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6
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1 #!/usr/bin/env python
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2 import json
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3 import optparse
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4 import urllib
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5 import os.path
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6 import os
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7 from operator import itemgetter
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8 import tarfile
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9
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10 __version__ = "1.0.0"
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11 CHUNK_SIZE = 2**20 #1mb
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12 VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ '
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13
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14
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15 def splitext(path):
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16 for ext in ['.tar.gz', '.tar.bz2']:
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17 if path.endswith(ext):
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18 path, ext = path[:-len(ext)], path[-len(ext):]
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19 break
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20 else:
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21 path, ext = os.path.splitext(path)
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22 return path, ext[1:]
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23
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24
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25 def chunk_write( source_stream, target_stream, source_method = "read", target_method="write" ):
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26 source_method = getattr( source_stream, source_method )
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27 target_method = getattr( target_stream, target_method )
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28 while True:
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29 chunk = source_method( CHUNK_SIZE )
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30 if chunk:
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31 target_method( chunk )
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32 else:
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33 break
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34
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35
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36 def deconstruct_multi_filename( multi_filename ):
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37 keys = [ 'primary', 'id', 'name', 'visible', 'file_type' ]
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38 return ( dict( zip( keys, multi_filename.split('_') ) ) )
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39
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40
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41 def construct_multi_filename( id, name, file_type ):
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42 """ Implementation of *Number of Output datasets cannot be determined until tool run* from documentation_.
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43 .. _documentation: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
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44 """
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45 filename = "%s_%s_%s_%s_%s" % ( 'primary', id, name, 'visible', file_type )
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46 return filename
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47
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48
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49 def download_from_query( query_data, target_output_filename ):
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50 """ Download file from the json data and write it to target_output_filename.
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51 """
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52 query_url = query_data.get( 'url' )
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53 query_file_type = query_data.get( 'extension' )
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54 query_stream = urllib.urlopen( query_url )
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55 output_stream = open( target_output_filename, 'wb' )
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56 chunk_write( query_stream, output_stream )
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57 query_stream.close()
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58 output_stream.close()
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59
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12
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60 def store_file_from_archive( file_object, target_output_filename, isString=False ):
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6
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61 """ Store file after extracting from archive and organize them as a collection using the structure
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62 (collection-name)_(file-name).ext as file name
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63 """
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64 output_stream = open( target_output_filename, 'wb' )
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12
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65 #chunk_write( file_object.read(), output_stream )
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66 if not isString:
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67 output_stream.write(file_object.read())
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68 else:
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69 output_stream.write(file_object)
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6
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70 output_stream.close()
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71
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72
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73 def download_extra_data( query_ext_data, base_path ):
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74 """ Download any extra data defined in the JSON.
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75 NOTE: the "path" value is a relative path to the file on our
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76 file system. This is slightly dangerous and we should make every effort
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77 to avoid a malicious absolute path to write the file elsewhere on the
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78 filesystem.
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79 """
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80 for ext_data in query_ext_data:
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81 if not os.path.exists( base_path ):
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82 os.mkdir( base_path )
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83 query_stream = urllib.urlopen( ext_data.get( 'url' ) )
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84 ext_path = ext_data.get( 'path' )
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85 os.makedirs( os.path.normpath( '/'.join( [ base_path, os.path.dirname( ext_path ) ] ) ) )
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86 output_stream = open( os.path.normpath( '/'.join( [ base_path, ext_path ] ) ), 'wb' )
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87 chunk_write( query_stream, output_stream )
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88 query_stream.close()
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89 output_stream.close()
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90
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91
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92 def metadata_to_json( dataset_id, metadata, filename, ds_type='dataset', primary=False):
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93 """ Return line separated JSON """
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94 meta_dict = dict( type = ds_type,
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95 ext = metadata.get( 'extension' ),
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96 filename = filename,
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97 name = metadata.get( 'name' ),
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98 metadata = metadata.get( 'metadata', {} ) )
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99 if metadata.get( 'extra_data', None ):
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100 meta_dict[ 'extra_files' ] = '_'.join( [ filename, 'files' ] )
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101 if primary:
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102 meta_dict[ 'base_dataset_id' ] = dataset_id
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103 else:
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104 meta_dict[ 'dataset_id' ] = dataset_id
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105 return "%s\n" % json.dumps( meta_dict )
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106
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107
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16
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108 def walk_on_archive(target_output_filename, check_ext, archive_name, appdata_path, db_key="?"):
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12
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109 archive_name = archive_name.replace("_", "-").replace(".", "-")
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110 with tarfile.open( target_output_filename, check_ext ) as tf:
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111 for entry in tf:
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112 if entry.isfile():
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113 fileobj = tf.extractfile( entry )
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114 # reserve the underscore for the collection searator
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115 filename = os.path.basename( entry.name ).replace("_", "-")
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116 extension = splitext( filename )[1]
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16
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117 # pattern: (?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)_(?P<ext>[^_]+)_(?P<dbkey>[^_]+)
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12
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118 if (len(extension) > 0):
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18
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119 filename = (filename[0:len(filename)-(len(extension)+1)]).replace(".", "-") + "." + extension + "_" + extension
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12
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120 else:
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121 extension = "auto"
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16
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122 filename_with_collection_prefix = archive_name + "_" + filename + "_" + db_key
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12
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123 target_entry_output_filename = os.path.join(appdata_path, filename_with_collection_prefix)
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124 store_file_from_archive( fileobj, target_entry_output_filename )
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125 return True
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126
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127
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128 def download_files_and_write_metadata(query_item, json_params, output_base_path, metadata_parameter_file, primary, appdata_path, options, args):
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6
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129 """ Main work function that operates on the JSON representation of
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130 one dataset and its metadata. Returns True.
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131 """
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132 dataset_url, output_filename, \
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133 extra_files_path, file_name, \
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134 ext, out_data_name, \
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135 hda_id, dataset_id = set_up_config_values(json_params)
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136 extension = query_item.get( 'extension' )
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14
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137 url = query_item.get( 'url' )
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12
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138 filename = query_item.get( 'name' )
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139
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140 check_ext = ""
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14
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141 if ( url.endswith( "gz" ) ):
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12
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142 check_ext = "r:gz"
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14
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143 elif ( url.endswith( "bz2" ) ):
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12
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144 check_ext = "r:bz2"
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14
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145 elif ( url.endswith( "tar" ) ):
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12
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146 check_ext = "r:"
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147 isArchive = bool( check_ext and check_ext.strip() )
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148
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6
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149 extra_data = query_item.get( 'extra_data', None )
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150 if primary:
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151 filename = ''.join( c in VALID_CHARS and c or '-' for c in filename )
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152 name = construct_multi_filename( hda_id, filename, extension )
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153 target_output_filename = os.path.normpath( '/'.join( [ output_base_path, name ] ) )
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12
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154 if isArchive is False:
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155 metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
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156 target_output_filename,
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157 ds_type='new_primary_dataset',
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158 primary=primary) )
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6
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159 else:
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160 target_output_filename = output_filename
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12
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161 if isArchive is False:
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162 metadata_parameter_file.write( metadata_to_json( dataset_id, query_item,
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163 target_output_filename,
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164 ds_type='dataset',
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165 primary=primary) )
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166
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14
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167 if isArchive is False:
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168 download_from_query( query_item, target_output_filename )
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169 else:
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170 target_output_path = os.path.join(appdata_path, filename)
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171 download_from_query( query_item, target_output_path )
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6
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172 if extra_data:
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173 extra_files_path = ''.join( [ target_output_filename, 'files' ] )
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174 download_extra_data( extra_data, extra_files_path )
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175
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10
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176 """ the following code handles archives and decompress them in a collection """
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12
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177 if ( isArchive ):
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16
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178 db_key = "?"
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179 archive_metadata = query_item.get( 'metadata', None )
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180 if archive_metadata is not None:
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181 try:
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182 db_key = archive_metadata.get( 'db_key' )
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183 except:
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184 pass
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185 walk_on_archive(target_output_path, check_ext, filename, appdata_path, db_key)
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12
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186
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6
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187 return True
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188
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189
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190 def set_up_config_values(json_params):
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191 """ Parse json_params file and return a tuple of necessary configuration
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192 values.
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193 """
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194 datasource_params = json_params.get( 'param_dict' )
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195 dataset_url = datasource_params.get( 'URL' )
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196 output_filename = datasource_params.get( 'output1', None )
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197 output_data = json_params.get( 'output_data' )
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198 extra_files_path, file_name, ext, out_data_name, hda_id, dataset_id = \
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199 itemgetter('extra_files_path', 'file_name', 'ext', 'out_data_name', 'hda_id', 'dataset_id')(output_data[0])
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200 return (dataset_url, output_filename,
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201 extra_files_path, file_name,
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202 ext, out_data_name,
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203 hda_id, dataset_id)
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204
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205
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14
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206 def download_from_json_data( options, args ):
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6
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207 """ Parse the returned JSON data and download files. Write metadata
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208 to flat JSON file.
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209 """
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210 output_base_path = options.path
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211 appdata_path = options.appdata
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212 if not os.path.exists(appdata_path):
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213 os.makedirs(appdata_path)
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214
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215 # read tool job configuration file and parse parameters we need
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14
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216 json_params = json.loads( open( options.json_param_file, 'r' ).read() )
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12
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217
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6
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218 dataset_url, output_filename, \
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219 extra_files_path, file_name, \
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220 ext, out_data_name, \
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221 hda_id, dataset_id = set_up_config_values(json_params)
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222 # line separated JSON file to contain all dataset metadata
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223 metadata_parameter_file = open( json_params['job_config']['TOOL_PROVIDED_JOB_METADATA_FILE'], 'wb' )
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224
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225 # get JSON response from data source
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226 # TODO: make sure response is not enormous
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14
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227 query_params = json.loads(urllib.urlopen( dataset_url ).read())
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6
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228 # download and write files
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20
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229 primary = False
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230 #primary = True
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6
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231 # query_item, hda_id, output_base_path, dataset_id
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232 for query_item in query_params:
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233 if isinstance( query_item, list ):
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234 # TODO: do something with the nested list as a collection
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235 for query_subitem in query_item:
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236 primary = download_files_and_write_metadata(query_subitem, json_params, output_base_path,
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237 metadata_parameter_file, primary, appdata_path, options, args)
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6
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238
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239 elif isinstance( query_item, dict ):
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240 primary = download_files_and_write_metadata(query_item, json_params, output_base_path,
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12
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241 metadata_parameter_file, primary, appdata_path, options, args)
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6
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242 metadata_parameter_file.close()
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243
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244 def __main__():
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245 """ Read the JSON return from a data source. Parse each line and request
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246 the data, download to "newfilepath", and write metadata.
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247
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248 Schema
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249 ------
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250
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251 [ {"url":"http://url_of_file",
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252 "name":"encode WigData",
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253 "extension":"wig",
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254 "metadata":{"db_key":"hg19"},
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255 "extra_data":[ {"url":"http://url_of_ext_file",
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256 "path":"rel/path/to/ext_file"}
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257 ]
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258 }
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259 ]
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260
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261 """
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262 # Parse the command line options
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263 usage = "Usage: json_data_source_mod.py max_size --json_param_file filename [options]"
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264 parser = optparse.OptionParser(usage = usage)
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265 parser.add_option("-j", "--json_param_file", type="string",
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266 action="store", dest="json_param_file", help="json schema return data")
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267 parser.add_option("-p", "--path", type="string",
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268 action="store", dest="path", help="new file path")
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269 parser.add_option("-a", "--appdata", type="string",
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270 action="store", dest="appdata", help="appdata folder name")
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271 parser.add_option("-v", "--version", action="store_true", dest="version",
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272 default=False, help="display version and exit")
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273
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274 (options, args) = parser.parse_args()
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275 if options.version:
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276 print __version__
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277 else:
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278 download_from_json_data( options, args )
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279
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280
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281 if __name__ == "__main__": __main__()
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