python2.7/subprocess.py", line 1308, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
It tells me the file doesn't exist now.
The only possibility I can think of is that maybe the executable itself is being found and run fine, but the executable is failing saying that something it needs (what?) isn't found. I'm not sure how I would test this theory, though... or even if it's possible.
Another possibility might be some kind of permissions issue? Although I can't think of why I would have proper permissions to see the file but then I suddenly wouldn't be able to see it the moment I try running it.
Instead of using call, I should have used check_output. Then the error would have included all of the messages printed to stdout and stderr.
path = '/root/Cognos/Cognos/linuxi38664h/issetupnx'
from subprocess import check_output
check_output([path])
Then I would have gotten a more detailed message about how it failed to load shared libraries.
execute this code as root:
import subprocess as sp
path = '/root/Cognos/Cognos/linuxi38664h/issetupnx'
proc = sp.Popen([path],stdin=sp.PIPE)
proc.communicate()
I want to us traffic control of the Linux kernel with Python to simulate lost, corrupt and duplicate packages. I'm already able to configure this with the Linux Terminal, but I have to use python.
bash cmd works:
tc filter show dev eth1
python doesn't work:
>>> subprocess.call(["tc", "filter", "show", "dev", "eth1"])
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.6/subprocess.py", line 470, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.6/subprocess.py", line 623, in __init__
errread, errwrite)
File "/usr/lib/python2.6/subprocess.py", line 1141, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
Thanks.
The python subprocess doesn't know about your shell environment. So provide absolute path to your command, something like:
subprocess.call(["/sbin/tc", "filter", "show", "dev", "eth1"])
find the exact location with command which tc in your shell.
The basic way if you don't need any special control is to use os.system() to launch a command as if you were in your shell command line (no need to specify the full path if in your $PATH):
import os
os.system("tc filter show dev eth1")
This should work exactly as if you did in your cmd:
$ tc filter show dev eth1
So I have a python script that produces a networkx graph and exports it as .graphml and I want script to also be able to open cytoscape with the network loaded without any work on the users part. I understand:
cytoscape.bat -N C:\Somepath\with\a\networkx.graphml
and it works fine when I use it. As does:
cd "C:\Program Files\Cytoscape_v3.0.0"
cytoscape.bat
However, I can't seem to get either os.system or subprocess to run properly, my current configuration is:
p = subprocess.Popen("cytoscape.bat", cwd="C:/Program Files/Cytoscape_v3.0.0")
stdout, stderr = p.communicate()
But the throws a file-not-found-exception.
I've been reading up on other stackoverflow posts and python docs on running .bats and doing cmd operations, and can get the basics to work. However, this seems somewhat more complicated, and I'm not sure where I'm going wrong!
As requested I exceptions:
The file not found and incorrect path exceptions:
Traceback (most recent call last):
File "CytoScapeExporter.py", line 219, in <module>
p = subprocess.Popen("cytoscape.bat", cwd="\"C:/Program Files/Cytoscape_v3.0
.0\"")
File "C:\Python27\lib\subprocess.py", line 679, in __init__
errread, errwrite)
File "C:\Python27\lib\subprocess.py", line 896, in _execute_child
startupinfo)
WindowsError: [Error 267] The directory name is invalid
Traceback (most recent call last):
File "CytoScapeExporter.py", line 219, in <module>
p = subprocess.Popen("cytoscape.bat", cwd="C:/Program Files/Cytoscape_v3.0.0
")
File "C:\Python27\lib\subprocess.py", line 679, in __init__
errread, errwrite)
File "C:\Python27\lib\subprocess.py", line 896, in _execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified
A slightly different JVM error, it is produced by this code:
os.system("\"C:/Program Files/Cytoscape_v3.0.0/cytoscape.bat\"")
Error: missing `server' JVM at `C:\Program Files (x86)\Java\jre7\bin\server\jvm.
dll'.
Please install or use the JRE or JDK that contains these missing components.
C:\Program Files\Cytoscape_v3.0.0
From the documentation:
"If cwd is not None, the child’s current directory will be changed to cwd before it is executed. Note that this directory is not considered when searching the executable, so you can’t specify the program’s path relative to cwd."
You have to pass the full path of the command to subprocess.Popen.
So i am running into a problem using subprocess.call() and i think i may just be calling it wrong. I am using:
subprocess.call('testingosfile.py')
and i get the traceback:
Traceback (most recent call last):
File "<pyshell#14>", line 1, in <module>
subprocess.call('testingosfile.py')
File "C:\Python27\lib\subprocess.py", line 493, in call
return Popen(*popenargs, **kwargs).wait()
File "C:\Python27\lib\subprocess.py", line 679, in __init__
errread, errwrite)
File "C:\Python27\lib\subprocess.py", line 893, in _execute_child
startupinfo)
WindowsError: [Error 193] %1 is not a valid Win32 application
and the contents of testingosfile.py is:
print "hello world!"
raw_input('....')
how do i manage to get this running?
Thank you in advance for your replies.
The error message makes perfect sense - with subprocess, you can only start an executable. So, to fix it, you should start an executable. Specifically, you should start the Python interpreter and tell it to run your script. Something like
subprocess.call(['python.exe', 'testingosfile.py'])
should work, although you might have to provide the full path to the Python interpreter (I can't test at the moment).
However, have you considered importing testingosfile.py instead? Whenever you import a Python script, all the commands in that script are run. Using
import testingosfile
inside a function in order to execute the commands would be poor style, but you could package up the useful commands of testingosfile.py into some function. Then, you could use
import testingosfile
at the top of your main script, and just call that function whenever you want to print Hello World and get the user's input.
try subprocess.call("myfile.ext", shell=True)