Body

': + line = f1.readline() + f2.write(line) + lineStripped = line.lstrip() + lineStripped=lineStripped.rstrip() + else: + print line + + ## add new tool to f2 + f2.write(' \n') + + ## copy rest of f1 into f2 + while not lineStripped == '': + line = f1.readline() + f2.write(line) + lineStripped = line.lstrip() + lineStripped=lineStripped.rstrip() + else: + print line + + ##close f1 and f2 + f1.close() + f2.close() + + ##interchange modes of f1 and f2 + f1=open(galaxyhome+'/tool_conf.xml','w') + f1.seek(0,0) + f2=open(galaxyhome+'/tool_conf_backup.xml','r') + f2.seek(0,0) + + line = f2.readline() + f1.write(line) + + lineStripped=line.lstrip() + + ##write entire f2 into f1 (reverse roles) + while not lineStripped == '': + line = f2.readline() + f1.write(line) + lineStripped = line.lstrip() + lineStripped=lineStripped.rstrip() + else: + print line + + f1.close() + f2.close() diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/edit_tool_conf.pyc Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/edit_tool_conf.pyc has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/edit_tool_conf.py~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/edit_tool_conf.py~ Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,76 @@ +''' +@author Chaitanya Guttula, Sumedha Ganjoo +@see LICENSE (MIT style license file). +''' + +import os + +''' +Open the toolconf.xml file and adds the tool under 'Web Service Workflow Tools' that has been passed to it. + +''' + +__author__="Chaitanya Guttula, Sumedha Ganjoo" + +class editToolConfig(object): + def addTool(self,toolName): + galaxyhome=os.environ.get('GALAXY_HOME') + f1=open(galaxyhome+'/tool_conf.xml','r') + f1.seek(0,0) + f2=open(galaxyhome+'/tool_conf_backup.xml','w') + f2.seek(0,0) + + ##first copy everything upto WebServiceTool1.xml into another file f2 + line = f1.readline() + f2.write(line) + + lineStripped=line.lstrip() + lineStripped=lineStripped.rstrip() + + #add the workflow Web service invocation tool under Web Service Workflow Tools section + while not lineStripped == '

': + line = f1.readline() + f2.write(line) + lineStripped = line.lstrip() + lineStripped=lineStripped.rstrip() + else: + print line + + ## add new tool to f2 + f2.write(' \n') + + ## copy rest of f1 into f2 + while not lineStripped == '': + line = f1.readline() + f2.write(line) + lineStripped = line.lstrip() + lineStripped=lineStripped.rstrip() + else: + print line + + ##close f1 and f2 + f1.close() + f2.close() + + ##interchange modes of f1 and f2 + f1=open(galaxyhome+'/tool_conf.xml','w') + f1.seek(0,0) + f2=open(galaxyhome+'/tool_conf_backup.xml','r') + f2.seek(0,0) + + line = f2.readline() + f1.write(line) + + lineStripped=line.lstrip() + + ##write entire f2 into f1 (reverse roles) + while not lineStripped == '': + line = f2.readline() + f1.write(line) + lineStripped = line.lstrip() + lineStripped=lineStripped.rstrip() + else: + print line + + f1.close() + f2.close() diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/edit_tool_conf1.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/edit_tool_conf1.py Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,75 @@ +''' +@author Chaitanya Guttula, Sumedha Ganjoo +@see LICENSE (MIT style license file). +''' + +import os + +''' +Opens the toolconf.xml file and then adds the tool that is paased to it under Web Service tools +''' + +__author__="" + +class editToolConfig1(object): + def addTool(self,toolName): + galaxyhome=os.environ.get('GALAXY_HOME') + f1=open(galaxyhome+'/tool_conf.xml','r') + f1.seek(0,0) + f2=open(galaxyhome+'/tool_conf_backup.xml','w') + f2.seek(0,0) + + #copy everything from tool_conf.xml upto the section 'Web Service Tools' into another file f2 + line = f1.readline() + f2.write(line) + + lineStripped=line.lstrip() + lineStripped=lineStripped.rstrip() + + #add the one-time Web service invocation tool under Web Service Tools section + while not lineStripped == '

': + line = f1.readline() + f2.write(line) + lineStripped = line.lstrip() + lineStripped=lineStripped.rstrip() + else: + print line + + f2.write(' \n') + + #copy rest of tool_conf.xml file f2 + while not lineStripped == '': + line = f1.readline() + f2.write(line) + lineStripped = line.lstrip() + lineStripped=lineStripped.rstrip() + else: + print line + + ##close f1 and f2 + f1.close() + f2.close() + + ##interchange modes of f1 and f2 + f1=open(galaxyhome+'/tool_conf.xml','w') + f1.seek(0,0) + f2=open(galaxyhome+'/tool_conf_backup.xml','r') + f2.seek(0,0) + + line = f2.readline() + f1.write(line) + + lineStripped=line.lstrip() + lineStripped = lineStripped.rstrip() + + ##write entire f2 into f1 (reverse roles) + while not lineStripped == '': + line = f2.readline() + f1.write(line) + lineStripped = line.lstrip() + lineStripped = lineStripped.rstrip() + else: + print line + + f1.close() + f2.close() diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/generateClient.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/generateClient.py Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,864 @@ +''' +@author Chaitanya Guttula, Sumedha Ganjoo +@see LICENSE (MIT style license file). +''' + +import warnings + +with warnings.catch_warnings(): + warnings.simplefilter("ignore") + import platform + + from jpype._jpackage import JPackage + from jpype import * + import os.path + import sys + import string + from edit_tool_conf import * + from clientGenerator.msHandler import * + from clientGenerator.creatorEngineComplex import * + from clientGenerator.wsdl2path import * + from clientGenerator.paramConverter import * + + +class ClientGenerator(object): + + #instantiate a client for invocation of the selected method of a Web service in workflows + def __init__(self,webservice,operation,outputfile,servicetype): + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + self.operation = operation + self.webservice = webservice + #self.inputs = outputfile + self.outputfile = outputfile + self.galaxyhome=os.environ.get('GALAXY_HOME') + self.clientfile = '' + self.servicetype = servicetype + if self.servicetype == 'SOAP': + wLoad=wsdlLoader() + sys.path.append(self.galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator') + os.chdir(self.galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator') + + a = str(self.webservice).split('/') + wsdlnamelist = a[len(a)-1].split(".") + if len(wsdlnamelist)==1: + wsdlnamelist=a[len(a)-1].split('?') + print wsdlnamelist + + foldername=wsdlnamelist[0] + + path =self.galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/'+foldername + + #creates the client stubs + self.clientfile = wLoad.wsdlUrl2path(str(self.webservice),foldername) + + print 'Client file : ',self.clientfile + self.paramelement = None + + #replace '__tilda__' with '~' + #if(url.find('__tilda__')>-1): + # ulist = url.split('__tilda__') + #url = '~'.join(ulist) + #self.url = url + + ''' + Checks if a particular paramter is reuired or not. This is used only for soap web services. + ''' + def isRequired(self,param): + #j=0 + #for param in inputl: + cc = ClientCreator() + self.msinstance = cc.opname2inputClassOb(self.operation,self.clientfile) + test = MessageHandler() + required = False + if (param.find('|$|')>-1): + plist = param.split('|') + #root = test.getParameter(self.msinstance(),plist[0]) + k = 0 + iparam = '' + for p in plist: + if(k-1): + plist = param.split('|') + root = test.getParameter(self.msinstance(),plist[0]) + if not getattr(root,'nillable') and not getattr(paramelement,'nillable'): + required = True + return True + elif getattr(root,'nillable') or (not getattr(root,'nillable') and getattr(paramelement,'nillable')): + required = False + return False + else: + if not getattr(paramelement,'nillable'): + required = True + return True + elif getattr(paramelement,'nillable'): + required = False + return False + return required + + + #replace '**' with ' ' + def formatString(self,string): + l = string.split(' ') + return '**'.join(l) + + ''' + 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 + 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 + if it same as the opearation and web service. As the code is dependent on description of the toool xml file, any change in the description tag + of the tool xml file can impact this function. + ''' + def isToolPresent(self): + + f = open(self.galaxyhome+'/tool_conf.xml','r') + line = f.readline() + linestripped = line.lstrip() + linestripped = linestripped.rstrip() + + while linestripped != '

': + line = f.readline() + linestripped = line.lstrip() + linestripped = linestripped.rstrip() + + line = f.readline() + linestripped = line.lstrip() + linestripped = linestripped.rstrip() + + while linestripped != '

': + if linestripped.find('<') >-1: + toolparts = linestripped.split('"') + print '\ntoolparts are : ',toolparts + f1 = open(self.galaxyhome+'/tools/'+toolparts[-2],'r') + line1 = f1.readline() + while not line1.find('') >-1: + line1 = f1.readline() + + linestripped1 = line1.lstrip() + linestripped1 = linestripped1.rstrip() + descriptionparts=linestripped1.split(' ') + print '\nOperation : ',descriptionparts + service = '' + if(self.servicetype == 'SOAP'): + service = self.clientfile + elif self.servicetype == 'REST': + service = self.webservice + if(descriptionparts[5]==self.operation and descriptionparts[10] == service): + f.close() + f1.close() + return True + f1.close() + line = f.readline() + linestripped = line.lstrip() + linestripped = linestripped.rstrip() + + f.close() + return False + + + ''' + Creates a client file2 (xml file) for the given opertion in the SOAP web service + This operation is invokes standalone and is cannot be used in workflows + Then invokes another operation which adds this client file (tool) to the toolconfig.xml + under 'Web Service Tools' + + ''' + + def wsdlClient(self): + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + wLoad=wsdlLoader() + galaxyhome=os.environ.get('GALAXY_HOME') + sys.path.append(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator') + os.chdir(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator') + + a= str(self.webservice).split('/') + wsdlnamelist = a[len(a)-1].split(".") + if len(wsdlnamelist)==1: + wsdlnamelist=a[len(a)-1].split('?') + print wsdlnamelist + + foldername=wsdlnamelist[0] + + path =galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/'+foldername + + #creates the client stubs + clientfile=wLoad.wsdlUrl2path(str(self.webservice),foldername) + + webservice = clientfile#sys.argv[4] + #operation = sys.argv[3] + outputfile=open(self.outputfile,'w') + test = ClientCreator() + inputs= test.opname2inputs(self.operation,webservice) + inputl = nested2flatDict(inputs) + inputlist = inputl.keys() + #noOfInputs=inputlist.count() + count =0 + if (len(inputs)==0): + inputs={' ':' '} + #inputlist=inputs.keys() + for i in inputlist: + if count==0: + outputfile.write(i+'\t'+webservice+'\t'+self.operation+'\n') + else: + outputfile.write(i+'\n') + count=count+1 + + + cc = ClientCreator() + self.msinstance = cc.opname2inputClassOb(self.operation,webservice) + + ##generate client's xml + galaxyhome=os.environ.get('GALAXY_HOME') + + #./clients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation. + #read the count and increment it. + + clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','r') + clientCountFile.readline() + clientCountStr = clientCountFile.readline() + clientCount=string.atoi(clientCountStr) + clientCount=clientCount+1 + clientCountFile.close() + + clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','w') + clientCountFile.write(' \n') + clientCountFile.write(str(clientCount)+'\n') + clientCountFile.write(' \n') + clientCountFile.close() + + clientName = 'WebServiceclient_'+ str(clientCount) + + clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/'+clientName+'.xml','w') + clientXml.seek(0,0) + + clientXml.write('\n') + clientXml.write(' Client for operation : '+self.operation+' , Web service : '+webservice+' \n') + + #Only Required parameters + clientXml.write(' \n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output $servicetype ' +webservice+' '+self.operation) + + #clientXml.write(' \n client_1.py \n' +' $output \n ' +self.webservice+' \n '+self.operation+'\n') + ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop + test = MessageHandler() + j=0 + for param in inputl: + if self.isRequired(param): + clientXml.write(' "'+param+'"') + clientXml.write(' $param'+str(j)) + j=j+1 + + + #Both Required and optional paramters + clientXml.write(' #else #client_1.py'+' $output $servicetype ' +webservice+' '+self.operation+'\n') + + ''' + Required parameters - If the parameter is complex type (tree structure) then the the parameter is required + only if both the root node and the leaf node are required (i.e. both root and leaf have attribute nillable as false) + ''' + + j=0 + for param in inputl: + if self.isRequired(param): + clientXml.write(' "'+param+'"') + clientXml.write(' $param'+str(j)) + j=j+1 + + + ''' + Optional parameters - If the parameter is complex type (tree structure) then the the paramter is optional + if its root element is optional (i.e. root has attribute nillable as true) even if the leaf node (element) + is required (i.e. leaf element has attribute nillable as false) + ''' + for param in inputl: + if not self.isRequired(param): + clientXml.write(' "'+param+'"') + clientXml.write(' $param'+str(j)) + j=j+1 + + +#params for array type +# for param in self.inputs: + # paramelement = test.getParameter(self.msinstance(),param) + # if getattr(paramelement,'nillable')==True: + # if string.find(param,"|0|")>-1: + # ele = string(param,"|0|") + # for param in self.inputs: + + + # clientXml.write(' "'+param+'"') + # clientXml.write(' $cond_source.param' + str(j)) + # j=j+1 + + clientXml.write(' #end if \n\n') + + +# for param in self.inputs: + # paramelement = test.getParameter(self.msinstance(),param) + # if getattr(paramelement,'nillable')==False or getattr(paramelement,'minOccurs')==1: + # clientXml.write(' "'+param+'"\n') + # clientXml.write(' $param'+str(j)+'\n') + # j=j+1 + + + #clientXml.write('\n') + + #start writing inputs + ##write inputs depending on required or not. if not required den dont display + ##if required- den check default value, and if options exist.Depending on that + ##decide the type of parameter and options + ##The input servicetype tells what type of webservice it is wether SOAP or REST - Useful during invocation of the web servcie + clientXml.write(' \n') + clientXml.write(' \n') + + + j=0 + for param in inputl: + if self.isRequired(param): + pName = getattr(self.paramelement,'pname') + clientXml.write('\n') + j=j+1 + + clientXml.write('\n \n \n \n \n \n') + clientXml.write(' \n ') + clientXml.write(' \n') + + for param in inputl: + if not self.isRequired(param): + pName = getattr(self.paramelement,'pname') + clientXml.write('\n') + j=j+1 + + + clientXml.write('\n') + +# j=0 + # for param in self.inputs: + # paramelement = test.getParameter(self.msinstance(),param) + # if not getattr(paramelement,'nillable'): + # pName = getattr(paramelement,'pname')#param.getName() + # clientXml.write('\n') + # j=j+1 + + clientXml.write('\n \n \n \n') + + clientXml.write(' \n') + paramtype = None + for param in inputl: + if self.isRequired(param): + if isinstance(self.paramelement,ZSI.TC.String): + paramtype = 'String' + elif isinstance(self.paramelement,ZSI.TCnumbers.FPfloat): + paramtype = 'Floating point' + elif isinstance(self.paramelement,ZSI.TC.Boolean): + paramtype = 'Boolean' + elif isinstance(self.paramelement,ZSI.TCnumbers.Iint): + paramtype = 'Integer' + clientXml.write('\n.. class:: infomark\n\n**TIP:** About '+ getattr(self.paramelement,'pname') +': type is ' + paramtype + '\n') + + + + + clientXml.write(' \n') + +# clientXml.write(' \n') + + # j=0 + # for param in params: + # clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n') + + # clientXml.write(' \n') + # clientXml.write('') + clientXml.close() + editor = editToolConfig1() + editor.addTool(clientName) + + ##later add help feature + + + def wadlClient(self): + ##parse wadl + pkg=JPackage('lsdis') + urlToPass=java.net.URL(self.webservice) + wadlUrl = self.webservice + + webserviceId = ''#self.operation + resUrl = self.operation + + urls = [] + methods = [] + params = [] + docs = [] + + WADLParserDriver=pkg.WADLParserDriver + wPD=WADLParserDriver() + wPD.parse(urlToPass) + urls = wPD.getUrl() + methods = wPD.getCompleteMethodList() + + #write into the output file information about the method and Web service to be invoked. + f=open(self.outputfile,'w') + f.write(self.webservice) + f.write('\n'+ resUrl) + + a= str(self.webservice).split('/') + wadlnamelist = a[len(a)-1].split(".") + if len(wadlnamelist)==1: + wadlnamelist=a[len(a)-1].split('?') + print wadlnamelist + + wadlname=wadlnamelist[0] + + + #get parameters for the selected method of the Web service + i=0 + for method in methods: + x = str(method.getId()) + y = str(urls.get(i)) + webserviceId = x + #if x==webserviceId: + if y == resUrl : + params = method.getRequest().getParams() + break + i=i+1 + + f.write('\n'+webserviceId) + galaxyhome=os.environ.get('GALAXY_HOME') + + methodname = resUrl.split('/') + + #./clients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation. + #read the count and increment it. + clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','r') + clientCountFile.readline() + clientCountStr = clientCountFile.readline() + clientCount=string.atoi(clientCountStr) + clientCount=clientCount+1 + clientCountFile.close() + + clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','w') + + clientCountFile.write(' \n') + clientCountFile.write(str(clientCount)+'\n') + clientCountFile.write(' \n') + + #include the count in the tool's name and id to uniquely identify it. + clientName = 'WebServiceclient_'+ str(clientCount) + + #create a new xml file under ./clients/ + clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/'+clientName+'.xml','w') + clientXml.seek(0,0) + + #write the tool id, name and description + clientXml.write('\n') + clientXml.write(' Client for method : '+self.operation+' , Web service : '+self.webservice+' \n') + + #the one-time invocation tool/client for a REST Web service invokes ./clients/client_1.py to invoke the Web service + #write the command tag to specify the arguments passed to this client_1.py + clientXml.write(' \n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output $servicetype ' +resUrl) + + j=0 + + for param in params: + if param.isRequired(): + clientXml.write(' '+self.formatString(param.getName())) + clientXml.write(' $param' + str(j)) + j=j+1 + clientXml.write(' #else #client_1.py'+' $output $servicetype ' +resUrl) + j=0 + for param in params: + if param.isRequired(): + clientXml.write(' '+self.formatString(param.getName())) + clientXml.write(' $param' + str(j)) + j=j+1 + + for param in params: + if not param.isRequired(): + clientXml.write(' '+self.formatString(param.getName())) + clientXml.write(' $cond_source.param' + str(j)) + j=j+1 + clientXml.write(' #end if \n\n') + + #start writing inputs + ##write inputs depending on required or not. if not required den dont display + ##if required- den check default value, and if options exist.Depending on that + ##decide the type of parameter and options + ##The input servicetype tells what type of webservice it is wether SOAP or REST - Useful during invocation of the web servcie + clientXml.write(' \n') + clientXml.write(' ') + + #create a param for each required parameter described in the WADL. Check if defaults and options are specified in the WADL + j=0 + for param in params: + if param.isRequired(): + pName = param.getName() + for doc in param.getDocs(): + if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT": + pName = doc.getInnerText() + if param.getOptions().size()==0: + clientXml.write('\n') + j=j+1 + else: + clientXml.write('\n' ) + for option in param.getOptions(): + clientXml.write(' \n ') + clientXml.write(' \n') + j=j+1 + + #create a conditional param for each optional parameter described in the WADL. + clientXml.write('\n \n \n \n \n \n') + clientXml.write(' \n ') + clientXml.write(' \n') + for param in params: + if not param.isRequired(): + pName = param.getName() + for doc in param.getDocs(): + if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT": + pName = doc.getInnerText() + if param.getOptions().size()==0: + clientXml.write('\n') + j=j+1 + else: + clientXml.write('\n' ) + for option in param.getOptions(): + clientXml.write(' \n ') + clientXml.write(' \n') + j=j+1 + + + clientXml.write('\n') + clientXml.write('\n \n \n \n') + + #write information about each parameter in the help section + clientXml.write(' \n') + + clientXml.write('Replace white space with ** in all parameter values\n') + + for param in params: + if param.isRequired(): + pName = param.getName() + for doc in param.getDocs(): + if doc.getTitle()=="prompt" or doc.getTitle()=="Prompt" or doc.getTitle()=="PROMPT": + pName = doc.getInnerText() + clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ pName +' type is ' + param.getType()+'\n') + + clientXml.write(' \n') + + + #adds the newly created tool to tool_conf.xml in Galaxy under the 'Web Service Tools' section. + editor = editToolConfig1() + editor.addTool(clientName) + + ##later add help feature + + + def sawadlClient(self): + ##parse sawadl + javahome = os.environ.get('JAVA_HOME') + galaxyhome=os.environ.get('GALAXY_HOME') + classpath= galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/bin' + jarpath = galaxyhome + '/tools/WebServiceToolWorkflow_REST_SOAP/lib/' + machine = platform.machine() + + #if machine == 'x86_64' : + # print 'a' + # startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath) + #elif machine == 'i686' : + # print 'b' + # 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 : + # print 'c' + # System.exit("Could not identify machine, please specify path to libjvm.so") + + + pkg=JPackage('edu.uga.cs.lsdis.meteors.wadls') + pkgModel =JPackage('org.semanticweb.owlapi.model') + pkgApiBinding =JPackage('org.semanticweb.owlapi.apibinding') + pkgVocab = JPackage('org.semanticweb.owlapi.vocab') + + DOCUMENT_IRI = "http://cs.uga.edu/~ganjoo/galaxy/EDAM.owl" + + sawadlUrl = self.webservice + + webserviceId = ''#self.methodName + resUrl = self.operation + + urls = [] + methods = [] + params = [] + annotationSet = [] + + SAWADLParserDriver=pkg.SAWADLParserDriver + sawPD=SAWADLParserDriver() + sawPD.parse(sawadlUrl) + urls = sawPD.getUrl() + methods = sawPD.getCompleteMethodList() + + IRI = pkgModel.IRI + OWLRDFVocabulary = pkgVocab.OWLRDFVocabulary + OWLManager = pkgApiBinding.OWLManager + OWLLiteral = pkgModel.OWLLiteral + owlOntManager = OWLManager.createOWLOntologyManager() + ontology = owlOntManager.loadOntologyFromOntologyDocument(IRI.create(DOCUMENT_IRI)) + dataFactory = owlOntManager.getOWLDataFactory() + propertyComment = dataFactory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI()) + + f=open(self.outputfile,'w') + f.write(sawadlUrl) + f.write(resUrl+'\t') + + + i=0 + for method in methods: + x = str(method.getName()) + y = str(urls.get(i)) + #if x == webserviceId : + webserviceId = x + if y == resUrl : + params = method.getRequest().getParamList() + break + i=i+1 + + f.write(webserviceId) + + + ##generate client's xml + galaxyhome=os.environ.get('GALAXY_HOME') + + #./clients/ClientCount.xml keeps the count of the clients/tools currently registered in Galaxy for Web service invocation. + #read the count and increment it. + + clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','r') + clientCountFile.readline() + clientCountStr = clientCountFile.readline() + clientCount=string.atoi(clientCountStr) + clientCount=clientCount+1 + clientCountFile.close() + + clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','w') + clientCountFile.write(' \n') + clientCountFile.write(str(clientCount)+'\n') + clientCountFile.write(' \n') + + clientName = 'WebServiceclient_'+ str(clientCount) + + clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/'+clientName+'.xml','w') + clientXml.seek(0,0) + + clientXml.write('\n') + clientXml.write(' Client for method: '+webserviceId+' , Web service: '+self.webservice+' \n') + + + clientXml.write(' \n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output $servicetype ' +resUrl) + ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop + + + j=0 + for param in params: + if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE': + clientXml.write(' '+self.formatString(param.getName())+'\n') + clientXml.write(' $param' + str(j)+'\n') + j=j+1 + + clientXml.write(' #else #client_1.py'+' $output $servicetype ' +resUrl) + j=0 + for param in params: + if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE': + clientXml.write(' '+self.formatString(param.getName())) + clientXml.write(' $param' + str(j)) + j=j+1 + + for param in params: + if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE': + clientXml.write(' '+self.formatString(param.getName())) + clientXml.write(' $cond_source.param' + str(j)) + j=j+1 + + clientXml.write('#end if \n \n') + + #start writing inputs + ##write inputs depending on required or not. if not required den dont display + ##if required- den check default value, and if options exist.Depending on that + ##decide the type of parameter and options + ##The input param servicetype tells what type of webservice it is wether SOAP or REST - Useful during invocation of the web servcie + clientXml.write(' \n') + cleintXml.write(' ') + + j=0 + for param in params: + if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE': + f.write('\n '+ param.getName() + ' options: '+str(param.getOptionvalue().size())) + if param.getOptionvalue().size()==0: + clientXml.write('\n') + j=j+1 + else: + clientXml.write('\n' ) + for option in param.getOptionvalue(): + clientXml.write(' \n ') + clientXml.write(' \n') + j=j+1 + + + clientXml.write('\n \n \n \n \n \n') + clientXml.write(' \n ') + clientXml.write(' \n') + + for param in params: + if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE': + f.write('\n '+ param.getName() + ' options: '+str(param.getOptionvalue().size())) + if param.getOptionvalue().size()==0: + clientXml.write('\n') + j=j+1 + else: + clientXml.write('\n' ) + for option in param.getOptionvalue(): + clientXml.write(' \n ') + clientXml.write(' \n') + j=j+1 + + clientXml.write('\n\n') + + clientXml.write('\n \n \n \n') + + clientXml.write(' \n') + for param in params: + if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE': + clientXml.write('\n.. class:: infomark\n\n**TIP:** About '+ param.getName() +': type is ' + param.getType()) + + modelRef = sawPD.getCompleteModelReference(param) + if not modelRef is None: + paramClass = dataFactory.getOWLClass(IRI.create(modelRef)); + annotationSet = paramClass.getAnnotations(ontology,propertyComment) + for annotation in annotationSet: + if isinstance(annotation.getValue(),OWLLiteral): + val = annotation.getValue() + if val.isOWLStringLiteral() and not val.isOWLTypedLiteral(): + print 'val.getLiteral()=' + val.getLiteral() + clientXml.write(', description from ontology is "' + val.getLiteral()+'"') + break + clientXml.write('\n') + clientXml.write(' \n') + editor = editToolConfig1() + editor.addTool(clientName) + + ##later add help feature + + def wsdlRESTClient(self): + ##parse wadl + 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() + + if machine == 'x86_64' : + print 'a' + startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath) + elif machine == 'i686' : + print 'b' + 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 : + print 'c' + System.exit("Could not identify machine, please specify path to libjvm.so") + + + pkg=JPackage('lsdis') + wsdlUrl = self.webserviceId + + webserviceId = ''#self.methodName + resUrl = self.resourceName + + urls = [] + methods = [] + params = [] + paramTypes = [] + + WSDLParserDriver =pkg.WSDLParserDriver + wPD=WSDLParserDriver() + wPD.parse(wsdlUrl) + methods = wPD.getCompleteMethodList() + urls = wPD.getUrl() + + f=open(self.Ofile,'w') + f.write(wsdlUrl) + f.write('\n'+ resUrl) + f.write('\n'+webserviceId) + + + i=0 + for method in methods: + x = str(method.getName().getLocalPart()) + y = str(url.get(i)) + webserviceId = x + if y == resUrl : + wPD.getParameters(x) + f.write('method matched') + paramTypes = wPD.getParamTypeList() + params = wPD.getParamList() + break + i=i+1 + + + + + ##generate client's xml + galaxyhome=os.environ.get('GALAXY_HOME') + + clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','r') + clientCountFile.readline() + clientCountStr = clientCountFile.readline() + clientCount=string.atoi(clientCountStr) + clientCount=clientCount+1 + clientCountFile.close() + + clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','w') + clientCountFile.write(' \n') + clientCountFile.write(str(clientCount)+'\n') + clientCountFile.write(' \n') + + + + + clientName = 'WebServiceclient_'+ str(clientCount) + + clientXml=open(galaxyhome+'/tools/WebServiceTool/clients/'+clientName+'.xml','w') + clientXml.seek(0,0) + + clientXml.write('\n') + clientXml.write(' Client for method: '+webserviceId+' , Web service: '+self.webservice+' \n') + + + clientXml.write(' \n client_1.py \n'+' $output \n $servicetype\n ' +resUrl+'\n') + ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop + + j=0 + for param in params: + clientXml.write(' '+self.formatString(param)+'\n') + clientXml.write(' $param' + str(j)+'\n') + j=j+1 + clientXml.write('\n') + + ##write inputs depending on required or not. if not required den dont display + ##if required- den check default value, and if options exist.Depending on that + ##decide the type of parameter and options + clientXml.write(' \n') + cleintXml.write(' ') + + j=0 + for param in params: + clientXml.write('\n') + j=j+1 + + + + clientXml.write('\n \n \n \n') + + clientXml.write(' \n') + + clientXml.write('** Replace white with ** in all parameter values **\n') + + j=0 + for param in params: + clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n') + + clientXml.write(' \n') + editor = editToolConfig() + editor.addTool(clientName) + + ##later add help feature + + +# Addedfor testing purpose + +if __name__ == "__main__": + + test = ClientGenerator1('http://www.cs.uga.edu/~guttula/wublast.wsdl','run',None,'SOAP') + present = test.isToolPresent() + required = test.isRequired('_parameters|_sequence') + print 'required : ',required diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/generateClient1_mc.py~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/generateClient1_mc.py~ Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,599 @@ +#generates client for a web service to be used as standalone +import warnings + +with warnings.catch_warnings(): + warnings.simplefilter("ignore") + import platform + + from jpype._jpackage import JPackage + from jpype import * + import os.path + import sys + import string + from edit_tool_conf1 import * + from msHandler import * + from creatorEngineComplex import * + +class ClientGenerator1(object): + + def __init__(self,webservice,operation,inputs): + self.webservice = webservice + self.operation = operation + #self.resourceName=resourceName + self.inputs = inputs + cc = ClientCreator() + self.msinstance = cc.opname2inputClassOb(self.operation,self.webservice) + + def formatString(self,string): + l = string.split(' ') + return '**'.join(l) + + def isRequired(self,param): + required = False + if param.find('|')>-1 : + plist = param.split('|') + root = test.getParameter(self.msinstance(),plist[0]) # Added + if (param.find('|$|')>-1): + print 'plist-------->',plist + k = 0 + iparam = '' + for p in plist: + if(k \n') + clientCountFile.write(str(clientCount)+'\n') + clientCountFile.write(' \n') + clientCountFile.close() + + + + + clientName = 'client_'+ str(clientCount) + + clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/'+clientName+'.xml','w') + clientXml.seek(0,0) + + clientXml.write('\n') + clientXml.write(' Client for operation : '+self.operation+' , Web service: '+self.webservice+' \n') + + clientXml.write(' \n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output ' +self.webservice+' '+self.operation) + + #clientXml.write(' \n client_1.py \n' +' $output \n ' +self.webservice+' \n '+self.operation+'\n') + ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop + test = MessageHandler() + j=0 + for param in self.inputs: + required = False + if param.find('|')>-1 : + plist = param.split('|') + root = test.getParameter(self.msinstance(),plist[0]) # Added + if (param.find('|$|')>-1): + print 'plist-------->',plist + k = 0 + iparam = '' + for p in plist: + if(k-1 : + plist = param.split('|') + root = test.getParameter(self.msinstance(),plist[0]) + if (param.find('|$|')>-1): + plist = param.split('|') + print 'plist-------->',plist + k = 0 + iparam = '' + for p in plist: + if(k-1 : + plist = param.split('|') + root = test.getParameter(self.msinstance(),plist[0]) + if (param.find('|$|')>-1): + plist = param.split('|') + print 'plist-------->',plist + k = 0 + iparam = '' + for p in plist: + if(k-1: + # ele = string(param,"|0|") + # for param in self.inputs: + + + # clientXml.write(' "'+param+'"') + # clientXml.write(' $cond_source.param' + str(j)) + # j=j+1 + + clientXml.write(' #end if \n\n') + + +# for param in self.inputs: + # paramelement = test.getParameter(self.msinstance(),param) + # if getattr(paramelement,'nillable')==False or getattr(paramelement,'minOccurs')==1: + # clientXml.write(' "'+param+'"\n') + # clientXml.write(' $param'+str(j)+'\n') + # j=j+1 + + + #clientXml.write('\n') + + ##write inputs depending on required or not. if not required den dont display + ##if required- den check default value, and if options exist.Depending on that + ##decide the type of parameter and options + clientXml.write(' \n') + + j=0 + for param in self.inputs: + required = False + if param.find('|')>-1 : + plist = param.split('|') + root = test.getParameter(self.msinstance(),plist[0]) + if (param.find('|$|')>-1): + plist = param.split('|') + print 'plist-------->',plist + k = 0 + iparam = '' + for p in plist: + if(k-1): + # plist = param.split('|') + # print 'plist-------->',plist + # k = 0 + # param = '' + # for p in plist: + # if(k\n') + j=j+1 + + + clientXml.write('\n \n \n \n \n \n') + clientXml.write(' \n ') + clientXml.write(' \n') + for param in self.inputs: + required = False + if param.find('|')>-1 : + plist = param.split('|') + root = test.getParameter(self.msinstance(),plist[0]) + if (param.find('|$|')>-1): + plist = param.split('|') + print 'plist-------->',plist + k = 0 + iparam = '' + for p in plist: + if(k-1): + # plist = param.split('|') + # print 'plist-------->',plist + # k = 0 + # param = '' + # for p in plist: + # if(k\n') + j=j+1 + + + + clientXml.write('\n') + +# j=0 + # for param in self.inputs: + # paramelement = test.getParameter(self.msinstance(),param) + # if not getattr(paramelement,'nillable'): + # pName = getattr(paramelement,'pname')#param.getName() + # clientXml.write('\n') + # j=j+1 + + clientXml.write('\n \n \n \n') + clientXml.write(' \n') + paramtype = None + for param in self.inputs: + required = False + if param.find('|')>-1 : + plist = param.split('|') + root = test.getParameter(self.msinstance(),plist[0]) + if (param.find('|$|')>-1): + plist = param.split('|') + print 'plist-------->',plist + k = 0 + iparam = '' + for p in plist: + if(k-1): + # plist = param.split('|') + # print 'plist-------->',plist + # k = 0 + # param = '' + # for p in plist: + # if(k\n') + +# clientXml.write(' \n') + + # j=0 + # for param in params: + # clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n') + + # clientXml.write(' \n') + # clientXml.write('') + clientXml.close() + editor = editToolConfig1() + editor.addTool(clientName) + + ##later add help feature + + + def sawsdlClient(self): + ##parse wadl + javahome = os.environ.get('JAVA_HOME') + galaxyhome=os.environ.get('GALAXY_HOME') + classpath= galaxyhome + '/tools/WebServiceTool/WodenWSDLParser/bin' + jarpath = galaxyhome + '/tools/WebServiceTool/WodenWSDLParser/lib/' + machine = platform.machine() + + if machine == 'x86_64' : + print 'a' + startJVM("%s/jre/lib/amd64/server/libjvm.so" % javahome,"-ea", "-Djava.class.path=%s" % classpath,"-Djava.ext.dirs=%s" % jarpath) + elif machine == 'i686' : + print 'b' + 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 : + print 'c' + System.exit("Could not identify machine, please specify path to libjvm.so") + + + pkg=JPackage('lsdis') + wsdlUrl = self.url + + webserviceId = self.methodName + resUrl = self.resourceName + + urls = [] + methods = [] + params = [] + paramTypes = [] + + WSDLParserDriver =pkg.WSDLParserDriver + wPD=WSDLParserDriver() + wPD.parse(wsdlUrl) + methods = wPD.getCompleteMethodList() + urls = wPD.getUrl() + + f=open(self.Ofile,'w') + f.write(wsdlUrl) + f.write('\n'+ resUrl) + f.write('\n'+webserviceId) + + + i=0 + for method in methods: + x = str(method.getName().getLocalPart()) + if x == webserviceId : + wPD.getParameters(x) + f.write('method matched') + paramTypes = wPD.getParamTypeList() + params = wPD.getParamList() + break + i=i+1 + + + + + ##generate client's xml + galaxyhome=os.environ.get('GALAXY_HOME') + + clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','r') + clientCountFile.readline() + clientCountStr = clientCountFile.read(1) + clientCount=string.atoi(clientCountStr) + clientCount=clientCount+1 + clientCountFile.close() + + clientCountFile=open(galaxyhome+'/tools/WebServiceTool/clients/ClientCount.xml','w') + clientCountFile.write(' \n') + clientCountFile.write(str(clientCount)) + clientCountFile.write(' \n') + + + + + clientName = 'client_'+ str(clientCount) + + clientXml=open(galaxyhome+'/tools/WebServiceTool/clients/'+clientName+'.xml','w') + clientXml.seek(0,0) + + clientXml.write('\n') + clientXml.write(' Client for method: '+self.methodName+' , Web service: '+self.url+' \n') + + + clientXml.write(' \n client_1.py \n'+' $output \n ' +resUrl+'\n') + ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop + + j=0 + for param in params: + clientXml.write(' '+self.formatString(param)+'\n') + clientXml.write(' $param' + str(j)+'\n') + j=j+1 + clientXml.write('\n') + + ##write inputs depending on required or not. if not required den dont display + ##if required- den check default value, and if options exist.Depending on that + ##decide the type of parameter and options + clientXml.write(' \n') + + j=0 + for param in params: + clientXml.write('\n') + j=j+1 + + + + clientXml.write('\n \n \n \n') + + clientXml.write(' \n') + + clientXml.write('** Replace white with ** in all parameter values **\n') + + j=0 + for param in params: + clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n') + + clientXml.write(' \n') + editor = editToolConfig1() + editor.addTool(clientName) + + ##later add help feature diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/getMethods_m.py --- /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 + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/getMethods_m.pyc Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/getMethods_m.pyc has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/getMethods_m.py~ --- /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 + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/.classpath --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/.classpath Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,7 @@ + + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/.project --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/.project Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,17 @@ + + + SAWADLParser + + + + + + org.eclipse.jdt.core.javabuilder + + + + + + org.eclipse.jdt.core.javanature + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/3A4_PurchaseOrder_CoreElements.xsd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/3A4_PurchaseOrder_CoreElements.xsd Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,447 @@ + + + + + + Authors: Michal Zaremba, Holger Lausen +$Revision: 1.2 $ +$Date: 2006/03/22 17:05:21 $ + +This XML Core Elements has been created on the basis of the RosettaNet specification (http://rosettanet.org/) +and is solely intended for the Semantic Web Challenge (http://www.sws-challenge.org/). + + + + + + Unformatted text. + + + + + + + + + The name of a business entity. + + + + + + + + + + The collection of business properties that describe a business identity and location. + + + + + + + + + + The first line of a physical address. + + + + + + + + + + The name of a city. + + + + + + + + + + Code identifying geographic location as specified by a national postal code. + + + + + + + + The actual physical location of an entity as prescribed by local postal authorities, including country identification as it relates to the party or a product. + + + + + + + + + + + + + The collection of business properties that identify and describe the actual physical location of an entity as prescribed by local postal authorities, including country identification. + + + + + + + + + + The collection of business properties that describe a business partners' identity, their contact information, where they are physically located and their function in a supply chain. + + + + + + + + + + + + The collection of business properties that describe a business partners' role in a partner interface process. + + + + + + + + + + + + Magnitude of currency amount. + + + + + + + + The collection of business properties that describe the monetary amount defined by a specified currency. + + + + + + + + + + + Total price for an entire business document. + + + + + + + + + + The partner and/or location to which the product must be delivered. + + + + + + + + + + Specifies a specific date. Date stamp based on the ISO 8601 specification. The "Z" following the day identifier (DD) is used to indicate Coordinated Universal Time. Informal format: YYYYMMDDZ + + + + + + + + The collection of business properties that describe the occurrence of the public conveyance of goods as a commercial enterprise. + + + + + + + + + + + The date a transportation event is requested to occur. + + + + + + + + + + Used to indicate "Yes", "No" statements. + + + + + + + + Indicates whether the order is a drop shipment. + + + + + + + + + + The role receiving the document in a business document exchange. + + + + + + + + + + Unique tracking identification number that identifies a request. + + + + + + + + + + Unique identifier, i.e. a numeric value or alphanumeric value, for a business document. + + + + + + + + Number of the line in the document. + + + + + + + + The information that identifies the business document being sent. This identifier is used to represent the specific business document associated with the defined business process. + + + + + + + + + + Specifies an instance in time. Based on the ISO 8601 specification where "YYYY" represents the year, "MM" the month and "DD" the day. The letter "T" is the date/time separator and "hh", "mm", "ss.sss" represent hour, minute and second respectively. This representation is immediately followed by a "Z" to indicate Coordinated Universal Time. Informal format: YYYYMMDDThhmmss + + + + + + + + The date-time stamp indicating when this business document was generated. + + + + + + + + + + Name of the contact person(s) within the organization. + + + + + + + + + + Electronic mail address. + + + + + + + + The electro-technical communication number, e.g., telephone number, facsimile number, pager number. + + + + + + + + The date-time that the requesting business document was generated. This is the same as the date-time stamp of the original business document. + + + + + + + + + + The monetary total associated with a line item. + + + + + + + + + + The price requested for a unit of product. + + + + + + + + + + Global unique product identifier. RosettaNet has adopted the Global Trade Identification Number (GTIN). + + + + + + + + The collection of business properties that describe proprietary and global identifier information regarding a product. + + + + + + + + + + Line number assigned to an item by the product buyer. + + + + + + + + + + A quantity specifying the number of product units. + + + + + + + + Quantity of product shipped. + + + + + + + + + + The collection of business properties that describe information regarding the quantity of the product shipped. + + + + + + + + + + + The quantity of product requested. + + + + + + + + + + The numerical schema designed to achieve contact via telephone. + + + + + + + + + + Quantity of product shipped currently scheduled for shipment. + + + + + + + + + + The collection of business properties that provide communication and address information for contacting a person, organization or business. + + + + + + + + + + + + Agreed upon sale price for each unit ordered. + + + + + + + + + + The role initiating a business document exchange. + + + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/3A4_PurchaseOrder_Dictionary.xsd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/3A4_PurchaseOrder_Dictionary.xsd Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,1031 @@ + + + + + Authors: Michal Zaremba, Holger Lausen +$Revision: 1.2 $ +$Date: 2006/03/06 15:30:27 $ + +This XML Dictionary has been created on the basis of the RosettaNet specification (http://rosettanet.org/) +and is solely intended for the Semantic Web Challenge (http://www.sws-challenge.org/). + + + + A code identifying type of exception process in order to enable the back-end integration. + + + + + + + + + + + + + + Code identifying the three character currency code specified in ISO 4217-1995. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Code identifying a party's role in the supply chain. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Code identifying a product unit of measure. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Code identifying category specification for a purchase order. + + + + + + + + + + + + + + + + + + + + PO generated to exchange a product that is not related to Warranty Replacement. + + + + + + + + + for mass production wafer + + + + + + + PO generated to replenish stock to achieve target levels. + + + + + + Before the yield is qualifed, the buyer requests the wafer manufacturer to produce the wafer according to the current spec., however, the manufacturer is not responsible for the yield + + + + + + + applicable to a single geographical site + + + + + + + + applicable to worldwide + + + + + + + + Code identifying an event during the transportation of a shipment. + + + + + + The event representing when the product should arrive on the recipient's dock. + + + + + The event representing when the product is scheduled to be picked up from the shipper's dock. + + + + + The event representing when the product is requested to ship. + + + + + + + + Code identifying the status of a purchase order. + + + + + + + + + + + + Code identifying the three character currency code specified in ISO 4217-1995. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/3A4_Simplified_PurchaseOrderRequest.xsd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/3A4_Simplified_PurchaseOrderRequest.xsd Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,76 @@ + + + + + Authors: Michal Zaremba, Holger Lausen +$Revision: 1.6 $ +$Date: 2006/04/12 16:32:29 $ + +This XML Schema has been created on the basis of the RosettaNet specification (http://rosettanet.org/) +and is solely intended for the Semantic Web Challenge (http://www.sws-challenge.org/). The Schema has +been simplified in several aspect, e.g. all Tax related aspect have been deleted for the saint of simplicity. + + + + + + + + + + + + + + + + + The collection of business properties that describe a buyer's offer to purchase a quantity of products at an agreed price and schedule. + + + + + + + + + + + + + + + The collection of business properties that describe a business document entry for a product. + + + + + + + + + + + + + + + + + The collection of business properties that describe various types of product quantity used in an ordering process. + + + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/AcknowledgementOfReceipt.xsd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/AcknowledgementOfReceipt.xsd Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,43 @@ + + + + + Authors: Michal Zaremba, Holger Lausen +$Revision: 1.1 $ +$Date: 2006/03/06 17:45:10 $ + +This XML Schema has been created on the basis of the RosettaNet specification (http://rosettanet.org/) +and is solely intended for the Semantic Web Challenge (http://www.sws-challenge.org/). + + + + + Business information returned to a requesting party to verify business document receipt. + + + + + + + + + + Information required to support non-repudiation of receipt. + + + + + + + + + + The base-64 encoded digest of the entire original mime message received. The digest MUST use the same algorithm as the original signed message. + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/NewTemplate.sawadl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/NewTemplate.sawadl Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,37 @@ + + + + + + + + + + + + + + Min Molecular Weight (Daltons) + + + + + + + + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/NewTemplate.sawadl~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/NewTemplate.sawadl~ Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + Min Molecular Weight (Daltons) + + + + + + + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/NewsSearchResponse.xsd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/NewsSearchResponse.xsd Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/Template.sawadl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/Template.sawadl Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,34 @@ + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/sample.wadl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/sample.wadl Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/xml.xsd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/Files/xml.xsd Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,146 @@ + + + + + + See http://www.w3.org/XML/1998/namespace.html and + http://www.w3.org/TR/REC-xml for information about this namespace. + + This schema document describes the XML namespace, in a form + suitable for import by other schema documents. + + Note that local names in this namespace are intended to be defined + only by the World Wide Web Consortium or its subgroups. The + following names are currently defined in this namespace and should + not be used with conflicting semantics by any Working Group, + specification, or document instance: + + base (as an attribute name): denotes an attribute whose value + provides a URI to be used as the base for interpreting any + relative URIs in the scope of the element on which it + appears; its value is inherited. This name is reserved + by virtue of its definition in the XML Base specification. + + id (as an attribute name): denotes an attribute whose value + should be interpreted as if declared to be of type ID. + The xml:id specification is not yet a W3C Recommendation, + but this attribute is included here to facilitate experimentation + with the mechanisms it proposes. Note that it is _not_ included + in the specialAttrs attribute group. + + lang (as an attribute name): denotes an attribute whose value + is a language code for the natural language of the content of + any element; its value is inherited. This name is reserved + by virtue of its definition in the XML specification. + + space (as an attribute name): denotes an attribute whose + value is a keyword indicating what whitespace processing + discipline is intended for the content of the element; its + value is inherited. This name is reserved by virtue of its + definition in the XML specification. + + Father (in any context at all): denotes Jon Bosak, the chair of + the original XML Working Group. This name is reserved by + the following decision of the W3C XML Plenary and + XML Coordination groups: + + In appreciation for his vision, leadership and dedication + the W3C XML Plenary on this 10th day of February, 2000 + reserves for Jon Bosak in perpetuity the XML name + xml:Father + + + + + This schema defines attributes and an attribute group + suitable for use by + schemas wishing to allow xml:base, xml:lang, xml:space or xml:id + attributes on elements they define. + + To enable this, such a schema must import this schema + for the XML namespace, e.g. as follows: + <schema . . .> + . . . + <import namespace="http://www.w3.org/XML/1998/namespace" + schemaLocation="http://www.w3.org/2001/xml.xsd"/> + + Subsequently, qualified reference to any of the attributes + or the group defined below will have the desired effect, e.g. + + <type . . .> + . . . + <attributeGroup ref="xml:specialAttrs"/> + + will define a type which will schema-validate an instance + element with any of those attributes + + + + In keeping with the XML Schema WG's standard versioning + policy, this schema document will persist at + http://www.w3.org/2005/08/xml.xsd. + At the date of issue it can also be found at + http://www.w3.org/2001/xml.xsd. + The schema document at that URI may however change in the future, + in order to remain compatible with the latest version of XML Schema + itself, or with the XML namespace itself. In other words, if the XML + Schema or XML namespaces change, the version of this document at + http://www.w3.org/2001/xml.xsd will change + accordingly; the version at + http://www.w3.org/2005/08/xml.xsd will not change. + + + + + + Attempting to install the relevant ISO 2- and 3-letter + codes as the enumerated possible values is probably never + going to be a realistic possibility. See + RFC 3066 at http://www.ietf.org/rfc/rfc3066.txt and the IANA registry + at http://www.iana.org/assignments/lang-tag-apps.htm for + further information. + + The union allows for the 'un-declaration' of xml:lang with + the empty string. + + + + + + + + + + + + + + + + + + + + + + + + See http://www.w3.org/TR/xmlbase/ for + information about this attribute. + + + + + + See http://www.w3.org/TR/xml-id/ for + information about this attribute. + + + + + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/bin/.classpath --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/bin/.classpath Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,6 @@ + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/bin/.project --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/bin/.project Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,17 @@ + + + SAWADALParser + + + + + + org.eclipse.jdt.core.javabuilder + + + + + + org.eclipse.jdt.core.javanature + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/bin/Parser.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/bin/Parser.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/bin/edu/uga/cs/lsdis/meteors/wadls/ApplicationImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/bin/edu/uga/cs/lsdis/meteors/wadls/ApplicationImpl.class has changed diff -r 000000000000 -r 049760c677de 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-r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/euPathWADL/GenesByMolecularWeight.sawadl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/euPathWADL/GenesByMolecularWeight.sawadl Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,169 @@ + + + + + + Molecular Weight + + Find genes whose unmodified protein product has a molecular weight in a range that you specify. + + + Find genes whose unmodified protein product has a molecular weight in a range that you specify. + Molecular weights are machine calculated from the raw translation and does not take into account any protein or residue modifications. For translations containing ambiguous amino acid codes (B, Z, X) we calculate the average of the upper and lower bound of the molecular weight. + + + + +Organism +Organism + +Entamoeba dispar,Entamoeba histolytica,Entamoeba invadens,Cryptosporidium parvum,Cryptosporidium hominis,Cryptosporidium muris,Giardia Assemblage A isolate WB,Giardia Assemblage B isolate GS,Giardia Assemblage E isolate P15,Encephalitozoon cuniculi,Encephalitozoon intestinalis,Plasmodium falciparum,Plasmodium vivax,Plasmodium yoelii,Plasmodium berghei,Plasmodium chabaudi,Plasmodium knowlesi,Toxoplasma gondii,Neospora caninum,Trichomonas vaginalis,Trypanosoma cruzi,Leishmania braziliensis,Leishmania infantum,Leishmania major,Leishmania mexicana,Trypanosoma brucei,Trypanosoma congolense,Trypanosoma vivax +p + +Provide one or more values. Use comma as a delimter. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Min Molecular Weight (Daltons) +Lower bound for the protein molecular weight +10000 + + + +Max Molecular Weight (Daltons) +Upper bound for the protein molecular weight +50000 + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/euPathWADL/GenesByMolecularWeight.sawadl~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/euPathWADL/GenesByMolecularWeight.sawadl~ Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,169 @@ + + + + + + Molecular Weight + + Find genes whose unmodified protein product has a molecular weight in a range that you specify. + + + Find genes whose unmodified protein product has a molecular weight in a range that you specify. + Molecular weights are machine calculated from the raw translation and does not take into account any protein or residue modifications. For translations containing ambiguous amino acid codes (B, Z, X) we calculate the average of the upper and lower bound of the molecular weight. + + + + +Organism +Organism + +Entamoeba dispar,Entamoeba histolytica,Entamoeba invadens,Cryptosporidium parvum,Cryptosporidium hominis,Cryptosporidium muris,Giardia Assemblage A isolate WB,Giardia Assemblage B isolate GS,Giardia Assemblage E isolate P15,Encephalitozoon cuniculi,Encephalitozoon intestinalis,Plasmodium falciparum,Plasmodium vivax,Plasmodium yoelii,Plasmodium berghei,Plasmodium chabaudi,Plasmodium knowlesi,Toxoplasma gondii,Neospora caninum,Trichomonas vaginalis,Trypanosoma cruzi,Leishmania braziliensis,Leishmania infantum,Leishmania major,Leishmania mexicana,Trypanosoma brucei,Trypanosoma congolense,Trypanosoma vivax +p + +Provide one or more values. Use comma as a delimter. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +Min Molecular Weight (Daltons) +Lower bound for the protein molecular weight +10000 + + + +Max Molecular Weight (Daltons) +Upper bound for the protein molecular weight +50000 + + + + + + + + + + + + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/.classpath --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/.classpath Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,6 @@ + + + + + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/.project --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/.project Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,17 @@ + + + SAWADALParser + + + + + + org.eclipse.jdt.core.javabuilder + + + + + + org.eclipse.jdt.core.javanature + + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/Parser.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/Parser.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/Parser.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/Parser.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,47 @@ +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Vector; + +import javax.wadls.Application; +import javax.wadls.Method; +import javax.wadls.Param; +import javax.wadls.Request; +import javax.wadls.Resource; +import javax.wadls.WADLSException; +import javax.wadls.factory.WADLFactory; +import javax.wadls.xml.WADLReader; +import javax.xml.namespace.QName; + +import edu.uga.cs.lsdis.meteors.wadls.Constants; +import edu.uga.cs.lsdis.meteors.wadls.ParamImpl; +import edu.uga.cs.lsdis.meteors.wadls.SAWADLParserDriver; + + +public class Parser { + + + public static void main(String[] args){ + +// //String consumerWADLS="http://localhost:9090/testcase2/Template.sawadl"; +// String consumerWADLS="/home/ganjoo/parser/SAWADLParser/Files/Template.sawadl"; +// WADLReader wadlReader; +// try { +// wadlReader = WADLFactory.newInstance().newWADLReader(); +// wadlReader.setFeature(Constants.FEATURE_PARSE_SAWADL,true); +// //wadlReader.setExtensionRegistry(new PopulatedExtensionRegistry()); +// Application app = wadlReader.readWADL(consumerWADLS); +// + SAWADLParserDriver spd = new SAWADLParserDriver(); + //String fileURL = "/home/ganjoo/parser/SAWADLParser/Files/sample.wadl"; + String fileURL = "/home/ganjoo/parser/SAWADLParser/euPathWADL/GenesByMolecularWeight.sawadl"; + try { + spd.parse(fileURL); + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + + + } + } diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ApplicationImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ApplicationImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ApplicationImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ApplicationImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,606 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls; + +import java.net.URI; +import java.util.*; + +import javax.wadls.*; +import javax.wadls.extensions.*; +import javax.wadls.extensions.ExtensionRegistry; +import javax.xml.namespace.*; +import org.w3c.dom.*; + +/** + * This class represents a WSDLS definition. + * + * @author Zixin Wu (wuzixin@uga.edu) + * @author Paul Fremantle + * @author Nirmal Mukhi + * @author Matthew J. Duftler + * @author namelessNerd + */ +public class ApplicationImpl implements Application +{ + protected String documentBaseURI = null; + protected QName name = null; + protected String targetNamespace = null; + protected Map namespaces = new HashMap(); + protected Map includes = new HashMap(); + protected Params params = null; + protected Grammars grammars = null; + protected Map resources = new HashMap(); + protected Element docEl = null; + protected String resourcespath=null; + protected List extElements = new Vector(); + + // added by namelessNerd + protected List modelReferenceList= new ArrayList(); + protected List ontologyNamespaces= new ArrayList(); + // end namelessNerd additions + + protected ExtensionRegistry extReg = null; + + public static final long serialVersionUID = 1; + + /** + * Get all the Parts which has a modelReference with the specified namespace and concept. + * @param namespace The namespace of the modelReference + * @param concept The concept of the modelReference + * @return All the Parts which has a modelReference with the specified namespace and concept. + */ + + /** + * Get all the Operations which has a modelReference with the specified namespace and concept. + * @param namespace The namespace of the modelReference + * @param concept The concept of the modelReference + * @return All the Operations which has a modelReference with the specified namespace and concept. + */ + public List getMethodsByModelReference(URI namespace, String concept){ + //TODO not implemented yet. + return null; + } + + + /** + * Get all the XSD Elements which has a modelReference with the specified namespace and concept. + * @param namespace The namespace of the modelReference + * @param concept The concept of the modelReference + * @return All the XSD Elements which has a modelReference with the specified namespace and concept. + */ + public List getXSDElementsByModelReference(URI namespace, String concept){ + //TODO not implemented yet. + return null; + } + + /** + * Get all the XSD ComplexTypes which has a modelReference with the specified namespace and concept. + * @param namespace The namespace of the modelReference + * @param concept The concept of the modelReference + * @return All the XSD ComplexTypes which has a modelReference with the specified namespace and concept. + */ + public List getXSDComplexTypeByModelReference(URI namespace, String concept){ + //TODO not implemented yet. + return null; + } + + + /** + * Set the document base URI of this definition. Can be used to + * represent the origin of the Definition, and can be exploited + * when resolving relative URIs (e.g. in <import>s). + * + * @param documentBaseURI the document base URI of this definition + */ + + /** + * Create a new modelReference. + * + * @return the newly created modelReference. + */ + public ModelReference createModelReference(){ + return new ModelReferenceImpl(); + } + + + + /** + * Create a new precondition. + * + * @return the newly created precondition + */ + public PreCondition createPreCondition(){ + return new OperationAddOnImpl(); + } + + /** + * Create a new effect. + * + * @return the newly created effect + */ + public Effect createEffect(){ + return new OperationAddOnImpl(); + } + + public void setDocumentBaseURI(String documentBaseURI) + { + this.documentBaseURI = documentBaseURI; + } + + + /** + * Get the document base URI of this definition. + * + * @return the document base URI + */ + public String getDocumentBaseURI() + { + return documentBaseURI; + } + + public void setResourcesPath(String resourcespath) + { + this.resourcespath = resourcespath; + } + + + /** + * Get the document base URI of this definition. + * + * @return the document base URI + */ + public String getResourcesPath() + { + return resourcespath; + } + + /** + * Set the name of this definition. + * + * @param name the desired name + */ + public void setQName(QName name) + { + this.name = name; + } + + /** + * Get the name of this definition. + * + * @return the definition name + */ + public QName getQName() + { + return name; + } + + /** + * Set the target namespace in which WSDL elements are defined. + * + * @param targetNamespace the target namespace + */ + public void setTargetNamespace(String targetNamespace) + { + this.targetNamespace = targetNamespace; + } + + /** + * Get the target namespace in which the WSDL elements + * are defined. + * + * @return the target namespace + */ + public String getTargetNamespace() + { + return targetNamespace; + } + + /** + * Get the target namespace in which the WSDL elements + * are defined. + * + * @return the target namespace + */ + public List getAllModelReference() + { + // grabModel + return modelReferenceList; + } + + /** + * This is a way to add a namespace association to a definition. + * It is similar to adding a namespace prefix declaration to the + * top of a <wsdl:definition> element. This has nothing to do + * with the <wsdl:import> element; there are separate methods for + * dealing with information described by <wsdl:import> elements. + * + * @param prefix the prefix to use for this namespace (when + * rendering this information as XML). Use null or an empty string + * to describe the default namespace (i.e. xmlns="..."). + * @param namespaceURI the namespace URI to associate the prefix + * with. If you use null, the namespace association will be removed. + */ + public void addNamespace(String prefix, String namespaceURI) + { + if (prefix == null) + { + prefix = ""; + } + + if (namespaceURI != null) + { + namespaces.put(prefix, namespaceURI); + } + else + { + namespaces.remove(prefix); + } + } + + /** + * Get the namespace URI associated with this prefix. Or null if + * there is no namespace URI associated with this prefix. This is + * unrelated to the <wsdl:import> element. + * + * @see #addNamespace(String, String) + * @see #getPrefix(String) + */ + public String getNamespace(String prefix) + { + if (prefix == null) + { + prefix = ""; + } + + return (String)namespaces.get(prefix); + } + + /** + * Get a prefix associated with this namespace URI. Or null if + * there are no prefixes associated with this namespace URI. This is + * unrelated to the <wsdl:import> element. + * + * @see #addNamespace(String, String) + * @see #getNamespace(String) + */ + public String getPrefix(String namespaceURI) + { + if (namespaceURI == null) + { + return null; + } + + Iterator entryIterator = namespaces.entrySet().iterator(); + + while (entryIterator.hasNext()) + { + Map.Entry entry = (Map.Entry)entryIterator.next(); + String prefix = (String)entry.getKey(); + String assocNamespaceURI = (String)entry.getValue(); + + if (namespaceURI.equals(assocNamespaceURI)) + { + return prefix; + } + } + + return null; + } + + /** + * Get all namespace associations in this definition. The keys are + * the prefixes, and the namespace URIs are the values. This is + * unrelated to the <wsdl:import> element. + * + * @see #addNamespace(String, String) + */ + public Map getNamespaces() + { + return namespaces; + } + + /** + * Set the types section. + */ + public void setParams(Params params) + { + this.params = params; + } + + public void setGrammars(Grammars grammars) + { + this.grammars = grammars; + } + /** + * Get the types section. + * + * @return the types section + */ + public Params getParams() + { + return params; + } + + public Grammars getGrammars() + { + return grammars; + } + + /** + * Add an import to this WADL description. + * + * @param importDef the import to be added + */ + public void addInclude(Include includeApp) + { + String namespaceURI = includeApp.getNamespaceURI(); + List includeList = (List)includes.get(namespaceURI); + + if (includeList == null) + { + includeList = new Vector(); + + includes.put(namespaceURI, includeList); + } + + includeList.add(includeApp); + } + + /** + * Get the list of imports for the specified namespaceURI. + * + * @param namespaceURI the namespaceURI associated with the + * desired imports. + * @return a list of the corresponding imports, or null if + * there weren't any matching imports + */ + public List getIncludes(String namespaceURI) + { + return (List)includes.get(namespaceURI); + } + + /** + * Get a map of lists containing all the imports defined here. + * The map's keys are the namespaceURIs, and the map's values + * are lists. There is one list for each namespaceURI for which + * imports have been defined. + */ + public Map getIncludes() + { + return includes; + } + + + /** + * Add a portType to this WSDL description. + * + * @param portType the portType to be added + */ + public void addResource(Resource portType) + { + resources.put(portType.getQName(), portType); + + } + + /** + * Get the specified portType. Also checks imported documents. + * + * @param name the name of the desired portType. + * @return the corresponding portType, or null if there wasn't + * any matching portType + */ + public Resource getResource(QName name) + { + Resource resource = (Resource)resources.get(name); + + if (resource == null && name != null) + { + resource = (Resource)getFromIncludes(Constants.ELEM_RESOURCE, name); + } + + return resource; + } + + /** + * Remove the specified portType from this definition. + * + * @param name the name of the portType to remove + * @return the portType previously associated with this qname, if there + * was one; may return null + */ + public Resource removeResource(QName name) + { + return (Resource)resources.remove(name); + } + + /** + * Get all the portTypes defined here. + */ + public Map getResources() + { + return resources; + } + + + /** + * Set the documentation element for this document. This dependency + * on org.w3c.dom.Element should eventually be removed when a more + * appropriate way of representing this information is employed. + * + * @param docEl the documentation element + */ + public void setDocumentationElement(Element docEl) + { + this.docEl = docEl; + } + + /** + * Get the documentation element. This dependency on org.w3c.dom.Element + * should eventually be removed when a more appropriate way of + * representing this information is employed. + * + * @return the documentation element + */ + public Element getDocumentationElement() + { + return docEl; + } + + /** + * Get all the extensibility elements defined here. + */ + public List getExtensibilityElements() + { + return extElements; + } + + + /** + * Create a new import. + * + * @return the newly created import + */ + public Include createInclude() + { + return new IncludeImpl(); + } + + /** + * Create a new input. + * + * @return the newly created input + */ + public Request createRequest() + { + return new RequestImpl(); + } + + + /** + * Create a new operation. + * + * @return the newly created operation + */ + public Method createMethod() + { + return new MethodImpl(); + } + + /** + * Create a new output. + * + * @return the newly created output + */ + public Response createResponse() + { + return new ResponseImpl(); + } + + /** + * Create a new port type. + * + * @return the newly created port type + */ + public Resource createResource() + { + return new ResourceImpl(); + } + + /** + * Create a new types section. + * + * @return the newly created types section + */ + public Params createParams() + { + return new ParamsImpl(this); + } + public Grammars createGrammars() + { + return new GrammarsImpl(this); + } + + private Object getFromIncludes(String typeOfApplication, QName name) + { + Object ret = null; + List includeList = getIncludes(name.getNamespaceURI()); + + if (includeList != null) + { + Iterator includeIterator = includeList.iterator(); + + while (includeIterator.hasNext()) + { + Include includeApp = (Include)includeIterator.next(); + + if (includeApp != null) + { + Application includedApp = includeApp.getApplication(); + + if (includedApp != null) + { + /* + These object comparisons will work fine because + this private method is only called from within + this class, using only the pre-defined constants + from the Constants class as the typeOfDefinition + argument. + */ + if (typeOfApplication == Constants.ELEM_RESOURCE) + { + ret = includedApp.getResource(name); + } + + if (ret != null) + { + return ret; + } + } + } + } + } + + return ret; + } + + public String toString() + { + StringBuffer strBuf = new StringBuffer(); + + strBuf.append("Definition: name=" + name + + " targetNamespace=" + targetNamespace); + + if (includes != null) + { + Iterator includeIterator = includes.values().iterator(); + + while (includeIterator.hasNext()) + { + strBuf.append("\n" + includeIterator.next()); + } + } + + if (params != null) + { + strBuf.append("\n" + params); + } + + + + if (resources != null) + { + Iterator resourceIterator = resources.values().iterator(); + + while (resourceIterator.hasNext()) + { + strBuf.append("\n" + resourceIterator.next()); + } + } + + + return strBuf.toString(); + } + +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/Constants$SemanticExtensionType.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/Constants$SemanticExtensionType.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/Constants.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/Constants.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/Constants.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/Constants.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,191 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls; + +import javax.xml.namespace.*; + +/** + * This class contains the constatns of WSDLS + * @author Zixin Wu (wuzixin@uga.edu) + * @author Matthew J. Duftler (duftler@us.ibm.com) + */ +public class Constants +{ + // Namespace URIs. + public static final String NS_URI_WADL = + "http://wadl.dev.java.net/2009/02"; + + public static final String NS_URI_WADLS = + "http://lsdis.cs.uga.edu/projects/meteor-s/wadl-s/examples/WSSemantics.xsd"; + public static final String NS_URI_SAWADL = + "http://www.w3.org/2002/ws/sawadl/spec/sawadl#"; + public static final String NS_URI_XMLNS = + "http://www.w3.org/2000/xmlns/"; + + //Prefix + public static final String PREFIX_WSDLS = + "wssem"; + + // Top-level element names. + public static final String ELEM_DEFINITIONS = "application"; + public static final String ELEM_GRAMMARS = "grammars"; + public static final String ELEM_PARAM = "param"; + public static final String ELEM_TYPES = "types"; + public static final String ELEM_RESOURCE = "resource"; + // Non top-level element names. + public static final String ELEM_OPERATION = "method"; + public static final String ELEM_PRECON = "precondition"; + public static final String ELEM_EFFECT = "effect"; + public static final String ELEM_INPUT = "request"; + public static final String ELEM_OUTPUT = "response"; + public static final String ELEM_HREF = "href"; + public static final String ELEM_RESOURCES = "resources"; + public static final String ELEM_INCLUDE = "include"; + public static final String ELEM_IMPORT = "import"; + public static final String ELEM_DOCUMENTATION = "doc"; + public static final String ELEM_REPRESENTATION = "representation"; + + + // Top-level qualified element names. + public static final QName Q_ELEM_DEFINITIONS = + new QName(NS_URI_WADL, ELEM_DEFINITIONS); + public static final QName Q_ELEM_TYPES = + new QName(NS_URI_WADL, ELEM_TYPES); + public static final QName Q_ELEM_GRAMMARS = + new QName(NS_URI_WADL, ELEM_GRAMMARS); + public static final QName Q_ELEM_PARAM = + new QName(NS_URI_WADL, ELEM_PARAM); + public static final QName Q_ELEM_RESOURCE = + new QName(NS_URI_WADL, ELEM_RESOURCE); + public static final QName Q_ELEM_RESOURCES = + new QName(NS_URI_WADL, ELEM_RESOURCES); + + // Non top-level qualified element names. + public static final QName Q_ELEM_OPERATION = + new QName(NS_URI_WADL, ELEM_OPERATION); + public static QName Q_ELEM_PRECON; + public static QName Q_ELEM_EFFECT; + public static QName Q_ELEM_CATEGORY; + public static final QName Q_ELEM_INPUT = + new QName(NS_URI_WADL, ELEM_INPUT); + public static final QName Q_ELEM_OUTPUT = + new QName(NS_URI_WADL, ELEM_OUTPUT); + public static final QName Q_ELEM_DOCUMENTATION = + new QName(NS_URI_WADL, ELEM_DOCUMENTATION); + public static final QName Q_ELEM_REPRESENTATION = + new QName(NS_URI_WADL, ELEM_REPRESENTATION); + public static final QName Q_ELEM_INCLUDE = + new QName(NS_URI_WADL, ELEM_INCLUDE); + + // Attribute names. + public static final String ATTR_NAME = "name"; + public static final String PARAM_STYLE = "style"; + public static final String PARAM_NAME = "name"; + public static final String PARAM_TYPE = "type"; + public static final String PARAM_REQUIRED = "required"; + public static final String PARAM_DEFAULT = "default"; + public static final String OPTION_VALUE = "value"; + public static final String ATTR_BASE = "base"; + public static final String REQUEST_ELEMENT_NAME ="element"; + public static final String ATTR_PRE = "precondition"; + public static final String ID_NAME = "id"; + public static final String RESOURCE_ATTR_NAME = "path"; + public static final String ATTR_TARGET_NAMESPACE = "targetNamespace"; + public static final String ATTR_ELEMENT = "element"; + public static final String ATTR_TYPE = "type"; + public static final String ATTR_MESSAGE = "message"; + public static final String ATTR_MODELREF = "modelReference"; + public static final String ATTR_LIFTINGSCHEMAMAPPING = "liftingSchemaMapping"; + public static final String ATTR_LOWERINGSCHEMAMAPPING = "loweringSchemaMapping"; + public static final String ATTR_PARAMETER_ORDER = "parameterOrder"; + public static final String ATTR_EXPRESSION = "expression"; + public static final String ATTR_BINDING = "binding"; + public static final String ATTR_XMLNS = "xmlns"; + public static final String ATTR_NAMESPACE = "namespace"; + public static final String ATTR_LOCATION = "location"; + public static final String ATTR_REQUIRED = "required"; + public static final String ATTR_TAXONOMYURI = "taxonomyURI"; + public static final String ATTR_TAXONOMYCODE = "taxonomyCode"; + + // Lists of native attribute names. + public static final String[] PART_ATTR_NAMES = + new String[]{ATTR_NAME, ATTR_TYPE, ATTR_ELEMENT, ATTR_MODELREF}; + public static final String[] BINDING_ATTR_NAMES = + new String[]{ATTR_NAME, ATTR_TYPE}; + public static final String[] BINDING_FAULT_ATTR_NAMES = + new String[]{ATTR_NAME}; + public static final String[] BINDING_INPUT_ATTR_NAMES = + new String[]{ATTR_NAME}; + public static final String[] BINDING_OPERATION_ATTR_NAMES = + new String[]{ATTR_NAME}; + public static final String[] BINDING_OUTPUT_ATTR_NAMES = + new String[]{ATTR_NAME}; + public static final String[] FAULT_ATTR_NAMES = + new String[]{ATTR_NAME, ATTR_MESSAGE}; + public static final String[] IMPORT_ATTR_NAMES = + new String[]{ATTR_NAMESPACE, ATTR_LOCATION}; + public static final String[] INPUT_ATTR_NAMES = + new String[]{ATTR_NAME, ATTR_MESSAGE}; + public static final String[] CATEGORY_ATTR_NAMES = + new String[]{ATTR_NAME, ATTR_TAXONOMYURI, ATTR_TAXONOMYCODE}; + public static final String[] OPADDON_ATTR_NAMES = + new String[]{ATTR_NAME, ATTR_EXPRESSION}; + public static final String[] MESSAGE_ATTR_NAMES = + new String[]{ATTR_NAME}; + public static final String[] OPERATION_ATTR_NAMES = + new String[]{ATTR_NAME, ATTR_PARAMETER_ORDER}; + public static final String[] OUTPUT_ATTR_NAMES = + new String[]{ATTR_NAME, ATTR_MESSAGE}; + public static final String[] PORT_ATTR_NAMES = + new String[]{ATTR_NAME, ATTR_BINDING}; + public static final String[] PORT_TYPE_ATTR_NAMES = + new String[]{RESOURCE_ATTR_NAME}; + public static final String[] SERVICE_ATTR_NAMES = + new String[]{ATTR_NAME}; + public static final String[] TYPES_ATTR_NAMES = + new String[]{}; + + // Qualified attribute names. + public static final QName Q_ATTR_REQUIRED = + new QName(NS_URI_WADL, ATTR_REQUIRED); + public static QName Q_ATTR_MODELREF; + public static QName Q_ATTR_LIFTINGSCHEMAMAPPING; + public static QName Q_ATTR_LOWERINGSCHEMAMAPPING; + + // XML Declaration string. + public static final String XML_DECL_DEFAULT = "UTF-8"; + public static final String XML_DECL_START = + ""; + + // Feature names. + public static final String FEATURE_VERBOSE = "javax.wsdl.verbose"; + public static final String FEATURE_IMPORT_DOCUMENTS = + "javax.wsdl.importDocuments"; + public static final String FEATURE_PARSE_SAWSDL = "urn:w3.org:sawsdl"; + public static final String FEATURE_PARSE_SAWADL = "urn:w3.org:sawadl"; + + public static enum SemanticExtensionType { + WADLS, SAWADL; + } + + public static final void setSemanticExtensionURI(SemanticExtensionType type) { + String uri = NS_URI_WADLS; + if(type == SemanticExtensionType.SAWADL) + uri = NS_URI_SAWADL; + + Q_ELEM_PRECON = + new QName(uri, ELEM_PRECON); + Q_ELEM_EFFECT = + new QName(uri, ELEM_EFFECT); + Q_ATTR_MODELREF = + new QName(uri, ATTR_MODELREF); + Q_ATTR_LIFTINGSCHEMAMAPPING = + new QName(uri, ATTR_LIFTINGSCHEMAMAPPING); + Q_ATTR_LOWERINGSCHEMAMAPPING = + new QName(uri, ATTR_LOWERINGSCHEMAMAPPING); + } + +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/GrammarsImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/GrammarsImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/GrammarsImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/GrammarsImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,272 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls; + +import java.net.URISyntaxException; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Vector; + +import javax.wadls.Application; +import javax.wadls.ModelReference; +import javax.wadls.Grammars; +import javax.wadls.WADLSException; +import javax.wadls.extensions.schema.Schema; +import javax.wadls.extensions.ExtensibilityElement; +import javax.xml.namespace.QName; + +import org.w3c.dom.Attr; +import org.w3c.dom.Element; + +import edu.uga.cs.lsdis.meteors.wadls.util.SchemaUtils; + +/** + * This class represents the <types> section of a WSDL document. + * + * @author Zixin Wu (wuzixin@uga.edu) + * @author Matthew J. Duftler (duftler@us.ibm.com) + */ +public class GrammarsImpl implements Grammars +{ + protected Application app = null; //WADLS Definition + protected List modelReferences = null; + protected Element docEl = null; + protected List extElements = new Vector(); + protected Map allSchemas = null; + + + public static final long serialVersionUID = 1; + + public GrammarsImpl(Application app){ + this.app = app; + } + + public List getTopLevelSchemas(){ + return SchemaUtils.getSchemas(this.extElements); + } + + /** + * Get the DOM elements of all the schemas in this Types. + * @return A list of DOM elements of all the schemas in this Types. + */ + public Map getSchemas(){ + return this.allSchemas; + } + + public void setSchemas(Map allSchemas){ + this.allSchemas = allSchemas; + } + + + /** + * Get the DOM element of the first schema in this Types. + * @return The DOM element of the first schema in this Types. + */ + public Schema getFirstSchema(){ + return SchemaUtils.getFirstSchema(this.extElements); + } + public ModelReference getModelReference(){ + if(modelReferences == null) + return null; + return modelReferences.get(0); + } + + public List getModelReferences(Element startElement, String path, Application app) throws WADLSException, URISyntaxException { + Element el = getXSDEle(startElement, path); + if (el == null) + return null; + String attrModelReference = el.getAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_MODELREF); + if (attrModelReference.equals("")) + return null; + List mrefs = ModelReferenceImpl.getModelReferences(attrModelReference, app); + if(mrefs.size() == 0) + return null; + return mrefs; + } + public ModelReference getModelReference(Element startElement, String path, Application app) throws WADLSException, URISyntaxException{ + List mrefs = getModelReferences(startElement, path, app); + return mrefs.get(0); + } + + + private Element getXSDEle(Element startElement, String path) throws WADLSException{ + if (path == null || path == "") + return startElement; + String eleName = startElement.getLocalName(); + if (eleName.equals("element")){ //search the target from (); + modelReferences.add(0, modelReference); + } + + public List getModelReferences() { + return modelReferences; + } + + public void setModelReferences(List refs) { + modelReferences = refs; + } + + /** + * Set the documentation element for this document. This dependency + * on org.w3c.dom.Element should eventually be removed when a more + * appropriate way of representing this information is employed. + * + * @param docEl the documentation element + */ + public void setDocumentationElement(Element docEl) + { + this.docEl = docEl; + } + + public void setModelReferences(Element startElement, String path, List refs) throws WADLSException { + for(ModelReference ref : refs) { + addModelReference(startElement, path, ref); + } + } + + public void addModelReference(Element startElement, String path, ModelReference modelReference) throws WADLSException{ + Element el = getXSDEle(startElement, path); + + if (modelReference != null){ + String strModelReference = modelReference.value(); + Attr attr = el.getAttributeNodeNS( + Constants.NS_URI_WADLS, Constants.ATTR_MODELREF); + if(attr == null) { + attr = el.getOwnerDocument().createAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_MODELREF); + attr.setPrefix(Constants.PREFIX_WSDLS); + el.setAttributeNodeNS(attr); + } + String value = attr.getValue(); + if(value != null) { + value += " " + strModelReference; + } else { + value = strModelReference; + } + attr.setValue(value); + modelReference.setParent(el); + } + else + el.removeAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_MODELREF); + } + + + /** + * Get the documentation element. This dependency on org.w3c.dom.Element + * should eventually be removed when a more appropriate way of + * representing this information is employed. + * + * @return the documentation element + */ + public Element getDocumentationElement() + { + return docEl; + } + + public void setLoweringSchemaMapping(Element startElement, String path, String schemaMapping) throws WADLSException{ + Element el = getXSDEle(startElement, path); + if (schemaMapping != null){ + Attr attr = el.getOwnerDocument().createAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LOWERINGSCHEMAMAPPING); + attr.setPrefix(Constants.PREFIX_WSDLS); + attr.setValue(schemaMapping); + el.setAttributeNodeNS(attr); + } + else + el.removeAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LOWERINGSCHEMAMAPPING); + } + + public void setLiftingSchemaMapping(Element startElement, String path, String schemaMapping) throws WADLSException{ + Element el = getXSDEle(startElement, path); + if (schemaMapping != null){ + Attr attr = el.getOwnerDocument().createAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LIFTINGSCHEMAMAPPING); + attr.setPrefix(Constants.PREFIX_WSDLS); + attr.setValue(schemaMapping); + el.setAttributeNodeNS(attr); + } + else + el.removeAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LIFTINGSCHEMAMAPPING); + } + public String getLoweringSchemaMapping(Element startElement, String path) throws WADLSException{ + Element el = getXSDEle(startElement, path); + if (el == null) + return null; + String attrSchemaMapping = el.getAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LOWERINGSCHEMAMAPPING); + if (attrSchemaMapping == "") + return null; + return attrSchemaMapping; + + } + + public String getLiftingSchemaMapping(Element startElement, String path) throws WADLSException{ + Element el = getXSDEle(startElement, path); + if (el == null) + return null; + String attrSchemaMapping = el.getAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LIFTINGSCHEMAMAPPING); + if (attrSchemaMapping == "") + return null; + return attrSchemaMapping; + + } + + + /** + * Add an extensibility element. + * + * @param extElement the extensibility element to be added + */ + + + /** + * Get all the extensibility elements defined here. + */ + + + public String toString() + { + StringBuffer strBuf = new StringBuffer(); + + strBuf.append("Types:"); + + if (extElements != null) + { + Iterator extIterator = extElements.iterator(); + + while (extIterator.hasNext()) + { + strBuf.append("\n" + extIterator.next()); + } + } + + return strBuf.toString(); + } + + +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/IncludeImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/IncludeImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/IncludeImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/IncludeImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,207 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls; + +import java.util.*; + +import javax.wadls.*; +import javax.xml.namespace.*; +import org.w3c.dom.*; + +/** + * This class represents an import, and may contain a reference + * to the imported definition. + * + * @author Matthew J. Duftler (duftler@us.ibm.com) + */ +public class IncludeImpl implements Include +{ + protected String namespaceURI = null; + protected String locationURI = null; + /* + This would need to be made into a generic reference to handle other + types of referenced documents. + */ + protected Application application = null; + protected Element docEl = null; + protected Map extensionAttributes = new HashMap(); + protected List nativeAttributeNames = + Arrays.asList(Constants.IMPORT_ATTR_NAMES); + + public static final long serialVersionUID = 1; + + public void setNamespaceURI(String namespaceURI) + { + this.namespaceURI = namespaceURI; + } + + public String getNamespaceURI() + { + return namespaceURI; + } + + public void setLocationURI(String locationURI) + { + this.locationURI = locationURI; + } + + public String getLocationURI() + { + return locationURI; + } + + /** + * This property can be used to hang a referenced Definition, + * and the top-level Definition (i.e. the one with the <import>) + * will use this Definition when resolving referenced WSDL parts. + * This would need to be made into a generic reference to handle + * other types of referenced documents. + */ + public void setApplication(Application application) + { + this.application = application; + } + + /** + * This property can be used to hang a referenced Definition, + * and the top-level Definition (i.e. the one with the <import>) + * will use this Definition when resolving referenced WSDL parts. + * This would need to be made into a generic reference to handle + * other types of referenced documents. + */ + public Application getApplication() + { + return application; + } + + /** + * Set the documentation element for this document. This dependency + * on org.w3c.dom.Element should eventually be removed when a more + * appropriate way of representing this information is employed. + * + * @param docEl the documentation element + */ + public void setDocumentationElement(Element docEl) + { + this.docEl = docEl; + } + + /** + * Get the documentation element. This dependency on org.w3c.dom.Element + * should eventually be removed when a more appropriate way of + * representing this information is employed. + * + * @return the documentation element + */ + public Element getDocumentationElement() + { + return docEl; + } + + /** + * Set an extension attribute on this element. Pass in a null value to remove + * an extension attribute. + * + * @param name the extension attribute name + * @param value the extension attribute value. Can be a String, a QName, a + * List of Strings, or a List of QNames. + * + * @see #getExtensionAttribute + * @see #getExtensionAttributes + * @see ExtensionRegistry#registerExtensionAttributeType + * @see ExtensionRegistry#queryExtensionAttributeType + */ + public void setExtensionAttribute(QName name, Object value) + { + if (value != null) + { + extensionAttributes.put(name, value); + } + else + { + extensionAttributes.remove(name); + } + } + + /** + * Retrieve an extension attribute from this element. If the extension + * attribute is not defined, null is returned. + * + * @param name the extension attribute name + * + * @return the value of the extension attribute, or null if + * it is not defined. Can be a String, a QName, a List of Strings, or a List + * of QNames. + * + * @see #setExtensionAttribute + * @see #getExtensionAttributes + * @see ExtensionRegistry#registerExtensionAttributeType + * @see ExtensionRegistry#queryExtensionAttributeType + */ + public Object getExtensionAttribute(QName name) + { + return extensionAttributes.get(name); + } + + /** + * Get the map containing all the extension attributes defined + * on this element. The keys are the qnames of the attributes. + * + * @return a map containing all the extension attributes defined + * on this element + * + * @see #setExtensionAttribute + * @see #getExtensionAttribute + */ + public Map getExtensionAttributes() + { + return extensionAttributes; + } + + /** + * Get the list of local attribute names defined for this element in + * the WSDL specification. + * + * @return a List of Strings, one for each local attribute name + */ + public List getNativeAttributeNames() + { + return nativeAttributeNames; + } + + public String toString() + { + StringBuffer strBuf = new StringBuffer(); + + strBuf.append("Import:"); + + if (namespaceURI != null) + { + strBuf.append("\nnamespaceURI=" + namespaceURI); + } + + if (locationURI != null) + { + strBuf.append("\nlocationURI=" + locationURI); + } + + if (application != null) + { + strBuf.append("\napplication=" + application); + } + + Iterator keys = extensionAttributes.keySet().iterator(); + + while (keys.hasNext()) + { + QName name = (QName)keys.next(); + + strBuf.append("\nextension attribute: " + name + "=" + + extensionAttributes.get(name)); + } + + return strBuf.toString(); + } +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/MethodImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/MethodImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/MethodImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/MethodImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,274 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Vector; +import javax.wadls.Effect; +import javax.wadls.Request; +import javax.wadls.ModelReference; +import javax.wadls.Method; +import javax.wadls.Response; +import javax.wadls.PreCondition; +import org.w3c.dom.Element; + +/** + * This class represents a WSDL operation. + * It includes information on input, output and fault + * messages associated with usage of the operation. + * + * @author Zixin Wu (wuzixin@uga.edu) + * @author Paul Fremantle (pzf@us.ibm.com) + * @author Nirmal Mukhi (nmukhi@us.ibm.com) + * @author Matthew J. Duftler (duftler@us.ibm.com) + */ +public class MethodImpl implements Method +{ + protected String name = null; + protected Request request = null; + protected Response response = null; + protected List modelRefs = null; + protected PreCondition preCondition = null; + protected Effect effect = null; + protected List parameterOrder = null; + protected Element docEl = null; + protected List extElements = new Vector(); + protected boolean isUndefined = true; + + public static final long serialVersionUID = 1; + + + public void addModelReference (ModelReference modelReference){ + if (this.modelRefs == null) + modelRefs= new ArrayList (); + modelRefs.add(modelReference); + } + + + /** + * Get the modelReference of this operation. + * + * @return the modelReference value + */ + + public ModelReference getModelReference(){ + if(modelRefs == null) + return null; + return modelRefs.get(0); + } + + /** + * Set the precondition of this operation. + * + * @param preCondition the desired precondition + */ + public void setPreCondition(PreCondition preCondition){ + this.preCondition = preCondition; + } + + /** + * Get the precondition of this operation. + * + * @return the precondition + */ + public PreCondition getPreCondition(){ + return this.preCondition; + } + + /** + * Set the effect of this operation. + * + * @param effect the desired effect + */ + public void setEffect(Effect effect){ + this.effect = effect; + } + + /** + * Get the effect of this operation. + * + * @return The effect + */ + public Effect getEffect(){ + return this.effect; + } + + /** + * Set the name of this operation. + * + * @param name the desired name + */ + public void setName(String name) + { + this.name = name; + } + + /** + * Get the name of this operation. + * + * @return the operation name + */ + public String getName() + { + return name; + } + + /** + * Set the input message specification for this operation. + * + * @param input the new input message + */ + public void setRequest(Request request) + { + this.request = request; + } + + /** + * Get the input message specification for this operation. + * + * @return the input message + */ + public Request getRequest() + { + return request; + } + + /** + * Set the output message specification for this operation. + * + * @param output the new output message + */ + public void setResponse(Response response) + { + this.response = response; + } + + /** + * Get the output message specification for this operation. + * + * @return the output message specification for the operation + */ + public Response getResponse() + { + return response; + } + + + + /** + * Set the parameter ordering for a request-response, + * or solicit-response operation. + * + * @param parameterOrder a list of named parameters + * containing the part names to reflect the desired + * order of parameters for RPC-style operations + */ + public void setParameterOrdering(List parameterOrder) + { + this.parameterOrder = parameterOrder; + } + + /** + * Get the parameter ordering for this operation. + * + * @return the parameter ordering, a list consisting + * of message part names + */ + public List getParameterOrdering() + { + return parameterOrder; + } + + /** + * Set the documentation element for this document. This dependency + * on org.w3c.dom.Element should eventually be removed when a more + * appropriate way of representing this information is employed. + * + * @param docEl the documentation element + */ + public void setDocumentationElement(Element docEl) + { + this.docEl = docEl; + } + + /** + * Get the documentation element. This dependency on org.w3c.dom.Element + * should eventually be removed when a more appropriate way of + * representing this information is employed. + * + * @return the documentation element + */ + public Element getDocumentationElement() + { + return docEl; + } + + public void setUndefined(boolean isUndefined) + { + this.isUndefined = isUndefined; + } + + public boolean isUndefined() + { + return isUndefined; + } + + public String toString() + { + StringBuffer strBuf = new StringBuffer(); + + strBuf.append("Operation: name=" + name); + + if (parameterOrder != null) + { + strBuf.append("\nparameterOrder=" + parameterOrder); + } + + + if (request != null) + { + strBuf.append("\n" + request); + } + + if (response != null) + { + strBuf.append("\n" + response); + } + + if (modelRefs != null) + for(ModelReference ref : modelRefs) { + strBuf.append('\n'); + strBuf.append(ref); + } + /* if (modelRef != null) + { + strBuf.append("\n" + modelRef); + }*/ + + if (preCondition != null) + { + strBuf.append("\n" + preCondition); + } + + if (effect != null) + { + strBuf.append("\n" + effect); + } + + return strBuf.toString(); + } + + public List getModelReferences() { + return modelRefs; + } + + public void setModelReferences(List refs) { + modelRefs = refs; + } +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ModelReferenceImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ModelReferenceImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ModelReferenceImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ModelReferenceImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,217 @@ +package edu.uga.cs.lsdis.meteors.wadls; + +import java.net.URI; +import java.net.URISyntaxException; +import java.util.ArrayList; +import java.util.List; + +import javax.wadls.Application; +import javax.wadls.ModelReference; +import javax.wadls.WADLSException; + +/** + * This class represents a ModelReference. + * + * @author Zixin Wu (wuzixin@uga.edu) + * + */ +public class ModelReferenceImpl implements ModelReference { + + /** + * The URI of the ontology used in the model reference + */ + protected URI namespace; + + /** + * The parent WSDL-S element of this model reference + */ + protected Object parent; + + /** + * The NS Prefix of the model reference + */ + protected String prefix; + + /** + * The ontology concept of this model reference + */ + protected String concept; + + /** + * Get the concept of this modelReference. + * @return The concept of this modelReference. + */ + public String getConcept(){ + return this.concept; + } + + /** + * Set the concept of this modelReference + * @param concept The desired concept of this modelReference + */ + public void setConcept(String concept){ + this.concept = concept; + } + + /** + * Get the prefix of this modelReference + * @return The prefix of this modelReference + */ + public String getPrefix(){ + return this.prefix; + } + + /** + * Set the prefix of the ontology used in this modelReference + * @param prefix The desired prefix of the ontology used in this modelReference + */ + public void setPrefix(String prefix){ + this.prefix = prefix; + } + + /** + * Get the namespace of the ontology used in this modelReference + * @return The namespace of the ontology used in this modelReference + */ + public URI getNamespace(){ + return this.namespace; + } + + /** + * Set the namespace of the ontology used in this modelReference + * @param nameSpace The desired namespace of the ontology used in this modelReference + */ + public void setNamespace(String nameSpace) + throws URISyntaxException{ + //System.out.println("namespace is "+nameSpace); + this.namespace = new URI(nameSpace); + } + + /** + * Get the parent object of this modelReference + * @return The parent object of this modelReference + */ + public Object getParent(){ + return this.parent; + } + + /** + * Set the parent object of this modelReference + * @param parent The desired parent object of this modelReference + */ + public void setParent(Object parent){ + this.parent = parent; + } + + /** + * Return a formatted string representing this modelReference. + * @return A formatted string representing this modelReference. + */ + public String value(){ + if (this.concept == null || this.namespace == null) + return null; + return (this.namespace + "#" + this.concept); + } + + public String toString(){ + if (this.concept == null) + return null; + if (this.prefix != null){ //use the prefix + return (this.prefix + "#" + this.concept); + } + else if (this.namespace != null){ //use the namespace + return (this.namespace + "#" + this.concept); + } + else + return null; + } + + public static List getModelReferences(String mrefs, Application app) throws URISyntaxException, WADLSException { + String[] refs = mrefs.split(" "); + List list = new ArrayList(refs.length); + for(String ref : refs) { + ModelReference mr = app.createModelReference(); + mr.valueOf(ref, app); + list.add(mr); + } + return list; + } + + public void valueOf(String modelReferenceAsString, Application app) throws URISyntaxException, WADLSException{ + int index = modelReferenceAsString.indexOf('#'); + String prefix = (index != -1) + ? modelReferenceAsString.substring(0, index) + : null; + String namespaceURI = prefix; + String localPart = null; + + //System.out.println("Namespace URI:"+namespaceURI); + //assume the user give prefix#localName + if (prefix != null){ + //try to find a namespaceURI for that prefix + String tmpNamespaceURI = app.getNamespace(prefix); + //System.out.println("Temp Namespace URI:"+tmpNamespaceURI); + if(tmpNamespaceURI != null) { //the user did give prefix + namespaceURI = tmpNamespaceURI.substring(0, tmpNamespaceURI.length()); + } + else{ //the user gave namespaceURI instead of prefix + //try to find a prefix for that namespaceURI + prefix = app.getPrefix(namespaceURI); + if (prefix == null) + prefix = app.getPrefix(namespaceURI+"#"); + } + localPart = modelReferenceAsString.substring(index + 1); + } + else if (!prefix.equals("")){ //no prefix or namespaceURI is given, but '#' is included + //use target namespace + namespaceURI = app.getTargetNamespace(); + prefix = app.getPrefix(namespaceURI); + localPart = modelReferenceAsString.substring(1); + } + else{ + throw new IllegalArgumentException( + "No Namespace URI is provided for this modelReference: " + + modelReferenceAsString + + "."); + } + + if (namespaceURI != null){ + System.out.println("namespaceURI is "+namespaceURI); + this.setNamespace(namespaceURI); + //System.out.println("Concept:"+localPart); + this.setConcept(localPart); + this.setPrefix(prefix); + } + else{ + String faultCode = (prefix == null) + ? WADLSException.NO_PREFIX_SPECIFIED + : WADLSException.UNBOUND_PREFIX; + + WADLSException wadlExc = new WADLSException(faultCode, + "Unable to determine " + + "namespace of '" + + modelReferenceAsString + "'."); + + throw wadlExc; + } + } + + /** + * Equals method overriden to compare two modelreferences. + * We campare the namespace and the concept name (literally) + * @param obj + */ + public boolean equals(Object obj) { + if (!(obj instanceof ModelReference)){ + return false; + }else{ + ModelReference ref = (ModelReference)obj; + return (concept.equals(ref.getConcept()) && + namespace.equals(ref.getNamespace())); + } + } + + public int hashCode(){ + return this.value().hashCode(); + } +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/OperationAddOnImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/OperationAddOnImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/OperationAddOnImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/OperationAddOnImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,223 @@ +/* + * Created on Apr 4, 2005 + * + */ +package edu.uga.cs.lsdis.meteors.wadls; + +import java.util.*; + +import javax.wadls.*; +import javax.xml.namespace.*; + +import org.w3c.dom.*; + +/** + * This class represents an instance of PreCondition or Effect, + * + * @author Zixin Wu + */ +public class OperationAddOnImpl implements PreCondition, Effect +{ + protected String name = null; + protected List modelReferences = null; + protected String expression = null; + protected Element docEl = null; + protected Map extensionAttributes = new HashMap(); + protected List nativeAttributeNames = + Arrays.asList(Constants.OPADDON_ATTR_NAMES); + + public static final long serialVersionUID = 1; + + /** + * Set the name. + * + * @param name the desired name + */ + public void setName(String name) + { + this.name = name; + } + + /** + * Get the name. + * + * @return the name + */ + public String getName() + { + return name; + } + + /** + * Get the modelReference. + * + * @return The modelReference + */ + public ModelReference getModelReference(){ + if(modelReferences == null) + return null; + return modelReferences.get(0); + } + + /** + * Set the modelReference. + * + * @param modelReference The desired modelReference. + */ + public void addModelReference(ModelReference modelReference){ + if(modelReferences == null) + modelReferences = new ArrayList(); + modelReferences.add(0, modelReference); + } + + /** + * Set the expression. + * + * @param expression The desired expression. + */ + public void setExpression(String expression){ + this.expression = expression; + } + + /** + * Get the expression. + * + * @return The expression. + */ + public String getExpression(){ + return this.expression; + } + + /** + * Set the documentation element for this document. This dependency + * on org.w3c.dom.Element should eventually be removed when a more + * appropriate way of representing this information is employed. + * + * @param docEl the documentation element + */ + public void setDocumentationElement(Element docEl) + { + this.docEl = docEl; + } + + /** + * Get the documentation element. This dependency on org.w3c.dom.Element + * should eventually be removed when a more appropriate way of + * representing this information is employed. + * + * @return the documentation element + */ + public Element getDocumentationElement() + { + return docEl; + } + + /** + * Set an extension attribute on this element. Pass in a null value to remove + * an extension attribute. + * + * @param name the extension attribute name + * @param value the extension attribute value. Can be a String, a QName, a + * List of Strings, or a List of QNames. + * + * @see #getExtensionAttribute + * @see #getExtensionAttributes + * @see ExtensionRegistry#registerExtensionAttributeType + * @see ExtensionRegistry#queryExtensionAttributeType + */ + public void setExtensionAttribute(QName name, Object value) + { + if (value != null) + { + extensionAttributes.put(name, value); + } + else + { + extensionAttributes.remove(name); + } + } + + /** + * Retrieve an extension attribute from this element. If the extension + * attribute is not defined, null is returned. + * + * @param name the extension attribute name + * + * @return the value of the extension attribute, or null if + * it is not defined. Can be a String, a QName, a List of Strings, or a List + * of QNames. + * + * @see #setExtensionAttribute + * @see #getExtensionAttributes + * @see ExtensionRegistry#registerExtensionAttributeType + * @see ExtensionRegistry#queryExtensionAttributeType + */ + public Object getExtensionAttribute(QName name) + { + return extensionAttributes.get(name); + } + + /** + * Get the map containing all the extension attributes defined + * on this element. The keys are the qnames of the attributes. + * + * @return a map containing all the extension attributes defined + * on this element + * + * @see #setExtensionAttribute + * @see #getExtensionAttribute + */ + public Map getExtensionAttributes() + { + return extensionAttributes; + } + + /** + * Get the list of local attribute names defined for this element in + * the WSDLS specification. + * + * @return a List of Strings, one for each local attribute name + */ + public List getNativeAttributeNames() + { + return nativeAttributeNames; + } + + public String toString() + { + StringBuffer strBuf = new StringBuffer(); + + strBuf.append("name=" + name); + + strBuf.append("\nmodelReference="); + for(ModelReference ref : modelReferences) { + strBuf.append(ref.toString()); + strBuf.append('\n'); + } + + if (expression != null) + { + strBuf.append("\nexpression=" + expression); + } + +// Iterator keys = extensionAttributes.keySet().iterator(); +// +// while (keys.hasNext()) +// { +// QName name = (QName)keys.next(); +// +// strBuf.append("\nextension attribute: " + name + "=" + +// extensionAttributes.get(name)); +// } + + return strBuf.toString(); + } + + public List getModelReferences() { + return modelReferences; + } + + public void setModelReferences(List refs) { + modelReferences = refs; + } +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ParamImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ParamImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ParamImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ParamImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,212 @@ +/* + * Copyright (c) 2009 Srikalyan Swayampakula.. All rights reserved. + * + * Author : Srikalyan Swayampakula. . + * Name of the File : Param.java . + * Created on : Nov 22, 2009 at 4:03:57 PM . + * + * Redistribution and use in source and binary forms, with or without + * modification, are permitted provided that the following conditions + * are met: + * + * 1. Redistributions of source code must retain the above + * copyright notice, this list of conditions and the following + * disclaimer. + * 2. Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions and the following + * disclaimer in the documentation and/or other materials + * provided with the distribution. + * 3. Neither the name of the University of Georgia nor the names + * of its contributors may be used to endorse or promote + * products derived from this software without specific prior + * written permission. + * + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND + * CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, + * INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF + * MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE + * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR + * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, + * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR + * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) + * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN + * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR + * OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, + * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + */ +package edu.uga.cs.lsdis.meteors.wadls; + +import java.net.URI; +import java.util.ArrayList; +import java.util.List; +import java.util.Vector; + +import javax.wadls.Param; + +/** + * + * @author Srikalyan Swayampakula. + */ +public class ParamImpl implements Param +{ + + List optionvalue = new Vector(); + protected String name; + protected String style; + protected String id; + protected String type; + protected String default1; + protected String required = "false"; + protected boolean repeation = false; + protected String fixed; + protected String path; + protected String modelreference =null; + protected String liftingschemamapping=null; + protected String loweringschemamapping=null; + + + + public String getModelreference() { + return modelreference; + } + + public void setModelreference(String modelreference) { + this.modelreference = modelreference; + } + + public String getLiftingschemamapping() { + return liftingschemamapping; + } + + public void setLiftingschemamapping(String liftingschemamapping) { + this.liftingschemamapping = liftingschemamapping; + } + + public String getLoweringschemamapping() { + return loweringschemamapping; + } + + public void setLoweringschemamapping(String loweringschemamapping) { + this.loweringschemamapping = loweringschemamapping; + } + + public List getOptionvalue() { + return optionvalue; + } + + public void setOptionvalue(List optionvalue) { + this.optionvalue = optionvalue; + } + + public ParamImpl() + { + } + + public ParamImpl(URI href, String name, String style, String id, String type, String default1, String fixed, String path) + { + + + this.name = name; + this.style = style; + this.id = id; + this.type = type; + this.default1 = default1; + this.fixed = fixed; + this.path = path; + } + + public String getDefault1() + { + return default1; + } + + public void setDefault1(String default1) + { + this.default1 = default1; + } + + + + public String getFixed() + { + return fixed; + } + + public void setFixed(String fixed) + { + this.fixed = fixed; + } + + + public String getId() + { + return id; + } + + public void setId(String id) + { + this.id = id; + } + + public String getName() + { + return name; + } + + public void setName(String name) + { + this.name = name; + } + + + public String getPath() + { + return path; + } + + public void setPath(String path) + { + this.path = path; + } + + public boolean isRepeation() + { + return repeation; + } + + public void setRepeation(boolean repeation) + { + this.repeation = repeation; + } + + public String getRequired() + { + return required; + } + + public void setRequired(String required) + { + this.required = required; + } + + public String getStyle() + { + return style; + } + + public void setStyle(String style) + { + this.style = style; + } + + public String getType() + { + return type; + } + + public void setType(String type) + { + this.type = type; + } +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ParamsImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ParamsImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ParamsImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ParamsImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,347 @@ +package edu.uga.cs.lsdis.meteors.wadls; + +import java.net.URISyntaxException; +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Vector; + +import javax.wadls.Application; +import javax.wadls.ModelReference; +import javax.wadls.Params; +import javax.wadls.WADLSException; +import javax.wadls.extensions.schema.Schema; +import javax.xml.namespace.QName; + +import org.w3c.dom.Attr; +import org.w3c.dom.Element; + +import edu.uga.cs.lsdis.meteors.wadls.util.SchemaUtils; + +/** + * This class represents the <types> section of a WSDL document. + * + * @author Zixin Wu (wuzixin@uga.edu) + * @author Matthew J. Duftler (duftler@us.ibm.com) + */ +public class ParamsImpl implements Params +{ + protected List modelRefs = null; + protected Application app = null; //WSDLS Definition + protected Element docEl = null; + protected List extElements = new Vector(); + protected Map allSchemas = null; + + public static final long serialVersionUID = 1; + + public ParamsImpl(Application app){ + this.app = app; + } + + public List getTopLevelSchemas(){ + return SchemaUtils.getSchemas(this.extElements); + } + + /** + * Get the DOM elements of all the schemas in this Types. + * @return A list of DOM elements of all the schemas in this Types. + */ + public Map getSchemas(){ + return this.allSchemas; + } + + public void setSchemas(Map allSchemas){ + this.allSchemas = allSchemas; + } + + + + public void addModelReference (ModelReference modelReference){ + if (this.modelRefs == null) + modelRefs= new ArrayList (); + modelRefs.add(modelReference); + } + + + /** + * Get the modelReference of this operation. + * + * @return the modelReference value + */ + + public ModelReference getModelReference(){ + if(modelRefs == null) + return null; + return modelRefs.get(0); + } + /** + * Get the DOM element of the first schema in this Types. + * @return The DOM element of the first schema in this Types. + */ + public Schema getFirstSchema(){ + return SchemaUtils.getFirstSchema(this.extElements); + } + public List getModelReferences() { + return modelRefs; + } + public void setModelReferences(List refs) { + modelRefs = refs; + } + /** + * Get the XSD simpleType with the given name. + * @param name The QName of the type + * @return A DOM Element representing the simpleType + * @throws WADLSException + */ + + public Element getXSDElement(String xpath) throws WADLSException{ + Element returnElt = null; + Map schemas = this.getSchemas(); + Iterator it = schemas.values().iterator(); + while(it.hasNext()){ + Schema schema = (Schema)(it.next()); + Element schemaEle = schema.getElement(); + returnElt = this.getXSDElement(schemaEle, xpath); + if (returnElt != null) + return returnElt; + } + return null; + } + + /** + * Get the modelReference on the element located by the given path. + * @param startElement The starting element of the path + * @param path + * @return The modelReference + */ + public ModelReference getModelReference(Element startElement, String path, Application app) throws WADLSException, URISyntaxException{ + List mrefs = getModelReferences(startElement, path, app); + return mrefs.get(0); + } + + /** + * Set the modelReference on the element located by the given path. + * @param startElement The starting element of the path + * @param path + * @param modelReference The desired modelReference + */ + public void addModelReference(Element startElement, String path, ModelReference modelReference) throws WADLSException{ + Element el = getXSDEle(startElement, path); + + if (modelReference != null){ + String strModelReference = modelReference.value(); + Attr attr = el.getAttributeNodeNS( + Constants.NS_URI_WADLS, Constants.ATTR_MODELREF); + if(attr == null) { + attr = el.getOwnerDocument().createAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_MODELREF); + attr.setPrefix(Constants.PREFIX_WSDLS); + el.setAttributeNodeNS(attr); + } + String value = attr.getValue(); + if(value != null) { + value += " " + strModelReference; + } else { + value = strModelReference; + } + attr.setValue(value); + modelReference.setParent(el); + } + else + el.removeAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_MODELREF); + } + + /** + * Get the liftingSchemaMapping on the element located by the given path. + * @param startElement The starting element of the path + * @param path + * @return The schemaMapping value + */ + public String getLiftingSchemaMapping(Element startElement, String path) throws WADLSException{ + Element el = getXSDEle(startElement, path); + if (el == null) + return null; + String attrSchemaMapping = el.getAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LIFTINGSCHEMAMAPPING); + if (attrSchemaMapping == "") + return null; + return attrSchemaMapping; + } + + /** + * Get the loweringSchemaMapping on the element located by the given path. + * @param startElement The starting element of the path + * @param path + * @return The schemaMapping value + */ + public String getLoweringSchemaMapping(Element startElement, String path) throws WADLSException{ + Element el = getXSDEle(startElement, path); + if (el == null) + return null; + String attrSchemaMapping = el.getAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LOWERINGSCHEMAMAPPING); + if (attrSchemaMapping == "") + return null; + return attrSchemaMapping; + } + + /** + * Set the liftingSchemaMapping on the element located by the given path. + * @param startElement The starting element of the path + * @param path + * @param schemaMapping The desired schemaMapping + */ + public void setLiftingSchemaMapping(Element startElement, String path, String schemaMapping) throws WADLSException{ + Element el = getXSDEle(startElement, path); + if (schemaMapping != null){ + Attr attr = el.getOwnerDocument().createAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LIFTINGSCHEMAMAPPING); + attr.setPrefix(Constants.PREFIX_WSDLS); + attr.setValue(schemaMapping); + el.setAttributeNodeNS(attr); + } + else + el.removeAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LIFTINGSCHEMAMAPPING); + } + + /** + * Set the loweringSchemaMapping on the element located by the given path. + * @param startElement The starting element of the path + * @param path + * @param schemaMapping The desired schemaMapping + */ + public void setLoweringSchemaMapping(Element startElement, String path, String schemaMapping) throws WADLSException{ + Element el = getXSDEle(startElement, path); + if (schemaMapping != null){ + Attr attr = el.getOwnerDocument().createAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LOWERINGSCHEMAMAPPING); + attr.setPrefix(Constants.PREFIX_WSDLS); + attr.setValue(schemaMapping); + el.setAttributeNodeNS(attr); + } + else + el.removeAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_LOWERINGSCHEMAMAPPING); + } + + private Element getXSDEle(Element startElement, String path) throws WADLSException{ + if (path == null || path == "") + return startElement; + String eleName = startElement.getLocalName(); + if (eleName.equals("element")){ //search the target from getModelReferences(Element startElement, String path, Application app) throws WADLSException, URISyntaxException { + Element el = getXSDEle(startElement, path); + if (el == null) + return null; + String attrModelReference = el.getAttributeNS(Constants.NS_URI_WADLS, Constants.ATTR_MODELREF); + if (attrModelReference.equals("")) + return null; + List mrefs = ModelReferenceImpl.getModelReferences(attrModelReference, app); + if(mrefs.size() == 0) + return null; + return mrefs; + } + public void setModelReferences(Element startElement, String path, List refs) throws WADLSException { + for(ModelReference ref : refs) { + addModelReference(startElement, path, ref); + } + } +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/RequestImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/RequestImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/RequestImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/RequestImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,205 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls; + +import java.util.*; + +import javax.wadls.*; +import javax.wadls.ModelReference; +import javax.xml.namespace.*; +import org.w3c.dom.*; + +/** + * This class represents an input message, and contains the name + * of the input and the message itself. + * + * @author Matthew J. Duftler + */ +public class RequestImpl implements Request +{ + protected String name = null; + List inputXSDList = new Vector(); + List paramList = new Vector(); + protected List modelReferences = null; + protected Element docEl = null; + protected Map extensionAttributes = new HashMap(); + protected List nativeAttributeNames = + Arrays.asList(Constants.INPUT_ATTR_NAMES); + + public static final long serialVersionUID = 1; + + /** + * Set the name of this input message. + * + * @param name the desired name + */ + public void setName(String name) + { + this.name = name; + } + public List getModelReferences() { + return modelReferences; + } + + public void setModelReferences(List refs) { + modelReferences = refs; + } + public ModelReference getModelReference(){ + if(modelReferences == null) + return null; + return modelReferences.get(0); + } + + /** + * Set the modelReference. + * + * @param modelReference The desired modelReference. + */ + public void addModelReference(ModelReference modelReference){ + if(modelReferences == null) + modelReferences = new ArrayList(); + modelReferences.add(0, modelReference); + } + /** + * Get the name of this input message. + * + * @return the input message name + */ + public String getName() + { + return name; + } + + public void setInputXSDList(List inputXSDList){ + this.inputXSDList=inputXSDList; + } + public List getInputXSDList(){ + + return this.inputXSDList; + } + + + public void setParamList(List paramList){ + this.paramList=paramList; + } + public List getParamList(){ + + return this.paramList; + } + + /** + * Set the documentation element for this document. This dependency + * on org.w3c.dom.Element should eventually be removed when a more + * appropriate way of representing this information is employed. + * + * @param docEl the documentation element + */ + public void setDocumentationElement(Element docEl) + { + this.docEl = docEl; + } + + /** + * Get the documentation element. This dependency on org.w3c.dom.Element + * should eventually be removed when a more appropriate way of + * representing this information is employed. + * + * @return the documentation element + */ + public Element getDocumentationElement() + { + return docEl; + } + + /** + * Set an extension attribute on this element. Pass in a null value to remove + * an extension attribute. + * + * @param name the extension attribute name + * @param value the extension attribute value. Can be a String, a QName, a + * List of Strings, or a List of QNames. + * + * @see #getExtensionAttribute + * @see #getExtensionAttributes + * @see ExtensionRegistry#registerExtensionAttributeType + * @see ExtensionRegistry#queryExtensionAttributeType + */ + public void setExtensionAttribute(QName name, Object value) + { + if (value != null) + { + extensionAttributes.put(name, value); + } + else + { + extensionAttributes.remove(name); + } + } + + /** + * Retrieve an extension attribute from this element. If the extension + * attribute is not defined, null is returned. + * + * @param name the extension attribute name + * + * @return the value of the extension attribute, or null if + * it is not defined. Can be a String, a QName, a List of Strings, or a List + * of QNames. + * + * @see #setExtensionAttribute + * @see #getExtensionAttributes + * @see ExtensionRegistry#registerExtensionAttributeType + * @see ExtensionRegistry#queryExtensionAttributeType + */ + public Object getExtensionAttribute(QName name) + { + return extensionAttributes.get(name); + } + + /** + * Get the map containing all the extension attributes defined + * on this element. The keys are the qnames of the attributes. + * + * @return a map containing all the extension attributes defined + * on this element + * + * @see #setExtensionAttribute + * @see #getExtensionAttribute + */ + public Map getExtensionAttributes() + { + return extensionAttributes; + } + + /** + * Get the list of local attribute names defined for this element in + * the WSDL specification. + * + * @return a List of Strings, one for each local attribute name + */ + public List getNativeAttributeNames() + { + return nativeAttributeNames; + } + + public String toString() + { + StringBuffer strBuf = new StringBuffer(); + + strBuf.append("Input: name=" + name); + + Iterator keys = extensionAttributes.keySet().iterator(); + + while (keys.hasNext()) + { + QName name = (QName)keys.next(); + + strBuf.append("\nextension attribute: " + name + "=" + + extensionAttributes.get(name)); + } + + return strBuf.toString(); + } +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ResourceImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ResourceImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ResourceImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ResourceImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,364 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls; + +import java.util.*; + +import javax.wadls.*; +import javax.wadls.ModelReference; +import javax.xml.namespace.*; +import org.w3c.dom.*; + +/** + * This class represents a port type. It contains information about + * operations associated with this port type. + * + * @author Paul Fremantle + * @author Nirmal Mukhi + * @author Matthew J. Duftler + * @author Zixin Wu + */ +public class ResourceImpl implements Resource +{ + protected QName name = null; + protected List modelReferences = null; + protected List methods = new Vector(); + protected List categories = new Vector(); + protected Element docEl = null; + protected Map extensionAttributes = new HashMap(); + protected List nativeAttributeNames = + Arrays.asList(Constants.PORT_TYPE_ATTR_NAMES); + protected boolean isUndefined = true; + + public static final long serialVersionUID = 1; + + + /** + * Get the category specifications in this portType. + * @return All the categories in this portType. + */ + public List getCategories() + { + return this.categories; + } + + /** + * Set the name of this port type. + * + * @param name the desired name + */ + public void setQName(QName name) + { + this.name = name; + } + + /** + * Get the name of this port type. + * + * @return the port type name + */ + public QName getQName() + { + return name; + } + + /** + * Add an operation to this port type. + * + * @param operation the operation to be added + */ + public void addMethod(Method operation) + { + methods.add(operation); + } + + /** + * Get the specified operation. Note that operation names can + * be overloaded within a PortType. In case of overloading, the + * names of the input and output messages can be used to further + * refine the search. + * + * @param name the name of the desired operation. + * @param inputName the name of the input message; if this is null + * it will be ignored. + * @param outputName the name of the output message; if this is null + * it will be ignored. + * @return the corresponding operation, or null if there wasn't + * any matching operation + */ + public Method getMethod(String name, + String inputName, + String outputName) + { + boolean found = false; + Method ret = null; + Iterator opIterator = methods.iterator(); + + while (opIterator.hasNext()) + { + Method op = (Method)opIterator.next(); + String opName = op.getName(); + + if (name != null && opName != null) + { + if (!name.equals(opName)) + { + op = null; + } + } + else if (name != null || opName != null) + { + op = null; + } + + if (op != null && inputName != null) + { + + String defaultInputName = opName; + defaultInputName = opName + "Request"; + boolean specifiedDefault = inputName.equals(defaultInputName); + Request input = op.getRequest(); + + if (input != null) + { + String opInputName = input.getName(); + + if (opInputName == null) + { + if (!specifiedDefault) + { + op = null; + } + } + else if (!opInputName.equals(inputName)) + { + op = null; + } + } + else + { + op = null; + } + } + + if (op != null && outputName != null) + { + String defaultOutputName = opName; + defaultOutputName = opName + "Response"; + boolean specifiedDefault = outputName.equals(defaultOutputName); + Response output = op.getResponse(); + + if (output != null) + { + String opOutputName = output.getName(); + + if (opOutputName == null) + { + if (!specifiedDefault) + { + op = null; + } + } + else if (!opOutputName.equals(outputName)) + { + op = null; + } + } + else + { + op = null; + } + } + + if (op != null) + { + if (found) + { + throw new IllegalArgumentException("Duplicate operation with " + + "name=" + name + + (inputName != null + ? ", inputName=" + inputName + : "") + + (outputName != null + ? ", outputName=" + outputName + : "") + + ", found in portType '" + + getQName() + "'."); + } + else + { + found = true; + ret = op; + } + } + } + + return ret; + } + public ModelReference getModelReference(){ + if(modelReferences == null) + return null; + return modelReferences.get(0); + } + + /** + * Set the modelReference. + * + * @param modelReference The desired modelReference. + */ + public void addModelReference(ModelReference modelReference){ + if(modelReferences == null) + modelReferences = new ArrayList(); + modelReferences.add(0, modelReference); + } + public List getModelReferences() { + return modelReferences; + } + + public void setModelReferences(List refs) { + modelReferences = refs; + } + /** + * Get all the operations defined here. + */ + public List getMethods() + { + return methods; + } + + /** + * Set the documentation element for this document. This dependency + * on org.w3c.dom.Element should eventually be removed when a more + * appropriate way of representing this information is employed. + * + * @param docEl the documentation element + */ + public void setDocumentationElement(Element docEl) + { + this.docEl = docEl; + } + + /** + * Get the documentation element. This dependency on org.w3c.dom.Element + * should eventually be removed when a more appropriate way of + * representing this information is employed. + * + * @return the documentation element + */ + public Element getDocumentationElement() + { + return docEl; + } + + public void setUndefined(boolean isUndefined) + { + this.isUndefined = isUndefined; + } + + public boolean isUndefined() + { + return isUndefined; + } + + /** + * Set an extension attribute on this element. Pass in a null value to remove + * an extension attribute. + * + * @param name the extension attribute name + * @param value the extension attribute value. Can be a String, a QName, a + * List of Strings, or a List of QNames. + * + * @see #getExtensionAttribute + * @see #getExtensionAttributes + * @see ExtensionRegistry#registerExtensionAttributeType + * @see ExtensionRegistry#queryExtensionAttributeType + */ + public void setExtensionAttribute(QName name, Object value) + { + if (value != null) + { + extensionAttributes.put(name, value); + } + else + { + extensionAttributes.remove(name); + } + } + + /** + * Retrieve an extension attribute from this element. If the extension + * attribute is not defined, null is returned. + * + * @param name the extension attribute name + * + * @return the value of the extension attribute, or null if + * it is not defined. Can be a String, a QName, a List of Strings, or a List + * of QNames. + * + * @see #setExtensionAttribute + * @see #getExtensionAttributes + * @see ExtensionRegistry#registerExtensionAttributeType + * @see ExtensionRegistry#queryExtensionAttributeType + */ + public Object getExtensionAttribute(QName name) + { + return extensionAttributes.get(name); + } + + /** + * Get the map containing all the extension attributes defined + * on this element. The keys are the qnames of the attributes. + * + * @return a map containing all the extension attributes defined + * on this element + * + * @see #setExtensionAttribute + * @see #getExtensionAttribute + */ + public Map getExtensionAttributes() + { + return extensionAttributes; + } + + /** + * Get the list of local attribute names defined for this element in + * the WSDL specification. + * + * @return a List of Strings, one for each local attribute name + */ + public List getNativeAttributeNames() + { + return nativeAttributeNames; + } + + public String toString() + { + StringBuffer strBuf = new StringBuffer(); + + strBuf.append("PortType: name=" + name); + + if (methods != null) + { + Iterator opIterator = methods.iterator(); + + while (opIterator.hasNext()) + { + strBuf.append("\n" + opIterator.next()); + } + } + + Iterator keys = extensionAttributes.keySet().iterator(); + + while (keys.hasNext()) + { + QName name = (QName)keys.next(); + + strBuf.append("\nextension attribute: " + name + "=" + + extensionAttributes.get(name)); + } + + return strBuf.toString(); + } +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ResponseImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ResponseImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ResponseImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/ResponseImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,205 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls; + +import java.util.*; + +import javax.wadls.*; +import javax.xml.namespace.*; +import org.w3c.dom.*; + +/** + * This class represents an output message, and contains the name + * of the output and the message itself. + * + * @author Matthew J. Duftler + */ +public class ResponseImpl implements Response +{ + protected String name = null; + List inputXSDList = new Vector(); + List paramList = new Vector(); + protected List modelReferences = null; + protected Element docEl = null; + protected Map extensionAttributes = new HashMap(); + protected List nativeAttributeNames = + Arrays.asList(Constants.OUTPUT_ATTR_NAMES); + + public static final long serialVersionUID = 1; + + /** + * Set the name of this output message. + * + * @param name the desired name + */ + public void setName(String name) + { + this.name = name; + } + + public void setInputXSDList(List inputXSDList){ + this.inputXSDList=inputXSDList; + } + public List getInputXSDList(){ + + return this.inputXSDList; + } + + + public void setParamList(List paramList){ + this.paramList=paramList; + } + public List getParamList(){ + + return this.paramList; + } + /** + * Get the name of this output message. + * + * @return the output message name + */ + public String getName() + { + return name; + } + + + /** + * Set the documentation element for this document. This dependency + * on org.w3c.dom.Element should eventually be removed when a more + * appropriate way of representing this information is employed. + * + * @param docEl the documentation element + */ + public void setDocumentationElement(Element docEl) + { + this.docEl = docEl; + } + public ModelReference getModelReference(){ + if(modelReferences == null) + return null; + return modelReferences.get(0); + } + + /** + * Set the modelReference. + * + * @param modelReference The desired modelReference. + */ + public void addModelReference(ModelReference modelReference){ + if(modelReferences == null) + modelReferences = new ArrayList(); + modelReferences.add(0, modelReference); + } + public List getModelReferences() { + return modelReferences; + } + + public void setModelReferences(List refs) { + modelReferences = refs; + } + /** + * Get the documentation element. This dependency on org.w3c.dom.Element + * should eventually be removed when a more appropriate way of + * representing this information is employed. + * + * @return the documentation element + */ + public Element getDocumentationElement() + { + return docEl; + } + + /** + * Set an extension attribute on this element. Pass in a null value to remove + * an extension attribute. + * + * @param name the extension attribute name + * @param value the extension attribute value. Can be a String, a QName, a + * List of Strings, or a List of QNames. + * + * @see #getExtensionAttribute + * @see #getExtensionAttributes + * @see ExtensionRegistry#registerExtensionAttributeType + * @see ExtensionRegistry#queryExtensionAttributeType + */ + public void setExtensionAttribute(QName name, Object value) + { + if (value != null) + { + extensionAttributes.put(name, value); + } + else + { + extensionAttributes.remove(name); + } + } + + /** + * Retrieve an extension attribute from this element. If the extension + * attribute is not defined, null is returned. + * + * @param name the extension attribute name + * + * @return the value of the extension attribute, or null if + * it is not defined. Can be a String, a QName, a List of Strings, or a List + * of QNames. + * + * @see #setExtensionAttribute + * @see #getExtensionAttributes + * @see ExtensionRegistry#registerExtensionAttributeType + * @see ExtensionRegistry#queryExtensionAttributeType + */ + public Object getExtensionAttribute(QName name) + { + return extensionAttributes.get(name); + } + + /** + * Get the map containing all the extension attributes defined + * on this element. The keys are the qnames of the attributes. + * + * @return a map containing all the extension attributes defined + * on this element + * + * @see #setExtensionAttribute + * @see #getExtensionAttribute + */ + public Map getExtensionAttributes() + { + return extensionAttributes; + } + + /** + * Get the list of local attribute names defined for this element in + * the WSDL specification. + * + * @return a List of Strings, one for each local attribute name + */ + public List getNativeAttributeNames() + { + return nativeAttributeNames; + } + + public String toString() + { + StringBuffer strBuf = new StringBuffer(); + + strBuf.append("Output: name=" + name); + + + Iterator keys = extensionAttributes.keySet().iterator(); + + while (keys.hasNext()) + { + QName name = (QName)keys.next(); + + strBuf.append("\nextension attribute: " + name + "=" + + extensionAttributes.get(name)); + } + + return strBuf.toString(); + } +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/SAWADLParserDriver.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/SAWADLParserDriver.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/SAWADLParserDriver.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/SAWADLParserDriver.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,153 @@ +package edu.uga.cs.lsdis.meteors.wadls; + +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Vector; + +import javax.wadls.Application; +import javax.wadls.Method; +import javax.wadls.Param; +import javax.wadls.Request; +import javax.wadls.Resource; +import javax.wadls.WADLSException; +import javax.wadls.factory.WADLFactory; +import javax.wadls.xml.WADLReader; +import javax.xml.namespace.QName; + + +public class SAWADLParserDriver { + + + private List completeMethodList = new ArrayList(); + private List url = new ArrayList(); + private List paramList = new ArrayList(); + private List paramTypeList = new ArrayList(); + private List paramModelRef = new ArrayList(); + private Application application; + + + public List getCompleteMethodList() { + return completeMethodList; + } + + public List getUrl() { + return url; + } + + public List getParamList() { + return paramList; + } + public List getParamTypeList() { + return paramTypeList; + } + + + + + public static void main(String[] args) throws Exception { + + //WADLParserDriver mpw = new WADLParserDriver(); + //mpw.parse(new URL(args[0])); + SAWADLParserDriver spd = new SAWADLParserDriver(); + //String fileURL = "/home/ganjoo/parser/SAWADLParser/Files/sample.wadl"; + String fileURL = "/home/ganjoo/parser/SAWADLParser/euPathWADL/GenesByTextSearch.sawadl"; + //String fileURL = "http://cs.uga.edu/~ganjoo/galaxy/GenesByTextSearch.sawadl"; + spd.parse(fileURL); + } + + public void parse(String fileURL) throws Exception { + int i=0; + Map resources = new HashMap(); + List methods = new Vector(); + List paramList = new Vector(); + + //URL fileURL = new URL("http://www.eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.wadl"); + WADLReader wadlReader; + try { + wadlReader = WADLFactory.newInstance().newWADLReader(); + wadlReader.setFeature(Constants.FEATURE_PARSE_SAWADL,true); + //wadlReader.setExtensionRegistry(new PopulatedExtensionRegistry()); + Application app = wadlReader.readWADL(fileURL); + this.application = app; + + + String temp = ""; + String tempHref=""; + int count =0; + Map resourceMap = app.getResources(); + for(Map.Entry entry : resourceMap.entrySet() ){ + count++; + Resource resource = (Resource) entry.getValue(); + // System.out.println("Resource " + count + "is " + resource.getQName().getNamespaceURI()); + + methods = resource.getMethods(); + + for(int j =0;j + */ +public class SchemaConstants { + + //Schema attribute names + public static final String ATTR_ID = "id"; + public static final String ATTR_SCHEMA_LOCATION = "schemaLocation"; + public static final String ATTR_HREF = "href"; + public static final String ATTR_NAME = "name"; + public static final String ATTR_TYPE = "type"; + public static final String ATTR_REF = "ref"; + public static final String ATTR_BASE = "base"; + public static final String ATTR_MAXOCCURS = "maxOccurs"; + public static final String ATTR_MINOCCURS = "minOccurs"; + + //Schema element names + public static final String ELEM_SCHEMA = "schema"; + public static final String ELEM_INCLUDE = "include"; + public static final String ELEM_REDEFINE = "redefine"; + public static final String ELEM_ELEMENT = "element"; + public static final String ELEM_SIMPLETYPE = "simpleType"; + public static final String ELEM_COMPLEXTYPE = "complexType"; + public static final String ELEM_ALL = "all"; + public static final String ELEM_SEQUENCE = "sequence"; + public static final String ELEM_CHOICE = "choice"; + public static final String ELEM_COMPLEXCONTENT = "complexContent"; + public static final String ELEM_RESTRICTION = "restriction"; + public static final String ELEM_EXTENSION = "extension"; + public static final String ELEM_GROUP = "group"; + + //Schema uri + public static final String NS_URI_XSD_1998 = + "http://www.w3.org/XML/1998/namespace"; + public static final String NS_URI_WADL = + "http://wadl.dev.java.net/2009/02"; + public static final String NS_URI_XSD_1999 = + "http://www.w3.org/1999/XMLSchema"; + public static final String NS_URI_XSD_2000 = + "http://www.w3.org/2000/10/XMLSchema"; + public static final String NS_URI_XSD_2001 = + "http://www.w3.org/2001/XMLSchema"; + public static final List XSD_STR_LIST = Arrays.asList(new String[] + {NS_URI_XSD_1998, NS_URI_XSD_1999, NS_URI_XSD_2000, NS_URI_XSD_2001}); + + //Schema qnames + public static final QName Q_ELEM_XSD_1999 = + new QName(NS_URI_XSD_1999, ELEM_SCHEMA); + public static final QName Q_ELEM_XSD_2000 = + new QName(NS_URI_XSD_2000, ELEM_SCHEMA); + public static final QName Q_ELEM_XSD_2001 = + new QName(NS_URI_XSD_2001, ELEM_SCHEMA); + public static final List XSD_QNAME_LIST = Arrays.asList(new QName[] + {Q_ELEM_XSD_1999, Q_ELEM_XSD_2000, Q_ELEM_XSD_2001}); + + //Schema import qnames + public static final QName Q_ELEM_IMPORT_XSD_1999 = new QName( + NS_URI_XSD_1999, Constants.ELEM_IMPORT); + public static final QName Q_ELEM_IMPORT_XSD_2000 = new QName( + NS_URI_XSD_2000, Constants.ELEM_IMPORT); + public static final QName Q_ELEM_IMPORT_XSD_2001 = new QName( + NS_URI_XSD_2001, Constants.ELEM_IMPORT); + public static final List XSD_IMPORT_QNAME_LIST = Arrays.asList(new QName[] + { Q_ELEM_IMPORT_XSD_1999, Q_ELEM_IMPORT_XSD_2000, Q_ELEM_IMPORT_XSD_2001 }); + + + //Schema include qnames + public static final QName Q_ELEM_INCLUDE_XSD_1999 = new QName( + NS_URI_XSD_1999, ELEM_INCLUDE); + public static final QName Q_ELEM_INCLUDE_XSD_2000 = new QName( + NS_URI_XSD_2000, ELEM_INCLUDE); + public static final QName Q_ELEM_INCLUDE_XSD_2001 = new QName( + NS_URI_XSD_2001, ELEM_INCLUDE); + public static final QName Q_ELEM_INCLUDE_WADL = new QName( + NS_URI_WADL, ELEM_INCLUDE); + + public static final List XSD_INCLUDE_QNAME_LIST = Arrays.asList(new QName[] + { Q_ELEM_INCLUDE_XSD_1999, Q_ELEM_INCLUDE_XSD_2000, Q_ELEM_INCLUDE_XSD_2001,Q_ELEM_INCLUDE_WADL }); + + //Schema redefine qnames + public static final QName Q_ELEM_REDEFINE_XSD_1999 = new QName( + NS_URI_XSD_1999, ELEM_REDEFINE); + public static final QName Q_ELEM_REDEFINE_XSD_2000 = new QName( + NS_URI_XSD_2000, ELEM_REDEFINE); + public static final QName Q_ELEM_REDEFINE_XSD_2001 = new QName( + NS_URI_XSD_2001, ELEM_REDEFINE); + public static final List XSD_REDEFINE_QNAME_LIST = Arrays.asList(new QName[] + { Q_ELEM_REDEFINE_XSD_1999, Q_ELEM_REDEFINE_XSD_2000, Q_ELEM_REDEFINE_XSD_2001 }); + + +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaDeserializer.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaDeserializer.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaDeserializer.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaDeserializer.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,196 @@ +/* + * (c) Copyright IBM Corp 2004, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.extensions.schema; + +import java.io.Serializable; +import java.util.Hashtable; +import java.util.Map; + +import javax.wadls.Application; +import javax.wadls.WADLSException; +import javax.wadls.extensions.ExtensionDeserializer; +import javax.wadls.extensions.schema.Schema; +import javax.wadls.extensions.schema.SchemaImport; +import javax.wadls.extensions.schema.SchemaReference; +import javax.wadls.xml.WADLLocator; +import javax.wadls.WADLSException; +import javax.wadls.extensions.ExtensibilityElement; +import javax.wadls.extensions.ExtensionRegistry; +import javax.xml.namespace.QName; + +import org.w3c.dom.Element; + + +import edu.uga.cs.lsdis.meteors.wadls.extensions.schema.SchemaConstants; +import edu.uga.cs.lsdis.meteors.wadls.Constants; +import edu.uga.cs.lsdis.meteors.wadls.util.xml.DOMUtils; +import edu.uga.cs.lsdis.meteors.wadls.util.xml.QNameUtils; + +/** + * This class is used to deserialize <schema> elements into + * Schema instances. + * + * @see SchemaImpl + * @see SchemaSerializer + * + * @author Jeremy Hughes + */ +public class SchemaDeserializer implements Serializable +{ + + // Need to set this since a Definition is serializable and it contains an + // extension registry which contains one of these + public static final long serialVersionUID = 1; + + private final Map allReferencedSchemas = new Hashtable(); + + private static ThreadLocal wsdlLocator = new ThreadLocal(); + + /** + * Set the WSDLLocator to be used by the deserializer on this thread. + * + * @param loc The WSDLLocator to be used. + * + * @see WSDLLocator + */ + public static void setLocator(WADLLocator loc) + { + wsdlLocator.set(loc); + } + public Schema unmarshall(QName elementType, + Element el, + Application def) +throws WADLSException +{ + +Schema schema = new SchemaImpl(); + +schema.setElementType(elementType); +schema.setElement(el); +schema.setDocumentBaseURI(def.getDocumentBaseURI()); + +//TODO: check if the 'required' attribute needs to be set + +// Go through the schema Element looking for child schemas +if(elementType.getLocalPart().equalsIgnoreCase("include")){ + + Element tempEl = el; + + QName tempElType = QNameUtils.newQName(tempEl); + + // Create the appropriate SchemaReference subclass to represent + // an , an or a + + SchemaReference sr = null; + String locationURI = null; + + + if (SchemaConstants.XSD_INCLUDE_QNAME_LIST.contains(tempElType)) + { + + // Create a new include. Don't use the + // ExtensionRegistry.createExtension() + // method as a Schema include is not a WSDL import. + sr = schema.createInclude(); + + sr.setId(DOMUtils.getAttribute(tempEl, SchemaConstants.ATTR_ID)); + + locationURI = DOMUtils.getAttribute(tempEl, SchemaConstants.ATTR_HREF); + + sr.setSchemaLocationURI(locationURI); + + // Now the include is set up except for the pointer to the + // referenced LWS, add the include to the LightWeightSchema. + schema.addInclude(sr); + } + +} +else{ +Element tempEl = DOMUtils.getFirstChildElement(el); + + +for (; tempEl != null; tempEl = DOMUtils.getNextSiblingElement(tempEl)) +{ + +QName tempElType = QNameUtils.newQName(tempEl); + +// Create the appropriate SchemaReference subclass to represent +// an , an or a + +SchemaReference sr = null; +String locationURI = null; + +if (SchemaConstants.XSD_IMPORT_QNAME_LIST.contains(tempElType)) +{ + + +// Create a new import. Don't use the +// ExtensionRegistry.createExtension() +// method as a Schema import is not a WSDL import. +SchemaImport im = schema.createImport(); + + +im.setId(DOMUtils.getAttribute(tempEl, SchemaConstants.ATTR_ID)); +im.setNamespaceURI(DOMUtils.getAttribute(tempEl, Constants.ATTR_NAMESPACE)); + +locationURI = DOMUtils.getAttribute(tempEl, SchemaConstants.ATTR_SCHEMA_LOCATION); +im.setSchemaLocationURI(locationURI); + +// Now the import is set up except for the point to the +// referenced LWS, add the import to the LightWeightSchema. +schema.addImport(im); +} +else +if (SchemaConstants.XSD_INCLUDE_QNAME_LIST.contains(tempElType)) +{ + +// Create a new include. Don't use the +// ExtensionRegistry.createExtension() +// method as a Schema include is not a WSDL import. +sr = schema.createInclude(); + +sr.setId(DOMUtils.getAttribute(tempEl, SchemaConstants.ATTR_ID)); + +locationURI = DOMUtils.getAttribute(tempEl, SchemaConstants.ATTR_SCHEMA_LOCATION); + +sr.setSchemaLocationURI(locationURI); + +// Now the include is set up except for the pointer to the +// referenced LWS, add the include to the LightWeightSchema. +schema.addInclude(sr); +} +else +if (SchemaConstants.XSD_REDEFINE_QNAME_LIST.contains(tempElType)) +{ +// Create a new redefine. Don't use the +// ExtensionRegistry.createExtension() method as a Schema redefine +// is not a WSDL import. +sr = schema.createRedefine(); + +sr.setId(DOMUtils.getAttribute(tempEl, SchemaConstants.ATTR_ID)); + +locationURI = DOMUtils.getAttribute(tempEl, SchemaConstants.ATTR_SCHEMA_LOCATION); + +sr.setSchemaLocationURI(locationURI); + +// Now the redefine is set up except for the pointer to the +// referenced LWS, add the redefine to the LightWeightSchema. +schema.addRedefine(sr); +} +else +{ +// The element isn't one we're interested in so look at the next +// one +continue; +} + +} //end for +} + +return schema; +} + + +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,235 @@ +/* + * (c) Copyright IBM Corp 2004, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.extensions.schema; + +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Vector; + +import javax.wadls.extensions.schema.Schema; +import javax.wadls.extensions.schema.SchemaImport; +import javax.wadls.extensions.schema.SchemaReference; +import javax.xml.namespace.QName; + +import org.w3c.dom.Element; + +/** + * This class is used to wrap schema elements. It holds the DOM Element to the + * <schema> element. + * + * @see SchemaSerializer + * @see SchemaDeserializer + * + * @author Jeremy Hughes + */ +public class SchemaImpl implements Schema +{ + protected QName elementType = null; + // Uses the wrapper type so we can tell if it was set or not. + protected Boolean required = null; + protected Element element = null; + + public static final long serialVersionUID = 1; + + /* + * imports is a Map of Lists with key of the import's namespace URI. Each List + * contains the SchemaImport objects for that namespace. There can be more + * than one SchemaImport in a List - one for each schemaLocation attribute + * setting. + */ + private Map imports = new HashMap(); + + /* + * includes is a List of Include objects for the targetNamespace of the + * enclosing schema. There is one Include in the List for each + * element in the XML Schema. + */ + private List includes = new Vector(); + + /* + * redefines is a list of Redefine obejcts for the targetNamespace of the + * enclosing schema. There is one Redefine in the List for each + * element in the XML Schema. + */ + private List redefines = new Vector(); + + private String documentBaseURI = null; + + /** + * Get a map of lists containing all the imports defined here. The map's keys + * are Strings representing the namespace URIs, and the map's values are + * lists. There is one list for each namespace URI for which imports have been + * defined. + * + * @return a Map of Lists of Import instances keyed off the import's namespace + */ + public Map getImports() + { + return this.imports; + } + + /** + * Create a new schema import. + * + * @return the newly created schema import + */ + public SchemaImport createImport() + { + return new SchemaImportImpl(); + } + + /** + * Add an import to this LightWeightSchema + * + * @param importSchema the import to be added + */ + public void addImport(SchemaImport importSchema) + { + String namespaceURI = importSchema.getNamespaceURI(); + List importList = (List) this.imports.get(namespaceURI); + + if (importList == null) + { + importList = new Vector(); + + this.imports.put(namespaceURI, importList); + } + + importList.add(importSchema); + } + + /** + * Get list of includes defined here. + * + * @return a List of SchemaReference instances representing the schema + * includes. + */ + + public List getIncludes() + { + return this.includes; + } + + public SchemaReference createInclude() + { + return new SchemaReferenceImpl(); + } + + public void addInclude(SchemaReference includeSchema) + { + this.includes.add(includeSchema); + } + + public List getRedefines() + { + return this.redefines; + } + + public SchemaReference createRedefine() + { + return new SchemaReferenceImpl(); + } + + public void addRedefine(SchemaReference redefineSchema) + { + this.redefines.add(redefineSchema); + } + + public String toString() + { + StringBuffer strBuf = new StringBuffer(); + + strBuf.append("SchemaExtensibilityElement (" + this.elementType + "):"); + strBuf.append("\nrequired=" + this.required); + + if (this.element != null) + { + strBuf.append("\nelement=" + this.element); + } + + return strBuf.toString(); + } + + /** + * Set the type of this extensibility element. + * + * @param elementType the type + */ + public void setElementType(QName elementType) + { + this.elementType = elementType; + } + + /** + * Get the type of this extensibility element. + * + * @return the extensibility element's type + */ + public QName getElementType() + { + return elementType; + } + + /** + * Set whether or not the semantics of this extension + * are required. Relates to the wsdl:required attribute. + */ + public void setRequired(Boolean required) + { + this.required = required; + } + + /** + * Get whether or not the semantics of this extension + * are required. Relates to the wsdl:required attribute. + */ + public Boolean getRequired() + { + return required; + } + + /** + * Set the DOM Element that represents this schema element. + * + * @param element the DOM element representing this schema + */ + public void setElement(Element element) + { + this.element = element; + } + + /** + * Get the DOM Element that represents this schema element. + * + * @return the DOM element representing this schema + */ + public Element getElement() + { + return element; + } + + /** + * Set the document base URI of this schema definition. Can be used to + * represent the origin of the schema, and can be exploited when resolving + * relative URIs (e.g. in <import>s). + * + * @param documentBaseURI the document base URI of this schema + */ + public void setDocumentBaseURI(String documentBaseURI) + { + this.documentBaseURI = documentBaseURI; + } + + /** + * Get the document base URI of this schema + * + * @return the document base URI + */ + public String getDocumentBaseURI() + { + return this.documentBaseURI; + } +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaImportImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaImportImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaImportImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaImportImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,33 @@ +/* + * (c) Copyright IBM Corp 2004, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.extensions.schema; + +import javax.wadls.extensions.schema.SchemaImport; + +/** + * @author Jeremy Hughes + */ +public class SchemaImportImpl extends SchemaReferenceImpl implements SchemaImport +{ + public static final long serialVersionUID = 1; + + private String namespace = null; + + /** + * @return Returns the namespace. + */ + public String getNamespaceURI() + { + return this.namespace; + } + + /** + * @param namespace The namespace to set. + */ + public void setNamespaceURI(String namespace) + { + this.namespace = namespace; + } +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaReferenceImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaReferenceImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaReferenceImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaReferenceImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,71 @@ +/* + * (c) Copyright IBM Corp 2004, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.extensions.schema; + +import javax.wadls.extensions.schema.Schema; +import javax.wadls.extensions.schema.SchemaReference; + +/** + * @author Jeremy Hughes + */ +public class SchemaReferenceImpl implements SchemaReference +{ + + public static final long serialVersionUID = 1; + + private String id = null; + + private String schemaLocation = null; + + private Schema referencedSchema = null; + + /** + * @return Returns the id. + */ + public String getId() + { + return this.id; + } + + /** + * @param id The id to set. + */ + public void setId(String id) + { + this.id = id; + } + + /** + * @return Returns the schemaLocation. + */ + public String getSchemaLocationURI() + { + return this.schemaLocation; + } + + /** + * @param schemaLocation The schemaLocation to set. + */ + public void setSchemaLocationURI(String schemaLocation) + { + this.schemaLocation = schemaLocation; + } + + /** + * @return Returns the importedSchema. + */ + public Schema getReferencedSchema() + { + return this.referencedSchema; + } + + /** + * @param referencedSchema The importedSchema to set. + */ + public void setReferencedSchema(Schema referencedSchema) + { + this.referencedSchema = referencedSchema; + } +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaSerializer.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaSerializer.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaSerializer.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/extensions/schema/SchemaSerializer.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,50 @@ +/* + * (c) Copyright IBM Corp 2004, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.extensions.schema; + +import java.io.PrintWriter; +import java.io.Serializable; + +import javax.wadls.Application; +import javax.wadls.WADLSException; +import javax.wadls.extensions.ExtensionDeserializer; +import javax.wadls.extensions.schema.Schema; +import javax.wadls.extensions.ExtensionSerializer; +import javax.wadls.WADLSException; +import javax.wadls.extensions.ExtensibilityElement; +import javax.wadls.extensions.ExtensionRegistry; +import javax.xml.namespace.QName; + +import edu.uga.cs.lsdis.meteors.wadls.util.xml.DOM2Writer; + +/** + * This class is used to serialize Schema instances + * into the PrintWriter. + * + * @see SchemaImpl + * @see SchemaDeserializer + * + * @author Jeremy Hughes + */ +public class SchemaSerializer implements ExtensionSerializer,Serializable +{ + public static final long serialVersionUID = 1; + public void marshall(Class parentType, + QName elementType, + ExtensibilityElement extension, + PrintWriter pw, + Application def, + ExtensionRegistry extReg) + throws WADLSException +{ +Schema schema = (Schema)extension; + +pw.print(" "); + +DOM2Writer.serializeAsXML(schema.getElement(), pw); + +pw.println(); +} +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/factory/WADLFactoryImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/factory/WADLFactoryImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/factory/WADLFactoryImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/factory/WADLFactoryImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,52 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.factory; + +import javax.wadls.*; +import javax.wadls.extensions.*; +import javax.wadls.factory.*; +import javax.wadls.xml.*; + +import edu.uga.cs.lsdis.meteors.wadls.*; +import edu.uga.cs.lsdis.meteors.wadls.xml.*; + +/** + * This class is a concrete implementation of the abstract class + * WSDLFactory. Some ideas used here have been shamelessly + * copied from the wonderful JAXP and Xerces work. + * + * @author Matthew J. Duftler (duftler@us.ibm.com) + */ +public class WADLFactoryImpl extends WADLFactory +{ + /** + * Create a new instance of a Definition, with an instance + * of a PopulatedExtensionRegistry as its ExtensionRegistry. + * + * @see edu.uga.cs.lsdis.meteors.wadls.extensions.PopulatedExtensionRegistry + */ + public Application newApplication() + { + Application app = new ApplicationImpl(); + return app; + } + + /** + * Create a new instance of a WSDLReader. + */ + public WADLReader newWADLReader() + { + return new WADLReaderImpl(); + } + + /** + * Create a new instance of a WSDLWriter. + */ + public WADLWriter newWADLWriter() + { + return new WADLWriterImpl(); + } + +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/IOUtils.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/IOUtils.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/IOUtils.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/IOUtils.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,36 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.util; + +import java.io.*; + +/** + * This file is a collection of input/output utilities. + * + * @author Sanjiva Weerawarana + * @author Matthew J. Duftler + */ +public class IOUtils { + // debug flag - generates debug stuff if true + static boolean debug = false; + + ////////////////////////////////////////////////////////////////////////// + + public static String getStringFromReader (Reader reader) throws IOException { + BufferedReader bufIn = new BufferedReader(reader); + StringWriter swOut = new StringWriter(); + PrintWriter pwOut = new PrintWriter(swOut); + String tempLine; + + while ((tempLine = bufIn.readLine()) != null) { + pwOut.println(tempLine); + } + + pwOut.flush(); + + return swOut.toString(); + } +} + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/ObjectRegistry.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/ObjectRegistry.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/ObjectRegistry.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/ObjectRegistry.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,55 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.util; + +import java.util.*; + +/** + * The ObjectRegistry is used to do name-to-object reference lookups. + * If an ObjectRegistry is passed as a constructor argument, then this + * ObjectRegistry will be a cascading registry: when a lookup is + * invoked, it will first look in its own table for a name, and if it's not + * there, it will cascade to the parent ObjectRegistry. + * All registration is always local. [??] + * + * @author Sanjiva Weerawarana + * @author Matthew J. Duftler + */ +public class ObjectRegistry { + Hashtable reg = new Hashtable (); + ObjectRegistry parent = null; + + public ObjectRegistry () { + } + + public ObjectRegistry (ObjectRegistry parent) { + this.parent = parent; + } + + // register an object + public void register (String name, Object obj) { + reg.put (name, obj); + } + + // unregister an object (silent if unknown name) + public void unregister (String name) { + reg.remove (name); + } + + // lookup an object: cascade up if needed + public Object lookup (String name) throws IllegalArgumentException { + Object obj = reg.get (name); + + if (obj == null && parent != null) { + obj = parent.lookup (name); + } + + if (obj == null) { + throw new IllegalArgumentException ("object '" + name + "' not in registry"); + } + + return obj; + } +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/SchemaUtils.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/SchemaUtils.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/SchemaUtils.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/SchemaUtils.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,543 @@ +/* + * Created on Apr 10, 2005 + * + */ +package edu.uga.cs.lsdis.meteors.wadls.util; + +import java.util.ArrayList; +import java.util.Iterator; +import java.util.List; +import java.util.Map; + +import javax.wadls.Grammars; +import javax.wadls.Params; +import javax.wadls.WADLSException; +import javax.wadls.extensions.schema.Schema; +import javax.xml.namespace.QName; + +import org.w3c.dom.DOMException; +import org.w3c.dom.Element; +import org.w3c.dom.Node; +import org.w3c.dom.NodeList; + +import edu.uga.cs.lsdis.meteors.wadls.Constants; +import edu.uga.cs.lsdis.meteors.wadls.extensions.schema.SchemaConstants; +import edu.uga.cs.lsdis.meteors.wadls.util.xml.QNameUtils; +import edu.uga.cs.lsdis.meteors.wadls.util.xml.XPathUtils; + +/** + * This file is a collection of utilities which find the location of a XML/XSD Element by using the given path. + * @author Zixin Wu + * + */ + +public class SchemaUtils { + + /** + * Search an XML element in the schemas contained in the given Types. + * @param types Search in the schemas contained in this WSDLS Types. + * @param tagName XML Element name of the desired element. + * @param elementName The value of the attribute "name" of the desired element. + * @return An XML element whose XML Element name is "tagName" and whose attribute "name" is "elementName". + * @throws WADLSException + */ + public static Element findXMLEleInSchemas(Grammars grammars, String tagName, QName elementName) throws WADLSException{ + Map schemas = grammars.getSchemas(); + Iterator it = schemas.values().iterator(); + while(it.hasNext()){ + Schema schema = (Schema)(it.next()); + Element schemaEle = schema.getElement(); + if (schemaEle.getAttribute(Constants.ATTR_TARGET_NAMESPACE).equals(elementName.getNamespaceURI())){ + Element foundEle = findXMLEleByName(schemaEle, tagName, elementName); + if (foundEle != null) + return foundEle; + } + } + return null; + } + + /** + * Search the element whose XML Element name is "tagName" and whose attribute "name" is "elementName", + * in the startElement, search in only one level depth. + * @param startElement Start searching from this XML Element. + * @param tagName XML Element name of the desired element. + * @param elementName The value of the attribute "name" of the desired element. + * @return An XML element whose XML Element name is "tagName" and whose attribute "name" is "elementName". + * @throws WADLSException + */ + public static Element findXMLEleByName(Element startElement, String tagName, QName elementName) throws WADLSException{ + NodeList nodeList = startElement.getChildNodes(); + //find the element with the required name as an attribute + int listLength = nodeList.getLength(); + for(int i=0;i + //get the QName of typeAttr + QName typeQName = QNameUtils.getQName(typeAttr, startElement); + if (SchemaConstants.XSD_STR_LIST.contains(typeQName.getNamespaceURI())){ + //primitive data type + WADLSException wsdlsExc = new WADLSException(WADLSException.PATH_ERROR, + "Primitive type cannot has path"); + wsdlsExc.setLocation(XPathUtils.getXPathExprFromNode(startElement)); + throw wsdlsExc; + } + else{ + //find the complexType with the given type QName + Element complexTypeElement = findXMLEleInSchemas(grammars, SchemaConstants.ELEM_COMPLEXTYPE, typeQName); + if (complexTypeElement != null) + return findXSDEleOnComplexType(complexTypeElement, path, grammars); + else + //cannot find in complexType + throw new DOMException(DOMException.NOT_FOUND_ERR, "cannot find complexType by the given path"); + } + } + else{ + //No type, look for complexType in the subNodes + Element complexElement = findXMLEleByName(startElement, SchemaConstants.ELEM_COMPLEXTYPE, null); + if (complexElement != null) + return findXSDEleOnComplexType(complexElement, path, grammars); + else{ + WADLSException wsdlsExc = new WADLSException(WADLSException.NOT_FOUND_ELE_BY_PATH, + "cannot find complexType matching the path"); + wsdlsExc.setLocation(XPathUtils.getXPathExprFromNode(startElement)); + throw wsdlsExc; + } + } + } + } + + public static Element findXSDEleOnEle(Element startElement, String path, Params params) throws WADLSException{ + /*String refAttr = startElement.getAttribute(SchemaConstants.ATTR_REF); + if (refAttr != ""){ + //look for the referenced element + QName elementQName = QNameUtils.getQName(refAttr, startElement); + Element refenecedElement = findXMLEleInSchemas(params, SchemaConstants.ELEM_ELEMENT, elementQName); + if (refenecedElement != null) + return findXSDEleOnEle(refenecedElement, path, grammars); + else{ + throw new DOMException(DOMException.NOT_FOUND_ERR, "Cannot find referenced element"); + } + } + else{ + if (path == "") + return startElement; + + String typeAttr = startElement.getAttribute(SchemaConstants.ATTR_TYPE); + if (typeAttr != ""){ //<... type="..."> + //get the QName of typeAttr + QName typeQName = QNameUtils.getQName(typeAttr, startElement); + if (SchemaConstants.XSD_STR_LIST.contains(typeQName.getNamespaceURI())){ + //primitive data type + WADLSException wsdlsExc = new WADLSException(WADLSException.PATH_ERROR, + "Primitive type cannot has path"); + wsdlsExc.setLocation(XPathUtils.getXPathExprFromNode(startElement)); + throw wsdlsExc; + } + else{ + //find the complexType with the given type QName + Element complexTypeElement = findXMLEleInSchemas(grammars, SchemaConstants.ELEM_COMPLEXTYPE, typeQName); + if (complexTypeElement != null) + return findXSDEleOnComplexType(complexTypeElement, path, grammars); + else + //cannot find in complexType + throw new DOMException(DOMException.NOT_FOUND_ERR, "cannot find complexType by the given path"); + } + } + else{ + //No type, look for complexType in the subNodes + Element complexElement = findXMLEleByName(startElement, SchemaConstants.ELEM_COMPLEXTYPE, null); + if (complexElement != null) + return findXSDEleOnComplexType(complexElement, path, grammars); + else{ + WADLSException wsdlsExc = new WADLSException(WADLSException.NOT_FOUND_ELE_BY_PATH, + "cannot find complexType matching the path"); + wsdlsExc.setLocation(XPathUtils.getXPathExprFromNode(startElement)); + throw wsdlsExc; + } + } + }*/ + return startElement; + } + + /** + * Search an XSD Element from the XSD complexType. + * @param complexTypeElement Start searching from this XSD ComplexType + * @param path + * @param types WSDLS Types + * @return An XSD Element + * @throws WADLSException + */ + public static Element findXSDEleOnComplexType(Element complexTypeElement, String path, Grammars grammars) throws WADLSException{ + if (path == null || path == "") + return null; + //look for the matching element. + String splitedPath[] = splitPath(path); + String elementName = splitedPath[0]; + path = splitedPath[1]; + Element targetElement = findXSDEleInComplexType(complexTypeElement, elementName, grammars); + if (targetElement != null) + return findXSDEleOnEle(targetElement, path, grammars); + else{ + WADLSException wsdlsExc = new WADLSException(WADLSException.NOT_FOUND_ELE_BY_PATH, + "Cannot find the element matching the path"); + wsdlsExc.setLocation(XPathUtils.getXPathExprFromNode(complexTypeElement)); + throw wsdlsExc; + } + } + + public static Element findXSDEleOnComplexType(Element complexTypeElement, String path, Params params) throws WADLSException{ + /*if (path == null || path == "") + return null; + //look for the matching element. + String splitedPath[] = splitPath(path); + String elementName = splitedPath[0]; + path = splitedPath[1]; + Element targetElement = findXSDEleInComplexType(complexTypeElement, elementName, grammars); + if (targetElement != null) + return findXSDEleOnEle(targetElement, path, grammars); + else{ + WADLSException wsdlsExc = new WADLSException(WADLSException.NOT_FOUND_ELE_BY_PATH, + "Cannot find the element matching the path"); + wsdlsExc.setLocation(XPathUtils.getXPathExprFromNode(complexTypeElement)); + throw wsdlsExc; + }*/ + return complexTypeElement; + } + + /** + * Search an XSD Element recursively inside of the complexType. + * @param startElement + * @param elementName The desired attribute "name" + * @param types WSDL Types + * @return A XSD Element + * @throws WADLSException + */ + public static Element findXSDEleInComplexType(Element startElement, String elementName, Grammars grammars) throws WADLSException{ + NodeList subNodes = startElement.getChildNodes(); + int length = subNodes.getLength(); + for(int i=0;i + Element returnElement = findXSDEleInComplexType(currentElement, elementName, grammars); + if (returnElement != null) + return returnElement; + else{ + String baseAttr = currentElement.getAttribute(SchemaConstants.ATTR_BASE); + QName baseQName = QNameUtils.getQName(baseAttr, currentElement); + Element baseElement = findXMLEleInSchemas(grammars, SchemaConstants.ELEM_COMPLEXTYPE, baseQName); + return findXSDEleInComplexType(baseElement, elementName, grammars); + } + } + else if (localPart.equals(SchemaConstants.ELEM_GROUP)){ + //find . + String refAttr = currentElement.getAttribute(SchemaConstants.ATTR_REF); + if (refAttr != ""){ + //look for the referenced + QName groupQName = QNameUtils.getQName(refAttr, currentElement); + Element groupElement = findXMLEleInSchemas(grammars, SchemaConstants.ELEM_GROUP, groupQName); + if (groupElement != null){ + //try to find it in the referenced + Element returnElement = findXSDEleInComplexType(groupElement, elementName, grammars); + if (returnElement != null) + return returnElement; + else + //Not in the referenced + continue; + } + else + throw new DOMException(DOMException.NOT_FOUND_ERR, "Cannot find the referenced group"); + } + else + //Just skip it, call this method recursively. + return findXSDEleInComplexType(currentElement, elementName, grammars); + } + } + return null; + } + + /** + * return the first schema in the given extensible elements. + * @param extElements Search the first schema in this extensible elements. + * @return The first schema in the given extensible elements. + * @throws WADLSException + */ + public static Schema getFirstSchema(List extElements){ + if (extElements == null) + return null; + Object schemaObj = extElements.iterator().next(); + if (schemaObj == null) + return null; + /* ExtensibilityElement schemaEE = (ExtensibilityElement) schemaObj; + if (SchemaConstants.XSD_QNAME_LIST.contains(schemaEE.getElementType())) + return (Schema)schemaObj; + else*/ + return null; + } + + /** + * return all schemas in the given extensible elements. + * @param extElements Search the first schema in this extensible elements. + * @return All schemas in the given extensible elements. + * @throws WADLSException + */ + public static List getSchemas(List extElements){ + List schemas = new ArrayList(); + if (extElements != null){ + Iterator it = extElements.iterator(); + while(it.hasNext()){ + Object schemaObj = it.next(); + if (schemaObj == null) + continue; + /*ExtensibilityElement schemaEE = (ExtensibilityElement) schemaObj; + if (SchemaConstants.XSD_QNAME_LIST.contains(schemaEE.getElementType())) + schemas.add((Schema)schemaObj);*/ + } + } + return schemas; + } + + /** + * This method split the path string, return a string array, + * whose first dim is the string before the first '/' , + * and the second dim is the remaining string. + * @param path The path to be splitted. + * @return The splitted string. + */ + public static String[] splitPath(String path){ + String returnStr[] = new String[2]; //the string before '/' + int slashPosition = path.indexOf('/'); + if (slashPosition == -1){ + //no deeper path + returnStr[0] = path; + returnStr[1] = ""; + } + else{ + returnStr[0] = path.substring(0, slashPosition); + returnStr[1] = path.substring(slashPosition+1); + //if the remaining path is "/", empty it. + if (returnStr[1] == "/") returnStr[1] = ""; + } + return returnStr; + } + +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/StringUtils.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/StringUtils.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/StringUtils.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/StringUtils.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,230 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.util; + +import java.io.*; +import java.util.*; +import java.net.URL; +import java.net.MalformedURLException; + +/** + * Deals with strings (probably need to elaborate some more). + * + * @author Matthew J. Duftler + */ +public class StringUtils +{ + public static final String lineSeparator = + System.getProperty("line.separator", "\n"); + public static final String lineSeparatorStr = cleanString(lineSeparator); + + // Ensure that escape sequences are passed through properly. + public static String cleanString(String str) + { + if (str == null) + return null; + else + { + char[] charArray = str.toCharArray(); + StringBuffer sBuf = new StringBuffer(); + + for (int i = 0; i < charArray.length; i++) + switch (charArray[i]) + { + case '\"' : sBuf.append("\\\""); + break; + case '\\' : sBuf.append("\\\\"); + break; + case '\n' : sBuf.append("\\n"); + break; + case '\r' : sBuf.append("\\r"); + break; + default : sBuf.append(charArray[i]); + break; + } + + return sBuf.toString(); + } + } + + /* + This method will return the correct name for a class object representing + a primitive, a single instance of a class, as well as n-dimensional arrays + of primitives or instances. This logic is needed to handle the string returned + from Class.getName(). If the class object represents a single instance (or + a primitive), Class.getName() returns the fully-qualified name of the class + and no further work is needed. However, if the class object represents an + array (of n dimensions), Class.getName() returns a Descriptor (the Descriptor + grammar is defined in section 4.3 of the Java VM Spec). This method will + parse the Descriptor if necessary. + */ + public static String getClassName(Class targetClass) + { + String className = targetClass.getName(); + + return targetClass.isArray() ? parseDescriptor(className) : className; + } + + /* + See the comment above for getClassName(targetClass)... + */ + private static String parseDescriptor(String className) + { + char[] classNameChars = className.toCharArray(); + int arrayDim = 0; + int i = 0; + + while (classNameChars[i] == '[') + { + arrayDim++; + i++; + } + + StringBuffer classNameBuf = new StringBuffer(); + + switch (classNameChars[i++]) + { + case 'B' : classNameBuf.append("byte"); + break; + case 'C' : classNameBuf.append("char"); + break; + case 'D' : classNameBuf.append("double"); + break; + case 'F' : classNameBuf.append("float"); + break; + case 'I' : classNameBuf.append("int"); + break; + case 'J' : classNameBuf.append("long"); + break; + case 'S' : classNameBuf.append("short"); + break; + case 'Z' : classNameBuf.append("boolean"); + break; + case 'L' : classNameBuf.append(classNameChars, + i, classNameChars.length - i - 1); + break; + } + + for (i = 0; i < arrayDim; i++) + classNameBuf.append("[]"); + + return classNameBuf.toString(); + } + + /* + @param contextURL the context in which to attempt to resolve the spec. + Effectively a document base. + */ + public static URL getURL(URL contextURL, String spec) + throws MalformedURLException + { + if (contextURL != null) + { + File tempFile = new File(spec); + + if (tempFile.isAbsolute()) + { + return tempFile.toURL(); + } + } + + try + { + return new URL(contextURL, spec); + } + catch (MalformedURLException e) + { + if (contextURL == null) + { + return new File(spec).toURL(); + } + else + { + throw e; + } + } + } + + /* + Returns an InputStream for reading from the specified resource, if the + resource points to a stream. + */ + public static InputStream getContentAsInputStream(URL url) + throws SecurityException, + IllegalArgumentException, + IOException + { + if (url == null) + { + throw new IllegalArgumentException("URL cannot be null."); + } + + try + { + Object content = url.getContent(); + + if (content == null) + { + throw new IllegalArgumentException("No content."); + } + + if (content instanceof InputStream) + { + return (InputStream)content; + } + else + { + throw new IllegalArgumentException((content instanceof String) + ? (String)content + : "This URL points to a: " + + StringUtils.getClassName(content.getClass())); + } + } + catch (SecurityException e) + { + throw new SecurityException("Your JVM's SecurityManager has " + + "disallowed this."); + } + catch (FileNotFoundException e) + { + throw new FileNotFoundException("This file was not found: " + url); + } + } + + public static List parseNMTokens(String nmTokens) + { + StringTokenizer strTok = new StringTokenizer(nmTokens, " "); + List tokens = new Vector(); + + while (strTok.hasMoreTokens()) + { + tokens.add(strTok.nextToken()); + } + + return tokens; + } + + public static String getNMTokens(List list) + { + if (list != null) + { + StringBuffer strBuf = new StringBuffer(); + int size = list.size(); + + for (int i = 0; i < size; i++) + { + String token = (String)list.get(i); + + strBuf.append((i > 0 ? " " : "") + token); + } + + return strBuf.toString(); + } + else + { + return null; + } + } +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/DOM2Writer.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/DOM2Writer.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/DOM2Writer.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/DOM2Writer.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,427 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.util.xml; + +import java.io.*; +import java.util.*; +import org.w3c.dom.*; + +import edu.uga.cs.lsdis.meteors.wadls.*; +import edu.uga.cs.lsdis.meteors.wadls.util.*; + +/** + * This class is a utility to serialize a DOM node as XML. This class + * uses the DOM Level 2 APIs. + * The main difference between this class and DOMWriter is that this class + * generates and prints out namespace declarations. + * + * @author Matthew J. Duftler (duftler@us.ibm.com) + * @author Joseph Kesselman + */ +public class DOM2Writer +{ + /** + * The namespaceURI represented by the prefix xmlns. + */ + private static String NS_URI_XMLNS = "http://www.w3.org/2000/xmlns/"; + + /** + * The namespaceURI represented by the prefix xml. + */ + private static String NS_URI_XML = "http://www.w3.org/XML/1998/namespace"; + + private static Map xmlEncodingMap = new HashMap(); + + static + { + xmlEncodingMap.put(null, Constants.XML_DECL_DEFAULT); + xmlEncodingMap.put(System.getProperty("file.encoding"), + Constants.XML_DECL_DEFAULT); + xmlEncodingMap.put("UTF8", "UTF-8"); + xmlEncodingMap.put("UTF-16", "UTF-16"); + xmlEncodingMap.put("UnicodeBig", "UTF-16"); + xmlEncodingMap.put("UnicodeLittle", "UTF-16"); + xmlEncodingMap.put("ASCII", "US-ASCII"); + xmlEncodingMap.put("ISO8859_1", "ISO-8859-1"); + xmlEncodingMap.put("ISO8859_2", "ISO-8859-2"); + xmlEncodingMap.put("ISO8859_3", "ISO-8859-3"); + xmlEncodingMap.put("ISO8859_4", "ISO-8859-4"); + xmlEncodingMap.put("ISO8859_5", "ISO-8859-5"); + xmlEncodingMap.put("ISO8859_6", "ISO-8859-6"); + xmlEncodingMap.put("ISO8859_7", "ISO-8859-7"); + xmlEncodingMap.put("ISO8859_8", "ISO-8859-8"); + xmlEncodingMap.put("ISO8859_9", "ISO-8859-9"); + xmlEncodingMap.put("ISO8859_13", "ISO-8859-13"); + xmlEncodingMap.put("ISO8859_15_FDIS", "ISO-8859-15"); + xmlEncodingMap.put("GBK", "GBK"); + xmlEncodingMap.put("Big5", "Big5"); + } + + /** + * Return a string containing this node serialized as XML. + */ + public static String nodeToString(Node node) + { + StringWriter sw = new StringWriter(); + + serializeAsXML(node, sw); + + return sw.toString(); + } + + + /** + * Print an XML declaration before serializing the element. + */ + public static void serializeElementAsDocument(Element el, Writer writer) + { + PrintWriter pw = new PrintWriter(writer); + String javaEncoding = (writer instanceof OutputStreamWriter) + ? ((OutputStreamWriter) writer).getEncoding() + : null; + + String xmlEncoding = java2XMLEncoding(javaEncoding); + + if (xmlEncoding != null) + { + pw.println(Constants.XML_DECL_START + + xmlEncoding + + Constants.XML_DECL_END); + } + else + { + pw.println(""); + } + + serializeAsXML(el, writer); + } + + /** + * Serialize this node into the writer as XML. + */ + public static void serializeAsXML(Node node, Writer writer) + { + ObjectRegistry namespaceStack = new ObjectRegistry(); + + namespaceStack.register("xml", NS_URI_XML); + + PrintWriter pw = new PrintWriter(writer); + String javaEncoding = (writer instanceof OutputStreamWriter) + ? ((OutputStreamWriter) writer).getEncoding() + : null; + + print(node, namespaceStack, pw, java2XMLEncoding(javaEncoding)); + } + + private static void print(Node node, ObjectRegistry namespaceStack, + PrintWriter out, String xmlEncoding) + { + if (node == null) + { + return; + } + + boolean hasChildren = false; + int type = node.getNodeType(); + + switch (type) + { + case Node.DOCUMENT_NODE : + { + if (xmlEncoding != null) + { + out.println(Constants.XML_DECL_START + + xmlEncoding + + Constants.XML_DECL_END); + } + else + { + out.println(""); + } + + NodeList children = node.getChildNodes(); + + if (children != null) + { + int numChildren = children.getLength(); + + for (int i = 0; i < numChildren; i++) + { + print(children.item(i), namespaceStack, out, xmlEncoding); + } + } + break; + } + + case Node.ELEMENT_NODE : + { + namespaceStack = new ObjectRegistry(namespaceStack); + + out.print('<' + node.getNodeName()); + + String elPrefix = node.getPrefix(); + String elNamespaceURI = node.getNamespaceURI(); + + if (elPrefix != null && elNamespaceURI != null) + { + boolean prefixIsDeclared = false; + + try + { + String namespaceURI = (String)namespaceStack.lookup(elPrefix); + + if (elNamespaceURI.equals(namespaceURI)) + { + prefixIsDeclared = true; + } + } + catch (IllegalArgumentException e) + { + // ignore this and carry on + } + + if (!prefixIsDeclared) + { + printNamespaceDecl(node, namespaceStack, out); + } + } + + NamedNodeMap attrs = node.getAttributes(); + int len = (attrs != null) ? attrs.getLength() : 0; + + for (int i = 0; i < len; i++) + { + Attr attr = (Attr)attrs.item(i); + + out.print(' ' + attr.getNodeName() +"=\"" + + normalize(attr.getValue()) + '\"'); + + String attrPrefix = attr.getPrefix(); + String attrNamespaceURI = attr.getNamespaceURI(); + + if (attrPrefix != null && attrNamespaceURI != null) + { + boolean prefixIsDeclared = false; + + try + { + String namespaceURI = (String)namespaceStack.lookup(attrPrefix); + + if (attrNamespaceURI.equals(namespaceURI)) + { + prefixIsDeclared = true; + } + } + catch (IllegalArgumentException e) + { + // ignore this and carry on + } + + if (!prefixIsDeclared) + { + printNamespaceDecl(attr, namespaceStack, out); + } + } + } + + NodeList children = node.getChildNodes(); + + if (children != null) + { + int numChildren = children.getLength(); + + hasChildren = (numChildren > 0); + + if (hasChildren) + { + out.print('>'); + } + + for (int i = 0; i < numChildren; i++) + { + print(children.item(i), namespaceStack, out, xmlEncoding); + } + } + else + { + hasChildren = false; + } + + if (!hasChildren) + { + out.print("/>"); + } + break; + } + + case Node.ENTITY_REFERENCE_NODE : + { + out.print('&'); + out.print(node.getNodeName()); + out.print(';'); + break; + } + + case Node.CDATA_SECTION_NODE : + { + out.print(""); + break; + } + + case Node.TEXT_NODE : + { + out.print(normalize(node.getNodeValue())); + break; + } + + case Node.COMMENT_NODE : + { + out.print(""); + break; + } + + case Node.PROCESSING_INSTRUCTION_NODE : + { + out.print(" 0) + { + out.print(' '); + out.print(data); + } + + out.println("?>"); + break; + } + } + + if (type == Node.ELEMENT_NODE && hasChildren == true) + { + out.print("'); + hasChildren = false; + } + } + + public static String java2XMLEncoding(String javaEnc) + { + return (String)xmlEncodingMap.get(javaEnc); + } + + + private static void printNamespaceDecl(Node node, + ObjectRegistry namespaceStack, + PrintWriter out) + { + switch (node.getNodeType()) + { + case Node.ATTRIBUTE_NODE : + { + printNamespaceDecl(((Attr)node).getOwnerElement(), node, + namespaceStack, out); + break; + } + + case Node.ELEMENT_NODE : + { + printNamespaceDecl((Element)node, node, namespaceStack, out); + break; + } + } + } + + private static void printNamespaceDecl(Element owner, Node node, + ObjectRegistry namespaceStack, + PrintWriter out) + { + String namespaceURI = node.getNamespaceURI(); + String prefix = node.getPrefix(); + + if (!(namespaceURI.equals(NS_URI_XMLNS) && prefix.equals("xmlns"))) + { + if (DOMUtils.getAttributeNS(owner, NS_URI_XMLNS, prefix) == null) + { + out.print(" xmlns:" + prefix + "=\"" + namespaceURI + '\"'); + } + } + else + { + prefix = node.getLocalName(); + namespaceURI = node.getNodeValue(); + } + + namespaceStack.register(prefix, namespaceURI); + } + + private static String normalize(String s) + { + StringBuffer str = new StringBuffer(); + int len = (s != null) ? s.length() : 0; + + for (int i = 0; i < len; i++) + { + char ch = s.charAt(i); + + switch (ch) + { + case '<' : + { + str.append("<"); + break; + } + case '>' : + { + str.append(">"); + break; + } + case '&' : + { + str.append("&"); + break; + } + case '"' : + { + str.append("""); + break; + } + case '\n' : + { + if (i > 0) + { + char lastChar = str.charAt(str.length() - 1); + + if (lastChar != '\r') + { + str.append(StringUtils.lineSeparator); + } + else + { + str.append('\n'); + } + } + else + { + str.append(StringUtils.lineSeparator); + } + break; + } + default : + { + str.append(ch); + } + } + } + + return (str.toString()); + } +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/DOMUtils.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/DOMUtils.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/DOMUtils.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/DOMUtils.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,641 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.util.xml; + +import java.io.*; +import java.util.*; +import org.w3c.dom.*; + +import javax.wadls.*; +import javax.xml.namespace.*; + +public class DOMUtils { + /** + * The namespaceURI represented by the prefix xmlns. + */ + private static String NS_URI_XMLNS = "http://www.w3.org/2000/xmlns/"; + + private static final String ATTR_XMLNS = "xmlns"; + + /** + * Returns a list of attributes of an element. Returns an + * empty list if the element has no attributes. Does not + * include namespace declarations. + * + * @param el Element whose attributes are returned + * @return the List of Attr + */ + static public List getAttributes (Element el) { + String nodename, prefix = null; + List attrs = new Vector(); + NamedNodeMap attrMap = el.getAttributes(); + for(int i = 0; i < attrMap.getLength(); i++) + { + nodename = attrMap.item(i).getNodeName(); + prefix = attrMap.item(i).getPrefix(); + + if (ATTR_XMLNS.equals(nodename) || ATTR_XMLNS.equals(prefix)) + { + //ignore namespace declarations + continue; + } + else + { + attrs.add(attrMap.item(i)); + } + } + + return attrs; + } + + /** + * Returns the value of an attribute of an element. Returns null + * if the attribute is not found (whereas Element.getAttribute + * returns "" if an attrib is not found). This method should be + * used for elements that support extension attributes because it + * does not track unexpected attributes. + * + * @param el Element whose attrib is looked for + * @param attrName name of attribute to look for + * @return the attribute value + */ + static public String getAttribute (Element el, String attrName) { + String sRet = null; + Attr attr = el.getAttributeNode(attrName); + + if (attr != null) { + sRet = attr.getValue(); + } + return sRet; + } + + /** + * Returns the value of an attribute of an element. Returns null + * if the attribute is not found (whereas Element.getAttribute + * returns "" if an attrib is not found). This method should be + * used for elements that do not support extension attributes + * because it tracks the element's remaining attributes so that + * eventually any unexpected attributes can be identified. + * + * @param el Element whose attrib is looked for + * @param attrName name of attribute to look for + * @param remainingAttrs List of remaining attributes + * @return the attribute value + */ + static public String getAttribute (Element el, String attrName, List remainingAttrs) { + String sRet = null; + Attr attr = el.getAttributeNode(attrName); + + if (attr != null) { + sRet = attr.getValue(); + remainingAttrs.remove(attr); + } + return sRet; + } + + /** + * Returns the value of an attribute of an element. Returns null + * if the attribute is not found (whereas Element.getAttributeNS + * returns "" if an attrib is not found). + * + * @param el Element whose attrib is looked for + * @param namespaceURI namespace URI of attribute to look for + * @param localPart local part of attribute to look for + * @return the attribute value + */ + static public String getAttributeNS (Element el, + String namespaceURI, + String localPart) { + String sRet = null; + Attr attr = el.getAttributeNodeNS (namespaceURI, localPart); + + if (attr != null) { + sRet = attr.getValue (); + } + + return sRet; + } + + /** + * Returns the value of an attribute of an element. Returns null + * if the attribute is not found (whereas Element.getAttributeNS + * returns "" if an attrib is not found). + * + * @param el Element whose attrib is looked for + * @param namespaceURI namespace URI of attribute to look for + * @param localPart local part of attribute to look for + * @return the attribute value + */ + static public String getAttributeNS (Element el, + String namespaceURI, + String localPart, + List remainingAttrs) { + String sRet = null; + Attr attr = el.getAttributeNodeNS (namespaceURI, localPart); + + if (attr != null) { + sRet = attr.getValue(); + remainingAttrs.remove(attr); + } + + return sRet; + } + + /** + * Concat all the text and cdata node children of this elem and return + * the resulting text. + * + * @param parentEl the element whose cdata/text node values are to + * be combined. + * @return the concatanated string. + */ + static public String getChildCharacterData (Element parentEl) { + if (parentEl == null) { + return null; + } + Node tempNode = parentEl.getFirstChild(); + StringBuffer strBuf = new StringBuffer(); + CharacterData charData; + + while (tempNode != null) { + switch (tempNode.getNodeType()) { + case Node.TEXT_NODE : + case Node.CDATA_SECTION_NODE : charData = (CharacterData)tempNode; + strBuf.append(charData.getData()); + break; + } + tempNode = tempNode.getNextSibling(); + } + return strBuf.toString(); + } + + /** + * Return the first child element of the given element. Null if no + * children are found. + * + * @param elem Element whose child is to be returned + * @return the first child element. + */ + public static Element getFirstChildElement (Element elem) { + for (Node n = elem.getFirstChild (); n != null; n = n.getNextSibling ()) { + if (n.getNodeType () == Node.ELEMENT_NODE) { + return (Element) n; + } + } + return null; + } + + /** + * Return the next sibling element of the given element. Null if no + * more sibling elements are found. + * + * @param elem Element whose sibling element is to be returned + * @return the next sibling element. + */ + public static Element getNextSiblingElement (Element elem) { + for (Node n = elem.getNextSibling (); n != null; n = n.getNextSibling ()) { + if (n.getNodeType () == Node.ELEMENT_NODE) { + return (Element) n; + } + } + return null; + } + + /** + * Return the first child element of the given element which has the + * given attribute with the given value. + * + * @param elem the element whose children are to be searched + * @param attrName the attrib that must be present + * @param attrValue the desired value of the attribute + * + * @return the first matching child element. + */ + public static Element findChildElementWithAttribute (Element elem, + String attrName, + String attrValue) { + for (Node n = elem.getFirstChild (); n != null; n = n.getNextSibling ()) { + if (n.getNodeType () == Node.ELEMENT_NODE) { + if (attrValue.equals (DOMUtils.getAttribute ((Element) n, attrName))) { + return (Element) n; + } + } + } + return null; + } + + /** + * Count number of children of a certain type of the given element. + * + * @param elem the element whose kids are to be counted + * + * @return the number of matching kids. + */ + public static int countKids (Element elem, short nodeType) { + int nkids = 0; + for (Node n = elem.getFirstChild (); n != null; n = n.getNextSibling ()) { + if (n.getNodeType () == nodeType) { + nkids++; + } + } + return nkids; + } + + /** + * Given a prefix and a node, return the namespace URI that the prefix + * has been associated with. This method is useful in resolving the + * namespace URI of attribute values which are being interpreted as + * QNames. If prefix is null, this method will return the default + * namespace. + * + * @param context the starting node (looks up recursively from here) + * @param prefix the prefix to find an xmlns:prefix=uri for + * + * @return the namespace URI or null if not found + */ + public static String getNamespaceURIFromPrefix (Node context, + String prefix) { + short nodeType = context.getNodeType (); + Node tempNode = null; + + switch (nodeType) + { + case Node.ATTRIBUTE_NODE : + { + tempNode = ((Attr) context).getOwnerElement (); + break; + } + case Node.ELEMENT_NODE : + { + tempNode = context; + break; + } + default : + { + tempNode = context.getParentNode (); + break; + } + } + + while (tempNode != null && tempNode.getNodeType () == Node.ELEMENT_NODE) + { + Element tempEl = (Element) tempNode; + String namespaceURI = null; + if (prefix == null){ + namespaceURI = getAttribute (tempEl, "xmlns"); + if (namespaceURI == null) + namespaceURI = getAttribute (tempEl, "targetNamespace"); + } + else + namespaceURI = getAttributeNS (tempEl, NS_URI_XMLNS, prefix); + + if (namespaceURI != null) + { + return namespaceURI; + } + else + { + tempNode = tempEl.getParentNode (); + } + } + + return null; + } + + public static QName getQName(String prefixedValue, + Element contextEl, + Application app) + throws WADLSException + { + int index = prefixedValue.indexOf(':'); + String prefix = (index != -1) + ? prefixedValue.substring(0, index) + : null; + String localPart = prefixedValue.substring(index + 1); + String namespaceURI = getNamespaceURIFromPrefix(contextEl, prefix); + + if (namespaceURI != null) + { + registerUniquePrefix(prefix, namespaceURI, app); + + return new QName(namespaceURI, localPart); + } + else + { + String faultCode = (prefix == null) + ? WADLSException.NO_PREFIX_SPECIFIED + : WADLSException.UNBOUND_PREFIX; + + WADLSException wsdlExc = new WADLSException(faultCode, + "Unable to determine " + + "namespace of '" + + prefixedValue + "'."); + + wsdlExc.setLocation(XPathUtils.getXPathExprFromNode(contextEl)); + + throw wsdlExc; + } + } + + public static void registerUniquePrefix(String prefix, + String namespaceURI, + Application app) + { + String tempNSUri = app.getNamespace(prefix); + + if (tempNSUri != null && tempNSUri.equals(namespaceURI)) + { + return; + } + + while (tempNSUri != null && !tempNSUri.equals(namespaceURI)) + { + prefix += "_"; + tempNSUri = app.getNamespace(prefix); + } + + app.addNamespace(prefix, namespaceURI); + } + + /** + * This method should be used for elements that support extension attributes + * because it does not track the remaining attributes to test for unexpected + * attributes. + */ + public static QName getQualifiedAttributeValue(Element el, + String attrName, + String elDesc, + boolean isRequired, + Application app) + throws WADLSException + { + String attrValue = DOMUtils.getAttribute(el, attrName); + + if (attrValue != null) + { + return getQName(attrValue, el, app); + } + else if (isRequired) + { + WADLSException wsdlExc = new WADLSException(WADLSException.INVALID_WADL, + "The '" + attrName + + "' attribute must be " + + "specified for every " + + elDesc + " element."); + + wsdlExc.setLocation(XPathUtils.getXPathExprFromNode(el)); + + throw wsdlExc; + } + else + { + return null; + } + } + + /** + * This method should be used for elements that do not support extension attributes + * because it tracks the remaining attributes so that eventually any + * unexpected attributes can be identified. + */ + public static QName getQualifiedAttributeValue(Element el, + String attrName, + String elDesc, + boolean isRequired, + Application app, + List remainingAttrs) + throws WADLSException + { + String attrValue = null; + + attrValue = DOMUtils.getAttribute(el, attrName, remainingAttrs); + + if (attrValue != null) + { + return getQName(attrValue, el, app); + } + else if (isRequired) + { + WADLSException wsdlExc = new WADLSException(WADLSException.INVALID_WADL, + "The '" + attrName + + "' attribute must be " + + "specified for every " + + elDesc + " element."); + + wsdlExc.setLocation(XPathUtils.getXPathExprFromNode(el)); + + throw wsdlExc; + } + else + { + return null; + } + } + + public static void throwWADLException(Element location) throws WADLSException + { + String elName = QNameUtils.newQName(location).toString(); + + WADLSException wsdlExc = new WADLSException(WADLSException.INVALID_WADL, + "Encountered unexpected element '" + + elName + "'."); + + wsdlExc.setLocation(XPathUtils.getXPathExprFromNode(location)); + + throw wsdlExc; + } + + public static void throwWADLException(Element location, List remainingAttrs) throws WADLSException + { + String elName = QNameUtils.newQName(location).toString(); + + StringBuffer sb = new StringBuffer(); + ListIterator i = remainingAttrs.listIterator(); + while (i.hasNext()) + { + String attrName = QNameUtils.newQName((Attr)i.next()).toString(); + sb.append(attrName); + sb.append( i.hasNext() ? " " : ""); + } + + WADLSException wsdlExc = new WADLSException(WADLSException.INVALID_WADL, + "Element '" + + elName + + "' contained unexpected attributes: '" + + sb.toString() + + "'"); + + wsdlExc.setLocation(XPathUtils.getXPathExprFromNode(location)); + + throw wsdlExc; + } + + public static void printAttribute(String name, + String value, + PrintWriter pw) + { + if (value != null) + { + pw.print(' ' + name + "=\"" + cleanString(value) + '\"'); + } + } + + /** + * Prints attributes with qualified names. + */ + public static void printQualifiedAttribute(QName name, + String value, + Application app, + PrintWriter pw) + throws WADLSException + { + if (name != null) + { + printAttribute(getQualifiedValue(name.getNamespaceURI(), + name.getLocalPart(), + app), + value, + pw); + } + } + + public static void printQualifiedAttribute(QName name, + QName value, + Application app, + PrintWriter pw) + throws WADLSException + { + if (value != null) + { + printAttribute(getQualifiedValue(name.getNamespaceURI(), + name.getLocalPart(), + app), + getQualifiedValue(value.getNamespaceURI(), + value.getLocalPart(), + app), + pw); + } + } + + public static void printQualifiedAttribute(String name, + QName value, + Application app, + PrintWriter pw) + throws WADLSException + { + if (value != null) + { + printAttribute(name, + getQualifiedValue(value.getNamespaceURI(), + value.getLocalPart(), + app), + pw); + } + } + + public static String getQualifiedValue(String namespaceURI, + String localPart, + Application app) + throws WADLSException + { + String prefix = null; + + if (namespaceURI != null && !namespaceURI.equals("")) + { + prefix = getPrefix(namespaceURI, app); + } + + return ((prefix != null && !prefix.equals("")) + ? prefix + ":" + : "") + localPart; + } + + public static String getPrefix(String namespaceURI, + Application app) + throws WADLSException + { + String prefix = app.getPrefix(namespaceURI); + + if (prefix == null) + { + throw new WADLSException(WADLSException.OTHER_ERROR, + "Can't find prefix for '" + namespaceURI + + "'. Namespace prefixes must be set on the" + + " Definition object using the " + + "addNamespace(...) method."); + } + + return prefix; + } + + public static String cleanString(String orig) + { + if (orig == null) + { + return ""; + } + + StringBuffer strBuf = new StringBuffer(); + char[] chars = orig.toCharArray(); + boolean inCDATA = false; + + for (int i = 0; i < chars.length; i++) + { + if (!inCDATA) + { + switch (chars[i]) + { + case '&' : strBuf.append("&"); + break; + case '\"' : strBuf.append("""); + break; + case '\'' : strBuf.append("'"); + break; + case '<' : + { + if (chars.length >= i + 9) + { + String tempStr = new String(chars, i, 9); + + if (tempStr.equals("' : strBuf.append(">"); + break; + default : strBuf.append(chars[i]); + break; + } + } + else + { + strBuf.append(chars[i]); + + if (chars[i] == '>' + && chars[i - 1] == ']' + && chars[i - 2] == ']') + { + inCDATA = false; + } + } + } + + return strBuf.toString(); + } +} + diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/QNameUtils.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/QNameUtils.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/QNameUtils.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/QNameUtils.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,132 @@ +/* + * (c) Copyright IBM Corp 2002, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.util.xml; + +import javax.wadls.Application; +import javax.wadls.WADLSException; +import javax.xml.XMLConstants; +import javax.xml.namespace.*; + +import org.w3c.dom.*; + +public class QNameUtils +{ + public static boolean matches(QName qname, Node node) + { + return (node != null && qname.equals(newQName(node))); + } + + public static QName newQName(Node node) + { + if (node != null) + { + // System.out.println("node:namespace uri is " + node.getNamespaceURI()); + QName q = new QName(node.getNamespaceURI(), node.getLocalName()); + //System.out.println("Qname generated is "+q); + return q; + + } + else + { + return new QName(null, null); + } + } + + public static QName getQName(String prefixedValue, + Element contextEl) + throws WADLSException{ + int index = prefixedValue.indexOf(':'); + String prefix = (index != -1) + ? prefixedValue.substring(0, index) + : null; + String localPart = prefixedValue.substring(index + 1); + String namespaceURI = DOMUtils.getNamespaceURIFromPrefix(contextEl, prefix); + + if (namespaceURI != null) + return new QName(namespaceURI, localPart); + else{ + String faultCode = (prefix == null) + ? WADLSException.NO_PREFIX_SPECIFIED + : WADLSException.UNBOUND_PREFIX; + + WADLSException wsdlExc = new WADLSException(faultCode, + "Unable to determine " + + "namespace of '" + + prefixedValue + "'."); + + wsdlExc.setLocation(XPathUtils.getXPathExprFromNode(contextEl)); + + throw wsdlExc; + } + } + + /** + * Parse a string, return a QName. + * The String can be only in the form of "{namespace}localpart" + * @param qNameAsString + * @return A QName by parsing the given string. + */ + public static QName generateQName(String qNameAsString){ + return generateQName(qNameAsString, null); + } + + /** + * Parse a string, return a QName. + * The String may be in the form of "prefix:localpart" or "{namespace}localpart" + * @param qNameAsString + * @param wsdlDef Wsdl definition for the purpose of getting URI from prefix, and vice versa. + * @return A QName by paring the given string. + */ + public static QName generateQName(String qNameAsString, Application wadlApp){ + String nsURI = null; + String prefix = null; + String localPart = null; + + if (qNameAsString == null) { + throw new IllegalArgumentException("cannot create QName from \"null\" or \"\" String"); + } + + if (qNameAsString.charAt(0) == '{') { //namespace + localpart + int endOfNamespaceURI = qNameAsString.indexOf('}'); + if (endOfNamespaceURI == -1) { + throw new IllegalArgumentException( + "cannot create QName from \"" + + qNameAsString + + "\", missing closing \"}\""); + } + else{ + nsURI = qNameAsString.substring(1, endOfNamespaceURI); + //get prefix from wsdls definition + if (wadlApp != null) + prefix = wadlApp.getPrefix(nsURI); + localPart = qNameAsString.substring(endOfNamespaceURI + 1); + return new QName(nsURI, localPart, nsURI); + } + + } + else{ + int endOfPrefix = qNameAsString.indexOf(':'); //try prefix + + if (endOfPrefix == -1){ //localpart only, use tagetNamespace from wsdls definition + if (wadlApp != null) + nsURI = wadlApp.getTargetNamespace(); + else + nsURI = XMLConstants.NULL_NS_URI; + return new QName(nsURI, qNameAsString); + } + else if (wadlApp != null){ //prefix + localpart + prefix = qNameAsString.substring(1, endOfPrefix); + nsURI = wadlApp.getNamespace(prefix); + localPart = qNameAsString.substring(endOfPrefix + 1); + return new QName(nsURI, localPart, nsURI); + } + else + throw new IllegalArgumentException( + "cannot create QName from \"" + + qNameAsString + + "\", no URI and no wsdl definition is given"); + } + } +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/XPathUtils.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/XPathUtils.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/XPathUtils.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/util/xml/XPathUtils.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,197 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.util.xml; + +import java.util.Vector; +import org.w3c.dom.*; + +/** + * A XPathUtils ... + * + * @author Matthew J. Duftler (duftler@us.ibm.com) + * @author Sanjiva Weerawarana (sanjiva@watson.ibm.com) + */ +public class XPathUtils +{ + private static Node getPreviousTypedNode(Node node, short nodeType) + { + node = node.getPreviousSibling(); + + while (node != null && node.getNodeType() != nodeType) + { + node = node.getPreviousSibling(); + } + + return node; + } + + private static Node getNextTypedNode(Node node, short nodeType) + { + node = node.getNextSibling(); + + while (node != null && node.getNodeType() != nodeType) + { + node = node.getNextSibling(); + } + + return node; + } + + private static String getValue(Node node, short nodeType) + { + switch (nodeType) + { + case Node.ELEMENT_NODE : + return ((Element)node).getTagName(); + + case Node.TEXT_NODE : + return ((Text)node).getData(); + + case Node.PROCESSING_INSTRUCTION_NODE : + return ((ProcessingInstruction)node).getData(); + + default : + return ""; + } + } + + private static short getNodeType(Node node) + { + return (node != null ? node.getNodeType() : -1); + } + + private static String getXPathFromVector(Vector path) + { + StringBuffer strBuf = new StringBuffer(); + int length = path.size(); + + for (int i = 0; i < length; i++) + { + Node tempNode = (Node)path.elementAt(i); + short nodeType = getNodeType(tempNode); + String targetValue = getValue(tempNode, nodeType); + int position = 1; + + tempNode = getPreviousTypedNode(tempNode, nodeType); + + while (tempNode != null) + { + if (nodeType == Node.ELEMENT_NODE) + { + if (getValue(tempNode, nodeType).equals(targetValue)) + { + position++; + } + } + else + { + position++; + } + + tempNode = getPreviousTypedNode(tempNode, nodeType); + } + + boolean hasMatchingSiblings = (position > 1); + + if (!hasMatchingSiblings) + { + tempNode = (Node)path.elementAt(i); + tempNode = getNextTypedNode(tempNode, nodeType); + + while (!hasMatchingSiblings && tempNode != null) + { + if (nodeType == Node.ELEMENT_NODE) + { + if (getValue(tempNode, nodeType).equals(targetValue)) + { + hasMatchingSiblings = true; + } + else + { + tempNode = getNextTypedNode(tempNode, nodeType); + } + } + else + { + hasMatchingSiblings = true; + } + } + } + + String step; + + switch (nodeType) + { + case Node.TEXT_NODE : + step = "text()"; + break; + case Node.PROCESSING_INSTRUCTION_NODE : + step = "processing-instruction()"; + break; + default : + step = targetValue; + break; + } + + if (step != null && step.length() > 0) + { + strBuf.append('/' + step); + } + + if (hasMatchingSiblings) + { + strBuf.append("[" + position + "]"); + } + } + + return strBuf.toString(); + } + + private static Vector getVectorPathFromNode(Node node) + { + Vector path = new Vector(); + + while (node != null) + { + path.insertElementAt(node, 0); + node = node.getParentNode(); + } + + return path; + } + + /** + * Generates an XPath expression that will return only the given node as its + * result. This method only works for element, text, document and PI nodes. + * + * @param node the node to generate an XPath expression for. This node must + * be an element node, a text node, a document node, or a processing + * instruction node. + * @return an XPath expression that will return only the given node as its + * result. + * @exception IllegalArgumentException if the given node is not an element, + * text, document or PI node. + */ + public static String getXPathExprFromNode(Node node) + throws IllegalArgumentException + { + short nodeType = getNodeType(node); + + switch (nodeType) + { + case Node.ELEMENT_NODE : + case Node.TEXT_NODE : + case Node.PROCESSING_INSTRUCTION_NODE : + return getXPathFromVector(getVectorPathFromNode(node)); + + case Node.DOCUMENT_NODE : + return "/"; + + default : + throw new IllegalArgumentException("Only works for element, text, " + + "document, and PI nodes."); + } + } +} \ No newline at end of file diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/xml/WADLReaderImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/xml/WADLReaderImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/xml/WADLReaderImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/xml/WADLReaderImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,1727 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.xml; + +import java.io.*; +import java.net.*; +import java.util.*; + +import javax.xml.namespace.*; +import javax.xml.parsers.*; +import org.w3c.dom.*; +import org.xml.sax.*; + +import javax.wadls.*; +import javax.wadls.extensions.*; +import javax.wadls.extensions.schema.Schema; +import javax.wadls.extensions.schema.SchemaReference; +import javax.wadls.factory.*; +import javax.wadls.xml.*; +import javax.wadls.Effect; +import javax.wadls.PreCondition; +import javax.wadls.extensions.ExtensionRegistry; + + + +import javax.wadls.extensions.ExtensibilityElement; +import javax.wadls.extensions.ExtensionDeserializer; +import javax.wadls.factory.WADLFactory; + +import edu.uga.cs.lsdis.meteors.wadls.*; +import edu.uga.cs.lsdis.meteors.wadls.extensions.schema.SchemaConstants; +import edu.uga.cs.lsdis.meteors.wadls.extensions.schema.SchemaSerializer; +import edu.uga.cs.lsdis.meteors.wadls.util.*; +import edu.uga.cs.lsdis.meteors.wadls.util.xml.*; +import edu.uga.cs.lsdis.meteors.wadls.Constants; +import edu.uga.cs.lsdis.meteors.wadls.util.xml.QNameUtils; +import edu.uga.cs.lsdis.meteors.wadls.util.StringUtils; +import edu.uga.cs.lsdis.meteors.wadls.util.xml.XPathUtils; +import edu.uga.cs.lsdis.meteors.wadls.extensions.schema.SchemaDeserializer; + + +/** + * This class describes a collection of methods + * that enable conversion of a WSDL-S document (in XML, + * following the WSDL schema described in the WSDL + * specification) into a WSDL-S model. + * + * @author Zixin Wu (wuzixin@uga.edu) + * @author Matthew J. Duftler + * @author Nirmal Mukhi + */ +public class WADLReaderImpl implements WADLReader +{ + + static { + Constants.setSemanticExtensionURI(Constants.SemanticExtensionType.SAWADL); + } + // Used for determining the style of operations. + private static final List STYLE_ONE_WAY = + Arrays.asList(new String[]{Constants.ELEM_INPUT}); + private static final List STYLE_REQUEST_RESPONSE = + Arrays.asList(new String[]{Constants.ELEM_INPUT, Constants.ELEM_OUTPUT}); + private static final List STYLE_SOLICIT_RESPONSE = + Arrays.asList(new String[]{Constants.ELEM_OUTPUT, Constants.ELEM_INPUT}); + private static final List STYLE_NOTIFICATION = + Arrays.asList(new String[]{Constants.ELEM_OUTPUT}); + + protected boolean verbose = true; + protected ExtensionRegistry extReg = null; + protected boolean importDocuments = true; + protected boolean parseSAWSDL = false; + protected String factoryImplName = null; + protected WADLLocator loc = null; + + //Contains all schemas used by this wsdl, either in-line or nested + //via wsdl imports or schema imports, includes or redefines + protected Map allSchemas = new Hashtable(); + + private String WORKING_SEMANTIC_NAMESPACE = Constants.NS_URI_SAWADL; + + + /** + * Sets the specified feature to the specified value. + *

+ * The supported features are: + *

+ * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + * + *
Name Description Default Value
javax.wsdls.verbose If set to true, status messages will be displayed. true
javax.wsdls.importDocuments If set to true, imported WSDL documents will be + * retrieved and processed. true
+ *

Name	Description	Default Value
javax.wsdls.verbose	If set to true, status messages will be displayed.	true
javax.wsdls.importDocuments	If set to true, imported WSDL documents will be + * retrieved and processed.	true

+ * All feature names must be fully-qualified, Java package style. All + * names starting with javax.wsdls. are reserved for features defined + * by the JWSDL specification. It is recommended that implementation- + * specific features be fully-qualified to match the package name + * of that implementation. For example: com.abc.featureName + * + * @param name the name of the feature to be set. + * @param value the value to set the feature to. + * @throws IllegalArgumentException if the feature name is not recognized. + * @see #getFeature(String) + */ + public void setFeature(String name, boolean value) + throws IllegalArgumentException + { + if (name == null) + { + throw new IllegalArgumentException("Feature name must not be null."); + } + + if (name.equals(Constants.FEATURE_VERBOSE)) + { + verbose = value; + } + else if (name.equals(Constants.FEATURE_IMPORT_DOCUMENTS)) + { + importDocuments = value; + } else if(name.equals(Constants.FEATURE_PARSE_SAWADL)) { + if(value) { + WORKING_SEMANTIC_NAMESPACE = Constants.NS_URI_SAWADL; + Constants.setSemanticExtensionURI(Constants.SemanticExtensionType.SAWADL); + } else { + WORKING_SEMANTIC_NAMESPACE = Constants.NS_URI_WADLS; + Constants.setSemanticExtensionURI(Constants.SemanticExtensionType.WADLS); + } + parseSAWSDL = value; + } + else + { + throw new IllegalArgumentException("Feature name '" + name + + "' not recognized."); + } + } + + /** + * Gets the value of the specified feature. + * + * @param name the name of the feature to get the value of. + * @throws IllegalArgumentException if the feature name is not recognized. + * @see #setFeature(String, boolean) + */ + public boolean getFeature(String name) throws IllegalArgumentException + { + if (name == null) + { + throw new IllegalArgumentException("Feature name must not be null."); + } + + if (name.equals(Constants.FEATURE_VERBOSE)) + { + return verbose; + } + else if (name.equals(Constants.FEATURE_IMPORT_DOCUMENTS)) + { + return importDocuments; + } + else + { + throw new IllegalArgumentException("Feature name '" + name + + "' not recognized."); + } + } + + public void setExtensionRegistry(ExtensionRegistry extReg) + { + this.extReg = extReg; + } + + /** + * Get the extension registry, if one was set. Default is + * null. + */ + public ExtensionRegistry getExtensionRegistry() + { + return extReg; + } + + /** + * Set the extension registry to be used when reading + * WSDL documents into a WSDL definition. If an + * extension registry is set, that is the extension + * registry that will be set as the extensionRegistry + * property of the definitions resulting from invoking + * readWSDL(...). Default is null. + * + * @param extReg the extension registry to use for new + * definitions + */ + + + + + /** + * Set a different factory implementation to use for + * creating definitions when reading WSDL documents. + * As some WSDLReader implementations may only be + * capable of creating definitions using the same + * factory implementation from which the reader was + * obtained, this method is optional. Default is null. + * + * @param factoryImplName the fully-qualified class name of the + * class which provides a concrete implementation of the abstract + * class WSDLFactory. + * @throws UnsupportedOperationException if this method + * is invoked on an implementation which does not + * support it. + */ + public void setFactoryImplName(String factoryImplName) + throws UnsupportedOperationException + { + this.factoryImplName = factoryImplName; + } + + /** + * Get the factoryImplName, if one was set. Default is null. + */ + public String getFactoryImplName() + { + return factoryImplName; + } + + protected Application parseApplications(String documentBaseURI, + Element defEl, + Map importedDefs) + throws WADLSException, URISyntaxException + { + checkElementName(defEl, Constants.Q_ELEM_DEFINITIONS); + + WADLFactory factory = (factoryImplName != null) + ? WADLFactory.newInstance(factoryImplName) + : WADLFactory.newInstance(); + Application def = factory.newApplication(); + + + + String name = DOMUtils.getAttribute(defEl, Constants.ATTR_NAME); + String targetNamespace = DOMUtils.getAttribute(defEl, + Constants.ATTR_TARGET_NAMESPACE); + System.out.println("Target Name Space:"+targetNamespace); + NamedNodeMap attrs = defEl.getAttributes(); + + if (documentBaseURI != null) + { + def.setDocumentBaseURI(documentBaseURI); + } + + if (name != null) + { + def.setQName(new QName(targetNamespace, name)); + } + + if (targetNamespace != null) + { + def.setTargetNamespace(targetNamespace); + } + + int size = attrs.getLength(); + + for (int i = 0; i < size; i++) + { + Attr attr = (Attr)attrs.item(i); + String namespaceURI = attr.getNamespaceURI(); + String localPart = attr.getLocalName(); + String value = attr.getValue(); + + + if (namespaceURI != null && namespaceURI.equals(Constants.NS_URI_XMLNS)) + { + if (localPart != null && !localPart.equals(Constants.ATTR_XMLNS)) + { + System.out.println("LocalPart is set to "+localPart+" and it's value is "+value); + def.addNamespace(localPart, value); + } + else + { + System.out.println("LocalPart is set to null and it's value is "+value); + def.addNamespace(null, value); + } + } + } + + Element tempEl = DOMUtils.getFirstChildElement(defEl); + System.out.println("%%%% "); + System.out.println("%%%% First Child: "+tempEl.getNodeName()); + + while (tempEl != null) + { + if (QNameUtils.matches(Constants.Q_ELEM_DOCUMENTATION, tempEl)) + { + System.out.println("%%%% Documentation Element:"+tempEl.getTextContent()); + def.setDocumentationElement(tempEl); + } + else if (QNameUtils.matches(Constants.Q_ELEM_GRAMMARS, tempEl)) + { + System.out.println("%%%% Grammars element is parsed."); + def.setGrammars(parseGrammars(tempEl, def)); + } + else if (QNameUtils.matches(Constants.Q_ELEM_RESOURCES, tempEl)){ + + System.out.println("%%%% Resources Element is parsed."); + String path = DOMUtils.getAttribute(tempEl, Constants.ATTR_BASE); + def.setResourcesPath(path); + System.out.println("Resources path is:"+path); + Element tempEl1 = DOMUtils.getFirstChildElement(tempEl); + for (; tempEl1 != null; tempEl1 = DOMUtils.getNextSiblingElement(tempEl1)){ + if (QNameUtils.matches(Constants.Q_ELEM_RESOURCE, tempEl1)) + { + def.addResource(parseResource(tempEl1, def)); + } + } + + } + else{ + + } + + tempEl = DOMUtils.getNextSiblingElement(tempEl); + } + + return def; + } + + protected Include parseInclude(Element importEl, + Application def, + Map importedDefs) + throws WADLSException + { + Include importDef = def.createInclude(); + + try + { + String namespaceURI = DOMUtils.getAttribute(importEl, + Constants.ATTR_NAMESPACE); + String locationURI = DOMUtils.getAttribute(importEl, + Constants.ATTR_LOCATION); + String contextURI = null; + + if (namespaceURI != null) + { + importDef.setNamespaceURI(namespaceURI); + } + + if (locationURI != null) + { + importDef.setLocationURI(locationURI); + + if (importDocuments) + { + try + { + contextURI = def.getDocumentBaseURI(); + Application importedDef = null; + InputStream inputStream = null; + InputSource inputSource = null; + URL url = null; + + if (loc != null) + { + inputSource = loc.getImportInputSource(contextURI, locationURI); + + /* + We now have available the latest import URI. This might + differ from the locationURI so check the importedDefs for it + since it is this that we pass as the documentBaseURI later. + */ + String liu = loc.getLatestImportURI(); + + importedDef = (Application)importedDefs.get(liu); + } + else + { + URL contextURL = (contextURI != null) + ? StringUtils.getURL(null, contextURI) + : null; + + url = StringUtils.getURL(contextURL, locationURI); + importedDef = (Application)importedDefs.get(url.toString()); + + if (importedDef == null) + { + inputStream = StringUtils.getContentAsInputStream(url); + + if (inputStream != null) + { + inputSource = new InputSource(inputStream); + } + } + } + + if (importedDef == null) + { + if (inputSource == null) + { + throw new WADLSException(WADLSException.OTHER_ERROR, + "Unable to locate imported document " + + "at '" + locationURI + "'" + + (contextURI == null + ? "." + : ", relative to '" + contextURI + + "'.")); + } + + inputSource.setSystemId(url.toString()); + Document doc = getDocument(inputSource, url.toString()); + + if (inputStream != null) + { + inputStream.close(); + } + + Element documentElement = doc.getDocumentElement(); + + /* + Check if it's a wsdl document. + If it's not, don't retrieve and process it. + This should later be extended to allow other types of + documents to be retrieved and processed, such as schema + documents (".xsd"), etc... + */ + if (QNameUtils.matches(Constants.Q_ELEM_DEFINITIONS, + documentElement)) + { + if (verbose) + { + System.out.println("Retrieving document at '" + locationURI + + "'" + + (contextURI == null + ? "." + : ", relative to '" + contextURI + "'.")); + } + + String urlString = + (loc != null) + ? loc.getLatestImportURI() + : (url != null) + ? url.toString() + : locationURI; + + importedDef = readWADL(urlString, + documentElement, + importedDefs); + } + else + { + QName docElementQName = QNameUtils.newQName(documentElement); + + if (SchemaConstants.XSD_QNAME_LIST.contains(docElementQName)) + { + WADLFactory factory = + (factoryImplName != null) + ? WADLFactory.newInstance(factoryImplName) + : WADLFactory.newInstance(); + + importedDef = factory.newApplication(); + + + String urlString = + (loc != null) + ? loc.getLatestImportURI() + : (url != null) + ? url.toString() + : locationURI; + + importedDef.setDocumentBaseURI(urlString); + + Params types = importedDef.createParams(); + importedDef.setParams(types); + } + } + } + + if (importedDef != null) + { + importDef.setApplication(importedDef); + } + } + catch (WADLSException e) + { + throw e; + } + catch (Throwable t) + { + throw new WADLSException(WADLSException.OTHER_ERROR, + "Unable to resolve imported document at '" + + locationURI + + (contextURI == null + ? "'." : "', relative to '" + contextURI + "'") + , t); + } + } //end importDocs + } //end locationURI + + } + catch (WADLSException e) + { + if (e.getLocation() == null) + { + e.setLocation(XPathUtils.getXPathExprFromNode(importEl)); + } + else + { + //If definitions are being parsed recursively for nested imports + //the exception location must be built up recursively too so + //prepend this element's xpath to exception location. + String loc = XPathUtils.getXPathExprFromNode(importEl) + e.getLocation(); + e.setLocation(loc); + } + + throw e; + } + + Element tempEl = DOMUtils.getFirstChildElement(importEl); + + while (tempEl != null) + { + if (QNameUtils.matches(Constants.Q_ELEM_DOCUMENTATION, tempEl)) + { + importDef.setDocumentationElement(tempEl); + } + else + { + DOMUtils.throwWADLException(tempEl); + } + + tempEl = DOMUtils.getNextSiblingElement(tempEl); + } + + + return importDef; + + } + + + + protected Grammars parseGrammars(Element typesEl, Application def) + throws WADLSException + { + Grammars grammars = def.createGrammars(); + List schemaList =new Vector(); + List docElement =new Vector(); + List targetNS =new Vector(); + Element tempEl = DOMUtils.getFirstChildElement(typesEl); + QName tempElType; + + while (tempEl != null) + { + tempElType = QNameUtils.newQName(tempEl); + + if (QNameUtils.matches(Constants.Q_ELEM_DOCUMENTATION, tempEl)) + { + grammars.setDocumentationElement(tempEl); + } + else if (QNameUtils.matches(Constants.Q_ELEM_INCLUDE, tempEl)) + { + String xsd = DOMUtils.getAttribute(tempEl, Constants.ELEM_HREF); + schemaList.add(xsd); + System.out.println("Xsd element in Grammars tag:"+xsd); + + docElement.add(parseSchema(tempEl,def)); + //targetNS.add(parseSchemaNS(tempEl,def)); + List remainingAttrs = DOMUtils.getAttributes(tempEl); + //the element qname indicates it is a schema. + String modelReference = DOMUtils.getAttributeNS(tempEl, + WORKING_SEMANTIC_NAMESPACE, + Constants.ATTR_MODELREF, + remainingAttrs); + System.out.println("XSD Element's model reference is:"+modelReference); + if (modelReference != null) + { + try { + parseModelReference(modelReference, def, grammars); + } catch (URISyntaxException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + /*ModelReference mr = def.createModelReference(); + mr.valueOf(modelReference, def); + mr.setParent(preCondition); + preCondition.addModelReference(mr);*/ + } + + } + + tempEl = DOMUtils.getNextSiblingElement(tempEl); + } + grammars.setSchemas(this.allSchemas); + Map temp = grammars.getSchemas(); + System.out.println("Schemas added to grammars class:"+temp.size()); + return grammars; + } + + +protected Schema parseSchema(Element el,Application def) + throws WADLSException + { + /* + * This method returns ExtensibilityElement rather than Schema because we + * do not insist that a suitable XSD schema deserializer is registered. + * PopulatedExtensionRegistry registers SchemaDeserializer by default, but + * if the user chooses not to register a suitable deserializer then the + * UnknownDeserializer will be used, returning an UnknownExtensibilityElement. + */ + + + Schema schema = null; + SchemaReference schemaRef = null; + try + { + + QName elementType = QNameUtils.newQName(el); + + edu.uga.cs.lsdis.meteors.wadls.extensions.schema.SchemaDeserializer scDS = new edu.uga.cs.lsdis.meteors.wadls.extensions.schema.SchemaDeserializer(); + + //Now unmarshall the DOM element. + Schema ee = + scDS.unmarshall(elementType, el, def); + + if (ee instanceof Schema) + { + + schema = (Schema) ee; + } + String location = null; + + //Keep track of parsed schemas to avoid duplicating Schema objects + //through duplicate or circular references (eg: A imports B imports A). + if (schema.getDocumentBaseURI() != null) + { + + + this.allSchemas.put(schema.getDocumentBaseURI(), schema); + } + + ArrayList allSchemaRefs = new ArrayList(); + + Collection ic = schema.getImports().values(); + + + Iterator importsIterator = ic.iterator(); + while(importsIterator.hasNext()) + { + allSchemaRefs.addAll( (Collection) importsIterator.next() ); + } + + allSchemaRefs.addAll(schema.getIncludes()); + allSchemaRefs.addAll(schema.getRedefines()); + + //Then, retrieve the schema referred to by each schema reference. If the + //schema has been read in previously, use the existing schema object. + //Otherwise unmarshall the DOM element into a new schema object. + + ListIterator schemaRefIterator = allSchemaRefs.listIterator(); + + + while(schemaRefIterator.hasNext()){ + + try + { + schemaRef = (SchemaReference) schemaRefIterator.next(); + + if (schemaRef.getSchemaLocationURI() == null) + { + + //cannot get the referenced schema, so ignore this schema reference + continue; + } + + if (verbose) + { + System.out.println("change: Retrieving schema at '" + + schemaRef.getSchemaLocationURI() + + (schema.getDocumentBaseURI() == null + ? "'." + : "', relative to '" + + schema.getDocumentBaseURI() + "'.")); + } + + + InputStream inputStream = null; + InputSource inputSource = null; + + + + //This is the child schema referred to by the schemaReference + Schema referencedSchema = null; + + //This is the child schema's location obtained from the WSDLLocator or the URL + + + if (loc != null) + { + + //Try to get the referenced schema using the wsdl locator + inputSource = loc.getImportInputSource( + schema.getDocumentBaseURI(), schemaRef.getSchemaLocationURI()); + + if (inputSource == null) + { + throw new WADLSException(WADLSException.OTHER_ERROR, + "Unable to locate with a locator " + + "the schema referenced at '" + + schemaRef.getSchemaLocationURI() + + "' relative to document base '" + + schema.getDocumentBaseURI() + "'"); + } + location = loc.getLatestImportURI(); + + + //if a schema from this location has been read previously, use it. + referencedSchema = (Schema) this.allSchemas.get(location); + } + else + { + // We don't have a wsdl locator, so try to retrieve the schema by its URL + + String contextURI = schema.getDocumentBaseURI(); + URL contextURL = (contextURI != null) ? StringUtils.getURL(null, contextURI) : null; + //System.out.println("%%%% Context URL OF SCHEMA:"+contextURL); + URL url = StringUtils.getURL(contextURL, schemaRef.getSchemaLocationURI()); + //System.out.println("%%%%URL :"+url); + location = url.toExternalForm(); + //System.out.println("%%%% schema location:"+location); + //if a schema from this location has been retrieved previously, use it. + referencedSchema = (Schema) this.allSchemas.get(location); + + if (referencedSchema == null) + { + //System.out.println("%%%% Referenced Schema is equal to null"); + // We haven't read this schema in before so do it now + inputStream = url.openStream(); + + if (inputStream != null) + { + inputSource = new InputSource(inputStream); + } + + if (inputSource == null) + { + throw new WADLSException(WADLSException.OTHER_ERROR, + "Unable to locate with a url " + + "the document referenced at '" + + schemaRef.getSchemaLocationURI() + + "'" + + (contextURI == null ? "." : ", relative to '" + + contextURI + "'.")); + } + } + + } //end if loc + + // If we have not previously read the schema, get its DOM element now. + if (referencedSchema == null) + { + //System.out.println("%%%% Referenced Schema is equal to null 2"); + inputSource.setSystemId(location); + Document doc = getDocument(inputSource, location); + + if (inputStream != null) + { + inputStream.close(); + } + + Element documentElement = doc.getDocumentElement(); + NodeList nodeList = documentElement.getChildNodes(); + + /*for(int i=0; i inputXSDList = new ArrayList(10); + List paramList = new ArrayList(20); + Element tempEl = DOMUtils.getFirstChildElement(inputEl); + List remainingAttrs = DOMUtils.getAttributes(inputEl); + String modelReference = DOMUtils.getAttributeNS(inputEl, + WORKING_SEMANTIC_NAMESPACE, + Constants.ATTR_MODELREF, + remainingAttrs); + System.out.println("Model reference for request:"+modelReference); + if (modelReference != null) + { + try { + parseModelReference(modelReference, def, input); + } catch (URISyntaxException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + /*ModelReference mr = def.createModelReference(); + mr.valueOf(modelReference, def); + mr.setParent(preCondition); + preCondition.addModelReference(mr);*/ + } + while (tempEl != null) + { + if (QNameUtils.matches(Constants.Q_ELEM_DOCUMENTATION, tempEl)) + { + input.setDocumentationElement(tempEl); + } + else if (QNameUtils.matches(Constants.Q_ELEM_REPRESENTATION, tempEl)) + { + String inputXSD = DOMUtils.getAttribute(tempEl, Constants.REQUEST_ELEMENT_NAME); + //input.setName(inputXSD); + inputXSDList.add(inputXSD); + System.out.println("InPut XSD : "+inputXSD); + } + else if (QNameUtils.matches(Constants.Q_ELEM_PARAM, tempEl)) + { + System.out.println("New paramter is added to request"); + Param param = new ParamImpl(); + List remainingParamAttrs = DOMUtils.getAttributes(tempEl); + String parammodelReference = DOMUtils.getAttributeNS(tempEl, + WORKING_SEMANTIC_NAMESPACE, + Constants.ATTR_MODELREF, + remainingAttrs); + String liftingschema = DOMUtils.getAttributeNS(tempEl, + WORKING_SEMANTIC_NAMESPACE, + Constants.ATTR_LIFTINGSCHEMAMAPPING, + remainingAttrs); + String loweringschema = DOMUtils.getAttributeNS(tempEl, + WORKING_SEMANTIC_NAMESPACE, + Constants.ATTR_LOWERINGSCHEMAMAPPING, + remainingAttrs); + + param.setModelreference(parammodelReference); + param.setLiftingschemamapping(liftingschema); + param.setLoweringschemamapping(loweringschema); + //param.setModelreference(liftingschema); + //param.setModelreference(loweringschema); + + String style = DOMUtils.getAttribute(tempEl, Constants.PARAM_STYLE); + System.out.println("Param Style:"+style); + String type = DOMUtils.getAttribute(tempEl, Constants.PARAM_TYPE); + System.out.println("Param Type:"+type); + + param.setName(DOMUtils.getAttribute(tempEl, Constants.PARAM_NAME)); + param.setDefault1(DOMUtils.getAttribute(tempEl, Constants.PARAM_DEFAULT)); + param.setRequired(DOMUtils.getAttribute(tempEl, Constants.PARAM_REQUIRED)); + + + if(type!=null){ + param.setType(type); + } + + List optionValue = new ArrayList(30); + Element paramoption = DOMUtils.getFirstChildElement(tempEl); + + + for (; paramoption != null; paramoption = DOMUtils.getNextSiblingElement(paramoption)) + { + if(paramoption.getLocalName().toString().equals("option")){ + optionValue.add(DOMUtils.getAttribute(paramoption, Constants.OPTION_VALUE)); + System.out.println("Param Option Value:"+DOMUtils.getAttribute(paramoption, Constants.OPTION_VALUE)); + } + } + + param.setOptionvalue(optionValue); + + + paramList.add(param); + + } + else + { + DOMUtils.throwWADLException(tempEl); + } + tempEl = DOMUtils.getNextSiblingElement(tempEl); + } + + input.setInputXSDList(inputXSDList); + input.setParamList(paramList); + return input; + } + + protected Response parseResponse(Element outputEl, Application def) + throws WADLSException + { + Response output = def.createResponse(); + List outputXSDList = new ArrayList(10); + List paramList = new ArrayList(20); + String name = DOMUtils.getAttribute(outputEl, Constants.ATTR_NAME); + QName messageName = getQualifiedAttributeValue(outputEl, + Constants.ATTR_MESSAGE, + Constants.ELEM_OUTPUT, + def); + + if (name != null) + { + output.setName(name); + } + List remainingAttrs = DOMUtils.getAttributes(outputEl); + String modelReference = DOMUtils.getAttributeNS(outputEl, + WORKING_SEMANTIC_NAMESPACE, + Constants.ATTR_MODELREF, + remainingAttrs); + System.out.println("Model reference for response:"+modelReference); + if (modelReference != null) + { + try { + parseModelReference(modelReference, def, output); + } catch (URISyntaxException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + /*ModelReference mr = def.createModelReference(); + mr.valueOf(modelReference, def); + mr.setParent(preCondition); + preCondition.addModelReference(mr);*/ + } + Element tempEl = DOMUtils.getFirstChildElement(outputEl); + + while (tempEl != null) + { + if (QNameUtils.matches(Constants.Q_ELEM_DOCUMENTATION, tempEl)) + { + output.setDocumentationElement(tempEl); + } + else if (QNameUtils.matches(Constants.Q_ELEM_REPRESENTATION, tempEl)) + { + String outputXSD = DOMUtils.getAttribute(tempEl, Constants.REQUEST_ELEMENT_NAME); + //output.setName(outputXSD); + outputXSDList.add(outputXSD); + System.out.println("OutPut XSD:"+outputXSD); + + } + else if (QNameUtils.matches(Constants.Q_ELEM_PARAM, tempEl)) + { + Param param = new ParamImpl(); + List remainingParamAttrs = DOMUtils.getAttributes(tempEl); + String parammodelReference = DOMUtils.getAttributeNS(tempEl, + WORKING_SEMANTIC_NAMESPACE, + Constants.ATTR_MODELREF, + remainingAttrs); + String liftingschema = DOMUtils.getAttributeNS(tempEl, + WORKING_SEMANTIC_NAMESPACE, + Constants.ATTR_LIFTINGSCHEMAMAPPING, + remainingAttrs); + String loweringschema = DOMUtils.getAttributeNS(tempEl, + WORKING_SEMANTIC_NAMESPACE, + Constants.ATTR_LOWERINGSCHEMAMAPPING, + remainingAttrs); + + param.setModelreference(parammodelReference); + param.setModelreference(liftingschema); + param.setModelreference(loweringschema); + + String style = DOMUtils.getAttribute(tempEl, Constants.PARAM_STYLE); + String type = DOMUtils.getAttribute(tempEl, Constants.PARAM_TYPE); + + param.setName(DOMUtils.getAttribute(tempEl, Constants.PARAM_NAME)); + param.setDefault1(DOMUtils.getAttribute(tempEl, Constants.PARAM_DEFAULT)); + param.setRequired(DOMUtils.getAttribute(tempEl, Constants.PARAM_REQUIRED)); + + if(style.equalsIgnoreCase("query") && type!=null){ + param.setType(type); + } + else{ + List optionValue = new ArrayList(30); + Element paramoption = DOMUtils.getFirstChildElement(tempEl); + + + for (; paramoption != null; paramoption = DOMUtils.getNextSiblingElement(paramoption)) + { + optionValue.add(DOMUtils.getAttribute(paramoption, Constants.OPTION_VALUE)); + } + + param.setOptionvalue(optionValue); + } + + paramList.add(param); + + } + + else + { + DOMUtils.throwWADLException(tempEl); + } + + tempEl = DOMUtils.getNextSiblingElement(tempEl); + } + + output.setInputXSDList(outputXSDList); + output.setParamList(paramList); + + return output; + } + + protected PreCondition parsePreCondition(Element preConEl, Application def) + throws WADLSException, URISyntaxException + { + PreCondition preCondition = def.createPreCondition(); + + //String name = DOMUtils.getAttribute(preConEl, Constants.ATTR_NAME); + String attrModelReference = DOMUtils.getQualifiedValue(WORKING_SEMANTIC_NAMESPACE, Constants.ATTR_MODELREF, def); + String modelReference = DOMUtils.getAttribute(preConEl, attrModelReference); + String expression = DOMUtils.getAttribute(preConEl, Constants.ATTR_EXPRESSION); + System.out.println("Pre Condition:"+expression); + + + if (modelReference != null) + { + parseModelReference(modelReference, def, preCondition); + /*ModelReference mr = def.createModelReference(); + mr.valueOf(modelReference, def); + mr.setParent(preCondition); + preCondition.addModelReference(mr);*/ + } + + if (expression != null) + { + preCondition.setExpression(expression); + } + + +// parseExtensibilityAttributes(preConEl, PreCondition.class, preCondition, def); + + return preCondition; + } + + protected Effect parseEffect(Element effectEl, Application def) + throws WADLSException, URISyntaxException + { + Effect effect = def.createEffect(); + //String name = DOMUtils.getAttribute(effectEl, Constants.ATTR_NAME); + String attrModelReference = DOMUtils.getQualifiedValue(WORKING_SEMANTIC_NAMESPACE, Constants.ATTR_MODELREF, def); + String modelReference = DOMUtils.getAttribute(effectEl, attrModelReference); + String expression = DOMUtils.getAttribute(effectEl, Constants.ATTR_EXPRESSION); + System.out.println("EFFECT:"+expression); + + /*if (name != null) + { + effect.setName(name); + }*/ + + if (modelReference != null) + { + parseModelReference(modelReference, def, effect); + /*ModelReference mr = def.createModelReference(); + mr.valueOf(modelReference, def); + mr.setParent(effect); + effect.addModelReference(mr);*/ + } + + if (expression != null) + { + effect.setExpression(expression); + } + + +// parseExtensibilityAttributes(effectEl, Effect.class, effect, def); + + return effect; + } + + /** + * This method should be used for elements that support extension + * attributes because it does not track unexpected remaining attributes. + */ + private static QName getQualifiedAttributeValue(Element el, + String attrName, + String elDesc, + Application def) + throws WADLSException + { + try + { + return DOMUtils.getQualifiedAttributeValue(el, + attrName, + elDesc, + false, + def); + } + catch (WADLSException e) + { + if (e.getFaultCode().equals(WADLSException.NO_PREFIX_SPECIFIED)) + { + String attrValue = DOMUtils.getAttribute(el, attrName); + + return new QName(attrValue); + } + else + { + throw e; + } + } + } + + /** + * This method should be used for elements that do not support extension + * attributes because it tracks unexpected remaining attributes. + */ + private static QName getQualifiedAttributeValue(Element el, + String attrName, + String elDesc, + Application def, + List remainingAttrs) + throws WADLSException + { + try + { + return DOMUtils.getQualifiedAttributeValue(el, + attrName, + elDesc, + false, + def, + remainingAttrs); + } + catch (WADLSException e) + { + if (e.getFaultCode().equals(WADLSException.NO_PREFIX_SPECIFIED)) + { + String attrValue = DOMUtils.getAttribute(el, attrName, remainingAttrs); + + return new QName(attrValue); + } + else + { + throw e; + } + } + } + + private static void checkElementName(Element el, QName qname) + throws WADLSException + { + System.out.println("Element Name:"+el); + System.out.println("Q Name:"+qname.toString()); + if (!QNameUtils.matches(qname, el)) + { + WADLSException wsdlExc = new WADLSException(WADLSException.INVALID_WADL, + "Expected element '" + + qname + "'."); + + wsdlExc.setLocation(XPathUtils.getXPathExprFromNode(el)); + + throw wsdlExc; + } + } + + private static Document getDocument(InputSource inputSource, + String desc) throws WADLSException + { + DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); + + factory.setNamespaceAware(true); + factory.setValidating(false); + + try + { + DocumentBuilder builder = factory.newDocumentBuilder(); + Document doc = builder.parse(inputSource); + + return doc; + } + catch (Throwable t) + { + throw new WADLSException(WADLSException.XSDPARSER_ERROR, + "Problem parsing '" + desc + "'.", + t); + } + } + + /** + * Read the WSDL document accessible via the given input stream + * @param wsdlIS a InputStream for a WSDL XML definition + * @return the definition. + * @throws WADLSException + */ + public Application readWADL(InputStream wsdlIS) + throws WADLSException + { + try + { + InputSource inputSource = new InputSource(wsdlIS); + Document doc = getDocument(inputSource, ""); + + wsdlIS.close(); + + //note that documentBaseURI will be null + //importing wsdl or schema should use absolution path/URL + Application def = readWADL(null, doc); + + return def; + } + catch (WADLSException e) + { + throw e; + } + catch (Throwable t) + { + throw new WADLSException(WADLSException.OTHER_ERROR, + "Unable to resolve imported document at '", t); + } + } + + /** + * Read the WSDL document accessible via the specified + * URI into a WSDL definition. + * + * @param wsdlURI a URI (can be a filename or URL) pointing to a + * WSDL XML definition. + * @return the definition. + */ + public Application readWADL(String wsdlURI) throws WADLSException + { + return readWADL(null, wsdlURI); + } + + /** + * Read the WSDL document accessible via the specified + * URI into a WSDL definition. + * + * @param contextURI the context in which to resolve the + * wsdlURI, if the wsdlURI is relative. Can be null, in which + * case it will be ignored. + * @param wsdlURI a URI (can be a filename or URL) pointing to a + * WSDL XML definition. + * @return the definition. + */ + public Application readWADL(String contextURI, String wsdlURI) + throws WADLSException + { + try + { + if (verbose) + { + System.out.println("Retrieving document at '" + wsdlURI + "'" + + (contextURI == null + ? "." + : ", relative to '" + contextURI + "'.")); + } + + URL contextURL = (contextURI != null) + ? StringUtils.getURL(null, contextURI) + : null; + URL url = StringUtils.getURL(contextURL, wsdlURI); + InputStream inputStream = url.openStream(); + InputSource inputSource = new InputSource(inputStream); + inputSource.setSystemId(url.toString()); + Document doc = getDocument(inputSource, url.toString()); + + inputStream.close(); + + Application def = readWADL(url.toString(), doc); + + return def; + } + catch (WADLSException e) + { + throw e; + } + catch (Throwable t) + { + throw new WADLSException(WADLSException.OTHER_ERROR, + "Unable to resolve imported document at '" + + wsdlURI + + (contextURI == null + ? "'." + : "', relative to '" + contextURI + "'.") + , t); + } + } + + /** + * Read the specified <wsdl:definitions> element into a WSDL + * definition. + * + * @param documentBaseURI the document base URI of the WSDL definition + * described by the element. Will be set as the documentBaseURI + * of the returned Definition. Can be null, in which case it + * will be ignored. + * @param definitionsElement the <wsdl:definitions> element + * @return the definition described by the element. + * @throws URISyntaxException + */ + public Application readWADL(String documentBaseURI, + Element definitionsElement) + throws WADLSException, URISyntaxException + { + return readWADL(documentBaseURI, definitionsElement, null); + } + + protected Application readWADL(String documentBaseURI, + Element definitionsElement, + Map importedDefs) + throws WADLSException, URISyntaxException + { + return parseApplications(documentBaseURI, definitionsElement, importedDefs); + } + + /** + * Read the specified WSDL document into a WSDL definition. + * + * @param documentBaseURI the document base URI of the WSDL definition + * described by the document. Will be set as the documentBaseURI + * of the returned Definition. Can be null, in which case it + * will be ignored. + * @param wsdlDocument the WSDL document, an XML + * document obeying the WSDL schema. + * @return the definition described in the document. + * @throws URISyntaxException + */ + public Application readWADL(String documentBaseURI, Document wsdlDocument) + throws WADLSException, URISyntaxException + { + return readWADL(documentBaseURI, wsdlDocument.getDocumentElement()); + } + + /** + * Read a WSDL document into a WSDL definition. + * + * @param documentBaseURI the document base URI of the WSDL definition + * described by the document. Will be set as the documentBaseURI + * of the returned Definition. Can be null, in which case it + * will be ignored. + * @param inputSource an InputSource pointing to the + * WSDL document, an XML document obeying the WSDL schema. + * @return the definition described in the document pointed to + * by the InputSource. + * @throws URISyntaxException + */ + public Application readWADL(String documentBaseURI, InputSource inputSource) + throws WADLSException, URISyntaxException + { + return readWADL(documentBaseURI, + getDocument(inputSource, "- WSDL Document -")); + } + + /** + * Read a WSDL document into a WSDL definition. + * + * @param locator A WSDLLocator object used to provide InputSources + * pointing to the wsdl file. + * @return the definition described in the document + * @throws URISyntaxException + */ + public Application readWADL(WADLLocator locator) throws WADLSException, URISyntaxException + { + InputSource is = locator.getBaseInputSource(); + String base = locator.getBaseURI(); + + if (is == null) + { + throw new WADLSException(WADLSException.OTHER_ERROR, + "Unable to locate document at '" + base + "'."); + } + + this.loc = locator; + + if (verbose) + { + System.out.println("Retrieving document at '" + base + "'."); + } + + return readWADL(base, is); + } + + protected List parseModelReference (String modelReference, Application def, ModelReferenceExtensible op) throws URISyntaxException,WADLSException{ + List modelReferenceList= new ArrayList(); + String [] modelRefs= modelReference.split("\\s"); + ModelReference currentModelReference; + for(int modelRefsIT= 0;modelRefsIT parseModelReference(String modelReferences, Application def) throws URISyntaxException, WADLSException { + return ModelReferenceImpl.getModelReferences(modelReferences, def); + } +} diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/xml/WADLWriterImpl.class Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/xml/WADLWriterImpl.class has changed diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/xml/WADLWriterImpl.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/edu/uga/cs/lsdis/meteors/wadls/xml/WADLWriterImpl.java Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,696 @@ +/* + * (c) Copyright IBM Corp 2001, 2005 + */ + +package edu.uga.cs.lsdis.meteors.wadls.xml; + +import java.io.*; +import java.net.URISyntaxException; +import java.util.*; +import javax.xml.namespace.*; +import javax.xml.parsers.*; +import org.w3c.dom.*; +import org.xml.sax.*; + +import javax.wadls.*; +import javax.wadls.extensions.*; +import javax.wadls.factory.*; +import javax.wadls.xml.*; + +import edu.uga.cs.lsdis.meteors.wadls.*; +import edu.uga.cs.lsdis.meteors.wadls.util.*; +import edu.uga.cs.lsdis.meteors.wadls.util.xml.*; + +/** + * This class describes a collection of methods + * that allow a WSDL-S model to be written to a writer + * in an XML format that follows the WSDL schema. + * + * @author Zixin Wu (wuzixin@uga.edu) + * @author Matthew J. Duftler + * @author Nirmal Mukhi + */ +public class WADLWriterImpl implements WADLWriter +{ + /** + * Sets the specified feature to the specified value. + *

+ * There are no minimum features that must be supported. + *

Usage:


+   *
+   *
  java edu.uga.cs.lsdis.meteors.wsdls.xml.WSDLWriterImpl filename|URL
+   *
+   *
    This test driver simply reads a WSDL document into a model
+   *    (using a WSDLReader), and then serializes it back to
+   *    standard out. In effect, it performs a round-trip test on
+   *    the specified WSDL document.
+ * @throws URISyntaxException 
+   */
+  public static void main(String[] argv) throws WADLSException, URISyntaxException
+  {
+    if (argv.length == 1)
+    {
+      WADLFactory wsdlFactory = WADLFactory.newInstance();
+      WADLReader  wsdlReader  = wsdlFactory.newWADLReader();
+      WADLWriter  wsdlWriter  = wsdlFactory.newWADLWriter();
+
+      wsdlWriter.writeWADL(wsdlReader.readWADL(null, argv[0]), System.out);
+    }
+    else
+    {
+      System.err.println("Usage:");
+      System.err.println();
+      System.err.println("  java " + WADLWriterImpl.class.getName() +
+                         " filename|URL");
+      System.err.println();
+      System.err.println("This test driver simply reads a WSDL document " +
+                         "into a model (using a WSDLReader), and then " +
+                         "serializes it back to standard out. In effect, " +
+                         "it performs a round-trip test on the specified " +
+                         "WSDL document.");
+    }
+  }
+}
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Application.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Application.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Application.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Application.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,268 @@
+package javax.wadls;
+
+import java.net.URI;
+import java.util.*;
+import org.w3c.dom.*;
+
+import javax.wadls.Params;
+import javax.wadls.extensions.ExtensionRegistry;
+import javax.xml.namespace.*;
+
+/**
+ * This interface represents a WADLS Application
+ *
+ */
+public interface Application extends java.io.Serializable
+{
+
+ 	/**
+  	 * Get all the Operations which has a modelReference with the specified namespace and concept.
+  	 * @param namespace The namespace of the modelReference
+  	 * @param concept The concept of the modelReference
+  	 * @return All the Operations which has a modelReference with the specified namespace and concept.
+  	 */
+	
+	
+	List getMethodsByModelReference(URI namespace, String concept);
+
+  	/**
+  	 * Get all the XSD Elements which has a modelReference with the specified namespace and concept.
+  	 * @param namespace The namespace of the modelReference
+  	 * @param concept The concept of the modelReference
+  	 * @return All the XSD Elements which has a modelReference with the specified namespace and concept.
+  	 */
+	List getXSDElementsByModelReference(URI namespace, String concept);
+	
+  	/**
+  	 * Get all the XSD ComplexTypes which has a modelReference with the specified namespace and concept.
+  	 * @param namespace The namespace of the modelReference
+  	 * @param concept The concept of the modelReference
+  	 * @return All the XSD ComplexTypes which has a modelReference with the specified namespace and concept.
+  	 */
+	List getXSDComplexTypeByModelReference(URI namespace, String concept);
+
+  /**
+   * Set the document base URI of this definition. Can be used to
+   * represent the origin of the Definition, and can be exploited
+   * when resolving relative URIs (e.g. in <import>s).
+   *
+   * @param documentBaseURI the document base URI of this definition
+   */
+  public void setDocumentBaseURI(String documentBaseURI);
+
+  /**
+   * Get the document base URI of this definition.
+   *
+   * @return the document base URI
+   */
+  public String getDocumentBaseURI();
+
+  public String getResourcesPath();
+  public void setResourcesPath(String path);
+  /**
+   * Set the name of this definition.
+   *
+   * @param name the desired name
+   */
+  public void setQName(QName name);
+
+  /**
+   * Get the name of this definition.
+   *
+   * @return the definition name
+   */
+  public QName getQName();
+
+  /**
+   * Set the target namespace in which WADL elements are defined.
+   *
+   * @param targetNamespace the target namespace
+   */
+  public void setTargetNamespace(String targetNamespace);
+
+  /**
+   * Get the target namespace in which the WADL elements
+   * are defined.
+   *
+   * @return the target namespace
+   */
+  public String getTargetNamespace();
+
+  /**
+   * This is a way to add a namespace association to a definition.
+   * It is similar to adding a namespace prefix declaration to the
+   * top of a <wsdl:definition> element. This has nothing to do
+   * with the <wsdl:import> element; there are separate methods for
+   * dealing with information described by <wsdl:import> elements.
+   *
+   * @param prefix the prefix to use for this namespace (when
+   * rendering this information as XML). Use null or an empty string
+   * to describe the default namespace (i.e. xmlns="...").
+   * @param namespaceURI the namespace URI to associate the prefix
+   * with. If you use null, the namespace association will be removed.
+   */
+   public void addNamespace(String prefix, String namespaceURI);
+
+   /**
+    * Get the namespace URI associated with this prefix. Or null if
+    * there is no namespace URI associated with this prefix. This is
+    * unrelated to the <wsdl:import> element.
+    *
+    * @see #addNamespace(String, String)
+    * @see #getPrefix(String)
+    */
+   public String getNamespace(String prefix);
+   
+   public void setGrammars(Grammars grammars);
+   public Grammars getGrammars();
+
+   /**
+    * Get the types section.
+    *
+    * @return the types section
+    */
+   public Params getParams();
+   public void setParams(Params params);
+   /**
+    * Get a prefix associated with this namespace URI. Or null if
+    * there are no prefixes associated with this namespace URI. This is
+    * unrelated to the <wsdl:import> element.
+    *
+    * @see #addNamespace(String, String)
+    * @see #getNamespace(String)
+    */
+   public String getPrefix(String namespaceURI);
+
+   /**
+    * Get all namespace associations in this application. The keys are
+    * the prefixes, and the namespace URIs are the values. This is
+    * unrelated to the <wsdl:import> element.
+    *
+    * @see #addNamespace(String, String)
+    */
+   public Map getNamespaces();
+
+
+  /**
+   * Add an import to this WADL description.
+   *
+   * @param importDef the import to be added
+   */
+  public void addInclude(Include includeApp);
+
+  /**
+   * Get the list of imports for the specified namespaceURI.
+   *
+   * @param namespaceURI the namespaceURI associated with the
+   * desired imports.
+   * @return a list of the corresponding imports, or null if
+   * there weren't any matching imports
+   */
+  public List getIncludes(String namespaceURI);
+
+  /**
+   * Get a map of lists containing all the imports defined here.
+   * The map's keys are the namespaceURIs, and the map's values
+   * are lists. There is one list for each namespaceURI for which
+   * imports have been defined.
+   */
+  public Map getIncludes();
+
+  
+  /**
+   * Add a portType to this WADL description.
+   *
+   * @param resource the resource to be added
+   */
+  public void addResource(Resource resource);
+
+  /**
+   * Get the specified resource. Also checks imported documents.
+   *
+   * @param name the name of the desired resource.
+   * @return the corresponding resource, or null if there wasn't
+   * any matching resource
+   */
+  public Resource getResource(QName name);
+
+  /**
+   * Remove the specified resource from this app.
+   *
+   * @param name the name of the resource to remove
+   * @return the resource previously associated with this qname, if there
+   * was one; may return null
+   */
+  public Resource removeResource(QName name);
+
+  /**
+   * Get all the resources defined here.
+   */
+  public Map getResources();
+
+  /**
+   * Set the documentation element for this document. This dependency
+   * on org.w3c.dom.Element should eventually be removed when a more
+   * appropriate way of representing this information is employed.
+   *
+   * @param docEl the documentation element
+   */
+  public void setDocumentationElement(Element docEl);
+
+  /**
+   * Get the documentation element. This dependency on org.w3c.dom.Element
+   * should eventually be removed when a more appropriate way of
+   * representing this information is employed.
+   *
+   * @return the documentation element
+   */
+  public Element getDocumentationElement();
+
+ 
+  public ModelReference createModelReference();
+
+  /**
+   * Create a new precondition.
+   *
+   * @return the newly created precondition
+   */
+  public PreCondition createPreCondition();
+
+  /**
+   * Create a new effect.
+   *
+   * @return the newly created effect
+   */
+  public Effect createEffect();
+
+  public Include createInclude();
+
+  /**
+   * Create a new input.
+   *
+   * @return the newly created input
+   */
+  public Request createRequest();
+
+  
+  /**
+   * Create a new operation.
+   *
+   * @return the newly created operation
+   */
+  public Method createMethod();
+
+  /**
+   * Create a new output.
+   *
+   * @return the newly created output
+   */
+  public Response createResponse();
+
+
+
+  public Resource createResource();
+
+ 
+  public Params createParams();
+  public Grammars createGrammars();
+ }
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Effect.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Effect.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Effect.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Effect.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,59 @@
+package javax.wadls;
+
+import org.w3c.dom.*;
+
+
+/**
+ * This interface represents an effect.
+ *
+ * @author Zixin Wu
+ */
+public interface Effect extends java.io.Serializable, ModelReferenceExtensible
+{
+	/**
+	 * Set the name of this effect.
+	 *
+	 * @param name the desired name
+	 */
+	public void setName(String name);
+	
+	/**
+	 * Get the name of this effect.
+	 *
+	 * @return the effect name
+	 */
+	public String getName();
+	
+	/**
+	 * Set the expression of this effect.
+	 *
+	 * @param expression The desired expression.
+	 */
+	public void setExpression(String expression);
+	
+	/**
+	 * Get the expression of this effect.
+	 *
+	 * @return The expression.
+	 */
+	public String getExpression();
+	
+	/**
+	 * Set the documentation element for this document. This dependency
+	 * on org.w3c.dom.Element should eventually be removed when a more
+	 * appropriate way of representing this information is employed.
+	 *
+	 * @param docEl the documentation element
+	 */
+	public void setDocumentationElement(Element docEl);
+	
+	/**
+	 * Get the documentation element. This dependency on org.w3c.dom.Element
+	 * should eventually be removed when a more appropriate way of
+	 * representing this information is employed.
+	 *
+	 * @return the documentation element
+	 */
+	public Element getDocumentationElement();
+	
+}
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Grammars.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Grammars.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Grammars.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Grammars.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,103 @@
+
+package javax.wadls;
+
+import java.net.URISyntaxException;
+import java.util.List;
+import java.util.Map;
+
+import javax.wadls.extensions.ElementExtensible;
+import javax.wadls.extensions.schema.Schema;
+import javax.wadls.Application;
+import javax.wadls.ModelReference;
+import javax.wadls.WADLSException;
+import javax.xml.namespace.QName;
+
+import org.w3c.dom.Element;
+
+/**
+ * This interface represents the <types> section of a WSDL document.
+ * 
+ * @author Zixin Wu (wuzixin@uga.edu)
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public interface Grammars extends java.io.Serializable,ModelReferenceExtensible
+{public List getTopLevelSchemas();
+
+/**
+ * Get the DOM elements of all the schemas in this Types.
+ * @return A list of DOM elements of all the schemas in this Types.
+ */
+public Map getSchemas();
+
+public void setSchemas(Map allSchemas);
+
+
+
+/**
+ * Get the DOM element of the first schema in this Types.
+ * @return The DOM element of the first schema in this Types.
+ */
+public Schema getFirstSchema();
+
+public ModelReference getModelReference(Element startElement, String path, Application app) throws WADLSException, URISyntaxException;
+
+/**
+ * Set the modelReference on the element located by the given path.
+ * @param startElement The starting element of the path
+ * @param path
+ * @param modelReference The desired modelReference
+ */
+public void addModelReference(Element startElement, String path, ModelReference modelReference) throws WADLSException;
+
+public void setModelReferences(Element startElement, String path, List refs) throws WADLSException;
+
+/**
+ * Get the LiftingSchemaMapping on the element located by the given path.
+ * @param startElement The starting element of the path
+ * @param path
+ * @return The schemaMapping value
+ */
+public String getLiftingSchemaMapping(Element startElement, String path) throws WADLSException;
+
+/**
+ * Set the LiftingSchemaMapping on the element located by the given path.
+ * @param startElement The starting element of the path
+ * @param path
+ * @param schemaMapping The desired schemaMapping
+ */
+public void setLiftingSchemaMapping(Element startElement, String path, String schemaMapping) throws WADLSException;
+
+/**
+ * Get the LiftingSchemaMapping on the element located by the given path.
+ * @param startElement The starting element of the path
+ * @param path
+ * @return The schemaMapping value
+ */
+public String getLoweringSchemaMapping(Element startElement, String path) throws WADLSException;
+
+/**
+ * Set the LiftingSchemaMapping on the element located by the given path.
+ * @param startElement The starting element of the path
+ * @param path
+ * @param schemaMapping The desired schemaMapping
+ */
+public void setLoweringSchemaMapping(Element startElement, String path, String schemaMapping) throws WADLSException;
+
+/**
+ * Set the documentation element for this document. This dependency
+ * on org.w3c.dom.Element should eventually be removed when a more
+ * appropriate way of representing this information is employed.
+ *
+ * @param docEl the documentation element
+ */
+public void setDocumentationElement(Element docEl);
+
+/**
+ * Get the documentation element. This dependency on org.w3c.dom.Element
+ * should eventually be removed when a more appropriate way of
+ * representing this information is employed.
+ *
+ * @return the documentation element
+ */
+public Element getDocumentationElement();
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Include.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Include.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Include.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Include.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,78 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls;
+
+import org.w3c.dom.*;
+
+
+
+/**
+ * This interface represents an import, and may contain a reference
+ * to the imported definition.
+ *
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public interface Include extends java.io.Serializable
+{
+  /**
+   * Set the namespace URI of this import.
+   *
+   * @param namespaceURI the desired namespace URI
+   */
+  public void setNamespaceURI(String namespaceURI);
+
+  /**
+   * Get the namespace URI of this import.
+   */
+  public String getNamespaceURI();
+
+  /**
+   * Set the location URI of this import.
+   *
+   * @param locationURI the desired location URI
+   */
+  public void setLocationURI(String locationURI);
+
+  /**
+   * Get the location URI of this import.
+   */
+  public String getLocationURI();
+
+  /**
+   * This property can be used to hang a referenced Definition,
+   * and the top-level Definition (i.e. the one with the <import>)
+   * will use this Definition when resolving referenced WSDL parts.
+   * This would need to be made into a generic reference to handle
+   * other types of referenced documents.
+   */
+  public void setApplication(Application app);
+
+  /**
+   * This property can be used to hang a referenced Definition,
+   * and the top-level Definition (i.e. the one with the <import>)
+   * will use this Definition when resolving referenced WSDL parts.
+   * This would need to be made into a generic reference to handle
+   * other types of referenced documents.
+   */
+  public Application getApplication();
+
+  /**
+   * Set the documentation element for this document. This dependency
+   * on org.w3c.dom.Element should eventually be removed when a more
+   * appropriate way of representing this information is employed.
+   *
+   * @param docEl the documentation element
+   */
+  public void setDocumentationElement(Element docEl);
+
+  /**
+   * Get the documentation element. This dependency on org.w3c.dom.Element
+   * should eventually be removed when a more appropriate way of
+   * representing this information is employed.
+   *
+   * @return the documentation element
+   */
+  public Element getDocumentationElement();
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Method.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Method.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Method.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Method.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,142 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls;
+
+import java.util.List;
+import java.util.Map;
+import org.w3c.dom.Element;
+
+
+/**
+ * This interface represents a WSDL operation.
+ * It includes information on input, output and fault
+ * messages associated with usage of the operation.
+ *
+ * @author Zixin Wu (wuzixin@uga.edu)
+ * @author Paul Fremantle (pzf@us.ibm.com)
+ * @author Nirmal Mukhi (nmukhi@us.ibm.com)
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public interface Method extends java.io.Serializable, ModelReferenceExtensible
+{
+	
+	/**
+	 * Set the precondition of this operation.
+	 *
+	 * @param preCondition the desired precondition
+	 */
+	public void setPreCondition(PreCondition preCondition);
+	
+	/**
+	 * Get the precondition of this operation.
+	 *
+	 * @return the precondition
+	 */
+	public PreCondition getPreCondition();
+	
+	/**
+	 * Set the effect of this operation.
+	 *
+	 * @param effect the desired effect
+	 */
+	public void setEffect(Effect effect);
+	
+	/**
+	 * Get the effect of this operation.
+	 *
+	 * @return The effect
+	 */
+	public Effect getEffect();
+	
+	/**
+	 * Set the name of this operation.
+	 *
+	 * @param name the desired name
+	 */
+	public void setName(String name);
+	
+	/**
+	 * Get the name of this operation.
+	 *
+	 * @return the operation name
+	 */
+	public String getName();
+	
+	/**
+	 * Set the input message specification for this operation.
+	 *
+	 * @param input the new input message
+	 */
+	public void setRequest(Request request);
+	
+	/**
+	 * Get the input message specification for this operation.
+	 *
+	 * @return the input message
+	 */
+	public Request getRequest();
+	
+	/**
+	 * Set the output message specification for this operation.
+	 *
+	 * @param output the new output message
+	 */
+	public void setResponse(Response response);
+	
+	/**
+	 * Get the output message specification for this operation.
+	 *
+	 * @return the output message specification for the operation
+	 */
+	public Response getResponse();
+	
+	
+	/**
+	 * Set the style for this operation (request-response,
+	 * one way, solicit-response or notification).
+	 *
+	 * @param style the new operation style
+
+	/**
+	 * Set the parameter ordering for a request-response,
+	 * or solicit-response operation.
+	 *
+	 * @param parameterOrder a list of named parameters
+	 * containing the part names to reflect the desired
+	 * order of parameters for RPC-style operations
+	 */
+	public void setParameterOrdering(List parameterOrder);
+	
+	/**
+	 * Get the parameter ordering for this operation.
+	 *
+	 * @return the parameter ordering, a list consisting
+	 * of message part names
+	 */
+	public List getParameterOrdering();
+	
+	/**
+	 * Set the documentation element for this document. This dependency
+	 * on org.w3c.dom.Element should eventually be removed when a more
+	 * appropriate way of representing this information is employed.
+	 *
+	 * @param docEl the documentation element
+	 */
+	public void setDocumentationElement(Element docEl);
+	
+	/**
+	 * Get the documentation element. This dependency on org.w3c.dom.Element
+	 * should eventually be removed when a more appropriate way of
+	 * representing this information is employed.
+	 *
+	 * @return the documentation element
+	 */
+	public Element getDocumentationElement();
+	
+	public void setUndefined(boolean isUndefined);
+	
+	public boolean isUndefined();
+
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/ModelReference.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/ModelReference.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/ModelReference.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/ModelReference.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,77 @@
+package javax.wadls;
+
+import java.net.URI;
+import java.net.URISyntaxException;
+
+/**
+ * This interface represents a ModelReference.
+ * 
+ * @author Zixin Wu (wuzixin@uga.edu)
+ *
+ */
+public interface ModelReference {
+
+	/**
+	 * Get the concept of this modelReference.
+	 * @return The concept of this modelReference.
+	 */
+	public String getConcept();
+
+	/**
+	 * Set the concept of this modelReference.
+	 * @param concept The desired concept of this modelReference.
+	 */
+	public void setConcept(String concept);
+
+	/**
+	 * Get the prefix of this modelReference
+	 * @return The prefix  of this modelReference
+	 */
+	public String getPrefix();
+
+	/**
+	 * Set the prefix of the ontology used in this modelReference
+	 * @param prefix The desired prefix of the ontology used in this modelReference
+	 */
+	public void setPrefix(String prefix);
+
+	/**
+	 * Get the namespace of the ontology used in this modelReference
+	 * @return The namespace of the ontology used in this modelReference
+	 */
+	public URI getNamespace();
+
+	/**
+	 * Set the namespace of the ontology used in this modelReference
+	 * @param nameSpace The desired namespace of the ontology used in this modelReference
+	 */
+	public void setNamespace(String nameSpace)
+			throws URISyntaxException;
+
+	/**
+	 * Get the parent object of this modelReference
+	 * @return The parent object of this modelReference
+	 */
+	public Object getParent();
+
+	/**
+	 * Set the parent object of this modelReference
+	 * @param parent The desired parent object of this modelReference
+	 */
+	public void setParent(Object parent);
+	
+	/**
+	 * Set the value of this modelReference by parsing the formatted string.
+	 * @param modelReferenceAsString The formatted string
+	 * @param def WSDLS definition
+	 * @throws URISyntaxException 
+	 * @throws WSDLSException 
+	 */
+	public void valueOf(String modelReferenceAsString, Application app) throws URISyntaxException, WADLSException;
+	
+	/**
+	 * Return a formatted string representing this modelReference.
+	 * @return A formatted string representing this modelReference.
+	 */
+	public String value();
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/ModelReferenceExtensible.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/ModelReferenceExtensible.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/ModelReferenceExtensible.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/ModelReferenceExtensible.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,40 @@
+package javax.wadls;
+
+import java.util.List;
+
+/**
+ * This interface marks a WADL param being allowed to have a
+ * javax.wadls.ModelReference for SAWADL.
+ * 
+ * @author Douglas Brewer
+ */
+public interface ModelReferenceExtensible {
+
+	/**
+	 * Add a single ModelReference to the Element.
+	 * 
+	 * @param modelReference The ModelReference.
+	 */
+	public void addModelReference(ModelReference modelReference);
+	
+	/**
+	 * Get the first ModelReference in the list of ModelReferences.
+	 * 
+	 * @return The first ModelReference.
+	 */
+	public ModelReference getModelReference();
+	
+	/**
+	 * Get all the ModelReferences of the Element.
+	 * 
+	 * @return A list of ModelReferences.
+	 */
+	public List getModelReferences();
+	
+	/**
+	 * Set the ModelReferences of this Element.
+	 * 
+	 * @param refs The ModelReferences for this Element.
+	 */
+	public void setModelReferences(List refs);
+}
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Param.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Param.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Param.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Param.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,98 @@
+/*
+ * Copyright (c) 2009 Srikalyan Swayampakula.. All rights reserved.
+ * 
+ *   Author : Srikalyan Swayampakula. .
+ *   Name of the File : Param.java .
+ *   Created on : Nov 22, 2009 at 4:03:57 PM .
+ * 
+ *  Redistribution and use in source and binary forms, with or without
+ *  modification, are permitted provided that the following conditions
+ *  are met:
+ * 
+ *  1. Redistributions of source code must retain the above
+ *     copyright notice, this list of conditions and the following
+ *     disclaimer.
+ *  2. Redistributions in binary form must reproduce the above
+ *     copyright notice, this list of conditions and the following
+ *     disclaimer in the documentation and/or other materials
+ *     provided with the distribution.
+ *  3. Neither the name of the University of Georgia nor the names
+ *     of its contributors may be used to endorse or promote
+ *     products derived from this software without specific prior
+ *     written permission.
+ * 
+ *  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
+ *  CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
+ *  INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+ *  MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ *  DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ *  CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ *  SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+ *  BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ *  SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ *  HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ *  CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+ *  OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
+ *  EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+package javax.wadls;
+
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ * @author Srikalyan Swayampakula.
+ */
+public interface Param extends java.io.Serializable
+{
+	
+     
+    
+    public String getModelreference();
+    
+    public void setModelreference(String modelreference);
+
+	public String getLiftingschemamapping();
+
+	public void setLiftingschemamapping(String liftingschemamapping) ;
+	public String getLoweringschemamapping() ;
+
+	public void setLoweringschemamapping(String loweringschemamapping) ;
+
+	public List getOptionvalue() ;
+
+	public void setOptionvalue(List optionvalue) ;
+	
+    public String getDefault1();
+    public void setDefault1(String default1);
+
+
+
+    public String getFixed();
+
+    public void setFixed(String fixed);
+
+
+    public String getId();
+    public void setId(String id);
+
+    public String getName();
+
+    public void setName(String name);
+   
+    public String getPath();
+    public void setPath(String path);
+    public boolean isRepeation();
+    public void setRepeation(boolean repeation);
+    public String getRequired();
+
+    public void setRequired(String required);
+    public String getStyle();
+
+    public void setStyle(String style);
+    public String getType();
+
+    public void setType(String type);
+}
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Params.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Params.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Params.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Params.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,117 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls;
+
+import java.net.URISyntaxException;
+import java.util.List;
+import java.util.Map;
+import javax.wadls.extensions.schema.Schema;
+import javax.xml.namespace.QName;
+
+import org.w3c.dom.Element;
+
+/**
+ * This interface represents the <types> section of a WSDL document.
+ * 
+ * @author Zixin Wu (wuzixin@uga.edu)
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public interface Params extends java.io.Serializable,ModelReferenceExtensible
+{
+	/**
+	 * Get the XSD simpleType with the given name.
+	 * @param name The QName of the type
+	 * @return A DOM Element representing the simpleType
+	 * @throws WADLSException 
+	 */
+	
+	public Element getXSDElement(String xpath) throws WADLSException;
+	
+	/**
+	 * Return a list of XSD elements contained in the startElement, search in only 1 level depth. 
+	 * @param startXSDElement
+	 * @return A list of XSD elements contained in the startElement. If no XSD element is contained, the list has 0 element.
+	 * @throws WADLSException
+	 */
+	public List getXSDElementsInComplexType(Element startXSDElement) throws WADLSException;
+	
+	/**
+	 * Return a list of XSD elements contained in the startElement, search in only 1 level depth. 
+	 * @param startXSDComplexType
+	 * @return A list of XSD elements contained in the startElement. If no XSD element is contained, the list has 0 element.
+	 * @throws WADLSException
+	 */
+	public List getXSDElementsInElement(Element startXSDComplexType) throws WADLSException;
+	
+	/**
+	 * Get the modelReference on the element located by the given path.
+	 * @param startElement The starting element of the path
+	 * @param path
+	 * @return The modelReference
+	 */
+	public ModelReference getModelReference(Element startElement, String path, Application app) throws WADLSException, URISyntaxException;
+	
+	/**
+	 * Set the modelReference on the element located by the given path.
+	 * @param startElement The starting element of the path
+	 * @param path
+	 * @param modelReference The desired modelReference
+	 */
+	public void addModelReference(Element startElement, String path, ModelReference modelReference) throws WADLSException;
+	
+	public List getModelReferences(Element startElement, String path, Application app) throws WADLSException, URISyntaxException;
+	
+	public void setModelReferences(Element startElement, String path, List refs) throws WADLSException;
+	
+	/**
+	 * Get the LiftingSchemaMapping on the element located by the given path.
+	 * @param startElement The starting element of the path
+	 * @param path
+	 * @return The schemaMapping value
+	 */
+	public String getLiftingSchemaMapping(Element startElement, String path) throws WADLSException;
+	
+	/**
+	 * Set the LiftingSchemaMapping on the element located by the given path.
+	 * @param startElement The starting element of the path
+	 * @param path
+	 * @param schemaMapping The desired schemaMapping
+	 */
+	public void setLiftingSchemaMapping(Element startElement, String path, String schemaMapping) throws WADLSException;
+	
+	/**
+	 * Get the LiftingSchemaMapping on the element located by the given path.
+	 * @param startElement The starting element of the path
+	 * @param path
+	 * @return The schemaMapping value
+	 */
+	public String getLoweringSchemaMapping(Element startElement, String path) throws WADLSException;
+	
+	/**
+	 * Set the LiftingSchemaMapping on the element located by the given path.
+	 * @param startElement The starting element of the path
+	 * @param path
+	 * @param schemaMapping The desired schemaMapping
+	 */
+	public void setLoweringSchemaMapping(Element startElement, String path, String schemaMapping) throws WADLSException;
+
+	/**
+	 * Set the documentation element for this document. This dependency
+	 * on org.w3c.dom.Element should eventually be removed when a more
+	 * appropriate way of representing this information is employed.
+	 *
+	 * @param docEl the documentation element
+	 */
+	public void setDocumentationElement(Element docEl);
+	
+	/**
+	 * Get the documentation element. This dependency on org.w3c.dom.Element
+	 * should eventually be removed when a more appropriate way of
+	 * representing this information is employed.
+	 *
+	 * @return the documentation element
+	 */
+	public Element getDocumentationElement();
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/PreCondition.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/PreCondition.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/PreCondition.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/PreCondition.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,49 @@
+
+package javax.wadls;
+
+
+
+import org.w3c.dom.Element;
+
+/**
+ * This interface represents a precondition.
+ *
+ * @author Zixin Wu
+ */
+public interface PreCondition extends java.io.Serializable,ModelReferenceExtensible
+{
+		
+	/**
+	 * Set the expression of this precondition.
+	 *
+	 * @param expression The desired expression.
+	 */
+	public void setExpression(String expression);
+	
+	/**
+	 * Get the expression of this precondition.
+	 *
+	 * @return The expression.
+	 */
+	public String getExpression();
+	
+    public void setName(String name);
+	
+	/**
+	 * Get the name of this precondition.
+	 *
+	 * @return the precondition name
+	 */
+	public String getName();
+	
+	public void setDocumentationElement(Element docEl);
+	
+	/**
+	 * Get the documentation element. This dependency on org.w3c.dom.Element
+	 * should eventually be removed when a more appropriate way of
+	 * representing this information is employed.
+	 *
+	 * @return the documentation element
+	 */
+	public Element getDocumentationElement();
+}
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Request.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Request.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Request.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Request.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,60 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls;
+
+import java.util.List;
+
+import org.w3c.dom.*;
+
+
+
+/**
+ * This interface represents an input message, and contains the name
+ * of the input and the message itself.
+ *
+ * @author Matthew J. Duftler
+ */
+public interface Request extends java.io.Serializable,ModelReferenceExtensible
+{
+  /**
+   * Set the name of this input message.
+   *
+   * @param name the desired name
+   */
+  public void setName(String name);
+  
+  
+  
+  /**
+   * Get the name of this input message.
+   *
+   * @return the input message name
+   */
+  public String getName();
+  public void setParamList(List paramList);
+  public List getParamList();
+
+
+  public void setInputXSDList(List inputXSDList);
+  public List getInputXSDList();
+
+  /**
+   * Set the documentation element for this document. This dependency
+   * on org.w3c.dom.Element should eventually be removed when a more
+   * appropriate way of representing this information is employed.
+   *
+   * @param docEl the documentation element
+   */
+  public void setDocumentationElement(Element docEl);
+
+  /**
+   * Get the documentation element. This dependency on org.w3c.dom.Element
+   * should eventually be removed when a more appropriate way of
+   * representing this information is employed.
+   *
+   * @return the documentation element
+   */
+  public Element getDocumentationElement();
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Resource.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Resource.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Resource.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Resource.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,90 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls;
+
+import java.util.*;
+import org.w3c.dom.*;
+import javax.xml.namespace.*;
+
+
+/**
+ * This interface represents a port type. It contains information about
+ * operations associated with this port type.
+ *
+ * @author Paul Fremantle
+ * @author Nirmal Mukhi
+ * @author Matthew J. Duftler
+ * @author Zixin Wu
+ */
+public interface Resource extends java.io.Serializable,ModelReferenceExtensible
+{
+
+	  
+  /**
+   * Set the name of this port type.
+   *
+   * @param name the desired name
+   */
+  public void setQName(QName name);
+
+  /**
+   * Get the name of this port type.
+   *
+   * @return the port type name
+   */
+  public QName getQName();
+
+  /**
+   * Add an operation to this port type.
+   *
+   * @param operation the operation to be added
+   */
+  public void addMethod(Method method);
+
+  /**
+   * Get the specified operation. Note that operation names can
+   * be overloaded within a PortType. In case of overloading, the
+   * names of the input and output messages can be used to further
+   * refine the search.
+   *
+   * @param name the name of the desired operation.
+   * @param inputName the name of the input message; if this is null
+   * it will be ignored.
+   * @param outputName the name of the output message; if this is null
+   * it will be ignored.
+   * @return the corresponding operation, or null if there wasn't
+   * any matching operation
+   */
+  public Method getMethod(String name,
+                                String inputName,
+                                String outputName);
+
+  /**
+   * Get all the operations defined here.
+   */
+  public List getMethods();
+
+  /**
+   * Set the documentation element for this document. This dependency
+   * on org.w3c.dom.Element should eventually be removed when a more
+   * appropriate way of representing this information is employed.
+   *
+   * @param docEl the documentation element
+   */
+  public void setDocumentationElement(Element docEl);
+
+  /**
+   * Get the documentation element. This dependency on org.w3c.dom.Element
+   * should eventually be removed when a more appropriate way of
+   * representing this information is employed.
+   *
+   * @return the documentation element
+   */
+  public Element getDocumentationElement();
+
+  public void setUndefined(boolean isUndefined);
+
+  public boolean isUndefined();
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Response.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Response.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Response.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/Response.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,56 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls;
+
+import java.util.List;
+
+import org.w3c.dom.*;
+
+/**
+ * This interface represents an output message, and contains the name
+ * of the output and the message itself.
+ *
+ * @author Matthew J. Duftler
+ */
+public interface Response extends java.io.Serializable,ModelReferenceExtensible
+{
+  /**
+   * Set the name of this output message.
+   *
+   * @param name the desired name
+   */
+  public void setName(String name);
+
+  /**
+   * Get the name of this output message.
+   *
+   * @return the output message name
+   */
+  public String getName();
+
+  public void setParamList(List paramList);
+  public List getParamList();
+
+
+  public void setInputXSDList(List inputXSDList);
+  public List getInputXSDList();
+  /**
+   * Set the documentation element for this document. This dependency
+   * on org.w3c.dom.Element should eventually be removed when a more
+   * appropriate way of representing this information is employed.
+   *
+   * @param docEl the documentation element
+   */
+  public void setDocumentationElement(Element docEl);
+
+  /**
+   * Get the documentation element. This dependency on org.w3c.dom.Element
+   * should eventually be removed when a more appropriate way of
+   * representing this information is employed.
+   *
+   * @return the documentation element
+   */
+  public Element getDocumentationElement();
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/WADLSException.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/WADLSException.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/WADLSException.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/WADLSException.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,140 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls;
+
+import java.io.*;
+
+/**
+ * This class represents a WADLS Exception
+ * @author Zixin Wu
+ *
+ */
+public class WADLSException extends Exception
+{
+  public static final long serialVersionUID = 1;
+
+  public static final String INVALID_WADL = "INVALID_WADL";
+  public static final String XSDPARSER_ERROR = "XSDPARSER_ERROR";
+  public static final String OTHER_ERROR = "OTHER_ERROR";
+  public static final String CONFIGURATION_ERROR = "CONFIGURATION_ERROR";
+  public static final String UNBOUND_PREFIX = "UNBOUND_PREFIX";
+  public static final String NO_PREFIX_SPECIFIED = "NO_PREFIX_SPECIFIED";
+  public static final String PATH_ERROR = "PATH_ERROR";
+  public static final String NOT_FOUND_ELE_BY_PATH = "NOT_FOUND_ELE_BY_PATH";
+  public static final String NOT_FOUND_SCHEMA = "NOT_FOUND_SCHEMA";
+  public static final String NOT_FOUND_ELE_IN_PART = "NOT_FOUND_ELE_IN_PART";
+
+  private String faultCode = null;
+  private Throwable targetThrowable = null;
+  private String location = null;
+
+  public WADLSException(String faultCode, String msg, Throwable t)
+  {
+    super(msg);
+    setFaultCode(faultCode);
+    setTargetException(t);
+  }
+
+  public WADLSException(String faultCode, String msg)
+  {
+    this(faultCode, msg, null);
+  }
+
+  public void setFaultCode(String faultCode)
+  {
+    this.faultCode = faultCode;
+  }
+
+  public String getFaultCode()
+  {
+    return faultCode;
+  }
+
+  public void setTargetException(Throwable targetThrowable)
+  {
+    this.targetThrowable = targetThrowable;
+  }
+
+  public Throwable getTargetException()
+  {
+    return targetThrowable;
+  }
+
+  /**
+   * Set the location using an XPath expression. Used for error messages.
+   *
+   * @param location an XPath expression describing the location where
+   * the exception occurred.
+   */
+  public void setLocation(String location)
+  {
+    this.location = location;
+  }
+
+  /**
+   * Get the location, if one was set. Should be an XPath expression which
+   * is used for error messages.
+   */
+  public String getLocation()
+  {
+    return location;
+  }
+
+  public String getMessage()
+  {
+    StringBuffer strBuf = new StringBuffer();
+
+    strBuf.append("WADLSException");
+
+    if (location != null)
+    {
+      try
+      {
+        strBuf.append(" (at " + location + ")");
+      }
+      catch (IllegalArgumentException e)
+      {
+      }
+    }
+
+    if (faultCode != null)
+    {
+      strBuf.append(": faultCode=" + faultCode);
+    }
+
+    String thisMsg = super.getMessage();
+    String targetMsg = (targetThrowable != null)
+                       ? targetThrowable.getMessage()
+                       : null;
+
+    if (thisMsg != null
+        && (targetMsg == null || !thisMsg.equals(targetMsg)))
+    {
+      strBuf.append(": " + thisMsg);
+    }
+
+    if (targetMsg != null)
+    {
+      strBuf.append(": " + targetMsg);
+    }
+
+    return strBuf.toString();
+  }
+
+  public String toString()
+  {
+    StringWriter sw = new StringWriter();
+    PrintWriter pw = new PrintWriter(sw);
+
+    pw.print(getMessage() + ": ");
+
+    if (targetThrowable != null)
+    {
+      targetThrowable.printStackTrace(pw);
+    }
+
+    return sw.toString();
+  }
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/AttributeExtensible.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/AttributeExtensible.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/AttributeExtensible.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/AttributeExtensible.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,76 @@
+
+
+package javax.wadls.extensions;
+
+import java.util.*;
+import javax.xml.namespace.*;
+
+/**
+ * Classes that implement this interface can contain extensibility
+ * attributes.
+ *
+ * @author Matthew J. Duftler
+ * @author Paul Fremantle
+ */
+public interface AttributeExtensible
+{
+  public static final int NO_DECLARED_TYPE = -1;
+  public static final int STRING_TYPE = 0;
+  public static final int QNAME_TYPE = 1;
+  public static final int LIST_OF_STRINGS_TYPE = 2;
+  public static final int LIST_OF_QNAMES_TYPE = 3;
+
+  /**
+   * Set an extension attribute on this element. Pass in a null value to remove
+   * an extension attribute.
+   *
+   * @param name the extension attribute name
+   * @param value the extension attribute value. Can be a String, a QName, a
+   * List of Strings, or a List of QNames.
+   *
+   * @see #getExtensionAttribute
+   * @see #getExtensionAttributes
+   * @see ExtensionRegistry#registerExtensionAttributeType
+   * @see ExtensionRegistry#queryExtensionAttributeType
+   */
+  public void setExtensionAttribute(QName name, Object value);
+
+  /**
+   * Retrieve an extension attribute from this element. If the extension
+   * attribute is not defined, null is returned.
+   *
+   * @param name the extension attribute name
+   *
+   * @return the value of the extension attribute, or null if
+   * it is not defined. Can be a String, a QName, a List of Strings, or a List
+   * of QNames.
+   *
+   * @see #setExtensionAttribute
+   * @see #getExtensionAttributes
+   * @see ExtensionRegistry#registerExtensionAttributeType
+   * @see ExtensionRegistry#queryExtensionAttributeType
+   */
+  public Object getExtensionAttribute(QName name);
+
+  /**
+   * Get the map containing all the extension attributes defined
+   * on this element. The keys are the qnames of the attributes.
+   *
+   * @return a map containing all the extension attributes defined
+   * on this element
+   *
+   * @see #setExtensionAttribute
+   * @see #getExtensionAttribute
+   * @see ExtensionRegistry#registerExtensionAttributeType
+   * @see ExtensionRegistry#queryExtensionAttributeType
+   */
+  public Map getExtensionAttributes();
+
+  /**
+   * Get the list of local attribute names defined for this element in
+   * the WSDL specification.
+   *
+   * @return a List of Strings, one for each local attribute name
+   */
+  public List getNativeAttributeNames();
+}
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ElementExtensible.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ElementExtensible.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ElementExtensible.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ElementExtensible.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,32 @@
+/*
+ * (c) Copyright IBM Corp 2004, 2005 
+ */
+
+package javax.wadls.extensions;
+
+import java.util.*;
+
+import javax.wadls.extensions.ExtensibilityElement;
+
+/**
+ * Classes that implement this interface can contain extensibility
+ * elements.
+ * 
+ * @author John Kaputin
+ */
+public interface ElementExtensible {
+    
+    /**
+     * Add an extensibility element.
+     *
+     * @param extElement the extensibility element to be added
+     */
+    public void addExtensibilityElement(ExtensibilityElement extElement);
+
+    /**
+     * Get all the extensibility elements defined here.
+     */
+    public List getExtensibilityElements();
+
+
+}
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensibilityElement.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensibilityElement.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensibilityElement.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensibilityElement.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,42 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls.extensions;
+
+import javax.xml.namespace.*;
+
+/**
+ * This interface should be implemented by classes intending to represent
+ * extensions.
+ *
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public interface ExtensibilityElement
+{
+  /**
+   * Set the type of this extensibility element.
+   *
+   * @param elementType the type
+   */
+  public void setElementType(QName elementType);
+
+  /**
+   * Get the type of this extensibility element.
+   *
+   * @return the extensibility element's type
+   */
+  public QName getElementType();
+
+  /**
+   * Set whether or not the semantics of this extension
+   * are required. Relates to the wsdl:required attribute.
+   */
+  public void setRequired(Boolean required);
+
+  /**
+   * Get whether or not the semantics of this extension
+   * are required. Relates to the wsdl:required attribute.
+   */
+  public Boolean getRequired();
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionDeserializer.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionDeserializer.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionDeserializer.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionDeserializer.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,44 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls.extensions;
+
+import org.w3c.dom.*;
+
+import javax.wadls.*;
+import javax.xml.namespace.*;
+
+/**
+ * This interface should be implemented by classes which deserialize
+ * org.w3c.dom.Elements into extension-specific instances of
+ * ExtensibilityElement.
+ *
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public interface ExtensionDeserializer
+{
+  /**
+   * This method deserializes elements into instances of classes
+   * which implement the ExtensibilityElement interface. The
+   * return value should be explicitly cast to the more-specific
+   * implementing type.
+   *
+   * @param parentType a class object indicating where in the WSDL
+   * document this extensibility element was encountered. For
+   * example, javax.wsdls.Binding.class would be used to indicate
+   * this element was encountered as an immediate child of
+   * a  element.
+   * @param elementType the qname of the extensibility element
+   * @param el the extensibility element to deserialize
+   * @param def the definition this extensibility element was
+   * encountered in
+   * @param extReg the ExtensionRegistry to use (if needed again)
+   */
+  public ExtensibilityElement unmarshall(Class parentType,
+                                         QName elementType,
+                                         Element el,
+                                         Application app,
+                                         ExtensionRegistry extReg)
+                                           throws WADLSException;
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionRegistry.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionRegistry.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionRegistry.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionRegistry.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,466 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls.extensions;
+
+import java.util.*;
+
+import javax.wadls.*;
+import javax.xml.namespace.*;
+
+/**
+ * This class is used to associate serializers, deserializers, and
+ * Java implementation types with extensibility elements.
+ *
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public class ExtensionRegistry implements java.io.Serializable
+{
+  public static final long serialVersionUID = 1;
+
+  /**
+   * Creates the extension registry, and sets the defaultSerializer
+   * and defaultDeserializer properties to instances of an
+   * UnknownExtensionSerializer, and an UnknownExtensionDeserializer,
+   * respectively.
+   */
+  public ExtensionRegistry()
+  {
+    setDefaultSerializer(new UnknownExtensionSerializer());
+    setDefaultDeserializer(new UnknownExtensionDeserializer());
+  }
+
+  /*
+    This is a Map of Maps. The top-level Map is keyed by (Class)parentType,
+    and the inner Maps are keyed by (QName)elementType.
+  */
+  protected Map serializerReg = new Hashtable();
+  /*
+    This is a Map of Maps. The top-level Map is keyed by (Class)parentType,
+    and the inner Maps are keyed by (QName)elementType.
+  */
+  protected Map deserializerReg = new Hashtable();
+  /*
+    This is a Map of Maps. The top-level Map is keyed by (Class)parentType,
+    and the inner Maps are keyed by (QName)elementType.
+  */
+  protected Map extensionTypeReg = new Hashtable();
+  protected ExtensionSerializer defaultSer = null;
+  protected ExtensionDeserializer defaultDeser = null;
+  /*
+    This is a Map of Maps. The top-level Map is keyed by (Class)parentType,
+    and the inner Maps are keyed by (QName)attrName.
+  */
+  protected Map extensionAttributeTypeReg = new Hashtable();
+
+  /**
+   * Set the serializer to be used when none is found for an extensibility
+   * element. Set this to null to have an exception thrown when
+   * unexpected extensibility elements are encountered. Default value is
+   * an instance of UnknownExtensionSerializer.
+   *
+   * @see UnknownExtensionSerializer
+   */
+  public void setDefaultSerializer(ExtensionSerializer defaultSer)
+  {
+    this.defaultSer = defaultSer;
+  }
+
+  /**
+   * Get the serializer to be used when none is found for an extensibility
+   * element. Default value is an instance of UnknownExtensionSerializer.
+   *
+   * @see UnknownExtensionSerializer
+   */
+  public ExtensionSerializer getDefaultSerializer()
+  {
+    return defaultSer;
+  }
+
+  /**
+   * Set the deserializer to be used when none is found for an encountered
+   * element. Set this to null to have an exception thrown when
+   * unexpected extensibility elements are encountered. Default value is
+   * an instance of UnknownExtensionDeserializer.
+   *
+   * @see UnknownExtensionDeserializer
+   */
+  public void setDefaultDeserializer(ExtensionDeserializer defaultDeser)
+  {
+    this.defaultDeser = defaultDeser;
+  }
+
+  /**
+   * Get the deserializer to be used when none is found for an encountered
+   * element. Default value is an instance of UnknownExtensionDeserializer.
+   *
+   * @see UnknownExtensionDeserializer
+   */
+  public ExtensionDeserializer getDefaultDeserializer()
+  {
+    return defaultDeser;
+  }
+
+  /**
+   * Declare that the specified serializer should be used to serialize
+   * all extensibility elements with a qname matching elementType, when
+   * encountered as children of the specified parentType.
+   *
+   * @param parentType a class object indicating where in the WSDL
+   * definition this extension was encountered. For
+   * example, javax.wsdls.Binding.class would be used to indicate
+   * this extensibility element was found in the list of
+   * extensibility elements belonging to a javax.wsdls.Binding.
+   * @param elementType the qname of the extensibility element
+   * @param es the extension serializer to use
+   *
+   * @see #querySerializer(Class, QName)
+   */
+  public void registerSerializer(Class parentType,
+                                 QName elementType,
+                                 ExtensionSerializer es)
+  {
+    Map innerSerializerReg = (Map)serializerReg.get(parentType);
+
+    if (innerSerializerReg == null)
+    {
+      innerSerializerReg = new Hashtable();
+
+      serializerReg.put(parentType, innerSerializerReg);
+    }
+
+    innerSerializerReg.put(elementType, es);
+  }
+
+  /**
+   * Declare that the specified deserializer should be used to deserialize
+   * all extensibility elements with a qname matching elementType, when
+   * encountered as immediate children of the element represented by the
+   * specified parentType.
+   *
+   * @param parentType a class object indicating where in the WSDL
+   * document this extensibility element was encountered. For
+   * example, javax.wsdls.Binding.class would be used to indicate
+   * this element was encountered as an immediate child of
+   * a <wsdl:binding> element.
+   * @param elementType the qname of the extensibility element
+   * @param ed the extension deserializer to use
+   *
+   * @see #queryDeserializer(Class, QName)
+   */
+  public void registerDeserializer(Class parentType,
+                                   QName elementType,
+                                   ExtensionDeserializer ed)
+  {
+    Map innerDeserializerReg = (Map)deserializerReg.get(parentType);
+
+    if (innerDeserializerReg == null)
+    {
+      innerDeserializerReg = new Hashtable();
+
+      deserializerReg.put(parentType, innerDeserializerReg);
+    }
+
+    innerDeserializerReg.put(elementType, ed);
+  }
+
+  /**
+   * Look up the serializer to use for the extensibility element with
+   * the qname elementType, which was encountered as a child of the
+   * specified parentType.
+   *
+   * @param parentType a class object indicating where in the WSDL
+   * definition this extension was encountered. For
+   * example, javax.wsdls.Binding.class would be used to indicate
+   * this extensibility element was found in the list of
+   * extensibility elements belonging to a javax.wsdls.Binding.
+   * @param elementType the qname of the extensibility element
+   *
+   * @return the extension serializer, if one was found. If none was
+   * found, the behavior depends on the value of the defaultSerializer
+   * property. If the defaultSerializer property is set to a non-null
+   * value, that value is returned; otherwise, a WSDLSException is
+   * thrown.
+   *
+   * @see #registerSerializer(Class, QName, ExtensionSerializer)
+   * @see #setDefaultSerializer(ExtensionSerializer)
+   */
+  public ExtensionSerializer querySerializer(Class parentType,
+                                             QName elementType)
+                                               throws WADLSException
+  {
+    Map innerSerializerReg = (Map)serializerReg.get(parentType);
+    ExtensionSerializer es = null;
+
+    if (innerSerializerReg != null)
+    {
+      es = (ExtensionSerializer)innerSerializerReg.get(elementType);
+    }
+
+    if (es == null)
+    {
+      es = defaultSer;
+    }
+
+    if (es == null)
+    {
+      throw new WADLSException(WADLSException.CONFIGURATION_ERROR,
+                              "No ExtensionSerializer found " +
+                              "to serialize a '" + elementType +
+                              "' element in the context of a '" +
+                              parentType.getName() + "'.");
+    }
+
+    return es;
+  }
+
+  /**
+   * Look up the deserializer for the extensibility element with the
+   * qname elementType, which was encountered as an immediate child
+   * of the element represented by the specified parentType.
+   *
+   * @param parentType a class object indicating where in the WSDL
+   * document this extensibility element was encountered. For
+   * example, javax.wsdls.Binding.class would be used to indicate
+   * this element was encountered as an immediate child of
+   * a <wsdl:binding> element.
+   * @param elementType the qname of the extensibility element
+   *
+   * @return the extension deserializer, if one was found. If none was
+   * found, the behavior depends on the value of the defaultDeserializer
+   * property. If the defaultDeserializer property is set to a non-null
+   * value, that value is returned; otherwise, a WSDLSException is thrown.
+   *
+   * @see #registerDeserializer(Class, QName, ExtensionDeserializer)
+   * @see #setDefaultDeserializer(ExtensionDeserializer)
+   */
+  public ExtensionDeserializer queryDeserializer(Class parentType,
+                                                 QName elementType)
+                                                   throws WADLSException
+  {
+	  
+	  System.out.println("%%%% Inside Query Deserializer");
+    Map innerDeserializerReg = (Map)deserializerReg.get(parentType);
+    System.out.println("%%%% inner DeserializerReg Size:"+innerDeserializerReg.size());
+    ExtensionDeserializer ed = null;
+
+    if (innerDeserializerReg != null)
+    {
+    	System.out.println("%%%% Inner Deserializer not null");
+      ed = (ExtensionDeserializer)innerDeserializerReg.get(elementType);
+      System.out.println("%%%% Ed string "+ed.toString());
+    }
+
+    if (ed == null)
+    {
+      ed = defaultDeser;
+      System.out.println("%%%% Default Deser String:"+defaultDeser.toString());
+    }
+
+    if (ed == null)
+    {
+      throw new WADLSException(WADLSException.CONFIGURATION_ERROR,
+                              "No ExtensionDeserializer found " +
+                              "to deserialize a '" + elementType +
+                              "' element in the context of a '" +
+                              parentType.getName() + "'.");
+    }
+
+    return ed;
+  }
+
+  /**
+   * Returns a set of QNames representing the extensibility elements
+   * that are allowed as children of the specified parent type.
+   * Basically, this method returns the keys associated with the set
+   * of extension deserializers registered for this parent type.
+   * Returns null if no extension deserializers are registered for
+   * this parent type.
+   */
+  public Set getAllowableExtensions(Class parentType)
+  {
+    Map innerDeserializerReg = (Map)deserializerReg.get(parentType);
+
+    return (innerDeserializerReg != null)
+           ? innerDeserializerReg.keySet()
+           : null;
+  }
+
+  /**
+   * Declare that the specified extensionType is the concrete
+   * class which should be used to represent extensibility elements
+   * with qnames matching elementType, that are intended to exist as
+   * children of the specified parentType.
+   *
+   * @param parentType a class object indicating where in the WSDL
+   * definition this extension would exist. For example,
+   * javax.wsdls.Binding.class would be used to indicate
+   * this extensibility element would be added to the list of
+   * extensibility elements belonging to a javax.wsdls.Binding,
+   * after being instantiated.
+   * @param elementType the qname of the extensibility element
+   * @param extensionType the concrete class which should be instantiated
+   *
+   * @see #createExtension(Class, QName)
+   */
+  public void mapExtensionTypes(Class parentType,
+                                QName elementType,
+                                Class extensionType)
+  {
+    Map innerExtensionTypeReg = (Map)extensionTypeReg.get(parentType);
+
+    if (innerExtensionTypeReg == null)
+    {
+      innerExtensionTypeReg = new Hashtable();
+
+      extensionTypeReg.put(parentType, innerExtensionTypeReg);
+    }
+
+    innerExtensionTypeReg.put(elementType, extensionType);
+  }
+
+  /**
+   * Create an instance of the type which was declared to be used to
+   * represent extensibility elements with qnames matching elementType,
+   * when intended to exist as children of the specified parentType.
+   * This method allows a user to instantiate an extensibility element
+   * without having to know the implementing type.
+   *
+   * @param parentType a class object indicating where in the WSDL
+   * definition this extension will exist. For example,
+   * javax.wsdls.Binding.class would be used to indicate
+   * this extensibility element is going to be added to the list of
+   * extensibility elements belonging to a javax.wsdls.Binding,
+   * after being instantiated.
+   * @param elementType the qname of the extensibility element
+   *
+   * @return a new instance of the type used to represent the
+   * specified extension
+   *
+   * @see #mapExtensionTypes(Class, QName, Class)
+   */
+  public ExtensibilityElement createExtension(Class parentType,
+                                              QName elementType)
+                                                throws WADLSException
+  {
+    Map innerExtensionTypeReg = (Map)extensionTypeReg.get(parentType);
+    Class extensionType = null;
+
+    if (innerExtensionTypeReg != null)
+    {
+      extensionType = (Class)innerExtensionTypeReg.get(elementType);
+    }
+
+    if (extensionType == null)
+    {
+      throw new WADLSException(WADLSException.CONFIGURATION_ERROR,
+                              "No Java extensionType found " +
+                              "to represent a '" + elementType +
+                              "' element in the context of a '" +
+                              parentType.getName() + "'.");
+    }
+    else if (!(ExtensibilityElement.class.isAssignableFrom(extensionType)))
+    {
+      throw new WADLSException(WADLSException.CONFIGURATION_ERROR,
+                              "The Java extensionType '" +
+                              extensionType.getName() + "' does " +
+                              "not implement the ExtensibilityElement " +
+                              "interface.");
+    }
+
+    try
+    {
+      ExtensibilityElement ee = (ExtensibilityElement)extensionType.newInstance();
+      
+      if (ee.getElementType() == null)
+      {
+        ee.setElementType(elementType);
+      }
+      
+      return ee;
+    }
+    catch (Exception e)
+    {
+      /*
+        Catches:
+                 InstantiationException
+                 IllegalAccessException
+      */
+      throw new WADLSException(WADLSException.CONFIGURATION_ERROR,
+                              "Problem instantiating Java " +
+                              "extensionType '" + extensionType.getName() +
+                              "'.",
+                              e);
+    }
+  }
+
+  /**
+   * Declare that the type of the specified extension attribute, when it occurs
+   * as an attribute of the specified parent type, should be assumed to be
+   * attrType.
+   *
+   * @param parentType a class object indicating where in the WSDL
+   * document this extensibility attribute was encountered. For
+   * example, javax.wsdls.Binding.class would be used to indicate
+   * this attribute was defined on a <wsdl:binding> element.
+   * @param attrName the qname of the extensibility attribute
+   * @param attrType one of the constants defined on the AttributeExtensible
+   * class
+   *
+   * @see #queryExtensionAttributeType(Class, QName)
+   * @see AttributeExtensible
+   */
+  public void registerExtensionAttributeType(Class parentType,
+                                             QName attrName,
+                                             int attrType)
+  {
+    Map innerExtensionAttributeTypeReg =
+      (Map)extensionAttributeTypeReg.get(parentType);
+
+    if (innerExtensionAttributeTypeReg == null)
+    {
+      innerExtensionAttributeTypeReg = new Hashtable();
+
+      extensionAttributeTypeReg.put(parentType, innerExtensionAttributeTypeReg);
+    }
+
+    innerExtensionAttributeTypeReg.put(attrName, new Integer(attrType));
+  }
+
+  /**
+   * Look up the type of the extensibility attribute with the qname attrName,
+   * which was defined on an element represented by the specified parentType.
+   *
+   * @param parentType a class object indicating where in the WSDL
+   * document this extensibility attribute was encountered. For
+   * example, javax.wsdls.Binding.class would be used to indicate
+   * this attribute was defined on a <wsdl:binding> element.
+   * @param attrName the qname of the extensibility attribute
+   *
+   * @return one of the constants defined on the AttributeExtensible class
+   *
+   * @see #registerExtensionAttributeType(Class, QName, int)
+   * @see AttributeExtensible
+   */
+  public int queryExtensionAttributeType(Class parentType, QName attrName)
+  {
+    Map innerExtensionAttributeTypeReg =
+      (Map)extensionAttributeTypeReg.get(parentType);
+    Integer attrType = null;
+
+    if (innerExtensionAttributeTypeReg != null)
+    {
+      attrType = (Integer)innerExtensionAttributeTypeReg.get(attrName);
+    }
+
+    if (attrType != null)
+    {
+      return attrType.intValue();
+    }
+    else
+    {
+      return AttributeExtensible.NO_DECLARED_TYPE;
+    }
+  }
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionSerializer.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionSerializer.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionSerializer.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/ExtensionSerializer.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,43 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls.extensions;
+
+import java.io.*;
+
+import javax.wadls.*;
+import javax.xml.namespace.*;
+
+/**
+ * This interface should be implemented by classes which serialize
+ * extension-specific instances of ExtensibilityElement into the
+ * PrintWriter.
+ *
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public interface ExtensionSerializer
+{
+  /**
+   * This method serializes extension-specific instances of
+   * ExtensibilityElement into the PrintWriter.
+   *
+   * @param parentType a class object indicating where in the WSDL
+   * definition this extension was encountered. For
+   * example, javax.wsdls.Binding.class would be used to indicate
+   * this extensibility element was found in the list of
+   * extensibility elements belonging to a javax.wsdls.Binding.
+   * @param elementType the qname of the extensibility element
+   * @param extension the extensibility element to serialize
+   * @param def the definition this extensibility element was
+   * encountered in
+   * @param extReg the ExtensionRegistry to use (if needed again)
+   */
+  public void marshall(Class parentType,
+                       QName elementType,
+                       ExtensibilityElement extension,
+                       PrintWriter pw,
+                       Application app,
+                       ExtensionRegistry extReg)
+                         throws WADLSException;
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensibilityElement.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensibilityElement.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensibilityElement.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensibilityElement.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,100 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls.extensions;
+
+import org.w3c.dom.*;
+import javax.xml.namespace.*;
+
+/**
+ * This class is used to wrap arbitrary elements.
+ *
+ * @see UnknownExtensionSerializer
+ * @see UnknownExtensionDeserializer
+ *
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public class UnknownExtensibilityElement implements ExtensibilityElement,
+                                                    java.io.Serializable
+{
+  protected QName elementType = null;
+  // Uses the wrapper type so we can tell if it was set or not.
+  protected Boolean required = null;
+  protected Element element = null;
+
+  public static final long serialVersionUID = 1;
+
+  /**
+   * Set the type of this extensibility element.
+   *
+   * @param elementType the type
+   */
+  public void setElementType(QName elementType)
+  {
+    this.elementType = elementType;
+  }
+
+  /**
+   * Get the type of this extensibility element.
+   *
+   * @return the extensibility element's type
+   */
+  public QName getElementType()
+  {
+    return elementType;
+  }
+
+  /**
+   * Set whether or not the semantics of this extension
+   * are required. Relates to the wsdl:required attribute.
+   */
+  public void setRequired(Boolean required)
+  {
+    this.required = required;
+  }
+
+  /**
+   * Get whether or not the semantics of this extension
+   * are required. Relates to the wsdl:required attribute.
+   */
+  public Boolean getRequired()
+  {
+    return required;
+  }
+
+  /**
+   * Set the Element for this extensibility element.
+   *
+   * @param element the unknown element that was encountered
+   */
+  public void setElement(Element element)
+  {
+    this.element = element;
+  }
+
+  /**
+   * Get the Element for this extensibility element.
+   *
+   * @return the unknown element that was encountered
+   */
+  public Element getElement()
+  {
+    return element;
+  }
+
+  public String toString()
+  {
+    StringBuffer strBuf = new StringBuffer();
+
+    strBuf.append("UnknownExtensibilityElement (" + elementType + "):");
+    strBuf.append("\nrequired=" + required);
+
+    if (element != null)
+    {
+      strBuf.append("\nelement=" + element);
+    }
+
+    return strBuf.toString();
+  }
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensionDeserializer.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensionDeserializer.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensionDeserializer.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensionDeserializer.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,55 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls.extensions;
+
+import org.w3c.dom.*;
+
+import javax.wadls.*;
+import javax.xml.namespace.*;
+
+import edu.uga.cs.lsdis.meteors.wadls.*;
+import edu.uga.cs.lsdis.meteors.wadls.util.xml.*;
+
+/**
+ * This class is used to deserialize arbitrary elements into
+ * UnknownExtensibilityElement instances.
+ *
+ * @see UnknownExtensibilityElement
+ * @see UnknownExtensionSerializer
+ *
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public class UnknownExtensionDeserializer implements ExtensionDeserializer,
+                                                     java.io.Serializable
+{
+  public static final long serialVersionUID = 1;
+
+  public ExtensibilityElement unmarshall(Class parentType,
+                                         QName elementType,
+                                         Element el,
+                                         Application app,
+                                         ExtensionRegistry extReg)
+                                           throws WADLSException
+  {
+	  System.out.println("%%%% Inside UnMarshall for Element:"+el.getNodeName());
+    UnknownExtensibilityElement unknownExt = new UnknownExtensibilityElement();
+    String requiredStr = DOMUtils.getAttributeNS(el,
+                                                 Constants.NS_URI_WADL,
+                                                 Constants.ATTR_REQUIRED);
+
+    System.out.println("%%%% Required Str:"+requiredStr);
+    System.out.println("%%%% Element Type To String:"+elementType.toString());
+    unknownExt.setElementType(elementType);
+
+    if (requiredStr != null)
+    {
+      unknownExt.setRequired(new Boolean(requiredStr));
+    }
+
+    unknownExt.setElement(el);
+
+    return unknownExt;
+  }
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensionSerializer.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensionSerializer.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensionSerializer.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/UnknownExtensionSerializer.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,45 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls.extensions;
+
+import java.io.*;
+
+import javax.wadls.*;
+import javax.xml.namespace.*;
+
+import edu.uga.cs.lsdis.meteors.wadls.util.xml.*;
+
+/**
+ * This class is used to serialize UnknownExtensibilityElement instances
+ * into the PrintWriter.
+ *
+ * @see UnknownExtensibilityElement
+ * @see UnknownExtensionDeserializer
+ *
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public class UnknownExtensionSerializer implements ExtensionSerializer,
+                                                   Serializable
+{
+  public static final long serialVersionUID = 1;
+
+  public void marshall(Class parentType,
+                       QName elementType,
+                       ExtensibilityElement extension,
+                       PrintWriter pw,
+                       Application app,
+                       ExtensionRegistry extReg)
+                         throws WADLSException
+  {
+    UnknownExtensibilityElement unknownExt =
+      (UnknownExtensibilityElement)extension;
+
+    pw.print("    ");
+
+    DOM2Writer.serializeAsXML(unknownExt.getElement(), pw);
+
+    pw.println();
+  }
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/Schema.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/Schema.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/Schema.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/Schema.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,146 @@
+/*
+ * (c) Copyright IBM Corp 2004, 2005 
+ */
+
+package javax.wadls.extensions.schema;
+
+import java.io.Serializable;
+import java.util.List;
+import java.util.Map;
+
+import javax.wadls.extensions.ExtensibilityElement;
+import javax.xml.namespace.QName;
+
+import org.w3c.dom.Element;
+
+/**
+ * Represents a schema element.
+ * This is a lightweight schema wrapper that provides access to 
+ * the schema DOM element, but does not parse the schema details. 
+ * The implementor may provide alternative schema parsing if required.
+ * 
+ * @author Jeremy Hughes
+ *
+ */
+public interface Schema extends Serializable 
+{
+    /**
+     * Get a map of lists containing all the imports defined here.
+     * The map's keys are the namespaceURIs, and the map's values
+     * are lists. There is one list for each namespaceURI for which
+     * imports have been defined.
+     *
+     * @return a map of lists of schema imports
+     */
+	
+	public void setElementType(QName elementType);
+
+	  /**
+	   * Get the type of this extensibility element.
+	   *
+	   * @return the extensibility element's type
+	   */
+	  public QName getElementType();
+
+	  /**
+	   * Set whether or not the semantics of this extension
+	   * are required. Relates to the wsdl:required attribute.
+	   */
+	  public void setRequired(Boolean required);
+
+	  /**
+	   * Get whether or not the semantics of this extension
+	   * are required. Relates to the wsdl:required attribute.
+	   */
+	  public Boolean getRequired();
+    public Map getImports();
+    
+    /**
+     * Create a new schema import
+     *
+     * @return the newly created schema import
+     */
+    public SchemaImport createImport();
+    
+    /**
+     * Add an import to this LightWeightSchema
+     *
+     * @param importSchema the import to be added
+     */
+    public void addImport(SchemaImport importSchema);
+    
+    /**
+     * Get a list containing all of the includes defined here.
+     * The list elements are schema references.
+     * 
+     * @return a list of schema references.
+     */
+    public List getIncludes();
+    
+    /**
+     * Create a new schema reference to represent an include.
+     *
+     * @return the newly created SchemaReference
+     */
+    public SchemaReference createInclude();
+    
+    /**
+     * Add an include to this LightWeightSchema
+     *
+     * @param includeSchema The include to be added, represented as a SchemaReference
+     */
+    public void addInclude(SchemaReference includeSchema);
+    
+    /**
+     * Get a list containing all of the redefines defined here.
+     * The list elements are schema references.
+     * 
+     * @return a list of schema references.
+     */
+    public List getRedefines();
+    
+    /**
+     * Create a new schema reference to represent a redefine.
+     *
+     * @return the newly created SchemaReference
+     */
+    public SchemaReference createRedefine();
+    
+    /**
+     * Add a redefine to this LightWeightSchema
+     *
+     * @param redefineSchema The redefine to be added, represented as a SchemaReference
+     */
+    public void addRedefine(SchemaReference redefineSchema);
+    
+    /**
+     * Set the DOM Element that represents this schema element.
+     *
+     * @param element the DOM element representing this schema
+     */
+    public void setElement(Element element);
+
+    /**
+     * Get the DOM Element that represents this schema element.
+     *
+     * @return the DOM element representing this schema
+     */
+    public Element getElement();
+    
+    /**
+     * Set the document base URI of this schema definition. Can be used to
+     * represent the origin of the schema, and can be exploited
+     * when resolving relative URIs (e.g. in <import>s).
+     *
+     * @param documentBaseURI the document base URI of this schema
+     */
+    public void setDocumentBaseURI(String documentBaseURI);
+
+    /**
+     * Get the document base URI of this schema
+     *
+     * @return the document base URI
+     */
+    public String getDocumentBaseURI();
+
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/SchemaImport.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/SchemaImport.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/SchemaImport.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/SchemaImport.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,25 @@
+/*
+ * (c) Copyright IBM Corp 2004, 2005 
+ */
+
+package javax.wadls.extensions.schema;
+
+
+/**
+ * Represents an import element within a schema element.
+ * Similar to an include or redefine, but includes a namespace.
+ * 
+ * @author Jeremy Hughes 
+ */
+public interface SchemaImport extends SchemaReference
+{
+  /**
+   * @return Returns the namespace.
+   */
+  public abstract String getNamespaceURI();
+
+  /**
+   * @param namespace The namespace to set.
+   */
+  public abstract void setNamespaceURI(String namespace);
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/SchemaReference.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/SchemaReference.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/SchemaReference.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/extensions/schema/SchemaReference.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,60 @@
+/*
+ * (c) Copyright IBM Corp 2004, 2005 
+ */
+
+package javax.wadls.extensions.schema;
+
+
+import java.io.Serializable;
+
+import javax.wadls.extensions.schema.Schema;
+
+/**
+ * Represents an include or a redefine element within a schema element.
+ * 
+ * @author Jeremy Hughes 
+ */
+public interface SchemaReference extends Serializable
+{
+    /**
+     * Gets the ID attribute of the referenced schema.
+     * 
+     * @return the id string 
+     */
+    public abstract String getId();
+
+    /**
+     * Sets the ID attribute of the referenced schema.
+     * 
+     * @param id The id string to set.
+     */
+    public abstract void setId(String id);
+
+    /**
+     * Gets the schemaLocation attribute of the referenced schema.
+     * 
+     * @return the schemaLocation string.
+     */
+    public abstract String getSchemaLocationURI();
+
+    /**
+     * Sets the schemaLocation attribute of the referenced schema.
+     * 
+     * @param schemaLocation The schemaLocation string to set.
+     */
+    public abstract void setSchemaLocationURI(String schemaLocation);
+
+    /**
+     * Gets the referenced schema, represented as a LightWeightSchema.
+     * 
+     * @return the referenced LightWeightSchema.
+     */
+    public abstract Schema getReferencedSchema();
+
+    /**
+     * Sets the referenced schema to a LightWeightSchema.
+     * 
+     * @param referencedSchema The LightWeightSchema to set.
+     */
+    public abstract void setReferencedSchema(Schema referencedSchema);
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/factory/WADLFactory.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/factory/WADLFactory.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/factory/WADLFactory.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/factory/WADLFactory.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,183 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls.factory;
+
+import java.io.*;
+import java.util.*;
+
+import javax.wadls.*;
+import javax.wadls.xml.*;
+
+/**
+ * This abstract class defines a factory API that enables applications
+ * to obtain a WSDLFactory capable of producing new Definitions, new
+ * WSDLReaders, and new WSDLWriters.
+ * 
+ * Some ideas used here have been shamelessly copied from the
+ * wonderful JAXP and Xerces work.
+ *
+ * @author Matthew J. Duftler (duftler@us.ibm.com)
+ */
+public abstract class WADLFactory
+{
+  private static final String PROPERTY_NAME =
+    "javax.wadls.factory.WADLFactory";
+  private static final String PROPERTY_FILE_NAME =
+    "wadl.properties";
+  private static final String DEFAULT_FACTORY_IMPL_NAME =
+    "edu.uga.cs.lsdis.meteors.wadls.factory.WADLFactoryImpl";
+
+  private static String fullPropertyFileName = null;
+
+  /**
+   * Get a new instance of a WSDLFactory. This method
+   * follows (almost) the same basic sequence of steps that JAXP
+   * follows to determine the fully-qualified class name of the
+   * class which implements WSDLFactory. The steps (in order)
+   * are:
+   *+   *  Check the javax.wsdls.factory.WSDLFactory system property.
+   *  Check the lib/wsdl.properties file in the JRE directory. The key
+   * will have the same name as the above system property.
+   *  Use the default value.
+   *
+   * Once an instance of a WSDLFactory is obtained, invoke
+   * newDefinition(), newWSDLReader(), or newWSDLWriter(), to create
+   * the desired instances.
+   */
+  public static WADLFactory newInstance() throws WADLSException
+  {
+    String factoryImplName = findFactoryImplName();
+
+    return newInstance(factoryImplName);
+  }
+
+  /**
+   * Get a new instance of a WSDLFactory. This method
+   * returns an instance of the class factoryImplName.
+   * Once an instance of a WSDLFactory is obtained, invoke
+   * newDefinition(), newWSDLReader(), or newWSDLWriter(), to create
+   * the desired instances.
+   *
+   * @param factoryImplName the fully-qualified class name of the
+   * class which provides a concrete implementation of the abstract
+   * class WSDLFactory.
+   */
+  public static WADLFactory newInstance(String factoryImplName)
+    throws WADLSException
+  {
+    if (factoryImplName != null)
+    {
+      try
+      {
+        Class cl = Class.forName(factoryImplName);
+
+        return (WADLFactory)cl.newInstance();
+      }
+      catch (Exception e)
+      {
+        /*
+          Catches:
+                   ClassNotFoundException
+                   InstantiationException
+                   IllegalAccessException
+        */
+        throw new WADLSException(WADLSException.CONFIGURATION_ERROR,
+                                "Problem instantiating factory " +
+                                "implementation.",
+                                e);
+      }
+    }
+    else
+    {
+      throw new WADLSException(WADLSException.CONFIGURATION_ERROR,
+                              "Unable to find name of factory " +
+                              "implementation.");
+    }
+  }
+
+  /**
+   * Create a new instance of a Definition.
+   */
+  public abstract Application newApplication();
+
+  /**
+   * Create a new instance of a WSDLReader.
+   */
+  public abstract WADLReader newWADLReader();
+
+  /**
+   * Create a new instance of a WSDLWriter.
+   */
+  public abstract WADLWriter newWADLWriter();
+
+
+  private static String findFactoryImplName()
+  {
+    String factoryImplName = null;
+
+    // First, check the system property.
+    try
+    {
+      factoryImplName = System.getProperty(PROPERTY_NAME);
+
+      if (factoryImplName != null)
+      {
+        return factoryImplName;
+      }
+    }
+    catch (SecurityException e)
+    {
+    }
+
+    // Second, check the properties file.
+    String propFileName = getFullPropertyFileName();
+
+    if (propFileName != null)
+    {
+      try
+      {
+        Properties properties = new Properties();
+        File propFile = new File(propFileName);
+        FileInputStream fis = new FileInputStream(propFile);
+
+        properties.load(fis);
+        fis.close();
+
+        factoryImplName = properties.getProperty(PROPERTY_NAME);
+
+        if (factoryImplName != null)
+        {
+          return factoryImplName;
+        }
+      }
+      catch (IOException e)
+      {
+      }
+    }
+
+    // Third, return the default.
+    return DEFAULT_FACTORY_IMPL_NAME;
+  }
+
+  private static String getFullPropertyFileName()
+  {
+    if (fullPropertyFileName == null)
+    {
+      try
+      {
+        String javaHome = System.getProperty("java.home");
+
+        fullPropertyFileName = javaHome + File.separator + "lib" +
+                               File.separator + PROPERTY_FILE_NAME;
+      }
+      catch (SecurityException e)
+      {
+      }
+    }
+
+    return fullPropertyFileName;
+  }
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLLocator.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLLocator.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLLocator.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLLocator.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,56 @@
+/*
+ * (c) Copyright IBM Corp 2002, 2005 
+ */
+
+package javax.wadls.xml;
+
+import org.xml.sax.*;
+
+/**
+ * This interface can act as an additional layer of indirection between
+ * a WSDLReader and the actual location of WSDL documents. One
+ * use could be to retrieve WSDL documents from JAR files, while still
+ * retaining the ability to resolve imported documents using relative
+ * URIs.
+ *
+ * @author Owen Burroughs (owenb@uk.ibm.com)
+ *
+ * @see WSDLReader#readWSDL(WSDLLocator)
+ */
+public interface WADLLocator
+{
+  /**
+   * Returns an InputSource "pointed at" the base document.
+   * 
+   * @return the InputSource object or null if the base document could
+   * not be found
+   */
+  public InputSource getBaseInputSource();
+
+  /**
+   * Returns an InputSource "pointed at" an imported wsdl document.
+   *
+   * @param parentLocation a URI specifying the location of the
+   * document doing the importing. This can be null if the import location
+   * is not relative to the parent location.
+   * @param importLocation a URI specifying the location of the
+   * document to import. This might be relative to the parent document's
+   * location.
+   * @return the InputSource object or null if the import cannot be found.
+   */
+  public InputSource getImportInputSource(String parentLocation,
+                                          String importLocation);
+
+  /**
+   * Returns a URI representing the location of the base document.
+   */
+  public String getBaseURI();
+
+  /**
+   * Returns a URI representing the location of the last import document
+   * to be resolved. This is used in resolving nested imports where an
+   * import location is relative to the parent document.
+   */
+  public String getLatestImportURI();
+}
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLReader.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLReader.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLReader.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLReader.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,178 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls.xml;
+
+import java.io.InputStream;
+import java.net.URISyntaxException;
+
+import org.w3c.dom.*;
+import org.xml.sax.*;
+
+import javax.wadls.*;
+import javax.wadls.extensions.*;
+import javax.wadls.extensions.ExtensionRegistry;
+
+/**
+ * This interface describes a collection of methods
+ * that enable conversion of a WSDL document (in XML,
+ * following the WSDL schema described in the WSDL
+ * specification) into a WSDL model.
+ *
+ * @author Matthew J. Duftler
+ */
+public interface WADLReader
+{
+  /**
+   * Sets the specified feature to the specified value.
+   * 
+   * The minimum features that must be supported are:
+   * 

+   * 
+   *   
+   *     
+   *     
+   *     
+   *   
+   *   
+   *     
+   *     
+   *     
+   *   
+   *   
+   *     
+   *     
+   *     
+   *   
+   * Name Description Default Value
javax.wsdls.verbose If set to true, status messages will be displayed. true
javax.wsdls.importDocuments If set to true, imported WSDL documents will be
+   *         retrieved and processed. true
+   * 

+   * All feature names must be fully-qualified, Java package style. All
+   * names starting with javax.wsdls. are reserved for features defined
+   * by the JWSDL specification. It is recommended that implementation-
+   * specific features be fully-qualified to match the package name
+   * of that implementation. For example: com.abc.featureName
+   *
+   * @param name the name of the feature to be set.
+   * @param value the value to set the feature to.
+   * @throws IllegalArgumentException if the feature name is not recognized.
+   * @see #getFeature(String)
+   */
+		  
+  public void setFeature(String name, boolean value)
+    throws IllegalArgumentException;
+
+  /**
+   * Gets the value of the specified feature.
+   *
+   * @param name the name of the feature to get the value of.
+   * @throws IllegalArgumentException if the feature name is not recognized.
+   * @see #setFeature(String, boolean)
+   */
+  public boolean getFeature(String name) throws IllegalArgumentException;
+
+
+
+  /**
+   * Set a different factory implementation to use for
+   * creating definitions when reading WSDL documents.
+   * As some WSDLReader implementations may only be
+   * capable of creating definitions using the same
+   * factory implementation from which the reader was
+   * obtained, this method is optional. Default is null.
+   *
+   * @param factoryImplName the fully-qualified class name of the
+   * class which provides a concrete implementation of the abstract
+   * class WSDLFactory.
+   * @throws UnsupportedOperationException if this method
+   * is invoked on an implementation which does not
+   * support it.
+   */
+  public void setFactoryImplName(String factoryImplName)
+    throws UnsupportedOperationException;
+
+  /**
+   * Get the factoryImplName, if one was set. Default is null.
+   */
+  public String getFactoryImplName();
+
+  public Application readWADL(InputStream wadlIS) throws WADLSException;
+
+  /**
+   * Read the WSDL document accessible via the specified
+   * URI into a WSDL definition.
+   *
+   * @param wsdlURI a URI (can be a filename or URL) pointing to a
+   * WSDL XML definition.
+   * @return the definition.
+   */
+  public Application readWADL(String wadlURI) throws WADLSException;
+
+  /**
+   * Read the WSDL document accessible via the specified
+   * URI into a WSDL definition.
+   *
+   * @param contextURI the context in which to resolve the
+   * wsdlURI, if the wsdlURI is relative. Can be null, in which
+   * case it will be ignored.
+   * @param wsdlURI a URI (can be a filename or URL) pointing to a
+   * WSDL XML definition.
+   * @return the definition.
+   */
+  public Application readWADL(String contextURI, String wadlURI)
+    throws WADLSException;
+
+  /**
+   * Read the specified <wsdl:definitions> element into a WSDL
+   * definition.
+   *
+   * @param documentBaseURI the document base URI of the WSDL definition
+   * described by the element. Will be set as the documentBaseURI
+   * of the returned Definition. Can be null, in which case it
+   * will be ignored.
+   * @param definitionsElement the <wsdl:definitions> element
+   * @return the definition described by the element.
+   */
+  public Application readWADL(String documentBaseURI,
+                             Element definitionsElement)
+                               throws WADLSException, URISyntaxException;
+
+  /**
+   * Read the specified WSDL document into a WSDL definition.
+   *
+   * @param documentBaseURI the document base URI of the WSDL definition
+   * described by the document. Will be set as the documentBaseURI
+   * of the returned Definition. Can be null, in which case it
+   * will be ignored.
+   * @param wsdlDocument the WSDL document, an XML 
+   * document obeying the WSDL schema.
+   * @return the definition described in the document.
+   */
+  public Application readWADL(String documentBaseURI, Document wadlDocument)
+    throws WADLSException, URISyntaxException;
+
+  /**
+   * Read a WSDL document into a WSDL definition.
+   *
+   * @param documentBaseURI the document base URI of the WSDL definition
+   * described by the document. Will be set as the documentBaseURI
+   * of the returned Definition. Can be null, in which case it
+   * will be ignored.
+   * @param inputSource an InputSource pointing to the
+   * WSDL document, an XML document obeying the WSDL schema.
+   * @return the definition described in the document pointed to
+   * by the InputSource.
+   */
+  public Application readWADL(String documentBaseURI, InputSource inputSource)
+    throws WADLSException, URISyntaxException;
+
+  /**
+   * Read a WSDL document into a WSDL definition.
+   *
+   * @param locator A WSDLLocator object used to provide InputSources
+   * pointing to the wsdl file.
+   * @return the definition described in the document
+   */
+  public Application readWADL(WADLLocator locator) throws WADLSException, URISyntaxException;
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLWriter.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLWriter.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLWriter.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/wadls/xml/WADLWriter.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,73 @@
+/*
+ * (c) Copyright IBM Corp 2001, 2005 
+ */
+
+package javax.wadls.xml;
+
+import java.io.*;
+import java.net.URISyntaxException;
+
+import org.w3c.dom.*;
+
+import javax.wadls.*;
+
+/**
+ * This interface describes a collection of methods
+ * that allow a WSDL model to be written to a writer
+ * in an XML format that follows the WSDL schema.
+ *
+ * @author Matthew J. Duftler
+ */
+public interface WADLWriter
+{
+  /**
+   * Sets the specified feature to the specified value.
+   * 

+   * There are no minimum features that must be supported.
+   * 

+   * All feature names must be fully-qualified, Java package style. All
+   * names starting with javax.wsdls. are reserved for features defined
+   * by the JWSDL specification. It is recommended that implementation-
+   * specific features be fully-qualified to match the package name
+   * of that implementation. For example: com.abc.featureName
+   *
+   * @param name the name of the feature to be set.
+   * @param value the value to set the feature to.
+   * @throws IllegalArgumentException if the feature name is not recognized.
+   * @see #getFeature(String)
+   */
+  public void setFeature(String name, boolean value)
+    throws IllegalArgumentException;
+
+  /**
+   * Gets the value of the specified feature.
+   *
+   * @param name the name of the feature to get the value of.
+   * @throws IllegalArgumentException if the feature name is not recognized.
+   * @see #setFeature(String, boolean)
+   */
+  public boolean getFeature(String name) throws IllegalArgumentException;
+
+  /**
+   * Return a document generated from the specified WSDL model.
+   */
+  public Document getDocument(Application wadlApp) throws WADLSException, URISyntaxException;
+
+  /**
+   * Write the specified WSDL definition to the specified Writer.
+   *
+   * @param wsdlDef the WSDL definition to be written.
+   * @param sink the Writer to write the xml to.
+   */
+  public void writeWADL(Application wadlApp, Writer sink)
+    throws WADLSException, URISyntaxException;
+
+  /**
+   * Write the specified WSDL definition to the specified OutputStream.
+   *
+   * @param wsdlDef the WSDL definition to be written.
+   * @param sink the OutputStream to write the xml to.
+   */
+  public void writeWADL(Application wadlApp, OutputStream sink)
+    throws WADLSException, URISyntaxException;
+}
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/xml/namespace/QName.class
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/xml/namespace/QName.class has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/xml/namespace/QName.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/SAWADLParser/src/javax/xml/namespace/QName.java	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,415 @@
+//$Id: QName.java,v 1.10 2004/02/09 23:41:21 jsuttor Exp $
+
+/*
+ * Copyright 2004 Sun Microsystems, Inc.  All rights reserved.
+ * SUN PROPRIETARY/CONFIDENTIAL. Use is subject to license terms.
+ */
+
+package javax.xml.namespace;
+
+import java.io.Serializable;
+
+import javax.xml.XMLConstants;
+
+/** 
+ * 
QName represents a qualified name
+ * as defined in the XML specifications: XML Schema Part2:
+ * Datatypes specification, Namespaces
+ * in XML, Namespaces
+ * in XML Errata.
+ *
+ * The value of a QName contains a Namespace
+ * URI, local part and
+ * prefix.
+ *
+ * The prefix is included in QName to retain lexical
+ * information when present in an {@link
+ * javax.xml.transform.Source XML input source}. The prefix is
+ * NOT used in {@link #equals(Object)
+ * QName.equals(Object)} or to compute the {@link #hashCode()
+ * QName.hashCode()}.  Equality and the hash code are defined using
+ * only the Namespace URI and local part.
+ *
+ * If not specified, the Namespace URI is set to {@link
+ * javax.xml.XMLConstants#NULL_NS_URI XMLConstants.NULL_NS_URI}.
+ * If not specified, the prefix is set to {@link
+ * javax.xml.XMLConstants#DEFAULT_NS_PREFIX
+ * XMLConstants.DEFAULT_NS_PREFIX}.
+ *
+ * QName is immutable.
+ *
+ * @author Jeff Suttor
+ * @version $Revision: 1.10 $, $Date: 2004/02/09 23:41:21 $
+ * @see XML Schema Part2: Datatypes specification
+ * @see Namespaces in XML
+ * @see Namespaces in XML Errata
+ * @since 1.5
+ */
+
+public class QName implements Serializable {
+
+    /**
+     * Stream Unique Identifier.
+     */
+    private static final long serialVersionUID = 4418622981026545151L;
+
+    /**
+     * Namespace URI of this QName.
+     */
+    private final String namespaceURI;
+
+    /**
+     * local part of this QName.
+     */
+    private final String localPart;
+
+    /**
+     * prefix of this QName.
+     */
+    private final String prefix;
+
+    /** 
+     * QName constructor specifying the Namespace URI
+     * and local part.
+     *
+     * If the Namespace URI is null, it is set to
+     * {@link javax.xml.XMLConstants#NULL_NS_URI
+     * XMLConstants.NULL_NS_URI}.  This value represents no
+     * explicitly defined Namespace as defined by the Namespaces
+     * in XML specification.  This action preserves compatible
+     * behavior with QName 1.0.  Explicitly providing the {@link
+     * javax.xml.XMLConstants#NULL_NS_URI
+     * XMLConstants.NULL_NS_URI} value is the preferred coding
+     * style.
+     *
+     * If the local part is null an
+     * IllegalArgumentException is thrown.
+     * A local part of "" is allowed to preserve
+     * compatible behavior with QName 1.0. 
+     *
+     * When using this constructor, the prefix is set to {@link
+     * javax.xml.XMLConstants#DEFAULT_NS_PREFIX
+     * XMLConstants.DEFAULT_NS_PREFIX}.
+     *
+     * The Namespace URI is not validated as a
+     * URI reference.
+     * The local part is not validated as a
+     * NCName
+     * as specified in Namespaces
+     * in XML.
+     *
+     * @param namespaceURI Namespace URI of the QName
+     * @param localPart    local part of the QName
+     * 
+     * @see #QName(String namespaceURI, String localPart, String
+     * prefix) QName(String namespaceURI, String localPart, String
+     * prefix)
+     */
+    public QName(final String namespaceURI, final String localPart) {
+        this(namespaceURI, localPart, XMLConstants.DEFAULT_NS_PREFIX);
+    }
+
+    /** 
+     * QName constructor specifying the Namespace URI,
+     * local part and prefix.
+     *
+     * If the Namespace URI is null, it is set to
+     * {@link javax.xml.XMLConstants#NULL_NS_URI
+     * XMLConstants.NULL_NS_URI}.  This value represents no
+     * explicitly defined Namespace as defined by the Namespaces
+     * in XML specification.  This action preserves compatible
+     * behavior with QName 1.0.  Explicitly providing the {@link
+     * javax.xml.XMLConstants#NULL_NS_URI
+     * XMLConstants.NULL_NS_URI} value is the preferred coding
+     * style.
+     * 
+     * If the local part is null an
+     * IllegalArgumentException is thrown.
+     * A local part of "" is allowed to preserve
+     * compatible behavior with QName 1.0. 
+     * 
+     * If the prefix is null, an
+     * IllegalArgumentException is thrown.  Use {@link
+     * javax.xml.XMLConstants#DEFAULT_NS_PREFIX
+     * XMLConstants.DEFAULT_NS_PREFIX} to explicitly indicate that no
+     * prefix is present or the prefix is not relevant.
+     *
+     * The Namespace URI is not validated as a
+     * URI reference.
+     * The local part and prefix are not validated as a
+     * NCName
+     * as specified in Namespaces
+     * in XML.
+     *
+     * @param namespaceURI Namespace URI of the QName
+     * @param localPart    local part of the QName
+     * @param prefix       prefix of the QName
+     */
+    public QName(String namespaceURI, String localPart, String prefix) {
+
+        // map null Namespace URI to default to preserve compatibility with QName 1.0
+        if (namespaceURI == null) {
+            this.namespaceURI = XMLConstants.NULL_NS_URI;
+        } else {
+            this.namespaceURI = namespaceURI;
+        }
+
+        // local part is required.  "" is allowed to preserve compatibility with QName 1.0        
+        if (localPart == null) {
+            throw new IllegalArgumentException("local part cannot be \"null\" when creating a QName");
+        }
+        this.localPart = localPart;
+
+        // prefix is required        
+        if (prefix == null) {
+            throw new IllegalArgumentException("prefix cannot be \"null\" when creating a QName");
+        }
+        this.prefix = prefix;
+    }
+
+    /** 
+     * QName constructor specifying the local part.
+     *
+     * If the local part is null an
+     * IllegalArgumentException is thrown.
+     * A local part of "" is allowed to preserve
+     * compatible behavior with QName 1.0. 
+     *
+     * When using this constructor, the Namespace URI is set to
+     * {@link javax.xml.XMLConstants#NULL_NS_URI
+     * XMLConstants.NULL_NS_URI} and the prefix is set to {@link
+     * javax.xml.XMLConstants#DEFAULT_NS_PREFIX
+     * XMLConstants.DEFAULT_NS_PREFIX}.
+     *
+     * In an XML context, all Element and Attribute names exist
+     * in the context of a Namespace.  Making this explicit during the
+     * construction of a QName helps prevent hard to
+     * diagnosis XML validity errors.  The constructors {@link
+     * #QName(String namespaceURI, String localPart) QName(String
+     * namespaceURI, String localPart)} and
+     * {@link #QName(String namespaceURI, String localPart, String prefix)} 
+     * are preferred.
+     * 
+     * The local part is not validated as a
+     * NCName
+     * as specified in Namespaces
+     * in XML.
+     *
+     * @param localPart local part of the QName
+     * @see #QName(String namespaceURI, String localPart) QName(String
+     * namespaceURI, String localPart)
+     * @see #QName(String namespaceURI, String localPart, String
+     * prefix) QName(String namespaceURI, String localPart, String
+     * prefix)
+     */
+    public QName(String localPart) {
+        this(
+            XMLConstants.NULL_NS_URI,
+            localPart,
+            XMLConstants.DEFAULT_NS_PREFIX);
+    }
+    
+    /** 
+     * Get the Namespace URI of this QName.
+     *
+     * @return Namespace URI of this QName
+     */
+    public String getNamespaceURI() {
+        return namespaceURI;
+    }
+
+    /**
+     * Get the local part of this QName.
+     *
+     *  @return local part of this QName
+     */
+    public String getLocalPart() {
+        return localPart;
+    }
+
+    /** 
+     * Get the prefix of this QName.
+     *
+     * The prefix assigned to a QName might
+     * NOT be valid in a different
+     * context. For example, a QName may be assigned a
+     * prefix in the context of parsing a document but that prefix may
+     * be invalid in the context of a different document.
+     *
+     *  @return prefix of this QName
+     */
+    public String getPrefix() {
+        return prefix;
+    }
+
+    /**
+     * Test this QName for equality with another
+     * Object.
+     *
+     * If the Object to be tested is not a
+     * QName or is null, then this method
+     * returns false.
+     *
+     * Two QNames are considered equal if and only if
+     * both the Namespace URI and local part are equal. This method
+     * uses String.equals() to check equality of the
+     * Namespace URI and local part. The prefix is
+     * NOT used to determine equality.
+     *
+     * This method satisfies the general contract of {@link
+     * java.lang.Object#equals(Object) Object.equals(Object)}
+     *
+     * @param objectToTest the Object to test for
+     * equality with this QName
+     * @return true if the given Object is
+     * equal to this QName else false
+     */
+    public final boolean equals(Object objectToTest) {
+        if (objectToTest == null || !(objectToTest instanceof QName)) {
+            return false;
+        }
+
+        QName qName = (QName) objectToTest;
+
+        return namespaceURI.equals(qName.namespaceURI)
+            && localPart.equals(qName.localPart);
+    }
+
+    /**
+     * Generate the hash code for this QName.
+     *
+     * The hash code is calculated using both the Namespace URI and
+     * the local part of the QName.  The prefix is
+     * NOT used to calculate the hash
+     * code.
+     *
+     * This method satisfies the general contract of {@link
+     * java.lang.Object#hashCode() Object.hashCode()}.
+     *
+     * @return hash code for this QName Object
+     */
+    public final int hashCode() {
+        return namespaceURI.hashCode() ^ localPart.hashCode();
+    }
+
+	/** 
+	 * String representation of this
+	 * QName.
+	 *
+	 * The commonly accepted way of representing a QName
+	 * as a String was defined
+	 * by James Clark.  Although this is not a standard
+	 * specification, it is in common use,  e.g. {@link javax.xml.transform.Transformer#setParameter(String name, Object value)}.
+	 * This implementation represents a QName as:
+	 * "{" + Namespace URI + "}" + local part.  If the Namespace URI
+	 * .equals(XMLConstants.NULL_NS_URI), only the
+	 * local part is returned.  An appropriate use of this method is
+	 * for debugging or logging for human consumption.
+	 *
+	 * Note the prefix value is NOT
+	 * returned as part of the String representation.
+	 *  
+	 * This method satisfies the general contract of {@link
+	 * java.lang.Object#toString() Object.toString()}.
+	 *
+	 *  @return String representation of this QName
+	 */
+    public String toString() {
+        if (namespaceURI.equals(XMLConstants.NULL_NS_URI)) {
+            return localPart;
+        } else {
+            return "{" + namespaceURI + "}" + localPart;
+        }
+    }
+
+    /** 
+     * QName derived from parsing the formatted
+     * String.
+     *
+     * If the String is null or does not conform to
+     * {@link #toString() QName.toString()} formatting, an
+     * IllegalArgumentException is thrown.
+     *  
+     * The String MUST be in the
+     * form returned by {@link #toString() QName.toString()}.
+
+	 * The commonly accepted way of representing a QName
+	 * as a String was defined
+	 * by James Clark.  Although this is not a standard
+	 * specification, it is in common use,  e.g. {@link javax.xml.transform.Transformer#setParameter(String name, Object value)}.
+     * This implementation parses a String formatted
+     * as: "{" + Namespace URI + "}" + local part.  If the Namespace
+     * URI .equals(XMLConstants.NULL_NS_URI), only the
+     * local part should be provided.
+     *
+     * The prefix value CANNOT be
+     * represented in the String and will be set to
+     * {@link javax.xml.XMLConstants#DEFAULT_NS_PREFIX
+     * XMLConstants.DEFAULT_NS_PREFIX}.
+     *
+     * This method does not do full validation of the resulting
+     * QName. 
+     * 
The Namespace URI is not validated as a
+     * URI reference.
+     * The local part is not validated as a
+     * NCName
+     * as specified in
+     * Namespaces in XML.
+     *
+     * @param qNameAsString String representation
+     * of the QName
+     * @return QName corresponding to the given String
+     * @see #toString() QName.toString()
+     */
+    public static QName valueOf(String qNameAsString) {
+
+        // null is not valid
+        if (qNameAsString == null) {
+            throw new IllegalArgumentException("cannot create QName from \"null\" or \"\" String");
+        }
+
+        // "" local part is valid to preserve compatible behavior with QName 1.0
+        if (qNameAsString.length() == 0) {
+            return new QName(
+                XMLConstants.NULL_NS_URI,
+                qNameAsString,
+                XMLConstants.DEFAULT_NS_PREFIX);
+        }
+
+        // local part only?
+        if (qNameAsString.charAt(0) != '{') {
+            return new QName(
+                XMLConstants.NULL_NS_URI,
+                qNameAsString,
+                XMLConstants.DEFAULT_NS_PREFIX);
+        }
+
+        // Namespace URI improperly specified?
+        if (qNameAsString.startsWith("{" + XMLConstants.NULL_NS_URI + "}")) {
+            throw new IllegalArgumentException(
+                "Namespace URI .equals(XMLConstants.NULL_NS_URI), "
+                + ".equals(\"" + XMLConstants.NULL_NS_URI + "\"), "
+                + "only the local part, "
+                + "\"" + qNameAsString.substring(2 + XMLConstants.NULL_NS_URI.length()) + "\", "
+                + "should be provided.");
+        }
+
+        // Namespace URI and local part specified
+        int endOfNamespaceURI = qNameAsString.indexOf('}');
+        if (endOfNamespaceURI == -1) {
+            throw new IllegalArgumentException(
+                "cannot create QName from \""
+                    + qNameAsString
+                    + "\", missing closing \"}\"");
+        }
+        return new QName(
+            qNameAsString.substring(1, endOfNamespaceURI),
+            qNameAsString.substring(endOfNamespaceURI + 1),
+            XMLConstants.DEFAULT_NS_PREFIX);
+    }
+}
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/owlapi-bin.jar
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/owlapi-bin.jar has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/owlapi-src.jar
Binary file WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/lib/owlapi-src.jar has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/refreshTool.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/refreshTool.py	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,16 @@
+'''
+@author  Sumedha Ganjoo
+@see     LICENSE (MIT style license file).
+'''
+
+import os.path
+import sys
+
+outputfile=open(sys.argv[2],'w')
+outputfile.seek(0,0)
+outputfile.write('\n Tool added...For independent use, find the tool under Web Service Tools on the left side window, \n and for use in workflows find the tool under Web Service Workflow Tools. \n If the tool is not visible click on "Galaxy" on the top left corner of this window to refresh the page.')
+
+
+
+
+    
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/refreshTool.py~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/refreshTool.py~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,16 @@
+'''
+@author  Sumedha Ganjoo
+@see     LICENSE (MIT style license file).
+'''
+
+import os.path
+import sys
+
+outputfile=open(sys.argv[2],'w')
+outputfile.seek(0,0)
+outputfile.write('\n Tool added...For independent use, find the tool under Web Service Tools on the left side window, \n and for use in workflows find the tool under Web Service Workflow Tools. \n If the tool is not visible click on "Galaxy" on the top left corner of this window to refresh the page.')
+
+
+
+
+    
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/refreshTool.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/refreshTool.xml	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,34 @@
+
+ 
+
+	refreshTool.py
+	$input
+	$output
+
+  
+   
+    
+   
+   
+  
+  
+     
+  
+  
+  
+  
+
+.. class:: infomark
+
+**TIP: After step c refresh the page.**
+
+**Your tool(s) can now be found under Web Service Tools and Web Service Workflow Tools in the tools section on the left.**
+      
+Web Service Tools are used to invoke web services independently.
+Web Service Workflow Tools can be used in creating workflows.
+  
+*NOTE: Step a, Step b and Step c merely add this tool to Galaxy. To use the tool, go to the Tools section on left
+and find the tool under Select Web Service Tools and Select Web Service Workflow Tools.*
+  
+
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/refreshTool.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/refreshTool.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,34 @@
+
+ 
+
+	refreshTool.py
+	$input
+	$output
+
+  
+   
+    
+   
+   
+  
+  
+     
+  
+  
+  
+  
+
+.. class:: infomark
+
+**TIP: After step c refresh the page.**
+
+**Your tool(s) can now be found under Web Service Tools and Web Service Workflow Tools in the tools section on the left.**
+      
+Web Service Tools are used to invoke web services independently.
+Web Service Workflow Tools can be used in creating workflows.
+  
+*NOTE: Step a, Step b and Step c merely add this tool to Galaxy. To use the tool, go to the Tools section on left
+and find the tool under Select Web Service Tools and Select Web Service Workflow Tools.*
+  
+
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/suite_config.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/suite_config.xml	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,17 @@
+
+        This suite contains all the tools required to register Web services to Galaxy
+        
+        
+             This tool takes the URL of an external Web service. The URL should point to the description document of a Web service.
+            
+        
+        
+             This tool lets the user choose operations from the Web service description document, as each operation has to be registered with Galaxy individually.
+            
+        
+        
+             Adds tool to Galaxy and refreshes toolbox. 
+            
+                
+
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/suite_config.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/suite_config.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,17 @@
+
+        This suite contains all the tools required to register Web services to Galaxy
+        
+        
+             This tool takes the URL of an external Web service. The URL should point to the description document of a Web service.
+            
+        
+        
+             This tool lets the user choose a method and a resource from the Web service description document, as each method has to be registered with Galaxy individually.
+            
+        
+        
+             Adds tool to Galaxy and refreshes toolbox. 
+            
+                
+
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,3 @@
+ 
+6
+ 
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/ClientCount.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,3 @@
+ 
+0
+ 
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_1.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_1.py	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,192 @@
+'''
+@author  Chaitanya Guttula, Sumedha Ganjoo
+@see     LICENSE (MIT style license file).
+'''
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+import warnings
+with warnings.catch_warnings():
+    warnings.simplefilter("ignore")
+    import sys
+    import os
+    import urllib
+    import time
+    
+    """
+    
+    This script takes the values of the input parameters of the
+    web service from the user and invokes the web service.
+    The URL to the WSDL is the command line argument
+
+    """
+    servicetype = sys.argv[2]
+    if servicetype=='SOAP':
+        galaxyhome=os.environ.get('GALAXY_HOME')
+        sys.path.append(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/')
+        os.chdir(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/')
+        from creatorEngineComplex import *
+        from wsdl2path import *
+        from paramConverter import *
+        from ZSI.writer import SoapWriter
+        from msHandler import *
+
+        webservice = str(sys.argv[5])
+        operation = str(sys.argv[6])
+        resultfile=open(sys.argv[1],'w')
+        length=len(sys.argv)
+        inputdict={}
+        i=7
+        test=ClientCreator()
+        while(i>=7 and i<(length-1)):
+            key=sys.argv[i]
+            print 'key is : ',key
+            #if(sys.argv[i+1]=='ZSI.TC.String'):
+            val=sys.argv[i+1]
+            while(val.find('__at__')>-1):
+                vlist = val.split('__at__')
+                val = '@'.join(vlist)
+            while(val.find('__sq__')>-1):
+                vlist = val.split('__sq__')
+                val = ''.join(vlist)
+            while(val.find('__gt__')>-1):
+                vlist = val.split('__gt__')
+                val = '>'.join(vlist)
+            while(val.find('***')>-1):
+                vlist = val.split('***')
+                val = '\n'.join(vlist)
+            while(val.find('**')>-1):
+                vlist = val.split('**')
+                val = ' '.join(vlist)
+            #if(val.find(',')>-1):
+            #    print 'found ,'
+            #    vlist = val.split(',')
+            #    val = '\',\''.join(vlist)
+                
+                
+            #if(val.find('__sq__')>-1):
+             #   j=i+4
+              #  val=val.lstrip('__sq__')
+               # while(str(sys.argv[j]).find('__sq__')==-1):
+                #    val=val+' '+sys.argv[j]
+                 #   j=j+1
+                #val=val+' '+(str(sys.argv[j]).rstrip('__sq__'))
+                #i=j-3
+
+        #elif((sys.argv[i+1]=='ZSI.TC.Integer')or (sys.argv[i+1]=='ZSI.TCnumbers.Iint')):
+        #   val=int(sys.argv[i+1])
+       #elif(sys.argv[i+1]=='ZSI.TC.Decimal'):
+         #   val=float(sys.argv[i+1])
+        #elif(sys.argv[i+2]=='Yes'):
+         #   valFile=open(sys.argv[i+3],'r')
+          #  val=valFile.read()
+        #else:
+        #   val=sys.argv[i+1]
+            if val == 'fileInput':
+                f = open(sys.argv[i+2])
+                #line = f.readline()
+                val = ''
+                #for j in line:
+                #   val = val+j
+                #linestripped = line.strip('\n')
+                for line in f:
+                    #line = f.readline().strip('\n')
+                    #line = line.strip(' ')
+                        
+                    val = val+line
+                val = val.strip("\n")
+                print val
+                i = i+1
+            
+            if(val != "0"): 
+                inputdict[key]= val
+            #resultfile.write('value is :'+ val+'\n')
+            
+            i=i+2
+        if len(inputdict) == 0:
+            inputdic = {}
+        else:
+            inputdic = flat2nestedDict(inputdict)    
+        print 'The webservice is : ',operation,' ',webservice #added
+        result = None
+        try:
+            result = test.invokeOp(operation,webservice,inputdic)
+        except:
+            pass
+        print 'The result before is ',result
+        while result == None:
+            time.sleep(2)
+            print 'in loop'
+            try:
+                result = test.invokeOp(operation,webservice,inputdic)
+            except:
+                pass
+            print 'result in loop ',result
+        
+        print 'The result after is',result
+
+        mshandler = MessageHandler()
+        resultDict={}
+        resultDict=mshandler.flatten(result)   #mshandler.msParser(responseInstance)
+        flat =  nested2flatDict(resultDict)
+	result=flat
+
+        # Writing the output to he o/p file when the result is parsed
+        for r in result:
+           if type(result[r])==list:
+                   for i in result[r]:
+                           resultfile.write(str(i)+'\n')
+                           print str(i)
+           else:
+                   resultfile.write(str(result[r])+'\n')
+
+        #Writes the result without parsinf in the XML format it gets.
+        #sw = SoapWriter(header=False, envelope=False);
+        #res = test.opname2outputClassOb(operation,webservice)
+        #res_tc = getattr(res,'typecode')
+        #ofwhat = res_tc.ofwhat;
+        #for tc in ofwhat :
+        #    sw.serialize(getattr(result, tc.aname), tc);
+        #    doc = sw.dom.getDocument();
+        #    fp = open(sys.argv[1], 'w');
+        #    try :
+        #        doc.writexml(fp, '\t', '', '\n');
+        #    finally :
+        #        fp.close();
+   
+
+    elif servicetype == 'REST':
+
+        outputFile = open(sys.argv[1],'w')
+        resUrl = sys.argv[3]
+
+        if(resUrl.find('__tilda__')>-1):
+            ulist = resUrl.split('__tilda__')
+            resUrl = '~'.join(ulist)
+    
+        paramdict={}
+        length=(len(sys.argv))
+
+        i=6
+        while( i>=6 and i<(length-1)):
+            key=sys.argv[i]
+            val=sys.argv[i+1]
+            if val=='fileInput':
+                print '##########fileInput found#############'
+                f=open(sys.argv[i+2])
+                line = f.readline().strip('\n')
+                line = line.strip(' ')
+                val = line        
+                i=i+1
+    
+            while(val.find('**')>-1):
+                vlist = val.split('**')
+        	val = ' '.join(vlist)
+            print key + '\t' + val
+            paramdict[key]=val
+            i=i+2
+
+        params = urllib.urlencode(paramdict)
+        data = urllib.urlopen(resUrl, params).read()
+        outputFile.write(data)
+        outputFile.close()
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_1.py~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_1.py~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,185 @@
+'''
+@author  Chaitanya Guttula, Sumedha Ganjoo
+@see     LICENSE (MIT style license file).
+'''
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+import warnings
+with warnings.catch_warnings():
+    warnings.simplefilter("ignore")
+    import sys
+    import os
+    import urllib
+    import time
+    
+    """
+    
+    This script takes the values of the input parameters of the
+    web service from the user and invokes the web service.
+    The URL to the WSDL is the command line argument
+
+    """
+    servicetype = sys.argv[2]
+    if servicetype=='SOAP':
+        galaxyhome=os.environ.get('GALAXY_HOME')
+        sys.path.append(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/')
+        os.chdir(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/')
+        from creatorEngineComplex import *
+        from wsdl2path import *
+        from paramConverter import *
+        from ZSI.writer import SoapWriter
+
+        webservice = str(sys.argv[5])
+        operation = str(sys.argv[6])
+        resultfile=open(sys.argv[1],'w')
+        length=len(sys.argv)
+        inputdict={}
+        i=7
+        test=ClientCreator()
+        while(i>=7 and i<(length-1)):
+            key=sys.argv[i]
+            print 'key is : ',key
+            #if(sys.argv[i+1]=='ZSI.TC.String'):
+            val=sys.argv[i+1]
+            while(val.find('__at__')>-1):
+                vlist = val.split('__at__')
+                val = '@'.join(vlist)
+            while(val.find('__sq__')>-1):
+                vlist = val.split('__sq__')
+                val = ''.join(vlist)
+            while(val.find('__gt__')>-1):
+                vlist = val.split('__gt__')
+                val = '>'.join(vlist)
+            while(val.find('***')>-1):
+                vlist = val.split('***')
+                val = '\n'.join(vlist)
+            while(val.find('**')>-1):
+                vlist = val.split('**')
+                val = ' '.join(vlist)
+            #if(val.find(',')>-1):
+            #    print 'found ,'
+            #    vlist = val.split(',')
+            #    val = '\',\''.join(vlist)
+                
+                
+            #if(val.find('__sq__')>-1):
+             #   j=i+4
+              #  val=val.lstrip('__sq__')
+               # while(str(sys.argv[j]).find('__sq__')==-1):
+                #    val=val+' '+sys.argv[j]
+                 #   j=j+1
+                #val=val+' '+(str(sys.argv[j]).rstrip('__sq__'))
+                #i=j-3
+
+        #elif((sys.argv[i+1]=='ZSI.TC.Integer')or (sys.argv[i+1]=='ZSI.TCnumbers.Iint')):
+        #   val=int(sys.argv[i+1])
+       #elif(sys.argv[i+1]=='ZSI.TC.Decimal'):
+         #   val=float(sys.argv[i+1])
+        #elif(sys.argv[i+2]=='Yes'):
+         #   valFile=open(sys.argv[i+3],'r')
+          #  val=valFile.read()
+        #else:
+        #   val=sys.argv[i+1]
+            if val == 'fileInput':
+                f = open(sys.argv[i+2])
+                #line = f.readline()
+                val = ''
+                #for j in line:
+                #   val = val+j
+                #linestripped = line.strip('\n')
+                for line in f:
+                    #line = f.readline().strip('\n')
+                    #line = line.strip(' ')
+                        
+                    val = val+line
+                val = val.strip("\n")
+                print val
+                i = i+1
+            
+            if(val != "0"): 
+                inputdict[key]= val
+            #resultfile.write('value is :'+ val+'\n')
+            
+            i=i+2
+        if len(inputdict) == 0:
+            inputdic = {}
+        else:
+            inputdic = flat2nestedDict(inputdict)    
+        print 'The webservice is : ',operation,' ',webservice #added
+        result = None
+        try:
+            result = test.invokeOp(operation,webservice,inputdic)
+        except:
+            pass
+        print 'The result before is ',result
+        while result == None:
+            time.sleep(2)
+            print 'in loop'
+            try:
+                result = test.invokeOp(operation,webservice,inputdic)
+            except:
+                pass
+            print 'result in loop ',result
+        
+        print 'The result after is',result
+
+        # Writing the output to he o/p file when the result is parsed
+        for r in result:
+            if type(result[r])==list:
+                    for i in result[r]:
+                            resultfile.write(str(i)+'\n')
+                            print str(i)
+            else:
+                    resultfile.write(str(result[r])+'\n')
+
+        #Writes the result without parsinf in the XML format it gets.
+        #sw = SoapWriter(header=False, envelope=False);
+        #res = test.opname2outputClassOb(operation,webservice)
+        #res_tc = getattr(res,'typecode')
+        #ofwhat = res_tc.ofwhat;
+        #for tc in ofwhat :
+        #    sw.serialize(getattr(result, tc.aname), tc);
+        #    doc = sw.dom.getDocument();
+        #    fp = open(sys.argv[1], 'w');
+        #    try :
+        #        doc.writexml(fp, '\t', '', '\n');
+        #    finally :
+        #        fp.close();
+   
+
+    elif servicetype == 'REST':
+
+        outputFile = open(sys.argv[1],'w')
+        resUrl = sys.argv[3]
+
+        if(resUrl.find('__tilda__')>-1):
+            ulist = resUrl.split('__tilda__')
+            resUrl = '~'.join(ulist)
+    
+        paramdict={}
+        length=(len(sys.argv))
+
+        i=6
+        while( i>=6 and i<(length-1)):
+            key=sys.argv[i]
+            val=sys.argv[i+1]
+            if val=='fileInput':
+                print '##########fileInput found#############'
+                f=open(sys.argv[i+2])
+                line = f.readline().strip('\n')
+                line = line.strip(' ')
+                val = line        
+                i=i+1
+    
+            while(val.find('**')>-1):
+                vlist = val.split('**')
+        	val = ' '.join(vlist)
+            print key + '\t' + val
+            paramdict[key]=val
+            i=i+2
+
+        params = urllib.urlencode(paramdict)
+        data = urllib.urlopen(resUrl, params).read()
+        outputFile.write(data)
+        outputFile.close()
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_1.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_1.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,60 @@
+
+   Client for method: genesbymolecularweight , Web service: http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.wadl 
+  
+  client_1.py 
+  $output 
+  http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml
+  organism
+  $param0
+  min_molecular_weight
+  $param1
+  max_molecular_weight
+  $param2
+
+  
+
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+
+
+
+  
+    
+  
+  
+.. class:: infomark
+
+**TIP:** organism type is xsd:string
+
+**TIP:** min_molecular_weight type is xsd:string
+
+**TIP:** max_molecular_weight type is xsd:string
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_10.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_10.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,50 @@
+
+   Client for method: poll , Web service: http://om.cs.uga.edu/demo/clustalW2.wadl 
+  
+  #client_1.py 
+  $output 
+  http://www.ebi.ac.uk/Tools/services/restwublast/result
+  jobId
+#if $source0.source0_source=="user" $source0.user_param0 #else $source0.cached_param0 #end if
+  resultType
+#if $source1.source1_source=="user" $source1.user_param1 #else $source1.cached_param1 #end if
+#if $cond_source.optional_param_source=="yes"#else 
+#end if
+
+  
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+   
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** jobId type is xsd:string
+
+.. class:: infomark
+
+**TIP:** resultType type is xsd:string
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_14.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_14.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,431 @@
+
+   Client for operation : run , Web service: wublast.wublast_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services         run
+	"_parameters|_sequence"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_stype"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_program"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_email"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	"_parameters|_database|_string|$|"
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services            run
+	"_parameters|_sequence"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_stype"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_program"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_email"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	"_parameters|_database|_string|$|"
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+	"_parameters|_sensitivity"
+	 #if $cond_source.source5.source5_source=="user":
+	 $cond_source.source5.user_param5
+	 #else:
+	 fileInput
+	 $cond_source.source5.cached_param5
+	 #end if
+	"_parameters|_topcombon"
+	 #if $cond_source.source6.source6_source=="user":
+	 $cond_source.source6.user_param6
+	 #else:
+	 fileInput
+	 $cond_source.source6.cached_param6
+	 #end if
+	"_parameters|_filter"
+	 #if $cond_source.source7.source7_source=="user":
+	 $cond_source.source7.user_param7
+	 #else:
+	 fileInput
+	 $cond_source.source7.cached_param7
+	 #end if
+	"_parameters|_alignments"
+	 #if $cond_source.source8.source8_source=="user":
+	 $cond_source.source8.user_param8
+	 #else:
+	 fileInput
+	 $cond_source.source8.cached_param8
+	 #end if
+	"_parameters|_scores"
+	 #if $cond_source.source9.source9_source=="user":
+	 $cond_source.source9.user_param9
+	 #else:
+	 fileInput
+	 $cond_source.source9.cached_param9
+	 #end if
+	"_parameters|_viewfilter"
+	 #if $cond_source.source10.source10_source=="user":
+	 $cond_source.source10.user_param10
+	 #else:
+	 fileInput
+	 $cond_source.source10.cached_param10
+	 #end if
+	"_parameters|_sort"
+	 #if $cond_source.source11.source11_source=="user":
+	 $cond_source.source11.user_param11
+	 #else:
+	 fileInput
+	 $cond_source.source11.cached_param11
+	 #end if
+	"_parameters|_strand"
+	 #if $cond_source.source12.source12_source=="user":
+	 $cond_source.source12.user_param12
+	 #else:
+	 fileInput
+	 $cond_source.source12.cached_param12
+	 #end if
+	"_parameters|_align"
+	 #if $cond_source.source13.source13_source=="user":
+	 $cond_source.source13.user_param13
+	 #else:
+	 fileInput
+	 $cond_source.source13.cached_param13
+	 #end if
+	"_parameters|_matrix"
+	 #if $cond_source.source14.source14_source=="user":
+	 $cond_source.source14.user_param14
+	 #else:
+	 fileInput
+	 $cond_source.source14.cached_param14
+	 #end if
+	"_title"
+	 #if $cond_source.source15.source15_source=="user":
+	 $cond_source.source15.user_param15
+	 #else:
+	 fileInput
+	 $cond_source.source15.cached_param15
+	 #end if
+	"_parameters|_stats"
+	 #if $cond_source.source16.source16_source=="user":
+	 $cond_source.source16.user_param16
+	 #else:
+	 fileInput
+	 $cond_source.source16.cached_param16
+	 #end if
+	"_parameters|_exp"
+	 #if $cond_source.source17.source17_source=="user":
+	 $cond_source.source17.user_param17
+	 #else:
+	 fileInput
+	 $cond_source.source17.cached_param17
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About sequence: type is String
+
+.. class:: infomark
+
+**TIP:** About stype: type is String
+
+.. class:: infomark
+
+**TIP:** About program: type is String
+
+.. class:: infomark
+
+**TIP:** About email: type is String
+
+.. class:: infomark
+
+**TIP:** About database: type is String
+  
+
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_16.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_16.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,431 @@
+
+   Client for operation : run , Web service: wublast.wublast_services 
+  
+  	client_2.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services         run
+	"_parameters|_sequence"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_stype"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_program"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_email"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	"_parameters|_database|_string|$|"
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services            run
+	"_parameters|_sequence"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_stype"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_program"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_email"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	"_parameters|_database|_string|$|"
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+	"_parameters|_sensitivity"
+	 #if $cond_source.source5.source5_source=="user":
+	 $cond_source.source5.user_param5
+	 #else:
+	 fileInput
+	 $cond_source.source5.cached_param5
+	 #end if
+	"_parameters|_topcombon"
+	 #if $cond_source.source6.source6_source=="user":
+	 $cond_source.source6.user_param6
+	 #else:
+	 fileInput
+	 $cond_source.source6.cached_param6
+	 #end if
+	"_parameters|_filter"
+	 #if $cond_source.source7.source7_source=="user":
+	 $cond_source.source7.user_param7
+	 #else:
+	 fileInput
+	 $cond_source.source7.cached_param7
+	 #end if
+	"_parameters|_alignments"
+	 #if $cond_source.source8.source8_source=="user":
+	 $cond_source.source8.user_param8
+	 #else:
+	 fileInput
+	 $cond_source.source8.cached_param8
+	 #end if
+	"_parameters|_scores"
+	 #if $cond_source.source9.source9_source=="user":
+	 $cond_source.source9.user_param9
+	 #else:
+	 fileInput
+	 $cond_source.source9.cached_param9
+	 #end if
+	"_parameters|_viewfilter"
+	 #if $cond_source.source10.source10_source=="user":
+	 $cond_source.source10.user_param10
+	 #else:
+	 fileInput
+	 $cond_source.source10.cached_param10
+	 #end if
+	"_parameters|_sort"
+	 #if $cond_source.source11.source11_source=="user":
+	 $cond_source.source11.user_param11
+	 #else:
+	 fileInput
+	 $cond_source.source11.cached_param11
+	 #end if
+	"_parameters|_strand"
+	 #if $cond_source.source12.source12_source=="user":
+	 $cond_source.source12.user_param12
+	 #else:
+	 fileInput
+	 $cond_source.source12.cached_param12
+	 #end if
+	"_parameters|_align"
+	 #if $cond_source.source13.source13_source=="user":
+	 $cond_source.source13.user_param13
+	 #else:
+	 fileInput
+	 $cond_source.source13.cached_param13
+	 #end if
+	"_parameters|_matrix"
+	 #if $cond_source.source14.source14_source=="user":
+	 $cond_source.source14.user_param14
+	 #else:
+	 fileInput
+	 $cond_source.source14.cached_param14
+	 #end if
+	"_title"
+	 #if $cond_source.source15.source15_source=="user":
+	 $cond_source.source15.user_param15
+	 #else:
+	 fileInput
+	 $cond_source.source15.cached_param15
+	 #end if
+	"_parameters|_stats"
+	 #if $cond_source.source16.source16_source=="user":
+	 $cond_source.source16.user_param16
+	 #else:
+	 fileInput
+	 $cond_source.source16.cached_param16
+	 #end if
+	"_parameters|_exp"
+	 #if $cond_source.source17.source17_source=="user":
+	 $cond_source.source17.user_param17
+	 #else:
+	 fileInput
+	 $cond_source.source17.cached_param17
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About sequence: type is String
+
+.. class:: infomark
+
+**TIP:** About stype: type is String
+
+.. class:: infomark
+
+**TIP:** About program: type is String
+
+.. class:: infomark
+
+**TIP:** About email: type is String
+
+.. class:: infomark
+
+**TIP:** About database: type is String
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_17.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_17.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,62 @@
+
+   Client for operation : run , Web service: wublast.wublast_services 
+  
+ #if $cond_source.optional_param_source=="no" #client_3.py $output $servicetype wublast.wublast_services  run	"_parameters|_sequence" $param0	"_parameters|_stype" $param1	"_parameters|_program" $param2	"_email" $param3	"_parameters|_database|_string|$|" $param4 #else #client_3.py $output $servicetype wublast.wublast_services    run
+	"_parameters|_sequence" $param0	"_parameters|_stype" $param1	"_parameters|_program" $param2	"_email" $param3	"_parameters|_database|_string|$|" $param4	"_parameters|_sensitivity" $param5	"_parameters|_topcombon" $param6	"_parameters|_filter" $param7	"_parameters|_alignments" $param8	"_parameters|_scores" $param9	"_parameters|_viewfilter" $param10	"_parameters|_sort" $param11	"_parameters|_strand" $param12	"_parameters|_align" $param13	"_parameters|_matrix" $param14	"_title" $param15	"_parameters|_stats" $param16	"_parameters|_exp" $param17 #end if 
+
+  
+    
+
+
+
+
+
+
+  
+ 
+  
+  
+ 
+ 
+  
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About sequence: type is String
+
+.. class:: infomark
+
+**TIP:** About stype: type is String
+
+.. class:: infomark
+
+**TIP:** About program: type is String
+
+.. class:: infomark
+
+**TIP:** About email: type is String
+
+.. class:: infomark
+
+**TIP:** About database: type is String
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_2.py~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_2.py~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,160 @@
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+import warnings
+with warnings.catch_warnings():
+    warnings.simplefilter("ignore")
+
+    import sys
+    import os
+    import time
+    galaxyhome=os.environ.get('GALAXY_HOME')
+    sys.path.append(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/')    
+    from creatorEngineComplex import *
+    from wsdl2path import *
+    from paramConverter import *
+    from ZSI.writer import SoapWriter
+    from collections import deque
+
+__author__="Shefali Shastri"
+
+def main():
+    """
+
+    This script takes the values of the input parameters of the
+    web service from the user and invokes the web service.
+    The URL to the WSDL is the command line argument
+
+    """
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+
+        #galaxyhome=os.environ.get('GALAXY_HOME')
+        #sys.path.append(galaxyhome+'/tools/SOAPclient/clients/clientGenerator/')
+        os.chdir(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clientGenerator/')
+        webservice = str(sys.argv[5])
+        #print 'WS ', webservice
+        operation = str(sys.argv[6])
+        #print 'OP ',operation
+        resultfile=open(sys.argv[1],'w')
+        length=len(sys.argv)
+        inputdict={}
+        i=7
+        test=ClientCreator()
+        while(i>=7 and i<(length-1)):
+            key=sys.argv[i]
+            print 'key is : ',key
+            #if(sys.argv[i+1]=='ZSI.TC.String'):
+            val=sys.argv[i+1]
+            while(val.find('__at__')>-1):
+                vlist = val.split('__at__')
+                val = '@'.join(vlist)
+            while(val.find('__sq__')>-1):
+                vlist = val.split('__sq__')
+                val = ''.join(vlist)
+            while(val.find('__gt__')>-1):
+                vlist = val.split('__gt__')
+                val = '>'.join(vlist)
+            while(val.find('***')>-1):
+                vlist = val.split('***')
+                val = '\n'.join(vlist)
+            while(val.find('**')>-1):
+                vlist = val.split('**')
+                val = ' '.join(vlist)
+            while(val.find('__ob__')>-1):
+                vlist = val.split('__ob__')
+                val = '['.join(vlist)
+            while(val.find('__cb__')>-1):
+                vlist = val.split('__cb__')
+                val = ']'.join(vlist)
+            
+            print 'value is : ',val
+            
+                #if(val.find('__sq__')>-1):
+                 #   j=i+4
+                  #  val=val.lstrip('__sq__')
+                   # while(str(sys.argv[j]).find('__sq__')==-1):
+                    #    val=val+' '+sys.argv[j]
+                     #   j=j+1
+                    #val=val+' '+(str(sys.argv[j]).rstrip('__sq__'))
+                    #i=j-3
+
+            #elif((sys.argv[i+1]=='ZSI.TC.Integer')or (sys.argv[i+1]=='ZSI.TCnumbers.Iint')):
+             #   val=int(sys.argv[i+1])
+            #elif(sys.argv[i+1]=='ZSI.TC.Decimal'):
+             #   val=float(sys.argv[i+1])
+            #elif(sys.argv[i+2]=='Yes'):
+             #   valFile=open(sys.argv[i+3],'r')
+              #  val=valFile.read()
+            #else:
+             #   val=sys.argv[i+1]
+            if val == 'fileInput':
+                f = open(sys.argv[i+2])
+                #line = f.readline()
+                val = ''
+                #for j in line:
+                 #   val = val+j
+                #linestripped = line.strip('\n')
+                for line in f:
+                    #line = f.readline().strip('\n')
+                    #line = line.strip(' ')
+                    
+                    val = val+line
+                val = val.strip("\n")
+                print val
+                i = i+1
+                
+            if(val != "0"): 
+                inputdict[key] = val
+            #resultfile.write('value is :'+ val+'\n')
+            
+            i=i+2
+        print inputdict
+        if len(inputdict) == 0:
+            print 'empty inputs'
+            inputdic = {}
+        else:
+            inputdic = flat2nestedDict(inputdict)    
+        print 'the inputs are',inputdic
+        result = None
+        try:
+            result = test.invokeOp(operation,webservice,inputdic)
+        except:
+            pass
+        print 'The result before is ',result
+        #print ps
+        while result == None:
+            time.sleep(2)
+            print 'in loop'
+            result = test.invokeOp(operation,webservice,inputdic)
+        
+        print 'The result after is',result
+
+        # Writing the output to he o/p file when the result is parsed
+        for r in result:
+            if type(result[r])==list:
+                    for i in result[r]:
+                            resultfile.write(str(i)+'\n')
+                            print str(i)
+            else:
+                    resultfile.write(str(result[r])+'\n')
+
+        #Writes the result without parsinf in the XML format it gets.
+        #sw = SoapWriter(header=False, envelope=False);
+        #res = test.opname2outputClassOb(operation,webservice)
+        #res_tc = getattr(res,'typecode')
+        #ofwhat = res_tc.ofwhat;
+        #for tc in ofwhat :
+        #    sw.serialize(getattr(result, tc.aname), tc);
+        #    doc = sw.dom.getDocument();
+        #    fp = open(sys.argv[1], 'w');
+        #    try :
+        #        doc.writexml(fp, '\t', '', '\n');
+        #    finally :
+        #        fp.close();
+    
+
+
+
+if __name__ == "__main__":
+    main();
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_2.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_2.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,239 @@
+
+   Client for method: genesbymolecularweight , Web service: http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.wadl 
+   
+  	client_1.py 
+	#if $cond_source.optional_param_source=="no":
+  	$output 
+	http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml
+	organism
+	 #if $source0.source0_source=="user": 
+	 $source0.user_param0 
+         #else: 
+	 $source0.cached_param0 
+	 #end if
+	min_molecular_weight
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1 
+	 #else:
+	 $source1.cached_param1 
+	 #end if
+	max_molecular_weight
+	 #if $source2.source2_source=="user":
+ 	 $source2.user_param2 
+	 #else:
+	 $source2.cached_param2 
+	 #end if
+   	#else:
+	organism
+	 #if $source0.source0_source=="user": 
+	 $source0.user_param0 
+         #else: 
+	 $source0.cached_param0 
+	 #end if
+	min_molecular_weight
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1 
+	 #else:
+	 $source1.cached_param1 
+	 #end if
+	max_molecular_weight
+	 #if $source2.source2_source=="user":
+ 	 $source2.user_param2 
+	 #else:
+	 $source2.cached_param2 
+	 #end if
+	o-fields
+	 #if $cond_source.source3.source3_source=="user": 
+	 $cond_source.source3.user_param3 
+	 #else:
+	 $cond_source.source3.cached_param3 
+	 #end if
+	o-tables
+    	 #if $cond_source.source4.source4_source=="user":
+     	 $cond_source.source4.user_param4 
+    	 #else:
+     	 $cond_source.source4.cached_param4 
+    	 #end if 
+   	#end if
+
+  
+
+     
+       
+       
+    
+    
+    
+      
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+   
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** Organism type is xsd:string
+
+.. class:: infomark
+
+**TIP:** Min Molecular Weight (Daltons) type is xsd:string
+
+.. class:: infomark
+
+**TIP:** Max Molecular Weight (Daltons) type is xsd:string
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_38.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_38.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,279 @@
+
+   Client for method: genesbygenetype , Web service: http://eupathdb.org/eupathdb/webservices/GeneQuestions/GenesByGeneType.wadl 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+        $method
+     http://eupathdb.org/webservices/GeneQuestions
+	organism
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	includePseudogenes
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	geneType
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+    $url
+    $method
+http://eupathdb.org/webservices/GeneQuestions
+	organism
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	includePseudogenes
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	geneType
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	o-fields
+	 #if $cond_source.source3.source3_source=="user":
+	 $cond_source.source3.user_param3
+	 #else:
+	 fileInput
+	 $cond_source.source3.cached_param3
+	 #end if
+	o-tables
+	 #if $cond_source.source4.source4_source=="user":
+	 $cond_source.source4.user_param4
+	 #else:
+	 fileInput
+	 $cond_source.source4.cached_param4
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+    
+      
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+    
+      
+       
+       
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+    
+      
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+      
+ 
+ 
+     
+   
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+ 
+ 
+
+  
+    
+  
+  
+Replace white space with ** in all parameter values
+
+.. class:: infomark
+
+**TIP:** Organism type is xsd:string
+
+.. class:: infomark
+
+**TIP:** Include Pseudogenes type is xsd:string
+
+.. class:: infomark
+
+**TIP:** Gene type type is xsd:string
+  
+
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_4.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_4.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,250 @@
+
+   Client for method: genesbymolecularweight , Web service: http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.wadl 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml
+	organism
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	min_molecular_weight
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	max_molecular_weight
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+   	#else:
+  	$output
+	http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml
+	organism
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	min_molecular_weight
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	max_molecular_weight
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	o-fields
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	o-tables
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+   	#end if
+
+  
+
+     
+       
+       
+    
+    
+    
+      
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+   
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+ 
+ 
+
+  
+    
+  
+  
+Replace white space with ** in all parameter values
+
+.. class:: infomark
+
+**TIP:** Organism type is xsd:string
+
+.. class:: infomark
+
+**TIP:** Min Molecular Weight (Daltons) type is xsd:string
+
+.. class:: infomark
+
+**TIP:** Max Molecular Weight (Daltons) type is xsd:string
+  
+
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_45.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_45.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,431 @@
+
+   Client for operation : run , Web service : wublast.wublast_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services         run
+	"_parameters|_sequence"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_stype"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_program"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_email"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	"_parameters|_database|_string|$|"
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services            run
+	"_parameters|_sequence"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_stype"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_program"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_email"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	"_parameters|_database|_string|$|"
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+	"_parameters|_sensitivity"
+	 #if $cond_source.source5.source5_source=="user":
+	 $cond_source.source5.user_param5
+	 #else:
+	 fileInput
+	 $cond_source.source5.cached_param5
+	 #end if
+	"_parameters|_topcombon"
+	 #if $cond_source.source6.source6_source=="user":
+	 $cond_source.source6.user_param6
+	 #else:
+	 fileInput
+	 $cond_source.source6.cached_param6
+	 #end if
+	"_parameters|_filter"
+	 #if $cond_source.source7.source7_source=="user":
+	 $cond_source.source7.user_param7
+	 #else:
+	 fileInput
+	 $cond_source.source7.cached_param7
+	 #end if
+	"_parameters|_alignments"
+	 #if $cond_source.source8.source8_source=="user":
+	 $cond_source.source8.user_param8
+	 #else:
+	 fileInput
+	 $cond_source.source8.cached_param8
+	 #end if
+	"_parameters|_scores"
+	 #if $cond_source.source9.source9_source=="user":
+	 $cond_source.source9.user_param9
+	 #else:
+	 fileInput
+	 $cond_source.source9.cached_param9
+	 #end if
+	"_parameters|_viewfilter"
+	 #if $cond_source.source10.source10_source=="user":
+	 $cond_source.source10.user_param10
+	 #else:
+	 fileInput
+	 $cond_source.source10.cached_param10
+	 #end if
+	"_parameters|_sort"
+	 #if $cond_source.source11.source11_source=="user":
+	 $cond_source.source11.user_param11
+	 #else:
+	 fileInput
+	 $cond_source.source11.cached_param11
+	 #end if
+	"_parameters|_strand"
+	 #if $cond_source.source12.source12_source=="user":
+	 $cond_source.source12.user_param12
+	 #else:
+	 fileInput
+	 $cond_source.source12.cached_param12
+	 #end if
+	"_parameters|_align"
+	 #if $cond_source.source13.source13_source=="user":
+	 $cond_source.source13.user_param13
+	 #else:
+	 fileInput
+	 $cond_source.source13.cached_param13
+	 #end if
+	"_parameters|_matrix"
+	 #if $cond_source.source14.source14_source=="user":
+	 $cond_source.source14.user_param14
+	 #else:
+	 fileInput
+	 $cond_source.source14.cached_param14
+	 #end if
+	"_title"
+	 #if $cond_source.source15.source15_source=="user":
+	 $cond_source.source15.user_param15
+	 #else:
+	 fileInput
+	 $cond_source.source15.cached_param15
+	 #end if
+	"_parameters|_stats"
+	 #if $cond_source.source16.source16_source=="user":
+	 $cond_source.source16.user_param16
+	 #else:
+	 fileInput
+	 $cond_source.source16.cached_param16
+	 #end if
+	"_parameters|_exp"
+	 #if $cond_source.source17.source17_source=="user":
+	 $cond_source.source17.user_param17
+	 #else:
+	 fileInput
+	 $cond_source.source17.cached_param17
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About sequence: type is String
+
+.. class:: infomark
+
+**TIP:** About stype: type is String
+
+.. class:: infomark
+
+**TIP:** About program: type is String
+
+.. class:: infomark
+
+**TIP:** About email: type is String
+
+.. class:: infomark
+
+**TIP:** About database: type is String
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_5.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_5.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,115 @@
+
+   Client for method: getDDBJEntry , Web service: http://cs.uga.edu/~ganjoo/galaxy/DDBJGetEntry.wadl 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	http://www.xml.nig.ac.jp/rest/Invoke
+	service
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 $source0.cached_param0
+	 #end if
+	method
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 $source1.cached_param1
+	 #end if
+	accession
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 $source2.cached_param2
+	 #end if
+   	#else:
+  	$output
+	http://www.xml.nig.ac.jp/rest/Invoke
+	service
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 $source0.cached_param0
+	 #end if
+	method
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 $source1.cached_param1
+	 #end if
+	accession
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+   	#end if
+
+  
+
+     
+       
+       
+    
+    
+    
+      
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+    
+      
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+  
+ 
+  
+   
+  
+  
+  
+     
+     
+     
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** Service to be invoked  type is xsd:string
+
+.. class:: infomark
+
+**TIP:** Method to be used type is xsd:string
+
+.. class:: infomark
+
+**TIP:** DDBJ accession number type is xsd:string
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_55.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_55.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,135 @@
+
+   Client for operation : getResult , Web service : wublast.wublast_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services         getResult
+	"_type"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_jobId"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services            getResult
+	"_type"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_jobId"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_parameter|0|_name"
+	 #if $cond_source.source2.source2_source=="user":
+	 $cond_source.source2.user_param2
+	 #else:
+	 fileInput
+	 $cond_source.source2.cached_param2
+	 #end if
+	"_parameters|_parameter|0|_value|_string|$|"
+	 #if $cond_source.source3.source3_source=="user":
+	 $cond_source.source3.user_param3
+	 #else:
+	 fileInput
+	 $cond_source.source3.cached_param3
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About type: type is String
+
+.. class:: infomark
+
+**TIP:** About jobId: type is String
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_57.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_57.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,155 @@
+
+   Client for operation : fetchBatch , Web service : WSDbfetchDoclit.WSDBFetchDoclitServerService_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+WSDbfetchDoclit.WSDBFetchDoclitServerService_services         fetchBatch
+	"_format"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_db"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_style"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_ids"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+WSDbfetchDoclit.WSDBFetchDoclitServerService_services            fetchBatch
+	"_format"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_db"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_style"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_ids"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About format: type is String
+
+.. class:: infomark
+
+**TIP:** About db: type is String
+
+.. class:: infomark
+
+**TIP:** About style: type is String
+
+.. class:: infomark
+
+**TIP:** About ids: type is String
+  
+
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_59.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_59.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,135 @@
+
+   Client for operation : getResult , Web service : clustalw2.clustalw2_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+clustalw2.clustalw2_services         getResult
+	"_type"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_jobId"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+clustalw2.clustalw2_services            getResult
+	"_type"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_jobId"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_parameter|0|_name"
+	 #if $cond_source.source2.source2_source=="user":
+	 $cond_source.source2.user_param2
+	 #else:
+	 fileInput
+	 $cond_source.source2.cached_param2
+	 #end if
+	"_parameters|_parameter|0|_value|_string|$|"
+	 #if $cond_source.source3.source3_source=="user":
+	 $cond_source.source3.user_param3
+	 #else:
+	 fileInput
+	 $cond_source.source3.cached_param3
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About type: type is String
+
+.. class:: infomark
+
+**TIP:** About jobId: type is String
+  
+
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_61.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_61.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,524 @@
+
+   Client for operation : run , Web service : clustalw2.clustalw2_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+clustalw2.clustalw2_services         run
+	"_email"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+clustalw2.clustalw2_services            run
+	"_email"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_sequence"
+	 #if $cond_source.source1.source1_source=="user":
+	 $cond_source.source1.user_param1
+	 #else:
+	 fileInput
+	 $cond_source.source1.cached_param1
+	 #end if
+	"_parameters|_pwmatrix"
+	 #if $cond_source.source2.source2_source=="user":
+	 $cond_source.source2.user_param2
+	 #else:
+	 fileInput
+	 $cond_source.source2.cached_param2
+	 #end if
+	"_parameters|_dnamatrix"
+	 #if $cond_source.source3.source3_source=="user":
+	 $cond_source.source3.user_param3
+	 #else:
+	 fileInput
+	 $cond_source.source3.cached_param3
+	 #end if
+	"_parameters|_gapopen"
+	 #if $cond_source.source4.source4_source=="user":
+	 $cond_source.source4.user_param4
+	 #else:
+	 fileInput
+	 $cond_source.source4.cached_param4
+	 #end if
+	"_parameters|_pairgap"
+	 #if $cond_source.source5.source5_source=="user":
+	 $cond_source.source5.user_param5
+	 #else:
+	 fileInput
+	 $cond_source.source5.cached_param5
+	 #end if
+	"_parameters|_pwdnamatrix"
+	 #if $cond_source.source6.source6_source=="user":
+	 $cond_source.source6.user_param6
+	 #else:
+	 fileInput
+	 $cond_source.source6.cached_param6
+	 #end if
+	"_parameters|_outorder"
+	 #if $cond_source.source7.source7_source=="user":
+	 $cond_source.source7.user_param7
+	 #else:
+	 fileInput
+	 $cond_source.source7.cached_param7
+	 #end if
+	"_parameters|_iteration"
+	 #if $cond_source.source8.source8_source=="user":
+	 $cond_source.source8.user_param8
+	 #else:
+	 fileInput
+	 $cond_source.source8.cached_param8
+	 #end if
+	"_parameters|_noendgaps"
+	 #if $cond_source.source9.source9_source=="user":
+	 $cond_source.source9.user_param9
+	 #else:
+	 fileInput
+	 $cond_source.source9.cached_param9
+	 #end if
+	"_parameters|_pwgapopen"
+	 #if $cond_source.source10.source10_source=="user":
+	 $cond_source.source10.user_param10
+	 #else:
+	 fileInput
+	 $cond_source.source10.cached_param10
+	 #end if
+	"_parameters|_ktup"
+	 #if $cond_source.source11.source11_source=="user":
+	 $cond_source.source11.user_param11
+	 #else:
+	 fileInput
+	 $cond_source.source11.cached_param11
+	 #end if
+	"_parameters|_alignment"
+	 #if $cond_source.source12.source12_source=="user":
+	 $cond_source.source12.user_param12
+	 #else:
+	 fileInput
+	 $cond_source.source12.cached_param12
+	 #end if
+	"_parameters|_matrix"
+	 #if $cond_source.source13.source13_source=="user":
+	 $cond_source.source13.user_param13
+	 #else:
+	 fileInput
+	 $cond_source.source13.cached_param13
+	 #end if
+	"_parameters|_score"
+	 #if $cond_source.source14.source14_source=="user":
+	 $cond_source.source14.user_param14
+	 #else:
+	 fileInput
+	 $cond_source.source14.cached_param14
+	 #end if
+	"_title"
+	 #if $cond_source.source15.source15_source=="user":
+	 $cond_source.source15.user_param15
+	 #else:
+	 fileInput
+	 $cond_source.source15.cached_param15
+	 #end if
+	"_parameters|_gapext"
+	 #if $cond_source.source16.source16_source=="user":
+	 $cond_source.source16.user_param16
+	 #else:
+	 fileInput
+	 $cond_source.source16.cached_param16
+	 #end if
+	"_parameters|_clustering"
+	 #if $cond_source.source17.source17_source=="user":
+	 $cond_source.source17.user_param17
+	 #else:
+	 fileInput
+	 $cond_source.source17.cached_param17
+	 #end if
+	"_parameters|_numiter"
+	 #if $cond_source.source18.source18_source=="user":
+	 $cond_source.source18.user_param18
+	 #else:
+	 fileInput
+	 $cond_source.source18.cached_param18
+	 #end if
+	"_parameters|_pwgapext"
+	 #if $cond_source.source19.source19_source=="user":
+	 $cond_source.source19.user_param19
+	 #else:
+	 fileInput
+	 $cond_source.source19.cached_param19
+	 #end if
+	"_parameters|_topdiags"
+	 #if $cond_source.source20.source20_source=="user":
+	 $cond_source.source20.user_param20
+	 #else:
+	 fileInput
+	 $cond_source.source20.cached_param20
+	 #end if
+	"_parameters|_window"
+	 #if $cond_source.source21.source21_source=="user":
+	 $cond_source.source21.user_param21
+	 #else:
+	 fileInput
+	 $cond_source.source21.cached_param21
+	 #end if
+	"_parameters|_gapdist"
+	 #if $cond_source.source22.source22_source=="user":
+	 $cond_source.source22.user_param22
+	 #else:
+	 fileInput
+	 $cond_source.source22.cached_param22
+	 #end if
+	"_parameters|_type"
+	 #if $cond_source.source23.source23_source=="user":
+	 $cond_source.source23.user_param23
+	 #else:
+	 fileInput
+	 $cond_source.source23.cached_param23
+	 #end if
+	"_parameters|_output"
+	 #if $cond_source.source24.source24_source=="user":
+	 $cond_source.source24.user_param24
+	 #else:
+	 fileInput
+	 $cond_source.source24.cached_param24
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About email: type is String
+  
+
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_7.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_7.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,483 @@
+
+   Client for method: runclustalW2 , Web service: http://om.cs.uga.edu/demo/clusatlW2.wadl 
+  
+  #client_1.py 
+  $output 
+  http://www.ebi.ac.uk/Tools/services/restclustalw2/run
+  email
+#if $source0.source0_source=="user" $source0.user_param0 #else $source0.cached_param0 #end if
+#if $cond_source.optional_param_source=="yes"  type
+#if $cond_source.source1.source1_source=="user" $cond_source.source1.user_param1 #else $cond_source.source1.cached_param1 #end if
+  title
+#if $cond_source.source2.source2_source=="user" $cond_source.source2.user_param2 #else $cond_source.source2.cached_param2 #end if
+  output
+#if $cond_source.source3.source3_source=="user" $cond_source.source3.user_param3 #else $cond_source.source3.cached_param3 #end if
+  alignments
+#if $cond_source.source4.source4_source=="user" $cond_source.source4.user_param4 #else $cond_source.source4.cached_param4 #end if
+  outorder
+#if $cond_source.source5.source5_source=="user" $cond_source.source5.user_param5 #else $cond_source.source5.cached_param5 #end if
+  sequence
+#if $cond_source.source6.source6_source=="user" $cond_source.source6.user_param6 #else $cond_source.source6.cached_param6 #end if
+  ktup
+#if $cond_source.source7.source7_source=="user" $cond_source.source7.user_param7 #else $cond_source.source7.cached_param7 #end if
+  window
+#if $cond_source.source8.source8_source=="user" $cond_source.source8.user_param8 #else $cond_source.source8.cached_param8 #end if
+  score
+#if $cond_source.source9.source9_source=="user" $cond_source.source9.user_param9 #else $cond_source.source9.cached_param9 #end if
+  topdiag
+#if $cond_source.source10.source10_source=="user" $cond_source.source10.user_param10 #else $cond_source.source10.cached_param10 #end if
+  pairgap
+#if $cond_source.source11.source11_source=="user" $cond_source.source11.user_param11 #else $cond_source.source11.cached_param11 #end if
+  pwmatrix
+#if $cond_source.source12.source12_source=="user" $cond_source.source12.user_param12 #else $cond_source.source12.cached_param12 #end if
+  pwdnamatrix
+#if $cond_source.source13.source13_source=="user" $cond_source.source13.user_param13 #else $cond_source.source13.cached_param13 #end if
+  pwgapopen
+#if $cond_source.source14.source14_source=="user" $cond_source.source14.user_param14 #else $cond_source.source14.cached_param14 #end if
+  pwgapext
+#if $cond_source.source15.source15_source=="user" $cond_source.source15.user_param15 #else $cond_source.source15.cached_param15 #end if
+  matrix
+#if $cond_source.source16.source16_source=="user" $cond_source.source16.user_param16 #else $cond_source.source16.cached_param16 #end if
+  dnamatrix
+#if $cond_source.source17.source17_source=="user" $cond_source.source17.user_param17 #else $cond_source.source17.cached_param17 #end if
+  gapopen
+#if $cond_source.source18.source18_source=="user" $cond_source.source18.user_param18 #else $cond_source.source18.cached_param18 #end if
+  noendgaps
+#if $cond_source.source19.source19_source=="user" $cond_source.source19.user_param19 #else $cond_source.source19.cached_param19 #end if
+  gapext
+#if $cond_source.source20.source20_source=="user" $cond_source.source20.user_param20 #else $cond_source.source20.cached_param20 #end if
+  gapext
+#if $cond_source.source21.source21_source=="user" $cond_source.source21.user_param21 #else $cond_source.source21.cached_param21 #end if
+  iteration
+#if $cond_source.source22.source22_source=="user" $cond_source.source22.user_param22 #else $cond_source.source22.cached_param22 #end if
+  numiter
+#if $cond_source.source23.source23_source=="user" $cond_source.source23.user_param23 #else $cond_source.source23.cached_param23 #end if
+#else 
+#end if
+
+  
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+   
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** email type is xsd:string
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_8.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_8.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,431 @@
+
+   Client for operation : run , Web service: wublast.wublast_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services         run
+	"_parameters|_sequence"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_stype"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_program"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_email"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	"_parameters|_database|_string|$|"
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services            run
+	"_parameters|_sequence"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_stype"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_program"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_email"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	"_parameters|_database|_string|$|"
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+	"_parameters|_sensitivity"
+	 #if $cond_source.source5.source5_source=="user":
+	 $cond_source.source5.user_param5
+	 #else:
+	 fileInput
+	 $cond_source.source5.cached_param5
+	 #end if
+	"_parameters|_topcombon"
+	 #if $cond_source.source6.source6_source=="user":
+	 $cond_source.source6.user_param6
+	 #else:
+	 fileInput
+	 $cond_source.source6.cached_param6
+	 #end if
+	"_parameters|_filter"
+	 #if $cond_source.source7.source7_source=="user":
+	 $cond_source.source7.user_param7
+	 #else:
+	 fileInput
+	 $cond_source.source7.cached_param7
+	 #end if
+	"_parameters|_alignments"
+	 #if $cond_source.source8.source8_source=="user":
+	 $cond_source.source8.user_param8
+	 #else:
+	 fileInput
+	 $cond_source.source8.cached_param8
+	 #end if
+	"_parameters|_scores"
+	 #if $cond_source.source9.source9_source=="user":
+	 $cond_source.source9.user_param9
+	 #else:
+	 fileInput
+	 $cond_source.source9.cached_param9
+	 #end if
+	"_parameters|_viewfilter"
+	 #if $cond_source.source10.source10_source=="user":
+	 $cond_source.source10.user_param10
+	 #else:
+	 fileInput
+	 $cond_source.source10.cached_param10
+	 #end if
+	"_parameters|_sort"
+	 #if $cond_source.source11.source11_source=="user":
+	 $cond_source.source11.user_param11
+	 #else:
+	 fileInput
+	 $cond_source.source11.cached_param11
+	 #end if
+	"_parameters|_strand"
+	 #if $cond_source.source12.source12_source=="user":
+	 $cond_source.source12.user_param12
+	 #else:
+	 fileInput
+	 $cond_source.source12.cached_param12
+	 #end if
+	"_parameters|_align"
+	 #if $cond_source.source13.source13_source=="user":
+	 $cond_source.source13.user_param13
+	 #else:
+	 fileInput
+	 $cond_source.source13.cached_param13
+	 #end if
+	"_parameters|_matrix"
+	 #if $cond_source.source14.source14_source=="user":
+	 $cond_source.source14.user_param14
+	 #else:
+	 fileInput
+	 $cond_source.source14.cached_param14
+	 #end if
+	"_title"
+	 #if $cond_source.source15.source15_source=="user":
+	 $cond_source.source15.user_param15
+	 #else:
+	 fileInput
+	 $cond_source.source15.cached_param15
+	 #end if
+	"_parameters|_stats"
+	 #if $cond_source.source16.source16_source=="user":
+	 $cond_source.source16.user_param16
+	 #else:
+	 fileInput
+	 $cond_source.source16.cached_param16
+	 #end if
+	"_parameters|_exp"
+	 #if $cond_source.source17.source17_source=="user":
+	 $cond_source.source17.user_param17
+	 #else:
+	 fileInput
+	 $cond_source.source17.cached_param17
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About sequence: type is String
+
+.. class:: infomark
+
+**TIP:** About stype: type is String
+
+.. class:: infomark
+
+**TIP:** About program: type is String
+
+.. class:: infomark
+
+**TIP:** About email: type is String
+
+.. class:: infomark
+
+**TIP:** About database: type is String
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_86.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_86.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,431 @@
+
+   Client for operation : run , Web service : wublast.wublast_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services         run
+	"_parameters|_sequence"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_stype"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_program"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_email"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	"_parameters|_database|_string|$|"
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services            run
+	"_parameters|_sequence"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_parameters|_stype"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_program"
+	 #if $source2.source2_source=="user":
+	 $source2.user_param2
+	 #else:
+	 fileInput
+	 $source2.cached_param2
+	 #end if
+	"_email"
+	 #if $source3.source3_source=="user":
+	 $source3.user_param3
+	 #else:
+	 fileInput
+	 $source3.cached_param3
+	 #end if
+	"_parameters|_database|_string|$|"
+	 #if $source4.source4_source=="user":
+	 $source4.user_param4
+	 #else:
+	 fileInput
+	 $source4.cached_param4
+	 #end if
+	"_parameters|_sensitivity"
+	 #if $cond_source.source5.source5_source=="user":
+	 $cond_source.source5.user_param5
+	 #else:
+	 fileInput
+	 $cond_source.source5.cached_param5
+	 #end if
+	"_parameters|_topcombon"
+	 #if $cond_source.source6.source6_source=="user":
+	 $cond_source.source6.user_param6
+	 #else:
+	 fileInput
+	 $cond_source.source6.cached_param6
+	 #end if
+	"_parameters|_filter"
+	 #if $cond_source.source7.source7_source=="user":
+	 $cond_source.source7.user_param7
+	 #else:
+	 fileInput
+	 $cond_source.source7.cached_param7
+	 #end if
+	"_parameters|_alignments"
+	 #if $cond_source.source8.source8_source=="user":
+	 $cond_source.source8.user_param8
+	 #else:
+	 fileInput
+	 $cond_source.source8.cached_param8
+	 #end if
+	"_parameters|_scores"
+	 #if $cond_source.source9.source9_source=="user":
+	 $cond_source.source9.user_param9
+	 #else:
+	 fileInput
+	 $cond_source.source9.cached_param9
+	 #end if
+	"_parameters|_viewfilter"
+	 #if $cond_source.source10.source10_source=="user":
+	 $cond_source.source10.user_param10
+	 #else:
+	 fileInput
+	 $cond_source.source10.cached_param10
+	 #end if
+	"_parameters|_sort"
+	 #if $cond_source.source11.source11_source=="user":
+	 $cond_source.source11.user_param11
+	 #else:
+	 fileInput
+	 $cond_source.source11.cached_param11
+	 #end if
+	"_parameters|_strand"
+	 #if $cond_source.source12.source12_source=="user":
+	 $cond_source.source12.user_param12
+	 #else:
+	 fileInput
+	 $cond_source.source12.cached_param12
+	 #end if
+	"_parameters|_align"
+	 #if $cond_source.source13.source13_source=="user":
+	 $cond_source.source13.user_param13
+	 #else:
+	 fileInput
+	 $cond_source.source13.cached_param13
+	 #end if
+	"_parameters|_matrix"
+	 #if $cond_source.source14.source14_source=="user":
+	 $cond_source.source14.user_param14
+	 #else:
+	 fileInput
+	 $cond_source.source14.cached_param14
+	 #end if
+	"_title"
+	 #if $cond_source.source15.source15_source=="user":
+	 $cond_source.source15.user_param15
+	 #else:
+	 fileInput
+	 $cond_source.source15.cached_param15
+	 #end if
+	"_parameters|_stats"
+	 #if $cond_source.source16.source16_source=="user":
+	 $cond_source.source16.user_param16
+	 #else:
+	 fileInput
+	 $cond_source.source16.cached_param16
+	 #end if
+	"_parameters|_exp"
+	 #if $cond_source.source17.source17_source=="user":
+	 $cond_source.source17.user_param17
+	 #else:
+	 fileInput
+	 $cond_source.source17.cached_param17
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About sequence: type is String
+
+.. class:: infomark
+
+**TIP:** About stype: type is String
+
+.. class:: infomark
+
+**TIP:** About program: type is String
+
+.. class:: infomark
+
+**TIP:** About email: type is String
+
+.. class:: infomark
+
+**TIP:** About database: type is String
+  
+
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_9.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_9.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,240 @@
+
+   Client for method: genesbymolecularweight , Web service: http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.wadl 
+  
+  	#client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml
+	organism
+	 #if $source0.source0_source=="user"
+	 $source0.user_param0
+	 #else:
+	 $source0.cached_param0
+	 #end if
+	min_molecular_weight
+	 #if $source1.source1_source=="user"
+	 $source1.user_param1
+	 #else:
+	 $source1.cached_param1
+	 #end if
+	max_molecular_weight
+	 #if $source2.source2_source=="user"
+	 $source2.user_param2
+	 #else:
+	 $source2.cached_param2
+	 #end if
+   	#else:  	$output
+	http://eupathdb.org/webservices/GeneQuestions/GenesByMolecularWeight.xml
+	organism
+	 #if $source0.source0_source=="user"
+	 $source0.user_param0
+	 #else:
+	 $source0.cached_param0
+	 #end if
+	min_molecular_weight
+	 #if $source1.source1_source=="user"
+	 $source1.user_param1
+	 #else:
+	 $source1.cached_param1
+	 #end if
+	max_molecular_weight
+	 #if $source2.source2_source=="user"
+	 $source2.user_param2
+	 #else:
+	 $source2.cached_param2
+	 #end if
+	o-fields
+	 #if $source3.source3_source=="user"
+	 $source3.user_param3
+	 #else:
+	 $source3.cached_param3
+	 #end if
+	o-tables
+	 #if $source4.source4_source=="user"
+	 $source4.user_param4
+	 #else:
+	 $source4.cached_param4
+	 #end if
+   	#end if
+
+  
+
+     
+       
+       
+    
+    
+    
+      
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+       
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+   
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+
+
+   
+     
+  
+
+         
+ 
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+  
+      
+ 
+
+  
+  
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** Organism type is xsd:string
+
+.. class:: infomark
+
+**TIP:** Min Molecular Weight (Daltons) type is xsd:string
+
+.. class:: infomark
+
+**TIP:** Max Molecular Weight (Daltons) type is xsd:string
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_90.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/client_90.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,135 @@
+
+   Client for operation : getResult , Web service : wublast.wublast_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services         getResult
+	"_type"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_jobId"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services            getResult
+	"_type"
+	 #if $source0.source0_source=="user":
+	 $source0.user_param0
+	 #else:
+	 fileInput
+	 $source0.cached_param0
+	 #end if
+	"_jobId"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_parameter|0|_name"
+	 #if $cond_source.source2.source2_source=="user":
+	 $cond_source.source2.user_param2
+	 #else:
+	 fileInput
+	 $cond_source.source2.cached_param2
+	 #end if
+	"_parameters|_parameter|0|_value|_string|$|"
+	 #if $cond_source.source3.source3_source=="user":
+	 $cond_source.source3.user_param3
+	 #else:
+	 fileInput
+	 $cond_source.source3.cached_param3
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+   
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About type: type is String
+
+.. class:: infomark
+
+**TIP:** About jobId: type is String
+  
+
\ No newline at end of file
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/workflowclient.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/workflowclient.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,73 @@
+
+   Client for operation : filetersequences , Web service : filter.filter_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	    $output
+	    $servicetype
+        $url
+        $method
+        clustalw2.clustalw2_services         getResult
+	    "_sequenceid"
+	    #if $source0.source0_source=="user":
+	       $source0.user_param0
+	    #else:
+	       fileInput
+	       $source0.cached_param0
+	    #end if
+   	#else:
+  	    $output
+	    $servicetype
+        $url
+        $method
+        clustalw2.clustalw2_services            getResult
+	    "_sequenceid"
+	    #if $source0.source0_source=="user":
+	        $source0.user_param0
+	    #else:
+	       fileInput
+	       $source0.cached_param0
+	    #end if
+   	#end if
+
+  
+     
+     
+     
+    
+         
+           
+           
+        
+        
+          
+        
+        
+             
+        
+    
+   
+         
+             
+             
+         
+         
+        
+         
+        
+    
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About type: type is String
+
+.. class:: infomark
+
+**TIP:** About jobId: type is String
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/workflowclient_1.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/workflowclients/workflowclient_1.xml~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,110 @@
+
+   Client for operation : getXMLResult , Web service : wublast.wublast_services 
+  
+  	client_1.py
+	#if $cond_source.optional_param_source=="no":
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services         getResult
+	"_jobId"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+   	#else:
+  	$output
+	$servicetype
+      $url
+      $method
+wublast.wublast_services            getResult
+	"_jobId"
+	 #if $source1.source1_source=="user":
+	 $source1.user_param1
+	 #else:
+	 fileInput
+	 $source1.cached_param1
+	 #end if
+	"_parameters|_parameter|0|_name"
+	 #if $cond_source.source2.source2_source=="user":
+	 $cond_source.source2.user_param2
+	 #else:
+	 fileInput
+	 $cond_source.source2.cached_param2
+	 #end if
+	"_parameters|_parameter|0|_value|_string|$|"
+	 #if $cond_source.source3.source3_source=="user":
+	 $cond_source.source3.user_param3
+	 #else:
+	 fileInput
+	 $cond_source.source3.cached_param3
+	 #end if
+   	#end if
+
+  
+     
+     
+     
+    
+     
+       
+       
+    
+    
+      
+ 
+ 
+     
+ 
+     
+   
+  
+  
+  
+     
+     
+     
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+
+
+   
+     
+  
+
+         
+ 
+
+  
+  
+   
+ 
+ 
+
+  
+    
+  
+  
+
+.. class:: infomark
+
+**TIP:** About type: type is String
+
+.. class:: infomark
+
+**TIP:** About jobId: type is String
+  
+
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WsExtension InstallationGuide.pdf
Binary file WebServiceExtensionsV1.1/WsExtension InstallationGuide.pdf has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/WsExtensions DeveloperGuide.pdf
Binary file WebServiceExtensionsV1.1/WsExtensions DeveloperGuide.pdf has changed
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/install.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/install.py	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,406 @@
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+
+__author__ = "Chaitanya Guttula"
+
+
+import os
+import sys
+from shutil import copytree, ignore_patterns
+
+galaxyhome=os.environ.get('GALAXY_HOME')
+#print galaxyhome
+
+#os.mkdir(galaxyhome+'/GAL')
+dirfilelist=os.listdir(galaxyhome+'/tools')
+exist = False
+for dirfile in dirfilelist:
+    if dirfile == 'WebServiceToolWorkflow_REST_SOAP':
+        exist = True
+        break
+
+if exist:
+    print 'WebServiceToolWorkflow_REST_SOAP is already present in '+galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP'
+else:
+    copytree('WebServiceToolWorkflow_REST_SOAP',galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP', ignore=ignore_patterns('*.pyc', 'tmp*'))
+    print 'Copied the folder \'WebServiceToolWorkflow_REST_SOAP\' to '+galaxyhome+'/tools'
+
+f1=open(galaxyhome+'/tool_conf.xml','r')
+f1.seek(0,0)
+f2=open(galaxyhome+'/tool_conf_backup.xml','w')
+f2.seek(0,0)
+
+#copy the first line  into another file f2
+line = f1.readline()
+#f2.write(line)
+
+lineStripped=line.lstrip()
+lineStripped=lineStripped.rstrip()
+
+#Flags for verifying that the tool is not already installed
+tool_present = False
+webservice_present = False
+workflow_present = False
+
+# Check of the tools are already installed or not
+# and sets the flags to true if they are already installed 
+while not lineStripped == '':
+    line = f1.readline()
+    lineStripped = line.lstrip()
+    lineStripped=lineStripped.rstrip()          
+    if(lineStripped.find('')>-1):
+            line = f1.readline()
+    
+    if lineStripped == '':
+        tool_present = True
+    elif lineStripped == '':
+        webservice_present = True
+    elif lineStripped == '':
+        workflow_present = True
+
+
+f1.seek(0,0)
+line = f1.readline()
+f2.write(line)
+
+lineStripped=line.lstrip()
+lineStripped=lineStripped.rstrip()
+
+# copy to the file f2 till 
+while not lineStripped == '':
+    line = f1.readline()
+    f2.write(line)
+    lineStripped = line.lstrip()
+    lineStripped = lineStripped.rstrip()
+
+# Check if the tool is not installed and then add it to the file f2
+if not tool_present:
+    f2.write('  \n')
+    f2.write('    \n')
+    f2.write('    \n')
+    f2.write('    \n')
+    f2.write('  \n')
+    print 'The "Add Web Service Tool" added successfully'
+else:
+    print 'The "Add Web service tool" tool is already present'
+
+
+# Check if the section "Web Service Tools" is not installed and then add it to the file f2
+if not webservice_present:
+    f2.write('  \n')
+    f2.write('\n')
+    f2.write('  \n')
+    print 'The "Web Service Tools" added successfully'
+else:
+    print 'The section "Web Service Tools" is already present'
+
+
+# Check if the Section "Web Service Workflow Tools" is not installed and then add it to the file f2
+if not workflow_present:
+    f2.write('  \n')
+    f2.write('\n')
+    f2.write('  \n')
+    print 'The section "Web Service Workflow Tools" is added successfully'
+else:
+    print 'The section "Web Service Workflow Tools" is already present'
+
+
+#copy rest of tool_conf.xml file to f2
+while not lineStripped == '':
+    line = f1.readline()
+    f2.write(line)
+    lineStripped = line.lstrip()
+    lineStripped=lineStripped.rstrip()          
+#else:
+#    print line
+
+##close f1 and f2
+f1.close()
+f2.close()
+
+##interchange modes of f1 and f2
+f1=open(galaxyhome+'/tool_conf.xml','w')
+f1.seek(0,0)
+f2=open(galaxyhome+'/tool_conf_backup.xml','r')
+f2.seek(0,0)
+
+line = f2.readline()
+f1.write(line)
+
+lineStripped=line.lstrip()
+lineStripped = lineStripped.rstrip()
+
+##write entire f2 into f1 (reverse roles)
+while not lineStripped == '':
+    line = f2.readline()
+    f1.write(line)
+    lineStripped = line.lstrip()
+    lineStripped = lineStripped.rstrip()        
+#else:
+#    print line
+
+f1.close()
+f2.close()
+
+
+# Adding Code to __init__.py in lib/galaxy/tools folder in Galaxy for disabling Web service stand alone tools in Workflows
+f1 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','r')
+f1.seek(0,0)
+
+exist = False
+line = f1.readline()
+linestripped = line.lstrip()
+linestripped = linestripped.rstrip()
+while line != '':
+#    if(linsetripped.find('\'\'\'')>-1):
+#        line = f1.readline()
+#        while(not line.find('\'\'\'')>-1):
+#            line = f1.readline()
+    if(linestripped == 'if self.id.find("WebService")>-1:'):
+        exist = True
+        break
+    line = f1.readline()
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+
+if exist :
+    print 'Workflow code is already present in __init__.py'
+else:
+    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','w')
+    f2.seek(0,0)
+    f1.seek(0,0)
+    line = f1.readline()
+    f2.write(line)
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+    while not (linestripped.find('def check_workflow_compatible(')>-1): 
+        line = f1.readline()
+        linestripped = line.lstrip()
+        linestripped = linestripped.rstrip()
+        f2.write(line)
+    if line.find('(')>-1:
+        while not line.find(')')>-1:
+            line = f1.readline()
+            f2.write(line)
+        
+    line = f1.readline()
+    while line.find('#')>-1:
+        f2.write(line)
+        line = f1.readline()
+        
+    indent=0
+    while (line[indent] == ' '):
+        indent = indent+1
+    
+    space = ''
+    for i in range(0,indent):    
+        space +=' '
+        
+    f2.write(space+'#############\n')    
+    f2.write(space+'#added by Chaitany Guttula, chaitu86@uga.edu - to disable webservice standalone tools in Workflows\n')
+    f2.write(space+'if self.id.find("WebService")>-1:\n')
+    f2.write(space+'    return False\n')
+    f2.write(space+'#############\n')
+
+    f2.write(line)
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+    
+    f1.close()
+    f2.close()
+
+    f1 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','r')
+    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','w')
+
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+    
+    f1.close()
+    f2.close()
+    print 'Workflow disabling Code added to __init__.py'
+    
+
+
+# Adding Code to __init__.py in lib/galaxy/tools folder in Galaxy for invoking the refresh functionality
+f1 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','r')
+f1.seek(0,0)
+
+exist = False
+line = f1.readline()
+linestripped = line.lstrip()
+linestripped = linestripped.rstrip()
+while line != '':
+#    if(linsetripped.find('\'\'\'')>-1):
+#        line = f1.readline()
+#        while(not line.find('\'\'\'')>-1):
+#            line = f1.readline()
+    if(linestripped == 'if self.id == \'WebService_REFRESH_ID\':'):
+        exist = True
+        break
+    line = f1.readline()
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+
+if exist :
+    print 'Refresh code is already present in __init__.py'
+else:
+    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','w')
+    f2.seek(0,0)
+    f1.seek(0,0)
+    line = f1.readline()
+    f2.write(line)
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+    while not (linestripped.find('def execute(')>-1): 
+        line = f1.readline()
+        linestripped = line.lstrip()
+        linestripped = linestripped.rstrip()
+        f2.write(line)
+    if line.find('(')>-1:
+        while not line.find(')')>-1:
+            line = f1.readline()
+            f2.write(line)
+        
+    line = f1.readline()
+    while line.find('#')>-1:
+        f2.write(line)
+        line = f1.readline()
+        
+    indent=0
+    while (line[indent] == ' '):
+        indent = indent+1
+    
+    space = ''
+    for i in range(0,indent):    
+        space +=' '
+        
+    f2.write(space+'#############\n')    
+    f2.write(space+'#add code to verify if user has administrative privileges\n')
+    f2.write(space+'#added by sumedha ganjoo, sganjoo@uga.edu - to refresh toolbox\n')
+    f2.write(space+'if self.id == \'WebService_REFRESH_ID\':\n')
+    f2.write(space+'    self.app.refreshToolBox()\n')
+    f2.write(space+'#############\n')
+
+    f2.write(line)
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+    
+    f1.close()
+    f2.close()
+
+    f1 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','r')
+    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','w')
+
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+    
+    f1.close()
+    f2.close()
+    print 'Refresh Code added to __init__.py'
+    
+    
+# Adding Code to app.py in lib/galaxy folder in Galaxy for invoking the refresh functionality
+f1 = open(galaxyhome+'/lib/galaxy/app.py','r')
+
+f1.seek(0,0)
+
+exist = False
+line = f1.readline()
+linestripped = line.lstrip()
+linestripped = linestripped.rstrip()
+while line != '':
+    if(linestripped == 'def refreshToolBox( self ):'):
+        exist = True
+        break
+    line = f1.readline()
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+
+if exist:
+    print 'Refresh code is already present in app.py'
+else:
+    f2 = open(galaxyhome+'/lib/galaxy/app_backup.py','w')
+    f2.seek(0,0)
+    f1.seek(0,0)
+    line = f1.readline()
+    f2.write(line)
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+    while not (line.find('class UniverseApplication')>-1): 
+        line = f1.readline()
+        linestripped = line.lstrip()
+        linestripped = linestripped.rstrip()
+        f2.write(line)
+    if line.find('(')>-1:
+        while not line.find(')')>-1:
+            line = f1.readline()
+            f2.write(line)
+        
+    line = f1.readline()
+    
+    while line.find('#')>-1:
+        f2.write(line)
+        line = f1.readline()
+    
+    
+    indent=0
+    while (line[indent] == ' '):
+        indent = indent+1
+
+    space = ''
+    for i in range(0,indent):    
+        space +=' '
+    
+    f2.write(space+'#############\n')    
+    f2.write(space+'#added by sumedha ganjoo, sganjoo@uga.edu\n')
+    f2.write(space+'def refreshToolBox( self ):\n')
+    f2.write(space+'    self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self )\n')
+    f2.write(space+'#############\n\n')
+
+    f2.write(line)
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+
+    f1.close()
+    f2.close()
+
+    f1 = open(galaxyhome+'/lib/galaxy/app_backup.py','r')
+    f2 = open(galaxyhome+'/lib/galaxy/app.py','w')
+    
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+
+    f1.close()
+    f2.close()
+    print 'Refresh code is added to app.py'
+    
+    
+    
+print '****Installation of tool is complete. Now reload galaxy to use the installed tool****'    
+    
diff -r 000000000000 -r 049760c677de WebServiceExtensionsV1.1/install.py~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceExtensionsV1.1/install.py~	Tue Jul 05 19:34:18 2011 -0400
@@ -0,0 +1,406 @@
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+
+__author__ = "Chaitanya Guttula"
+
+
+import os
+import sys
+from shutil import copytree, ignore_patterns
+
+galaxyhome=os.environ.get('GALAXY_HOME')
+#print galaxyhome
+
+#os.mkdir(galaxyhome+'/GAL')
+dirfilelist=os.listdir(galaxyhome+'/tools')
+exist = False
+for dirfile in dirfilelist:
+    if dirfile == 'WebServiceToolWorkflow_REST_SOAP':
+        exist = True
+        break
+
+if exist:
+    print 'WebServiceToolWorkflow_REST_SOAP is already present in '+galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP'
+else:
+    copytree('WebServiceToolWorkflow_REST_SOAP',galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP', ignore=ignore_patterns('*.pyc', 'tmp*'))
+    print 'Copied the folder \'WebServiceToolWorkflow_REST_SOAP\' to '+galaxyhome+'/tools'
+
+f1=open(galaxyhome+'/tool_conf.xml','r')
+f1.seek(0,0)
+f2=open(galaxyhome+'/tool_conf_backup.xml','w')
+f2.seek(0,0)
+
+#copy the first line  into another file f2
+line = f1.readline()
+#f2.write(line)
+
+lineStripped=line.lstrip()
+lineStripped=lineStripped.rstrip()
+
+#Flags for verifying that the tool is not already installed
+tool_present = False
+webservice_present = False
+workflow_present = False
+
+# Check of the tools are already installed or not
+# and sets the flags to true if they are already installed 
+while not lineStripped == '':
+    line = f1.readline()
+    lineStripped = line.lstrip()
+    lineStripped=lineStripped.rstrip()          
+    if(lineStripped.find('')>-1):
+            line = f1.readline()
+    
+    if lineStripped == '':
+        tool_present = True
+    elif lineStripped == '':
+        webservice_present = True
+    elif lineStripped == '':
+        workflow_present = True
+
+
+f1.seek(0,0)
+line = f1.readline()
+f2.write(line)
+
+lineStripped=line.lstrip()
+lineStripped=lineStripped.rstrip()
+
+# copy to the file f2 till 
+while not lineStripped == '':
+    line = f1.readline()
+    f2.write(line)
+    lineStripped = line.lstrip()
+    lineStripped = lineStripped.rstrip()
+
+# Check if the tool is not installed and then add it to the file f2
+if not tool_present:
+    f2.write('  \n')
+    f2.write('    \n')
+    f2.write('    \n')
+    f2.write('    \n')
+    f2.write('  \n')
+    print 'The "Add Web Service Tool" added successfully'
+else:
+    print 'The "Add Web service tool" tool is already present'
+
+
+# Check if the section "Web Service Tools" is not installed and then add it to the file f2
+if not webservice_present:
+    f2.write('  \n')
+    f2.write('\n')
+    f2.write('  \n')
+    print 'The "Web Service Tools" added successfully'
+else:
+    print 'The section "Web Service Tools" is already present'
+
+
+# Check if the Section "Web Service Workflow Tools" is not installed and then add it to the file f2
+if not workflow_present:
+    f2.write('  \n')
+    f2.write('\n')
+    f2.write('  \n')
+    print 'The section "Web Service Workflow Tools" is added successfully'
+else:
+    print 'The section "Web Service Workflow Tools" is already present'
+
+
+#copy rest of tool_conf.xml file to f2
+while not lineStripped == '':
+    line = f1.readline()
+    f2.write(line)
+    lineStripped = line.lstrip()
+    lineStripped=lineStripped.rstrip()          
+#else:
+#    print line
+
+##close f1 and f2
+f1.close()
+f2.close()
+
+##interchange modes of f1 and f2
+f1=open(galaxyhome+'/tool_conf.xml','w')
+f1.seek(0,0)
+f2=open(galaxyhome+'/tool_conf_backup.xml','r')
+f2.seek(0,0)
+
+line = f2.readline()
+f1.write(line)
+
+lineStripped=line.lstrip()
+lineStripped = lineStripped.rstrip()
+
+##write entire f2 into f1 (reverse roles)
+while not lineStripped == '':
+    line = f2.readline()
+    f1.write(line)
+    lineStripped = line.lstrip()
+    lineStripped = lineStripped.rstrip()        
+#else:
+#    print line
+
+f1.close()
+f2.close()
+
+
+# Adding Code to __init__.py in lib/galaxy/tools folder in Galaxy for disabling Web service stand alone tools in Workflows
+f1 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','r')
+f1.seek(0,0)
+
+exist = False
+line = f1.readline()
+linestripped = line.lstrip()
+linestripped = linestripped.rstrip()
+while line != '':
+#    if(linsetripped.find('\'\'\'')>-1):
+#        line = f1.readline()
+#        while(not line.find('\'\'\'')>-1):
+#            line = f1.readline()
+    if(linestripped == 'if self.id.find("WebService")>-1:'):
+        exist = True
+        break
+    line = f1.readline()
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+
+if exist :
+    print 'Workflow code is already present in __init__.py'
+else:
+    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','w')
+    f2.seek(0,0)
+    f1.seek(0,0)
+    line = f1.readline()
+    f2.write(line)
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+    while not (linestripped.find('def check_workflow_compatible(')>-1): 
+        line = f1.readline()
+        linestripped = line.lstrip()
+        linestripped = linestripped.rstrip()
+        f2.write(line)
+    if line.find('(')>-1:
+        while not line.find(')')>-1:
+            line = f1.readline()
+            f2.write(line)
+        
+    line = f1.readline()
+    while line.find('#')>-1:
+        f2.write(line)
+        line = f1.readline()
+        
+    indent=0
+    while (line[indent] == ' '):
+        indent = indent+1
+    
+    space = ''
+    for i in range(0,indent):    
+        space +=' '
+        
+    f2.write(space+'#############\n')    
+    f2.write(space+'#added by Chaitany Guttula, chaitu86@uga.edu - to disable webservice standalone tools in Workflows\n')
+    f2.write(space+'if self.id.find("WebService")>-1:\n')
+    f2.write(space+'    return False\n')
+    f2.write(space+'#############\n')
+
+    f2.write(line)
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+    
+    f1.close()
+    f2.close()
+
+    f1 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','r')
+    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','w')
+
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+    
+    f1.close()
+    f2.close()
+    print 'Workflow disabling Code added to __init__.py'
+    
+
+
+# Adding Code to __init__.py in lib/galaxy/tools folder in Galaxy for invoking the refresh functionality
+f1 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','r')
+f1.seek(0,0)
+
+exist = False
+line = f1.readline()
+linestripped = line.lstrip()
+linestripped = linestripped.rstrip()
+while line != '':
+#    if(linsetripped.find('\'\'\'')>-1):
+#        line = f1.readline()
+#        while(not line.find('\'\'\'')>-1):
+#            line = f1.readline()
+    if(linestripped == 'if self.id == \'WebService_REFRESH_ID\':'):
+        exist = True
+        break
+    line = f1.readline()
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+
+if exist :
+    print 'Refresh code is already present in __init__.py'
+else:
+    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','w')
+    f2.seek(0,0)
+    f1.seek(0,0)
+    line = f1.readline()
+    f2.write(line)
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+    while not (linestripped.find('def execute(')>-1): 
+        line = f1.readline()
+        linestripped = line.lstrip()
+        linestripped = linestripped.rstrip()
+        f2.write(line)
+    if line.find('(')>-1:
+        while not line.find(')')>-1:
+            line = f1.readline()
+            f2.write(line)
+        
+    line = f1.readline()
+    while line.find('#')>-1:
+        f2.write(line)
+        line = f1.readline()
+        
+    indent=0
+    while (line[indent] == ' '):
+        indent = indent+1
+    
+    space = ''
+    for i in range(0,indent):    
+        space +=' '
+        
+    f2.write(space+'#############\n')    
+    f2.write(space+'#add code to verify if user has administrative privileges\n')
+    f2.write(space+'#added by sumedha ganjoo, sganjoo@uga.edu - to refresh toolbox\n')
+    f2.write(space+'if self.id == \'WebService_REFRESH_ID\':\n')
+    f2.write(space+'    self.app.refreshToolBox()\n')
+    f2.write(space+'#############\n')
+
+    f2.write(line)
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+    
+    f1.close()
+    f2.close()
+
+    f1 = open(galaxyhome+'/lib/galaxy/tools/__init__backup.py','r')
+    f2 = open(galaxyhome+'/lib/galaxy/tools/__init__.py','w')
+
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+    
+    f1.close()
+    f2.close()
+    print 'Refresh Code added to __init__.py'
+    
+    
+# Adding Code to app.py in lib/galaxy folder in Galaxy for invoking the refresh functionality
+f1 = open(galaxyhome+'/lib/galaxy/app.py','r')
+
+f1.seek(0,0)
+
+exist = False
+line = f1.readline()
+linestripped = line.lstrip()
+linestripped = linestripped.rstrip()
+while line != '':
+    if(linestripped == 'def refreshToolBox( self ):'):
+        exist = True
+        break
+    line = f1.readline()
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+
+if exist:
+    print 'Refresh code is already present in app.py'
+else:
+    f2 = open(galaxyhome+'/lib/galaxy/app_backup.py','w')
+    f2.seek(0,0)
+    f1.seek(0,0)
+    line = f1.readline()
+    f2.write(line)
+    linestripped = line.lstrip()
+    linestripped = linestripped.rstrip()
+    while not (line.find('class UniverseApplication')>-1): 
+        line = f1.readline()
+        linestripped = line.lstrip()
+        linestripped = linestripped.rstrip()
+        f2.write(line)
+    if line.find('(')>-1:
+        while not line.find(')')>-1:
+            line = f1.readline()
+            f2.write(line)
+        
+    line = f1.readline()
+    
+    while line.find('#')>-1:
+        f2.write(line)
+        line = f1.readline()
+    
+    
+    indent=0
+    while (line[indent] == ' '):
+        indent = indent+1
+
+    space = ''
+    for i in range(0,indent):    
+        space +=' '
+    
+    f2.write(space+'#############\n')    
+    f2.write(space+'#added by sumedha ganjoo, sganjoo@uga.edu\n')
+    f2.write(space+'def refreshToolBox( self ):\n')
+    f2.write(space+'    self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self )\n')
+    f2.write(space+'#############\n\n')
+
+    f2.write(line)
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+
+    f1.close()
+    f2.close()
+
+    f1 = open(galaxyhome+'/lib/galaxy/app_backup.py','r')
+    f2 = open(galaxyhome+'/lib/galaxy/app.py','w')
+    
+    line = f1.readline()
+    f2.write(line)
+
+    while line != '':
+        line = f1.readline()
+        f2.write(line)
+
+    f1.close()
+    f2.close()
+    print 'Refresh code is added to app.py'
+    
+    
+    
+print '****Installation of tool is complete. Now reload galaxy to use the installed tool****'    
+