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1 #!/usr/bin/env python
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2 # Retrieves data from external data source applications and stores in a dataset file.
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3 # Data source application parameters are temporarily stored in the dataset file.
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4 import socket
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5 import urllib
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6 import sys
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7 import os
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8 import optparse
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9 import xml.etree.ElementTree as ElementTree
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10 from galaxy import eggs #eggs needs to be imported so that galaxy.util can find docutils egg...
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11 from galaxy.util.json import from_json_string, to_json_string
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12 from galaxy.util import get_charset_from_http_headers
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13 import galaxy.model # need to import model before sniff to resolve a circular import dependency
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14 from galaxy.datatypes import sniff
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15 from galaxy.datatypes.registry import Registry
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16 from galaxy.jobs import TOOL_PROVIDED_JOB_METADATA_FILE
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17
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18 assert sys.version_info[:2] >= ( 2, 4 )
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19
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20 def stop_err( msg ):
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21 sys.stderr.write( msg )
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22 sys.exit()
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23
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24 GALAXY_PARAM_PREFIX = 'GALAXY'
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25 GALAXY_ROOT_DIR = os.path.realpath( os.path.join( os.path.split( os.path.realpath( __file__ ) )[0], '..', '..' ) )
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26 GALAXY_DATATYPES_CONF_FILE = os.path.join( GALAXY_ROOT_DIR, 'datatypes_conf.xml' )
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27
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28 def load_input_parameters( filename, erase_file = True ):
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29 datasource_params = {}
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30 try:
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31 json_params = from_json_string( open( filename, 'r' ).read() )
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32 datasource_params = json_params.get( 'param_dict' )
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33 except:
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34 json_params = None
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35 for line in open( filename, 'r' ):
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36 try:
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37 line = line.strip()
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38 fields = line.split( '\t' )
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39 datasource_params[ fields[0] ] = fields[1]
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40 except:
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41 continue
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42 if erase_file:
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43 open( filename, 'w' ).close() #open file for writing, then close, removes params from file
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44 return json_params, datasource_params
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45
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46 def deconstruct_multi_filename( multi_filename ):
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47 keys = ['primary', 'id', 'name', 'visible', 'file_type', 'dbkey']
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48 return ( dict( zip( keys, multi_filename.split('_') ) ) )
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49
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50 def construct_multi_filename( id, name, file_type, dbkey=None):
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51 """ Implementation of *Number of Output datasets cannot be determined until tool run* from documentation_.
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52 .. _documentation: http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files
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53 """
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54 if dbkey:
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55 filename = "%s_%s_%s_%s_%s_%s" % ( 'primary', id, name, 'visible', file_type, dbkey )
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56 else:
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57 filename = "%s_%s_%s_%s_%s" % ( 'primary', id, name, 'visible', file_type )
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58
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59 return filename
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60
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61 def xml_save_to_newfile_directory( xmlfile, directory, id, enhanced_handling=False, datatypes_registry=None ):
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62 """ Open xmlfile, parse all URLs to fetch. Fetch each file, saving to ``directory``.
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63 Save first file for last and return for ``page``.
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64
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65 Schema
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66
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67 ::
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68
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69 <?xml version="1.0"?>
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70 <!DOCTYPE downloads [
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71 <!ELEMENT downloads (download)>
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72 <!ELEMENT download (resource,url,meta)>
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73 <!ELEMENT resource (#PCDATA)>
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74 <!ELEMENT url (#PCDATA)>
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75 <!ELEMENT id (#PCDATA)>
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76 <!ELEMENT meta (id,format,type,summary,feature,genome,technique,instrument,assay,sample,description,PMID)>
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77 <!ELEMENT id (#PCDATA)>
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78 <!ELEMENT format (#PCDATA)>
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79 <!ELEMENT type (#PCDATA)>
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80 <!ELEMENT summary (#PCDATA)>
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81 <!ELEMENT feature (#PCDATA)>
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82 <!ELEMENT genome (#PCDATA)>
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83 <!ELEMENT technique (#PCDATA)>
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84 <!ELEMENT instrument (#PCDATA)>
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85 <!ELEMENT assay (#PCDATA)>
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86 <!ELEMENT sample (#PCDATA)>
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87 <!ELEMENT description (#PCDATA)>
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88 <!ELEMENT PMID (#PCDATA)>
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89 ]>
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90 """
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91 root = ElementTree.fromstring(xmlfile.read())
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92 if root.tag != 'downloads':
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93 stop_err( 'The remote data source application has not sent back a URL parameter in the request.' )
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94 # traverse xml schema to find URLs, names, and dbkeys
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95 files_to_fetch = []
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96 complete = False
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97
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98 for child in root:
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99 if (child.tag == 'download') and (complete == True):
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100 files_to_fetch.append( ( construct_multi_filename( id, name, file_type, dbkey ), URL ) )
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101
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102 for sub in child:
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103 if sub.tag == 'url':
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104 URL = sub.text
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105 elif sub.tag == 'meta':
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106
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107 for meta in sub:
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108 if meta.tag == 'id':
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109 name = meta.text
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110 elif meta.tag == 'genome':
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111 dbkey = meta.text
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112 elif meta.tag == 'format':
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113 file_type = meta.text
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114 # hit the end of our schema
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115 files_to_fetch.append( ( construct_multi_filename( id, name, file_type, dbkey ), URL ) )
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116
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117 if len(files_to_fetch) > 1:
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118 for filename, URL in files_to_fetch[1:]:
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119 try:
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120 cur_filename = os.path.join( directory, filename )
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121 page = urllib.urlopen( URL )
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122 multi_dict = deconstruct_multi_filename( filename )
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123 cur_filename, is_multi_byte = sniff.stream_to_open_named_file( page, os.open( cur_filename, os.O_WRONLY | os.O_CREAT ), cur_filename, source_encoding=get_charset_from_http_headers( page.headers ) )
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124 if enhanced_handling:
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125 ext = sniff.handle_uploaded_dataset_file( cur_filename, datatypes_registry, ext = multi_dict['file_type'], is_multi_byte = is_multi_byte )
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126 except Exception, e:
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127 stop_err( 'Unable to fetch %s:\n%s' % ( URL, e ) )
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128
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129 # pass page back to main
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130 return ( files_to_fetch[0][0], urllib.urlopen( files_to_fetch[0][1] ) )
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131
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132 def __main__():
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133 # Parse the command line options
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134 usage = "Usage: ncbi_connector.py filename max_size [options]"
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135 parser = optparse.OptionParser(usage = usage)
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136 parser.add_option("-x", "--xml",
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137 action="store_true", dest="xmlfile", help="filename defines external resources as xml")
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138 parser.add_option("-i", "--id", type="string",
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139 action="store", dest="id", help="output id")
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140 parser.add_option("-p", "--path", type="string",
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141 action="store", dest="newfilepath", help="new file path")
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142
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143 (options, args) = parser.parse_args()
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144
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145 filename = args[0]
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146 try:
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147 max_file_size = int( args[1] )
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148 except:
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149 max_file_size = 0
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150
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151 job_params, params = load_input_parameters( filename )
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152 if job_params is None: #using an older tabular file
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153 enhanced_handling = False
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154 job_params = dict( param_dict = params )
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155 job_params[ 'output_data' ] = [ dict( out_data_name = 'output',
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156 ext = 'data',
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157 file_name = filename,
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158 extra_files_path = None ) ]
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159 job_params[ 'job_config' ] = dict( GALAXY_ROOT_DIR=GALAXY_ROOT_DIR, GALAXY_DATATYPES_CONF_FILE=GALAXY_DATATYPES_CONF_FILE, TOOL_PROVIDED_JOB_METADATA_FILE = TOOL_PROVIDED_JOB_METADATA_FILE )
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160 else:
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161 enhanced_handling = True
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162 json_file = open( job_params[ 'job_config' ][ 'TOOL_PROVIDED_JOB_METADATA_FILE' ], 'w' ) #specially named file for output junk to pass onto set metadata
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163
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164 datatypes_registry = Registry()
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165 datatypes_registry.load_datatypes( root_dir = job_params[ 'job_config' ][ 'GALAXY_ROOT_DIR' ], config = job_params[ 'job_config' ][ 'GALAXY_DATATYPES_CONF_FILE' ] )
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166
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167 URL = params.get( 'URL', None ) #using exactly URL indicates that only one dataset is being downloaded
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168 URL_method = params.get( 'URL_method', None )
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169
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170 # The Python support for fetching resources from the web is layered. urllib uses the httplib
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171 # library, which in turn uses the socket library. As of Python 2.3 you can specify how long
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172 # a socket should wait for a response before timing out. By default the socket module has no
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173 # timeout and can hang. Currently, the socket timeout is not exposed at the httplib or urllib2
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174 # levels. However, you can set the default timeout ( in seconds ) globally for all sockets by
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175 # doing the following.
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176 socket.setdefaulttimeout( 600 )
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177
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178 for data_dict in job_params[ 'output_data' ]:
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179 cur_filename = data_dict.get( 'file_name', filename )
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180 cur_URL = params.get( '%s|%s|URL' % ( GALAXY_PARAM_PREFIX, data_dict[ 'out_data_name' ] ), URL )
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181 if not cur_URL:
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182 open( cur_filename, 'w' ).write( "" )
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183 stop_err( 'The remote data source application has not sent back a URL parameter in the request.' )
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184
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185 # The following calls to urllib.urlopen() will use the above default timeout
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186 try:
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187 if not URL_method or URL_method == 'get':
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188 page = urllib.urlopen( cur_URL )
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189 elif URL_method == 'post':
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190 page = urllib.urlopen( cur_URL, urllib.urlencode( params ) )
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191 except Exception, e:
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192 stop_err( 'The remote data source application may be off line, please try again later. Error: %s' % str( e ) )
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193 if max_file_size:
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194 file_size = int( page.info().get( 'Content-Length', 0 ) )
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195 if file_size > max_file_size:
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196 stop_err( 'The size of the data (%d bytes) you have requested exceeds the maximum allowed (%d bytes) on this server.' % ( file_size, max_file_size ) )
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197 # If xmlfile is provided, fetch files 2 through n and save to new_file_path, replace page with file 1
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198 if options.xmlfile:
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199 multi_filename, page = xml_save_to_newfile_directory( page, options.newfilepath, options.id, enhanced_handling, datatypes_registry )
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200 multi_dict = deconstruct_multi_filename( multi_filename )
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201
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202 #do sniff stream for multi_byte
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203 try:
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204 cur_filename, is_multi_byte = sniff.stream_to_open_named_file( page, os.open( cur_filename, os.O_WRONLY | os.O_CREAT ), cur_filename, source_encoding=get_charset_from_http_headers( page.headers ) )
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205 except Exception, e:
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206 stop_err( 'Unable to fetch %s:\n%s' % ( cur_URL, e ) )
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207
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208 #here import checks that upload tool performs
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209 if enhanced_handling:
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210 try:
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211 ext = sniff.handle_uploaded_dataset_file( filename, datatypes_registry, ext = data_dict[ 'ext' ], is_multi_byte = is_multi_byte )
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212 except Exception, e:
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213 stop_err( str( e ) )
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214 info = dict( type = 'dataset',
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215 dataset_id = data_dict[ 'dataset_id' ],
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216 ext = ext)
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217
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218 json_file.write( "%s\n" % to_json_string( info ) )
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219
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220 if __name__ == "__main__": __main__()
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