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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. #
# #
########################################################################################
"""
Classes executing the command and managing the results
"""
import os
from logging import getLogger, shutdown as logging_shutdown
_log = logging.getLogger(__name__)
from Mobyle.MobyleLogger import MLogger
from Mobyle.Execution.ExecutionSystem import ExecutionSystem
from Mobyle.MobyleError import MobyleError
from Mobyle.Admin import Admin
from Mobyle.Status import Status
from Mobyle.ConfigManager import Config
_cfg = Config()
__extra_epydoc_fields__ = [('call', 'Called by','Called by')]
class Dummy(ExecutionSystem):
"""
Run the commandline by ???
"""
def run(self, commandLine , dirPath , serviceName , jobKey , jobState , queue , xmlEnv ):
"""
Run the commandLine
redirect the standard error and output on service.name.out and service.name.err, then restore the sys.stderr and sys.stdout
@return: the L{Mobyle.Status.Status} of this job and a message
@rtype: Status object
"""
jobKey = self.getKey()
fout = open( serviceName + ".out" , 'w' )
ferr = open( serviceName + ".err" , 'w' )
try:
## execute the commandline through your favorite execution system
pass
except OSError, err:
msg= "System execution failed: " + str(err)
self._logError( dirPath , serviceName ,jobKey,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %( self.serviceName ,
jobKey ,
msg
)
)
raise MobyleError , msg
adm = Admin( dirPath )
adm.setExecutionAlias( self.execution_config_alias ) ## store the alias of execution config used for this job
adm.setNumber( jobKey ) ## store the key to query/retrieve this job on this system execution
adm.commit()
## link the .admin file in ADMINDIR which looklike to a "process table"
linkName = ( "%s/%s.%s" %(self. _cfg.admindir() ,
serviceName ,
jobKey
)
)
try:
os.symlink(
os.path.join( self.dirPath , '.admin') ,
linkName
)
except OSError , err:
msg = "can't create symbolic link %s in ADMINDIR: %s" %( linkName , err )
self._logError( dirPath , serviceName ,jobKey,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %( serviceName ,
jobKey ,
msg
)
)
raise MobyleError , msg
logging_shutdown() #close all loggers see issue #1075
## wait the completion of the job
## THIS CLASS MUST BE SYNCHRON WITH THE JOB
MLogger(child = True ) #reopen the logger
try:
## remove the job from the ADMINDIR ( "process table" )
os.unlink( linkName )
except OSError , err:
msg = "can't remove symbolic link %s in ADMINDIR: %s" %( linkName , err )
self._logError( dirPath , serviceName ,jobKey,
userMsg = "Mobyle internal server error" ,
logMsg = None )
_log.critical( "%s/%s : %s" %( self.serviceName ,
jobKey ,
msg
)
)
raise MobyleError , msg
##close the standard output and standard error file
fout.close()
ferr.close()
oldStatus = self.status_manager.getStatus( dirPath )
#if the oldStatus is terminal ( finish error killed )
#I don't modify this status
if oldStatus.isEnded():
return oldStatus
else:
## analyse the returncode of the job
## and instanciate a Status according the returncode
## then return the Status
status = Status( code = 4 ) #finished
return status
def getStatus( self , key ):
"""
@param key: the value associate to the key "NUMBER" in Admin object (and .admin file )
@type key: string
@return: the status of the job corresponding to the key
@rtype: Mobyle.Status.Status instance
@call: by L{Utils.getStatus}
"""
##query your execution system about the job with this key
##translate the answer in mobyle compliant status and message
## for mobyle status see Mobyle.Status.Status
mobyle_status_code = 3 # running
message = "my job is running"
return Status( code = mobyle_status_code , message = message )
def kill( self , key ):
"""
kill a job
@param key : the value associate to the key "NUMBER" in Admin object (and .admin file )
@type key: string
@raise MobyleError: if can't kill the job
@call: by L{Utils.Mkill}
"""
return None
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