--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/getMethods_m.py	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,220 @@
+'''
+@author  Chaitanya Guttula
+@see     LICENSE (MIT style license file).
+'''
+
+
+# Author = Chaitanya Guttula
+
+import warnings
+
+with warnings.catch_warnings():
+    warnings.simplefilter("ignore")
+
+    import platform
+    import commands
+    import ZSI
+    import os
+    from clientGenerator.creatorEngineComplex import *
+    from clientGenerator.wsdl2path import *
+    from jpype._jpackage import JPackage
+    from jpype import *
+    import sys
+
+class Document(object):  
+
+    '''    
+        Method to get all the operations from the WSDL file and write it to Galaxy output datasets
+    '''
+     	    
+    def getWSDLMethods(self, url , outputFileUrl):
+        wLoad=wsdlLoader()
+        a= str(url).split('/')
+        wsdlnamelist = a[len(a)-1].split(".")
+        if len(wsdlnamelist)==1:
+    	    wsdlnamelist=a[len(a)-1].split('?')
+    	    print wsdlnamelist
+
+        foldername=wsdlnamelist[0]
+        
+        galaxyhome=os.environ.get('GALAXY_HOME')
+        path =galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/'+foldername
+        os.chdir(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/')
+        
+    #creates the client stubs
+        clientfile=wLoad.wsdlUrl2path(str(url),foldername)
+        
+    #Gets the list of operations
+        test=ClientCreator()
+        operations=test.path2Ops(str(clientfile)).keys()
+        
+    #COnvert ~ to __tilda__
+        if(url.find('~')>-1):
+            ulist = url.split('~')
+            url = '__tilda__'.join(ulist)
+
+
+    #Print all the operations and web service info to the Galaxy output dataset
+        outputfile=open(outputFileUrl,'w')
+        count=0
+        outputfile.seek(0,0)
+        for k in operations:
+            count=count+1
+            if(count==1):
+                outputfile.write(k+'\t'+clientfile+'\t'+url+'\n')
+    	    else:
+                outputfile.write(k+'\n')
+
+    #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.
+    def getWSDLRESTMethods(self, wsdlUrl, outputFileUrl ):
+        javahome = os.environ.get('JAVA_HOME')
+        galaxyhome=os.environ.get('GALAXY_HOME')
+        classpath= galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/WodenWSDLParser/bin'
+        jarpath = galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/WodenWSDLParser/lib/'
+        machine = platform.machine()
+        
+    #start JVM depending on the machine. The location of libjvm.so is assumed to be standard.
+    #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)
+        if machine == 'x86_64' :
+            startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
+        elif machine == 'i686' :
+            startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
+        elif machine == 'sun4u' :
+            startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
+        else :
+            System.exit("Could not identify machine, please specify path to libjvm.so")
+    
+        pkg=JPackage('lsdis')
+       
+        outputfile=open(outputFileUrl,'w')
+        outputfile.seek(0,0)
+        length=(len(sys.argv))
+    
+        urls = []
+        methods = []
+
+	if(wsdlUrl.find('__tilda__')>-1):
+	    ulist = wsdlUrl.split('__tilda__')
+	    urlToPass = '~'.join(ulist)
+
+        WSDLParserDriver=pkg.WSDLParserDriver
+        wPD=WSDLParserDriver()
+        wPD.parse(urlToPass)
+        urls = wPD.getUrl()
+        methods = wPD.getCompleteMethodList()
+        	            
+        i=0
+        for url in urls:
+           outputfile.write(wsdlUrl+"\t")
+           outputfile.write(str(methods[i].getName().getLocalPart())+"\t")
+           outputfile.write(str(url)+"\n")
+           i=i+1
+
+                
+
+    '''
+        Invoked to get methods described in a WADL document 
+    '''
+    def getWADLMethods(self, wadlUrl, outputFileUrl ):
+
+    #get environment variables JAVA_HOME and GALAXY_HOME
+        javahome = os.environ.get('JAVA_HOME')
+        galaxyhome=os.environ.get('GALAXY_HOME')
+
+    #classpath, jarpath are variables pointing to the java libraries required to parse a WADL document
+        classpath= galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/ParserForWADL/bin'
+        jarpath = galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/ParserForWADL/lib/'
+    
+    #start JVM depending on the machine. The location of libjvm.so is assumed to be standard.
+    #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)
+        machine = platform.machine()
+        if machine == 'x86_64' :
+            startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
+        elif machine == 'i686' :
+            startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
+        elif machine == 'sun4u' :
+            startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath)
+        else :
+            System.exit("Could not identify machine, please specify path to libjvm.so")
+        
+    #tell JPYPE that the package name is lsdis 
+        pkg=JPackage('lsdis')
+    
+        urlToPass=java.net.URL(wadlUrl)	
+
+    #convert __tilda__ to ~
+        if(wadlUrl.find('__tilda__')>-1):
+	        ulist = wadlUrl.split('__tilda__')
+	        urlToPass = java.net.URL('~'.join(ulist))
+        
+   
+        outputfile=open(outputFileUrl,'w')
+        outputfile.seek(0,0)
+         
+        urls = []
+        methods = []
+
+    #using JPYPE call appropriate Java classes and methods to parse the WADL document and get a list of methods defined in it
+        WADLParserDriver=pkg.WADLParserDriver
+        wPD=WADLParserDriver()
+        wPD.parse(urlToPass)
+        urls = wPD.getUrl()
+        methods = wPD.getCompleteMethodList()
+    
+    #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.
+        i=0
+        for url in urls:
+            outputfile.write(str(url)+"\t")
+            outputfile.write(str(methods[i].getId())+"\t")
+            outputfile.write(wadlUrl+"\n")
+            i=i+1
+     	    
+
+   
+    # invoked to get methods described in a SAWADL document    
+    def getSAWADLMethods(self, sawadlUrl, outputFileUrl ):
+        javahome = os.environ.get('JAVA_HOME')
+        galaxyhome=os.environ.get('GALAXY_HOME')
+        classpath= galaxyhome + '/tools/restclientSAWADL/lib/SAWADLParser/bin'
+        machine = platform.machine()
+        
+    #start JVM depending on the machine. The location of libjvm.so is assumed to be standard.
+    #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)        
+        if machine == 'x86_64' :
+            startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath)
+        elif machine == 'i686' :
+            startJVM("%s/jre/lib/i386/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath)
+        elif machine == 'sun4u' :
+            startJVM("%s/jre/lib/sparc/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath)            
+        else :
+            System.exit("Could not identify machine, please specify path to libjvm.so")
+    
+        pkg=JPackage('edu.uga.cs.lsdis.meteors.wadls')
+        
+
+   # Open the output file for galaxy
+        outputfile=open(outputFileUrl,'w')
+        outputfile.seek(0,0)
+   
+    	if(sawadlUrl.find('__tilda__')>-1):
+    	    ulist = sawadlUrl.split('__tilda__')
+    	    urlToPass = '~'.join(ulist)
+	         
+        urls = []
+        methods = []
+
+    #invoke the parser and get the method list
+        SAWADLParserDriver=pkg.SAWADLParserDriver
+        sawPD=SAWADLParserDriver()
+        sawPD.parse(urlToPass)
+        urls = sawPD.getUrl()
+        methods = sawPD.getCompleteMethodList()
+        
+    #Print the methods and service information to the 
+        i=0
+        for url in urls:
+           outputfile.write(sawadlUrl+"\t")
+           outputfile.write(str(methods[i].getName())+"\t")    
+           outputfile.write(str(url)+"\n")
+           i=i+1
+