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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3
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4 """
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5 A wrapper script for running the MINE.jar commands.
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6 """
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7
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8 import sys, optparse, os, tempfile, subprocess, shutil
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9
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10 CHUNK_SIZE = 2**20 #1mb
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11
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12 BASE_NAME = "galaxy_mime_file.txt"
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13 JOB_ID = "galaxy_mine"
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14
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15 def cleanup_before_exit( tmp_dir ):
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16 if tmp_dir and os.path.exists( tmp_dir ):
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17 print os.listdir( tmp_dir )
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18 shutil.rmtree( tmp_dir )
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19
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20 def open_file_from_option( filename, mode = 'rb' ):
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21 if filename:
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22 return open( filename, mode = mode )
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23 return None
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24
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25
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26 def __main__():
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27 #Parse Command Line
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28 parser = optparse.OptionParser()
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29 parser.add_option( '-j', '--jar', dest='jar', action='store', type="string", help='Location of JAR file' )
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30 parser.add_option( '-i', '--infile', dest='infile', action='store', type="string", help='infile' )
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31 parser.add_option( '-m', '--master_variable', dest='master_variable', action='store', type="string", help='master_variable' )
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32 parser.add_option( '-v', '--cv', dest='cv', action='store', type="string", help='cv' )
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33 parser.add_option( '-e', '--exp', dest='exp', action='store', type="string", help='exp' )
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34 parser.add_option( '-c', '--c', dest='c', action='store', type="string", help='c' )
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35 parser.add_option( '-p', '--permute', dest='permute', action='store_true', default=False, help='permute' )
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36 parser.add_option( '-o', '--output_results', dest='output_results', action='store', type="string", help='output_results' )
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37 parser.add_option( '-l', '--output_log', dest='output_log', action='store', type="string", help='output_log' )
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38 parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' )
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39 parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' )
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40 (options, args) = parser.parse_args()
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41
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42 tmp_dir = tempfile.mkdtemp( prefix='tmp-MINE-' )
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43 tmp_input_name = os.path.join( tmp_dir, BASE_NAME )
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44 if options.permute:
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45 permute = "-permute"
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46 else:
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47 permute = ""
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48
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49 os.symlink( options.infile, tmp_input_name )
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50
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51 cmd = 'java -jar "%s" "%s" %s -cv%s -exp%s -c%s %s "%s"' % ( options.jar, tmp_input_name, options.master_variable, options.cv, options.exp, options.c, permute, JOB_ID )
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52 print cmd
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53
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54 #set up stdout and stderr output options
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55 stdout = open_file_from_option( options.stdout, mode = 'wb' )
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56 stderr = open_file_from_option( options.stderr, mode = 'wb' )
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57 #if no stderr file is specified, we'll use our own
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58 if stderr is None:
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59 stderr = tempfile.NamedTemporaryFile( prefix="MINE-stderr-", dir=tmp_dir )
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60
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61 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
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62 return_code = proc.wait()
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63
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64 if return_code:
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65 stderr_target = sys.stderr
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66 else:
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67 stderr_target = sys.stdout
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68 stderr.flush()
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69 stderr.seek(0)
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70 while True:
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71 chunk = stderr.read( CHUNK_SIZE )
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72 if chunk:
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73 stderr_target.write( chunk )
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74 else:
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75 break
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76 stderr.close()
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77
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78 print os.listdir( tmp_dir )
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79
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80 shutil.move( '%s,%s,Results.csv' % ( tmp_input_name, JOB_ID ), options.output_results )
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81 shutil.move( '%s,%s,Status.csv' % ( tmp_input_name, JOB_ID ), options.output_log )
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82
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83 cleanup_before_exit( tmp_dir )
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84
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85 if __name__=="__main__": __main__()
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