Mercurial > repos > ganjoo > webservice_toolsuite
diff WebServiceToolWorkflow/generateClient.py~ @ 0:d5cd409b8a18 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | ganjoo |
|---|---|
| date | Tue, 07 Jun 2011 18:00:50 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/WebServiceToolWorkflow/generateClient.py~ Tue Jun 07 18:00:50 2011 -0400 @@ -0,0 +1,551 @@ +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 * + +class ClientGenerator(object): + + #instantiate a client for invocation of the selected method of a Web service in workflows + 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 ./workflowclients/ + 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 = [] + + #invoke the WADL parser packaged with this tool. + 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('\n in methods') + x = str(method.getId()) + y = str(urls.get(i)) + if x == webserviceId : + f.write('\n method matched') + f.write('\n y is' + y + ', resUrl is '+resUrl) + if y == resUrl : + f.write('res matched') + params = method.getRequest().getParams() + break + i=i+1 + + + + galaxyhome=os.environ.get('GALAXY_HOME') + + #./workflowclients/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/workflowclients/ClientCount.xml','r') + clientCountFile.readline() + clientCountStr = clientCountFile.read(1) + clientCount=string.atoi(clientCountStr) + clientCount=clientCount+1 + clientCountFile.close() + + clientCountFile=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/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 ./workflowclients/ + clientXml=open(galaxyhome+'/tools/WebServiceToolWorkflow/workflowclients/'+clientName+'.xml','w') + clientXml.seek(0,0) + + #write the tool id, name and description + clientXml.write('<tool id="' + clientName+'" name="' + self.methodName +' ">\n') + clientXml.write(' <description> Client for method: '+self.methodName+' , Web service: '+self.url+' </description>\n') + + #the workflow tool/client for a REST Web service invokes ./workflowclients/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 client_1.py\n'+' #if $cond_source.optional_param_source=="no":\n $output\n ' +resUrl+'\n') + + + j=0 + for param in params: + if param.isRequired(): + clientXml.write(' '+self.formatString(param.getName())+'\n #if $source'+str(j)+'.source'+str(j)+'_source=="user":\n $source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $source' + str(j) + '.cached_param' + str(j)+'\n #end if\n') + j=j+1 + + clientXml.write(' #else:\n $output\n ' +resUrl+'\n') + j=0 + for param in params: + if param.isRequired(): + clientXml.write(' '+self.formatString(param.getName())+'\n #if $source'+str(j)+'.source'+str(j)+'_source=="user":\n $source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $source' + str(j) + '.cached_param' + str(j)+'\n #end if\n') + j=j+1 + + for param in params: + if not param.isRequired(): + clientXml.write(' '+self.formatString(param.getName())+'\n #if $cond_source.source'+str(j)+'.source'+str(j)+'_source=="user":\n $cond_source.source'+str(j)+'.user_param'+str(j)+'\n #else:\n fileInput\n $cond_source.source' + str(j) + '.cached_param' + str(j)+'\n #end if\n') + j=j+1 + + clientXml.write(' #end if\n') + clientXml.write('</command>\n') + + #start writing inputs + clientXml.write(' <inputs>\n') + + #create a param for each required parameter described in the WADL. Check if defaults are specified. Create param such that + #it can either be given a value manually or the value can be taken from a previous step. + 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() + + clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+pName+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n') + if param.getOptions().size()==0: + clientXml.write(' <param format="text" size = "150" name = "user_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') + else: + clientXml.write(' <param name="user_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') + clientXml.write(' </when>\n') + clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + pName + '"/> \n </when></conditional>') + j=j+1 + + #create a conditional param for each optional parameter described in the WADL. Again the param can be given a value manually or the value can be taken from + #a previous step. + clientXml.write(' <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 <when value="no"> \n </when>\n <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() + + clientXml.write('\n<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+pName+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n</param>\n <when value="user">') + if param.getOptions().size()==0: + clientXml.write('<param format="text" size = "150" name = "user_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') + else: + clientXml.write('<param name="user_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') + clientXml.write(' </when>\n') + clientXml.write('<when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + pName + '"/> \n </when></conditional>\n') + j=j+1 + + + + clientXml.write(' </when>\n </conditional>\n</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 Workflow Tools' section. + editor = editToolConfig() + editor.addTool(clientName) + + + 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/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/WebServiceToolWorkflow/workflowclients/'+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: + if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE': + clientXml.write(' '+self.formatString(param.getName())+'\n#if $source'+str(j)+'.source'+str(j)+'_source=="user" $source'+str(j)+'.user_param'+str(j)+' #else $source' + str(j) + '.cached_param' + str(j)+' #end if\n') + j=j+1 + clientXml.write('#if $cond_source.optional_param_source=="yes"') + + 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())+'\n#if $cond_source.source'+str(j)+'.source'+str(j)+'_source=="user" $cond_source.source'+str(j)+'.user_param'+str(j)+' #else $cond_source.source' + str(j) + '.cached_param' + str(j)+' #end if\n') + j=j+1 + + clientXml.write('#else \n#end if\n') + 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: + if param.getRequired()=='true' or param.getRequired()=='True' or param.getRequired()=='TRUE': + clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+param.getName()+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n') + if param.getOptionvalue().size()==0: + clientXml.write(' <param format="text" size = "150" name = "user_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="user_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') + clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + param.getName() + '"/> \n </when></conditional>') + + clientXml.write(' <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 <when value="no"> \n </when>\n <when value="yes"> \n') + + for param in params: + if not param.getRequired()=='true' and not param.getRequired()=='True' and not param.getRequired()=='TRUE': + clientXml.write('<conditional name="source'+str(j)+'">\n <param name="source' + str(j)+'_source" type="select" label="'+param.getName()+' Source"> \n <option value="cached" selected="true">Param value will be taken from previous step</option> \n <option value="user">User will enter the param value</option> \n </param>\n <when value="user">\n') + if param.getOptionvalue().size()==0: + clientXml.write(' <param format="text" size = "150" name = "user_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="user_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') + clientXml.write(' <when value="cached">\n <param name = "cached_param'+ str(j)+'" type="data" label="Choose the step from which to get the parameter ' + param.getName() + '"/> \n </when></conditional>') + + 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 = editToolConfig() + 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') + + 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