view WebServiceExtensionsV1.1/WebServiceToolWorkflow_REST_SOAP/generateClient1_mc.py~ @ 0:049760c677de default tip

Galaxy WSExtensions added successfully

#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<len(plist)-3):
                        if(k==0):
                            iparam = iparam+(p)
                        else:
                            iparam = iparam+'|'+p
                        k=k+1
                paramelement = test.getParameter(self.msinstance(),iparam)
                #if not getattr(root,'nillable') or (getattr(root,'nillable') and not getattr(paramelement,'nillable')):
                #    required = True
            else:
                paramelement = test.getParameter(self.msinstance(),param)
            if not getattr(root,'nillable') or (getattr(root,'nillable') and not getattr(paramelement,'nillable')):
                required = True
        else:
            paramelement = test.getParameter(self.msinstance(),param)
            if getattr(paramelement,'nillable')==False:
                required = True
        return required 
            
    def wsdlClient(self):
        ##parse wsdl 
        '''javahome = os.environ.get('JAVA_HOME')
        galaxyhome=os.environ.get('GALAXY_HOME')
        classpath= galaxyhome + '/tools/SOAPclient/SimpleWSDLParser/build/classes'
        jarpath = galaxyhome + '/tools/SOAPclient/SimpleWSDLParser/dist/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 == 'i386' :
            print 'b'
            startJVM("/System/Library/Frameworks/JavaVM.framework/JavaVM","-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.wsdl')
        urlToPass=java.net.URL(self.url)
        wadlUrl = self.url
    
        webserviceId = self.methodName
        resUrl = self.resourceName
    
        urls = []
        methods = []
        params = []

        WADLParserDriver=pkg.WADLParserDriver
        wPD=WADLParserDriver()
        wPD.parse(urlToPass)
        urls = wPD.getUrl()
        methods = wPD.getCompleteMethodList()
       ''' 

        
        
        ##generate client's xml
        galaxyhome=os.environ.get('GALAXY_HOME')
        
        clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/ClientCount.xml','r')
	clientCountFile.readline()
        clientCountStr = clientCountFile.read(1)
        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 = 'client_'+ str(clientCount)
        
        clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow_REST_SOAP/clients/'+clientName+'.xml','w')
        clientXml.seek(0,0)
        
        clientXml.write('<tool id="' + clientName+'" name="' + self.operation +'">\n')
        clientXml.write('  <description> Client for operation : '+self.operation+' , Web service: '+self.webservice+' </description>\n')

        clientXml.write('  <command interpreter="python">\n #if $cond_source.optional_param_source=="no" #client_1.py'+' $output ' +self.webservice+'  '+self.operation)
        
        #clientXml.write('  <command interpreter="python">\n  client_1.py \n' +'  $output \n  ' +self.webservice+' \n  '+self.operation+'\n')
        ##write such that the parameters passed to client1.py(change name to clientName.py) are dependent on a for loop
        test = MessageHandler()
        j=0
        for param in self.inputs:
            required = False
            if param.find('|')>-1 :
                plist = param.split('|')
                root = test.getParameter(self.msinstance(),plist[0])  # Added
                if (param.find('|$|')>-1):
                    print 'plist-------->',plist
                    k = 0
                    iparam = ''
                    for p in plist:
                        if(k<len(plist)-3):
                            if(k==0):
                                iparam = iparam+(p)
                            else:
                                iparam = iparam+'|'+p
                            k=k+1
                    paramelement = test.getParameter(self.msinstance(),iparam)
                    #if (getattr(root,'nillable') and not getattr(paramelement,'nillable')):
                    #    required = True
                else:
                    paramelement = test.getParameter(self.msinstance(),param)
                if getattr(root,'nillable'):
                    required = False
                else:
                    #if (not getattr(root,'nillable')) or (getattr(root,'nillable') and not getattr(paramelement,'nillable')):
                    if (not getattr(paramelement,'nillable')): 
                        required = True
                    else:
                        required = False
                    
            else:
                paramelement = test.getParameter(self.msinstance(),param)
                if getattr(paramelement,'nillable')==False:
                    required = True
            if required:
                clientXml.write(' "'+param+'"')
                clientXml.write(' $param' + str(j))            
                j=j+1
        clientXml.write(' #else #client_1.py'+' $output ' +self.webservice+'    '+self.operation+'\n')
        j=0
        for param in self.inputs:
            required = False
            if param.find('|')>-1 :
                plist = param.split('|')
                root = test.getParameter(self.msinstance(),plist[0])
                if (param.find('|$|')>-1):
                    plist = param.split('|')
                    print 'plist-------->',plist
                    k = 0
                    iparam = ''
                    for p in plist:
                        if(k<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)
                if getattr(root,'nillable'):
                    required = False
                else:    
                    #if (getattr(root,'nillable') and not getattr(paramelement,'nillable')):
                    if (not getattr(paramelement,'nillable')): 
                        required = True
                    else:
                        required = False
            else:
                paramelement = test.getParameter(self.msinstance(),param)
                if getattr(paramelement,'nillable')==False:
                    required = True
            if required:
                clientXml.write(' "'+param+'"')
                clientXml.write(' $param' + str(j))            
                j=j+1
                
        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<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)
                if getattr(root,'nillable'):
                    required = False
                else:
                    #if (getattr(root,'nillable') and not getattr(paramelement,'nillable')):
                    if (not getattr(paramelement,'nillable')): 
                        required = True
                    else:
                        required = False
            else:
                paramelement = test.getParameter(self.msinstance(),param)
                if(not getattr(paramelement,'nillable')):
                    required = True
            if not required:#getattr(paramelement,'nillable')==True:
                clientXml.write(' "'+param+'"')
                clientXml.write(' $cond_source.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')
        
        ##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 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<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)
                if getattr(root,'nillable'):
                    required = False
                else:
                #if (getattr(root,'nillable') and not getattr(paramelement,'nillable')):
                    if (not getattr(paramelement,'nillable')): 
                        required = True
                    else:
                        required = False
            else:
                paramelement = test.getParameter(self.msinstance(),param)
                if getattr(paramelement,'nillable')==False:
                    required = True

            #if (param.find('|$|')>-1):
            #    plist = param.split('|')
            #    print 'plist-------->',plist
            #    k = 0
            #    param = ''
            #    for p in plist:
            #        if(k<len(plist)-3):
            #            if(k==0):
            #                param = param+(p)
            #            else:
            #                param = param+'|'+p
            #            k=k+1
            #paramelement = test.getParameter(self.msinstance(),param)
            if required:#getattr(paramelement,'nillable')==False:
                pName = getattr(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 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 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<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)
                if getattr(root,'nillable'):
                    required = False
                else:
                #if (getattr(root,'nillable') and not getattr(paramelement,'nillable')):
                    if (not getattr(paramelement,'nillable')): 
                        required = True
                    else:
                        required = False
            else:
                paramelement = test.getParameter(self.msinstance(),param)
                if getattr(paramelement,'nillable')==False:
                    required = True

        #    if (param.find('|$|')>-1):
        #        plist = param.split('|')
        #        print 'plist-------->',plist
        #        k = 0
        #        param = ''
        #        for p in plist:
        #            if(k<len(plist)-3):
        #                if(k==0):
        #                    param = param+(p)
        #               else:
        #                    param = param+'|'+p
        #                k=k+1
        #    paramelement = test.getParameter(self.msinstance(),param)
            if not required:#getattr(paramelement,'nillable'):
                pName = getattr(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 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<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)
                if getattr(root,'nillable'):
                    required = False
                else:
                #if (getattr(root,'nillable') and not getattr(paramelement,'nillable')):
                    if (not getattr(paramelement,'nillable')): 
                        required = True
                    else:
                        required = False
            else:
                paramelement = test.getParameter(self.msinstance(),param)
                if getattr(paramelement,'nillable')==False:
                    required = True

        #    if (param.find('|$|')>-1):
        #        plist = param.split('|')
        #        print 'plist-------->',plist
        #        k = 0
        #        param = ''
        #        for p in plist:
        #            if(k<len(plist)-3):
        #                if(k==0):
        #                    param = param+(p)
        #                else:
        #                    param = param+'|'+p
        #                k=k+1
        #    paramelement = test.getParameter(self.msinstance(),param)
            if required:#getattr(paramelement,'nillable')==False:
                if isinstance(paramelement,ZSI.TC.String):
                    paramtype = 'String'
                elif isinstance(paramelement,ZSI.TCnumbers.FPfloat):
                    paramtype = 'Floating point'
                elif isinstance(paramelement,ZSI.TC.Boolean):
                    paramtype = 'Boolean'
                elif isinstance(paramelement,ZSI.TCnumbers.Iint):
                    paramtype = 'Integer'
                clientXml.write('\n.. class:: infomark\n\n**TIP:** About '+ getattr(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 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('<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 = editToolConfig1()
        editor.addTool(clientName)
        
        ##later add help feature