Mercurial > repos > uga-galaxy-group > webservice_toolsuite_v1_1
diff WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/generateClient1.py~ @ 0:049760c677de default tip
Galaxy WSExtensions added successfully
| author | uga-galaxy-group |
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| date | Tue, 05 Jul 2011 19:34:18 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/generateClient1.py~ Tue Jul 05 19:34:18 2011 -0400 @@ -0,0 +1,919 @@ +''' +@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_conf1 import * + from clientGenerator.msHandler import * + from clientGenerator.creatorEngineComplex import * + from clientGenerator.wsdl2path import * + from clientGenerator.paramConverter import * + +__author__="" + +#generates client for a web service to be used as standalone +class ClientGenerator1(object): + + def __init__(self,webservice,operation,outputfile,servicetype):#,url): + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + self.webservice = webservice + self.operation = operation + self.inputs = outputfile + self.outputfile = outputfile + #self.url = url + + self.servicetype = servicetype + self.galaxyhome=os.environ.get('GALAXY_HOME') + self.clientfile = '' + 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 + + + + ''' Replaces space (' ') with '**' in the given string ''' + def formatString(self,string): + l = string.split(' ') + return '**'.join(l) + + 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<len(plist)-3): + if(k==0): + iparam = iparam+(p) + else: + iparam = iparam+'|'+p + k=k+1 + paramelement = test.getParameter(self.msinstance(),iparam) + else: + paramelement = test.getParameter(self.msinstance(),param) + self.paramelement = paramelement + if (param.find('|')>-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 fie, any change in the description + 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 != '<section name="Select Web Service Tool" id="WebServices">': + line = f.readline() + linestripped = line.lstrip() + linestripped = linestripped.rstrip() + + line = f.readline() + linestripped = line.lstrip() + linestripped = linestripped.rstrip() + + while linestripped != '</section>': + 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('<description>') >-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('<count> \n') + clientCountFile.write(str(clientCount)+'\n') + clientCountFile.write('</count> \n') + clientCountFile.close() + + clientName = 'WebServiceclient_'+ str(clientCount) + + clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/'+clientName+'.xml','w') + clientXml.seek(0,0) + + clientXml.write('<tool id="' + clientName+'" name="'+foldername+'.' + self.operation +'">\n') + clientXml.write(' <description> Client for operation : '+self.operation+' , Web service : '+webservice+' </description>\n') + + #Only Required parameters + clientXml.write(' <command interpreter="python">\n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output $servicetype ' +webservice+' '+self.operation) + + #clientXml.write(' <command interpreter="python">\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</command>\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('</command>\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(' <inputs>\n') + clientXml.write(' <param name="servicetype" type="hidden" value="SOAP" />\n') + + + j=0 + for param in inputl: + if self.isRequired(param): + pName = getattr(self.paramelement,'pname') + clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ') + clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n') + j=j+1 + + clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Show Optional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n') + clientXml.write('<when value="no"> \n </when>') + clientXml.write('<when value="yes"> \n') + + for param in inputl: + if not self.isRequired(param): + pName = getattr(self.paramelement,'pname') + clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ') + clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n') + j=j+1 + + + clientXml.write('</when>\n</conditional>') + +# 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('<param format="text" size = "150" name = "param'+str(j)+'" ') + # clientXml.write('type="text" label="'+pName+'" help="see tip below" />\n') + # j=j+1 + + clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n') + + clientXml.write(' <help>\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(' </help>\n</tool>') + +# clientXml.write(' <help>\n') + + # j=0 + # for param in params: + # clientXml.write('\n.. class:: infomark\n\n**TIP:** '+ param +' type is ' + paramTypes[j] +'\n') + + # clientXml.write(' </help>\n</tool>') + # clientXml.write('</tool>') + 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('<count> \n') + clientCountFile.write(str(clientCount)+'\n') + clientCountFile.write('</count> \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('<tool id="' + clientName+'1" name="'+wadlname+'.' + methodname[-1] +' ">\n') + clientXml.write(' <description> Client for method : '+self.operation+' , Web service : '+self.webservice+' </description>\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(' <command interpreter="python">\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</command>\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(' <inputs>\n') + clientXml.write(' <param name="servicetype" type="hidden" value="REST" />') + + #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('<param format="text" size = "150" name = "param'+str(j)+'" ') + if not param.getDefault1() == None: + clientXml.write('value="'+param.getDefault1()+'" ') + clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n') + j=j+1 + else: + clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' ) + for option in param.getOptions(): + clientXml.write(' <option value="'+self.formatString(option.getName())+'" ') + if option.getName() == param.getDefault1(): + clientXml.write('selected="true"') + clientXml.write('>'+option.getName()+'</option>\n ') + clientXml.write(' </param> \n') + j=j+1 + + #create a conditional param for each optional parameter described in the WADL. + clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Show Optional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n') + clientXml.write('<when value="no"> \n </when>') + clientXml.write('<when value="yes"> \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('<param format="text" size = "150" name = "param'+str(j)+'" ') + if not param.getDefault1() == None: + clientXml.write('value="'+param.getDefault1()+'" ') + clientXml.write('type="text" label="Enter '+pName+'" help="see tip below" />\n') + j=j+1 + else: + clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+pName+'" help="see tip below">\n' ) + for option in param.getOptions(): + clientXml.write(' <option value="'+self.formatString(option.getName())+'" ') + if option.getName() == param.getDefault1(): + clientXml.write('selected="true"') + clientXml.write('>'+option.getName()+'</option>\n ') + clientXml.write(' </param> \n') + j=j+1 + + + clientXml.write('</when>\n</conditional>') + clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n') + + #write information about each parameter in the help section + clientXml.write(' <help>\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(' </help>\n</tool>') + + + #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('<count> \n') + clientCountFile.write(str(clientCount)+'\n') + clientCountFile.write('</count> \n') + + clientName = 'WebServiceclient_'+ str(clientCount) + + clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/'+clientName+'.xml','w') + clientXml.seek(0,0) + + clientXml.write('<tool id="' + clientName+'1" name="' + webserviceId +'">\n') + clientXml.write(' <description> Client for method: '+webserviceId+' , Web service: '+self.webservice+' </description>\n') + + + clientXml.write(' <command interpreter="python">\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 </command>\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(' <inputs>\n') + cleintXml.write(' <param name="servicetype" type="hidden" value="REST"/>') + + 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('<param format="text" size = "150" name = "param'+str(j)+'" ') + if not param.getDefault1() == None: + clientXml.write('value="'+param.getDefault1()+'" ') + clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n') + j=j+1 + else: + clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' ) + for option in param.getOptionvalue(): + clientXml.write(' <option value="'+self.formatString(option)+'" ') + if option == param.getDefault1(): + clientXml.write('selected="true"') + clientXml.write('>'+option+'</option>\n ') + clientXml.write(' </param> \n') + j=j+1 + + + clientXml.write('\n <conditional name="cond_source"> \n <param name="optional_param_source" type="select" label="Display Optional Parameters">\n <option value="no" selected="true">no</option> \n <option value="yes">yes</option> \n </param>\n') + clientXml.write('<when value="no"> \n </when>') + clientXml.write('<when value="yes"> \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('<param format="text" size = "150" name = "param'+str(j)+'" ') + if not param.getDefault1() == None: + clientXml.write('value="'+param.getDefault1()+'" ') + clientXml.write('type="text" label="Enter '+param.getName()+'" help="see tip below" />\n') + j=j+1 + else: + clientXml.write('<param name="param'+str(j)+'" type="select" label="Select '+param.getName()+'" help="see tip below">\n' ) + for option in param.getOptionvalue(): + clientXml.write(' <option value="'+self.formatString(option)+'" ') + if option == param.getDefault1(): + clientXml.write('selected="true"') + clientXml.write('>'+option+'</option>\n ') + clientXml.write(' </param> \n') + j=j+1 + + clientXml.write('</when>\n</conditional>\n') + + clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n') + + clientXml.write(' <help>\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(' </help>\n</tool>') + 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('<count> \n') + clientCountFile.write(str(clientCount)+'\n') + clientCountFile.write('</count> \n') + + + + + clientName = 'WebServiceclient_'+ str(clientCount) + + clientXml=open(galaxyhome+'/tools/WebServiceTool/clients/'+clientName+'.xml','w') + clientXml.seek(0,0) + + clientXml.write('<tool id="' + clientName+'" name="' + webserviceId +'">\n') + clientXml.write(' <description> Client for method: '+webserviceId+' , Web service: '+self.webservice+' </description>\n') + + + clientXml.write(' <command interpreter="python">\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('</command>\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(' <inputs>\n') + cleintXml.write(' <param name="servicetype" type="hidden" value="REST"/>') + + j=0 + for param in params: + clientXml.write('<param format="text" size = "150" name = "param'+str(j)+'" ') + clientXml.write('type="text" label="'+param+'" help="see tip below" />\n') + j=j+1 + + + + clientXml.write('</inputs>\n <outputs>\n <data format="tabular" name="output" />\n </outputs>\n') + + clientXml.write(' <help>\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(' </help>\n</tool>') + 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