idx int64 0 63k | question stringlengths 61 4.03k | target stringlengths 6 1.23k |
|---|---|---|
46,200 | def _get_known_noncoding_het_snp ( data_dict ) : if data_dict [ 'gene' ] == '1' : return None if data_dict [ 'known_var' ] == '1' and data_dict [ 'ref_ctg_effect' ] == 'SNP' and data_dict [ 'smtls_nts' ] != '.' and ';' not in data_dict [ 'smtls_nts' ] : nucleotides = data_dict [ 'smtls_nts' ] . split ( ',' ) depths = d... | If ref is coding return None . If the data dict has a known snp and samtools made a call then return the string ref_name_change and the % of reads supporting the variant type . If noncoding but no samtools call then return None |
46,201 | def _has_match ( self , assembled_summary ) : if assembled_summary . startswith ( 'yes' ) : if self . data [ 0 ] [ 'var_only' ] == '0' or self . _to_cluster_summary_has_known_nonsynonymous ( assembled_summary ) == 'yes' : return 'yes' else : return 'no' else : return 'no' | assembled_summary should be output of _to_cluster_summary_assembled |
46,202 | def has_var_groups ( self ) : ids = set ( ) for d in self . data : if self . _has_known_variant ( d ) != 'no' and d [ 'var_group' ] != '.' : ids . add ( d [ 'var_group' ] ) return ids | Returns a set of the variant group ids that this cluster has |
46,203 | def column_summary_data ( self ) : assembled_summary = self . _to_cluster_summary_assembled ( ) pct_id , read_depth = self . _pc_id_and_read_depth_of_longest ( ) columns = { 'assembled' : self . _to_cluster_summary_assembled ( ) , 'match' : self . _has_match ( assembled_summary ) , 'ref_seq' : self . ref_name , 'pct_id... | Returns a dictionary of column name - > value for cluster - level results |
46,204 | def cat_files ( infiles , outfile ) : f_out = pyfastaq . utils . open_file_write ( outfile ) for filename in infiles : if os . path . exists ( filename ) : f_in = pyfastaq . utils . open_file_read ( filename ) for line in f_in : print ( line , end = '' , file = f_out ) pyfastaq . utils . close ( f_in ) pyfastaq . utils... | Cats all files in list infiles into outfile |
46,205 | def _check_spades_log_file ( logfile ) : f = pyfastaq . utils . open_file_read ( logfile ) for line in f : if line . startswith ( '== Error == system call for:' ) and line . rstrip ( ) . endswith ( 'finished abnormally, err code: -7' ) : pyfastaq . utils . close ( f ) print ( 'Error running SPAdes. Cannot continue. Th... | SPAdes can fail with a strange error . Stop everything if this happens |
46,206 | def _fix_contig_orientation ( contigs_fa , ref_fa , outfile , min_id = 90 , min_length = 20 , breaklen = 200 ) : if not os . path . exists ( contigs_fa ) : raise Error ( 'Cannot fix orientation of assembly contigs because file not found: ' + contigs_fa ) tmp_coords = os . path . join ( outfile + '.tmp.rename.coords' ) ... | Changes orientation of each contig to match the reference when possible . Returns a set of names of contigs that had hits in both orientations to the reference |
46,207 | def _parse_nucmer_coords_file ( coords_file , ref_name ) : file_reader = pymummer . coords_file . reader ( coords_file ) nucmer_hits = { } for hit in file_reader : assert hit . ref_name == ref_name contig = hit . qry_name if contig not in nucmer_hits : nucmer_hits [ contig ] = [ ] nucmer_hits [ contig ] . append ( copy... | Input is coords file made by self . _run_nucmer . Reference should have one sequence only . ref_name is name fo the reference sequence to sanity check the coords file . Returns dictionary . Key = assembly contig name . Value = list of nucmer hits to that contig |
46,208 | def _nucmer_hits_to_percent_identity ( nucmer_hits ) : percent_identities = { } max_lengths = { } for contig in nucmer_hits : max_length = - 1 percent_identity = 0 for hit in nucmer_hits [ contig ] : if hit . hit_length_qry > max_length : max_length = hit . hit_length_qry percent_identity = hit . percent_identity perce... | Input is hits made by self . _parse_nucmer_coords_file . Returns dictionary . key = contig name . Value = percent identity of hits to that contig |
46,209 | def _nucmer_hits_to_assembly_coords ( nucmer_hits ) : coords = { } for l in nucmer_hits . values ( ) : for hit in l : if hit . qry_name not in coords : coords [ hit . qry_name ] = [ ] coords [ hit . qry_name ] . append ( hit . qry_coords ( ) ) for scaff in coords : pyfastaq . intervals . merge_overlapping_in_list ( coo... | Input is hits made by self . _parse_nucmer_coords_file . Returns dictionary . key = contig name . Value = list of coords that match to the reference gene |
46,210 | def nucmer_hits_to_ref_coords ( cls , nucmer_hits , contig = None ) : coords = [ ] if contig is None : coords = { key : [ ] for key in nucmer_hits . keys ( ) } else : coords = { contig : [ ] } for key in coords : coords [ key ] = [ hit . ref_coords ( ) for hit in nucmer_hits [ key ] ] pyfastaq . intervals . merge_overl... | Input is hits made by self . _parse_nucmer_coords_file . Returns dictionary . Key = contig name . Value = list of coords in the reference sequence for that contig . if contig = contig_name then just gets the ref coords from that contig instead of using all the contigs |
46,211 | def nucmer_hits_to_ref_and_qry_coords ( cls , nucmer_hits , contig = None ) : if contig is None : ctg_coords = { key : [ ] for key in nucmer_hits . keys ( ) } else : ctg_coords = { contig : [ ] } ref_coords = { } for key in ctg_coords : hits = copy . copy ( nucmer_hits [ key ] ) hits . sort ( key = lambda x : len ( x .... | Same as nucmer_hits_to_ref_coords except removes containing hits first and returns ref and qry coords lists |
46,212 | def ref_cov_per_contig ( nucmer_hits ) : coords = AssemblyCompare . nucmer_hits_to_ref_coords ( nucmer_hits ) return { x : pyfastaq . intervals . length_sum_from_list ( coords [ x ] ) for x in coords } | Input is hits made by self . _parse_nucmer_coords_file . Returns dictionary . key = contig name . Value = number of bases that match to the reference sequence . |
46,213 | def _ref_covered_by_at_least_one_full_length_contig ( nucmer_hits , percent_threshold , max_nt_extend ) : for l in nucmer_hits . values ( ) : for hit in l : if ( ( 2 * max_nt_extend ) + len ( hit . ref_coords ( ) ) ) / hit . ref_length >= percent_threshold : return True return False | Returns true iff there exists a contig that completely covers the reference sequence nucmer_hits = hits made by self . _parse_nucmer_coords_file . |
46,214 | def nucmer_hit_containing_reference_position ( nucmer_hits , ref_name , ref_position , qry_name = None ) : for contig_name in nucmer_hits : for hit in nucmer_hits [ contig_name ] : if hit . ref_name == ref_name and ( qry_name is None or qry_name == hit . qry_name ) and hit . ref_coords ( ) . distance_to_point ( ref_pos... | Returns the first nucmer match found that contains the given reference location . nucmer_hits = hits made by self . _parse_nucmer_coords_file . Returns None if no matching hit found |
46,215 | def _get_exe ( prog ) : if prog in prog_to_env_var : env_var = prog_to_env_var [ prog ] if env_var in os . environ : return os . environ [ env_var ] return prog_to_default [ prog ] | Given a program name return what we expect its exectuable to be called |
46,216 | def fake_run ( self ) : clusters = { } used_names = set ( ) seq_reader = pyfastaq . sequences . file_reader ( self . infile ) for seq in seq_reader : if seq . id in used_names : raise Error ( 'Sequence name "' + seq . id + '" not unique. Cannot continue' ) clusters [ str ( len ( clusters ) + self . min_cluster_number )... | Doesn t actually run cd - hit . Instead puts each input sequence into its own cluster . So it s as if cdhit was run but didn t cluster anything |
46,217 | def run_get_clusters_from_file ( self , clusters_infile , all_ref_seqs , rename_dict = None ) : if rename_dict is None : rename_dict = { } seq_reader = pyfastaq . sequences . file_reader ( self . infile ) names_list_from_fasta_file = [ seq . id for seq in seq_reader ] names_set_from_fasta_file = set ( names_list_from_f... | Instead of running cdhit gets the clusters info from the input file . |
46,218 | def sam_pair_to_insert ( s1 , s2 ) : if s1 . is_unmapped or s2 . is_unmapped or ( s1 . tid != s2 . tid ) or ( s1 . is_reverse == s2 . is_reverse ) : return None if s1 . is_reverse : end = s1 . reference_end - 1 start = s2 . reference_start else : end = s2 . reference_end - 1 start = s1 . reference_start if start < end ... | Returns insert size from pair of sam records as long as their orientation is innies . Otherwise returns None . |
46,219 | def update_from_sam ( self , sam , sam_reader ) : if sam . is_unmapped or sam . mate_is_unmapped or ( sam . reference_id == sam . next_reference_id ) : return new_link = link . Link ( sam , sam_reader , self . ref_lengths ) read_name = sam . query_name if read_name in self . partial_links : new_link . merge ( self . pa... | Updates graph info from a pysam . AlignedSegment object |
46,220 | def _make_graph ( self , max_insert ) : if len ( self . partial_links ) != 0 : raise Error ( 'Error in _make_graph(). Cannot continue because there are partial links' ) self . contig_links = { } for key in self . links : for l in self . links [ key ] : insert_size = l . insert_size ( ) if insert_size <= max_insert : if... | helper function to construct graph from current state of object |
46,221 | def _sam_to_soft_clipped ( self , sam ) : if sam . is_unmapped : raise Error ( 'Cannot get soft clip info from an unmapped read' ) if sam . cigar is None or len ( sam . cigar ) == 0 : return False , False return ( sam . cigar [ 0 ] [ 0 ] == 4 , sam . cigar [ - 1 ] [ 0 ] == 4 ) | Returns tuple of whether or not the left and right end of the mapped read in the sam record is soft - clipped |
46,222 | def _report_line_to_dict ( cls , line ) : data = line . split ( '\t' ) if len ( data ) != len ( report . columns ) : return None d = dict ( zip ( report . columns , data ) ) for key in report . int_columns : try : d [ key ] = int ( d [ key ] ) except : assert d [ key ] == '.' for key in report . float_columns : try : d... | Takes report line string as input . Returns a dict of column name - > value in line |
46,223 | def _dict_to_report_line ( cls , report_dict ) : return '\t' . join ( [ str ( report_dict [ x ] ) for x in report . columns ] ) | Takes a report_dict as input and returns a report line |
46,224 | def _load_report ( infile ) : report_dict = { } f = pyfastaq . utils . open_file_read ( infile ) first_line = True for line in f : line = line . rstrip ( ) if first_line : expected_first_line = '#' + '\t' . join ( report . columns ) if line != expected_first_line : pyfastaq . utils . close ( f ) raise Error ( 'Error re... | Loads report file into a dictionary . Key = reference name . Value = list of report lines for that reference |
46,225 | def _filter_dicts ( self ) : keys_to_remove = set ( ) for ref_name in self . report : for ctg_name in self . report [ ref_name ] : self . report [ ref_name ] [ ctg_name ] = self . _filter_list_of_dicts ( self . report [ ref_name ] [ ctg_name ] ) if len ( self . report [ ref_name ] [ ctg_name ] ) == 0 : keys_to_remove .... | Filters out all the report_dicts that do not pass the cutoffs . If any ref sequence loses all of its report_dicts then it is completely removed . |
46,226 | def merge ( self , other ) : assert self . refnames == other . refnames assert self . dirs == other . dirs assert self . lengths == other . lengths for i in range ( 2 ) : if self . pos [ i ] is None : if other . pos [ i ] is None : raise Error ( 'Error merging these two links:\n' + str ( self ) + '\n' + str ( other ) )... | Merge another link into this one . Expected that each link was created from each mate from a pair . We only know both distances to contig ends when we have read info from both mappings in a BAM file . All other info should be the same . |
46,227 | def _load_fofn ( cls , fofn ) : filenames = { } f = pyfastaq . utils . open_file_read ( fofn ) for line in f : fields = line . rstrip ( ) . split ( ) if len ( fields ) == 1 : filenames [ fields [ 0 ] ] = None elif len ( fields ) == 2 : filenames [ fields [ 0 ] ] = fields [ 1 ] else : raise Error ( 'Error at the followi... | Returns dictionary of filename - > short name . Value is None whenever short name is not provided |
46,228 | def _filter_matrix_rows ( cls , matrix ) : indexes_to_keep = [ ] for i in range ( len ( matrix ) ) : keep_row = False for element in matrix [ i ] : if element not in { 'NA' , 'no' } : keep_row = True break if keep_row : indexes_to_keep . append ( i ) return [ matrix [ i ] for i in indexes_to_keep ] | matrix = output from _to_matrix |
46,229 | def _filter_matrix_columns ( cls , matrix , phandango_header , csv_header ) : indexes_to_keep = set ( ) for row in matrix : for i in range ( len ( row ) ) : if row [ i ] not in { 'NA' , 'no' } : indexes_to_keep . add ( i ) indexes_to_keep = sorted ( list ( indexes_to_keep ) ) for i in range ( len ( matrix ) ) : matrix ... | phandango_header csv_header matrix = output from _to_matrix |
46,230 | def _get_remaining_known_ref_variants ( known_ref_variants , used_ref_variants , nucmer_coords ) : variants = [ ] for ref_variant_pos , ref_variants_set in sorted ( known_ref_variants . items ( ) ) : for known_ref_variant in ref_variants_set : if known_ref_variant not in used_ref_variants : variant_pos_matches_contig =... | Finds variants where ref has the variant and so does the contig . Which means that there was no mummer call to flag it up so need to look through the known ref variants . Also need to check that the variant is in a nucmer match to an assembly contig . |
46,231 | def _samtools_depths_at_known_snps_all_wild ( sequence_meta , contig_name , cluster , variant_list ) : ref_nuc_range = sequence_meta . variant . nucleotide_range ( ) if ref_nuc_range is None : return None bases = [ ] ctg_nts = [ ] ref_nts = [ ] smtls_total_depths = [ ] smtls_nts = [ ] smtls_depths = [ ] contig_position... | Input is a known variants as sequence_metadata object . The assumption is that both the reference and the assembly have the variant type not wild type . The list variant_list should be a list of pymummer . variant . Variant objects only contaning variants to the relevant query contig |
46,232 | def abbr ( value : Any , limit : int = 20 ) -> str : rep = repr ( value ) if len ( rep ) > limit : if limit < 3 : raise ValueError ( 'Abbreviation limit may not be less than 3' ) rep = rep [ : limit - 3 ] + '...' return rep | Converts a value into its string representation and abbreviates that representation based on the given length limit if necessary . |
46,233 | def invalidate_value ( cls , value : Any , exc : Type [ Exception ] = EncodingTypeError , msg : Optional [ str ] = None , ) -> None : raise exc ( "Value `{rep}` of type {typ} cannot be encoded by {cls}{msg}" . format ( rep = abbr ( value ) , typ = type ( value ) , cls = cls . __name__ , msg = "" if msg is None else ( "... | Throws a standard exception for when a value is not encodable by an encoder . |
46,234 | def parse_tuple_type_str ( old_from_type_str ) : @ functools . wraps ( old_from_type_str ) def new_from_type_str ( cls , type_str , registry ) : normalized_type_str = normalize ( type_str ) abi_type = parse ( normalized_type_str ) type_str_repr = repr ( type_str ) if type_str != normalized_type_str : type_str_repr = '{... | Used by BaseCoder subclasses as a convenience for implementing the from_type_str method required by ABIRegistry . Useful if normalizing then parsing a tuple type string is required in that method . |
46,235 | def seek_in_frame ( self , pos , * args , ** kwargs ) : super ( ) . seek ( self . _total_offset + pos , * args , ** kwargs ) | Seeks relative to the total offset of the current contextual frames . |
46,236 | def push_frame ( self , offset ) : self . _frames . append ( ( offset , self . tell ( ) ) ) self . _total_offset += offset self . seek_in_frame ( 0 ) | Pushes a new contextual frame onto the stack with the given offset and a return position at the current cursor position then seeks to the new total offset . |
46,237 | def pop_frame ( self ) : try : offset , return_pos = self . _frames . pop ( ) except IndexError : raise IndexError ( 'no frames to pop' ) self . _total_offset -= offset self . seek ( return_pos ) | Pops the current contextual frame off of the stack and returns the cursor to the frame s return position . |
46,238 | def has_arrlist ( type_str ) : try : abi_type = grammar . parse ( type_str ) except exceptions . ParseError : return False return abi_type . arrlist is not None | A predicate that matches a type string with an array dimension list . |
46,239 | def is_base_tuple ( type_str ) : try : abi_type = grammar . parse ( type_str ) except exceptions . ParseError : return False return isinstance ( abi_type , grammar . TupleType ) and abi_type . arrlist is None | A predicate that matches a tuple type with no array dimension list . |
46,240 | def register ( self , lookup : Lookup , encoder : Encoder , decoder : Decoder , label : str = None ) -> None : self . register_encoder ( lookup , encoder , label = label ) self . register_decoder ( lookup , decoder , label = label ) | Registers the given encoder and decoder under the given lookup . A unique string label may be optionally provided that can be used to refer to the registration by name . |
46,241 | def unregister ( self , label : str ) -> None : self . unregister_encoder ( label ) self . unregister_decoder ( label ) | Unregisters the entries in the encoder and decoder registries which have the label label . |
46,242 | def copy ( self ) : cpy = type ( self ) ( ) cpy . _encoders = copy . copy ( self . _encoders ) cpy . _decoders = copy . copy ( self . _decoders ) return cpy | Copies a registry such that new registrations can be made or existing registrations can be unregistered without affecting any instance from which a copy was obtained . This is useful if an existing registry fulfills most of a user s needs but requires one or two modifications . In that case a copy of that registry can ... |
46,243 | def encode_single ( self , typ : TypeStr , arg : Any ) -> bytes : encoder = self . _registry . get_encoder ( typ ) return encoder ( arg ) | Encodes the python value arg as a binary value of the ABI type typ . |
46,244 | def encode_abi ( self , types : Iterable [ TypeStr ] , args : Iterable [ Any ] ) -> bytes : encoders = [ self . _registry . get_encoder ( type_str ) for type_str in types ] encoder = TupleEncoder ( encoders = encoders ) return encoder ( args ) | Encodes the python values in args as a sequence of binary values of the ABI types in types via the head - tail mechanism . |
46,245 | def is_encodable ( self , typ : TypeStr , arg : Any ) -> bool : encoder = self . _registry . get_encoder ( typ ) try : encoder . validate_value ( arg ) except EncodingError : return False except AttributeError : try : encoder ( arg ) except EncodingError : return False return True | Determines if the python value arg is encodable as a value of the ABI type typ . |
46,246 | def decode_single ( self , typ : TypeStr , data : Decodable ) -> Any : if not is_bytes ( data ) : raise TypeError ( "The `data` value must be of bytes type. Got {0}" . format ( type ( data ) ) ) decoder = self . _registry . get_decoder ( typ ) stream = ContextFramesBytesIO ( data ) return decoder ( stream ) | Decodes the binary value data of the ABI type typ into its equivalent python value . |
46,247 | def decode_abi ( self , types : Iterable [ TypeStr ] , data : Decodable ) -> Tuple [ Any , ... ] : if not is_bytes ( data ) : raise TypeError ( "The `data` value must be of bytes type. Got {0}" . format ( type ( data ) ) ) decoders = [ self . _registry . get_decoder ( type_str ) for type_str in types ] decoder = Tuple... | Decodes the binary value data as a sequence of values of the ABI types in types via the head - tail mechanism into a tuple of equivalent python values . |
46,248 | async def create_turn_endpoint ( protocol_factory , server_addr , username , password , lifetime = 600 , ssl = False , transport = 'udp' ) : loop = asyncio . get_event_loop ( ) if transport == 'tcp' : _ , inner_protocol = await loop . create_connection ( lambda : TurnClientTcpProtocol ( server_addr , username = usernam... | Create datagram connection relayed over TURN . |
46,249 | async def connect ( self ) : request = stun . Message ( message_method = stun . Method . ALLOCATE , message_class = stun . Class . REQUEST ) request . attributes [ 'LIFETIME' ] = self . lifetime request . attributes [ 'REQUESTED-TRANSPORT' ] = UDP_TRANSPORT try : response , _ = await self . request ( request ) except e... | Create a TURN allocation . |
46,250 | async def delete ( self ) : if self . refresh_handle : self . refresh_handle . cancel ( ) self . refresh_handle = None request = stun . Message ( message_method = stun . Method . REFRESH , message_class = stun . Class . REQUEST ) request . attributes [ 'LIFETIME' ] = 0 await self . request ( request ) logger . info ( '... | Delete the TURN allocation . |
46,251 | async def refresh ( self ) : while True : await asyncio . sleep ( 5 / 6 * self . lifetime ) request = stun . Message ( message_method = stun . Method . REFRESH , message_class = stun . Class . REQUEST ) request . attributes [ 'LIFETIME' ] = self . lifetime await self . request ( request ) logger . info ( 'TURN allocati... | Periodically refresh the TURN allocation . |
46,252 | async def send_data ( self , data , addr ) : channel = self . peer_to_channel . get ( addr ) if channel is None : channel = self . channel_number self . channel_number += 1 self . channel_to_peer [ channel ] = addr self . peer_to_channel [ addr ] = channel await self . channel_bind ( channel , addr ) header = struct . ... | Send data to a remote host via the TURN server . |
46,253 | def send_stun ( self , message , addr ) : logger . debug ( '%s > %s %s' , self , addr , message ) self . _send ( bytes ( message ) ) | Send a STUN message to the TURN server . |
46,254 | def get_extra_info ( self , name , default = None ) : if name == 'related_address' : return self . __inner_protocol . transport . get_extra_info ( 'sockname' ) elif name == 'sockname' : return self . __relayed_address return default | Return optional transport information . |
46,255 | def sendto ( self , data , addr ) : asyncio . ensure_future ( self . __inner_protocol . send_data ( data , addr ) ) | Sends the data bytes to the remote peer given addr . |
46,256 | def candidate_foundation ( candidate_type , candidate_transport , base_address ) : key = '%s|%s|%s' % ( candidate_type , candidate_transport , base_address ) return hashlib . md5 ( key . encode ( 'ascii' ) ) . hexdigest ( ) | See RFC 5245 - 4 . 1 . 1 . 3 . Computing Foundations |
46,257 | def candidate_priority ( candidate_component , candidate_type , local_pref = 65535 ) : if candidate_type == 'host' : type_pref = 126 elif candidate_type == 'prflx' : type_pref = 110 elif candidate_type == 'srflx' : type_pref = 100 else : type_pref = 0 return ( 1 << 24 ) * type_pref + ( 1 << 8 ) * local_pref + ( 256 - c... | See RFC 5245 - 4 . 1 . 2 . 1 . Recommended Formula |
46,258 | def to_sdp ( self ) : sdp = '%s %d %s %d %s %d typ %s' % ( self . foundation , self . component , self . transport , self . priority , self . host , self . port , self . type ) if self . related_address is not None : sdp += ' raddr %s' % self . related_address if self . related_port is not None : sdp += ' rport %s' % s... | Return a string representation suitable for SDP . |
46,259 | def can_pair_with ( self , other ) : a = ipaddress . ip_address ( self . host ) b = ipaddress . ip_address ( other . host ) return ( self . component == other . component and self . transport . lower ( ) == other . transport . lower ( ) and a . version == b . version ) | A local candidate is paired with a remote candidate if and only if the two candidates have the same component ID and have the same IP address version . |
46,260 | def candidate_pair_priority ( local , remote , ice_controlling ) : G = ice_controlling and local . priority or remote . priority D = ice_controlling and remote . priority or local . priority return ( 1 << 32 ) * min ( G , D ) + 2 * max ( G , D ) + ( G > D and 1 or 0 ) | See RFC 5245 - 5 . 7 . 2 . Computing Pair Priority and Ordering Pairs |
46,261 | def get_host_addresses ( use_ipv4 , use_ipv6 ) : addresses = [ ] for interface in netifaces . interfaces ( ) : ifaddresses = netifaces . ifaddresses ( interface ) for address in ifaddresses . get ( socket . AF_INET , [ ] ) : if use_ipv4 and address [ 'addr' ] != '127.0.0.1' : addresses . append ( address [ 'addr' ] ) f... | Get local IP addresses . |
46,262 | async def server_reflexive_candidate ( protocol , stun_server ) : loop = asyncio . get_event_loop ( ) stun_server = ( await loop . run_in_executor ( None , socket . gethostbyname , stun_server [ 0 ] ) , stun_server [ 1 ] ) request = stun . Message ( message_method = stun . Method . BINDING , message_class = stun . Clas... | Query STUN server to obtain a server - reflexive candidate . |
46,263 | def sort_candidate_pairs ( pairs , ice_controlling ) : def pair_priority ( pair ) : return - candidate_pair_priority ( pair . local_candidate , pair . remote_candidate , ice_controlling ) pairs . sort ( key = pair_priority ) | Sort a list of candidate pairs . |
46,264 | def send_stun ( self , message , addr ) : self . __log_debug ( '> %s %s' , addr , message ) self . transport . sendto ( bytes ( message ) , addr ) | Send a STUN message . |
46,265 | def add_remote_candidate ( self , remote_candidate ) : if self . _remote_candidates_end : raise ValueError ( 'Cannot add remote candidate after end-of-candidates.' ) if remote_candidate is None : self . _prune_components ( ) self . _remote_candidates_end = True return self . _remote_candidates . append ( remote_candida... | Add a remote candidate or signal end - of - candidates . |
46,266 | async def gather_candidates ( self ) : if not self . _local_candidates_start : self . _local_candidates_start = True addresses = get_host_addresses ( use_ipv4 = self . _use_ipv4 , use_ipv6 = self . _use_ipv6 ) for component in self . _components : self . _local_candidates += await self . get_component_candidates ( comp... | Gather local candidates . |
46,267 | def get_default_candidate ( self , component ) : for candidate in sorted ( self . _local_candidates , key = lambda x : x . priority ) : if candidate . component == component : return candidate | Gets the default local candidate for the specified component . |
46,268 | async def connect ( self ) : if not self . _local_candidates_end : raise ConnectionError ( 'Local candidates gathering was not performed' ) if ( self . remote_username is None or self . remote_password is None ) : raise ConnectionError ( 'Remote username or password is missing' ) for remote_candidate in self . _remote_... | Perform ICE handshake . |
46,269 | async def recvfrom ( self ) : if not len ( self . _nominated ) : raise ConnectionError ( 'Cannot receive data, not connected' ) result = await self . _queue . get ( ) if result [ 0 ] is None : raise ConnectionError ( 'Connection lost while receiving data' ) return result | Receive the next datagram . |
46,270 | async def sendto ( self , data , component ) : active_pair = self . _nominated . get ( component ) if active_pair : await active_pair . protocol . send_data ( data , active_pair . remote_addr ) else : raise ConnectionError ( 'Cannot send data, not connected' ) | Send a datagram on the specified component . |
46,271 | def set_selected_pair ( self , component , local_foundation , remote_foundation ) : protocol = None for p in self . _protocols : if ( p . local_candidate . component == component and p . local_candidate . foundation == local_foundation ) : protocol = p break remote_candidate = None for c in self . _remote_candidates : ... | Force the selected candidate pair . |
46,272 | def check_incoming ( self , message , addr , protocol ) : component = protocol . local_candidate . component remote_candidate = None for c in self . _remote_candidates : if c . host == addr [ 0 ] and c . port == addr [ 1 ] : remote_candidate = c assert remote_candidate . component == component break if remote_candidate... | Handle a succesful incoming check . |
46,273 | async def check_start ( self , pair ) : self . check_state ( pair , CandidatePair . State . IN_PROGRESS ) request = self . build_request ( pair ) try : response , addr = await pair . protocol . request ( request , pair . remote_addr , integrity_key = self . remote_password . encode ( 'utf8' ) ) except exceptions . Tran... | Starts a check . |
46,274 | def check_state ( self , pair , state ) : self . __log_info ( 'Check %s %s -> %s' , pair , pair . state , state ) pair . state = state | Updates the state of a check . |
46,275 | def _find_pair ( self , protocol , remote_candidate ) : for pair in self . _check_list : if ( pair . protocol == protocol and pair . remote_candidate == remote_candidate ) : return pair return None | Find a candidate pair in the check list . |
46,276 | def _prune_components ( self ) : seen_components = set ( map ( lambda x : x . component , self . _remote_candidates ) ) missing_components = self . _components - seen_components if missing_components : self . __log_info ( 'Components %s have no candidate pairs' % missing_components ) self . _components = seen_component... | Remove components for which the remote party did not provide any candidates . |
46,277 | def parse_message ( data , integrity_key = None ) : if len ( data ) < HEADER_LENGTH : raise ValueError ( 'STUN message length is less than 20 bytes' ) message_type , length , cookie , transaction_id = unpack ( '!HHI12s' , data [ 0 : HEADER_LENGTH ] ) if len ( data ) != HEADER_LENGTH + length : raise ValueError ( 'STUN ... | Parses a STUN message . |
46,278 | def connection_made ( self , transport : asyncio . BaseTransport ) -> None : if self . _stream_reader is None : raise SMTPServerDisconnected ( "Client not connected" ) self . _stream_reader . _transport = transport self . _over_ssl = transport . get_extra_info ( "sslcontext" ) is not None self . _stream_writer = asynci... | Modified connection_made that supports upgrading our transport in place using STARTTLS . |
46,279 | def upgrade_transport ( self , context : ssl . SSLContext , server_hostname : str = None , waiter : Awaitable = None , ) -> SSLProtocol : if self . _over_ssl : raise RuntimeError ( "Already using TLS." ) if self . _stream_reader is None or self . _stream_writer is None : raise SMTPServerDisconnected ( "Client not conne... | Upgrade our transport to TLS in place . |
46,280 | async def read_response ( self , timeout : NumType = None ) -> SMTPResponse : if self . _stream_reader is None : raise SMTPServerDisconnected ( "Client not connected" ) code = None response_lines = [ ] while True : async with self . _io_lock : line = await self . _readline ( timeout = timeout ) try : code = int ( line ... | Get a status reponse from the server . |
46,281 | async def write_and_drain ( self , data : bytes , timeout : NumType = None ) -> None : if self . _stream_writer is None : raise SMTPServerDisconnected ( "Client not connected" ) self . _stream_writer . write ( data ) async with self . _io_lock : await self . _drain_writer ( timeout ) | Format a command and send it to the server . |
46,282 | async def write_message_data ( self , data : bytes , timeout : NumType = None ) -> None : data = LINE_ENDINGS_REGEX . sub ( b"\r\n" , data ) data = PERIOD_REGEX . sub ( b".." , data ) if not data . endswith ( b"\r\n" ) : data += b"\r\n" data += b".\r\n" await self . write_and_drain ( data , timeout = timeout ) | Encode and write email message data . |
46,283 | async def execute_command ( self , * args : bytes , timeout : NumType = None ) -> SMTPResponse : command = b" " . join ( args ) + b"\r\n" await self . write_and_drain ( command , timeout = timeout ) response = await self . read_response ( timeout = timeout ) return response | Sends an SMTP command along with any args to the server and returns a response . |
46,284 | def last_ehlo_response ( self , response : SMTPResponse ) -> None : extensions , auth_methods = parse_esmtp_extensions ( response . message ) self . _last_ehlo_response = response self . esmtp_extensions = extensions self . server_auth_methods = auth_methods self . supports_esmtp = True | When setting the last EHLO response parse the message for supported extensions and auth methods . |
46,285 | async def helo ( self , hostname : str = None , timeout : DefaultNumType = _default ) -> SMTPResponse : if hostname is None : hostname = self . source_address async with self . _command_lock : response = await self . execute_command ( b"HELO" , hostname . encode ( "ascii" ) , timeout = timeout ) self . last_helo_respon... | Send the SMTP HELO command . Hostname to send for this command defaults to the FQDN of the local host . |
46,286 | async def help ( self , timeout : DefaultNumType = _default ) -> str : await self . _ehlo_or_helo_if_needed ( ) async with self . _command_lock : response = await self . execute_command ( b"HELP" , timeout = timeout ) success_codes = ( SMTPStatus . system_status_ok , SMTPStatus . help_message , SMTPStatus . completed ,... | Send the SMTP HELP command which responds with help text . |
46,287 | async def noop ( self , timeout : DefaultNumType = _default ) -> SMTPResponse : await self . _ehlo_or_helo_if_needed ( ) async with self . _command_lock : response = await self . execute_command ( b"NOOP" , timeout = timeout ) if response . code != SMTPStatus . completed : raise SMTPResponseException ( response . code ... | Send an SMTP NOOP command which does nothing . |
46,288 | async def vrfy ( self , address : str , timeout : DefaultNumType = _default ) -> SMTPResponse : await self . _ehlo_or_helo_if_needed ( ) parsed_address = parse_address ( address ) async with self . _command_lock : response = await self . execute_command ( b"VRFY" , parsed_address . encode ( "ascii" ) , timeout = timeou... | Send an SMTP VRFY command which tests an address for validity . Not many servers support this command . |
46,289 | async def expn ( self , address : str , timeout : DefaultNumType = _default ) -> SMTPResponse : await self . _ehlo_or_helo_if_needed ( ) parsed_address = parse_address ( address ) async with self . _command_lock : response = await self . execute_command ( b"EXPN" , parsed_address . encode ( "ascii" ) , timeout = timeou... | Send an SMTP EXPN command which expands a mailing list . Not many servers support this command . |
46,290 | async def quit ( self , timeout : DefaultNumType = _default ) -> SMTPResponse : await self . _ehlo_or_helo_if_needed ( ) async with self . _command_lock : response = await self . execute_command ( b"QUIT" , timeout = timeout ) if response . code != SMTPStatus . closing : raise SMTPResponseException ( response . code , ... | Send the SMTP QUIT command which closes the connection . Also closes the connection from our side after a response is received . |
46,291 | async def rcpt ( self , recipient : str , options : Iterable [ str ] = None , timeout : DefaultNumType = _default , ) -> SMTPResponse : await self . _ehlo_or_helo_if_needed ( ) if options is None : options = [ ] options_bytes = [ option . encode ( "ascii" ) for option in options ] to = b"TO:" + quote_address ( recipien... | Send an SMTP RCPT command which specifies a single recipient for the message . This command is sent once per recipient and must be preceded by MAIL . |
46,292 | async def data ( self , message : Union [ str , bytes ] , timeout : DefaultNumType = _default ) -> SMTPResponse : await self . _ehlo_or_helo_if_needed ( ) self . _raise_error_if_disconnected ( ) if timeout is _default : timeout = self . timeout if isinstance ( message , str ) : message = message . encode ( "ascii" ) as... | Send an SMTP DATA command followed by the message given . This method transfers the actual email content to the server . |
46,293 | async def ehlo ( self , hostname : str = None , timeout : DefaultNumType = _default ) -> SMTPResponse : if hostname is None : hostname = self . source_address async with self . _command_lock : response = await self . execute_command ( b"EHLO" , hostname . encode ( "ascii" ) , timeout = timeout ) self . last_ehlo_respon... | Send the SMTP EHLO command . Hostname to send for this command defaults to the FQDN of the local host . |
46,294 | def _reset_server_state ( self ) -> None : self . last_helo_response = None self . _last_ehlo_response = None self . esmtp_extensions = { } self . supports_esmtp = False self . server_auth_methods = [ ] | Clear stored information about the server . |
46,295 | def supported_auth_methods ( self ) -> List [ str ] : return [ auth for auth in self . AUTH_METHODS if auth in self . server_auth_methods ] | Get all AUTH methods supported by the both server and by us . |
46,296 | async def login ( self , username : str , password : str , timeout : DefaultNumType = _default ) -> SMTPResponse : await self . _ehlo_or_helo_if_needed ( ) if not self . supports_extension ( "auth" ) : raise SMTPException ( "SMTP AUTH extension not supported by server." ) response = None exception = None for auth_name ... | Tries to login with supported auth methods . |
46,297 | async def auth_crammd5 ( self , username : str , password : str , timeout : DefaultNumType = _default ) -> SMTPResponse : async with self . _command_lock : initial_response = await self . execute_command ( b"AUTH" , b"CRAM-MD5" , timeout = timeout ) if initial_response . code != SMTPStatus . auth_continue : raise SMTPA... | CRAM - MD5 auth uses the password as a shared secret to MD5 the server s response . |
46,298 | async def auth_plain ( self , username : str , password : str , timeout : DefaultNumType = _default ) -> SMTPResponse : username_bytes = username . encode ( "ascii" ) password_bytes = password . encode ( "ascii" ) username_and_password = b"\0" + username_bytes + b"\0" + password_bytes encoded = base64 . b64encode ( use... | PLAIN auth encodes the username and password in one Base64 encoded string . No verification message is required . |
46,299 | async def auth_login ( self , username : str , password : str , timeout : DefaultNumType = _default ) -> SMTPResponse : encoded_username = base64 . b64encode ( username . encode ( "ascii" ) ) encoded_password = base64 . b64encode ( password . encode ( "ascii" ) ) async with self . _command_lock : initial_response = awa... | LOGIN auth sends the Base64 encoded username and password in sequence . |
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