######################################################################################## # # # Author: Bertrand Neron, # # Organization:'Biological Software and Databases' Group, Institut Pasteur, Paris. # # Distributed under GPLv2 Licence. Please refer to the COPYING.LIB document. # # # ######################################################################################## """ Build the command from the parameters chosen by the users """ import os from StringIO import StringIO from Mobyle.MobyleError import MobyleError from logging import getLogger c_log = getLogger(__name__) b_log = getLogger( 'Mobyle.builder' ) from Mobyle.ConfigManager import Config _cfg = Config() __extra_epydoc_fields__ = [( 'call', 'Called by','Called by' )] class CommandBuilder: """ This class create the command from the parameters chosen by the users 3 main methods exist - buildLocalCommand: to build a unix command line for a local job - buildCGI : to build the url, to invoke a cgi - buildWS : to build the ,to call a WebService """ def __init__( self , job_dir = None ): self._commandLine = "" self._paramfileHandles = {} # the key is the filename, # the value is the StrinIO file object like def buildLocalCommand( self, service ): """ Build a unix command line from a - L{Service} instance @param service: the service which correspond to the programm asked by the user @type service: a - L{Service} instance @return: a String representing the command line """ debug = _cfg.debug( service.getName() ) commandIsInserted = False commandParameterName = service.getCommandParameterName() if commandParameterName: commandPos = service.getArgpos( commandParameterName ) else: commandPos = 0 if debug > 1: b_log.debug( """\n \t##################################################### \t# # \t# command line building # \t# # \t##################################################### \n""" ) myEvaluator = service.getEvaluator() for parameter in service.getAllParameterByArgpos(): paramName = parameter.getName() if debug > 1: b_log.debug( "--------------- " + paramName + " ---------------") b_log.debug( "commandIsInserted " + str( commandIsInserted ) ) b_log.debug( "service.getArgpos( paramName ) " + str( parameter.getArgpos())) if not commandIsInserted and parameter.getArgpos() >= commandPos: if parameter.iscommand(): #the command from parameter is priority vs command #the command comes from this parameter if debug > 1 : b_log.debug( "self._commandLine service.iscommand " + self._commandLine ) commandIsInserted = True else: #I insert the command from command tag in commandLine if debug > 1: b_log.debug( "self._commandLine = " + self._commandLine ) self._commandLine += " " + service.getCommand()[0] commandIsInserted = True if debug > 1: b_log.debug( "self._commandLine+ command = " + self._commandLine ) #set "vdef" and "value" in the protected namespace (evaluator) rawVdef = parameter.getVdef() if rawVdef is None: myEvaluator.setVar( 'vdef' , None ) convertedVdef = None #TODO a suprimmer qund b_log renove else: convertedVdef , mt = parameter.convert(rawVdef , parameter.getType() ) myEvaluator.setVar( 'vdef' , convertedVdef ) if debug > 1: b_log.debug( "rawVdef = " + str( rawVdef ) ) b_log.debug( "convertedVdef = " + str( convertedVdef ) ) b_log.debug( "myEvaluator.setVar( 'vdef' , "+ str( convertedVdef ) +" )") if ( myEvaluator.isDefined( paramName ) ) : # be careful we can't use the test: if servive.getValue(), # because, the value could be fill with False. # thus we must test if the value exist or not, and not test the value itself! myEvaluator.setVar( 'value', parameter.getValue( ) ) if debug > 1: b_log.debug( "myEvaluator.isDefined( " + paramName + " ) = True" ) b_log.debug( "myEvaluator.setVar( 'value' ,"+ str( parameter.getValue() ) + " )" ) else: myEvaluator.setVar( 'value' , convertedVdef ) if debug > 1: b_log.debug( "myEvaluator.isDefined( " + paramName + " ) = False" ) b_log.debug( "rawVdef = " + str( rawVdef ) ) b_log.debug( "convertedVdef = " + str( convertedVdef ) ) b_log.debug( "myEvaluator.setVar( 'value' , " + str( convertedVdef ) + " )" ) if parameter.precondHas_proglang( 'python' ): if debug > 1: b_log.debug("precondHas_proglang( "+ paramName +" , 'python' ) = True") allPrecondTrue = True preconds = parameter.getPreconds( proglang='python' ) for precond in preconds: if not myEvaluator.eval( precond ): if debug > 1: b_log.debug("eval( "+ precond +" ) = False") allPrecondTrue = False break else: if debug > 1: b_log.debug("eval( "+ precond +" ) = True") if not allPrecondTrue : continue #next parameter if parameter.formatHas_proglang( 'python' ): if debug > 1: b_log.debug("service.formatHas_proglang( "+ paramName +" , 'python' ) = True") format = parameter.getFormat( 'python' ) else: value = myEvaluator.getVar( 'value' ) if value is not None : if parameter.flistHas_proglang( value , 'python' ) : if debug > 1: b_log.debug("service.flistHas_proglang( "+ paramName +" , "+ str( value ) + " , 'python' ) = True") format = parameter.getFlistCode( value , 'python' ) else: format = None else: format = None if debug > 1: b_log.debug( "value = " + str( myEvaluator.getVar( 'value' )) + " type = "+ str(type( myEvaluator.getVar( 'value' ) ) ) ) b_log.debug( "vdef = " + str( myEvaluator.getVar( 'vdef' )) + " type = "+ str(type( myEvaluator.getVar( 'value' ) ) ) ) b_log.debug(" format = " + str( format ) ) if format : if parameter.hasParamfile(): #the Parameter.setParamfile method had already trim the spaces paramfileName = parameter.getParamfile() if paramfileName: if self._paramfileHandles.has_key( paramfileName ): paramfileHandle = self._paramfileHandles[ paramfileName ] else: try: paramfileHandle = self.openParamFile( paramfileName ) self._paramfileHandles[paramfileName] = paramfileHandle except IOError: raise MobyleError, "cannot open the file: "+str( paramfileName ) else : paramfileHandle = None else: if myEvaluator.getVar( 'value' ) is not None: if parameter.formatHas_proglang( 'perl' ) or parameter.flistHas_proglang( parameter.getValue() , 'perl' ) : if debug > 1: b_log.debug( "#################### WARNING ##############################################" ) b_log.debug( "the parameter " + paramName + " had a format code in Perl but not in Python" ) b_log.debug( "###########################################################################" ) continue try: arg = myEvaluator.eval( format ) except Exception, err: msg = "Error during evaluation of \"%s.%s\" format parameter: %s : \"%s\"" % ( service.getName(), paramName , format, err ) if debug > 1: b_log.debug( msg ) raise MobyleError , msg if paramfileHandle: if debug > 1: b_log.debug( ">> " + paramfileName + " , " + arg ) if arg : paramfileHandle.write( arg ) paramfileHandle.flush() else: self._commandLine = str( self._commandLine ) + str( arg ) if debug > 1: b_log.debug( "commandLine = " + self._commandLine ) if debug > 1: b_log.debug( "------------ end of parameter loop -------------" ) #=============================================================================== # # the environment is modified here ( it will be just before to do run in _batch ) to avoid # dramatic side effects on well of mobyle. # we usr the environment to find the right python everywhere in mobyle and if we modified the path # we could change the python used. # #=============================================================================== xmlEnv = {} if commandParameterName : #the command come from a parameter path = service.getEnv( 'PATH' ) else:#the command come from the element command in head path = service.getCommand()[2] path_env = service.getEnv( 'PATH' ) if path and path_env: path = "%s:%s" % ( path, path_env ) elif path_env: path = path_env if path : #os.environ['PATH'] = "%s:%s" %( path , os.environ['PATH']) xmlEnv[ 'PATH' ] = path if debug > 1: b_log.debug( "PATH= " + str( path ) ) else: if debug > 1 : b_log.debug( "PATH= "+ str( os.environ[ 'PATH' ] ) ) for varEnv in service.envVars(): envArg = service.getEnv( varEnv ).strip() if varEnv == 'PATH': continue else: xmlEnv[ varEnv ] = envArg for var, value in xmlEnv.items(): if value.startswith('()'): msg = 'Bash vulnerabilty Exploitation: service unsafe check env %s'% var c_log.critical("Security Error: %s : %s" % (service.getName(), msg)) raise MobyleError, msg #trim multi espaces , ... self._commandLine = ' '.join( self._commandLine.split() ) self._commandLine.strip() self._commandLine.replace( '"','\\"' ) self._commandLine.replace( '@','\@' ) self._commandLine.replace( '_SQ_',"\'" ) self._commandLine.replace( '_DQ_','\"' ) if debug > 1: b_log.debug( "Environment ="+str( xmlEnv ) ) b_log.debug( "command line= " + self._commandLine ) return { 'cmd' : self._commandLine , 'env' : xmlEnv , 'paramfiles': self._paramfileHandles } def __str__( self ): return str( self._commandLine ) def openParamFile(self , paramfileName ): return StringIO()