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1 #! /usr/bin/python
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2 # -*- coding: utf8 -*-
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3
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4 """#supported organisms soap - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
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5 #Copyright (C) 2015 Institut Curie
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6 #
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7 #This program is free software: you can redistribute it and/or modify
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8 #it under the terms of the GNU General Public License as published by
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9 #the Free Software Foundation, either version 3 of the License, or
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10 #(at your option) any later version.
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11 #
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12 #This program is distributed in the hope that it will be useful,
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13 #but WITHOUT ANY WARRANTY; without even the implied warranty of
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14 #MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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15 #GNU General Public License for more details.
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16 #
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17 #You should have received a copy of the GNU General Public License
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18 #along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 #
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20 ###########################################################'
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21 #
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22 #Recup organisms to each RSAT server and create loc files for Galaxy.
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23 #
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24 ###########################################################'
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25 #
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26 # Client to have list RSAT suppported organisms.
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27 #
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28 #
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29 #usage: supported-organisms_soap.py [-h] -f <OUTPUT_FORMAT> -galaxyPath <GALAXY_PATH>
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30 #
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31 #
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32 #optional arguments:
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33 # -h, --help show this help message and exit
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34 # -f <OUTPUT_FORMAT>, --format <OUTPUT_FORMAT>
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35 # Output format. Supported: html_list, html_table,
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36 # array, text, keys, names, sizes, full, tree,
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37 # html_tree.
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38 # -galaxyPath <GALAXY_PATH>, --galaxyPath <GALAXY_PATH>
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39 # Galaxy tool_data_path directory (e.i. /myGalaxy
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40 # /galaxy-dist/tool-data)
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41 #
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42 #Version 0.1 - 15/04/2015
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43 #
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44 ###########################################################'"""
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45 __author__ = 'Jocelyn Brayet'
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46 supportedOrganismsVersion = '0.1 - 15/04/2015'
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47
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48 ###########################################################'
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49 ## Import
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50
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51 import argparse
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52 import os
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53 import urllib
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54 from suds.client import Client
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55 import platform
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56
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57 ###########################################################'
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58
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59 ################################ functions ############################################################
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60 ## Define a function to make a service perform the desired request using provided arguments
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61 def call_run_service(rsat_service, args):
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62 """
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63 Run job in RSAT server.
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64 service -> RSAT web service
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65 args -> web service request
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66 """
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67
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68 result = rsat_service.supported_organisms(args)
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69 return result
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70
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71 def testNone(argument):
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72 """
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73 Test if argument is None or not.
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74 argument -> argument give by user
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75 """
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76
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77 if not argument is None:
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78 variable = argument[0]
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79 else:
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80 variable = ""
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81 return variable
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82
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83 def recupOrganisms(srv,request,dicServ,path):
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84
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85 """
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86 Recup RSAT organisms in each RSAT server.
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87 srv -> server key in server dictionary
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88 request -> job request
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89 dicServ -> server dictionary
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90 """
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91
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92 # Create the client
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93 client = Client(serverDict[srv])
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94 # Need service interface to perform requests
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95 rsat_service = client.service
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96
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97 # Define client header
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98
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99 userAgent = 'RSAT-Client/v%s (%s; Python %s; %s)' % (
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100 supportedOrganismsVersion,
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101 os.path.basename( __file__ ),
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102 platform.python_version(),
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103 platform.system()
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104 )
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105
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106 httpHeaders = {'User-agent': userAgent}
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107 client.set_options(headers=httpHeaders)
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108 client.set_options(timeout=300)
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109
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110 result = call_run_service(rsat_service, request)
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111
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112 ###########################################################'
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113 ## Display request results
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114
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115 print '###############################################'
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116 print 'Command performed on server'
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117 print ''
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118 print result.command
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119 print ''
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120 print '###############################################'
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121 print 'Result'
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122 print ''
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123 print result.client
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124
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125 resultsFile = open(path+"/"+"RSAT_organisms_"+srv+".loc","w")
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126 resultsFile.write(result.client)
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127 resultsFile.close()
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128
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129 ###########################################################'
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130
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131 ###########################################################'
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132 # server dictionary
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133 serverDict = {
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134
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135 #http://protists.rsat.eu/
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136 "fr_ens":"http://rsat01.biologie.ens.fr/rsa-tools/web_services/RSATWS.wsdl",
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137 "fr_mrs":"http://rsat-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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138 "fr_ro":"http://rsat.sb-roscoff.fr/web_services/RSATWS.wsdl",
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139 "fr_mrs_2":"http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl",
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140 "es":"http://floresta.eead.csic.es/rsat/web_services/RSATWS.wsdl",
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141 "mx":"http://embnet.ccg.unam.mx/rsa-tools/web_services/RSATWS.wsdl"
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142
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143 }
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144
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145
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146 if __name__ == '__main__':
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147
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148 # Create the parser
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149 parser = argparse.ArgumentParser(description='Client to download supported-organisms results from RSAT server.', epilog='Version '+supportedOrganismsVersion)
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150
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151 # List desired arguments
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152 parser.add_argument('-f', '--format', metavar='<OUTPUT_FORMAT>', type=str, nargs=1, help='Output format. Supported: html_list, html_table, array, text, keys, names, sizes, full, tree, html_tree.', required=True)
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153 parser.add_argument('-galaxyPath', '--galaxyPath', metavar='<GALAXY_PATH>', type=str, nargs=1, help='Galaxy tool_data_path directory (e.i. /myGalaxy/galaxy-dist/tool-data)', required=True)
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154
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155
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156 # Parse command line
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157 args = parser.parse_args()
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158
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159 # Get values to be used
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160 output_format = testNone(args.format)
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161 galaxyPath = testNone(args.galaxyPath)
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162
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163 supportedOrganismsRequest = {
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164
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165 'output' : 'client',
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166 'format' : output_format
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167
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168 }
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169
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170 for srv in serverDict:
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171
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172 recupOrganisms(srv,supportedOrganismsRequest,serverDict,galaxyPath)
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173
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174
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175
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