Mercurial > repos > ganjoo > webservice_toolsuite

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author ganjoo
date Tue, 07 Jun 2011 18:00:50 -0400
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d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 import warnings
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2
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3 with warnings.catch_warnings():
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4 warnings.simplefilter("ignore")
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5 import platform
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6
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7 from jpype._jpackage import JPackage
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8 from jpype import *
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9 import os.path
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10 import sys
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11
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12 class Document(object):
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13
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14 #invoked to get methods described in a WADL document
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15 def getWADLMethods(self, wadlUrl, outputFileUrl ):
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16
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17 #get environment variables JAVA_HOME and GALAXY_HOME
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18 javahome = os.environ.get('JAVA_HOME')
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19 galaxyhome=os.environ.get('GALAXY_HOME')
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20
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21 #classpath, jarpath are variables pointing to the java libraries required to parse a WADL document
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22 classpath= galaxyhome + '/tools/WebServiceTool/ParserForWADL/bin'
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23 jarpath = galaxyhome + '/tools/WebServiceTool/ParserForWADL/lib/'
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24
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25 #start JVM depending on the machine. The location of libjvm.so is assumed to be standard.
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26 #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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27 machine = platform.machine()
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28 if machine == 'x86_64' :
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29 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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30 elif machine == 'i686' :
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31 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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32 elif machine == 'sun4u' :
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33 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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34 else :
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35 System.exit("Could not identify machine, please specify path to libjvm.so")
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36
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37 #tell JPYPE that the package name is lsdis
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38 pkg=JPackage('lsdis')
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39
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40 urlToPass=java.net.URL(wadlUrl)
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41
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42 #convert __tilda__ to ~
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43 if(wadlUrl.find('__tilda__')>-1):
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44 ulist = wadlUrl.split('__tilda__')
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45 urlToPass = java.net.URL('~'.join(ulist))
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46
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47
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48 outputfile=open(outputFileUrl,'w')
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49 outputfile.seek(0,0)
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50
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51 urls = []
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52 methods = []
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53
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54 #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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55 WADLParserDriver=pkg.WADLParserDriver
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56 wPD=WADLParserDriver()
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57 wPD.parse(urlToPass)
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58 urls = wPD.getUrl()
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59 methods = wPD.getCompleteMethodList()
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60
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61 #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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62 i=0
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63 for url in urls:
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64 outputfile.write(wadlUrl+"\t")
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65 outputfile.write(str(methods[i].getId())+"\t")
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66 outputfile.write(str(url)+"\n")
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67 i=i+1
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68
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69
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70
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71 #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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72 def getWSDLMethods(self, wsdlUrl, outputFileUrl ):
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73 javahome = os.environ.get('JAVA_HOME')
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74 galaxyhome=os.environ.get('GALAXY_HOME')
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75 classpath= galaxyhome + '/tools/restClientWSDL/WodenWSDLParser/bin'
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76 jarpath = galaxyhome + '/tools/restClientWSDL/WodenWSDLParser/lib/'
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77 machine = platform.machine()
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78
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79 #start JVM depending on the machine. The location of libjvm.so is assumed to be standard.
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80 #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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81 if machine == 'x86_64' :
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82 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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83 elif machine == 'i686' :
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84 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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85 elif machine == 'sun4u' :
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86 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
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87 else :
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88 System.exit("Could not identify machine, please specify path to libjvm.so")
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89
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90 pkg=JPackage('lsdis')
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91
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92 outputfile=open(outputFileUrl,'w')
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93 outputfile.seek(0,0)
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94 length=(len(sys.argv))
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95
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96 urls = []
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97 methods = []
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98
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99 if(wsdlUrl.find('__tilda__')>-1):
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100 ulist = wsdlUrl.split('__tilda__')
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101 urlToPass = '~'.join(ulist)
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102
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103 WSDLParserDriver=pkg.WSDLParserDriver
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104 wPD=WSDLParserDriver()
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105 wPD.parse(urlToPass)
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106 urls = wPD.getUrl()
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107 methods = wPD.getCompleteMethodList()
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108
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109 i=0
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110 for url in urls:
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111 outputfile.write(wsdlUrl+"\t")
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112 outputfile.write(str(methods[i].getName().getLocalPart())+"\t")
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113 outputfile.write(str(url)+"\n")
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114 i=i+1
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115
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116
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117 # invoked to get methods described in a SAWADL document
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118 def getSAWADLMethods(self, sawadlUrl, outputFileUrl ):
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119 javahome = os.environ.get('JAVA_HOME')
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120 galaxyhome=os.environ.get('GALAXY_HOME')
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121 classpath= galaxyhome + '/tools/restclientSAWADL/lib/SAWADLParser/bin'
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122 machine = platform.machine()
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123
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124 #start JVM depending on the machine. The location of libjvm.so is assumed to be standard.
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125 #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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126 if machine == 'x86_64' :
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127 startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath)
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128 elif machine == 'i686' :
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129 startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath)
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130 elif machine == 'sun4u' :
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131 startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath)
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132 else :
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133 System.exit("Could not identify machine, please specify path to libjvm.so")
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134
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135 pkg=JPackage('edu.uga.cs.lsdis.meteors.wadls')
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137
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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138
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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139 outputfile=open(outputFileUrl,'w')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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140 outputfile.seek(0,0)
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141
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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142 if(sawadlUrl.find('__tilda__')>-1):
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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143 ulist = sawadlUrl.split('__tilda__')
d5cd409b8a18 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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144 urlToPass = '~'.join(ulist)
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145
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146 urls = []
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147 methods = []
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148
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149
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150 SAWADLParserDriver=pkg.SAWADLParserDriver
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151 sawPD=SAWADLParserDriver()
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152 sawPD.parse(urlToPass)
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153 urls = sawPD.getUrl()
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154 methods = sawPD.getCompleteMethodList()
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155
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156 i=0
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157 for url in urls:
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158 outputfile.write(sawadlUrl+"\t")
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159 outputfile.write(str(methods[i].getName())+"\t")
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160 outputfile.write(str(url)+"\n")
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161 i=i+1
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162
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164
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165
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166