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.
Related
I have installed exiftool (https://smarnach.github.io/pyexiftool/) and I am able to import the library, but I get the following error when trying to run the test data just to see if it works.
ERROR: test_get_metadata (__main__.TestExifTool)
----------------------------------------------------------------------
Traceback (most recent call last):
File "C:\Program Files\Python36\Lib\site-
packages\pyexiftool\test\test_exiftool.py", line 66, in test_get_metadata
with self.et:
File "C:\Program Files\Python36\lib\site-packages\exiftool.py", line 191, in __enter__
self.start()
File "C:\Program Files\Python36\lib\site-packages\exiftool.py", line 174, in start
stderr=devnull)
File "C:\Program Files\Python36\lib\subprocess.py", line 709, in __init__
restore_signals, start_new_session)
File "C:\Program Files\Python36\lib\subprocess.py", line 997, in _execute_child
startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
I also did run the setup code that is in the exiftool folder and still no luck. I think it might be a library issue or path or the (init.py) file, but I've tried several ways and so I'm here to ask if anyone else has a solution or ideas for me to try and fix it.
I'm running Python 3.6.6 and have tried other versions.
(I can run exiftool in command line, but I have encoded BASE64 images that exiftool doesnt work in command line to fully decode.)
Thank you StarGeek! The problem was that I didn't have the exiftool command tool (the separate application of exiftool) in the right PATH env variable. Once I added the application to the PATH env variables i got it to work. Also in the python exiftool code at line 70 it says that you have to have it in the path or direct it to the executable, that I had missed. Thanks again!
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()
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.
i installed python-nmap-0.1.4.tar.gz in pyhton27 in window. When i ran this http://codepad.org/vTu1Uw7I script, i got a few error. What those error mean?. Are those error happened because i used python-nmap-0.1.4.tar.gz in windows?.
Here is the error
Traceback (most recent call last):
File "C:/Python27/Lib/site-packages/nmap/run-nmap.py", line 3, in <module>
nm = nmap.PortScanner() # instantiate nmap.PortScanner object
File "C:/Python27/Lib/site-packages/nmap\nmap.py", line 118, in __init__
p = subprocess.Popen(['nmap', '-V'], bufsize=10000, stdout=subprocess.PIPE)
File "C:\Python27\lib\subprocess.py", line 711, in __init__
errread, errwrite)
File "C:\Python27\lib\subprocess.py", line 948, in _execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified
Here is the subprocess.py script
http://codepad.org/SpbV8muR
Seems that python-nmap is meant to be run on Linux… but you can still try to make it work on Windows. The problem is that it is trying to call nmap but the binary is not found in PATH.
Add the directory with nmap executable to you PATH variable. Here is a HOWTO.
I am trying to run an existing python code, and having issues with it.
This program required npm program installed and which is installed at C:\Program Files\nodejs\npm in my computer. When I run the following code, as a part of the whole program, it throws errors.
def popen_results(args):
proc = subprocess.Popen(args, stdout=subprocess.PIPE)
return proc.communicate()[0]
def installed():
"""docstring for npm_installed"""
return popen_results(["which", "npm"]).strip()
This is the complete stack of the error thrown--
Checking for node and dependencies
Traceback (most recent call last):
File "deploy\deploy.py", line 344, in <module>
main()
File "deploy\deploy.py", line 287, in main
if not check_deps():
File "deploy\deploy.py", line 201, in check_deps
return npm.check_dependencies()
File "C:\Documents and Settings\Sunil\workspace\khan\src\deploy\npm.py", line
38, in check_dependencies
if not installed():
File "C:\Documents and Settings\Sunil\workspace\khan\src\deploy\npm.py", line
13, in installed
return popen_results(["which", "npm"]).strip()
File "C:\Documents and Settings\Sunil\workspace\khan\src\deploy\npm.py", line
8, in popen_results
proc = subprocess.Popen(args, stdout=subprocess.PIPE)
File "C:\python25\lib\subprocess.py", line 594, in __init__
errread, errwrite)
File "C:\python25\lib\subprocess.py", line 822, in _execute_child
startupinfo)
WindowsError: [Error 2] The system cannot find the file specified
I agree with martineau, it is unable to find which. The script may have been written with the assumption it was going to be run in a unix environment which would most likely have the "which" command available and in the default PATH. Since it looks like you're running this on Windows, I don't think it's going to work.
It looks like there is some alternatives to which on Windows though, discussed here: Is there an equivalent to which on Windows?