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 killJob(jobID):
"""
@param jobID: the url of the job or a sequence of jobID
@type jobID: string or sequence of jobID
@return:
@rtype:
@raise MobyleError: if the job has no number or if the job doesn't exist anymore
@todo: tester la partie sge
"""
from types import StringTypes, TupleType, ListType
from Mobyle.MobyleError import MobyleError
from Mobyle.JobState import JobState, normUri
from Mobyle.Job import Job
from Mobyle.WorkflowJob import WorkflowJob
if isinstance(jobID, StringTypes):
jobIDs = [jobID]
elif isinstance(jobID, (ListType, TupleType)):
jobIDs = jobID
else:
raise MobyleError, "jobID must be a string or a Sequence of strings :%s" % type(jobID)
errors = []
for jobID in jobIDs:
try:
path = normUri(jobID)
except MobyleError, err:
errors.append((jobID, str(err)))
continue
if path[:4] == "http":
# the jobID is not on this Mobyle server
errors.append((jobID, "can't kill distant job"))
continue
js = JobState(uri=jobID)
if js.isWorkflow():
job = WorkflowJob(id=jobID)
else:
job = Job(ID=jobID)
try:
job.kill()
except MobyleError, err:
errors.append((jobID, str(err)))
continue
# Author: Herve Menager, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
from Mobyle.Workflow import Parser
from Mobyle.WorkflowJob import WorkflowJob
if __name__ == "__main__":
mp = Parser()
#wf = mp.parse('/tmp/workflow.xml') # 1st example
wf = mp.parse('/tmp/workflow2.xml') # 2nd example
class SessionFake(object):
def getKey(self):
return "workflowjobdemotestmodule"
wf.owner = SessionFake()
parameters = {'sequences': """>A
TTTT
>B
TATA""",
'alignment_format': 'PHYLIP'}
wj = WorkflowJob(workflow=wf,email='*****@*****.**')
print wj.id
#for key, value in parameters.items(): # set values for 1st example
# wj.set_value(key, value)
wj.srun() #synchronous calls
#wj.run #asynchronous calls