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1 """
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2 Binary classes
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3 """
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4
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5 import galaxy.datatypes.data
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6 from galaxy.datatypes.data import Data
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7 import galaxy.datatypes.sniff
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8 from galaxy.datatypes.sniff import *
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9
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10 import zipfile
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11 from urllib import urlencode, quote_plus
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12
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13 log = logging.getLogger(__name__)
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14
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15 # Cistrome Customized Datatypes
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16 class Eset( Data ):
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17 """Class describing an Expression Set"""
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18 file_ext = "eset"
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19 def set_peek( self, dataset, is_multi_byte=False ):
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20 if not dataset.dataset.purged:
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21 dataset.peek = "Expression set"
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22 dataset.blurb = data.nice_size( dataset.get_size() )
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23 else:
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24 dataset.peek = 'file does not exist'
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25 dataset.blurb = 'file purged from disk'
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26 def display_peek(self, dataset):
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27 try:
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28 return dataset.peek
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29 except:
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30 return "Expression set"
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31 def get_mime(self):
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32 """Returns the mime type of the datatype"""
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33
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34 class XysZip( Data ):
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35 """Class describing a zip archive of NimbleGen XYS files"""
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36 file_ext = "xys.zip"
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37 def set_peek( self, dataset, is_multi_byte=False ):
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38 if not dataset.dataset.purged:
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39 zip_file = zipfile.ZipFile( dataset.file_name, "r" )
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40 num_files = len( zip_file.namelist() )
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41 dataset.peek = "Archive of %s NimbleGen XYS files" % ( str( num_files - 1 ) )
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42 dataset.blurb = data.nice_size( dataset.get_size() )
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43 else:
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44 dataset.peek = 'file does not exist'
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45 dataset.blurb = 'file purged from disk'
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46 def display_peek(self, dataset):
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47 try:
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48 return dataset.peek
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49 except:
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50 return "NimbleGen XYS file archive (%s)" % ( data.nice_size( dataset.get_size() ) )
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51 def get_mime(self):
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52 """Returns the mime type of the datatype"""
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53 return 'application/zip'
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54
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55 class CelZip( Data ):
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56 """Class describing a zip archive of Affymetrix CEL files"""
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57 file_ext = "cel.zip"
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58 def set_peek( self, dataset, is_multi_byte=False ):
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59 if not dataset.dataset.purged:
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60 zip_file = zipfile.ZipFile( dataset.file_name, "r" )
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61 num_files = len( zip_file.namelist() )
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62 dataset.peek = "Archive of %s Affymetrix CEL files" % ( str( num_files - 1 ) )
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63 dataset.blurb = data.nice_size( dataset.get_size() )
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64 else:
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65 dataset.peek = 'file does not exist'
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66 dataset.blurb = 'file purged from disk'
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67 def display_peek(self, dataset):
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68 try:
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69 return dataset.peek
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70 except:
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71 return "Affymetrix CEL file archive (%s)" % ( data.nice_size( dataset.get_size() ) )
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72 def get_mime(self):
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73 """Returns the mime type of the datatype"""
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74 return 'application/zip'
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75
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76 class Cel( Data ):
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77 """Class describing an binary CEL file"""
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78 file_ext = "cel"
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79 def set_peek( self, dataset, is_multi_byte=False ):
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80 if not dataset.dataset.purged:
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81 export_url = "/history_add_to?" + urlencode({'history_id':dataset.history_id,'ext':'cel','name':'affymetrix cel file','info':'Cel file','dbkey':dataset.dbkey})
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82 dataset.peek = "Binary cel sequence file"
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83 dataset.blurb = data.nice_size( dataset.get_size() )
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84 else:
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85 dataset.peek = 'file does not exist'
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86 dataset.blurb = 'file purged from disk'
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87 def display_peek(self, dataset):
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88 try:
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89 return dataset.peek
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90 except:
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91 return "Binary cel sequence file (%s)" % ( data.nice_size( dataset.get_size() ) )
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92 def sniff( self, filename ):
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93 """
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94 Determines wether the file is in cel format
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95
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96 """
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97 parts = filename.lower().split('.')
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98 for p in parts:
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99 if p == 'cel':
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100 return True
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101 return False
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102
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103 def get_mime(self):
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104 """Returns the mime type of the datatype"""
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105 return 'application/octet-stream'
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106 # End
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