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1 #!/usr/bin/env python
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2
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3
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4 # borrowed from: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr and modified for use with Trinity tools.
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5
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6 """
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7 Wrapper that execute a program and its arguments but reports standard error
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8 messages only if the program exit status was not 0
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9 Example: ./stderr_wrapper.py myprog arg1 -f arg2
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10 """
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11
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12 import sys, subprocess, os
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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 TRINITY_BASE_DIR = ""
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17 if os.environ.has_key('TRINITY_HOME'):
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18 TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
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19 else:
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20 # Cicada Dennis added looking for the location of the Trinity program using the unix "which" utility.
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21 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
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22 try:
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23 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
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24 except:
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25 t, v, tb = sys.exc_info()
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26 sys.stderr.write("You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running this");
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27 raise t, v, tb
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28 else:
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29 output1, err1 = pipe1.communicate()
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30 # Take off the last part of the path (which is the Trinity command)
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31 TRINITY_BASE_DIR = "/".join(output1.split("/")[0:-1])
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32
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33 # get bindir
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34 bindir = sys.argv[0]
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35 bindir = bindir.split("/")
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36 if len(bindir) > 1:
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37 bindir.pop()
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38 bindir = "/".join(bindir)
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39 else:
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40 bindir = "."
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41
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42
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43 ## add locations of tools to path setting.
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44 TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt";
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45 for line in open(TOOL_PATHS_FILE):
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46 line = line.rstrip()
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47 os.environ['PATH'] += ":" + line
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48
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49
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50 def stop_err( msg ):
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51 sys.stderr.write( "%s\n" % msg )
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52 sys.exit()
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53
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54 def __main__():
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55 # Get command-line arguments
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56 args = sys.argv
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57 # Remove name of calling program, i.e. ./stderr_wrapper.py
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58 args.pop(0)
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59 # If there are no arguments left, we're done
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60 if len(args) == 0:
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61 return
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62
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63 # If one needs to silence stdout
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64 #args.append( ">" )
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65 #args.append( "/dev/null" )
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66
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67 args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]);
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68
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69 cmdline = " ".join(args)
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70
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71
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72
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73 try:
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74 # Run program
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75 err_capture = open("stderr.txt", 'w')
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76 proc = subprocess.Popen( args=cmdline, shell=True, stderr=err_capture, stdout=sys.stdout )
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77 returncode = proc.wait()
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78 err_capture.close()
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79
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80
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81 if returncode != 0:
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82 raise Exception
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83
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84 except Exception:
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85 # Running Grinder failed: write error message to stderr
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86 err_text = open("stderr.txt").readlines()
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87 stop_err( "ERROR:\n" + "\n".join(err_text))
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88
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89
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90 if __name__ == "__main__": __main__()
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