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1 #!/usr/bin/python
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2
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3 """
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4 Wrapper that executes a program with its arguments but reports standard error
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5 messages only if the program exit status was not 0. This is useful to prevent
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6 Galaxy to interpret that there was an error if something was printed on stderr,
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7 e.g. if this was simply a warning.
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8 Example: ./stderr_wrapper.py myprog arg1 -f arg2
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9 Author: Florent Angly
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10 """
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11
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12 import sys, subprocess
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13
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14 assert sys.version_info[:2] >= ( 2, 4 )
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15
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16 def stop_err( msg ):
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17 sys.stderr.write( "%s\n" % msg )
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18 sys.exit()
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19
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20 def __main__():
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21 # Get command-line arguments
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22 args = sys.argv
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23 # Remove name of calling program, i.e. ./stderr_wrapper.py
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24 args.pop(0)
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25 # If there are no arguments left, we're done
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26 if len(args) == 0:
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27 return
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28
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29 # If one needs to silence stdout
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30 args.append( ">" )
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31 args.append( "/dev/null" )
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32
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33 #cmdline = " ".join(args)
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34 #print cmdline
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35 try:
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36 # Run program
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37 proc = subprocess.Popen( args=args, shell=False, stderr=subprocess.PIPE )
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38 returncode = proc.wait()
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39 # Capture stderr, allowing for case where it's very large
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40 stderr = ''
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41 buffsize = 1048576
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42 try:
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43 while True:
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44 stderr += proc.stderr.read( buffsize )
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45 if not stderr or len( stderr ) % buffsize != 0:
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46 break
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47 except OverflowError:
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48 pass
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49 # Running Grinder failed: write error message to stderr
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50 if returncode != 0:
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51 raise Exception, stderr
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52 except Exception, e:
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53 # Running Grinder failed: write error message to stderr
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54 stop_err( 'Error: ' + str( e ) )
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55
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56
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57 if __name__ == "__main__": __main__()
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