grep: broken pipe error python 2.2

Question

I'm taking in a bunch of scripts, and creating a wrapper for them in python. I didn't create the scripts that were given to me. Currently I'm working with python 2.2, and the shell I'm using is a csh shell.

When I run the script in the following manner:

>> setenv some_var '/some/path/'
>> <some more setenv>
>> ./script -flag >& log.txt < /dev/null &

It run's perfectly fine.

The issue arises when I use a bash wrapper to call my python wrapper. My bash script (analysis.sh) is as follows:

#!/bin/bash
#environment variables
ENV1='/path/for/env1'
ENV2='/path/for/env2'

export ENV1
export ENV2

./run_analysis.py $@
exit

In my python file, all I'm basically doing is performing

....
os.system(script_path + script_name + script_flag)
....

Whenever I run the script in the following manner on csh shell:

./analysis.sh -flag script_name >& log.txt < /dev/null &

The script all of a sudden gives me a bunch of broken pipe errors ("grep: writing output: Broken pipe"). I know that the script does use a lot of grep. I just don't understand why these errors would pop up when I perform redirection. In python 2.2, only 'os' and 'commands' module exist. I'm forced to use these constraints.

Thank you.

score 0 · Answer 1 · answered Jul 17 '12 at 16:12

0

As soon as your script has written it's data and exited, it looks like grep (somewhere) is still expecting to be able to read from the pipe, which no longer exists as your script has excited - hence the broken pipe.

answered Jul 17 '12 at 16:12

Jon Clements

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So are you saying to get rid of the "exit" in the bash script? Why would it reach this statement? Wouldn't only reach here once ./run_analysis finished? – de1337ed Jul 17 '12 at 16:24
would I need to perform some sort of waitpid in the python script? – de1337ed Jul 17 '12 at 16:28

score 0 · Answer 2 · answered Jul 18 '12 at 06:20

0

I think the problem is that the environment variables set by the bash script are not being passed on to the python script's os.system() call. Consider setting those envars from within the python script. Itself.

answered Jul 18 '12 at 06:20

ZaSter

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score 0 · Answer 3 · answered Jul 19 '12 at 19:48

0

Figured it out.

I had to run the redirection command inside the os.system() call. It wasn't working if I ran it outside.

my final line was:

os.system(script_dir + script + script_flag + " >> log.txt 2>&1 < /dev/null &")

Thanks for help though.

answered Jul 19 '12 at 19:48

de1337ed

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grep: broken pipe error python 2.2

3 Answers3

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