--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/WebServiceToolWorkflow/generateClient1.py	Tue Jun 07 18:00:50 2011 -0400
@@ -0,0 +1,549 @@
+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 *
+    
+class ClientGenerator1(object):
+
+    #instantiate a client for one time invocation of the selected method of a Web service
+    def __init__(self,url,methodName,resourceName,fileName):
+        self.methodName = methodName
+        self.resourceName=resourceName
+        self.Ofile = fileName
+        #replace '__tilda__' with '~'        
+        if(url.find('__tilda__')>-1):
+            ulist = url.split('__tilda__')
+	    url = '~'.join(ulist)
+        self.url = url  
+
+    #replace '**' with ' '        
+    def formatString(self,string):
+        l = string.split(' ')
+        return '**'.join(l)
+
+    #generates a xml describing a client capable of invoking a Web service described 
+    #using a WADL document. Places this xml tool under ./clients/        
+    def wadlClient(self):
+        ##parse wadl 
+        #javahome = os.environ.get('JAVA_HOME')
+        #galaxyhome=os.environ.get('GALAXY_HOME')
+        #classpath= galaxyhome + '/tools/WebServiceToolWorkflow/ParserForWADL/bin'
+        #jarpath = galaxyhome + '/tools/WebServiceToolWorkflow/ParserForWADL/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')
+        urlToPass=java.net.URL(self.url)
+        wadlUrl = self.url
+    
+        webserviceId = self.methodName
+        resUrl = self.resourceName
+    
+        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.Ofile,'w')
+        f.write(wadlUrl)
+        f.write('\n'+ resUrl)
+        f.write('\n'+webserviceId)
+        
+
+        #get parameters for the selected method of the Web service
+        i=0
+        for method in methods:
+            f.write('in for loop')
+            x = str(method.getId())
+            y = str(urls.get(i))
+            if x == webserviceId :
+                f.write('method matched')
+                if y == resUrl : 
+                    f.write('res matched')
+                    params = method.getRequest().getParams()
+                    break
+            i=i+1    
+     
+        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/clients/ClientCount.xml','r')
+	clientCountFile.readline()
+        clientCountStr = clientCountFile.read(1)
+        clientCount=string.atoi(clientCountStr)
+        clientCount=clientCount+1
+        clientCountFile.close()
+        
+        clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','w')
+
+	clientCountFile.write('<count> \n')
+	clientCountFile.write(str(clientCount))
+	clientCountFile.write('</count> \n')
+	
+        #include the count in the tool's name and id to uniquely identify it.         
+        clientName = 'client_'+ str(clientCount)
+
+        #create a new xml file under ./clients/        
+        clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/'+clientName+'.xml','w')
+        clientXml.seek(0,0)
+
+        #write the tool id, name and description        
+        clientXml.write('<tool id="' + clientName+'1" name="' + self.methodName +'      ">\n')
+        clientXml.write('  <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </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 ' +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 ' +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
+        clientXml.write('  <inputs>\n') 
+        
+        #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 Additional 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/WebServiceTool/lib/SAWADLParser/bin'
+        jarpath = galaxyhome + '/tools/WebServiceTool/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.url
+    
+        webserviceId = self.methodName
+        resUrl = self.resourceName
+    
+        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.Ofile,'w')
+        f.write(sawadlUrl)
+        f.write('\n'+ resUrl)
+        f.write('\n'+webserviceId)
+        
+
+        i=0
+        for method in methods:
+            x = str(method.getName())
+            y = str(urls.get(i))
+            if x == webserviceId :
+                f.write('method matched')
+                if y == resUrl : 
+                    f.write('res matched')
+                    params = method.getRequest().getParamList()
+                    break
+            i=i+1    
+        
+
+        
+        
+        ##generate client's xml
+        galaxyhome=os.environ.get('GALAXY_HOME')
+        
+        clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','r')
+	clientCountFile.readline()
+        clientCountStr = clientCountFile.read(1)
+        clientCount=string.atoi(clientCountStr)
+        clientCount=clientCount+1
+        clientCountFile.close()
+        
+        clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/ClientCount.xml','w')
+	clientCountFile.write('<count> \n')
+	clientCountFile.write(str(clientCount))
+	clientCountFile.write('</count> \n')
+	
+        clientName = 'client_'+ str(clientCount)
+        
+        clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/clients/'+clientName+'.xml','w')
+        clientXml.seek(0,0)
+        
+        clientXml.write('<tool id="' + clientName+'1" name="' + self.methodName +'">\n')
+        clientXml.write('  <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')
+
+  
+        clientXml.write('  <command interpreter="python">\n  #if $cond_source.optional_param_source=="no" #client_1.py'+' $output ' +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 ' +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')
+        
+        ##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') 
+        
+        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 Additional 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 wsdlClient(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('<count> \n')
+	clientCountFile.write(str(clientCount))
+	clientCountFile.write('</count> \n')
+	
+        
+        
+        
+        clientName = 'client_'+ str(clientCount)
+        
+        clientXml=open(galaxyhome+'/tools/WebServiceTool/clients/'+clientName+'.xml','w')
+        clientXml.seek(0,0)
+        
+        clientXml.write('<tool id="' + clientName+'" name="' + self.methodName +'">\n')
+        clientXml.write('  <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n')
+
+  
+        clientXml.write('  <command interpreter="python">\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('</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') 
+        
+        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