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########################################################################################
# #
# Author: Herve Menager #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
"""
Mobyle.JobFacade
This module provides an simplified and seamless access to
- local jobs and
- remote jobs
"""
import os
import time #@UnresolvedImport
import urllib #@UnresolvedImport
import urllib2 #@UnresolvedImport
import simplejson #@UnresolvedImport
from logging import getLogger#@UnresolvedImport
j_log = getLogger(__name__)
acc_log = getLogger('Mobyle.access')
from Mobyle.MobyleJob import MobyleJob
from Mobyle.Parser import parseService
from Mobyle.JobState import JobState
from Mobyle.MobyleError import MobyleError, UserValueError, NoSpaceLeftError
from Mobyle.Registry import registry
from Mobyle.WorkflowJob import WorkflowJob
from Mobyle.Workflow import Workflow, Parser
from Mobyle.Service import Program
from Mobyle.Utils import getStatus as utils_getStatus , killJob as utils_killJob
from Mobyle.Status import Status
from Mobyle.StatusManager import StatusManager
from Mobyle.DataProvider import DataProvider
from JobState import ProgramJobState, WorkflowJobState
#BEGIN #819
from Mobyle.Service import MobyleType
from Mobyle.Classes.Core import AbstractTextDataType
#END #819
from Mobyle.ConfigManager import Config
_cfg = Config()
class JobFacade(object):
"""
JobFacade is an abstract class that is an access point to a Mobyle Job.
"""
def __init__(self, programUrl=None, workflowUrl=None, service=None, jobId=None,workflowId=None,email_notify='auto'):
if programUrl is not None:
self.programUrl = programUrl
elif workflowUrl is not None:
self.workflowUrl = workflowUrl
elif service is not None:
self.service = service
if jobId:
self.jobId = jobId
self.email_notify = email_notify
self.workflowId = workflowId
def _getFormValuesToAddToSession(self,session, param):
if param['srcFileName'] and not(param['value']):
param['userName'] = session.getData(param['srcFileName'])['userName']
if param['value'] and not(param['srcFileName']):
try:
param['srcFileName'] = \
session.addData( param['userName'], \
param['parameter'].getType(), \
content = param['value'], \
inputModes = [param['inputMode']])
except NoSpaceLeftError, err:
raise UserValueError(param.get('parameter'), msg=err.message)
return param['srcFileName']
def addJobToSession(self, session, jobInfo):
"""
links the job to a session by:
- adding the job to the session
- adding the inFile data to the session
- getting user file name from the session
@param session: the user "session"
@type session: Mobyle.Session
@param jobInfo: a dictionary containing job information such as id, date, etc.
@type: dictionary
"""
dataUsed = []
for paramName in self.service.getUserInputParameterByArgpos():
param = self.service.getParameter(paramName)
if param.isInfile():
if param.getDataType().isMultiple():
inputNames = set([inputName.partition('.')[0] for inputName in self.request.keys() if inputName.startswith(paramName+'[')])
valueToSet = [self._getFormValuesToAddToSession(session,self.params[inputName]) for inputName in inputNames if self.params.has_key(inputName)]
dataUsed.extend(valueToSet)
elif self.params.has_key(paramName):
valueToSet = self._getFormValuesToAddToSession(session,self.params[paramName])
dataUsed.append(valueToSet)
userName = self.servicePID + ' - ' + jobInfo['date']
session.addJob( jobInfo['id'],userName=userName,dataUsed=dataUsed)
jobInfo['userName'] = userName
return jobInfo
def _processFormParameterValue(self, param,inputName, index=0):
value, userName, src, srcFileName, inputMode = None, None, None, None, None
if param.isInfile():
inputMode = self.request.get(inputName+'.mode',"upload")
if self.request.has_key(inputName+".ref"):
srcFileName = self.request.get(inputName+".ref")
src = self.session
userName = self.request.get(inputName+".name")
elif self.request.has_key(inputName+".src"):
srcFileName = self.request.get(inputName+".srcFileName")
src = self.request.get(inputName+".src")
userName = self.request.get(inputName+".name")
else:
value = self.request.get(inputName)
userName = inputName + ".data"
else:
value = self.request.get(inputName, None)
if (value is not None and value!="") or srcFileName: # if the value is not null (or blank from BMID)...
self.params[inputName] = {'value': value,
'userName': userName ,
'srcFileName': srcFileName,
'src': src,
'inputMode': inputMode,
'parameter': param,
'index':index
}
def _processForm(self):
"""
process the cgi form:
- preprocessing infiles, parsing user and safe file names
- preprocessing boolean values, which have specific default values
- create a parameter values dictionary which is used later
"""
for paramName in self.service.getUserInputParameterByArgpos():
param = self.service.getParameter(paramName)
if param.getDataType().isMultiple():
inputNames = sorted(set([inputName.partition('.')[0] for inputName in self.request.keys() if inputName.startswith(paramName+'[')]))
idx=0
for inputName in inputNames:
self._processFormParameterValue(param,inputName,index=idx)
idx = idx + 1
else:
self._processFormParameterValue(param,paramName)
def parseService(self):
"""
initializes the self.service and self.servicePID properties corresponding to the service url
uses self.programUrl or self.workflowUrl
"""
if hasattr(self,'programUrl'):
self.service = parseService(self.programUrl)
self.servicePID = registry.programsByUrl[self.programUrl].pid
elif hasattr(self,'workflowUrl'):
mp = Parser()
self.service = mp.parse(self.workflowUrl)
self.service.url = self.workflowUrl
self.servicePID = registry.workflowsByUrl[ self.workflowUrl ].pid
def create(self, request_fs=None, request_dict=None, session=None,simulate=False):
"""
create sets up most of the class attributes TODO: check if this could be done in __init__?
"""
self.request = {}
if request_dict:
self.request = request_dict
elif request_fs:
for key in request_fs.keys():
self.request[key] = request_fs.getvalue(key)
serviceDef = None
if self.request.get('programName',None):
serviceDef = registry.programsByUrl[self.request.get('programName')]
elif self.request.get('workflowUrl',None):
serviceDef = registry.workflowsByUrl[ self.request.get( 'workflowUrl')]
simulate = simulate or self.request.get('mobyle:simulate', False)=='true'
if not(simulate) and not(session) and (serviceDef.server.name=='local' and not(serviceDef.isExported()))\
and not(self.workflowId and registry.isJobLocal(self.workflowId)):
# test if service is exported is needed unless it is only a simulation
raise MobyleError("unauthorized access to service %s@%s, which is restricted to local use." % (serviceDef.name,serviceDef.server.name))
self.email = self.request.get('email', None)
if not(self.email) and session:
self.email = session.getEmail()
self.parseService()
if hasattr(self.service,'pid'):
self.servicePID = self.service.pid
if (not(simulate) and not( self.email ) and not( _cfg.opt_email( self.servicePID ) ) ):
# test if email is needed unless it is only a simulation
return {"emailNeeded":"true"}
if (not(simulate) and session and not(session.isActivated())):
# test if session is active is needed unless it is only a simulation
return {"activationNeeded":"true"}
self.params = {}
self.session = session
self._processForm()
resp = self.submit(session,simulate)
if resp.has_key('id'):
self.jobId = resp['id']
resp['pid'] = str(registry.getJobPID(resp['id']))
# log the job in the access log
if not(resp.has_key('errormsg')):
msg = "%s %s %s %s %s" % (self.servicePID, # service PID
resp.get('pid','').replace(self.servicePID+'.',''), #job key
str(self.email), # user email
os.environ.get('REMOTE_HOST',os.environ.get('REMOTE_ADDR','local')), # ip or host
os.environ.get('HTTP_X_MOBYLEPORTALNAME','unknown') # client portal
)
acc_log.info( msg )
return resp
def getOutputParameterValues(self, name):
js = JobState(self.jobId)
outputRefs = js.getOutput(name)
values = []
if outputRefs:
for outputRef in outputRefs:
fh = js.open(outputRef[0])
value = ''.join( fh.readlines() )
values.append({'value':value,'ref':self.jobId+'/'+outputRef[0],'size':outputRef[1],'fmt':outputRef[2]})
return values
def getOutputParameterRefs(self, name):
js = JobState(self.jobId)
outputRefs = js.getOutput(name)
values = []
if outputRefs:
for outputRef in outputRefs:
values.append({'src':self.jobId,'srcFileName':outputRef[0],'size':outputRef[1],'fmt':outputRef[2]})
return values
def getFromService(cls, programUrl=None, workflowUrl=None, service=None,workflowId=None):
"""
create a new JobFacade from the service URL.
@param programUrl: service URL
@type session: string
@return: the appropriate job facade
@rtype: JobFacade
"""
j=None
if programUrl:
if registry.programsByUrl.has_key(programUrl):
if registry.programsByUrl[programUrl].server.name=='local':
j = LocalJobFacade(programUrl=programUrl, workflowId=workflowId)
else:
j = RemoteJobFacade(programUrl=programUrl, workflowId=workflowId)
else:
raise MobyleError(msg="Service for url %s cannot be found" % programUrl)
elif workflowUrl:
if registry.workflowsByUrl.has_key(workflowUrl):
if registry.workflowsByUrl[workflowUrl].server.name=='local':
j = LocalJobFacade(workflowUrl=workflowUrl, workflowId=workflowId)
else:
j = RemoteJobFacade(workflowUrl=workflowUrl, workflowId=workflowId)
else:
raise MobyleError(msg="Service for url %s cannot be found" % workflowUrl)
elif service is not None:
j = LocalJobFacade(service=service, workflowId=workflowId)
return j
getFromService = classmethod(getFromService)
def getFromJobId(cls, jobId):
"""
create a JobFacade to access an existing job.
@param jobId: the job identifier
@type jobId: string
@return: the appropriate job facade
@rtype: JobFacade
"""
jobState = JobState(jobId)
jfargs = {'jobId': jobState.getID(),'programUrl':None,'workflowUrl':None}
if jobState.isWorkflow():
jfargs['workflowUrl'] = jobState.getName()
else:
jfargs['programUrl']= jobState.getName()
# this id is identical to the one in parameter,
# except it has been normalized (may have removed
# trailing index.xml from the id)
if jobState.isLocal():
return(LocalJobFacade(**jfargs))
else:
return(RemoteJobFacade(**jfargs))
getFromJobId = classmethod(getFromJobId)
class RemoteJobFacade(JobFacade):
"""
RemoteJobFacade is a class that is an access point to a Mobyle Job on a remote server.
"""
def __init__(self, programUrl=None, workflowUrl=None, service=None, jobId=None ,workflowId=None ):
JobFacade.__init__(self,programUrl=programUrl, workflowUrl= workflowUrl, service=service, jobId=jobId ,workflowId = workflowId )
if hasattr(self,'programUrl'):
self.server = registry.programsByUrl[self.programUrl].server
else:
self.server = registry.workflowsByUrl[self.workflowUrl].server
self.endpoint = self.server.url
def submit(self, session=None, simulate=False):
"""
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
if simulate:
requestDict['mobyle:simulate'] = 'true'
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
def getStatus(self):
"""
gets the job status on the remote server
@return: job status information as a dictionary
@rtype: dictionary
"""
endpointUrl = self.endpoint + "/job_status.py"
requestDict = {}
requestDict['jobId'] = self.jobId
try:
response = self._remoteRequest(endpointUrl, requestDict)
except:
return {"errormsg":"A communication error happened while \
asking job status to the remote Portal"}
status = Status(string=response['status'], message=response['msg'])
return status
def getSubJobs(self):
"""
gets the list of subjobs (along with their status)
@return: subjobs list of dictionaries
@rtype: dictionary
"""
endpointUrl = self.endpoint + "/job_subjobs.py"
requestDict = {}
requestDict['jobId'] = self.jobId
response = self._remoteRequest(endpointUrl, requestDict)
rv= []
if response:
for job_entry in response:
if job_entry.has_key('jobSortDate'):
jobDate = time.strptime(job_entry['jobSortDate'],"%Y%m%d%H%M%S")
if job_entry.has_key('status'):
jobstatus = Status(string=job_entry['status'], message=job_entry.get('status_message'))
jobID = job_entry['url']
jobPID = self.server.name + '.' + job_entry['jobID']
serviceName = job_entry['programName']
rv.append({'jobID':jobID,
'jobPID':jobPID,
'userName':jobID,
'programName':serviceName,
'date':jobDate,
'status':jobstatus,
'owner':registry.getJobPID(self.jobId)
})
return rv
def killJob(self):
endpointUrl = self.endpoint + "/job_kill.py"
requestDict = {}
requestDict['jobId'] = self.jobId
try:
response = self._remoteRequest(endpointUrl, requestDict)
except:
return {"errormsg":"A communication error happened while \
asking job status to the remote Portal"}
return response
def _remoteRequest(self, url, requestDict):
"""
encodes and executes the proper request on the remote server, with
proper error logging
@param url: the target url
@type url: string
@param requestDict: the request parameters
@type requestDict: dictionary
@return: response as a dictionary
@rtype: dictionary
"""
data = urllib.urlencode(requestDict)
headers = { 'User-Agent' : 'Mobyle-1.0',
'X-MobylePortalName' : _cfg.portal_name() }
req = urllib2.Request(url, data,headers)
try:
handle = urllib2.urlopen(req)
except (urllib2.HTTPError), e:
j_log.error("Error during remote job communication for remote service %s \
to %s, HTTP response code = %s" % (self.programUrl, url, e.code))
return None
except (urllib2.URLError), e:
j_log.error("Error during remote job communication for remote service %s \
to %s, URL problem = %s" % (self.programUrl, url, e.reason))
return None
try:
str = handle.read()
jsonMap = simplejson.loads(str)
except ValueError, e:
j_log.error("Error during remote job communication for remote service %s \
to %s, bad response format: %s" % (self.programUrl, url, str(e)))
return None
return jsonMap
class LocalJobFacade(JobFacade):
"""
LocalJobFacade is a class that is an access point to a Mobyle Job on the local server.
"""
def submit(self, session=None, simulate=False):
"""
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,
debug = (None,1)[simulate],
email_notify=self.email_notify)
elif isinstance(self.service, Workflow):
self.job = WorkflowJob( workflow = self.service,
email = self.email,
session = session,
workflowID = self.workflowId,
#debug = (None,1)[simulate],
email_notify=self.email_notify)
else:
raise NotImplementedError("No Job can be instanciated for a %s service" % str(self.service.__class__))
for paramName in self.service.getUserInputParameterByArgpos():
param = self.service.getParameter(paramName)
try:
if param.getDataType().isMultiple():
inputNames = set([inputName.partition('.')[0] for inputName in self.request.keys() if inputName.startswith(paramName+'[')])
valueToSet = [self._getFormValueToSet(self.params[inputName]) for inputName in inputNames if self.params.has_key(inputName)]
else:
if self.params.has_key(paramName):
valueToSet = self._getFormValueToSet(self.params[paramName])
else:
continue
self.job.setValue(paramName, valueToSet)
except MobyleError , err:
if param.promptHas_lang( "en"):
userMsg = "Error while setting value for parameter: %s " % param.getPrompt( lang="en")
else:
userMsg = "Error while setting value for parameter: %s " % param.getName()
sm = StatusManager ()
sm.setStatus( self.job.getDir() , Status( code = 5 , message = userMsg ) )
raise err
# 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:
jobId = None
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
except MobyleError, e:
j_log.error(e, exc_info = True)
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()
return msg
def _getFormValueToSet(self,param):
if param['parameter'].isInfile():
if param['src']:
param['src'] = DataProvider.get(param['src'])
return (param['userName'], None, param['src'], param['srcFileName'],param['index'])
else:
return (param['userName'], param['value'], None, None,param['index'])
else:
return param['value']
def getStatus(self):
"""
gets the job status on the local server
@return: job status information as a dictionary
@rtype: dictionary
"""
return utils_getStatus( self.jobId )
def getSubJobs(self):
"""
gets the list of subjobs (along with their status)
@return: subjobs list of dictionaries
@rtype: list
"""
js = JobState(self.jobId)
if hasattr(js, 'getSubJobs'):
subjobs = js.getSubJobs()
subsubjobs = []
for s in subjobs:
s['jobPID'] = registry.getJobPID(self.jobId) + '::'+ registry.getJobPID(s['jobID'])
child_jf = JobFacade.getFromJobId(s['jobID'])
s['status'] = child_jf.getStatus()
for ss in child_jf.getSubJobs():
ss['jobPID'] = s['jobPID'] + '::' + registry.getJobPID(ss['jobID'])
schild_jf = JobFacade.getFromJobId(ss['jobID'])
ss['status'] = schild_jf.getStatus()
subsubjobs.append(ss)
subjobs.extend(subsubjobs)
return subjobs
else:
return []
def getExecutionDetails(self):
js = JobState(self.jobId)
execution_details = {}
if isinstance(js.state,ProgramJobState):
execution_details['cmd']=js.getCommandLine()
# TODO it should be specified if the contents
# of the paramfiles have to be sent back as well
execution_details['paramfiles']=js.getParamfiles()
# TODO the environment vars are not stored except in the .forChild.dump
# we can do something about it if necessary, otherwise accessing them
# is too much work...
#execution_details['env']=self.job._job.runner._xmlEnv
st = utils_getStatus( self.jobId )
execution_details['status']={'code':str(st),'message':st.message}
if st.isOnError():
execution_details['errormsg']=st.message
return execution_details
def killJob(self):
"""
"""
utils_killJob( self.jobId )
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