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comparison mine_wrapper.py @ 0:cad7e25f68db draft

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Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:30:14 -0400
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-1:000000000000 0:cad7e25f68db
1 #!/usr/bin/env python
2 #Dan Blankenberg
3
4 """
5 A wrapper script for running the MINE.jar commands.
6 """
7
8 import sys, optparse, os, tempfile, subprocess, shutil
9
10 CHUNK_SIZE = 2**20 #1mb
11
12 BASE_NAME = "galaxy_mime_file.txt"
13 JOB_ID = "galaxy_mine"
14
15 def cleanup_before_exit( tmp_dir ):
16 if tmp_dir and os.path.exists( tmp_dir ):
17 print os.listdir( tmp_dir )
18 shutil.rmtree( tmp_dir )
19
20 def open_file_from_option( filename, mode = 'rb' ):
21 if filename:
22 return open( filename, mode = mode )
23 return None
24
25
26 def __main__():
27 #Parse Command Line
28 parser = optparse.OptionParser()
29 parser.add_option( '-j', '--jar', dest='jar', action='store', type="string", help='Location of JAR file' )
30 parser.add_option( '-i', '--infile', dest='infile', action='store', type="string", help='infile' )
31 parser.add_option( '-m', '--master_variable', dest='master_variable', action='store', type="string", help='master_variable' )
32 parser.add_option( '-v', '--cv', dest='cv', action='store', type="string", help='cv' )
33 parser.add_option( '-e', '--exp', dest='exp', action='store', type="string", help='exp' )
34 parser.add_option( '-c', '--c', dest='c', action='store', type="string", help='c' )
35 parser.add_option( '-p', '--permute', dest='permute', action='store_true', default=False, help='permute' )
36 parser.add_option( '-o', '--output_results', dest='output_results', action='store', type="string", help='output_results' )
37 parser.add_option( '-l', '--output_log', dest='output_log', action='store', type="string", help='output_log' )
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.' )
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.' )
40 (options, args) = parser.parse_args()
41
42 tmp_dir = tempfile.mkdtemp( prefix='tmp-MINE-' )
43 tmp_input_name = os.path.join( tmp_dir, BASE_NAME )
44 if options.permute:
45 permute = "-permute"
46 else:
47 permute = ""
48
49 os.symlink( options.infile, tmp_input_name )
50
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 )
52 print cmd
53
54 #set up stdout and stderr output options
55 stdout = open_file_from_option( options.stdout, mode = 'wb' )
56 stderr = open_file_from_option( options.stderr, mode = 'wb' )
57 #if no stderr file is specified, we'll use our own
58 if stderr is None:
59 stderr = tempfile.NamedTemporaryFile( prefix="MINE-stderr-", dir=tmp_dir )
60
61 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
62 return_code = proc.wait()
63
64 if return_code:
65 stderr_target = sys.stderr
66 else:
67 stderr_target = sys.stdout
68 stderr.flush()
69 stderr.seek(0)
70 while True:
71 chunk = stderr.read( CHUNK_SIZE )
72 if chunk:
73 stderr_target.write( chunk )
74 else:
75 break
76 stderr.close()
77
78 print os.listdir( tmp_dir )
79
80 shutil.move( '%s,%s,Results.csv' % ( tmp_input_name, JOB_ID ), options.output_results )
81 shutil.move( '%s,%s,Status.csv' % ( tmp_input_name, JOB_ID ), options.output_log )
82
83 cleanup_before_exit( tmp_dir )
84
85 if __name__=="__main__": __main__()