diff mine_wrapper.py @ 0:cad7e25f68db draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mine_wrapper.py	Mon Jul 28 11:30:14 2014 -0400
@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+"""
+A wrapper script for running the MINE.jar commands.
+"""
+
+import sys, optparse, os, tempfile, subprocess, shutil
+
+CHUNK_SIZE = 2**20 #1mb
+
+BASE_NAME = "galaxy_mime_file.txt"
+JOB_ID = "galaxy_mine"
+
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        print os.listdir( tmp_dir )
+        shutil.rmtree( tmp_dir )
+
+def open_file_from_option( filename, mode = 'rb' ):
+    if filename:
+        return open( filename, mode = mode )
+    return None
+
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '-j', '--jar', dest='jar', action='store', type="string", help='Location of JAR file' )
+    parser.add_option( '-i', '--infile', dest='infile', action='store', type="string", help='infile' )
+    parser.add_option( '-m', '--master_variable', dest='master_variable', action='store', type="string", help='master_variable' )
+    parser.add_option( '-v', '--cv', dest='cv', action='store', type="string", help='cv' )
+    parser.add_option( '-e', '--exp', dest='exp', action='store', type="string", help='exp' )
+    parser.add_option( '-c', '--c', dest='c', action='store', type="string", help='c' )
+    parser.add_option( '-p', '--permute', dest='permute', action='store_true', default=False, help='permute' )
+    parser.add_option( '-o', '--output_results', dest='output_results', action='store', type="string", help='output_results' )
+    parser.add_option( '-l', '--output_log', dest='output_log', action='store', type="string", help='output_log' )
+    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.' )
+    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.' )
+    (options, args) = parser.parse_args()
+    
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-MINE-' )
+    tmp_input_name = os.path.join( tmp_dir, BASE_NAME )
+    if options.permute:
+        permute = "-permute"
+    else:
+        permute = ""
+    
+    os.symlink( options.infile, tmp_input_name )
+    
+    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 )
+    print cmd
+    
+    #set up stdout and stderr output options
+    stdout = open_file_from_option( options.stdout, mode = 'wb' )
+    stderr = open_file_from_option( options.stderr, mode = 'wb' )
+    #if no stderr file is specified, we'll use our own
+    if stderr is None:
+        stderr = tempfile.NamedTemporaryFile( prefix="MINE-stderr-", dir=tmp_dir )
+    
+    proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
+    return_code = proc.wait()
+    
+    if return_code:
+        stderr_target = sys.stderr
+    else:
+        stderr_target = sys.stdout
+    stderr.flush()
+    stderr.seek(0)
+    while True:
+        chunk = stderr.read( CHUNK_SIZE )
+        if chunk:
+            stderr_target.write( chunk )
+        else:
+            break
+    stderr.close()
+    
+    print os.listdir( tmp_dir )
+    
+    shutil.move( '%s,%s,Results.csv' % ( tmp_input_name, JOB_ID ), options.output_results )
+    shutil.move( '%s,%s,Status.csv' % ( tmp_input_name, JOB_ID ), options.output_log )
+    
+    cleanup_before_exit( tmp_dir )
+
+if __name__=="__main__": __main__()