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
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
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')
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')
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
