Develop Reference

Incorrect path to my file when I try to restart it

I am trying to execute this:
os.execv(sys.executable, ['python'] + sys.argv)
The result I am getting:
C:\Program Files\Python310\python.exe: can't find '__main__' module in 'c:\\Users\\user\\OneDrive\\Рабочий'
As you can see, the path after the 'module in' words is improper. I printed sys.argv and got:
c:/Users/user/OneDrive/Рабочий стол/myfolder/file.py

This is how to os.execv into another program passed in the command line:
# as execv_argv.py
import os
import sys
os.execv(sys.executable, [sys.executable] + sys.argv[1:])
and call with
python execv_argv.py "second exec.py"
Note os.execv with full sys.argv will call the parent again forever.

How can os.popen take argument externaly to run another script

I am trying to write a python CLI program using module python cmd. When I try to execute another python script in my CLI program my objective is I have some python script in other folder and CLI program in other folder. I am trying to execute those python script using CLI program.
Below is the os.popen method used to execute other script there is CLI program:
import cmd
import os
import sys
class demo(cmd.Cmd):
def do_shell(self,line,args):
"""hare is function to execute the other script"""
output = os.popen('xterm -hold -e python %s' % args).read()
output(sys.argv[1])
def do_quit(self,line):
return True
if __name__ == '__main__':
demo().cmdloop()
and hare is error:
(Cmd) shell demo-test.py
Traceback (most recent call last):
File "bemo.py", line 18, in <module>
demo().cmdloop()
File "/usr/lib/python2.7/cmd.py", line 142, in cmdloop
stop = self.onecmd(line)
File "/usr/lib/python2.7/cmd.py", line 221, in onecmd
return func(arg)
TypeError: do_shell() takes exactly 3 arguments (2 given)
there is some link to other cmd CLI program
1 = cmd – Create line-oriented command processors
2 = Console built with Cmd object (Python recipe)
and some screen shot's for more information:
Please run above code in your system.

As specified in the doc:
https://pymotw.com/2/cmd/index.html
do_shell is defined as such:
do_shell(self, args):
But you are defining it as
do_shell(self, line, args):
I think the intended use is define it as specified from the documentation.
I ran your code and followed your example. I replicated your error. I then, as specified in the documentation for do_shell, I changed the method to the as expected:
do_shell(self, args):
From there, the sys module was missing, so you need to import that as well (unless you did not copy it from your source). After that, I got an error for index out of range, probably because of the expectation of extra parameters needing to be passed.
Furthermore, because you are talking about Python scripts, I don't see the need for the extra commands you are adding, I simply changed the line to this:
output = os.popen('python %s' % args).read()
However, if there is a particular reason you need the xterm command, then you can probably put that back and it will work for your particular case.
I also, did not see the use case for this:
output(sys.argv[1])
I commented that out. I ran your code, and everything worked. I created a test file that just did a simple print and it ran successfully.
So, the code actually looks like this:
def do_shell(self, args):
"""hare is function to execute the other script"""
output = os.popen('python %s' % args).read()
print output
The full code should look like this:
import cmd
import os
import sys
class demo(cmd.Cmd):
def do_shell(self, args):
"""hare is function to execute the other script"""
output = os.popen('python %s' % args).read()
print output
def do_quit(self,line):
return True
if __name__ == '__main__':
demo().cmdloop()

Different results when running in python interpreter vs. script file

I am trying to use bash functions inside my python script to allow me to locate a specific directory and then grep a given file inside the directory. The catch is that I only have part of the directory name, so I need to use the bash function find to get the rest of the directory name (names are unique and will only ever return one folder)
The code I have so far is as follows:
def get_tag(part_of_foldername):
import subprocess
import os
p1 = subprocess.Popen(["find", "/path/to/directory", "-maxdepth", "1", "-name", "%s.*" % part_of_foldername, "-type", "d"], stdout=subprocess.PIPE)
directory = p1.communicate()[0].strip('\n')
os.chdir(directory)
p2 = subprocess.Popen(["grep", "STUFF_", ".hgtags"], stdout=subprocess.PIPE)
tag = p2.comminucate()[0].strip('\n')
return tag
Here is what's really strange. This code works when you enter it line by line into interactive, but not when it's run thru a script. It also works when you import the script file into interactive and call the function, but not when it's called by the main function. The traceback I get from running the script straight is as follows:
Traceback (most recent call last):
File "./integration.py", line 64, in <module>
main()
File "./integration.py", line 48, in main
tag = get_tag(folder)
File "./integration.py", line 9, in get_date
os.chdir(directory)
OSError: [Errno 2] No such file or directory: ''
And it's called in the main function like this:
if block_dict[block][0]=='0':
tag = get_tag(folder)
with "folder" being previously defined as a string.
Please note we use python 2.6 so I can't use the module check_output unfortunately.

Have you tried using the glob module as opposed to find?
import glob
glob.glob("/path/to/directory/*/SomeDir/path/*")
You can look past multiple dirctories using **:
glob.glob("/path/**/SomeDir/path/*")
and that would match /path/to/your/SomeDir/path/file.

evidently p1.communicate()[0].strip('\n') is returning an empty string. are you really using the hardcoded value "/path/to/directory" as in your example?

Check the result of p1.communicate()[0]. It maybe empty string.
. in "%s.*" % part_of_foldername seems to be the cause.
UPDATE
Found typo: comminucate -> comminucate
def get_tag(part_of_foldername):
p1 = subprocess.Popen(["find", "/path/to/directory", "-maxdepth", "1", "-name", "*%s*" % part_of_foldername, "-type", "d"], stdout=subprocess.PIPE)
out, err = p1.communicate()
directory = out.split('\n')[0]
p1.wait()
if directory:
os.chdir(directory)
p2 = subprocess.Popen(["grep", "STUFF_", ".hgtags"], stdout=subprocess.PIPE)
out, err = p2.communicate()
p2.wait()
return out.rstrip('\n')

Python subprocess Exec format error

Sorry if this question is dumb. I am using python subprocess statement to call a .bat file in Ubuntu (Natty 11.04), however, I got error messages:
Traceback (most recent call last):
File "pfam_picloud.py", line 40, in <module>
a=subprocess.Popen(src2, shell=0)
File "/usr/lib/python2.7/subprocess.py", line 672, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1213, in _execute_child
raise child_exception
run this python file
$python pfam_picloud.py
Python code (pfam_picloud.py)
#!/usr/bin/python
#
met="wTest.dvf"
run="run_pfam.bat"
inp="pfam_input.PFA"
import os
import stat
import shutil
import subprocess
import string
import random
# Generate a random ID for file save
def id_generator(size=6, chars=string.ascii_uppercase + string.digits):
return ''.join(random.choice(chars) for x in range(size))
name_temp=id_generator()
cwd=os.getcwd()
src=cwd
src1=cwd+'/'+name_temp
if not os.path.exists(src1):
os.makedirs(src1)
else:
shutil.rmtree(src1)
os.makedirs(src1)
##
shutil.copy(src+"/"+run,src1)
shutil.copy(src+"/"+met,src1)
shutil.copy(cwd+"/pfam_pi.exe",src1)
shutil.copy(src+"/"+inp,src1)
#
src2=src1+"/run_pfam.bat"
os.chdir(src1)
a=subprocess.Popen(src2, shell=0)
a.wait()
bash file (run_pfam.bat)
#!/bin/sh
./pfam_pi.exe pfam_input.PFA
I can successfully run this bash file in Ubuntu. So I guess, I messed up something in my Python script. Could anyone give me some suggestions? Thanks for any inputs.
EDIT
the file pfam_pi.exe is a Linux executable. I compiled it in Ubuntu. Sorry for the confusion.
update
Well, I got different types of error now.
1. With #!/bin/sh, it said No such file or directory.
2. With /bin/sh, it said exec format error.
3. If I sent everything as arguments a=subprocess.Popen(['./pfam_pi.exe', 'inp', 'src1'], shell=0), it said end of line symbol error

Since feature requests to mark a comment as an answer remain declined, I copy the above solution here.
#Ellioh: Thanks for your comments. I found once I changed the shell=1, problem is solved. – tao.hong

Try running wine (you should have it installed) and pass pfam_pi.exe to it as a parameter. Maybe pfam_pi.exe is not a Linux executable. :-) Certainly, executable file extensions are not meaningful on Linux, but probably it really is a Windows program, otherwise I hardly can imagine it named pfam_pi.exe.
However, if it is a Linux executable, note subprocess.Popen accepts a list of args (the first element is the program itself), not a command line:
>>> import shlex, subprocess
>>> command_line = raw_input()
/bin/vikings -input eggs.txt -output "spam spam.txt" -cmd "echo '$MONEY'"
>>> args = shlex.split(command_line)
>>> print args
['/bin/vikings', '-input', 'eggs.txt', '-output', 'spam spam.txt', '-cmd', "echo '$MONEY'"]
>>> p = subprocess.Popen(args) # Success!

subprocess can't get the stdin input from other process

I use subprocess exchange data between two process
I edit a repeat.py file with:
this file is a example from http://www.doughellmann.com/PyMOTW/subprocess/
import sys
sys.stderr.write('repeater.py: starting\n')
sys.stderr.flush()
while True:
next_line = sys.stdin.readline()
if not next_line:
break
sys.stdout.write(next_line)
sys.stdout.flush()
sys.stderr.write('repeater.py: exiting\n')
sys.stderr.flush()
and run this file in ipython
In [1]: import subprocess
In [2]: f=subprocess.Popen(['python','~/repeat.py'],shell=True,stdin=subprocess.PIPE,stdout=subprocess.PIPE)
In [3]: f.stdin.write('teststs\n')
In [4]: f.communicate()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
NameError: name 'teststs' is not defined
Out[4]: ('', None)
why teststs is not defined?

You seem to be starting an interactive Python session instead of running repeat.py. Try removing shell=True, it doesn't make sense together with a list of parameters. (Using shell=True is almost always a bad idea, by the way.)

This works with some strange behavior at first 5 key-presses. I don't know why. After that if works fine, and we have access to ls -l, cd, previous commands when press UP, seems command line has full functionality.
#!/bin/python3
import subprocess
import sys
proc = subprocess.Popen(['bash'])
while True:
buff = sys.stdin.readline()
stdoutdata, stderrdata = proc.communicate(buff)
if( stdoutdata ):
print( stdoutdata )
else:
print('n')
break
Here is my similar question.