annotate stderr_wrapper.py @ 11:fa1fa683bcf1 default tip

Added tool_data_table_conf.xml.sample

#!/usr/bin/env python

"""
Wrapper that executes a program with its arguments but reports standard error
messages only if the program exit status was not 0. This is useful to prevent
Galaxy to interpret that there was an error if something was printed on stderr,
e.g. if this was simply a warning.
Example: ./stderr_wrapper.py myprog arg1 -f arg2
Author: Florent Angly
"""

import sys, subprocess

assert sys.version_info[:2] >= ( 2, 4 )

def stop_err( msg ):
    sys.stderr.write( "%s\n" % msg )
    sys.exit()

def __main__():
    # Get command-line arguments
    args = sys.argv
    # Remove name of calling program, i.e. ./stderr_wrapper.py
    args.pop(0)
    # If there are no arguments left, we're done
    if len(args) == 0:
        return
   
    # If one needs to silence stdout 
    #args.append( ">" )
    #args.append( "/dev/null" )

    #cmdline = " ".join(args)
    #print cmdline
    try:
        # Run program
        proc = subprocess.Popen( args=args, shell=False, stderr=subprocess.PIPE )
        returncode = proc.wait()
        # Capture stderr, allowing for case where it's very large
        stderr = ''
        buffsize = 1048576
        try:
            while True:
                stderr += proc.stderr.read( buffsize )
                if not stderr or len( stderr ) % buffsize != 0:
                    break
        except OverflowError:
            pass
        # Running Grinder failed: write error message to stderr
        if returncode != 0:
            raise Exception, stderr
    except Exception, e:
        # Running Grinder failed: write error message to stderr
        stop_err( 'Error: ' + str( e ) )


if __name__ == "__main__": __main__()