def submit(self, session=None):
"""
submits the job on the local server
@param session: the session used to load infile values
@type session: Mobyle.Session
@return: job information as a dictionary
@rtype: dictionary
"""
try:
if isinstance(self.service, Program):
self.job = MobyleJob( service = self.service ,
email = self.email,
session = session,
workflowID = self.workflowId)
elif isinstance(self.service, Workflow):
self.job = WorkflowJob( workflow = self.service,
email = self.email,
session = session,
workflowID = self.workflowId)
else:
raise NotImplementedError("No Job can be instanciated for a %s service" % str(self.service.__class__))
for name, param in self.params.items():
if param['parameter'].isInfile():
if param['src']:
param['src'] = DataProvider.get(param['src'])
self.job.setValue(name, (param['userName'], None, param['src'], param['srcFileName']))
else:
self.job.setValue(name, (param['userName'], param['value'], None, None))
else:
if param['parameter'].getDataType().getName() == 'MultipleChoice':
from types import StringTypes
if isinstance( param['value'] , StringTypes ):
param['value'] = [ param['value'] ]
self.job.setValue(name, param['value'])
# run Job
self.job.run()
return {
'id': str(self.job.getJobid()),
'date':str(time.strftime( "%x %X", self.job.getDate())),
'status': str( self.job.getStatus() ),
}
except UserValueError, e:
if hasattr(e, 'message') and e.message:
msg = {'errormsg':str(e.message)}
else:
msg = {'errormsg':str(e)}
if hasattr(self, 'job') and self.job:
jobId = self.job.getJobid()
msg['id'] = str(jobId)
if hasattr(e, 'param') and e.param:
msg["errorparam"] = e.param.getName()
if jobId:
pid_str = str(registry.getJobPID(jobId))
else:
pid_str = "none"
j_log.error("user error in job %s (email %s): %s"% (pid_str, getattr(self,"email","anonymous"),str(e)))
return msg
def set_value(self, parameter_name, value=None, src=None, srcFileName=None):
wf_parameter = [p for p in self.workflow.parameters if p.name==parameter_name][0]
if value is not None:
log.debug("setting %s parameter value to %s" %(parameter_name, value))
elif src is not None:
log.debug("copying %s parameter value from %s/%s" %(parameter_name, src,srcFileName))
else:
log.error("no VALUE or SOURCE URL specified for %s parameter." % parameter_name)
""" set a parameter value """
self.parameters[parameter_name] = value
self.parameters[parameter_name + '.src'] = src
self.parameters[parameter_name + '.srcFileName'] = srcFileName
if value and value==wf_parameter.vdef:
log.debug("setting %s parameter value to default value %s" %(parameter_name, wf_parameter.vdef))
return
# save input value in a file
# link this file from the JobState xml
datatype_class = wf_parameter.type.datatype.class_name
datatype_superclass = wf_parameter.type.datatype.superclass_name
df = DataTypeFactory()
if (datatype_superclass in [None,""] ):
dt = df.newDataType(datatype_class)
else:
dt = df.newDataType(datatype_superclass, datatype_class)
mt = MobyleType(dt)
p = Parameter(mt, name=parameter_name)
p._isout = wf_parameter.isout
if dt.isFile():
file_name = parameter_name+'.data'
if src:
src = DataProvider.get(src)
file_name, size = mt.toFile( value , self , file_name, src , srcFileName )
if not(wf_parameter.isout):
self.jobState.setInputDataFile(parameter_name, (file_name, size, None))
else:
self.jobState.setOutputDataFile(parameter_name, [(file_name, size, None)])
else:
if not(wf_parameter.isout):
self.jobState.setInputDataValue(parameter_name, value)
else:
raise NotImplementedError() # so far Mobyle does not manage non-file outputs
self.jobState.commit()
def submit(self, session=None):
"""
submits the job on the remote server
@param session: the session used to load infile values
@type session: Mobyle.Session
@return: job information as a dictionary
@rtype: dictionary
"""
endpointUrl = self.endpoint + "/job_submit.py"
#values = self.request
for param in [param for param in self.params.values() \
if (param.has_key('parameter') \
and param['parameter'].isInfile())]:
# if param['srcFileName'] and not(param['value']):
# param['value'] = session.getContentData(param['srcFileName'], \
# forceFull = True)[1]
if param['srcFileName'] and not(param['value']):
param['src'] = DataProvider.get(param['src'])
param['value'] = urllib.urlopen('%s/%s' % (param['src'].getDir(), param['srcFileName'])).read()
#param['value'] = urllib.urlopen(param['src']+'/'+param['srcFileName']).read()
requestDict = {}
if hasattr(self, 'programUrl'):
requestDict['programName'] = self.programUrl
else:
requestDict['workflowUrl'] = self.workflowUrl
if self.email:
requestDict['email'] = self.email
requestDict['workflowId'] = self.workflowId
for name, param in self.params.items():
requestDict[name] = param['value']
try:
response = self._remoteRequest(endpointUrl, requestDict)
except:
return {"errormsg":"A communication error happened during the \
submission of your job to the remote Portal"}
return response
