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########################################################################################
# #
# Author: Bertrand Neron, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
import os
import random
from string import ascii_uppercase
import resource
import time
import logging
j_log = logging.getLogger( __name__ )
from Mobyle.JobState import JobState , path2url , url2path
from Mobyle.Admin import Admin
from Mobyle.Status import Status
from Mobyle.StatusManager import StatusManager
from Mobyle.MobyleError import MobyleError , UserValueError
from Mobyle.Utils import executionLoader
import Local.Policy
__extra_epydoc_fields__ = [('call', 'Called by','Called by')]
class Job:
"""
create the environment to run a job
- working directory creation
"""
def __init__(self, service=None , cfg=None , session = None , userEmail = None , workflowID = None , email_notify= 'auto' , ID = None, debug=None ):
"""
@param service:
@type service: a {Service} instance
@param cfg: a config object
@type cfg: L{ConfigManager.Config} instance
@param session:
@type session: a L{Session} instance
@param userEmail: the email of the user
@type userEmail: a L{Mobyle.Net.EmailAddress} instance
@param workflowID: the url of the workflow owner of this job
@type workflowID: string
@param email_notify: if the user must be or not notify of the results at the end of the Job.
the 3 authorized values for this argument are:
- 'true' to notify the results to the user
- 'false' to Not notify the results to the user
- 'auto' to notify the results based on the job elapsed time and the config EMAIL_DELAY
@type email_notify: string
"""
if cfg:
self.cfg = cfg
else:
from Mobyle.ConfigManager import Config
self.cfg = Config()
self._debug = debug
self.runner = None
self.session = session
self.userEmail = userEmail
self.workflowID = workflowID
self.sm = StatusManager()
if ID:
self.ID = ID
self.work_dir = url2path( ID )
self.jobState = JobState( uri = ID )
self.key = os.path.split( self.work_dir )[ 1 ]
else:
self.service = service
self.work_dir = None
self.jobState = None
self.cmdLine = None
self.key = self._newKey()
self.email_notify = email_notify
self.makeEnv()
self.ID = self.getURL()
def makeEnv( self, uri = None ):
"""
create the environment to run a job
- working directory creation
- fixing permission
- creation of the xml file index.xml
"""
basedir = self.cfg.results_path()
if not os.path.exists( basedir ):
msg = "directory " + str( basedir ) + " does not exist"
j_log.error(msg)
raise MobyleError, msg
if uri is None:
if self.session and self.service.getUrl().startswith(self.session.url):
name = 'user_defined'
else:
name = self.service.getName()
workdir = os.path.join( basedir , name , self.key )
if os.path.exists( workdir ):
msg = 'cannot make directory '+ str( workdir )+" : File exists"
j_log.error( msg )
raise MobyleError , msg
try:
os.makedirs( workdir , 0755 ) #create parent directory
except Exception , err:
j_log.critical( "unable to create job directory %s: %s " %( workdir , err ), exc_info = True )
raise MobyleError , "Internal server Error"
os.umask(0022)
self.work_dir = workdir
resource.setrlimit( resource.RLIMIT_CORE , (0 , 0) )
maxFileSize = self.cfg.filelimit()
resource.setrlimit( resource.RLIMIT_FSIZE , ( maxFileSize , maxFileSize ) )
self.date = time.localtime()
#be careful the order of setting informations in state is important
self.jobState = JobState( uri=workdir, service=self.service )
serviceName = self.service.getName()
jobID = self.getURL()
self.jobState.setName( self.service.getUrl() )
self.jobState.setHost( self.cfg.root_url() )
self.jobState.setID( jobID )
self.jobState.setDate( self.date )
if self.userEmail is not None:
self.jobState.setEmail( self.userEmail )
sessionKey = None
if self.session is not None:
sessionKey = self.session.getKey()
self.jobState.setSessionKey( sessionKey )
if self.workflowID is not None:
self.jobState.setWorkflowID( self.workflowID )
self.jobState.commit()
self.sm.create( self.work_dir , Status( code= 0 ) ) # building
try:
remote_host = os.environ['REMOTE_HOST']
except KeyError :
remote_host = "UNKNOWN"
try:
ip_addr = os.environ['REMOTE_ADDR']
except KeyError :
ip_addr = 'local'
remote = ip_addr+"\\"+remote_host
## Attention I'm building the job instance
## during the MobyleJob instanciation
## thus the job is not already add to the session
## this is done explicitly in the CGI when a value is submitted
Admin.create( self.work_dir , remote , serviceName , jobID ,
userEmail = self.userEmail ,
sessionID = sessionKey ,
workflowID = self.workflowID )
def _newKey(self):
"""
@return: a unique key which serve to indentify a job
@rtype: string
"""
#for PBS/SGE jobname, the first char of tmp dir must begin by a letter
letter = ascii_uppercase[ random.randrange( 0 , 26 ) ]
#max 15 chars for PBS jobname
strTime = "%.9f" % time.time()
strTime = strTime[-9:]
strPid = "%05d" % os.getpid()
strPid = strPid.replace( '.' , '' )[ -5 : ]
return letter + strPid + strTime
def setSession(self , session ):
self.session = session
sessionKey = self.session.getKey()
self.jobState.setSessionKey( sessionKey )
self.jobState.commit()
adm = Admin( self.work_dir )
adm.setSession( sessionKey )
adm.commit()
def getKey( self ):
"""
@return: the unique key of this job
@rtype: string
"""
return self.key
def getDate( self ):
"""
@return: the submission date of this job
@rtype: string
"""
return self.date
def getDir(self):
"""
@return: the absolute path to the directory where the job is executed
@rtype: string
"""
return self.work_dir
def getCommandLine(self):
if self.ID:
return self.jobState.getCommandLine()
else:
return self.cmdLine
def getURL(self):
"""
@return: the URL to the directory where the job is executed
@rtype: string
"""
url = path2url( self.work_dir )
return url
def getService( self ):
"""
@return: the instance of the service used for this job
@rtype: Service
"""
return self.service
def getServiceName(self):
return self.service.getName()
def getStatus(self):
return self.sm.getStatus( self.work_dir )
def getEmail( self ):
"""
@return: the email of the user or None if there is no email
@rtype: -L{Net.EmailAddress} instance
"""
return self.userEmail
def isLocal(self):
"""
@return: True if this job is on this server , False otherwise
@rtype: boolean
"""
return self.jobState.isLocal()
def run( self ):
"""
Run the Job (instanciate a CommandRunner)
@call: L{MobyleJob.run <MobyleJob>}
"""
from Mobyle.RunnerFather import CommandRunner
if self.jobState is None:
msg = "you must make an environment for the job before running it"
self._logError( logMsg = msg ,
userMsg = "Mobyle Internal server error"
)
raise MobyleError, msg
oldStatus = self.sm.getStatus( self.work_dir )
if oldStatus != Status( string="building" ):
msg = "try to run a Job which have %s status" % oldStatus
self._logError( logMsg = msg ,
userMsg = "Mobyle Internal server error"
)
raise MobyleError, msg
self.sm.setStatus( self.work_dir , Status( code = 1 ) )#submitted
self.runner = CommandRunner( self )
self.cmdLine = self.runner.getCmdLine()
debug = self._debug or self.cfg.debug( self.service.getName() )
if debug > 0 and debug < 3:# the job will not run
self.sm.setStatus( self.work_dir , Status( code = 4,message="job simulation only" ) )#finished
else:
if self.userEmail is not None :
try:
Local.Policy.allow_to_be_executed( self )
except UserValueError, err:
self._logError( userMsg = str(err) ) #set the job in status error
raise err
except AttributeError:
j_log.warning( "func allow_to_be_executed not found in Local.Policy: see Example.Local.Policy.py to update: all jobs are allowed")
#allow_to_be_executed is not in local policy
#so all jobs are allowed to run
pass
self.runner.run()
def kill( self ) :
adm = Admin( self.getDir() )
jobNum = adm.getNumber()
if jobNum is None:
raise MobyleError( "no jobNum for the job : %s" % self.ID )
try:
execKlass = executionLoader( jobID = self.ID )
execKlass.kill( jobNum )
self.sm.setStatus( self.work_dir , Status( code= 6 , message = "Your job has been cancelled" ) )
except MobyleError , err :
msg = "cannot kill job %s : %s" % ( self.ID , err)
j_log.error( msg )
raise MobyleError( msg )
def _logError( self , userMsg = None , logMsg = None ):
if userMsg :
self.sm.setStatus( self.work_dir , Status( code = 5 , message = userMsg ) ) #error
if logMsg :
j_log.error( "%s : %s : %s" %( self.service.getName() ,
self.getKey() ,
logMsg
)
)
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