def getDescription(self, tree_node):
if tree_node.parent:
service = tree_node.parent.GetFullName()
else:
service = tree_node.GetFullName()
import ZSI
self.Description_Text.configure(text_state='normal')
self.Description_Text.clear()
from ZSI.generate.wsdl2python import WriteServiceModule
from ZSI.wstools import WSDLTools
reader = WSDLTools.WSDLReader()
wsdl = reader.loadFromURL(self.Services_dict[service])
try:
wsdl.services['AppService']
except:
self.Description_Text.insert(
'end',
'Sorry, only Opal based web services are supported http://nbcr.net/services/opal'
)
self.Description_Text.configure(text_state='disabled')
return
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(\
self.URL + "/services/"+service)
req = getAppMetadataRequest()
resp = appServicePort.getAppMetadata(req)
self.Description_Text.configure(text_state='normal')
if resp._info:
self.Description_Text.insert('end', resp._usage + "\n\n")
self.Description_Text.insert('end', resp._info[0])
else:
self.Description_Text.insert('end', resp._usage)
self.Description_Text.configure(text_state='disabled')
def getDescription(self, tree_node):
if tree_node.parent:
service = tree_node.parent.GetFullName()
else:
service = tree_node.GetFullName()
import ZSI
self.Description_Text.configure(text_state = 'normal')
self.Description_Text.clear()
from ZSI.generate.wsdl2python import WriteServiceModule
from ZSI.wstools import WSDLTools
reader = WSDLTools.WSDLReader()
wsdl = reader.loadFromURL(self.Services_dict[service])
try:
wsdl.services['AppService']
except:
self.Description_Text.insert('end', 'Sorry, only Opal based web services are supported http://nbcr.net/services/opal')
self.Description_Text.configure(text_state = 'disabled')
return
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(\
self.URL + "/services/"+service)
req = getAppMetadataRequest()
resp = appServicePort.getAppMetadata(req)
self.Description_Text.configure(text_state = 'normal')
if resp._info:
self.Description_Text.insert('end',resp._usage+"\n\n")
self.Description_Text.insert('end',resp._info[0])
else:
self.Description_Text.insert('end',resp._usage)
self.Description_Text.configure(text_state = 'disabled')
def onStoppingExecution(self):
#kill running job
#TODO kill local running job
if (self.jobID != None):
#ok let's kill the running job
print "Killing job: " + self.jobID
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(self.opalNode.url)
destroyReq = destroyRequest(self.jobID)
resp = appServicePort.destroy(destroyReq)
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
class OpalServiceNode(NetworkNode):
"""A generic Opal Web Service Node that extends NetworkEditor.items.NetworkNode
and impliments common functionalty among Opal Web Service Nodes.
http://nbcr.net/services/opal
"""
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 runws(self):
"""
Runs Opal Web Service on a given port:
Returns resp if succeeded or
prints obID and resp._baseURL message if failed, and returns ""
"""
appServicePort = self.appLocator.getAppServicePort(self.service)
try:
self.resp = appServicePort.launchJob(self.req)
jobID = self.resp._jobID
self.resp = appServicePort.queryStatus(queryStatusRequest(jobID))
except Exception, inst:
from ZSI import FaultException
if isinstance(inst, FaultException):
tmp_str = inst.fault.AsSOAP()
tmp_str = tmp_str.split('<message>')
tmp_str = tmp_str[1].split('</message>')
if len(tmp_str[0]) > 500:
print tmp_str[0]
tmp_str[0] = tmp_str[0][0:500] + '...'
tkMessageBox.showerror("ERROR: ", tmp_str[0])
self.resp = None
return
while self.resp._code != 8:
time.sleep(1)
self.resp = appServicePort.queryStatus(queryStatusRequest(jobID))
if self.resp._code == 4:
print "jobID:", jobID, 'failed on', self.resp._baseURL
opener = urllib.FancyURLopener({})
errorMsg = opener.open(self.resp._baseURL + "/std.err").read()
tkMessageBox.showerror("Error!", errorMsg)
webbrowser.open(self.host + '/' + jobID)
return ""
self.outurl = self.host + '/' + jobID
self.resp = appServicePort.getOutputs(getOutputsRequest(jobID))
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')
class WebServices(MVCommand):
def __init__(self):
MVCommand.__init__(self)
rc = getResourceFolderWithVersion() + os.sep + 'ws' + os.sep
if not os.path.exists(rc):
os.mkdir(rc)
self.proxy_gama = rc + 'proxy_gama'
self.rc_ad = rc + "rc_ad"
self.login = False
if hasattr(self, 'vf.GUI.ROOT'):
self.dpf = Tkinter.StringVar(self.vf.GUI.ROOT)
self.gpf = Tkinter.StringVar(self.vf.GUI.ROOT)
self.prev_dir = Tkinter.StringVar(self.vf.GUI.ROOT)
self.ad_radio = Tkinter.IntVar(self.vf.GUI.ROOT)
else:
self.dpf = Tkinter.StringVar()
self.gpf = Tkinter.StringVar()
self.prev_dir = Tkinter.StringVar()
self.ad_radio = Tkinter.IntVar()
self.current_job = None
def guiCallback(self, event=None):
mainform = self.showForm('default', modal=0, blocking=1.,
initFunc=self.initForm)
def buildFormDescr(self, formName):
ifd = InputFormDescr(title = "AutoGrid/AutoDock Web Services")
#Web Services Login
ifd.append({'name':"LoginGroup", 'widgetType':Pmw.Group,
'container':{'LoginGroup':'w.interior()'},
'wcfg':{'tag_text':'Web Services Location'},
'gridcfg':{'sticky':'nswe'}
})
ifd.append({'widgetType':Pmw.ComboBox, 'name':'WS_address',
'parent':'LoginGroup',
'wcfg':{'scrolledlist_items':
('http://ws.nbcr.net/opal2/services',),
'listheight':50, 'dropdown':1, 'history':1,
'autoclear':1},
'gridcfg':{'sticky':'ew', 'row':0, 'column':0,
'columnspan':3}
})
# ifd.append({'widgetType':Tkinter.Label, 'name':'New_User',
# 'parent':'LoginGroup', 'wcfg':{'text':' New Users?',
# 'fg':'Blue','cursor':'hand1'},
# 'gridcfg':{'sticky':'w', 'row':1, 'column':0}
# })
# ifd.append({'widgetType':Tkinter.Label, 'name':'UserName_Label',
# 'parent':'LoginGroup', 'wcfg':{'text':'User Name'},
# 'gridcfg':{'sticky':'e', 'row':1, 'column':1}
# })
# ifd.append({'widgetType':Tkinter.Entry, 'name':'UserName_Entry',
# 'parent':'LoginGroup','wcfg':{},
# 'gridcfg':{'sticky':'ew', 'row':1, 'column':2}
# })
# ifd.append({'widgetType':Tkinter.Label, 'name':'Password_Label',
# 'parent':'LoginGroup', 'wcfg':{'text':'Password'},
# 'gridcfg':{'sticky':'e', 'row':2, 'column':1}
# })
# ifd.append({'widgetType':Tkinter.Entry, 'name':'Password_Entry',
# 'parent':'LoginGroup', 'wcfg':{'show':'*'},
# 'gridcfg':{'sticky':'ew', 'row':2, 'column':2}
# })
# ifd.append({'widgetType':Tkinter.Label, 'name':'Remember_Label',
# 'parent':'LoginGroup',
# 'wcfg':{'text':'Remember User Name and Password'},
# 'gridcfg':{'sticky':'e', 'row':3, 'column':0,'columnspan':2}
# })
# self.RememberLogin_var = Tkinter.BooleanVar()
# ifd.append({'widgetType':Tkinter.Checkbutton, 'name':'Remember_Checkbutton',
# 'parent':'LoginGroup', 'variable':self.RememberLogin_var,
# 'gridcfg':{'sticky':'w', 'row':3, 'column':2}
# })
#AutoGrid group
ifd.append({'name':"AutoGrid", 'widgetType':Pmw.Group,
'container':{'AutoGrid':'w.interior()'},
'wcfg':{'tag_text':'AutoGrid'},
'gridcfg':{'sticky':'nswe'}
})
ifd.append({'widgetType':Tkinter.Button, 'name':'Run_autogrid',
'parent':'AutoGrid',
'wcfg':{'text':'Run AutoGrid ',
'command':self.startAutogrid},
'gridcfg':{'sticky':'w', 'row':0, 'column':0}
})
ifd.append( {'name': 'gpf_entry', 'parent':'AutoGrid',
'widgetType':Tkinter.Entry,
'wcfg':{'width':30,'textvariable':self.gpf},
'gridcfg':{'sticky':'w','row':0,'column':1}
})
ifd.append({'name': 'browse_gpf', 'widgetType': Tkinter.Button,
'parent':'AutoGrid', 'text':'Browse',
'command':self.browse_gpf,
'gridcfg':{'sticky':'w','row':0, 'column':2}
})
#AutoDock group
ifd.append({'name':"AutoDock", 'widgetType':Pmw.Group,
'container':{'AutoDock':'w.interior()'},
'wcfg':{'tag_text':'AutoDock'},
'gridcfg':{'sticky':'nswe'}
})
ifd.append({'widgetType':Tkinter.Button, 'name':'Run_autodock',
'parent':'AutoDock',
'wcfg':{'text':'Run AutoDock',
'command':self.startAutodock},
'gridcfg':{'sticky':'w', 'row':0, 'column':0}
})
ifd.append( {'name': 'dpf_entry', 'parent':'AutoDock',
'widgetType':Tkinter.Entry,
'wcfg':{'width':30,'textvariable':self.dpf},
'gridcfg':{'sticky':'w','row':0,'column':1}
})
ifd.append({'name': 'browse_dpf', 'widgetType': Tkinter.Button,
'parent':'AutoDock', 'text':'Browse',
'command':self.browse_dpf,
'gridcfg':{'sticky':'w','row':0, 'column':2}
})
ifd.append({'name': 'ag_local', 'widgetType': Tkinter.Radiobutton,
'parent':'AutoDock', 'text':'Use local grids',
'tooltip':"This option sends locally stored grid files with Web Services request",
'wcfg':{'variable':self.ad_radio,'value':0},
'gridcfg':{'sticky':'w','row':1, 'column':0,'columnspan':2}
})
# ifd.append({'name': 'ag_before', 'widgetType': Tkinter.Radiobutton,
# 'parent':'AutoDock', 'text':'Run AutoGrid first',
# 'tooltip':"This option runs AutoGrid Web Services and uses resulting map files for AutoDock",
# 'wcfg':{'variable':self.ad_radio,'value':1,'state':'disabled'},
# 'gridcfg':{'sticky':'w','row':2, 'column':0,'columnspan':2}
# })
ifd.append({'name': 'use_remote', 'widgetType': Tkinter.Radiobutton,
'parent':'AutoDock', 'text':'Use grids from server directory',
'tooltip':"This option copies map files from previous AutoGrid run",
'wcfg':{'variable':self.ad_radio,'value':2,},
'gridcfg':{'sticky':'w','row':3, 'column':0,'columnspan':2}
})
ifd.append( {'name': 'remote_dir', 'parent':'AutoDock',
'widgetType':Tkinter.Entry,
'wcfg':{'width':23,'textvariable':self.prev_dir},
'gridcfg':{'sticky':'e','row':3,'column':1,'columnspan':2}
})
#Status
ifd.append({'name':"StatusGroup", 'widgetType':Pmw.Group,
'container':{'StatusGroup':'w.interior()'},
'wcfg':{'tag_text':'Web Services Status'},
'gridcfg':{'sticky':'nswe'}
})
ifd.append({'widgetType':Tkinter.Label, 'name':'status0',
'parent':'StatusGroup',
'wcfg':{'text':' ',},
'gridcfg':{'sticky':'w', 'row':0, 'column':0}
})
ifd.append({'widgetType':Tkinter.Label, 'name':'status1',
'parent':'StatusGroup',
'wcfg':{'text':' ',},
'gridcfg':{'sticky':'w', 'row':1, 'column':0}
})
ifd.append({'name':'WS_ProgressBar', 'widgetType':Tkinter.Frame,
'parent':'StatusGroup', 'wcfg':{'height':30},
'gridcfg':{'sticky':'ew', 'row':2,'column':0}
})
ifd.append({'widgetType':Tkinter.Label, 'name':'down_label',
'parent':'StatusGroup',
'wcfg':{'text':' ',},
'gridcfg':{'sticky':'w', 'row':3, 'column':0}
})
return ifd
def browse_gpf(self):
filename = askopenfilename(filetypes=[('Grid Parameter File','*.gpf')],\
title="Please Select Grid Parameter File",
parent=self.cmdForms['default'].root)
if filename:
self.gpf.set(filename)
self.cmdForms['default'].descr.entryByName['Run_autogrid']['widget'].configure(state='normal')
#self.cmdForms['default'].descr.entryByName['ag_before']['widget'].configure(state='normal')
def browse_dpf(self):
filename = askopenfilename(filetypes=[('Dock Parameter File','*.dpf')],\
title="Please Select Dock Parameter File",
parent=self.cmdForms['default'].root)
if filename:
self.dpf.set(filename)
self.cmdForms['default'].descr.entryByName['Run_autodock']['widget'].configure(state='normal')
def initForm(self, cmdForm=None):
cmdForm.descr.entryByName['WS_address']['widget'].selectitem(0)
# if not os.path.exists(self.rc_ad):
# open(self.rc_ad,'w')
# else:
# file = open(self.rc_ad)
# text = file.read()
# text = text.split()
# for line in text:
# tmp_line = line.split('User:'******'UserName_Entry']['wcfg']\
# ['textvariable'].set(tmp_line[1])
# tmp_line = line.split('Password:'******'Password_Entry']['wcfg']\
# ['textvariable'].set(tmp_line[1])
# file.close()
# def openurl(event):
# webbrowser.open('https://nbcr.net:8443/worksphere/start?cid=apply')
# cmdForm.descr.entryByName['New_User']['widget'].bind(sequence="<Button-1>",
# func=openurl)
if hasattr(self.vf,'dpo') and self.vf.dpo.dpf_filename:
self.dpf.set(self.vf.dpo.dpf_filename)
cmdForm.descr.entryByName['Run_autodock']['widget'].configure(state='normal')
else:
if not self.dpf.get():
cmdForm.descr.entryByName['Run_autodock']['widget'].configure(state='disabled')
if hasattr(self.vf,'gpo') and self.vf.gpo.gpf_filename:
self.gpf.set(self.vf.gpo.gpf_filename)
cmdForm.descr.entryByName['Run_autogrid']['widget'].configure(state='normal')
#cmdForm.descr.entryByName['ag_before']['widget'].configure(state='normal')
else:
if not self.gpf.get():
cmdForm.descr.entryByName['Run_autogrid']['widget'].configure(state='disabled')
self.progressBar = ProgressBar(
cmdForm.descr.entryByName['WS_ProgressBar']['widget'],
labelside=None, width=200, height=20, mode='percent')
self.progressBar.setLabelText('Progress...')
self.progressBar.set(0)
cmdForm.descr.entryByName['WS_ProgressBar']['widget'].grid_forget()
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 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 uploadFile(self, path):
"""
this function given a string containing a path creates a
InputFileType to be used with jobLaunch
"""
inputFile = ns0.InputFileType_Def('inputFile')
inputFile._name = os.path.basename(path)
if self.isOpal2():
#use attachment this is opal2 server
inputFile._attachment = open(path, "r")
else:
#it's not a opal2 server don't user attachment
infile = open(path, "r")
inputFile._contents = infile.read()
infile.close()
return inputFile
def isOpal2(self):
"""return True if we are using Opal2"""
print "self.host is: " + self.host
if self.host.find("/opal2/") != -1:
return True
else:
return False
def checkStatus(self):
resp = self.appServicePort.queryStatus(queryStatusRequest(self.JobID))
if resp._code == 8: # 8 = GramJob.STATUS_DONE
descr = self.cmdForms['default'].descr
descr.entryByName['status0']['widget'].configure(text=resp._message)
webbrowser.open(resp._baseURL)
descr.entryByName['status1']['widget'].configure(text=resp._baseURL,
fg='Blue',cursor='hand1')
def openurl(event):
webbrowser.open(resp._baseURL)
descr.entryByName['status1']['widget'].bind(sequence="<Button-1>",
func=openurl)
self.resp = self.appServicePort.getOutputs(getOutputsRequest(self.JobID))
descr.entryByName['WS_ProgressBar']['widget'].grid(sticky='ew',
row=2, column=0)
self.opener = urllib.FancyURLopener(cert_file=self.proxy_gama,
key_file=self.proxy_gama)
self.download_finished = False
self.new_download = True
self.file_counter = -1
inputs = [x for x in self.resp._outputFile if x._name[-3:] !='dlg']
if len(inputs) != len(self.resp._outputFile):
for input in inputs:
self.resp._outputFile.remove(input)
self.download()
return
else:
self.cmdForms['default'].descr.entryByName['status0']['widget'].\
configure(text = "Status: " + resp._message)
self.cmdForms['default'].descr.entryByName['status1']['widget'].\
configure(text = "")
self.vf.GUI.ROOT.after(5000, self.checkStatus)
def download(self):
if self.new_download:
self.file_counter += 1
if self.file_counter > self.resp._outputFile.__len__() - 1 :
self.cmdForms['default'].descr.entryByName['WS_ProgressBar']\
['widget'].grid_forget()
self.cmdForms['default'].descr.entryByName['down_label']\
['widget'].configure(text = "")
self.cmdForms['default'].descr.entryByName['Run_autogrid']\
['widget'].configure(state='normal')
return
self.progressBar.configure(progressformat='percent',
labeltext='Progress ... ', max =100)
self.progressBar.set(0)
remote_file = self.resp._outputFile[self.file_counter]
self.cmdForms['default'].descr.entryByName['down_label']['widget'].\
configure(text = "Downloading " + remote_file._name + " " +
str(self.file_counter+1) +" of " +
str(self.resp._outputFile.__len__()))
self._url = self.opener.open(remote_file._url)
try:
self._out = open(remote_file._name,"w")
except IOError:
showerror("Download Failed!",
"Permission denied: " +os.path.join(os.getcwd(),remote_file._name),
parent = self.cmdForms['default'].root)
return
bytes = int(self._url.headers.dict['content-length'])
self._progress_counter = 0
self._download_bytes = bytes/100
if self._download_bytes == 0: self._download_bytes = 1
self.new_download = False
self.vf.GUI.ROOT.after(1, self.download)
return
else:
self._progress_counter += 1
if self._progress_counter > 100:
self._progress_counter = 100
self.progressBar.set(self._progress_counter)
tmp = self._url.read(self._download_bytes)
if tmp:
self._out.write(tmp)
else:
self._url.close()
self._out.close()
self.new_download = True
self.vf.GUI.ROOT.after(50, self.download)
def validate_login(self):
self.login = False
from mglutil.web.services.SecuritymyproxyloginImplService_services import \
loginUserMyProxyRequestWrapper, \
SecuritymyproxyloginImplServiceLocator
gamaLoginLocator = SecuritymyproxyloginImplServiceLocator()
gamaLoginService = gamaLoginLocator.getSecuritymyproxyloginImpl(
ssl=1,transport=httplib.HTTPSConnection)
req = loginUserMyProxyRequestWrapper()
username = self.cmdForms['default'].descr.\
entryByName['UserName_Entry']['widget'].get()
passwd = self.cmdForms['default'].descr.\
entryByName['Password_Entry']['widget'].get()
if not username or not passwd:
showerror("Username or Password is missing",
"Login failed. Please type your User Name and Password,\
or click on New User?", parent = self.cmdForms['default'].root)
return "Failed"
req._username = username
req._passwd = passwd
resp = gamaLoginService.loginUserMyProxy(req)
f = open(self.proxy_gama, "w")
f.write(resp._loginUserMyProxyReturn)
f.close()
if self.RememberLogin_var.get():
file = open(self.rc_ad,'w')
user = self.cmdForms['default'].descr.entryByName\
['UserName_Entry']['widget'].get()
passwd = self.cmdForms['default'].descr.entryByName\
['Password_Entry']['widget'].get()
file.write("User:%s\nPassword:%s\n"%(user,passwd))
self.login = True
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
class OpalServiceNode(NetworkNode):
"""A generic Opal Web Service Node that extends NetworkEditor.items.NetworkNode
and impliments common functionalty among Opal Web Service Nodes.
http://nbcr.net/services/opal
"""
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 runws(self):
"""
Runs Opal Web Service on a given port:
Returns resp if succeeded or
prints obID and resp._baseURL message if failed, and returns ""
"""
appServicePort = self.appLocator.getAppServicePort(self.service)
try:
self.resp = appServicePort.launchJob(self.req)
jobID = self.resp._jobID
self.resp = appServicePort.queryStatus(queryStatusRequest(jobID))
except Exception, inst:
from ZSI import FaultException
if isinstance(inst, FaultException):
tmp_str = inst.fault.AsSOAP()
tmp_str = tmp_str.split('<message>')
tmp_str = tmp_str[1].split('</message>')
if len(tmp_str[0]) > 500:
print tmp_str[0]
tmp_str[0] = tmp_str[0][0:500] + '...'
tkMessageBox.showerror("ERROR: ",tmp_str[0])
self.resp = None
return
while self.resp._code != 8:
time.sleep(1)
self.resp = appServicePort.queryStatus(queryStatusRequest(jobID))
if self.resp._code == 4:
print "jobID:",jobID, 'failed on', self.resp._baseURL
opener = urllib.FancyURLopener({})
errorMsg = opener.open(self.resp._baseURL+"/std.err").read()
tkMessageBox.showerror("Error!",errorMsg)
webbrowser.open(self.host + '/' + jobID)
return ""
self.outurl = self.host + '/' + jobID
self.resp = appServicePort.getOutputs(getOutputsRequest(jobID))
