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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 logging
import types
import glob
from Mobyle.MobyleLogger import MLogger
MLogger()
from Mobyle.Net import EmailAddress , checkHost
from Mobyle.MobyleError import MobyleError , UserValueError , UnDefAttrError , ServiceError ,UnSupportedFormatError , EvaluationError
from Mobyle.Job import Job
from Mobyle.Evaluation import Evaluation
from Mobyle.JobState import JobState , url2path as jobState_url2path
from Mobyle.Utils import getStatus as utils_getStatus , safeFileName , makeService
from Mobyle.Status import Status
from Mobyle.StatusManager import StatusManager
from Mobyle.Admin import Admin
_extra_epydoc_fields__ = [('call', 'Called by','Called by')]
class MobyleJob:
"""this class is the interface with the cgis to submit a job"""
def __init__(self, progUrl= None , email = None , service = None, params = None, evaluator = None , ID = None , session = None , cfg = None , workflowID = None , email_notify= 'auto', debug=None):
"""
We could instanciate a MobyleJob whith a progName or directly with a Service instance , with params or a Evaluation instance.
if we instanciate a MobyleJob with a progName mobyleJob will instanciate a service corresponding to this name .
you could provide the user parameters in a dictionary params which will used to fill an Evalution instance or provide directly the Evaluation instance.
@param progUrl: the url of a xml file
@type progUrl: String
@param email: the user Email address where the results will be sent
@type email: string or L{EmailAddress}
@param service: if you want to run a service which is already instanciate
@type service: a L{Service} instance
@param evaluator: an Evaluation instance
@type evaluator: L{Evaluation}
@param ID: the url of job, if an id is specified
@type ID: string
@param cfg: a config object
@type cfg: L{ConfigManager.Config} instance
@param workflowID: the url of the workflow ownre 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
@raise L{MobyleError}: if the id is not a valid url a MobyleError is raised
@todo: estce que passer un evaluateur a MobyleJob a toujours un sens avec la nouvelle architecture (creation de fichiers ... l'evaluateur a un nom de fichier comme valeur comment recuperer le contenu)
"""
self.m_log = logging.getLogger( __name__ )
if cfg is None:
from Mobyle.ConfigManager import Config
self.cfg = Config()
else:
self.cfg = cfg
if ID:
self.jobState = JobState( ID )
self._job = None
self._hasRun = True
else:
self.build_log = logging.getLogger('Mobyle.builder')
if progUrl:
jobName = os.path.basename( progUrl )[:-4]
elif service:
jobName = service.getName()
else:
raise MobyleError, "you must provide either a service or a service name"
## check the service availablity
serviceID = 'local.'+jobName
if self.cfg.isDisabled( serviceID ):
if self.cfg.isDisabled():
raise MobyleError, "Sorry, the server is not available for now."
else:
raise MobyleError, "Sorry, the program " + jobName +" is not available for now."
try:
remoteHost = os.environ[ 'REMOTE_HOST' ]
except KeyError:
remoteHost = None
try:
ip = os.environ[ 'REMOTE_ADDR' ]
except KeyError :
ip = 'local'
self._remote =( ip , remoteHost )
if self._remote[1]:
remoteLog = self._remote[1] #the remote host
else:
remoteLog = self._remote[0] #the remote addr
if session :
email = session.getEmail()
if email:
self.userEmail = EmailAddress( session.getEmail() )
resp = self.userEmail.checkBlackList()
if not resp.status:
raise UserValueError( msg = resp.user_message )
else:
self.userEmail = None
elif email :
if isinstance( email , types.StringTypes ):
self.userEmail = EmailAddress( email )
else:
self.userEmail = email
resp = self.userEmail.check()
if not resp.status:
msg = "%s %s %s %s" %( jobName ,
unicode( str( self.userEmail ).decode('ascii', 'replace')).encode( 'ascii', 'replace' ) ,
remoteLog ,
"FORBIDDEN "+ resp.message
)
self.m_log.info( msg )
raise UserValueError( msg = resp.user_message )
else:
self.userEmail = None
email_notify = email_notify.lower()
resp = checkHost()
if not resp.status:
msg = "%s %s %s %s %s" %( jobName,
unicode( str( email ).decode('ascii', 'replace')).encode( 'ascii', 'replace' ) ,
remoteLog ,
"FORBIDDEN ",
resp.message
)
self.m_log.warning( msg )
raise UserValueError( msg = resp.user_message )
## building the MobyleJob
self.progUrl = progUrl
self._service = service
self.params = params # a garder??
self._evaluator = evaluator
self.session = session
self._job = None #an instance of Mobyle.Job
self.jobState = None #an instance of JobState
self._adm = None
self._hasRun = False
if params is None:
if service is None:
if progUrl is None:
### TODO il n'y a pas encore de job de cree donc logger cette erreur ?
raise MobyleError, "you must provide either a service or a service url"
else:
if evaluator is None or not evaluator.isFill():
#self._service = self._makeService( progUrl )
try:
self._service = makeService( progUrl )
except MobyleError , err :
self._logError( userMsg = "Mobyle internal server error" )
raise MobyleError( err )
self._service = makeService( progUrl )
self._evaluator = self._service.getEvaluator()
else:
if evaluator.isFill():
try:
self._service = makeService( progUrl )
except MobyleError , err :
self._logError( userMsg = "Mobyle internal server error")
raise MobyleError( err )
self._service.setEvaluator( evaluator )
else: #service is not None
if self._evaluator is None or not self._evaluator.isFill():
self._evaluator = self._service.getEvaluator()
else:
self._service.setEvaluator( evaluator )
self._debug = debug or self.cfg.debug( self._service.getName() )
self._job = Job( self._service ,
self.cfg ,
userEmail = self.userEmail ,
session = self.session ,
workflowID = workflowID ,
email_notify = email_notify,
debug=debug
)
else: #params is not None
if service is None:
if progUrl is None:
raise MobyleError,"you must provide either a service a service url"
else:
self._service = makeService( progUrl )
self._evaluator = self._service.getEvaluator()
else: #service is not None
self._evaluator = Evaluation()
self._service.setEvaluator( self._evaluator )
self._debug = self.cfg.debug( self._service.getName() )
self._job = Job( self._service ,
userEmail = self.userEmail ,
session = self.session ,
workflowID = workflowID ,
email_notify = email_notify
)
############ in all cases except ID ###################
if self._debug > 1:
self.build_log.debug( "MobyleJob : params= " + str( params ) )
self.jobState = self._job.jobState
self._adm = Admin( self._job.getDir() )
###############################################################
#
#
#
###############################################################
def setSession(self , session ):
self.session = session
if self._job is not None:
self._job.setSession( session )
def _toFileAndConvert(self, parameter , value):
paramName = parameter.getName()
if len( value ) != 5 :
msg = "Problem with the infile : " + paramName
self._logError( logMsg = msg ,
userMsg = "Internal Mobyle Server Error"
)
raise UserValueError( parameter = parameter , msg = msg )
else:
destFileName , data , src , srcFileName, idx = value
if not destFileName and not data and not src:
data = None
src = None
elif destFileName and not ( data or src ):
msg = "parameter %s: is empty. please check your data" % paramName
self._logError( logMsg = msg ,
userMsg = msg
)
raise UserValueError( parameter = parameter , msg = msg )
elif data and src:
msg = "parameter %s: you cannot specify data and source at the same time" % paramName
self._logError( logMsg = msg ,
userMsg = msg
)
raise UserValueError( parameter = parameter , msg = msg )
elif not srcFileName and not data and src:
msg = "parameter %s: if you specify a src, you must specify a src file name" % paramName
self._logError( logMsg = msg ,
userMsg = msg
)
raise UserValueError( parameter = parameter , msg = msg )
elif not srcFileName and data and not src:
srcFileName = paramName + ".data"
# I put systematically the value in index.xml even if its the
# same as the previous value because the value is a filename
# and 2 files with the same name could have different contents
##fileName = basename
acceptedMobyleType = parameter.getType()
dataType = acceptedMobyleType.getDataType()
paramName = parameter.getName()
try:
fileName, sizeIn = dataType.toFile( data, self._job , destFileName, src , srcFileName )
except MobyleError, err:
msg = "%s/%s : %s : %s"%( self._service.getName(), self.getJobid() , paramName, err)
self.m_log.error( msg )
raise MobyleError( msg )
detectedMobyleType = acceptedMobyleType.detect( ( self._job, fileName ) )
acceptedFormats = acceptedMobyleType.getAcceptedFormats()
if detectedMobyleType.dataFormat is None :
self.jobState.addInputDataFile( paramName, ( fileName , sizeIn , 'not detected' ) )
self.jobState.commit()
if not acceptedFormats:
return fileName
elif ( set( [ f for f , r in acceptedFormats] )- set( dataType.supportedFormat() ) ):
# format accepted by the parameter - format supported by the conevrters
# case of a not detected format but the parameter accept some formats not supported by converter
self.m_log.warning("%s/%s : %s : a data format which has not been detected has been accepted in job" %( self._service.getName(), self.getJobid() , paramName ))
return fileName
else:
# case of a not detected format and the all format accepetd by the parameter are supported by the converters
msg = "Your %s format cannot be detected: please submit your data in one of the following formats: %s"%( dataType.getName() , dataType.supportedFormat() )
sm = StatusManager()
sm.setStatus( self.getDir() , Status( code= 5 , message= msg ))
raise UserValueError( parameter = parameter ,
msg = msg )
else: #the format of the data has been detected
outFileName = None
if not acceptedFormats:#if there isn't any accepted format => all formats are available
self.jobState.addInputDataFile( paramName ,
( fileName , sizeIn , detectedMobyleType.dataFormat ) ,
fmtProgram = detectedMobyleType.format_program
)
self.jobState.commit()
return fileName
if self._debug > 1:
self.build_log.debug("self._service.setValue( %s , %s )" %( paramName , fileName ) )
else:# some accepted format are specified
for out_format , force_reformat in acceptedFormats:
if detectedMobyleType.dataFormat == out_format:
if force_reformat:
continue
else:
self.jobState.addInputDataFile( paramName ,
( fileName , sizeIn , detectedMobyleType.dataFormat ) ,
fmtProgram = detectedMobyleType.format_program
)
self.jobState.commit()
outFileName = fileName
break
else:
continue
if outFileName is None:#the data must be converted
try:
outFileName , convertedMobyleType = detectedMobyleType.convert( ( self._job, fileName ) , acceptedMobyleType )
sizeOut = os.path.getsize( os.path.join( self._job.getDir(),outFileName ) )
self.jobState.addInputDataFile( paramName ,
( fileName , sizeIn , detectedMobyleType.dataFormat ) ,
fmtProgram = convertedMobyleType.format_program ,
formattedFile = ( outFileName , sizeOut , convertedMobyleType.dataFormat )
)
self.jobState.commit()
except UnSupportedFormatError ,err :
self.m_log.error( "UnSupportedFormatError:%s"%err ,exc_info=True)
msg = str( err )
sm = StatusManager()
sm.setStatus( self.getDir() , Status( code= 5 , message= msg ))
raise UserValueError( parameter = parameter , msg = msg )
except Exception, err:
self.m_log.error( str(err), exc_info= True)
return outFileName
def setValue( self , paramName , value ):
"""
set the value for one parameter. the value is cast in the right type. if the value cannot be cast a UserValueError is raised
@param paramName: the name of the parameter
@type paramName: string
@param value : the value of the parameter
@type value:
- for simple type: any
- for the infile: a tuple ( destFileName , content , src , srcFileName )
- the name of the file
- the data the content of the file , string or None
- the src where the file could be retrieve, MobyleJob , Job or Session instance or None
data is specified when data is new on the server.
src is specified when the data already exists on the server.
you can't specify data and src in the same time
@raise: MobyleError if the paramName doesn't match with any parameter name
"""
if self._hasRun:
msg = "MobyleJob.setValue this job has already ran"
self._logError( logMsg = msg ,
userMsg = msg
)
raise MobyleError , msg
if self._debug > 1:
self.build_log.debug( "\n--------------------- MobyleJob set user value for " + paramName + "--------------------" )
if paramName in self._service.getAllParameterNameByArgpos():
parameter = self._service.getParameter( paramName )
acceptedMobyleType = parameter.getType()
dataType = acceptedMobyleType.getDataType()
if value == '' :
value = None
if self._service.isInfile( paramName ):
###############################################################
if dataType.isMultiple():
fileNames = []
value.sort(key=lambda item:item[4])
for item in value:
#destFileName , data , src , srcFileName, idx = item
#destFileName file name in the destination folder
#data file contents (if src is None)
#src: folder where the source file can be found (if data is None)
#srcFileName: file name in the src folder (if data is None)
#idx: index in the ordered list of values
#self.m_log.debug( "destFileName=%s ,data=%s , src=%s , srcFileName=%s"% (destFileName , data , src , srcFileName))
fileName = self._toFileAndConvert( parameter , item )
fileNames.append( fileName )
parameter.setValue( fileNames )
if self._debug > 1:
self.build_log.debug("self._service.setValue( %s , %s )" %( paramName , fileNames ) )
else:#parameter is represents One file
fileName = self._toFileAndConvert( parameter , value )
parameter.setValue( fileName )
else : #the parameter is not an infile
oldValue = parameter.getValue()
try:
detectedMobyleType = dataType.detect( value )
if dataType.getName() == 'MultipleChoice':
if isinstance(value, types.StringTypes):
value = [value]
converted_value , convertedMobyleType = detectedMobyleType.convert( value , acceptedMobyleType , separator = parameter.getSeparator())
else:
converted_value , convertedMobyleType = detectedMobyleType.convert( value , acceptedMobyleType)
parameter.setValue( converted_value )
if self._debug > 1:
try:
self.build_log.debug( "self._service.setValue( %s , %s )" %( paramName , converted_value ) )
except:
self.build_log.debug( "!!!!!!!! problem during reporting log !!!!!!!!!!!!" )
except UserValueError , err:
msg = str( err )
self._logError( logMsg = msg ,userMsg = msg)
raise UserValueError(parameter=parameter, msg=msg)
newValue = parameter.getValue( )
if newValue != oldValue :
rawVdef = parameter.getVdef()
if rawVdef is None:
vdef = None
else:
vdef , vdefMT = detectedMobyleType.convert( rawVdef , acceptedMobyleType )
if parameter.getType().getDataType().getName() == 'MultipleChoice':
if vdef is not None:
sep = parameter.getSeparator()
vdef = sep.join( vdef)
if newValue == vdef :
if oldValue is not None and oldValue != vdef:
self.jobState.delInputData( paramName )
self.jobState.commit()
else:
self.jobState.setInputDataValue( paramName , newValue )
self.jobState.commit()
else:
msg = "the parameter named : %s doesn't exist in %s" %( paramName ,
self._service.getName()
)
self._logError( logMsg = msg ,
userMsg = msg
)
raise UserValueError( msg = msg )
def _validateParameters(self):
"""
verifie que le parametre est valide cad si c'est un choice qu'il appartient bien a la liste si c'est une sequence passe dans squizz ...
@raise UserValueError: throws UserValueError raised by checkUser
"""
if self._debug > 1:
self.build_log.debug("""\n
\t################################################
\t# #
\t# validation beginning #
\t# #
\t################################################
\n""")
for paramName in self._service.getAllParameterNameByArgpos():
###################################################
# #
# check if parameter have a value #
# #
###################################################
value = self._service.getValue(paramName)
if self._debug > 1:
self.build_log.debug("------------- " + paramName + " -------------")
self.build_log.debug("value= %s : type= %s"%( value , type(value) ) )
self.build_log.debug("service.precondHas_proglang( %s , 'python' ) = %s " %(
paramName ,
self._service.precondHas_proglang( paramName , 'python' )
)
)
if self._service.precondHas_proglang( paramName , 'python' ):
preconds = self._service.getPreconds( paramName , proglang='python' )
allPrecondTrue = True
for precond in preconds:
try:
evaluatedPrecond = self._evaluator.eval( precond )
except EvaluationError, err:
self.build_log.error("ERROR during precond evaluation: %s : %s"%( precond, err ) )
msg = "ERROR during %s %s precond evaluation: %s : %s" % ( self._service.getName(),
paramName ,
precond ,
err
)
self._logError( logMsg = msg ,
userMsg = "Internal Server Error"
)
raise MobyleError( "Internal Server Error" )
if self._debug > 1:
self.build_log.debug("precond= " + precond )
self.build_log.debug("eval precond= " + str( evaluatedPrecond ))
if not evaluatedPrecond :
allPrecondTrue = False
break
if not allPrecondTrue :
if self._debug > 1:
self.build_log.debug("next parameter")
continue #next parameter
else:
if self._debug > 1:
if self._service.precondHas_proglang( paramName, 'perl' ) :
self.build_log.debug( "################ WARNING ###################" )
self.build_log.debug( "had a precond code in Perl but not in Python" )
self.build_log.debug( "############################################" )
if value is None :
if self._debug > 1:
self.build_log.debug( " value is None " )
if self._service.ismandatory( paramName ):
msg = "The mandatory Parameter : %s, must be specified " % paramName
self._logError( logMsg = msg ,
userMsg = msg
)
raise UserValueError(parameter = self._service.getParameter( paramName ) ,
msg = "This parameter is mandatory" )
if self._debug > 1:
self.build_log.debug( "call service.validate( " + paramName + " )" )
try:
self._service.validate( paramName )
except UserValueError , err:
msg = str(err)
self.build_log.debug( msg )
self._logError( logMsg = msg ,
userMsg = msg
)
raise UserValueError ,err
except MobyleError , err:
msg = str(err)
self.build_log.debug( msg )
self._logError( logMsg = msg ,
userMsg = "Mobyle Internal Server Error"
)
raise MobyleError , err
####################################################
# #
# check if the Parameter have a secure paramfile #
# #
####################################################
try:
if self._debug > 1:
self.build_log.debug( "check if the Parameter have a secure paramfile" )
paramfile = self._service.getParamfile( paramName )
try:
safeParamfile = safeFileName( paramfile )
except UserValueError , err :
msg = str( err )
self._logError( logMsg = msg ,
userMsg = msg
)
raise UserValueError( parameter= self._service.getParameter( paramName ), msg = msg )
if not safeParamfile or safeParamfile != paramfile :
msg = "The Parameter:%s, have an unsecure paramfile value: %s " %( paramName ,
paramfile
)
if self._debug < 2 :
self._logError( logMsg = None ,
userMsg = "Mobyle Internal Server Error"
)
self.m_log.critical( "%s/%s : %s" %( self._service.getName(),
self._job.getKey() ,
msg
)
)
else:
self._logError( logMsg = msg ,
userMsg = "Mobyle Internal Server Error"
)
raise MobyleError , "Mobyle Internal Server Error"
else:
if self._debug > 1:
self.build_log.debug( "paramfile = %s ...........OK" % paramfile )
except UnDefAttrError :
if self._debug > 1:
self.build_log.debug("no paramfile")
pass
def _collisions(self):
"""
check if there is no potential collisions between the infiles and the output masks.
if ther is a risk of collision the input file is renamed
"""
paramsOut = self._service.getAllOutParameter( )
evaluator = self._service.getEvaluator()
allMasks = []
potCollisions =[]
for paramName in paramsOut :
if self._service.precondHas_proglang( paramName , 'python' ):
preconds = self._service.getPreconds( paramName , proglang='python' )
allPrecondTrue = True
for precond in preconds:
if not evaluator.eval( precond ) :
allPrecondTrue = False
break
if not allPrecondTrue :
continue #next parameter
unixMasks = self._service.getFilenames( paramName , proglang = 'python' )
service_name = self._service.getName()
#unixMasks += ["%s.out"%service_name , "%s.err"%service_name ]
allMasks += unixMasks
workdir = self.getDir()
for mask in unixMasks:
mask = os.path.join( workdir , mask )
Files = glob.glob( mask )
if Files:
self.m_log.warning( 'Potential Collision: %s input files match the \"%s\" output parameter mask %s' %( Files ,
paramName,
mask
) )
potCollisions += [ os.path.basename( f ) for f in Files ]
infiles = self._service.getAllInFileParameter()
for infileName in potCollisions:
for parameter in infiles:
oldNames = self.jobState.getInput( parameter.getName())
oldNames = [ fileName for fileName , size , fmt in oldNames ]
for oldName in oldNames:
if oldName == infileName:
newName = "mob_%s_collision" %( infileName )
parameter.renameFile( workdir , oldName, newName )
values = parameter.getValue()
sep = parameter.getSeparator()
if sep is not None:
values = values.split( sep )
if oldName in values: #the collision can be between input before conversion and output so the oldname is not in evaluator (seq.out -> seq.fasta)
oldName_i = values.index( oldName )
values[ oldName_i ] = newName
parameter.setvalue( values )
else:
if oldName == values:
parameter.setValue( newName )
self.jobState.renameInputDataFile( parameter.getName() , oldName, newName )
self.jobState.commit()
self.m_log.warning( '%s/%s : Potential Collision : %s file was renamed into %s' %( self._service.getName(),
self._job.getKey() ,
oldName ,
newName )
)
for mask in allMasks :
mask = os.path.join( workdir , mask )
collideFiles = glob.glob( mask )
if collideFiles:
msg= '%s/%s : Potential Collision: %s input files output mask %s' %( self._service.getName(),
self._job.getKey() ,
collideFiles ,
mask
)
self._logError( userMsg = "Mobyle Internal Server Error",
logMsg = msg
)
raise MobyleError , msg
def run(self):
"""
run a job
@raise MobyleError: L{MobyleError} if the job dosen't exist. or if session is not activated
"""
if self._job is not None:
if not self.cfg.isAuthorized( self._service.getName() , self._remote[0] ):
msg = "Sorry, you are not allowed to run this service."
logMsg = " %s try to access restricted service"%self._remote[0]
self._logError( userMsg = msg ,
logMsg = logMsg,
)
raise MobyleError( msg )
if self.session and not self.session.isActivated():
self._logError( userMsg = "session is not activated : run aborted" ,
logMsg = "session \"%s\" is not activated : run aborted" % self.session.getKey()
)
raise MobyleError( "session is not activated" )
# for security reason
# I remove some unsuful variable form environment
# to avoid to propagate them in all cluster nodes
# waiting a better model
for envVar in [ 'CONTENT_LENGTH' ,
'CONTENT_TYPE' ,
'GATEWAY_INTERFACE' ,
'HTTP_ACCEPT' ,
'HTTP_ACCEPT_ENCODING',
'HTTP_ACCEPT_LANGUAGE',
'HTTP_CACHE_CONTROL' ,
'HTTP_ACCEPT_CHARSET' ,
'HTTP_COOKIE' ,
'HTTP_CONNECTION' ,
'HTTP_KEEP_ALIVE' ,
'HTTP_PRAGMA' ,
'HTTP_REFERER' ,
'HTTP_USER_AGENT' ,
'HTTP_X_PROTOTYPE_VERSION',
'HTTP_X_REQUESTED_WITH',
'QUERY_STRING' ,
'SERVER_ADMIN' ,
'REQUEST_METHOD' ,
'REQUEST_URI' ,
'SCRIPT_FILENAME' ,
'SCRIPT_NAME' ,
#'SERVER_NAME' ,
#'SERVER_PORT' ,
'SERVER_PROTOCOL' ,
'SERVER_SIGNATURE' ,
'SERVER_SOFTWARE' ,
]:
try:
del( os.environ[ envVar ])
except KeyError:
pass
for var in os.environ.keys():
if os.environ[var].startswith('()'):
self.m_log.critical( "Security Error: %s/%s : unsafe var %s=%s : Bash vulnerabilty Exploitation'" %
( self._service.getName() , self._job.key, var, os.environ[var] ))
self._logError(userMsg = "Mobyle internal server error")
raise MobyleError, "Mobyle internal server error"
self._validateParameters()
#do the controls specified in the Xml file
if self._debug > 1:
self.build_log.debug("""\n
\t################################################
\t# #
\t# xml controls beginning #
\t# #
\t################################################
\n""")
for paramName in self._service.getAllParameterNameByArgpos():
hasCtrl = self._service.has_ctrl( paramName )
hasScale = self._service.hasScale( paramName , proglang = 'python' )
if hasCtrl or hasScale:
if self._debug > 1:
self.build_log.debug("------------- " + paramName + " -------------")
self.build_log.debug("service.precondHas_proglang( %s , 'python' ) = %s " %(
paramName ,
self._service.precondHas_proglang( paramName , 'python' )
))
if self._service.precondHas_proglang( paramName , 'python' ):
preconds = self._service.getPreconds( paramName , proglang='python' )
allPrecondTrue = True
for precond in preconds:
evaluatedPrecond = self._evaluator.eval( precond )
if self._debug > 1:
self.build_log.debug("precond= " + precond )
self.build_log.debug("eval precond= " + str( evaluatedPrecond ))
if not evaluatedPrecond :
allPrecondTrue = False
break
if not allPrecondTrue :
if self._debug > 1:
self.build_log.debug("next parameter")
continue #next parameter
if hasCtrl:
if self._service.getValue( paramName ) is not None:
try:
self._service.doCtrls( paramName )
except ServiceError , err:
# when the parameterName doesn't exist
# or an error occured during the python code evaluation ( see parameter.doCrtls() )
msg = str( err )
self._logError( logMsg = msg , userMsg = "Internal Mobyle server Error" )
raise MobyleError , msg
except UserValueError , err:
msg = str( err )
self._logError( logMsg = msg , userMsg = msg )
raise err
else:
if self._debug > 1:
self.build_log.debug("undefined value: next parameter")
continue
if hasScale:
if self._debug > 1:
self.build_log.debug( paramName + " has scale= True" )
try:
isInScale = self._service.isInScale( paramName , proglang = 'python')
if self._debug > 1:
self.build_log.debug( "isInScale= " + str( isInScale ) )
if isInScale:
continue
else:
smin ,smax , incr = self._service.getScale( paramName , proglang = 'python')
msg = "%s value: %s is not in scale ( %s , %s )" %(
paramName ,
self._service.getValue( paramName ) ,
smin ,
smax )
self._logError( logMsg = msg , userMsg = msg )
parameter = self._service.getParameter( paramName )
raise UserValueError( parameter = parameter , msg = msg )
except ValueError , err :
msg = paramName + " value is None. Thus it is not in scale"
self._logError(logMsg = msg , userMsg = msg )
raise MobyleError , msg
else:
if self._debug > 1:
self.build_log.debug("has scale= False" )
continue
self._collisions()
self._hasRun = True
self._job.run()
return self._job.getURL()
else:
if self._hasRun:
msg = "MobyleJob.run this job has already ran"
else:
msg = "MobyleJob.run: can't run the job (%s). It doesn't exist" % self._job.getURL()
self._logError( logMsg = msg , userMsg = msg )
raise MobyleError , msg
####################################################################
#
# get job info
#
####################################################################
def getDir(self):
"""
@return: the directory absolute path where the job is executed
@rtype: string
@call: cgiJob.printResult()
"""
if self._job:
return self._job.getDir()
elif self.jobState:
url = self.jobState.getID()
return jobState_url2path( url )
else:
return None
def getDate(self):
"""
@return: the submission date of this job
@rtype: string
@call: cgiJob.submit()
"""
if self._job:
return self._job.getDate()
else:
return None
def getJobid(self):
"""
@return: url where the job is executed
@rtype: string
"""
if self.jobState:
return self.jobState.getID()
else:
return None
def getOutputs(self):
"""
@return: a dictionary where the keys are the parameter name and the values a list of files which are produced by this parameter.
@rtype: dict
"""
if self.jobState:
if self._hasRun:
return self.jobState.getOutputs()
else:
msg = "try to get results but the job had not run"
raise MobyleError , msg
else:
return None
def getOutput(self , paramName ):
"""
@return: the list of results files names. if there is no files for this parameter return None
@rtype: list of tuples ( string filename , long size , string fmt or None )
"""
if self.jobState:
if self._hasRun:
return self.jobState.getOutput( paramName )
else:
msg = "try to get result but the job had not run"
raise MobyleError , msg
else:
return None
def getOutputFile( self, fileName ):
"""
@param fileName:
@type fileName: String
@return: the content of a output file as a string
@rtype: string
@raise exception:
"""
if self.jobState:
if self._hasRun:
return self.jobState.getOutputFile( fileName )
else:
msg = "try to get result but the job had not run"
raise MobyleError , msg
else:
return None
def isLocal( self ):
"""
"""
if self.jobState:
return self.jobState.isLocal()
def getStatus(self):
"""
@return: the status of the job
@rtype: L{Mobyle.Status.Status} instance
"""
if self.jobState:
return utils_getStatus( self.jobState.getID() )
else:
return None
def isFinished(self):
"""
@return: True if the job is finished, False Otherwise
@rtype: boolean
"""
if self.jobState:
sm = StatusManager()
status = sm.getStatus( self.jobState.getDir() )
return status.isEnded()
else:
return None
def getCommandLine(self):
"""
@return: the Command line
@rtype: string
"""
if self.jobState:
if self._hasRun:
return self.jobState.getCommandLine()
else:
msg = "try to get the command but the job had not run"
raise MobyleError , msg
else:
return None
def getDataPrompt(self , paramName ):
"""
@return: the prompt for an In/Output parameter
@rtype: string
"""
if self.jobState:
if self._hasRun:
return self.jobState.getPrompt( paramName )
else:
msg = "try to get the command but the job had not run"
raise MobyleError , msg
else:
return None
def getStdout(self):
"""
@return: the content of the job stdout as a string
@rtype: string
@raise MobyleError: if the job is not finished raise a L{MobyleError}
"""
if self.jobState:
if self._hasRun:
return self.jobState.getStdout()
else:
msg = "try to get the job stdout, but the job had not run"
raise MobyleError , msg
else:
return None
def getStderr(self):
"""
@return: the content of the job stderr as a string
@rtype: string
@raise MobyleError: if the job is not finished raise a L{MobyleError}
"""
if self.jobState:
return self.jobState.getStderr()
else:
return None
def open(self , fileName ):
"""
return an file object if the file is local or a file like object if the file is distant
we could apply the same method on this object: read(), readline(), readlines(), close(). (unlike file the file like object doesn't implement an iterator).
@param fileName: the name of the file (given by getResults).
@type fileName: string
@return: a file or file like object, or None if the job isn't ran.
"""
if self.jobState:
return self.jobState.open( fileName )
else:
return None
def getArgs(self):
"""
read the parameters in the .index.xml file and return a dictionary containig these parameters
@return: the parameters of a job
@rtype: dictionary
"""
if self.jobState:
return self.jobState.getArgs()
else:
return None
def _logError( self , userMsg = None , logMsg = None ):
if userMsg:
sm = StatusManager ()
sm.setStatus( self.getDir() , Status( code = 5 , message = userMsg ) )
if logMsg :
self.m_log.error( "%s/%s : %s" %( self._service.getName() ,
self._job.getKey() ,
logMsg
)
)
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