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1 '''
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2 @author Chaitanya Guttula, Sumedha Ganjoo
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3 @see LICENSE (MIT style license file).
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4 '''
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5
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6 import warnings
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7
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8 with warnings.catch_warnings():
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9 warnings.simplefilter("ignore")
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10 import platform
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11
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12 from jpype._jpackage import JPackage
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13 from jpype import *
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14 import os.path
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15 import sys
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16 import string
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17 from edit_tool_conf1 import *
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18 from clientGenerator.msHandler import *
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19 from clientGenerator.creatorEngineComplex import *
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20 from clientGenerator.wsdl2path import *
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21 from clientGenerator.paramConverter import *
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22
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23 __author__=""
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24
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25 #generates client for a web service to be used as standalone
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26 class ClientGenerator1(object):
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27
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28 def __init__(self,webservice,operation,outputfile,servicetype):#,url):
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29 with warnings.catch_warnings():
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30 warnings.simplefilter("ignore")
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31 self.webservice = webservice
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32 self.operation = operation
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33 self.inputs = outputfile
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34 self.outputfile = outputfile
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35 #self.url = url
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36
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37 self.servicetype = servicetype
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38 self.galaxyhome=os.environ.get('GALAXY_HOME')
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39 self.clientfile = ''
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40 if self.servicetype == 'SOAP':
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41 wLoad=wsdlLoader()
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42 sys.path.append(self.galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator')
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43 os.chdir(self.galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator')
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44
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45 a = str(self.webservice).split('/')
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46 wsdlnamelist = a[len(a)-1].split(".")
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47 if len(wsdlnamelist)==1:
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48 wsdlnamelist=a[len(a)-1].split('?')
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49 print wsdlnamelist
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50
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51 foldername=wsdlnamelist[0]
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52
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53 path =self.galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/'+foldername
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54
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55 #creates the client stubs
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56 self.clientfile = wLoad.wsdlUrl2path(str(self.webservice),foldername)
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57
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58 print 'Client file : ',self.clientfile
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59 self.paramelement = None
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60
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61
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62
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63 ''' Replaces space (' ') with '**' in the given string '''
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64 def formatString(self,string):
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65 l = string.split(' ')
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66 return '**'.join(l)
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67
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68 def isRequired(self,param):
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69 #j=0
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70 #for param in inputl:
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71 cc = ClientCreator()
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72 self.msinstance = cc.opname2inputClassOb(self.operation,self.clientfile)
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73 test = MessageHandler()
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74 required = False
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75 if (param.find('|$|')>-1):
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76 plist = param.split('|')
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77 #root = test.getParameter(self.msinstance(),plist[0])
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78 k = 0
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79 iparam = ''
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80 for p in plist:
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81 if(k<len(plist)-3):
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82 if(k==0):
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83 iparam = iparam+(p)
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84 else:
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85 iparam = iparam+'|'+p
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86 k=k+1
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87 paramelement = test.getParameter(self.msinstance(),iparam)
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88 else:
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89 paramelement = test.getParameter(self.msinstance(),param)
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90 self.paramelement = paramelement
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91 if (param.find('|')>-1):
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92 plist = param.split('|')
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93 root = test.getParameter(self.msinstance(),plist[0])
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94 if not getattr(root,'nillable') and not getattr(paramelement,'nillable'):
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95 required = True
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96 return True
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97 elif getattr(root,'nillable') or (not getattr(root,'nillable') and getattr(paramelement,'nillable')):
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98 required = False
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99 return False
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100 else:
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101 if not getattr(paramelement,'nillable'):
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102 required = True
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103 return True
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104 elif getattr(paramelement,'nillable'):
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105 required = False
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106 return False
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107 return required
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108
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109
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110 #replace '**' with ' '
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111 def formatString(self,string):
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112 l = string.split(' ')
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113 return '**'.join(l)
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114
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115 '''
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116 Checks if the tool(operation) is already addded to Galaxy. It opens the tool_conf.xml file and loops through the "Web Service Workflow Tools" sections
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117 Then opens each and every tool (xml file) and looks for the description tag for the "Web Service" and "Client for Method" values and then checks
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118 if it same as the opearation and web service. As the code is dependent on description of the toool xml fie, any change in the description
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119 of the tool xml file can impact this function.
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120 '''
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121 def isToolPresent(self):
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122
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123 f = open(self.galaxyhome+'/tool_conf.xml','r')
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124 line = f.readline()
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125 linestripped = line.lstrip()
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126 linestripped = linestripped.rstrip()
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127
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128 while linestripped != '<section name="Select Web Service Tool" id="WebServices">':
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129 line = f.readline()
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130 linestripped = line.lstrip()
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131 linestripped = linestripped.rstrip()
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132
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133 line = f.readline()
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134 linestripped = line.lstrip()
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135 linestripped = linestripped.rstrip()
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136
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137 while linestripped != '</section>':
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138 if linestripped.find('<') >-1:
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139 toolparts = linestripped.split('"')
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140 print '\ntoolparts are : ',toolparts
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141 f1 = open(self.galaxyhome+'/tools/'+toolparts[-2],'r')
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142 line1 = f1.readline()
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143 while not line1.find('<description>') >-1:
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144 line1 = f1.readline()
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145
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146 linestripped1 = line1.lstrip()
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147 linestripped1 = linestripped1.rstrip()
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148 descriptionparts=linestripped1.split(' ')
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149 print '\nOperation : ',descriptionparts
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150 service = ''
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151 if(self.servicetype == 'SOAP'):
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152 service = self.clientfile
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153 elif self.servicetype == 'REST':
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154 service = self.webservice
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155 if(descriptionparts[5]==self.operation and descriptionparts[10] == service):
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156 f.close()
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157 f1.close()
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158 return True
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159 f1.close()
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160 line = f.readline()
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161 linestripped = line.lstrip()
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162 linestripped = linestripped.rstrip()
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163
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164 f.close()
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165 return False
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166
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167
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168 '''
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169 Creates a client file2 (xml file) for the given opertion in the SOAP web service
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170 This operation is invokes standalone and is cannot be used in workflows
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171 Then invokes another operation which adds this client file (tool) to the toolconfig.xml
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172 under 'Web Service Tools'
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173
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174 '''
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175
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176 def wsdlClient(self):
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177 with warnings.catch_warnings():
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178 warnings.simplefilter("ignore")
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179 wLoad=wsdlLoader()
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180 galaxyhome=os.environ.get('GALAXY_HOME')
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181 sys.path.append(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator')
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182 os.chdir(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator')
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183
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184 a= str(self.webservice).split('/')
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185 wsdlnamelist = a[len(a)-1].split(".")
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186 if len(wsdlnamelist)==1:
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187 wsdlnamelist=a[len(a)-1].split('?')
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188 print wsdlnamelist
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189
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190 foldername=wsdlnamelist[0]
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191
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192 path =galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/'+foldername
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193
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194 #creates the client stubs
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195 clientfile=wLoad.wsdlUrl2path(str(self.webservice),foldername)
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196
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197 webservice = clientfile#sys.argv[4]
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198 #operation = sys.argv[3]
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199 outputfile=open(self.outputfile,'w')
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200 test = ClientCreator()
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201 inputs= test.opname2inputs(self.operation,webservice)
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202 inputl = nested2flatDict(inputs)
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203 inputlist = inputl.keys()
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204 #noOfInputs=inputlist.count()
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205 count =0
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206 if (len(inputs)==0):
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207 inputs={' ':' '}
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208 #inputlist=inputs.keys()
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209 for i in inputlist:
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210 if count==0:
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211 outputfile.write(i+'\t'+webservice+'\t'+self.operation+'\n')
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212 else:
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213 outputfile.write(i+'\n')
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214 count=count+1
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215
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216
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217 cc = ClientCreator()
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218 self.msinstance = cc.opname2inputClassOb(self.operation,webservice)
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219
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220 ##generate client's xml
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221 galaxyhome=os.environ.get('GALAXY_HOME')
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222
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223 #./clients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation.
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224 #read the count and increment it.
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225
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226 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','r')
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227 clientCountFile.readline()
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228 clientCountStr = clientCountFile.readline()
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229 clientCount=string.atoi(clientCountStr)
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230 clientCount=clientCount+1
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231 clientCountFile.close()
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232
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233 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','w')
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234 clientCountFile.write('<count> \n')
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235 clientCountFile.write(str(clientCount)+'\n')
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236 clientCountFile.write('</count> \n')
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237 clientCountFile.close()
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238
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239 clientName = 'WebServiceclient_'+ str(clientCount)
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240
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241 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/'+clientName+'.xml','w')
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242 clientXml.seek(0,0)
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243
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244 clientXml.write('<tool id="' + clientName+'" name="'+foldername+'.' + self.operation +'">\n')
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245 clientXml.write(' <description> Client for operation : '+self.operation+' , Web service : '+webservice+' </description>\n')
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246
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247 #Only Required parameters
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248 clientXml.write(' <command interpreter="python">\n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output $servicetype ' +webservice+' '+self.operation)
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249
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250 #clientXml.write(' <command interpreter="python">\n client_1.py \n' +' $output \n ' +self.webservice+' \n '+self.operation+'\n')
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251 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
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252 test = MessageHandler()
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253 j=0
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254 for param in inputl:
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255 if self.isRequired(param):
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256 clientXml.write(' "'+param+'"')
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257 clientXml.write(' $param'+str(j))
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258 j=j+1
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259
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260
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261 #Both Required and optional paramters
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262 clientXml.write(' #else #client_1.py'+' $output $servicetype ' +webservice+' '+self.operation+'\n')
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263
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264 '''
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265 Required parameters - If the parameter is complex type (tree structure) then the the parameter is required
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266 only if both the root node and the leaf node are required (i.e. both root and leaf have attribute nillable as false)
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267 '''
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268
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269 j=0
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270 for param in inputl:
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271 if self.isRequired(param):
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272 clientXml.write(' "'+param+'"')
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273 clientXml.write(' $param'+str(j))
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274 j=j+1
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275
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276
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277 '''
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278 Optional parameters - If the parameter is complex type (tree structure) then the the paramter is optional
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279 if its root element is optional (i.e. root has attribute nillable as true) even if the leaf node (element)
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280 is required (i.e. leaf element has attribute nillable as false)
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281 '''
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282 for param in inputl:
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283 if not self.isRequired(param):
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284 clientXml.write(' "'+param+'"')
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285 clientXml.write(' $param'+str(j))
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286 j=j+1
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287
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288
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289 #params for array type
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290 # for param in self.inputs:
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291 # paramelement = test.getParameter(self.msinstance(),param)
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292 # if getattr(paramelement,'nillable')==True:
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293 # if string.find(param,"|0|")>-1:
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294 # ele = string(param,"|0|")
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295 # for param in self.inputs:
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296
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297
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298 # clientXml.write(' "'+param+'"')
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299 # clientXml.write(' $cond_source.param' + str(j))
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300 # j=j+1
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301
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302 clientXml.write(' #end if \n</command>\n')
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303
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304
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305 # for param in self.inputs:
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306 # paramelement = test.getParameter(self.msinstance(),param)
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307 # if getattr(paramelement,'nillable')==False or getattr(paramelement,'minOccurs')==1:
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308 # clientXml.write(' "'+param+'"\n')
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309 # clientXml.write(' $param'+str(j)+'\n')
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310 # j=j+1
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311
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312
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313 #clientXml.write('</command>\n')
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314
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315 #start writing inputs
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316 ##write inputs depending on required or not. if not required den dont display
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317 ##if required- den check default value, and if options exist.Depending on that
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318 ##decide the type of parameter and options
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319 ##The input servicetype tells what type of webservice it is wether SOAP or REST - Useful during invocation of the web servcie
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320 clientXml.write(' <inputs>\n')
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321 clientXml.write(' <param name="servicetype" type="hidden" value="SOAP" />\n')
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322
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323
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324 j=0
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325 for param in inputl:
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326 if self.isRequired(param):
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327 pName = getattr(self.paramelement,'pname')
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328 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
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329 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
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330 j=j+1
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331
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332 clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Show Optional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n')
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333 clientXml.write('<when value="no"> \n </when>')
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334 clientXml.write('<when value="yes"> \n')
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335
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336 for param in inputl:
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337 if not self.isRequired(param):
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338 pName = getattr(self.paramelement,'pname')
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339 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
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340 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
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341 j=j+1
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342
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343
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344 clientXml.write('</when>\n</conditional>')
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345
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346 # j=0
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347 # for param in self.inputs:
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348 # paramelement = test.getParameter(self.msinstance(),param)
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349 # if not getattr(paramelement,'nillable'):
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350 # pName = getattr(paramelement,'pname')#param.getName()
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351 # clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
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352 # clientXml.write('type="text" label="'+pName+'" help="see tip below" />\n')
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353 # j=j+1
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354
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355 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
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356
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357 clientXml.write(' <help>\n')
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358 paramtype = None
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359 for param in inputl:
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360 if self.isRequired(param):
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361 if isinstance(self.paramelement,ZSI.TC.String):
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362 paramtype = 'String'
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363 elif isinstance(self.paramelement,ZSI.TCnumbers.FPfloat):
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364 paramtype = 'Floating point'
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365 elif isinstance(self.paramelement,ZSI.TC.Boolean):
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366 paramtype = 'Boolean'
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367 elif isinstance(self.paramelement,ZSI.TCnumbers.Iint):
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368 paramtype = 'Integer'
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369 clientXml.write('\n.. class:: infomark\n\n**TIP:** About '+ getattr(self.paramelement,'pname') +': type is ' + paramtype + '\n')
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370
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371
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372
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373
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374 clientXml.write(' </help>\n</tool>')
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375
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376 # clientXml.write(' <help>\n')
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377
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378 # j=0
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379 # for param in params:
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380 # clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n')
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381
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|
382 # clientXml.write(' </help>\n</tool>')
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|
|
383 # clientXml.write('</tool>')
|
|
|
384 clientXml.close()
|
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|
385 editor = editToolConfig1()
|
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|
386 editor.addTool(clientName)
|
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387
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|
388 ##later add help feature
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|
389
|
|
|
390
|
|
|
391 def wadlClient(self):
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|
392 ##parse wadl
|
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|
393 pkg=JPackage('lsdis')
|
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|
394 urlToPass=java.net.URL(self.webservice)
|
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|
395 wadlUrl = self.webservice
|
|
|
396
|
|
|
397 webserviceId = ''#self.operation
|
|
|
398 resUrl = self.operation
|
|
|
399
|
|
|
400 urls = []
|
|
|
401 methods = []
|
|
|
402 params = []
|
|
|
403 docs = []
|
|
|
404
|
|
|
405 WADLParserDriver=pkg.WADLParserDriver
|
|
|
406 wPD=WADLParserDriver()
|
|
|
407 wPD.parse(urlToPass)
|
|
|
408 urls = wPD.getUrl()
|
|
|
409 methods = wPD.getCompleteMethodList()
|
|
|
410
|
|
|
411 #write into the output file information about the method and Web service to be invoked.
|
|
|
412 f=open(self.outputfile,'w')
|
|
|
413 f.write(self.webservice)
|
|
|
414 f.write('\n'+ resUrl)
|
|
|
415
|
|
|
416 a= str(self.webservice).split('/')
|
|
|
417 wadlnamelist = a[len(a)-1].split(".")
|
|
|
418 if len(wadlnamelist)==1:
|
|
|
419 wadlnamelist=a[len(a)-1].split('?')
|
|
|
420 print wadlnamelist
|
|
|
421
|
|
|
422 wadlname=wadlnamelist[0]
|
|
|
423
|
|
|
424
|
|
|
425 #get parameters for the selected method of the Web service
|
|
|
426 i=0
|
|
|
427 for method in methods:
|
|
|
428 x = str(method.getId())
|
|
|
429 y = str(urls.get(i))
|
|
|
430 webserviceId = x
|
|
|
431 #if x==webserviceId:
|
|
|
432 if y == resUrl :
|
|
|
433 params = method.getRequest().getParams()
|
|
|
434 break
|
|
|
435 i=i+1
|
|
|
436
|
|
|
437 f.write('\n'+webserviceId)
|
|
|
438 galaxyhome=os.environ.get('GALAXY_HOME')
|
|
|
439
|
|
|
440 methodname = resUrl.split('/')
|
|
|
441
|
|
|
442 #./clients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation.
|
|
|
443 #read the count and increment it.
|
|
|
444 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','r')
|
|
|
445 clientCountFile.readline()
|
|
|
446 clientCountStr = clientCountFile.readline()
|
|
|
447 clientCount=string.atoi(clientCountStr)
|
|
|
448 clientCount=clientCount+1
|
|
|
449 clientCountFile.close()
|
|
|
450
|
|
|
451 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','w')
|
|
|
452
|
|
|
453 clientCountFile.write('<count> \n')
|
|
|
454 clientCountFile.write(str(clientCount)+'\n')
|
|
|
455 clientCountFile.write('</count> \n')
|
|
|
456
|
|
|
457 #include the count in the tool's name and id to uniquely identify it.
|
|
|
458 clientName = 'WebServiceclient_'+ str(clientCount)
|
|
|
459
|
|
|
460 #create a new xml file under ./clients/
|
|
|
461 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/'+clientName+'.xml','w')
|
|
|
462 clientXml.seek(0,0)
|
|
|
463
|
|
|
464 #write the tool id, name and description
|
|
|
465 clientXml.write('<tool id="' + clientName+'1" name="'+wadlname+'.' + methodname[-1] +' ">\n')
|
|
|
466 clientXml.write(' <description> Client for method : '+self.operation+' , Web service : '+self.webservice+' </description>\n')
|
|
|
467
|
|
|
468 #the one-time invocation tool/client for a REST Web service invokes ./clients/client_1.py to invoke the Web service
|
|
|
469 #write the command tag to specify the arguments passed to this client_1.py
|
|
|
470 clientXml.write(' <command interpreter="python">\n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output $servicetype ' +resUrl)
|
|
|
471
|
|
|
472 j=0
|
|
|
473
|
|
|
474 for param in params:
|
|
|
475 if param.isRequired():
|
|
|
476 clientXml.write(' '+self.formatString(param.getName()))
|
|
|
477 clientXml.write(' $param' + str(j))
|
|
|
478 j=j+1
|
|
|
479 clientXml.write(' #else #client_1.py'+' $output $servicetype ' +resUrl)
|
|
|
480 j=0
|
|
|
481 for param in params:
|
|
|
482 if param.isRequired():
|
|
|
483 clientXml.write(' '+self.formatString(param.getName()))
|
|
|
484 clientXml.write(' $param' + str(j))
|
|
|
485 j=j+1
|
|
|
486
|
|
|
487 for param in params:
|
|
|
488 if not param.isRequired():
|
|
|
489 clientXml.write(' '+self.formatString(param.getName()))
|
|
|
490 clientXml.write(' $cond_source.param' + str(j))
|
|
|
491 j=j+1
|
|
|
492 clientXml.write(' #end if \n</command>\n')
|
|
|
493
|
|
|
494 #start writing inputs
|
|
|
495 ##write inputs depending on required or not. if not required den dont display
|
|
|
496 ##if required- den check default value, and if options exist.Depending on that
|
|
|
497 ##decide the type of parameter and options
|
|
|
498 ##The input servicetype tells what type of webservice it is wether SOAP or REST - Useful during invocation of the web servcie
|
|
|
499 clientXml.write(' <inputs>\n')
|
|
|
500 clientXml.write(' <param name="servicetype" type="hidden" value="REST" />')
|
|
|
501
|
|
|
502 #create a param for each required parameter described in the WADL. Check if defaults and options are specified in the WADL
|
|
|
503 j=0
|
|
|
504 for param in params:
|
|
|
505 if param.isRequired():
|
|
|
506 pName = param.getName()
|
|
|
507 for doc in param.getDocs():
|
|
|
508 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
|
|
|
509 pName = doc.getInnerText()
|
|
|
510 if param.getOptions().size()==0:
|
|
|
511 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
|
|
|
512 if not param.getDefault1() == None:
|
|
|
513 clientXml.write('value="'+param.getDefault1()+'" ')
|
|
|
514 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
|
|
|
515 j=j+1
|
|
|
516 else:
|
|
|
517 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )
|
|
|
518 for option in param.getOptions():
|
|
|
519 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')
|
|
|
520 if option.getName() == param.getDefault1():
|
|
|
521 clientXml.write('selected="true"')
|
|
|
522 clientXml.write('>'+option.getName()+'</option>\n ')
|
|
|
523 clientXml.write(' </param> \n')
|
|
|
524 j=j+1
|
|
|
525
|
|
|
526 #create a conditional param for each optional parameter described in the WADL.
|
|
|
527 clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Show Optional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n')
|
|
|
528 clientXml.write('<when value="no"> \n </when>')
|
|
|
529 clientXml.write('<when value="yes"> \n')
|
|
|
530 for param in params:
|
|
|
531 if not param.isRequired():
|
|
|
532 pName = param.getName()
|
|
|
533 for doc in param.getDocs():
|
|
|
534 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
|
|
|
535 pName = doc.getInnerText()
|
|
|
536 if param.getOptions().size()==0:
|
|
|
537 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
|
|
|
538 if not param.getDefault1() == None:
|
|
|
539 clientXml.write('value="'+param.getDefault1()+'" ')
|
|
|
540 clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n')
|
|
|
541 j=j+1
|
|
|
542 else:
|
|
|
543 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' )
|
|
|
544 for option in param.getOptions():
|
|
|
545 clientXml.write(' <option value="'+self.formatString(option.getName())+'" ')
|
|
|
546 if option.getName() == param.getDefault1():
|
|
|
547 clientXml.write('selected="true"')
|
|
|
548 clientXml.write('>'+option.getName()+'</option>\n ')
|
|
|
549 clientXml.write(' </param> \n')
|
|
|
550 j=j+1
|
|
|
551
|
|
|
552
|
|
|
553 clientXml.write('</when>\n</conditional>')
|
|
|
554 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
|
|
|
555
|
|
|
556 #write information about each parameter in the help section
|
|
|
557 clientXml.write(' <help>\n')
|
|
|
558
|
|
|
559 clientXml.write('Replace white space with ** in all parameter values\n')
|
|
|
560
|
|
|
561 for param in params:
|
|
|
562 if param.isRequired():
|
|
|
563 pName = param.getName()
|
|
|
564 for doc in param.getDocs():
|
|
|
565 if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT":
|
|
|
566 pName = doc.getInnerText()
|
|
|
567 clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ pName +' type is ' + param.getType()+'\n')
|
|
|
568
|
|
|
569 clientXml.write(' </help>\n</tool>')
|
|
|
570
|
|
|
571
|
|
|
572 #adds the newly created tool to tool_conf.xml in Galaxy under the 'Web Service Tools' section.
|
|
|
573 editor = editToolConfig1()
|
|
|
574 editor.addTool(clientName)
|
|
|
575
|
|
|
576 ##later add help feature
|
|
|
577
|
|
|
578
|
|
|
579 def sawadlClient(self):
|
|
|
580 ##parse sawadl
|
|
|
581 javahome = os.environ.get('JAVA_HOME')
|
|
|
582 galaxyhome=os.environ.get('GALAXY_HOME')
|
|
|
583 classpath= galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/bin'
|
|
|
584 jarpath = galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/lib/'
|
|
|
585 machine = platform.machine()
|
|
|
586
|
|
|
587 #if machine == 'x86_64' :
|
|
|
588 # print 'a'
|
|
|
589 # startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
|
|
|
590 #elif machine == 'i686' :
|
|
|
591 # print 'b'
|
|
|
592 # startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
|
|
|
593 #elif machine == 'sun4u' :
|
|
|
594 # startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
|
|
|
595 #else :
|
|
|
596 # print 'c'
|
|
|
597 # System.exit("Could not identify machine, please specify path to libjvm.so")
|
|
|
598
|
|
|
599
|
|
|
600 pkg=JPackage('edu.uga.cs.lsdis.meteors.wadls')
|
|
|
601 pkgModel =JPackage('org.semanticweb.owlapi.model')
|
|
|
602 pkgApiBinding =JPackage('org.semanticweb.owlapi.apibinding')
|
|
|
603 pkgVocab = JPackage('org.semanticweb.owlapi.vocab')
|
|
|
604
|
|
|
605 DOCUMENT_IRI = "http://cs.uga.edu/~ganjoo/galaxy/EDAM.owl"
|
|
|
606
|
|
|
607 sawadlUrl = self.webservice
|
|
|
608
|
|
|
609 webserviceId = ''#self.methodName
|
|
|
610 resUrl = self.operation
|
|
|
611
|
|
|
612 urls = []
|
|
|
613 methods = []
|
|
|
614 params = []
|
|
|
615 annotationSet = []
|
|
|
616
|
|
|
617 SAWADLParserDriver=pkg.SAWADLParserDriver
|
|
|
618 sawPD=SAWADLParserDriver()
|
|
|
619 sawPD.parse(sawadlUrl)
|
|
|
620 urls = sawPD.getUrl()
|
|
|
621 methods = sawPD.getCompleteMethodList()
|
|
|
622
|
|
|
623 IRI = pkgModel.IRI
|
|
|
624 OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary
|
|
|
625 OWLManager = pkgApiBinding.OWLManager
|
|
|
626 OWLLiteral = pkgModel.OWLLiteral
|
|
|
627 owlOntManager = OWLManager.createOWLOntologyManager()
|
|
|
628 ontology = owlOntManager.loadOntologyFromOntologyDocument(IRI.create(DOCUMENT_IRI))
|
|
|
629 dataFactory = owlOntManager.getOWLDataFactory()
|
|
|
630 propertyComment = dataFactory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI())
|
|
|
631
|
|
|
632 f=open(self.outputfile,'w')
|
|
|
633 f.write(sawadlUrl)
|
|
|
634 f.write(resUrl+'\t')
|
|
|
635
|
|
|
636
|
|
|
637 i=0
|
|
|
638 for method in methods:
|
|
|
639 x = str(method.getName())
|
|
|
640 y = str(urls.get(i))
|
|
|
641 #if x == webserviceId :
|
|
|
642 webserviceId = x
|
|
|
643 if y == resUrl :
|
|
|
644 params = method.getRequest().getParamList()
|
|
|
645 break
|
|
|
646 i=i+1
|
|
|
647
|
|
|
648 f.write(webserviceId)
|
|
|
649
|
|
|
650
|
|
|
651 ##generate client's xml
|
|
|
652 galaxyhome=os.environ.get('GALAXY_HOME')
|
|
|
653
|
|
|
654 #./clients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation.
|
|
|
655 #read the count and increment it.
|
|
|
656
|
|
|
657 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','r')
|
|
|
658 clientCountFile.readline()
|
|
|
659 clientCountStr = clientCountFile.readline()
|
|
|
660 clientCount=string.atoi(clientCountStr)
|
|
|
661 clientCount=clientCount+1
|
|
|
662 clientCountFile.close()
|
|
|
663
|
|
|
664 clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','w')
|
|
|
665 clientCountFile.write('<count> \n')
|
|
|
666 clientCountFile.write(str(clientCount)+'\n')
|
|
|
667 clientCountFile.write('</count> \n')
|
|
|
668
|
|
|
669 clientName = 'WebServiceclient_'+ str(clientCount)
|
|
|
670
|
|
|
671 clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/'+clientName+'.xml','w')
|
|
|
672 clientXml.seek(0,0)
|
|
|
673
|
|
|
674 clientXml.write('<tool id="' + clientName+'1" name="' + webserviceId +'">\n')
|
|
|
675 clientXml.write(' <description> Client for method: '+webserviceId+' , Web service: '+self.webservice+' </description>\n')
|
|
|
676
|
|
|
677
|
|
|
678 clientXml.write(' <command interpreter="python">\n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output $servicetype ' +resUrl)
|
|
|
679 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
|
|
|
680
|
|
|
681
|
|
|
682 j=0
|
|
|
683 for param in params:
|
|
|
684 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
|
|
|
685 clientXml.write(' '+self.formatString(param.getName())+'\n')
|
|
|
686 clientXml.write(' $param' + str(j)+'\n')
|
|
|
687 j=j+1
|
|
|
688
|
|
|
689 clientXml.write(' #else #client_1.py'+' $output $servicetype ' +resUrl)
|
|
|
690 j=0
|
|
|
691 for param in params:
|
|
|
692 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
|
|
|
693 clientXml.write(' '+self.formatString(param.getName()))
|
|
|
694 clientXml.write(' $param' + str(j))
|
|
|
695 j=j+1
|
|
|
696
|
|
|
697 for param in params:
|
|
|
698 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':
|
|
|
699 clientXml.write(' '+self.formatString(param.getName()))
|
|
|
700 clientXml.write(' $cond_source.param' + str(j))
|
|
|
701 j=j+1
|
|
|
702
|
|
|
703 clientXml.write('#end if \n </command>\n')
|
|
|
704
|
|
|
705 #start writing inputs
|
|
|
706 ##write inputs depending on required or not. if not required den dont display
|
|
|
707 ##if required- den check default value, and if options exist.Depending on that
|
|
|
708 ##decide the type of parameter and options
|
|
|
709 ##The input param servicetype tells what type of webservice it is wether SOAP or REST - Useful during invocation of the web servcie
|
|
|
710 clientXml.write(' <inputs>\n')
|
|
|
711 cleintXml.write(' <param name="servicetype" type="hidden" value="REST"/>')
|
|
|
712
|
|
|
713 j=0
|
|
|
714 for param in params:
|
|
|
715 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
|
|
|
716 f.write('\n '+ param.getName() + ' options: '+str(param.getOptionvalue().size()))
|
|
|
717 if param.getOptionvalue().size()==0:
|
|
|
718 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
|
|
|
719 if not param.getDefault1() == None:
|
|
|
720 clientXml.write('value="'+param.getDefault1()+'" ')
|
|
|
721 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')
|
|
|
722 j=j+1
|
|
|
723 else:
|
|
|
724 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' )
|
|
|
725 for option in param.getOptionvalue():
|
|
|
726 clientXml.write(' <option value="'+self.formatString(option)+'" ')
|
|
|
727 if option == param.getDefault1():
|
|
|
728 clientXml.write('selected="true"')
|
|
|
729 clientXml.write('>'+option+'</option>\n ')
|
|
|
730 clientXml.write(' </param> \n')
|
|
|
731 j=j+1
|
|
|
732
|
|
|
733
|
|
|
734 clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Display Optional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n')
|
|
|
735 clientXml.write('<when value="no"> \n </when>')
|
|
|
736 clientXml.write('<when value="yes"> \n')
|
|
|
737
|
|
|
738 for param in params:
|
|
|
739 if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE':
|
|
|
740 f.write('\n '+ param.getName() + ' options: '+str(param.getOptionvalue().size()))
|
|
|
741 if param.getOptionvalue().size()==0:
|
|
|
742 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
|
|
|
743 if not param.getDefault1() == None:
|
|
|
744 clientXml.write('value="'+param.getDefault1()+'" ')
|
|
|
745 clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n')
|
|
|
746 j=j+1
|
|
|
747 else:
|
|
|
748 clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' )
|
|
|
749 for option in param.getOptionvalue():
|
|
|
750 clientXml.write(' <option value="'+self.formatString(option)+'" ')
|
|
|
751 if option == param.getDefault1():
|
|
|
752 clientXml.write('selected="true"')
|
|
|
753 clientXml.write('>'+option+'</option>\n ')
|
|
|
754 clientXml.write(' </param> \n')
|
|
|
755 j=j+1
|
|
|
756
|
|
|
757 clientXml.write('</when>\n</conditional>\n')
|
|
|
758
|
|
|
759 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
|
|
|
760
|
|
|
761 clientXml.write(' <help>\n')
|
|
|
762 for param in params:
|
|
|
763 if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE':
|
|
|
764 clientXml.write('\n.. class:: infomark\n\n**TIP:** About '+ param.getName() +': type is ' + param.getType())
|
|
|
765
|
|
|
766 modelRef = sawPD.getCompleteModelReference(param)
|
|
|
767 if not modelRef is None:
|
|
|
768 paramClass = dataFactory.getOWLClass(IRI.create(modelRef));
|
|
|
769 annotationSet = paramClass.getAnnotations(ontology,propertyComment)
|
|
|
770 for annotation in annotationSet:
|
|
|
771 if isinstance(annotation.getValue(),OWLLiteral):
|
|
|
772 val = annotation.getValue()
|
|
|
773 if val.isOWLStringLiteral() and not val.isOWLTypedLiteral():
|
|
|
774 print 'val.getLiteral()=' + val.getLiteral()
|
|
|
775 clientXml.write(', description from ontology is "' + val.getLiteral()+'"')
|
|
|
776 break
|
|
|
777 clientXml.write('\n')
|
|
|
778 clientXml.write(' </help>\n</tool>')
|
|
|
779 editor = editToolConfig1()
|
|
|
780 editor.addTool(clientName)
|
|
|
781
|
|
|
782 ##later add help feature
|
|
|
783
|
|
|
784 def wsdlRESTClient(self):
|
|
|
785 ##parse wadl
|
|
|
786 javahome = os.environ.get('JAVA_HOME')
|
|
|
787 galaxyhome=os.environ.get('GALAXY_HOME')
|
|
|
788 classpath= galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/WodenWSDLParser/bin'
|
|
|
789 jarpath = galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/WodenWSDLParser/lib/'
|
|
|
790 machine = platform.machine()
|
|
|
791
|
|
|
792 if machine == 'x86_64' :
|
|
|
793 print 'a'
|
|
|
794 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
|
|
|
795 elif machine == 'i686' :
|
|
|
796 print 'b'
|
|
|
797 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
|
|
|
798 elif machine == 'sun4u' :
|
|
|
799 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
|
|
|
800 else :
|
|
|
801 print 'c'
|
|
|
802 System.exit("Could not identify machine, please specify path to libjvm.so")
|
|
|
803
|
|
|
804
|
|
|
805 pkg=JPackage('lsdis')
|
|
|
806 wsdlUrl = self.webserviceId
|
|
|
807
|
|
|
808 webserviceId = ''#self.methodName
|
|
|
809 resUrl = self.resourceName
|
|
|
810
|
|
|
811 urls = []
|
|
|
812 methods = []
|
|
|
813 params = []
|
|
|
814 paramTypes = []
|
|
|
815
|
|
|
816 WSDLParserDriver =pkg.WSDLParserDriver
|
|
|
817 wPD=WSDLParserDriver()
|
|
|
818 wPD.parse(wsdlUrl)
|
|
|
819 methods = wPD.getCompleteMethodList()
|
|
|
820 urls = wPD.getUrl()
|
|
|
821
|
|
|
822 f=open(self.Ofile,'w')
|
|
|
823 f.write(wsdlUrl)
|
|
|
824 f.write('\n'+ resUrl)
|
|
|
825 f.write('\n'+webserviceId)
|
|
|
826
|
|
|
827
|
|
|
828 i=0
|
|
|
829 for method in methods:
|
|
|
830 x = str(method.getName().getLocalPart())
|
|
|
831 y = str(url.get(i))
|
|
|
832 webserviceId = x
|
|
|
833 if y == resUrl :
|
|
|
834 wPD.getParameters(x)
|
|
|
835 f.write('method matched')
|
|
|
836 paramTypes = wPD.getParamTypeList()
|
|
|
837 params = wPD.getParamList()
|
|
|
838 break
|
|
|
839 i=i+1
|
|
|
840
|
|
|
841
|
|
|
842
|
|
|
843
|
|
|
844 ##generate client's xml
|
|
|
845 galaxyhome=os.environ.get('GALAXY_HOME')
|
|
|
846
|
|
|
847 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','r')
|
|
|
848 clientCountFile.readline()
|
|
|
849 clientCountStr = clientCountFile.readline()
|
|
|
850 clientCount=string.atoi(clientCountStr)
|
|
|
851 clientCount=clientCount+1
|
|
|
852 clientCountFile.close()
|
|
|
853
|
|
|
854 clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','w')
|
|
|
855 clientCountFile.write('<count> \n')
|
|
|
856 clientCountFile.write(str(clientCount)+'\n')
|
|
|
857 clientCountFile.write('</count> \n')
|
|
|
858
|
|
|
859
|
|
|
860
|
|
|
861
|
|
|
862 clientName = 'WebServiceclient_'+ str(clientCount)
|
|
|
863
|
|
|
864 clientXml=open(galaxyhome+'/tools/WebServiceTool/clients/'+clientName+'.xml','w')
|
|
|
865 clientXml.seek(0,0)
|
|
|
866
|
|
|
867 clientXml.write('<tool id="' + clientName+'" name="' + webserviceId +'">\n')
|
|
|
868 clientXml.write(' <description> Client for method: '+webserviceId+' , Web service: '+self.webservice+' </description>\n')
|
|
|
869
|
|
|
870
|
|
|
871 clientXml.write(' <command interpreter="python">\n client_1.py \n'+' $output \n $servicetype\n ' +resUrl+'\n')
|
|
|
872 ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
|
|
|
873
|
|
|
874 j=0
|
|
|
875 for param in params:
|
|
|
876 clientXml.write(' '+self.formatString(param)+'\n')
|
|
|
877 clientXml.write(' $param' + str(j)+'\n')
|
|
|
878 j=j+1
|
|
|
879 clientXml.write('</command>\n')
|
|
|
880
|
|
|
881 ##write inputs depending on required or not. if not required den dont display
|
|
|
882 ##if required- den check default value, and if options exist.Depending on that
|
|
|
883 ##decide the type of parameter and options
|
|
|
884 clientXml.write(' <inputs>\n')
|
|
|
885 cleintXml.write(' <param name="servicetype" type="hidden" value="REST"/>')
|
|
|
886
|
|
|
887 j=0
|
|
|
888 for param in params:
|
|
|
889 clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ')
|
|
|
890 clientXml.write('type="text" label="'+param+'" help="see tip below" />\n')
|
|
|
891 j=j+1
|
|
|
892
|
|
|
893
|
|
|
894
|
|
|
895 clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n')
|
|
|
896
|
|
|
897 clientXml.write(' <help>\n')
|
|
|
898
|
|
|
899 clientXml.write('** Replace white with ** in all parameter values **\n')
|
|
|
900
|
|
|
901 j=0
|
|
|
902 for param in params:
|
|
|
903 clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n')
|
|
|
904
|
|
|
905 clientXml.write(' </help>\n</tool>')
|
|
|
906 editor = editToolConfig()
|
|
|
907 editor.addTool(clientName)
|
|
|
908
|
|
|
909 ##later add help feature
|
|
|
910
|
|
|
911
|
|
|
912 # Addedfor testing purpose
|
|
|
913
|
|
|
914 if __name__ == "__main__":
|
|
|
915
|
|
|
916 test = ClientGenerator1('http://www.cs.uga.edu/~guttula/wublast.wsdl','run',None,'SOAP')
|
|
|
917 present = test.isToolPresent()
|
|
|
918 required = test.isRequired('_parameters|_sequence')
|
|
|
919 print 'required : ',required
|
