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1 #!/usr/bin/env python
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2 import optparse
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3 import os
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4 import sys
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5 import tempfile
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6 import shutil
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7 import subprocess
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8 import re
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9 import logging
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10 import urllib2
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11 from urlparse import urlparse
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12
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13
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14 assert sys.version_info[:2] >= (2, 6)
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15
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16 log = logging.getLogger(__name__)
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17
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18 CHUNK_SIZE = 2**20 #1mb
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19
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20 def stop_err(msg):
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21 sys.stderr.write("%s\n" % msg)
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22 sys.exit()
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23
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24 def download_from_url( url, output_dir, basename=None, ext=None ):
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25 o = urlparse(url)
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26 src_parts = os.path.basename(o.path).split('.',1)
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27 file_name = "%s.%s" % ( basename if basename else src_parts[0], ext if ext else src_parts[1] )
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28 file_path = os.path.join(output_dir,file_name)
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29 reader = urllib2.urlopen( url )
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30 writer = open(file_path,'wb')
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31 while True:
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32 data = reader.read( CHUNK_SIZE )
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33 if data:
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34 writer.write( data )
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35 else:
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36 break
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37 writer.close()
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38 reader.close()
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39 return file_path
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40
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41 def __main__():
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42 parser = optparse.OptionParser()
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43 parser.add_option( '-a', '--archive', dest='archive', default=None, help='URL to archive containing: <name>.wiff file <name>.wiff.scan <name>.wiff.mtd files' )
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44 parser.add_option( '-w', '--wiff', dest='wiff', default=None, help='URL to <name>.wiff file' )
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45 parser.add_option( '-s', '--scan', dest='scan', default=None, help='URL to <name>.wiff.scan file' )
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46 parser.add_option( '-m', '--mtd', dest='mtd', default=None, help='URL to <name>.wiff.mtd file' )
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47 parser.add_option( '-n', '--name', dest='name', default=None, help='base name for files' )
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48 parser.add_option( '-o', '--output_dir', dest='output_dir', default=None, help='dir to copy files into' )
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49 parser.add_option( '-f', '--output_file', dest='output_file', default=None, help='Galaxy dataset file' )
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50 (options, args) = parser.parse_args()
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51
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52 if not (options.archive or options.wiff):
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53 stop_err("No wiff input file specified")
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54 output_dir = os.getcwd()
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55 if options.output_dir:
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56 output_dir = options.output_dir
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57 if not os.path.exists( output_dir ):
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58 os.makedirs(output_dir)
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59 basename = options.name
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60 rval = ['<html><head><title>Wiff Composite Dataset %s</title></head><body><p/>' % (basename if basename else '')]
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61 rval.append('This composite dataset is composed of the following files:<p/><ul>')
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62 if options.wiff:
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63 file_path = download_from_url (options.wiff, output_dir, basename=basename, ext='wiff')
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64 rel_path = os.path.basename(file_path)
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65 os.symlink( rel_path, os.path.join(output_dir,'wiff'))
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66 rval.append( '<li><a href="%s" type="application/octet-stream">%s</a></li>' % ( rel_path, rel_path ) )
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67 print >> sys.stdout, "wiff: %s" % options.wiff
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68 if options.scan:
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69 file_path = download_from_url (options.scan, output_dir, basename=basename, ext='wiff.scan')
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70 rel_path = os.path.basename(file_path)
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71 os.symlink( rel_path, os.path.join(output_dir,'wiff_scan'))
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72 rval.append( '<li><a href="%s" type="application/octet-stream">%s</a></li>' % ( rel_path, rel_path ) )
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73 print >> sys.stdout, "scan: %s" % options.scan
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74 if options.mtd:
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75 file_path = download_from_url (options.mtd, output_dir, basename=basename, ext='wiff.mtd')
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76 rel_path = os.path.basename(file_path)
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77 os.symlink( rel_path, os.path.join(output_dir,'wiff_mtd'))
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78 rval.append( '<li><a href="%s" type="application/octet-stream">%s</a></li>' % ( rel_path, rel_path ) )
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79 print >> sys.stdout, "mtd: %s" % options.mtd
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80 if options.output_file:
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81 rval.append( '</ul></div></body></html>' )
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82 f = open(options.output_file,'a')
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83 f.write("\n".join( rval ))
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84 f.close()
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85
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86 if __name__ == '__main__':
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87 __main__()
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