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1 '''
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2 @author Chaitanya Guttula
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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
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7 # Author = Chaitanya Guttula
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8
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9 import warnings
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10
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11 with warnings.catch_warnings():
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12 warnings.simplefilter("ignore")
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13
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14 import platform
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15 import commands
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16 import ZSI
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17 import os
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18 from clientGenerator.creatorEngineComplex import *
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19 from clientGenerator.wsdl2path import *
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20 from jpype._jpackage import JPackage
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21 from jpype import *
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22 import sys
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23
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24 class Document(object):
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25
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26 '''
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27 Method to get all the operations from the WSDL file and write it to Galaxy output datasets
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28 '''
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29
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30 def getWSDLMethods(self, url , outputFileUrl):
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31 wLoad=wsdlLoader()
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32 a= str(url).split('/')
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33 wsdlnamelist = a[len(a)-1].split(".")
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34 if len(wsdlnamelist)==1:
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35 wsdlnamelist=a[len(a)-1].split('?')
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36 print wsdlnamelist
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37
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38 foldername=wsdlnamelist[0]
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39
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40 galaxyhome=os.environ.get('GALAXY_HOME')
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41 path =galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/'+foldername
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42 os.chdir(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/')
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43
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44 #creates the client stubs
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45 clientfile=wLoad.wsdlUrl2path(str(url),foldername)
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46
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47 #Gets the list of operations
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48 test=ClientCreator()
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49 operations=test.path2Ops(str(clientfile)).keys()
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50
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51 #COnvert ~ to __tilda__
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52 if(url.find('~')>-1):
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53 ulist = url.split('~')
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54 url = '__tilda__'.join(ulist)
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55
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56
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57 #Print all the operations and web service info to the Galaxy output dataset
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58 outputfile=open(outputFileUrl,'w')
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59 count=0
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60 outputfile.seek(0,0)
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61 for k in operations:
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62 count=count+1
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63 if(count==1):
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64 outputfile.write(k+'\t'+clientfile+'\t'+url+'\n')
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65 else:
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66 outputfile.write(k+'\n')
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67
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68 #invoked to get REST methods described in a WSDL 2.0 document. Steps are similar to getWADLMethods except the library to parse WSDL 2.0 is used.
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69 def getWSDLRESTMethods(self, wsdlUrl, outputFileUrl ):
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70 javahome = os.environ.get('JAVA_HOME')
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71 galaxyhome=os.environ.get('GALAXY_HOME')
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72 classpath= galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/WodenWSDLParser/bin'
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73 jarpath = galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/WodenWSDLParser/lib/'
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74 machine = platform.machine()
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75
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76 #start JVM depending on the machine. The location of libjvm.so is assumed to be standard.
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77 #you can replace lines 81 to 88, with startJVM("LOCATION OF YOUR LIBJVM.SO","-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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78 if machine == 'x86_64' :
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79 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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80 elif machine == 'i686' :
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81 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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82 elif machine == 'sun4u' :
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83 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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84 else :
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85 System.exit("Could not identify machine, please specify path to libjvm.so")
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86
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87 pkg=JPackage('lsdis')
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88
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89 outputfile=open(outputFileUrl,'w')
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90 outputfile.seek(0,0)
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91 length=(len(sys.argv))
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92
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93 urls = []
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94 methods = []
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95
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96 if(wsdlUrl.find('__tilda__')>-1):
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97 ulist = wsdlUrl.split('__tilda__')
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98 urlToPass = '~'.join(ulist)
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99
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100 WSDLParserDriver=pkg.WSDLParserDriver
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101 wPD=WSDLParserDriver()
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102 wPD.parse(urlToPass)
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103 urls = wPD.getUrl()
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104 methods = wPD.getCompleteMethodList()
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105
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106 i=0
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107 for url in urls:
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108 outputfile.write(wsdlUrl+"\t")
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109 outputfile.write(str(methods[i].getName().getLocalPart())+"\t")
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110 outputfile.write(str(url)+"\n")
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111 i=i+1
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112
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113
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114
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115 '''
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116 Invoked to get methods described in a WADL document
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117 '''
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118 def getWADLMethods(self, wadlUrl, outputFileUrl ):
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119
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120 #get environment variables JAVA_HOME and GALAXY_HOME
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121 javahome = os.environ.get('JAVA_HOME')
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122 galaxyhome=os.environ.get('GALAXY_HOME')
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123
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124 #classpath, jarpath are variables pointing to the java libraries required to parse a WADL document
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125 classpath= galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/ParserForWADL/bin'
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126 jarpath = galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/ParserForWADL/lib/'
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127
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128 #start JVM depending on the machine. The location of libjvm.so is assumed to be standard.
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129 #you can replace lines 28 to 35, with startJVM("LOCATION OF YOUR LIBJVM.SO","-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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130 machine = platform.machine()
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131 if machine == 'x86_64' :
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132 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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133 elif machine == 'i686' :
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134 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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135 elif machine == 'sun4u' :
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136 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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137 else :
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138 System.exit("Could not identify machine, please specify path to libjvm.so")
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139
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140 #tell JPYPE that the package name is lsdis
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141 pkg=JPackage('lsdis')
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142
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143 urlToPass=java.net.URL(wadlUrl)
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144
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145 #convert __tilda__ to ~
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146 if(wadlUrl.find('__tilda__')>-1):
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147 ulist = wadlUrl.split('__tilda__')
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148 urlToPass = java.net.URL('~'.join(ulist))
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149
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150
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151 outputfile=open(outputFileUrl,'w')
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152 outputfile.seek(0,0)
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153
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154 urls = []
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155 methods = []
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156
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157 #using JPYPE call appropriate Java classes and methods to parse the WADL document and get a list of methods defined in it
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158 WADLParserDriver=pkg.WADLParserDriver
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159 wPD=WADLParserDriver()
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160 wPD.parse(urlToPass)
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161 urls = wPD.getUrl()
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162 methods = wPD.getCompleteMethodList()
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163
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164 #write the url of the WADL and the list of methods to the output in a tabular format, for the Step 2 tool to read from.
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165 i=0
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166 for url in urls:
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167 outputfile.write(str(url)+"\t")
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168 outputfile.write(str(methods[i].getId())+"\t")
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169 outputfile.write(wadlUrl+"\n")
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170 i=i+1
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171
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172
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173
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174 # invoked to get methods described in a SAWADL document
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175 def getSAWADLMethods(self, sawadlUrl, outputFileUrl ):
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176 javahome = os.environ.get('JAVA_HOME')
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177 galaxyhome=os.environ.get('GALAXY_HOME')
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178 classpath= galaxyhome + '/tools/restclientSAWADL/lib/SAWADLParser/bin'
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179 machine = platform.machine()
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180
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181 #start JVM depending on the machine. The location of libjvm.so is assumed to be standard.
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182 #you can replace lines 126 to 133, with startJVM("LOCATION OF YOUR LIBJVM.SO","-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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183 if machine == 'x86_64' :
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184 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath)
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185 elif machine == 'i686' :
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186 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath)
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187 elif machine == 'sun4u' :
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188 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath)
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189 else :
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190 System.exit("Could not identify machine, please specify path to libjvm.so")
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191
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192 pkg=JPackage('edu.uga.cs.lsdis.meteors.wadls')
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193
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194
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195 # Open the output file for galaxy
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196 outputfile=open(outputFileUrl,'w')
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197 outputfile.seek(0,0)
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198
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199 if(sawadlUrl.find('__tilda__')>-1):
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200 ulist = sawadlUrl.split('__tilda__')
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201 urlToPass = '~'.join(ulist)
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202
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203 urls = []
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204 methods = []
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205
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206 #invoke the parser and get the method list
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207 SAWADLParserDriver=pkg.SAWADLParserDriver
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208 sawPD=SAWADLParserDriver()
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209 sawPD.parse(urlToPass)
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210 urls = sawPD.getUrl()
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211 methods = sawPD.getCompleteMethodList()
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212
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213 #Print the methods and service information to the
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214 i=0
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215 for url in urls:
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216 outputfile.write(sawadlUrl+"\t")
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217 outputfile.write(str(methods[i].getName())+"\t")
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218 outputfile.write(str(url)+"\n")
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219 i=i+1
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220
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