mengmengmmm/csn_python_trainuse_slice4 · Datasets at Hugging Face

idx int64 0 63k	question stringlengths 61 4.03k	target stringlengths 6 1.23k
6,900	def status ( * args , ** kwargs ) : def decor ( func ) : @ wraps ( func ) def wrapper ( * args , ** krgs ) : echo ( "[!] " + msg , end = " " , flush = True ) result = func ( * args , ** krgs ) echo ( fin , flush = True ) return result return wrapper fin = kwargs . pop ( 'fin' , "DONE." ) args = list ( args ) if len ( args ) > 1 and callable ( args [ 1 ] ) : msg = args . pop ( 0 ) func = args . pop ( 0 ) try : fargs = args . pop ( 0 ) except : fargs = [ ] try : fkrgs = args . pop ( 0 ) except : fkrgs = { } return decor ( func ) ( * fargs , ** fkrgs ) msg = args . pop ( 0 ) return decor	Prints a status message at the start and finish of an associated function . Can be used as a function decorator or as a function that accepts another function as the first parameter .
6,901	def fatal ( msg , exitcode = 1 , kwargs ) : pause_before_exit = kwargs . pop ( "pause" ) if "pause" in kwargs . keys ( ) else False echo ( "[FATAL] " + msg , kwargs ) if pause_before_exit : pause ( ) sys . exit ( exitcode )	Prints a message then exits the program . Optionally pause before exit with pause = True kwarg .
6,902	def hrule ( width = None , char = None ) : width = width or HRWIDTH char = char or HRCHAR return echo ( getline ( char , width ) )	Outputs or returns a horizontal line of the given character and width . Returns printed string .
6,903	def title ( msg ) : if sys . platform . startswith ( "win" ) : ctypes . windll . kernel32 . SetConsoleTitleW ( tounicode ( msg ) )	Sets the title of the console window .
6,904	def wrap ( item , args = None , krgs = None , kwargs ) : with Wrap ( kwargs ) : if callable ( item ) : args = args or [ ] krgs = krgs or { } item ( * args , ** krgs ) else : echo ( item )	Wraps the given item content between horizontal lines . Item can be a string or a function .
6,905	def _guess_name ( desc , taken = None ) : taken = taken or [ ] name = "" for word in desc . split ( ) : c = word [ 0 ] . lower ( ) if not c . isalnum ( ) : continue name += c if name not in taken : break count = 2 while name in taken : name = name + str ( count ) count += 1 return name	Attempts to guess the menu entry name from the function name .
6,906	def add ( self , name , desc , func = None , args = None , krgs = None ) : self . entries . append ( MenuEntry ( name , desc , func , args or [ ] , krgs or { } ) )	Add a menu entry .
6,907	def enum ( self , desc , func = None , args = None , krgs = None ) : name = str ( len ( self . entries ) + 1 ) self . entries . append ( MenuEntry ( name , desc , func , args or [ ] , krgs or { } ) )	Add a menu entry whose name will be an auto indexed number .
6,908	def run ( self , name ) : for entry in self . entries : if entry . name == name : run_func ( entry ) break	Runs the function associated with the given entry name .
6,909	def partition_scripts ( scripts , start_type1 , start_type2 ) : match , other = [ ] , [ ] for script in scripts : if ( HairballPlugin . script_start_type ( script ) == start_type1 or HairballPlugin . script_start_type ( script ) == start_type2 ) : match . append ( script ) else : other . append ( script ) return match , other	Return two lists of scripts out of the original scripts list .
6,910	def attribute_result ( cls , sprites ) : retval = dict ( ( x , True ) for x in cls . ATTRIBUTES ) for properties in sprites . values ( ) : for attribute , state in properties . items ( ) : retval [ attribute ] &= state != cls . STATE_MODIFIED return retval	Return mapping of attributes to if they were initialized or not .
6,911	def attribute_state ( cls , scripts , attribute ) : green_flag , other = partition_scripts ( scripts , cls . HAT_GREEN_FLAG , cls . HAT_CLONE ) block_set = cls . BLOCKMAPPING [ attribute ] state = cls . STATE_NOT_MODIFIED for script in green_flag : in_zone = True for name , level , _ in cls . iter_blocks ( script . blocks ) : if name == 'broadcast %s and wait' : in_zone = False if ( name , 'absolute' ) in block_set : if in_zone and level == 0 : if state == cls . STATE_NOT_MODIFIED : state = cls . STATE_INITIALIZED else : state = cls . STATE_MODIFIED elif in_zone : continue else : state = cls . STATE_MODIFIED break elif ( name , 'relative' ) in block_set : state = cls . STATE_MODIFIED break if state != cls . STATE_NOT_MODIFIED : return state for script in other : for name , _ , _ in cls . iter_blocks ( script . blocks ) : if name in [ x [ 0 ] for x in block_set ] : return cls . STATE_MODIFIED return cls . STATE_NOT_MODIFIED	Return the state of the scripts for the given attribute .
6,912	def output_results ( cls , sprites ) : print ( ' ' . join ( cls . ATTRIBUTES ) ) format_strs = [ '{{{}!s:^{}}}' . format ( x , len ( x ) ) for x in cls . ATTRIBUTES ] print ( ' ' . join ( format_strs ) . format ( ** cls . attribute_result ( sprites ) ) )	Output whether or not each attribute was correctly initialized .
6,913	def sprite_changes ( cls , sprite ) : retval = dict ( ( x , cls . attribute_state ( sprite . scripts , x ) ) for x in ( x for x in cls . ATTRIBUTES if x != 'background' ) ) return retval	Return a mapping of attributes to their initilization state .
6,914	def analyze ( self , scratch , ** kwargs ) : changes = dict ( ( x . name , self . sprite_changes ( x ) ) for x in scratch . sprites ) changes [ 'stage' ] = { 'background' : self . attribute_state ( scratch . stage . scripts , 'costume' ) } return { 'initialized' : changes }	Run and return the results of the AttributeInitialization plugin .
6,915	def variable_state ( cls , scripts , variables ) : def conditionally_set_not_modified ( ) : state = variables . get ( block . args [ 0 ] , None ) if state == cls . STATE_NOT_MODIFIED : variables [ block . args [ 0 ] ] = cls . STATE_MODIFIED green_flag , other = partition_scripts ( scripts , cls . HAT_GREEN_FLAG ) variables = dict ( ( x , cls . STATE_NOT_MODIFIED ) for x in variables ) for script in green_flag : in_zone = True for name , level , block in cls . iter_blocks ( script . blocks ) : if name == 'broadcast %s and wait' : in_zone = False if name == 'set %s effect to %s' : state = variables . get ( block . args [ 0 ] , None ) if state is None : continue if in_zone and level == 0 : if state == cls . STATE_NOT_MODIFIED : state = cls . STATE_INITIALIZED else : state = cls . STATE_MODIFIED elif in_zone : continue elif state == cls . STATE_NOT_MODIFIED : state = cls . STATE_MODIFIED variables [ block . args [ 0 ] ] = state elif name == 'change %s effect by %s' : conditionally_set_not_modified ( ) for script in other : for name , _ , block in cls . iter_blocks ( script . blocks ) : if name in ( 'change %s effect by %s' , 'set %s effect to %s' ) : conditionally_set_not_modified ( ) return variables	Return the initialization state for each variable in variables .
6,916	def analyze ( self , scratch , ** kwargs ) : variables = dict ( ( x , self . variable_state ( x . scripts , x . variables ) ) for x in scratch . sprites ) variables [ 'global' ] = self . variable_state ( self . iter_scripts ( scratch ) , scratch . stage . variables ) import pprint pprint . pprint ( variables ) return { 'variables' : variables }	Run and return the results of the VariableInitialization plugin .
6,917	def finalize ( self ) : print ( '{} default sprite names found:' . format ( self . total_default ) ) for name in self . list_default : print ( name )	Output the default sprite names found in the project .
6,918	def analyze ( self , scratch , ** kwargs ) : for sprite in self . iter_sprites ( scratch ) : for default in self . default_names : if default in sprite . name : self . total_default += 1 self . list_default . append ( sprite . name )	Run and return the results from the SpriteNaming plugin .
6,919	def prepare_request_params ( self , _query_params , _json_params ) : self . _query_params = dictset ( _query_params or self . request . params . mixed ( ) ) self . _json_params = dictset ( _json_params ) ctype = self . request . content_type if self . request . method in [ 'POST' , 'PUT' , 'PATCH' ] : if ctype == 'application/json' : try : self . _json_params . update ( self . request . json ) except simplejson . JSONDecodeError : log . error ( "Expecting JSON. Received: '{}'. " "Request: {} {}" . format ( self . request . body , self . request . method , self . request . url ) ) self . _json_params = BaseView . convert_dotted ( self . _json_params ) self . _query_params = BaseView . convert_dotted ( self . _query_params ) self . _params = self . _query_params . copy ( ) self . _params . update ( self . _json_params )	Prepare query and update params .
6,920	def set_override_rendered ( self ) : if '' in self . request . accept : self . request . override_renderer = self . _default_renderer elif 'application/json' in self . request . accept : self . request . override_renderer = 'nefertari_json' elif 'text/plain' in self . request . accept : self . request . override_renderer = 'string'	Set self . request . override_renderer if needed .
6,921	def _setup_aggregation ( self , aggregator = None ) : from nefertari . elasticsearch import ES if aggregator is None : aggregator = ESAggregator aggregations_enabled = ( ES . settings and ES . settings . asbool ( 'enable_aggregations' ) ) if not aggregations_enabled : log . debug ( 'Elasticsearch aggregations are not enabled' ) return index = getattr ( self , 'index' , None ) index_defined = index and index != self . not_allowed_action if index_defined : self . index = aggregator ( self ) . wrap ( self . index )	Wrap self . index method with ESAggregator .
6,922	def get_collection_es ( self ) : from nefertari . elasticsearch import ES return ES ( self . Model . __name__ ) . get_collection ( ** self . _query_params )	Query ES collection and return results .
6,923	def set_public_limits ( self ) : if self . request . method . upper ( ) in [ 'GET' , 'HEAD' ] : self . _query_params . process_int_param ( '_limit' , 20 ) if self . _auth_enabled and not getattr ( self . request , 'user' , None ) : wrappers . set_public_limits ( self )	Set public limits if auth is enabled and user is not authenticated .
6,924	def convert_ids2objects ( self ) : if not self . Model : log . info ( "%s has no model defined" % self . __class__ . __name__ ) return for field in self . _json_params . keys ( ) : if not engine . is_relationship_field ( field , self . Model ) : continue rel_model_cls = engine . get_relationship_cls ( field , self . Model ) self . id2obj ( field , rel_model_cls )	Convert object IDs from self . _json_params to objects if needed .
6,925	def setup_default_wrappers ( self ) : self . _after_calls [ 'index' ] = [ wrappers . wrap_in_dict ( self . request ) , wrappers . add_meta ( self . request ) , wrappers . add_object_url ( self . request ) , ] self . _after_calls [ 'show' ] = [ wrappers . wrap_in_dict ( self . request ) , wrappers . add_meta ( self . request ) , wrappers . add_object_url ( self . request ) , ] self . _after_calls [ 'create' ] = [ wrappers . wrap_in_dict ( self . request ) , wrappers . add_meta ( self . request ) , wrappers . add_object_url ( self . request ) , ] self . _after_calls [ 'update' ] = [ wrappers . wrap_in_dict ( self . request ) , wrappers . add_meta ( self . request ) , wrappers . add_object_url ( self . request ) , ] self . _after_calls [ 'replace' ] = [ wrappers . wrap_in_dict ( self . request ) , wrappers . add_meta ( self . request ) , wrappers . add_object_url ( self . request ) , ] if self . _auth_enabled : for meth in ( 'index' , 'show' , 'create' , 'update' , 'replace' ) : self . _after_calls [ meth ] += [ wrappers . apply_privacy ( self . request ) , ] for meth in ( 'update' , 'replace' , 'update_many' ) : self . _before_calls [ meth ] += [ wrappers . apply_request_privacy ( self . Model , self . _json_params ) , ]	Setup defaulf wrappers .
6,926	def register ( self ) : user , created = self . Model . create_account ( self . _json_params ) if not created : raise JHTTPConflict ( 'Looks like you already have an account.' ) self . request . _user = user pk_field = user . pk_field ( ) headers = remember ( self . request , getattr ( user , pk_field ) ) return JHTTPOk ( 'Registered' , headers = headers )	Register new user by POSTing all required data .
6,927	def register ( self ) : user , created = self . Model . create_account ( self . _json_params ) if user . api_key is None : raise JHTTPBadRequest ( 'Failed to generate ApiKey for user' ) if not created : raise JHTTPConflict ( 'Looks like you already have an account.' ) self . request . _user = user headers = remember ( self . request , user . username ) return JHTTPOk ( 'Registered' , headers = headers )	Register a new user by POSTing all required data .
6,928	def claim_token ( self , ** params ) : self . _json_params . update ( params ) success , self . user = self . Model . authenticate_by_password ( self . _json_params ) if success : headers = remember ( self . request , self . user . username ) return JHTTPOk ( 'Token claimed' , headers = headers ) if self . user : raise JHTTPUnauthorized ( 'Wrong login or password' ) else : raise JHTTPNotFound ( 'User not found' )	Claim current token by POSTing login and password .
6,929	def reset_token ( self , params ) : response = self . claim_token ( params ) if not self . user : return response self . user . api_key . reset_token ( ) headers = remember ( self . request , self . user . username ) return JHTTPOk ( 'Registered' , headers = headers )	Reset current token by POSTing login and password .
6,930	def _apply_nested_privacy ( self , data ) : kw = { 'is_admin' : self . is_admin , 'drop_hidden' : self . drop_hidden , } for key , val in data . items ( ) : if is_document ( val ) : data [ key ] = apply_privacy ( self . request ) ( result = val , kw ) elif isinstance ( val , list ) and val and is_document ( val [ 0 ] ) : data [ key ] = [ apply_privacy ( self . request ) ( result = doc , kw ) for doc in val ] return data	Apply privacy to nested documents .
6,931	def get_root_resource ( config ) : app_package_name = get_app_package_name ( config ) return config . registry . _root_resources . setdefault ( app_package_name , Resource ( config ) )	Returns the root resource .
6,932	def get_default_view_path ( resource ) : "Returns the dotted path to the default view class." parts = [ a . member_name for a in resource . ancestors ] + [ resource . collection_name or resource . member_name ] if resource . prefix : parts . insert ( - 1 , resource . prefix ) view_file = '%s' % '_' . join ( parts ) view = '%s:%sView' % ( view_file , snake2camel ( view_file ) ) app_package_name = get_app_package_name ( resource . config ) return '%s.views.%s' % ( app_package_name , view )	Returns the dotted path to the default view class .
6,933	def get_ancestors ( self ) : "Returns the list of ancestor resources." if self . _ancestors : return self . _ancestors if not self . parent : return [ ] obj = self . resource_map . get ( self . parent . uid ) while obj and obj . member_name : self . _ancestors . append ( obj ) obj = obj . parent self . _ancestors . reverse ( ) return self . _ancestors	Returns the list of ancestor resources .
6,934	def add_from_child ( self , resource , kwargs ) : new_resource = self . add ( resource . member_name , resource . collection_name , kwargs ) for child in resource . children : new_resource . add_from_child ( child , ** kwargs )	Add a resource with its all children resources to the current resource .
6,935	def add ( self , path ) : name_with_ext = os . path . split ( path ) [ 1 ] name = name_with_ext . split ( '.' ) [ 0 ] self . list . update ( { name : path } )	Add the path of a data set to the list of available sets
6,936	def unpack ( self , name ) : path = self . list [ name ] df = pd . read_pickle ( path , compression = 'gzip' ) return df	Unpacks a data set to a Pandas DataFrame
6,937	def six_frame ( genome , table , minimum = 10 ) : for seq in parse_fasta ( genome ) : dna = Seq ( seq [ 1 ] . upper ( ) . replace ( 'U' , 'T' ) , IUPAC . ambiguous_dna ) counter = 0 for sequence in [ 'f' , dna ] , [ 'rc' , dna . reverse_complement ( ) ] : direction , sequence = sequence for frame in range ( 0 , 3 ) : for prot in sequence [ frame : ] . translate ( table = table , to_stop = False ) . split ( '*' ) : if len ( prot ) < minimum : continue counter += 1 header = '%s_%s table=%s frame=%s-%s %s' % ( seq [ 0 ] . split ( ) [ 0 ] , counter , table , frame + 1 , direction , ' ' . join ( seq [ 0 ] . split ( ) [ 1 : ] ) ) yield [ header , prot ]	translate each sequence into six reading frames
6,938	def check_gaps ( matches , gap_threshold = 0 ) : gaps = [ ] prev = None for match in sorted ( matches , key = itemgetter ( 0 ) ) : if prev is None : prev = match continue if match [ 0 ] - prev [ 1 ] >= gap_threshold : gaps . append ( [ prev , match ] ) prev = match return [ [ i [ 0 ] [ 1 ] , i [ 1 ] [ 0 ] ] for i in gaps ]	check for large gaps between alignment windows
6,939	def check_overlap ( current , hit , overlap = 200 ) : for prev in current : p_coords = prev [ 2 : 4 ] coords = hit [ 2 : 4 ] if get_overlap ( coords , p_coords ) >= overlap : return True return False	determine if sequence has already hit the same part of the model indicating that this hit is for another 16S rRNA gene
6,940	def find_coordinates ( hmms , bit_thresh ) : seq2hmm = parse_hmm ( hmms , bit_thresh ) seq2hmm = best_model ( seq2hmm ) group2hmm = { } for seq , info in list ( seq2hmm . items ( ) ) : group2hmm [ seq ] = { } for group_num , group in enumerate ( hit_groups ( info [ 1 ] ) ) : best = sorted ( group , reverse = True , key = itemgetter ( - 1 ) ) [ 0 ] strand = best [ 5 ] coordinates = [ i [ 0 ] for i in group ] + [ i [ 1 ] for i in group ] coordinates = [ min ( coordinates ) , max ( coordinates ) , strand ] matches = [ i for i in group if i [ 5 ] == strand ] gaps = check_gaps ( matches ) group2hmm [ seq ] [ group_num ] = [ info [ 0 ] , strand , coordinates , matches , gaps ] return group2hmm	find 16S rRNA gene sequence coordinates
6,941	def get_info ( line , bit_thresh ) : if len ( line ) >= 18 : id , model , bit , inc = line [ 0 ] . split ( ) [ 0 ] , line [ 2 ] , float ( line [ 14 ] ) , line [ 16 ] sstart , send , strand = int ( line [ 7 ] ) , int ( line [ 8 ] ) , line [ 9 ] mstart , mend = int ( line [ 5 ] ) , int ( line [ 6 ] ) elif len ( line ) == 9 : if bit_thresh == 0 : print ( '# ssu-cmsearch does not include a model-specific inclusion threshold, ' , file = sys . stderr ) print ( '# please specify a bit score threshold' , file = sys . stderr ) exit ( ) id , model , bit = line [ 1 ] . split ( ) [ 0 ] , line [ 0 ] , float ( line [ 6 ] ) inc = '!' sstart , send = int ( line [ 2 ] ) , int ( line [ 3 ] ) mstart , mend = int ( 4 ) , int ( 5 ) if send >= sstart : strand = '+' else : strand = '-' else : print ( '# unsupported hmm format:' , file = sys . stderr ) print ( '# provide tabular output from ssu-cmsearch and cmsearch supported' , file = sys . stderr ) exit ( ) coords = [ sstart , send ] sstart , send = min ( coords ) , max ( coords ) mcoords = [ mstart , mend ] mstart , mend = min ( mcoords ) , max ( mcoords ) return id , model , bit , sstart , send , mstart , mend , strand , inc	get info from either ssu - cmsearch or cmsearch output
6,942	def check_buffer ( coords , length , buffer ) : s = min ( coords [ 0 ] , buffer ) e = min ( length - coords [ 1 ] , buffer ) return [ s , e ]	check to see how much of the buffer is being used
6,943	def _import_parsers ( ) : global ARCGIS_NODES global ARCGIS_ROOTS global ArcGISParser global FGDC_ROOT global FgdcParser global ISO_ROOTS global IsoParser global VALID_ROOTS if ARCGIS_NODES is None or ARCGIS_ROOTS is None or ArcGISParser is None : from gis_metadata . arcgis_metadata_parser import ARCGIS_NODES from gis_metadata . arcgis_metadata_parser import ARCGIS_ROOTS from gis_metadata . arcgis_metadata_parser import ArcGISParser if FGDC_ROOT is None or FgdcParser is None : from gis_metadata . fgdc_metadata_parser import FGDC_ROOT from gis_metadata . fgdc_metadata_parser import FgdcParser if ISO_ROOTS is None or IsoParser is None : from gis_metadata . iso_metadata_parser import ISO_ROOTS from gis_metadata . iso_metadata_parser import IsoParser if VALID_ROOTS is None : VALID_ROOTS = { FGDC_ROOT } . union ( ARCGIS_ROOTS + ISO_ROOTS )	Lazy imports to prevent circular dependencies between this module and utils
6,944	def _init_metadata ( self ) : if self . _data_map is None : self . _init_data_map ( ) validate_properties ( self . _data_map , self . _metadata_props ) for prop in self . _data_map : setattr ( self , prop , parse_property ( self . _xml_tree , None , self . _data_map , prop ) ) self . has_data = any ( getattr ( self , prop ) for prop in self . _data_map )	Dynamically sets attributes from a Dictionary passed in by children . The Dictionary will contain the name of each attribute as keys and either an XPATH mapping to a text value in _xml_tree or a function that takes no parameters and returns the intended value .
6,945	def _parse_complex ( self , prop ) : xpath_root = None xpath_map = self . _data_structures [ prop ] return parse_complex ( self . _xml_tree , xpath_root , xpath_map , prop )	Default parsing operation for a complex struct
6,946	def _parse_complex_list ( self , prop ) : xpath_root = self . _get_xroot_for ( prop ) xpath_map = self . _data_structures [ prop ] return parse_complex_list ( self . _xml_tree , xpath_root , xpath_map , prop )	Default parsing operation for lists of complex structs
6,947	def _parse_dates ( self , prop = DATES ) : return parse_dates ( self . _xml_tree , self . _data_structures [ prop ] )	Creates and returns a Date Types data structure parsed from the metadata
6,948	def _update_complex ( self , update_props ) : prop = update_props [ 'prop' ] xpath_root = self . _get_xroot_for ( prop ) xpath_map = self . _data_structures [ prop ] return update_complex ( xpath_root = xpath_root , xpath_map = xpath_map , update_props )	Default update operation for a complex struct
6,949	def _update_complex_list ( self , update_props ) : prop = update_props [ 'prop' ] xpath_root = self . _get_xroot_for ( prop ) xpath_map = self . _data_structures [ prop ] return update_complex_list ( xpath_root = xpath_root , xpath_map = xpath_map , update_props )	Default update operation for lists of complex structs
6,950	def spec ( self , postf_un_ops : str ) -> list : spec = [ ( l + op , { 'pat' : self . pat ( pat ) , 'postf' : self . postf ( r , postf_un_ops ) , 'regex' : None } ) for op , pat in self . styles . items ( ) for l , r in self . brackets ] spec [ 0 ] [ 1 ] [ 'regex' ] = self . regex_pat . format ( _ops_regex ( l for l , r in self . brackets ) , _ops_regex ( self . styles . keys ( ) ) ) return spec	Return prefix unary operators list
6,951	def one_symbol_ops_str ( self ) -> str : return re . escape ( '' . join ( ( key for key in self . ops . keys ( ) if len ( key ) == 1 ) ) )	Regex - escaped string with all one - symbol operators
6,952	def plot_gaps ( plot , columns ) : from plot_window import window_plot_convolve as plot_window plot_window ( [ [ 100 - i for i in columns ] ] , len ( columns ) * .01 , plot )	plot % of gaps at each position
6,953	def sample_group ( sid , groups ) : for name in groups : if sid in groups [ name ] . sids : return name	Iterate through all categories in an OrderedDict and return category name if SampleID present in that category .
6,954	def combine_sets ( * sets ) : combined = set ( ) for s in sets : combined . update ( s ) return combined	Combine multiple sets to create a single larger set .
6,955	def unique_otuids ( groups ) : uniques = { key : set ( ) for key in groups } for i , group in enumerate ( groups ) : to_combine = groups . values ( ) [ : i ] + groups . values ( ) [ i + 1 : ] combined = combine_sets ( * to_combine ) uniques [ group ] = groups [ group ] . difference ( combined ) return uniques	Get unique OTUIDs of each category .
6,956	def shared_otuids ( groups ) : for g in sorted ( groups ) : print ( "Number of OTUs in {0}: {1}" . format ( g , len ( groups [ g ] . results [ "otuids" ] ) ) ) number_of_categories = len ( groups ) shared = defaultdict ( ) for i in range ( 2 , number_of_categories + 1 ) : for j in combinations ( sorted ( groups ) , i ) : combo_name = " & " . join ( list ( j ) ) for grp in j : shared [ combo_name ] = groups [ j [ 0 ] ] . results [ "otuids" ] . copy ( ) for grp in j [ 1 : ] : shared [ combo_name ] . intersection_update ( groups [ grp ] . results [ "otuids" ] ) return shared	Get shared OTUIDs between all unique combinations of groups .
6,957	def write_uniques ( path , prefix , uniques ) : for group in uniques : fp = osp . join ( path , "{}_{}.txt" . format ( prefix , group ) ) with open ( fp , "w" ) as outf : outf . write ( "\n" . join ( uniques [ group ] ) )	Given a path the method writes out one file for each group name in the uniques dictionary with the file name in the pattern
6,958	def storeFASTA ( fastaFNH ) : fasta = file_handle ( fastaFNH ) . read ( ) return [ FASTARecord ( rec [ 0 ] . split ( ) [ 0 ] , rec [ 0 ] . split ( None , 1 ) [ 1 ] , "" . join ( rec [ 1 : ] ) ) for rec in ( x . strip ( ) . split ( "\n" ) for x in fasta . split ( ">" ) [ 1 : ] ) ]	Parse the records in a FASTA - format file by first reading the entire file into memory .
6,959	def parseFASTA ( fastaFNH ) : recs = [ ] seq = [ ] seqID = "" descr = "" for line in file_handle ( fastaFNH ) : line = line . strip ( ) if line [ 0 ] == ";" : continue if line [ 0 ] == ">" : if seq : recs . append ( FASTARecord ( seqID , descr , "" . join ( seq ) ) ) seq = [ ] line = line [ 1 : ] . split ( None , 1 ) seqID , descr = line [ 0 ] , line [ 1 ] else : seq . append ( line ) if seq : recs . append ( FASTARecord ( seqID , descr , "" . join ( seq ) ) ) return recs	Parse the records in a FASTA - format file keeping the file open and reading through one line at a time .
6,960	def get ( self , test_id ) : self . select ( '*' , 'test_id=?' , [ test_id ] ) row = self . _cursor . fetchone ( ) if not row : raise KeyError ( 'No report with test id %s in the DB' % test_id ) values = self . row_to_dict ( row ) content = self . _deserialize_dict ( values [ 'content' ] ) return Report . from_dict ( content )	get report by the test id
6,961	def _serialize_dict ( cls , data ) : return b64encode ( zlib . compress ( cPickle . dumps ( data , protocol = 2 ) ) ) . decode ( )	serializes a dictionary
6,962	def _deserialize_dict ( cls , data ) : return cPickle . loads ( zlib . decompress ( b64decode ( data . encode ( ) ) ) )	deserializes a dictionary
6,963	def _run_sequence ( self , sequence ) : self . _check_pause ( ) self . _pre_test ( ) session_data = self . target . get_session_data ( ) self . _test_info ( ) resp = None for edge in sequence : if edge . callback : edge . callback ( self , edge , resp ) session_data = self . target . get_session_data ( ) node = edge . dst node . set_session_data ( session_data ) resp = self . _transmit ( node ) return self . _post_test ( )	Run a single sequence
6,964	def _transmit ( self , node ) : payload = node . render ( ) . tobytes ( ) self . _last_payload = payload try : return self . target . transmit ( payload ) except Exception as e : self . logger . error ( 'Error in transmit: %s' , e ) raise	Transmit node data to target .
6,965	def _generate_rpc_method ( self , method ) : def _ ( ** kwargs ) : msg_id = self . get_unique_msg_id ( ) params = encode_data ( kwargs ) payload = { 'method' : method , 'params' : params , 'jsonrpc' : '2.0' , 'id' : msg_id } response = requests . post ( self . url , data = json . dumps ( payload ) , headers = self . headers ) . json ( ) if ( 'error' in response ) : if response [ 'error' ] [ 'code' ] == JSONRPC_NO_RESULT : return None raise Exception ( 'Got error from RPC server when called "%s" error: %s' % ( method , response [ 'error' ] ) ) if 'result' in response : result = decode_data ( response [ 'result' ] ) return result return _	Generate a function that performs rpc call
6,966	def _parse_request ( self ) : self . req_method = 'unknown' self . req_params = { } self . req_rpc_version = '2.0' self . req_id = 0 self . data = self . rfile . read ( int ( self . headers . get ( 'content-length' ) ) ) data_dict = json . loads ( self . data ) self . req_method = data_dict [ 'method' ] self . req_params = decode_data ( data_dict [ 'params' ] ) self . req_rpc_version = data_dict [ 'jsonrpc' ] self . req_id = data_dict [ 'id' ]	Parse the request
6,967	def send_result ( self , additional_dict ) : self . send_response ( 200 ) self . send_header ( "Content-type" , "application/json" ) response = { 'jsonrpc' : self . req_rpc_version , 'id' : self . req_id , } response . update ( additional_dict ) jresponse = json . dumps ( response ) self . send_header ( "Content-length" , len ( jresponse ) ) self . end_headers ( ) self . wfile . write ( jresponse . encode ( ) )	Send a result to the RPC client
6,968	def set_current_value ( self , value ) : self . _current_value = value self . _current_rendered = self . _encode_value ( self . _current_value ) return self . _current_rendered	Sets the current value of the field
6,969	def mutate ( self ) : self . _initialize ( ) if self . _exhausted ( ) : return False self . _current_index += 1 self . _mutate ( ) return True	Mutate the field
6,970	def render ( self , ctx = None ) : self . _initialize ( ) if not self . is_default ( ) : self . _current_rendered = self . _encode_value ( self . _current_value ) return self . _current_rendered	Render the current value of the field
6,971	def reset ( self ) : self . _current_index = - 1 self . _current_value = self . _default_value self . _current_rendered = self . _default_rendered self . offset = None	Reset the field to its default state
6,972	def resolve_field ( self , field ) : if isinstance ( field , BaseField ) : return field name = field if name . startswith ( '/' ) : return self . resolve_absolute_name ( name ) resolved_field = self . scan_for_field ( name ) if not resolved_field : container = self . enclosing if container : resolved_field = container . resolve_field ( name ) if not resolved_field : raise KittyException ( 'Could not resolve field by name (%s)' % name ) return resolved_field	Resolve a field from name
6,973	def stop ( self ) : self . _stop_event . set ( ) if self . _func_stop_event is not None : self . _func_stop_event . set ( ) self . join ( timeout = 1 ) if self . isAlive ( ) : print ( 'Failed to stop thread' )	stop the thread return after thread stopped
6,974	def _initialize ( self ) : if self . _field_name : self . _field = self . resolve_field ( self . _field_name ) if not self . _field : raise KittyException ( 'Could not resolve field name %s' % self . _field_name )	We override _initialize as we want to resolve the field each time
6,975	def _calculate ( self , field ) : encloser = field . enclosing if encloser : rendered = encloser . get_rendered_fields ( RenderContext ( self ) ) if field not in rendered : value = len ( rendered ) else : value = rendered . index ( field ) else : value = 0 return value	We want to avoid trouble so if the field is not enclosed by any other field we just return 0 .
6,976	def _calculate ( self , field ) : base_offset = 0 if self . base_field is not None : base_offset = self . base_field . offset target_offset = self . _field . offset if ( target_offset is None ) or ( base_offset is None ) : return 0 return target_offset - base_offset	If the offset is unknown return 0
6,977	def get_report ( self ) : report_dict = self . _meta_get_report ( ) report = Report . from_dict ( report_dict ) return report	need to wrap get_report since we need to parse the report
6,978	def setup ( self ) : if self . controller : self . controller . setup ( ) for monitor in self . monitors : monitor . setup ( )	Make sure the target is ready for fuzzing including monitors and controllers
6,979	def teardown ( self ) : if self . controller : self . controller . teardown ( ) for monitor in self . monitors : monitor . teardown ( )	Clean up the target once all tests are completed
6,980	def stop ( self ) : self . logger . info ( 'Stopping client fuzzer' ) self . _target_control_thread . stop ( ) self . target . signal_mutated ( ) super ( ClientFuzzer , self ) . stop ( )	Stop the fuzzing session
6,981	def _should_fuzz_node ( self , fuzz_node , stage ) : if stage == ClientFuzzer . STAGE_ANY : return True if fuzz_node . name . lower ( ) == stage . lower ( ) : if self . _index_in_path == len ( self . _fuzz_path ) - 1 : return True else : return False	The matching stage is either the name of the last node or ClientFuzzer . STAGE_ANY .
6,982	def get_mutation ( self , stage , data ) : payload = None if self . _keep_running ( ) : fuzz_node = self . _fuzz_path [ self . _index_in_path ] . dst if self . _should_fuzz_node ( fuzz_node , stage ) : fuzz_node . set_session_data ( data ) payload = fuzz_node . render ( ) . tobytes ( ) self . _last_payload = payload else : self . _update_path_index ( stage ) if payload : self . _notify_mutated ( ) self . _requested_stages . append ( ( stage , payload ) ) return payload	Get the next mutation if in the correct stage
6,983	def SInt64 ( value , min_value = None , max_value = None , encoder = ENC_INT_DEFAULT , fuzzable = True , name = None , full_range = False ) : return BitField ( value , 64 , signed = True , min_value = min_value , max_value = max_value , encoder = encoder , fuzzable = fuzzable , name = name , full_range = full_range )	Signed 64 - bit field
6,984	def BE8 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt8 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_BE , fuzzable = fuzzable , name = name , full_range = full_range )	8 - bit field Big endian encoded
6,985	def BE16 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt16 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_BE , fuzzable = fuzzable , name = name , full_range = full_range )	16 - bit field Big endian encoded
6,986	def BE32 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt32 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_BE , fuzzable = fuzzable , name = name , full_range = full_range )	32 - bit field Big endian encoded
6,987	def BE64 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt64 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_BE , fuzzable = fuzzable , name = name , full_range = full_range )	64 - bit field Big endian encoded
6,988	def LE8 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt8 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_LE , fuzzable = fuzzable , name = name , full_range = full_range )	8 - bit field Little endian encoded
6,989	def LE16 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt16 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_LE , fuzzable = fuzzable , name = name , full_range = full_range )	16 - bit field Little endian encoded
6,990	def LE32 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt32 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_LE , fuzzable = fuzzable , name = name , full_range = full_range )	32 - bit field Little endian encoded
6,991	def LE64 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt64 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_LE , fuzzable = fuzzable , name = name , full_range = full_range )	64 - bit field Little endian encoded
6,992	def _eintr_retry ( func , * args ) : while True : try : return func ( * args ) except ( OSError , select . error ) as e : if e . args [ 0 ] != errno . EINTR : raise	restart a system call interrupted by EINTR
6,993	def serve_forever ( self , poll_interval = 0.5 ) : self . __is_shut_down . clear ( ) try : while not self . __shutdown_request : r , w , e = _eintr_retry ( select . select , [ self ] , [ ] , [ ] , poll_interval ) if self in r : self . _handle_request_noblock ( ) finally : self . __shutdown_request = False self . __is_shut_down . set ( )	Handle one request at a time until shutdown . Polls for shutdown every poll_interval seconds . Ignores self . timeout . If you need to do periodic tasks do them in another thread .
6,994	def _handle_request_noblock ( self ) : try : request , client_address = self . get_request ( ) except socket . error : return if self . verify_request ( request , client_address ) : try : self . process_request ( request , client_address ) except : self . handle_error ( request , client_address ) self . shutdown_request ( request )	Handle one request without blocking .
6,995	def process_request ( self , request , client_address ) : self . finish_request ( request , client_address ) self . shutdown_request ( request )	Call finish_request .
6,996	def process_request_thread ( self , request , client_address ) : try : self . finish_request ( request , client_address ) self . shutdown_request ( request ) except Exception as e : self . logger . error ( e ) self . handle_error ( request , client_address ) self . shutdown_request ( request )	Process the request .
6,997	def handle_error ( self , request , client_address ) : self . logger . error ( '-' * 40 ) self . logger . error ( 'Exception happened during processing of request from %s:%s' % ( client_address [ 0 ] , client_address [ 1 ] ) ) self . logger . error ( traceback . format_exc ( ) ) self . logger . error ( '-' * 40 ) self . stop ( )	Add self . stop to make server stop
6,998	def _restart_target ( self ) : if self . _server : if self . _server . returncode is None : self . _server . kill ( ) time . sleep ( 0.2 ) self . _server = subprocess . Popen ( "python session_server.py" , stdout = subprocess . PIPE , stderr = subprocess . PIPE , shell = True ) time . sleep ( 0.2 )	Restart our Target .
6,999	def clear ( self ) : self . _data_fields = { } self . _sub_reports = { } self . set_status ( Report . FAILED if self . _default_failed else Report . PASSED ) self . add ( 'name' , self . _name ) self . add ( 'sub_reports' , [ ] )	Set the report to its defaults . This will clear the report keeping only the name and setting the failure status to the default .

6,900

def status ( * args , ** kwargs ) : def decor ( func ) : @ wraps ( func ) def wrapper ( * args , ** krgs ) : echo ( "[!] " + msg , end = " " , flush = True ) result = func ( * args , ** krgs ) echo ( fin , flush = True ) return result return wrapper fin = kwargs . pop ( 'fin' , "DONE." ) args = list ( args ) if len ( args ) > 1 and callable ( args [ 1 ] ) : msg = args . pop ( 0 ) func = args . pop ( 0 ) try : fargs = args . pop ( 0 ) except : fargs = [ ] try : fkrgs = args . pop ( 0 ) except : fkrgs = { } return decor ( func ) ( * fargs , ** fkrgs ) msg = args . pop ( 0 ) return decor

Prints a status message at the start and finish of an associated function . Can be used as a function decorator or as a function that accepts another function as the first parameter .

6,901

def fatal ( msg , exitcode = 1 , ** kwargs ) : pause_before_exit = kwargs . pop ( "pause" ) if "pause" in kwargs . keys ( ) else False echo ( "[FATAL] " + msg , ** kwargs ) if pause_before_exit : pause ( ) sys . exit ( exitcode )

Prints a message then exits the program . Optionally pause before exit with pause = True kwarg .

6,902

def hrule ( width = None , char = None ) : width = width or HRWIDTH char = char or HRCHAR return echo ( getline ( char , width ) )

Outputs or returns a horizontal line of the given character and width . Returns printed string .

6,903

def title ( msg ) : if sys . platform . startswith ( "win" ) : ctypes . windll . kernel32 . SetConsoleTitleW ( tounicode ( msg ) )

Sets the title of the console window .

6,904

def wrap ( item , args = None , krgs = None , ** kwargs ) : with Wrap ( ** kwargs ) : if callable ( item ) : args = args or [ ] krgs = krgs or { } item ( * args , ** krgs ) else : echo ( item )

Wraps the given item content between horizontal lines . Item can be a string or a function .

6,905

def _guess_name ( desc , taken = None ) : taken = taken or [ ] name = "" for word in desc . split ( ) : c = word [ 0 ] . lower ( ) if not c . isalnum ( ) : continue name += c if name not in taken : break count = 2 while name in taken : name = name + str ( count ) count += 1 return name

Attempts to guess the menu entry name from the function name .

6,906

def add ( self , name , desc , func = None , args = None , krgs = None ) : self . entries . append ( MenuEntry ( name , desc , func , args or [ ] , krgs or { } ) )

Add a menu entry .

6,907

def enum ( self , desc , func = None , args = None , krgs = None ) : name = str ( len ( self . entries ) + 1 ) self . entries . append ( MenuEntry ( name , desc , func , args or [ ] , krgs or { } ) )

Add a menu entry whose name will be an auto indexed number .

6,908

def run ( self , name ) : for entry in self . entries : if entry . name == name : run_func ( entry ) break

Runs the function associated with the given entry name .

6,909

def partition_scripts ( scripts , start_type1 , start_type2 ) : match , other = [ ] , [ ] for script in scripts : if ( HairballPlugin . script_start_type ( script ) == start_type1 or HairballPlugin . script_start_type ( script ) == start_type2 ) : match . append ( script ) else : other . append ( script ) return match , other

Return two lists of scripts out of the original scripts list .

6,910

def attribute_result ( cls , sprites ) : retval = dict ( ( x , True ) for x in cls . ATTRIBUTES ) for properties in sprites . values ( ) : for attribute , state in properties . items ( ) : retval [ attribute ] &= state != cls . STATE_MODIFIED return retval

Return mapping of attributes to if they were initialized or not .

6,911

def attribute_state ( cls , scripts , attribute ) : green_flag , other = partition_scripts ( scripts , cls . HAT_GREEN_FLAG , cls . HAT_CLONE ) block_set = cls . BLOCKMAPPING [ attribute ] state = cls . STATE_NOT_MODIFIED for script in green_flag : in_zone = True for name , level , _ in cls . iter_blocks ( script . blocks ) : if name == 'broadcast %s and wait' : in_zone = False if ( name , 'absolute' ) in block_set : if in_zone and level == 0 : if state == cls . STATE_NOT_MODIFIED : state = cls . STATE_INITIALIZED else : state = cls . STATE_MODIFIED elif in_zone : continue else : state = cls . STATE_MODIFIED break elif ( name , 'relative' ) in block_set : state = cls . STATE_MODIFIED break if state != cls . STATE_NOT_MODIFIED : return state for script in other : for name , _ , _ in cls . iter_blocks ( script . blocks ) : if name in [ x [ 0 ] for x in block_set ] : return cls . STATE_MODIFIED return cls . STATE_NOT_MODIFIED

Return the state of the scripts for the given attribute .

6,912

def output_results ( cls , sprites ) : print ( ' ' . join ( cls . ATTRIBUTES ) ) format_strs = [ '{{{}!s:^{}}}' . format ( x , len ( x ) ) for x in cls . ATTRIBUTES ] print ( ' ' . join ( format_strs ) . format ( ** cls . attribute_result ( sprites ) ) )

Output whether or not each attribute was correctly initialized .

6,913

def sprite_changes ( cls , sprite ) : retval = dict ( ( x , cls . attribute_state ( sprite . scripts , x ) ) for x in ( x for x in cls . ATTRIBUTES if x != 'background' ) ) return retval

Return a mapping of attributes to their initilization state .

6,914

def analyze ( self , scratch , ** kwargs ) : changes = dict ( ( x . name , self . sprite_changes ( x ) ) for x in scratch . sprites ) changes [ 'stage' ] = { 'background' : self . attribute_state ( scratch . stage . scripts , 'costume' ) } return { 'initialized' : changes }

Run and return the results of the AttributeInitialization plugin .

6,915

def variable_state ( cls , scripts , variables ) : def conditionally_set_not_modified ( ) : state = variables . get ( block . args [ 0 ] , None ) if state == cls . STATE_NOT_MODIFIED : variables [ block . args [ 0 ] ] = cls . STATE_MODIFIED green_flag , other = partition_scripts ( scripts , cls . HAT_GREEN_FLAG ) variables = dict ( ( x , cls . STATE_NOT_MODIFIED ) for x in variables ) for script in green_flag : in_zone = True for name , level , block in cls . iter_blocks ( script . blocks ) : if name == 'broadcast %s and wait' : in_zone = False if name == 'set %s effect to %s' : state = variables . get ( block . args [ 0 ] , None ) if state is None : continue if in_zone and level == 0 : if state == cls . STATE_NOT_MODIFIED : state = cls . STATE_INITIALIZED else : state = cls . STATE_MODIFIED elif in_zone : continue elif state == cls . STATE_NOT_MODIFIED : state = cls . STATE_MODIFIED variables [ block . args [ 0 ] ] = state elif name == 'change %s effect by %s' : conditionally_set_not_modified ( ) for script in other : for name , _ , block in cls . iter_blocks ( script . blocks ) : if name in ( 'change %s effect by %s' , 'set %s effect to %s' ) : conditionally_set_not_modified ( ) return variables

Return the initialization state for each variable in variables .

6,916

def analyze ( self , scratch , ** kwargs ) : variables = dict ( ( x , self . variable_state ( x . scripts , x . variables ) ) for x in scratch . sprites ) variables [ 'global' ] = self . variable_state ( self . iter_scripts ( scratch ) , scratch . stage . variables ) import pprint pprint . pprint ( variables ) return { 'variables' : variables }

Run and return the results of the VariableInitialization plugin .

6,917

def finalize ( self ) : print ( '{} default sprite names found:' . format ( self . total_default ) ) for name in self . list_default : print ( name )

Output the default sprite names found in the project .

6,918

def analyze ( self , scratch , ** kwargs ) : for sprite in self . iter_sprites ( scratch ) : for default in self . default_names : if default in sprite . name : self . total_default += 1 self . list_default . append ( sprite . name )

Run and return the results from the SpriteNaming plugin .

6,919

def prepare_request_params ( self , _query_params , _json_params ) : self . _query_params = dictset ( _query_params or self . request . params . mixed ( ) ) self . _json_params = dictset ( _json_params ) ctype = self . request . content_type if self . request . method in [ 'POST' , 'PUT' , 'PATCH' ] : if ctype == 'application/json' : try : self . _json_params . update ( self . request . json ) except simplejson . JSONDecodeError : log . error ( "Expecting JSON. Received: '{}'. " "Request: {} {}" . format ( self . request . body , self . request . method , self . request . url ) ) self . _json_params = BaseView . convert_dotted ( self . _json_params ) self . _query_params = BaseView . convert_dotted ( self . _query_params ) self . _params = self . _query_params . copy ( ) self . _params . update ( self . _json_params )

Prepare query and update params .

6,920

def set_override_rendered ( self ) : if '' in self . request . accept : self . request . override_renderer = self . _default_renderer elif 'application/json' in self . request . accept : self . request . override_renderer = 'nefertari_json' elif 'text/plain' in self . request . accept : self . request . override_renderer = 'string'

Set self . request . override_renderer if needed .

6,921

def _setup_aggregation ( self , aggregator = None ) : from nefertari . elasticsearch import ES if aggregator is None : aggregator = ESAggregator aggregations_enabled = ( ES . settings and ES . settings . asbool ( 'enable_aggregations' ) ) if not aggregations_enabled : log . debug ( 'Elasticsearch aggregations are not enabled' ) return index = getattr ( self , 'index' , None ) index_defined = index and index != self . not_allowed_action if index_defined : self . index = aggregator ( self ) . wrap ( self . index )

Wrap self . index method with ESAggregator .

6,922

def get_collection_es ( self ) : from nefertari . elasticsearch import ES return ES ( self . Model . __name__ ) . get_collection ( ** self . _query_params )

Query ES collection and return results .

6,923

def set_public_limits ( self ) : if self . request . method . upper ( ) in [ 'GET' , 'HEAD' ] : self . _query_params . process_int_param ( '_limit' , 20 ) if self . _auth_enabled and not getattr ( self . request , 'user' , None ) : wrappers . set_public_limits ( self )

Set public limits if auth is enabled and user is not authenticated .

6,924

def convert_ids2objects ( self ) : if not self . Model : log . info ( "%s has no model defined" % self . __class__ . __name__ ) return for field in self . _json_params . keys ( ) : if not engine . is_relationship_field ( field , self . Model ) : continue rel_model_cls = engine . get_relationship_cls ( field , self . Model ) self . id2obj ( field , rel_model_cls )

Convert object IDs from self . _json_params to objects if needed .

6,925

def setup_default_wrappers ( self ) : self . _after_calls [ 'index' ] = [ wrappers . wrap_in_dict ( self . request ) , wrappers . add_meta ( self . request ) , wrappers . add_object_url ( self . request ) , ] self . _after_calls [ 'show' ] = [ wrappers . wrap_in_dict ( self . request ) , wrappers . add_meta ( self . request ) , wrappers . add_object_url ( self . request ) , ] self . _after_calls [ 'create' ] = [ wrappers . wrap_in_dict ( self . request ) , wrappers . add_meta ( self . request ) , wrappers . add_object_url ( self . request ) , ] self . _after_calls [ 'update' ] = [ wrappers . wrap_in_dict ( self . request ) , wrappers . add_meta ( self . request ) , wrappers . add_object_url ( self . request ) , ] self . _after_calls [ 'replace' ] = [ wrappers . wrap_in_dict ( self . request ) , wrappers . add_meta ( self . request ) , wrappers . add_object_url ( self . request ) , ] if self . _auth_enabled : for meth in ( 'index' , 'show' , 'create' , 'update' , 'replace' ) : self . _after_calls [ meth ] += [ wrappers . apply_privacy ( self . request ) , ] for meth in ( 'update' , 'replace' , 'update_many' ) : self . _before_calls [ meth ] += [ wrappers . apply_request_privacy ( self . Model , self . _json_params ) , ]

Setup defaulf wrappers .

6,926

def register ( self ) : user , created = self . Model . create_account ( self . _json_params ) if not created : raise JHTTPConflict ( 'Looks like you already have an account.' ) self . request . _user = user pk_field = user . pk_field ( ) headers = remember ( self . request , getattr ( user , pk_field ) ) return JHTTPOk ( 'Registered' , headers = headers )

Register new user by POSTing all required data .

6,927

def register ( self ) : user , created = self . Model . create_account ( self . _json_params ) if user . api_key is None : raise JHTTPBadRequest ( 'Failed to generate ApiKey for user' ) if not created : raise JHTTPConflict ( 'Looks like you already have an account.' ) self . request . _user = user headers = remember ( self . request , user . username ) return JHTTPOk ( 'Registered' , headers = headers )

Register a new user by POSTing all required data .

6,928

def claim_token ( self , ** params ) : self . _json_params . update ( params ) success , self . user = self . Model . authenticate_by_password ( self . _json_params ) if success : headers = remember ( self . request , self . user . username ) return JHTTPOk ( 'Token claimed' , headers = headers ) if self . user : raise JHTTPUnauthorized ( 'Wrong login or password' ) else : raise JHTTPNotFound ( 'User not found' )

Claim current token by POSTing login and password .

6,929

def reset_token ( self , ** params ) : response = self . claim_token ( ** params ) if not self . user : return response self . user . api_key . reset_token ( ) headers = remember ( self . request , self . user . username ) return JHTTPOk ( 'Registered' , headers = headers )

Reset current token by POSTing login and password .

6,930

def _apply_nested_privacy ( self , data ) : kw = { 'is_admin' : self . is_admin , 'drop_hidden' : self . drop_hidden , } for key , val in data . items ( ) : if is_document ( val ) : data [ key ] = apply_privacy ( self . request ) ( result = val , ** kw ) elif isinstance ( val , list ) and val and is_document ( val [ 0 ] ) : data [ key ] = [ apply_privacy ( self . request ) ( result = doc , ** kw ) for doc in val ] return data

Apply privacy to nested documents .

6,931

def get_root_resource ( config ) : app_package_name = get_app_package_name ( config ) return config . registry . _root_resources . setdefault ( app_package_name , Resource ( config ) )

Returns the root resource .

6,932

def get_default_view_path ( resource ) : "Returns the dotted path to the default view class." parts = [ a . member_name for a in resource . ancestors ] + [ resource . collection_name or resource . member_name ] if resource . prefix : parts . insert ( - 1 , resource . prefix ) view_file = '%s' % '_' . join ( parts ) view = '%s:%sView' % ( view_file , snake2camel ( view_file ) ) app_package_name = get_app_package_name ( resource . config ) return '%s.views.%s' % ( app_package_name , view )

Returns the dotted path to the default view class .

6,933

def get_ancestors ( self ) : "Returns the list of ancestor resources." if self . _ancestors : return self . _ancestors if not self . parent : return [ ] obj = self . resource_map . get ( self . parent . uid ) while obj and obj . member_name : self . _ancestors . append ( obj ) obj = obj . parent self . _ancestors . reverse ( ) return self . _ancestors

Returns the list of ancestor resources .

6,934

def add_from_child ( self , resource , ** kwargs ) : new_resource = self . add ( resource . member_name , resource . collection_name , ** kwargs ) for child in resource . children : new_resource . add_from_child ( child , ** kwargs )

Add a resource with its all children resources to the current resource .

6,935

def add ( self , path ) : name_with_ext = os . path . split ( path ) [ 1 ] name = name_with_ext . split ( '.' ) [ 0 ] self . list . update ( { name : path } )

Add the path of a data set to the list of available sets

6,936

def unpack ( self , name ) : path = self . list [ name ] df = pd . read_pickle ( path , compression = 'gzip' ) return df

Unpacks a data set to a Pandas DataFrame

6,937

def six_frame ( genome , table , minimum = 10 ) : for seq in parse_fasta ( genome ) : dna = Seq ( seq [ 1 ] . upper ( ) . replace ( 'U' , 'T' ) , IUPAC . ambiguous_dna ) counter = 0 for sequence in [ 'f' , dna ] , [ 'rc' , dna . reverse_complement ( ) ] : direction , sequence = sequence for frame in range ( 0 , 3 ) : for prot in sequence [ frame : ] . translate ( table = table , to_stop = False ) . split ( '*' ) : if len ( prot ) < minimum : continue counter += 1 header = '%s_%s table=%s frame=%s-%s %s' % ( seq [ 0 ] . split ( ) [ 0 ] , counter , table , frame + 1 , direction , ' ' . join ( seq [ 0 ] . split ( ) [ 1 : ] ) ) yield [ header , prot ]

translate each sequence into six reading frames

6,938

def check_gaps ( matches , gap_threshold = 0 ) : gaps = [ ] prev = None for match in sorted ( matches , key = itemgetter ( 0 ) ) : if prev is None : prev = match continue if match [ 0 ] - prev [ 1 ] >= gap_threshold : gaps . append ( [ prev , match ] ) prev = match return [ [ i [ 0 ] [ 1 ] , i [ 1 ] [ 0 ] ] for i in gaps ]

check for large gaps between alignment windows

6,939

def check_overlap ( current , hit , overlap = 200 ) : for prev in current : p_coords = prev [ 2 : 4 ] coords = hit [ 2 : 4 ] if get_overlap ( coords , p_coords ) >= overlap : return True return False

determine if sequence has already hit the same part of the model indicating that this hit is for another 16S rRNA gene

6,940

def find_coordinates ( hmms , bit_thresh ) : seq2hmm = parse_hmm ( hmms , bit_thresh ) seq2hmm = best_model ( seq2hmm ) group2hmm = { } for seq , info in list ( seq2hmm . items ( ) ) : group2hmm [ seq ] = { } for group_num , group in enumerate ( hit_groups ( info [ 1 ] ) ) : best = sorted ( group , reverse = True , key = itemgetter ( - 1 ) ) [ 0 ] strand = best [ 5 ] coordinates = [ i [ 0 ] for i in group ] + [ i [ 1 ] for i in group ] coordinates = [ min ( coordinates ) , max ( coordinates ) , strand ] matches = [ i for i in group if i [ 5 ] == strand ] gaps = check_gaps ( matches ) group2hmm [ seq ] [ group_num ] = [ info [ 0 ] , strand , coordinates , matches , gaps ] return group2hmm

find 16S rRNA gene sequence coordinates

6,941

def get_info ( line , bit_thresh ) : if len ( line ) >= 18 : id , model , bit , inc = line [ 0 ] . split ( ) [ 0 ] , line [ 2 ] , float ( line [ 14 ] ) , line [ 16 ] sstart , send , strand = int ( line [ 7 ] ) , int ( line [ 8 ] ) , line [ 9 ] mstart , mend = int ( line [ 5 ] ) , int ( line [ 6 ] ) elif len ( line ) == 9 : if bit_thresh == 0 : print ( '# ssu-cmsearch does not include a model-specific inclusion threshold, ' , file = sys . stderr ) print ( '# please specify a bit score threshold' , file = sys . stderr ) exit ( ) id , model , bit = line [ 1 ] . split ( ) [ 0 ] , line [ 0 ] , float ( line [ 6 ] ) inc = '!' sstart , send = int ( line [ 2 ] ) , int ( line [ 3 ] ) mstart , mend = int ( 4 ) , int ( 5 ) if send >= sstart : strand = '+' else : strand = '-' else : print ( '# unsupported hmm format:' , file = sys . stderr ) print ( '# provide tabular output from ssu-cmsearch and cmsearch supported' , file = sys . stderr ) exit ( ) coords = [ sstart , send ] sstart , send = min ( coords ) , max ( coords ) mcoords = [ mstart , mend ] mstart , mend = min ( mcoords ) , max ( mcoords ) return id , model , bit , sstart , send , mstart , mend , strand , inc

get info from either ssu - cmsearch or cmsearch output

6,942

def check_buffer ( coords , length , buffer ) : s = min ( coords [ 0 ] , buffer ) e = min ( length - coords [ 1 ] , buffer ) return [ s , e ]

check to see how much of the buffer is being used

6,943

def _import_parsers ( ) : global ARCGIS_NODES global ARCGIS_ROOTS global ArcGISParser global FGDC_ROOT global FgdcParser global ISO_ROOTS global IsoParser global VALID_ROOTS if ARCGIS_NODES is None or ARCGIS_ROOTS is None or ArcGISParser is None : from gis_metadata . arcgis_metadata_parser import ARCGIS_NODES from gis_metadata . arcgis_metadata_parser import ARCGIS_ROOTS from gis_metadata . arcgis_metadata_parser import ArcGISParser if FGDC_ROOT is None or FgdcParser is None : from gis_metadata . fgdc_metadata_parser import FGDC_ROOT from gis_metadata . fgdc_metadata_parser import FgdcParser if ISO_ROOTS is None or IsoParser is None : from gis_metadata . iso_metadata_parser import ISO_ROOTS from gis_metadata . iso_metadata_parser import IsoParser if VALID_ROOTS is None : VALID_ROOTS = { FGDC_ROOT } . union ( ARCGIS_ROOTS + ISO_ROOTS )

Lazy imports to prevent circular dependencies between this module and utils

6,944

def _init_metadata ( self ) : if self . _data_map is None : self . _init_data_map ( ) validate_properties ( self . _data_map , self . _metadata_props ) for prop in self . _data_map : setattr ( self , prop , parse_property ( self . _xml_tree , None , self . _data_map , prop ) ) self . has_data = any ( getattr ( self , prop ) for prop in self . _data_map )

Dynamically sets attributes from a Dictionary passed in by children . The Dictionary will contain the name of each attribute as keys and either an XPATH mapping to a text value in _xml_tree or a function that takes no parameters and returns the intended value .

6,945

def _parse_complex ( self , prop ) : xpath_root = None xpath_map = self . _data_structures [ prop ] return parse_complex ( self . _xml_tree , xpath_root , xpath_map , prop )

Default parsing operation for a complex struct

6,946

def _parse_complex_list ( self , prop ) : xpath_root = self . _get_xroot_for ( prop ) xpath_map = self . _data_structures [ prop ] return parse_complex_list ( self . _xml_tree , xpath_root , xpath_map , prop )

Default parsing operation for lists of complex structs

6,947

def _parse_dates ( self , prop = DATES ) : return parse_dates ( self . _xml_tree , self . _data_structures [ prop ] )

Creates and returns a Date Types data structure parsed from the metadata

6,948

def _update_complex ( self , ** update_props ) : prop = update_props [ 'prop' ] xpath_root = self . _get_xroot_for ( prop ) xpath_map = self . _data_structures [ prop ] return update_complex ( xpath_root = xpath_root , xpath_map = xpath_map , ** update_props )

Default update operation for a complex struct

6,949

def _update_complex_list ( self , ** update_props ) : prop = update_props [ 'prop' ] xpath_root = self . _get_xroot_for ( prop ) xpath_map = self . _data_structures [ prop ] return update_complex_list ( xpath_root = xpath_root , xpath_map = xpath_map , ** update_props )

Default update operation for lists of complex structs

6,950

def spec ( self , postf_un_ops : str ) -> list : spec = [ ( l + op , { 'pat' : self . pat ( pat ) , 'postf' : self . postf ( r , postf_un_ops ) , 'regex' : None } ) for op , pat in self . styles . items ( ) for l , r in self . brackets ] spec [ 0 ] [ 1 ] [ 'regex' ] = self . regex_pat . format ( _ops_regex ( l for l , r in self . brackets ) , _ops_regex ( self . styles . keys ( ) ) ) return spec

Return prefix unary operators list

6,951

def one_symbol_ops_str ( self ) -> str : return re . escape ( '' . join ( ( key for key in self . ops . keys ( ) if len ( key ) == 1 ) ) )

Regex - escaped string with all one - symbol operators

6,952

def plot_gaps ( plot , columns ) : from plot_window import window_plot_convolve as plot_window plot_window ( [ [ 100 - i for i in columns ] ] , len ( columns ) * .01 , plot )

plot % of gaps at each position

6,953

def sample_group ( sid , groups ) : for name in groups : if sid in groups [ name ] . sids : return name

Iterate through all categories in an OrderedDict and return category name if SampleID present in that category .

6,954

def combine_sets ( * sets ) : combined = set ( ) for s in sets : combined . update ( s ) return combined

Combine multiple sets to create a single larger set .

6,955

def unique_otuids ( groups ) : uniques = { key : set ( ) for key in groups } for i , group in enumerate ( groups ) : to_combine = groups . values ( ) [ : i ] + groups . values ( ) [ i + 1 : ] combined = combine_sets ( * to_combine ) uniques [ group ] = groups [ group ] . difference ( combined ) return uniques

Get unique OTUIDs of each category .

6,956

def shared_otuids ( groups ) : for g in sorted ( groups ) : print ( "Number of OTUs in {0}: {1}" . format ( g , len ( groups [ g ] . results [ "otuids" ] ) ) ) number_of_categories = len ( groups ) shared = defaultdict ( ) for i in range ( 2 , number_of_categories + 1 ) : for j in combinations ( sorted ( groups ) , i ) : combo_name = " & " . join ( list ( j ) ) for grp in j : shared [ combo_name ] = groups [ j [ 0 ] ] . results [ "otuids" ] . copy ( ) for grp in j [ 1 : ] : shared [ combo_name ] . intersection_update ( groups [ grp ] . results [ "otuids" ] ) return shared

Get shared OTUIDs between all unique combinations of groups .

6,957

def write_uniques ( path , prefix , uniques ) : for group in uniques : fp = osp . join ( path , "{}_{}.txt" . format ( prefix , group ) ) with open ( fp , "w" ) as outf : outf . write ( "\n" . join ( uniques [ group ] ) )

Given a path the method writes out one file for each group name in the uniques dictionary with the file name in the pattern

6,958

def storeFASTA ( fastaFNH ) : fasta = file_handle ( fastaFNH ) . read ( ) return [ FASTARecord ( rec [ 0 ] . split ( ) [ 0 ] , rec [ 0 ] . split ( None , 1 ) [ 1 ] , "" . join ( rec [ 1 : ] ) ) for rec in ( x . strip ( ) . split ( "\n" ) for x in fasta . split ( ">" ) [ 1 : ] ) ]

Parse the records in a FASTA - format file by first reading the entire file into memory .

6,959

def parseFASTA ( fastaFNH ) : recs = [ ] seq = [ ] seqID = "" descr = "" for line in file_handle ( fastaFNH ) : line = line . strip ( ) if line [ 0 ] == ";" : continue if line [ 0 ] == ">" : if seq : recs . append ( FASTARecord ( seqID , descr , "" . join ( seq ) ) ) seq = [ ] line = line [ 1 : ] . split ( None , 1 ) seqID , descr = line [ 0 ] , line [ 1 ] else : seq . append ( line ) if seq : recs . append ( FASTARecord ( seqID , descr , "" . join ( seq ) ) ) return recs

Parse the records in a FASTA - format file keeping the file open and reading through one line at a time .

6,960

def get ( self , test_id ) : self . select ( '*' , 'test_id=?' , [ test_id ] ) row = self . _cursor . fetchone ( ) if not row : raise KeyError ( 'No report with test id %s in the DB' % test_id ) values = self . row_to_dict ( row ) content = self . _deserialize_dict ( values [ 'content' ] ) return Report . from_dict ( content )

get report by the test id

6,961

def _serialize_dict ( cls , data ) : return b64encode ( zlib . compress ( cPickle . dumps ( data , protocol = 2 ) ) ) . decode ( )

serializes a dictionary

6,962

def _deserialize_dict ( cls , data ) : return cPickle . loads ( zlib . decompress ( b64decode ( data . encode ( ) ) ) )

deserializes a dictionary

6,963

def _run_sequence ( self , sequence ) : self . _check_pause ( ) self . _pre_test ( ) session_data = self . target . get_session_data ( ) self . _test_info ( ) resp = None for edge in sequence : if edge . callback : edge . callback ( self , edge , resp ) session_data = self . target . get_session_data ( ) node = edge . dst node . set_session_data ( session_data ) resp = self . _transmit ( node ) return self . _post_test ( )

Run a single sequence

6,964

def _transmit ( self , node ) : payload = node . render ( ) . tobytes ( ) self . _last_payload = payload try : return self . target . transmit ( payload ) except Exception as e : self . logger . error ( 'Error in transmit: %s' , e ) raise

Transmit node data to target .

6,965

def _generate_rpc_method ( self , method ) : def _ ( ** kwargs ) : msg_id = self . get_unique_msg_id ( ) params = encode_data ( kwargs ) payload = { 'method' : method , 'params' : params , 'jsonrpc' : '2.0' , 'id' : msg_id } response = requests . post ( self . url , data = json . dumps ( payload ) , headers = self . headers ) . json ( ) if ( 'error' in response ) : if response [ 'error' ] [ 'code' ] == JSONRPC_NO_RESULT : return None raise Exception ( 'Got error from RPC server when called "%s" error: %s' % ( method , response [ 'error' ] ) ) if 'result' in response : result = decode_data ( response [ 'result' ] ) return result return _

Generate a function that performs rpc call

6,966

def _parse_request ( self ) : self . req_method = 'unknown' self . req_params = { } self . req_rpc_version = '2.0' self . req_id = 0 self . data = self . rfile . read ( int ( self . headers . get ( 'content-length' ) ) ) data_dict = json . loads ( self . data ) self . req_method = data_dict [ 'method' ] self . req_params = decode_data ( data_dict [ 'params' ] ) self . req_rpc_version = data_dict [ 'jsonrpc' ] self . req_id = data_dict [ 'id' ]

Parse the request

6,967

def send_result ( self , additional_dict ) : self . send_response ( 200 ) self . send_header ( "Content-type" , "application/json" ) response = { 'jsonrpc' : self . req_rpc_version , 'id' : self . req_id , } response . update ( additional_dict ) jresponse = json . dumps ( response ) self . send_header ( "Content-length" , len ( jresponse ) ) self . end_headers ( ) self . wfile . write ( jresponse . encode ( ) )

Send a result to the RPC client

6,968

def set_current_value ( self , value ) : self . _current_value = value self . _current_rendered = self . _encode_value ( self . _current_value ) return self . _current_rendered

Sets the current value of the field

6,969

def mutate ( self ) : self . _initialize ( ) if self . _exhausted ( ) : return False self . _current_index += 1 self . _mutate ( ) return True

Mutate the field

6,970

def render ( self , ctx = None ) : self . _initialize ( ) if not self . is_default ( ) : self . _current_rendered = self . _encode_value ( self . _current_value ) return self . _current_rendered

Render the current value of the field

6,971

def reset ( self ) : self . _current_index = - 1 self . _current_value = self . _default_value self . _current_rendered = self . _default_rendered self . offset = None

Reset the field to its default state

6,972

def resolve_field ( self , field ) : if isinstance ( field , BaseField ) : return field name = field if name . startswith ( '/' ) : return self . resolve_absolute_name ( name ) resolved_field = self . scan_for_field ( name ) if not resolved_field : container = self . enclosing if container : resolved_field = container . resolve_field ( name ) if not resolved_field : raise KittyException ( 'Could not resolve field by name (%s)' % name ) return resolved_field

Resolve a field from name

6,973

def stop ( self ) : self . _stop_event . set ( ) if self . _func_stop_event is not None : self . _func_stop_event . set ( ) self . join ( timeout = 1 ) if self . isAlive ( ) : print ( 'Failed to stop thread' )

stop the thread return after thread stopped

6,974

def _initialize ( self ) : if self . _field_name : self . _field = self . resolve_field ( self . _field_name ) if not self . _field : raise KittyException ( 'Could not resolve field name %s' % self . _field_name )

We override _initialize as we want to resolve the field each time

6,975

def _calculate ( self , field ) : encloser = field . enclosing if encloser : rendered = encloser . get_rendered_fields ( RenderContext ( self ) ) if field not in rendered : value = len ( rendered ) else : value = rendered . index ( field ) else : value = 0 return value

We want to avoid trouble so if the field is not enclosed by any other field we just return 0 .

6,976

def _calculate ( self , field ) : base_offset = 0 if self . base_field is not None : base_offset = self . base_field . offset target_offset = self . _field . offset if ( target_offset is None ) or ( base_offset is None ) : return 0 return target_offset - base_offset

If the offset is unknown return 0

6,977

def get_report ( self ) : report_dict = self . _meta_get_report ( ) report = Report . from_dict ( report_dict ) return report

need to wrap get_report since we need to parse the report

6,978

def setup ( self ) : if self . controller : self . controller . setup ( ) for monitor in self . monitors : monitor . setup ( )

Make sure the target is ready for fuzzing including monitors and controllers

6,979

def teardown ( self ) : if self . controller : self . controller . teardown ( ) for monitor in self . monitors : monitor . teardown ( )

Clean up the target once all tests are completed

6,980

def stop ( self ) : self . logger . info ( 'Stopping client fuzzer' ) self . _target_control_thread . stop ( ) self . target . signal_mutated ( ) super ( ClientFuzzer , self ) . stop ( )

Stop the fuzzing session

6,981

def _should_fuzz_node ( self , fuzz_node , stage ) : if stage == ClientFuzzer . STAGE_ANY : return True if fuzz_node . name . lower ( ) == stage . lower ( ) : if self . _index_in_path == len ( self . _fuzz_path ) - 1 : return True else : return False

The matching stage is either the name of the last node or ClientFuzzer . STAGE_ANY .

6,982

def get_mutation ( self , stage , data ) : payload = None if self . _keep_running ( ) : fuzz_node = self . _fuzz_path [ self . _index_in_path ] . dst if self . _should_fuzz_node ( fuzz_node , stage ) : fuzz_node . set_session_data ( data ) payload = fuzz_node . render ( ) . tobytes ( ) self . _last_payload = payload else : self . _update_path_index ( stage ) if payload : self . _notify_mutated ( ) self . _requested_stages . append ( ( stage , payload ) ) return payload

Get the next mutation if in the correct stage

6,983

def SInt64 ( value , min_value = None , max_value = None , encoder = ENC_INT_DEFAULT , fuzzable = True , name = None , full_range = False ) : return BitField ( value , 64 , signed = True , min_value = min_value , max_value = max_value , encoder = encoder , fuzzable = fuzzable , name = name , full_range = full_range )

Signed 64 - bit field

6,984

def BE8 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt8 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_BE , fuzzable = fuzzable , name = name , full_range = full_range )

8 - bit field Big endian encoded

6,985

def BE16 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt16 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_BE , fuzzable = fuzzable , name = name , full_range = full_range )

16 - bit field Big endian encoded

6,986

def BE32 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt32 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_BE , fuzzable = fuzzable , name = name , full_range = full_range )

32 - bit field Big endian encoded

6,987

def BE64 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt64 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_BE , fuzzable = fuzzable , name = name , full_range = full_range )

64 - bit field Big endian encoded

6,988

def LE8 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt8 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_LE , fuzzable = fuzzable , name = name , full_range = full_range )

8 - bit field Little endian encoded

6,989

def LE16 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt16 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_LE , fuzzable = fuzzable , name = name , full_range = full_range )

16 - bit field Little endian encoded

6,990

def LE32 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt32 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_LE , fuzzable = fuzzable , name = name , full_range = full_range )

32 - bit field Little endian encoded

6,991

def LE64 ( value , min_value = None , max_value = None , fuzzable = True , name = None , full_range = False ) : return UInt64 ( value , min_value = min_value , max_value = max_value , encoder = ENC_INT_LE , fuzzable = fuzzable , name = name , full_range = full_range )

64 - bit field Little endian encoded

6,992

def _eintr_retry ( func , * args ) : while True : try : return func ( * args ) except ( OSError , select . error ) as e : if e . args [ 0 ] != errno . EINTR : raise

restart a system call interrupted by EINTR

6,993

def serve_forever ( self , poll_interval = 0.5 ) : self . __is_shut_down . clear ( ) try : while not self . __shutdown_request : r , w , e = _eintr_retry ( select . select , [ self ] , [ ] , [ ] , poll_interval ) if self in r : self . _handle_request_noblock ( ) finally : self . __shutdown_request = False self . __is_shut_down . set ( )

Handle one request at a time until shutdown . Polls for shutdown every poll_interval seconds . Ignores self . timeout . If you need to do periodic tasks do them in another thread .

6,994

def _handle_request_noblock ( self ) : try : request , client_address = self . get_request ( ) except socket . error : return if self . verify_request ( request , client_address ) : try : self . process_request ( request , client_address ) except : self . handle_error ( request , client_address ) self . shutdown_request ( request )

Handle one request without blocking .

6,995

def process_request ( self , request , client_address ) : self . finish_request ( request , client_address ) self . shutdown_request ( request )

Call finish_request .

6,996

def process_request_thread ( self , request , client_address ) : try : self . finish_request ( request , client_address ) self . shutdown_request ( request ) except Exception as e : self . logger . error ( e ) self . handle_error ( request , client_address ) self . shutdown_request ( request )

Process the request .

6,997

def handle_error ( self , request , client_address ) : self . logger . error ( '-' * 40 ) self . logger . error ( 'Exception happened during processing of request from %s:%s' % ( client_address [ 0 ] , client_address [ 1 ] ) ) self . logger . error ( traceback . format_exc ( ) ) self . logger . error ( '-' * 40 ) self . stop ( )

Add self . stop to make server stop

6,998

def _restart_target ( self ) : if self . _server : if self . _server . returncode is None : self . _server . kill ( ) time . sleep ( 0.2 ) self . _server = subprocess . Popen ( "python session_server.py" , stdout = subprocess . PIPE , stderr = subprocess . PIPE , shell = True ) time . sleep ( 0.2 )

Restart our Target .

6,999

def clear ( self ) : self . _data_fields = { } self . _sub_reports = { } self . set_status ( Report . FAILED if self . _default_failed else Report . PASSED ) self . add ( 'name' , self . _name ) self . add ( 'sub_reports' , [ ] )

Set the report to its defaults . This will clear the report keeping only the name and setting the failure status to the default .