Example #1
0
    def __init__(self, service=None, **kw):
        apply( NetworkNode.__init__, (self,), kw )
        self.inNodeWidgetsVisibleByDefault = True
        from mglutil.web.services.AppService_client import AppServiceLocator, launchJobRequest, \
getOutputsRequest, queryStatusRequest
        from mglutil.web.services.AppService_types import ns0
        self.appLocator = AppServiceLocator()
        self.req = launchJobRequest()        
        self.inputFile = ns0.InputFileType_Def('inputFile')   

        self.widgetDescr['outputURL'] = {
            'class':'NECheckButton', 'master':'ParamPanel',
            'labelCfg':{'text':'output URL'},
            }    
        self.inputPortsDescr.append(datatype='boolean', name='outputURL')            
        self.outputPortsDescr.append(datatype='string', name='URL')    
        if service:   
            self.constrkw['service'] = `service`
            self.service = service
            self.host =  self.service[:7+self.service[7:].find('/')] #to get rid of part after http://ws.nbcr.net:8080
Example #2
0
    def __init__(self, service=None, **kw):
        apply(NetworkNode.__init__, (self, ), kw)
        self.inNodeWidgetsVisibleByDefault = True
        from mglutil.web.services.AppService_client import AppServiceLocator, launchJobRequest, \
getOutputsRequest, queryStatusRequest
        from mglutil.web.services.AppService_types import ns0
        self.appLocator = AppServiceLocator()
        self.req = launchJobRequest()
        self.inputFile = ns0.InputFileType_Def('inputFile')

        self.widgetDescr['outputURL'] = {
            'class': 'NECheckButton',
            'master': 'ParamPanel',
            'labelCfg': {
                'text': 'output URL'
            },
        }
        self.inputPortsDescr.append(datatype='boolean', name='outputURL')
        self.outputPortsDescr.append(datatype='string', name='URL')
        if service:
            self.constrkw['service'] = ` service `
            self.service = service
            self.host = self.service[:7 + self.service[7:].find(
                '/')]  #to get rid of part after http://ws.nbcr.net:8080
Example #3
0
    def startAutodock(self):

        self.cmdForms['default'].descr.entryByName['Run_autodock']['widget']\
                                                    .configure(state='disabled')
        dpf_file = self.dpf.get()
        if not os.path.exists(dpf_file):
            self.cmdForms['default'].descr.entryByName['status0']['widget'].\
            configure(text = 'ERROR: dpf file ' + fpf_file + ' does not exist!')
            return
        
        self.host = self.cmdForms['default'].descr.entryByName['WS_address']['widget'].get()
        
#        if not self.login :
#            self.cmdForms['default'].descr.entryByName['status0']['widget'].\
#                configure(text='Connecting to '+ self.host + ". Please wait...")
#            self.vf.GUI.ROOT.update()
#            f = self.validate_login()
#            if f == "Failed":
#                return

        self.appLocator = AppServiceLocator()
        self.req = launchJobRequest()
        input_file = os.path.basename(dpf_file)
        options = '-p ' +  input_file + ' -l ' + os.path.splitext(input_file)[0] + '.dlg'
        self.req._argList = options
        
        #input_dpf = ns0.InputFileType_Def('inputFile')
        #input_dpf._name = input_file
        dpfFile = open(dpf_file, 'r')
        dpfFileString = dpfFile.read()
        dpfFile.close()
        #input_dpf._contents = dpfFileString
        #DPF file
        inputFiles = []       
        inputFiles.append(self.uploadFile(dpf_file))
        
        
        run_option = self.ad_radio.get()
        if run_option == 0: # sends locally stored grid files
            inputs = re.findall("\w*.\w*\.map ",dpfFileString)
            inputs.extend(re.findall("\w*\.maps.fld",dpfFileString))
            inputs.extend(re.findall("\w*.pdbq[t]*",dpfFileString))
            for input in inputs:
                input = input.strip()
                #ws_input = ns0.InputFileType_Def('inputFile')
                #ws_input._name = input
                input_full_name = os.path.join(os.path.split(dpf_file)[0],input)
                #inputFile = open(input_full_name, 'r')
                #inputFileString = inputFile.read()
                #inputFile.close()
                #ws_input._contents = inputFileString
                inputFiles.append(self.uploadFile(input_full_name))
                
        elif run_option == 2: # runs AutoGrid first
            prev_dir = self.prev_dir.get()
            inputs = re.findall("\w*.\w*\.map ",dpfFileString)
            inputs.extend(re.findall("\w*\.maps.fld",dpfFileString))
            
            host = 'http://'+self.host.split('/')[2]
            for input in inputs:
                self.req._argList += " " +host+"/"+prev_dir+"/"+input
            pdbq_input = re.findall("\w*.pdbq[t]*",dpfFileString)
            pdbq_input = pdbq_input[0].strip()

            #ws_input = ns0.InputFileType_Def('inputFile')
            #ws_input._name = pdbq_input
            input_full_name = os.path.join(os.path.split(dpf_file)[0],pdbq_input)
            #inputFile = open(input_full_name, 'r')
            #inputFileString = inputFile.read()
            #inputFile.close()
            #ws_input._contents = inputFileString
            inputFiles.append(self.uploadFile(input_full_name))
        self.req._inputFile = inputFiles
        self.vf.GUI.ROOT.update()
        self.appServicePort = self.appLocator.getAppServicePort(
                                 self.host+'/AutodockOpalService',)
        resp = self.appServicePort.launchJob(self.req)

        self.JobID = resp._jobID
        self.cmdForms['default'].descr.entryByName['status0']['widget'].\
                                configure(text = 'Running Autodock Job ID: ' + self.JobID)
        self.vf.GUI.ROOT.update()
        self.vf.GUI.ROOT.after(5, self.checkStatus)
        self.cmdForms['default'].descr.entryByName['Run_autodock']['widget'].configure(state='normal')
Example #4
0
    def startAutogrid(self):
        self.cmdForms['default'].descr.entryByName['Run_autogrid']['widget']\
                                                    .configure(state='disabled')
        gpf_file = self.gpf.get()
        if not os.path.exists(gpf_file):
            self.cmdForms['default'].descr.entryByName['status0']['widget'].\
            configure(text = 'ERROR: gpf file ' + gpf_file + ' does not exist!')
            return
        
        self.host = self.cmdForms['default'].descr.entryByName['WS_address']['widget'].get()
        
#        if not self.login :
#            self.cmdForms['default'].descr.entryByName['status0']['widget'].\
#                configure(text='Connecting to '+ self.host + ". Please wait...")
#            self.vf.GUI.ROOT.update()
#            f = self.validate_login()
#            if f == "Failed":
#                return
        
        self.appLocator = AppServiceLocator()
        self.req = launchJobRequest()
        input_file = os.path.basename(gpf_file)
        options = '-p ' +  input_file + ' -l ' + os.path.splitext(input_file)[0] + '.glg'
        self.req._argList = options
        
        #input_gpf = ns0.InputFileType_Def('inputFile')
        #input_gpf._name = input_file
        gpfFile = open(gpf_file, 'r')
        gpfFileString = gpfFile.read()
        gpfFile.close()
        #input_gpf._contents = gpfFileString
        
        gpfFileString = gpfFileString.split('\n')
        for line in gpfFileString:
            if line[0:9] == 'receptor ':
                pdbqs = line.split()[1]
        
        #input_pdbqs = ns0.InputFileType_Def('inputFile')
        #input_pdbqs._name = pdbqs
        pdbqs = os.path.join(os.path.split(gpf_file)[0],pdbqs)
        #pdbqsFile = open(pdbqs, 'r')
        #pdbqsFileString = pdbqsFile.read()
        #pdbqsFile.close()
        #input_pdbqs._contents = pdbqsFileString
        
        inputFiles = []
        
        #inputFiles.append(input_gpf)
        #inputFiles.append(input_pdbqs)
        inputFiles.append(self.uploadFile(gpf_file))
        inputFiles.append(self.uploadFile(pdbqs))
        
        self.req._inputFile = inputFiles
        
        self.appServicePort = self.appLocator.getAppServicePort(
                                 self.host+'/AutogridOpalService')
        
        resp = self.appServicePort.launchJob(self.req)

        self.JobID = resp._jobID
        self.cmdForms['default'].descr.entryByName['status0']['widget'].\
                                configure(text = 'Running Autogrid Job ID: ' + self.JobID)
        self.vf.GUI.ROOT.update()
        self.vf.GUI.ROOT.after(5, self.checkStatus)
        self.cmdForms['default'].descr.entryByName['Run_autogrid']['widget'].configure(state='normal')
        self.prev_dir.set(self.JobID)
        self.cmdForms['default'].descr.entryByName['use_remote']['widget'].configure(state='normal')
Example #5
0
    def executeWebJob(self, url, commandline, inFilesPath, numProcs):
        """ 
            executeWebJob description:
            it execute a job through OpalInterface
            @input:
                -url: the url where to reach the Opal service
                -commandline the command line to use for the execution
                -inputFiles an array of input file to upload, it should contains an array of string with the path to the file
                -numProcs the number of processors to use
        """

        inputFiles = []

        if inFilesPath != None:
            for i in inFilesPath:
                inputFile = ns0.InputFileType_Def('inputFile')
                inputFile._name = os.path.basename(i)
                if self.isOpal2(url):
                    #use attachment this is opal2 server

                    if os.name == 'dos' or os.name == 'nt': 
                        inputFile._attachment = open(i, "rb")
                    else:
                        inputFile._attachment = open(i, "r")
                else:
                    #it's not a opal2 server don't user attachment
                    infile = open(i, "r")
                    inputFile._contents = infile.read()
                    infile.close()
                inputFiles.append(inputFile)

        appLocator = AppServiceLocator()
        appServicePort = appLocator.getAppServicePort(url)

        req = launchJobRequest()
        req._argList = commandline
        req._inputFile = inputFiles
        req._numProcs = numProcs

        if inputFiles != []:
            print "Uploading input files..."

        resp_s = -1

        while resp_s == -1:
            try:
                resp = appServicePort.launchJob(req)
                resp_s = 0
            except FaultException, inst:
                estr = inst.fault.AsSOAP()
                estr = estr.split("<message>")[1].split("</message>")[0]
                t = strftime("%Y-%m-%d %H:%M:%S", time.localtime())
                cte = time.mktime(datetime.now().timetuple())
                ete = cte + 60 * 60 + 10
                
                print "WARNING: " + t + " Opal FaultException from server: " + estr
                print "         will try again in about an hour" 
                while time.mktime(datetime.now().timetuple()) < ete:
                    if self.opalNode._vpe is not None:
                        self.opalNode._vpe.updateGuiCycle()
                        net = self.opalNode._node.network
                        if net.execStatus == 'stop':
                        #if self.opalNode._vpe.buttonBar.toolbarButtonDict['stop'].state == "disabled":
                            self.onStoppingExecution()
                            return None
                    time.sleep(0.5)
                pass
            except: # no internet