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########################################################################################
# #
# Author: Bertrand Neron, #
# Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. #
# Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. #
# #
########################################################################################
import logging
import sys
import os
import re
import types
MOBYLEHOME = None
if os.environ.has_key('MOBYLEHOME'):
MOBYLEHOME = os.environ['MOBYLEHOME']
if not MOBYLEHOME:
sys.exit('MOBYLEHOME must be defined in your environment')
if ( MOBYLEHOME ) not in sys.path:
sys.path.append( MOBYLEHOME )
if ( os.path.join( MOBYLEHOME , 'Src' ) ) not in sys.path:
sys.path.append( os.path.join( MOBYLEHOME , 'Src' ) )
from Dispatcher import DefaultDispatcher
from Mobyle.MobyleError import MobyleError , ConfigError
MOBYLEHTDOCS = None
class MetaSingleton(type):
def __init__(cls , name , bases , classdict ):
cls._ref = None
def __call__(cls , *args , **kwargs ):
if cls._ref:
return cls._ref
else:
instance = cls.__new__(cls, *args , **kwargs )
instance.__init__( *args , **kwargs )
cls._ref = instance
return instance
class Config( object ):
"""
this class is designed as the singleton pattern
(ref: Programmation Python , Tarek Ziade .p 483).
there is only one instance at once.
this class parse the file local/Config/Config.py
raise error fix default values raise error if needed.
all other Mobyle classes must use this class to access
to a configuration information.
"""
__metaclass__ = MetaSingleton
def __init__(self):
self.__version = '1.5.5'
import Local.Config.Config
import Local.Config.Execution
#############################
#
# logging
#
##############################
try:
self._logdir = Local.Config.Config.LOGDIR
except AttributeError:
self._logdir = "/dev/null"
msg = "LOGDIR not found in Local/Config/Config.py"
print >> sys.stderr, "%s . It sets to %s" % ( msg , self._logdir )
self.log = logging.getLogger('Mobyle.Config')
self.log.propagate = False
try:
defaultHandler = logging.FileHandler( os.path.join( self._logdir , 'error_log' ) , 'a')
except :
print >> sys.stderr , " WARNING : can't access to logfile. Logs will redirect to /dev/null"
defaultHandler = logging.FileHandler( '/dev/null' , 'a' )
defaultFormatter = logging.Formatter(
'%(name)-10s : %(levelname)-8s : L %(lineno)d : %(asctime)s : %(message)s' ,
'%a, %d %b %Y %H:%M:%S'
)
#defaultHandler.setLevel( logging.DEBUG )
defaultHandler.setFormatter( defaultFormatter )
self.log.addHandler( defaultHandler )
if os.path.exists( MOBYLEHOME ):
self._mobylehome = os.path.realpath( MOBYLEHOME )
else:
raise MobyleError , "MOBYLEHOME is not defined"
######################
#
# Mandatory values
#
######################
try: #old style config
if os.path.exists( Local.Config.Config.DOCUMENT_ROOT ):
self._mobyle_htdocs = os.path.realpath( Local.Config.Config.DOCUMENT_ROOT )
else:
msg = "DOCUMENT_ROOT: %s does not exist" % Local.Config.Config.DOCUMENT_ROOT
self.log.error( msg )
raise ConfigError , msg
except AttributeError:
if MOBYLEHTDOCS: #define by new installer
if os.path.exists( MOBYLEHTDOCS ):
self._mobyle_htdocs = os.path.realpath( MOBYLEHTDOCS )
else: #never happen ?
msg = "bad installation option --install-htdocs : %s no such directory " % MOBYLEHTDOCS
raise ConfigError , msg
else:
try: #define in Config.py witout installer but with new style config
if os.path.exists( Local.Config.Config.MOBYLEHTDOCS ):
self._mobyle_htdocs = os.path.realpath( Local.Config.Config.MOBYLEHTDOCS )
else:
msg = "MOBYLEHTDOCS: %s no such directory" % Local.Config.Config.MOBYLEHTDOCS
self.log.error( msg )
raise ConfigError , msg
except AttributeError:
msg = "error during installation or configuration MOBYLEHTDOCS not found"
self.log.error( msg )
raise ConfigError , msg
try:
self._root_url = Local.Config.Config.ROOT_URL.strip( '/' )
except AttributeError:
msg = "ROOT_URL not found in Local/Config/Config.py"
self.log.error( msg )
raise ConfigError , msg
try:
self._cgi_prefix = Local.Config.Config.CGI_PREFIX.strip( '/' )
except AttributeError:
msg = "CGI_PREFIX not found in Local/Config/Config.py"
self.log.error( msg )
raise ConfigError , msg
try:
self._htdocs_prefix = Local.Config.Config.HTDOCS_PREFIX.strip( '/' )
except AttributeError:
msg = "HTDOCS_PREFIX not found in Local/Config/Config.py"
self.log.error( "HTDOCS_PREFIX not found in Local/Config/Config.py" )
raise ConfigError , msg
if self._htdocs_prefix is not None :
self._portal_prefix = self._htdocs_prefix + '/portal'
self._portal_prefix = self._portal_prefix.lstrip( '/' )
self._portal_path = os.path.realpath( os.path.join( self._mobyle_htdocs , 'portal' ) )
######################
#
# default values
#
#######################
self._debug = 0
self._particular_debug = {}
self._accounting = False
self._session_debug = None
self._status_debug = False
if self._htdocs_prefix:
self._repository_url = "%s/%s/%s" % ( self._root_url , self._htdocs_prefix , 'data' )
else:
self._repository_url = "%s/%s" % ( self._root_url , 'data' )
self._results_url = "%s/%s" % ( self._repository_url , 'jobs' )
self._user_sessions_url = "%s/%s" % ( self._repository_url , 'sessions' )
self._servers_url = "%s/%s/%s" % ( self._repository_url , 'services' , 'servers' )
self._repository_path = os.path.realpath( os.path.join( self._mobyle_htdocs , 'data' ) )
self._services_path = os.path.realpath( os.path.join( self._repository_path , 'services' ) )
self._servers_path = os.path.realpath( os.path.join( self._services_path, 'servers' ) )
self._index_path = os.path.realpath( os.path.join( self._services_path ,'index' ) )
self._results_path = os.path.realpath( os.path.join( self._repository_path , 'jobs' ) )
self._user_sessions_path = os.path.realpath( os.path.join( self._repository_path , 'sessions' ) )
#OPENID
self._openidstore_path = os.path.realpath( os.path.join( self._repository_path , 'openidstore' ) )
self._binary_path = []
self._format_detector_cache_path = None
self._databanks_config = {}
self._dns_resolver = False
self._opt_email = False
self._particular_opt_email = {}
self._anonymous_session = "captcha"
self._authenticated_session = 'email'
#OPENID
self._openid = False
self._refresh_frequency = 240
self._dont_email_result = False
self._filelimit = 2147483648 # 2 Gib
self._sessionlimit = 52428800 # 50 Mib
self._previewDataLimit = 1048576 # 1 Mib
self._max_similar_job_per_user = 1
self._max_job_per_user = 0
self._result_remain = 10 # in day
self._lang = 'en'
self._email_delay = 20
self._dataconverter = {}
self._execution_system_alias = { 'SYS' : Local.Config.Execution.SYSConfig() }
self._dispatcher = DefaultDispatcher( { 'DEFAULT' : ( self._execution_system_alias[ 'SYS' ] , '' ) } )
self._services_deployment_include = { 'programs' : [ '*' ] ,
'workflows' : [ '*' ] ,
'viewers' : [ '*' ] ,
'tutorials' : [ '*' ] ,
}
self._services_deployment_exclude = { 'programs' : [] ,
'workflows' : [] ,
'viewers' : [] ,
'tutorials' : [] ,
}
self._module_init = None
self._module_load= {}
self._disable_all = False
self._disabled_services = []
self._authorized_services = {}
self._all_portals = {}
self._exported_services = []
try:
self._accounting = Local.Config.Config.ACCOUNTING
except AttributeError:
self.log.info( "ACCOUNTING not found in Local/Config/Config.py, set ACCOUNTING= %s" %self._accounting )
try:
self._session_debug = Local.Config.Config.SESSION_DEBUG
except AttributeError:
pass
try:
self._status_debug = Local.Config.Config.STATUS_DEBUG
except AttributeError:
pass
######################
#
# Directories
#
######################
## in htdocs ##
#OPENID
try:
if os.path.exists( Local.Config.Config.OPENIDSTORE_PATH ):
self._openidstore_path = os.path.realpath( Local.Config.Config.OPENIDSTORE_PATH )
else:
msg = "OPENIDSTORE_PATH: %s does not exit" % Local.Config.Config.OPENIDSTORE_PATH
self.log.error( msg )
raise ConfigError , msg
except AttributeError, err:
self.log.debug( "OPENIDSTORE_PATH not found in Local/Config/Config.py default value used : " +str( self._openidstore_path) )
## out web ##
self._admindir = os.path.join( self._results_path , 'ADMINDIR' )
try:
binary_path = []
for path in Local.Config.Config.BINARY_PATH:
binary_path.append( path )
self._binary_path = binary_path
except AttributeError:
self.log.warning( "BINARY_PATH not found in Local/Config/Config.py the default web server path will be used" )
try:
if os.path.exists( Local.Config.Config.FORMAT_DETECTOR_CACHE_PATH ):
self._format_detector_cache_path = os.path.realpath( Local.Config.Config.FORMAT_DETECTOR_CACHE_PATH )
else:
msg = "FORMAT_DETECTOR_CACHE_PATH: %s does not exit" % Local.Config.Config.FORMAT_DETECTOR_CACHE_PATH
self.log.error( msg )
raise ConfigError , msg
except AttributeError:
pass
try:
self._databanks_config = Local.Config.Config.DATABANKS_CONFIG
except AttributeError:
self.log.info( "No databanks are found in Local/Config/Config.py" )
#######################
#
# debug
#
#######################
try:
debug = Local.Config.Config.DEBUG
if debug >= 0 or debug <= 3:
self._debug = debug
else:
self.log.warning( "DEBUG must be >= 0 and <= 3 I found DEBUG =%s, DEBUG is set to %i" % ( debug , self._debug ) )
except AttributeError:
self.log.info( "DEBUG not found in Local/Config/Config.py, DEBUG is set to %i" % self._debug )
try:
self._particular_debug = Local.Config.Config.PARTICULAR_DEBUG
except AttributeError:
self.log.info( "PARTICULAR_DEBUG not found in Local/Config/Config.py" )
#######################
#
# Mail
#
#######################
try:
if type( Local.Config.Config.MAINTAINER ) == types.ListType or type( Local.Config.Config.MAINTAINER ) == types.TupleType :
self._maintainer = Local.Config.Config.MAINTAINER
else:
self._maintainer = [ Local.Config.Config.MAINTAINER ]
if type( Local.Config.Config.HELP ) == types.ListType or type( Local.Config.Config.HELP ) == types.TupleType :
self._help = Local.Config.Config.HELP
else:
self._help = [ Local.Config.Config.HELP ]
self._mailhost = Local.Config.Config.MAILHOST
except AttributeError, err:
msg = str(err).split()[-1] + "not found in Local/Config/Config.py"
self.log.error( msg )
raise ConfigError , msg
try:
self._sender = Local.Config.Config.SENDER
except AttributeError, err:
self._sender = ", ".join( self._help )
self.log.info( "SENDER not found in Local/Config/Config.py , set SENDER to HELP ")
try:
self._dns_resolver = Local.Config.Config.DNS_RESOLVER
except AttributeError:
self.log.info( "DNS_RESOLVER not found in Local/Config/Config.py, set DNS_RESOLVER to False" )
#######################
#
# Statistics
#
#######################
#GOOGLE ANALYTICS
try:
self._GAcode = Local.Config.Config.GACODE
except AttributeError:
self._GAcode = None
#######################
#
# Welcome page configuration
#
#######################
try:
self._welcome_config = Local.Config.Config.WELCOME_CONFIG
except AttributeError:
self._welcome_config = {}
#######################
#
# Portal customization
#
#######################
try:
self._custom_portal_header = Local.Config.Config.CUSTOM_PORTAL_HEADER
except AttributeError:
self._custom_portal_header = None
try:
self._custom_portal_footer = Local.Config.Config.CUSTOM_PORTAL_FOOTER
except AttributeError:
self._custom_portal_footer = None
#######################
#
# Authentication
#
#######################
#OPENID
try:
self._openid = Local.Config.Config.OPENID
except AttributeError:
self.log.info("OPENID not found in Local/Config/Config.py")
try:
self._opt_email = Local.Config.Config.OPT_EMAIL
except AttributeError:
self.log.info( "OPT_EMAIL not found in Local/Config/Config.py, set OPT_EMAIL to %s" % self._opt_email )
try:
self._particular_opt_email = Local.Config.Config.PARTICULAR_OPT_EMAIL
except AttributeError:
self.log.info( "PARTICULAR_OPT_EMAIL not found in Local/Config/Config.py, use OPT_EMAIL for all services" )
try:
self._anonymous_session = Local.Config.Config.ANONYMOUS_SESSION
try:
self._anonymous_session = self._anonymous_session.lower()
except AttributeError:
self._anonymous_session = "captcha"
self.log.warning( "ANONYMOUS_SESSION have a wrong value: " + str( Local.Config.Config.ANONYMOUS_SESSION ) + " , set to \"%s\"" %self._anonymous_session)
if self._anonymous_session == "yes" or self._anonymous_session == "y":
self._anonymous_session = "yes"
elif self._anonymous_session == "no" or self._anonymous_session == "n":
self._anonymous_session = "no"
elif self._anonymous_session != "captcha":
self._anonymous_session = "captcha"
self.log.warning( "ANONYMOUS_SESSION have a wrong value: " + str( Local.Config.Config.ANONYMOUS_SESSION ) + " , set to \"captcha\"" )
except AttributeError:
self.log.info( "ANONYMOUS_SESSION not found in Local/Config/Config.py, set to default value: \"%s\"" %self._anonymous_session )
try:
self._authenticated_session = Local.Config.Config.AUTHENTICATED_SESSION
if self._authenticated_session not in ( "email" ,"no" ,"yes" ):
self.log.warning( "AUTHENTICATED_SESSION have a wrong value: %s set to \"%s\""%( Local.Config.Config.AUTHENTICATED_SESSION ,
self._authenticated_session ) )
if self._anonymous_session == "no" and not self._authenticated_session :
msg = "anonymous session AND authenticated session are disabled. you can't disabled both"
self.log.error( msg )
raise ConfigError , msg
except AttributeError , err :
self.log.info( "AUTHENTICATED_SESSION not found in Local/Config/Config.py , set to default value: \"%s\"" %self._authenticated_session )
try:
self._refresh_frequency = Local.Config.Config.REFRESH_FREQUENCY
except AttributeError:
self.log.info( "REFRESH_FREQUENCY not found in Local/Config/Config.py, set to %s" % self._refresh_frequency )
########################
#
# results
#
########################
try:
self._dont_email_result = Local.Config.Config.DONT_EMAIL_RESULTS
except AttributeError:
self.log.info( "DONT_EMAIL_RESULTS not found in Local/Config/Config.py, set DONT_EMAIL_RESULTS to %s" %self._dont_email_result)
try:
self._maxmailsize = Local.Config.Config.MAXMAILSIZE
except AttributeError:
if not self._dont_email_result :
self.log.info("MAXMAILSIZE not found in Local/Config/Config.py but DONT_EMAIL_RESULTS is False, I set MAXMAILSIZE = 2 Mo")
self._maxmailsize = 2097152
else:
self._maxmailsize = None
try:
self._filelimit = int( Local.Config.Config.FILELIMIT )
except AttributeError:
self.log.info( "FILELIMIT not found in Local/Config/Config.py, set FILELIMIT to %d Gib" %( self._filelimit / 1073741824 ) )
except ValueError:
msg = "FILELIMIT have an invalid value : %s .\nIt must be an integer" % self._filelimit
self.log.error( msg )
raise ConfigError , msg
try:
self._sessionlimit = int( Local.Config.Config.SESSIONLIMIT )
except AttributeError:
self.log.info( "SESSIONLIMIT not found in Local/Config/Config.py, set SESSIONLIMIT to %d Mib" %( self._sessionlimit / 1048576 ) )
except ValueError:
msg = "SESSIONLIMIT have an invalid value : %s .\nIt must be an integer" % self._sessionlimit
self.log.error( msg )
raise ConfigError , msg
try:
self._previewDataLimit = int( Local.Config.Config.PREVIEW_DATA_LIMIT )
except AttributeError:
self.log.info( "PREVIEW_DATA_LIMIT not found in Local/Config/Config.py, set PREVIEW_DATA_LIMIT to %d Mib"%( self._previewDataLimit / 1048576 ) )
except ValueError:
msg = "PREVIEW_DATA_LIMIT have an invalid value : %s .\nIt must be an integer" % self._sessionlimit
self.log.error( msg )
raise ConfigError , msg
try:
self._result_remain = int( Local.Config.Config.RESULT_REMAIN )
except AttributeError:
self.log.info( "RESULT_REMAIN not found in Local/Config/Config.py, set RESULT_REMAIN to %d days" %( self._result_remain ))
except ValueError:
msg = "RESULT_REMAIN have an invalid value : %s .\nIt must be an integer" % Local.Config.Config.RESULT_REMAIN
self.log.error( msg )
raise ConfigError , msg
try:
self._max_similar_job_per_user = int( Local.Config.Config.MAX_SIMILAR_JOB_PER_USER )
if self._max_similar_job_per_user < 0 :
msg = "MAX_SIMILAR_JOB_PER_USER have an invalid value : %s .\nIt must be a positive or null integer" % Local.Config.Config.MAX_SIMILAR_JOB_PER_USER
self.log.error( msg )
raise ConfigError , msg
except AttributeError:
try:
self._max_similar_job_per_user = int( Local.Config.Config.SIMULTANEOUS_JOBS )
if self._max_similar_job_per_user < 0 :
msg = "SIMULTANEOUS_JOBS have an invalid value : %s .\nIt must be a positive or null integer" % Local.Config.Config.SIMULTANEOUS_JOBS
self.log.error( msg )
self.log.warning( "SIMULTANEOUS_JOBS has been replaced by MAX_SIMILAR_JOB_PER_USER please update you config (see UPDATE file)")
raise ConfigError , msg
except AttributeError:
self.log.info( "MAX_SIMILAR_JOB_PER_USER not found in Local/Config/Config.py, set MAX_SIMILAR_JOB_PER_USER to %d " %( self._max_similar_job_per_user ))
except ValueError:
msg = "SIMULTANEOUS_JOBS have an invalid value : %s .\nIt must be a positive or null integer" % Local.Config.Config.SIMULTANEOUS_JOBS
self.log.error( msg )
raise ConfigError , msg
except ValueError:
msg = "MAX_SIMILAR_JOB_PER_USER have an invalid value : %s .\nIt must be a positive or null integer" % Local.Config.Config.MAX_SIMILAR_JOB_PER_USER
self.log.error( msg )
raise ConfigError , msg
try:
self._max_job_per_user = int( Local.Config.Config.MAX_JOB_PER_USER )
if self._max_job_per_user < 0 :
msg = "MAX_JOB_PER_USER have an invalid value : %s .\nIt must be a positive or null integer" % Local.Config.Config.MAX_JOB_PER_USER
self.log.error( msg )
raise ConfigError , msg
except AttributeError:
self.log.info( "MAX_JOB_PER_USER not found in Local/Config/Config.py, users can submit as many jobs as they wants")
except ValueError:
msg = "MAX_JOB_PER_USER have an invalid value : %s .\nIt must be a positive or null integer" % Local.Config.Config.MAX_JOB_PER_USER
self.log.error( msg )
raise ConfigError , msg
#############################
#
# CONVERTER
#
#############################
try:
self._dataconverter = Local.Config.Config.DATA_CONVERTER
for dtype in Local.Config.Config.DATA_CONVERTER:
self._dataconverter[ dtype ] = Local.Config.Config.DATA_CONVERTER[ dtype ]
except AttributeError:
pass
##############################
#
# Misc
#
##############################
try:
self._lang = Local.Config.Config.LANG
except AttributeError:
self.log.info( "LANG not found in Local/Config/Config.py, set LANG to %s" % self._lang)
try:
self._email_delay = Local.Config.Config.EMAIL_DELAY
except AttributeError:
try:
self._email_delay = Local.Config.Config.TIMEOUT
self.log.info( "TIMEOUT is deprecated and replaced by EMAIL_DELAY, set EMAIL_DELAY to %d" % self._email_delay)
except AttributeError:
self.log.info( "EMAIL_DELAY not found in Local/Config/Config.py, set EMAIL_DELAY to %d" % self._email_delay)
##############################
#
# BATCH
#
##############################
try:
self._execution_system_alias = Local.Config.Config.EXECUTION_SYSTEM_ALIAS
except AttributeError:
msg = "EXECUTION_SYSTEM_ALIAS not found in Local/Config/Config.py, it is set to %s" % self._execution_system_alias.values()[0]
self.log.warning( msg )
if not self._execution_system_alias:
self._execution_system_alias = { 'SYS' : Local.Config.Execution.SYSConfig() }
msg = "EXECUTION_SYSTEM_ALIAS in Local/Config/Config.py is empty. it is fill with %s" % self._execution_system_alias[ 'SYS' ]
self.log.warning( msg )
try:
self._dispatcher = Local.Config.Config.DISPATCHER
except AttributeError:
default_alias_name , default_alias = self._execution_system_alias.items()[0]
msg = "DISPATCHER not found in Local/Config/Config.py, it is set to { 'DEFAULT' : %s }" % default_alias_name
self.log.warning( msg )
self._revert_alias = dict( [ ( config , alias ) for alias , config in self._execution_system_alias.items() ] )
try:
self._default_Q = Local.Config.Config.DEFAULT_Q
except AttributeError:
self._default_Q = 'mobyle'
self.log.info( "DEFAULT_Q not found in Local/Config/Config.py. it is set to mobyle" )
try:
self._particular_Q = Local.Config.Config.PARTICULAR_Q
except AttributeError:
self.log.info( "PARTICULAR_Q not found in Local/Config/Config.py" )
try:
self._module_init = Local.Config.Config.MODULE_INIT.strip()
except AttributeError:
self.log.info( "MODULE_INIT not found in Local/Config/Config.py" )
try:
self._module_load = Local.Config.Config.MODULE_LOAD
except AttributeError:
self.log.info( "MODULE_LOAD not found in Local/Config/Config.py" )
if self._module_load and not self._module_init:
msg = "MODULE_LOAD is specified Local/Config/Config.py but not MODULE_INIT"
self.log.error(msg)
raise ConfigError( msg )
elif self._module_init:
self._module_init = os.path.abspath(os.path.realpath( self._module_init ))
if not os.path.exists(self._module_init):
msg = "MODULE_INIT= %s: No such file" % self._module_init
self.log.error(msg)
raise ConfigError( msg )
##########################
#
# services publication
#
###########################
try:
self._services_deployment_exclude.update( Local.Config.Config.LOCAL_DEPLOY_EXCLUDE )
except ( AttributeError , NameError ):
self.log.info( "LOCAL_DEPLOY_EXCLUDE not found in Local/Config/Config.py" )
try:
self._services_deployment_include.update( Local.Config.Config.LOCAL_DEPLOY_INCLUDE )
except ( AttributeError , NameError ):
self.log.info( "LOCAL_DEPLOY_INCLUDE not found in Local/Config/Config.py" )
#############################
#
# disabled service
#
#############################
try:
self._disable_all = Local.Config.Config.DISABLE_ALL
except AttributeError:
msg = "DISABLE_ALL not found in Local/Config/Config.py,set to %s" % self._disable_all
self.log.info( msg )
try:
self._disabled_services = Local.Config.Config.DISABLED_SERVICES
except AttributeError:
msg = "DISABLED_SERVICES not found in Local/Config/Config.py,"
self.log.info( msg )
#########################################
#
# restriction services access
#
#########################################
try:
self._authorized_services = Local.Config.Config.AUTHORIZED_SERVICES
except AttributeError:
self.log.info( "AUTHORIZED_SERVICES not found in Local/Config/Config.py" )
#########################################
#
# Grid aspects
#
#########################################
self._portal_name = "anonymous"
try:
self._portal_name = Local.Config.Config.PORTAL_NAME
except AttributeError:
pass
self._simple_forms_active = False
try:
self._simple_forms_active = Local.Config.Config.SIMPLE_FORMS
except AttributeError:
pass
try:
self._all_portals = Local.Config.Config.PORTALS
for portal in self._all_portals .keys():
self._all_portals[ portal ][ 'url' ] = self._all_portals[ portal ][ 'url' ].rstrip( '/')
self._all_portals[ portal ][ 'repository' ] = "%s/%s" % ( self._all_portals[ portal ][ 'repository' ].rstrip( '/') ,
'data' )
#self._all_portals[ portal ][ 'jobsBase' ] = self._all_portals[ portal ][ 'jobsBase' ].rstrip( '/')
except KeyError , err:
msg = "error PORTALS : %s is not properly defined : %s" % ( portal , err )
self.log.warning( msg )
try:
del self._all_portals[ portal ]
except KeyError:
pass
self.log.warning( " the portal: %s will not be imported" % portal )
except AttributeError:
pass
try:
self._exported_services = Local.Config.Config.EXPORTED_SERVICES
except AttributeError:
self.log.info( "EXPORTED_SERVICES not found in Local/Config/Config.py" )
###############################
#
# accessors
#
##############################
def version( self ):
"""
@return: the version number of this Mobyle instance
@rtype:
"""
return self.__version
def debug( self , jobName = None ):
"""
Returns the debug level for a job or the default debug level if jobName is not specified
@param jobName:
@type jobName: string
@return: an int >=0 and <= 3
@rtype: int
"""
try:
debug = self._particular_debug[ jobName ]
except KeyError:
debug = self._debug
if debug < 0 or debug > 3:
if jobName is None:
msg =" DEBUG must be >= 0 and <= 3 I found DEBUG =%i, DEBUG is set to %i" % ( debug , self._debug )
else:
msg = jobName + " debug must be >= 0 and <= 3 I found %i, PARTICULAR_DEBUG[ '%s' ] is set it to %i" % ( debug ,
jobName ,
self._debug )
self.log.warning( msg )
return debug
def mobylehome( self ):
"""
@return: the absolute path to home of the project
@rtype: string
"""
return self._mobylehome
def document_root( self ):
"""
@return: the absolute path to the mobyle htdocs directory
@rtype: string
"""
return self._mobyle_htdocs
def root_url( self ):
"""
@return: the base url of the web server
@rtype: string
"""
return self._root_url
def results_url( self ):
"""
@return: the complete url of the jobs
@rtype: string
"""
return self._results_url
def results_path( self ):
"""
@return: the directory absolute path where are located the jobs
@rtype: string
"""
return self._results_path
def admindir(self):
"""
@return: the absolute path of the ADMINDIR
@rtype: string
"""
return self._admindir
def servers_url( self ):
"""
@return: the base url of the service definitions
@rtype: string
"""
return self._servers_url
def servers_path( self ):
"""
@return: the directory absolute path where are located the services
@rtype: string
"""
return self._servers_path
def services_path( self ):
"""
@return: the directory absolute path where are located the services
@rtype: string
"""
return self._services_path
def repository_path( self ):
"""
@return: the absolute path where are located the services, jobs, sessions ...
@rtype: string
"""
return self._repository_path
def repository_url( self ):
"""
@return: the url where are located the services, index , jobs, ...
@rtype: string
"""
return self._repository_url
def index_path( self ):
"""
@return: the directory absolute path where are located the indexes for this portal.
@rtype: string
"""
return self._index_path
def binary_path( self ):
"""
@return: the list of path where binaries must be search
@rtype: list of strings
"""
return self._binary_path
def format_detector_cache_path( self ):
"""
@return: the absolute path where the invalid sequences and alignment are dumped for analysis
@rtype: string
"""
return self._format_detector_cache_path
def user_sessions_path( self ):
"""
@return: the directory absolute path where are located the sessions
@rtype: string
"""
return self._user_sessions_path
def user_sessions_url( self ):
"""
@return: the complete url of the sessions
@rtype: string
"""
return self._user_sessions_url
def log_dir( self ):
"""
@return: the absolute path where located the log files
@rtype: string
"""
return self._logdir
def portal_url( self , relative = False ):
"""
@param relative:
@type relative: boolean
@return: if relative return the relative url of the portal otherwise return the absolute
url of the portal.
@rtype: string
"""
if relative:
return self._portal_prefix
else:
return "%s/%s" % ( self._root_url , self._portal_prefix )
def portal_path(self):
"""
@return: the absolute path to the portal
@rtype: string
"""
return self._portal_path
def cgi_url( self ):
"""
@return: the absolute url to the cgis
@rtype: string
"""
return "%s/%s" % ( self._root_url , self._cgi_prefix )
def getDatabanksConfig(self):
"""
@return: the list of databanks
along with their typing information and label
@rtype: dictionary
"""
return self._databanks_config
def maintainer( self ):
"""
@return: the email address of the Mobyle server maintainer
@rtype: list of string
"""
return self._maintainer
def mailHelp( self ):
"""
@return: The email address to the hot line for this Mobyle server
@rtype: list of string
"""
return self._help
def sender( self ):
"""
the sender address is used as From: for mail sent by mobyle
- notification of long job
- results
- session confirmation
@return: the sender email address ( From: ) of this Mobyle server
@rtype: string
"""
return self._sender
def mailhost( self ):
"""
@return: the mail transfert agent used to send emails
@rtype: string
"""
return self._mailhost
def opt_email( self , portalid = None ):
"""
@return: True if the user email is not mandatory to run a job, False otherwise
@rtype: Boolean
"""
if portalid is None:
return self._opt_email
else:
if portalid.find( '.' ) == -1:
portalid = "local.%s"%portalid
try:
return self._particular_opt_email[ portalid ]
except KeyError:
return self._opt_email
#OPENID
def openid( self ):
"""
@return: True if openid authentication is supported , False otherwise
@rtype: boolean
"""
return self._openid
#OPENID
def openidstore_path( self ):
"""
@return: the directory absolute path where is located the openid store
@rtype: string
"""
return self._openidstore_path
def anonymousSession( self ):
"""
@return:
- 'no' if the anonymous sessions are not allowed.
- 'yes' if the anonymous sessions are allowed, without any restrictions.
- 'captcha' if the anonymous sessions are allowed, with a captcha challenge.
@rtype: string
"""
return self._anonymous_session
def authenticatedSession( self ):
"""
@return:
- 'no' if authenticated session are not allowed.
- 'yes' if authenticated session are allowed and activated without any restriction.
- 'email' if authenticated session are allowed but an email confirmation is needed to activate it.
@rtype: string
"""
return self._authenticated_session
def refreshFrequency( self ):
"""
@return: portal refresh frequency, in seconds
@rtype: integer
"""
return self._refresh_frequency
def dnsResolver( self ):
"""
@return: True if the user email domain name is checked to have a mail server , False otherwise
@rtype: boolean
"""
return self._dns_resolver
def mailResults( self ):
"""
@return: dont_email_result , mailmaxsize in a tuple
@rtype: ( boolean , int )
"""
return ( self._dont_email_result , self._maxmailsize )
def remainResults( self ):
"""
@return: how long ( in days ) the results files remains on the server.
@rtype: int
"""
return self._result_remain
def max_similar_job_per_user( self ):
"""
@return: how many "indentical" jobs are allowed to be submit in same time.
"indentical" jobs means same email, same IP, same commandline.
@rtype: int (>=0)
"""
return self._max_similar_job_per_user
def max_job_per_user(self):
"""
@return: how many jobs are allowed to be submit in same time.
@rtype: int (>=0)
"""
return self._max_job_per_user
def lang( self ):
"""
@return: The default language used by this Mobyle server (used to internationalise the form)
(2 letter code )(default = "en")
@rtype: string
"""
return self._lang
def filelimit( self ):
"""
@return: the max size for one file generated by a service ( in byte ).
@rtype: int
"""
return self._filelimit
def sessionlimit( self ):
"""
@return: the max size for a session directory ( in byte )
@rtype: int
"""
return self._sessionlimit
def previewDataLimit( self ):
"""
@return: the max size for a result to be preview in job result ( in Byte ).
@rtype: int
"""
return self._previewDataLimit
def dataconverter(self, datatype):
"""
@param datatype: the name of a datatype as found in the xml of services
@type datatype: string
@return: list of dataconverter insntance for a given datatype
"""
try:
return self._dataconverter[ datatype ]
except KeyError:
return []
def data_conversions(self):
"""
data_conversions returns the list of conversion possibilities as a list of dictionnaries
computed from the configured converters
@type datatype: string
@return: list of dataconverter insntance for a given datatype
"""
list = []
for dts, entries in self._dataconverter.items():
for entry in entries:
for fts in entry.convertedFormat():
if fts[0] != fts[1]:
list.append({'dataType':dts, 'fromFormat':fts[0], 'toFormat':fts[1], 'using':entry.program_name})
return list
def email_delay( self ):
"""
@return: the time during the father process wait its child ( in sec ).
@rtype: int
"""
return self._email_delay
def getAliasFromConfig(self , config ):
try:
return self._revert_alias[ config ]
except KeyError:
raise ConfigError()
def getExecutionConfigFromAlias(self , alias ):
"""
@param alias: the symbolic name of a ExecutionConfig object in the Execution_CONFIG_ALIAS
@type alias: string
@return: the ExecutionConfig corresponding to the symbolic name alias
@rtype: ExecutionConfig
@raise KeyError: if alias doesn't match with any alias in Config.
"""
try:
return self._execution_system_alias[ alias ]
except KeyError , err:
raise err
def getDispatcher( self):
"""
@return: a L{Dispatcher}
@rtype: a L{Dispatcher} instance
"""
return self._dispatcher
def module(self, serviceName ):
"""
@param serviceName: the name of the service
@type serviceName: string
@return: the path to module init, and the module load to do if module is used or None otherwise
@rtype: tuple (string module_init_path , string module load) or None
"""
if not self._module_init:
return None
if serviceName in self._module_load:
module_load = self._module_load.get(serviceName)
elif 'DEFAULT' in self._module_load:
module_load = self._module_load['DEFAULT']
else:
#module_load is not defined for this interface and there is no default
#don't use module load
module_load = None
if module_load is not None:
return (self._module_init, module_load)
else:
return None
def accounting( self ):
"""
@return: True if the accounting is on, False otherwise.
@rtype: boolean
"""
return self._accounting
def session_debug( self ):
"""
@return: the debug level for the session specifique logger.
if there is no level specify in Config, return None
@rtype: int
"""
return self._session_debug
def status_debug( self ):
"""
@return: True if the debug log on status is on, False otherwise.
@rtype: boolean
"""
return self._status_debug
def isDisabled( self , portalID = None ):
"""
@param portalID: the portalID of a service.
The portalID is the portal name and service name separated by a dot like portal1.service1
local means the local portal
@type: string
@return: True if the service is disabled, False otherwise
@rtype: boolean
"""
if portalID is None:
return self._disable_all
else:
if self._disable_all :
return True
else:
pattern = self._disabled_services
if pattern :
pattern = '|'.join( pattern )
pattern = pattern.replace('.' , '\.' )
pattern = pattern.replace('*' , '.*')
pattern = "^(%s)$" % pattern
auto = re.compile( pattern )
else:
# by default if no pattern are specified all services are enabled
return False
if auto.search( portalID ):
return True
else:
return False
def restrictedServices( self ):
"""
@return: The list of service which have a restrictive access
@rtype: list of strings
"""
return self._authorized_services.keys()
def isAuthorized( self , serviceName , addr = None ):
"""
@param service: the name of the service
@type service: type
@param addr: the ip address to test. if addr is None the environment REMOTE_ADDR will be used
@type addr: string
@return: True if the user is authorized to used the service (based on IP), False otherwise.
@rtype: boolean
"""
if addr is None:
try:
addr = os.environ[ 'REMOTE_ADDR' ]
except KeyError:
return True
try:
pattern = self._authorized_services[ serviceName ]
except KeyError:
# by default if no pattern are specified there is no restriction
# to access to this service
return True
if pattern :
pattern = '|'.join( pattern )
pattern = pattern.replace('.' , '\.' )
pattern = pattern.replace('*' , '.*')
pattern = "^(%s)$" % pattern
auto = re.compile( pattern )
else:
# by default if no pattern are specified there is no restriction
# to access to this service
return True
if auto.search( addr ):
return True
else:
return False
def getPrivilegeTable( self ):
"""
@return: a dict where keys are the service names and values a list of Ip mask which are authorized to access to this service
@rtype: dict { string : [ strings ] }
"""
return self._authorized_services
def imported_services( self ):
"""
@return: the urls of the services imported by this server
@rtype: list of strings
"""
return self._imported_services
def exported_services( self ):
"""
@return: the name of the services which are exported by this server
@rtype: list of strings
"""
return self._exported_services
def portal_name( self ):
"""
@return: the name of the portal within a MobyleNet federation
@rtype: String
"""
return self._portal_name
def simple_forms_active( self ):
"""
@return: tells if "simple forms" should be displayed by default
@rtype: Boolean
"""
return self._simple_forms_active
def portals( self ):
"""
@return: all the Mobyle portals belonging to the "Mobyle grid"
@rtype: list of dictionaries { { 'server' : 'url of Mobyle server' ,
'email' : 'the contact email of this server' }
}
"""
return self._all_portals
def services_deployment_include(self, service_type = None ):
"""
@param service_type: the type of the service to deploy
@type service_type: string (for now the available keywords are 'programs' , 'workflows' and 'viewers'
@return: the services deployment include masks list
@rtype: list of strings
"""
if service_type is None:
return self._services_deployment_include
else:
try:
return self._services_deployment_include[ service_type ]
except KeyError:
raise KeyError( "the '%s' service type is not handled by Mobyle" %service_type )
def services_deployment_exclude(self, service_type = None ):
"""
@param service_type: the type of the service to not deploy
@type service_type: string (for now the available keywords are 'programs' , 'workflows' and 'viewers'
@return: the services deployment exclude masks list
@rtype: list of strings
"""
if service_type is None:
return self._services_deployment_exclude
else:
try:
return self._services_deployment_exclude[ service_type ]
except KeyError:
raise KeyError( "the '%s' service type is not handled by Mobyle" %service_type )
def GAcode(self):
"""
@return: the Google Analytics code if a GA account is used
@rtype: string or None
"""
return self._GAcode
def welcome_config(self):
"""
@return: the custom welcome page configuration
@rtype: dictionary with keys 'url' and 'format' (format can be html or atom for instance)
"""
return self._welcome_config
def custom_portal_header(self):
"""
@return: the custom portal header
@rtype: string containing an HTML chunk
"""
return self._custom_portal_header
def custom_portal_footer(self):
"""
@return: the custom portal footer
@rtype: string containing an HTML chunk
"""
return self._custom_portal_footer
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