idx int64 0 252k | question stringlengths 48 5.28k | target stringlengths 5 1.23k |
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5,000 | def weighted_mean ( data , weights = None ) : if weights is None : return mean ( data ) total_weight = float ( sum ( weights ) ) weights = [ weight / total_weight for weight in weights ] w_mean = 0 for i , weight in enumerate ( weights ) : w_mean += weight * data [ i ] return w_mean | Calculate the weighted mean of a list . |
5,001 | def median ( data ) : data . sort ( ) num_values = len ( data ) half = num_values // 2 if num_values % 2 : return data [ half ] return 0.5 * ( data [ half - 1 ] + data [ half ] ) | Calculate the median of a list . |
5,002 | def weighted_median ( data , weights = None ) : if weights is None : return median ( data ) midpoint = 0.5 * sum ( weights ) if any ( [ j > midpoint for j in weights ] ) : return data [ weights . index ( max ( weights ) ) ] if any ( [ j > 0 for j in weights ] ) : sorted_data , sorted_weights = zip ( * sorted ( zip ( da... | Calculate the weighted median of a list . |
5,003 | def init_app ( self , app , config_prefix = None ) : config_prefix = ( config_prefix or 'REDIS' ) . rstrip ( '_' ) . upper ( ) if not hasattr ( app , 'extensions' ) : app . extensions = dict ( ) if config_prefix . lower ( ) in app . extensions : raise ValueError ( 'Already registered config prefix {0!r}.' . format ( co... | Actual method to read Redis settings from app configuration and initialize the StrictRedis instance . |
5,004 | def _recursive_remove ( fs , path ) : if not fs . is_link ( path = path ) and fs . is_dir ( path = path ) : for child in fs . children ( path = path ) : _recursive_remove ( fs = fs , path = child ) fs . remove_empty_directory ( path = path ) else : fs . remove_file ( path = path ) | A recursive non - atomic directory removal . |
5,005 | def create ( name , create_file , open_file , remove_file , create_directory , list_directory , remove_empty_directory , temporary_directory , stat , lstat , link , readlink , realpath = _realpath , remove = _recursive_remove , ) : methods = dict ( create = create_file , open = lambda fs , path , mode = "r" : open_file... | Create a new kind of filesystem . |
5,006 | def _exists ( fs , path ) : try : fs . stat ( path ) except ( exceptions . FileNotFound , exceptions . NotADirectory ) : return False return True | Check that the given path exists on the filesystem . |
5,007 | def _is_dir ( fs , path ) : try : return stat . S_ISDIR ( fs . stat ( path ) . st_mode ) except exceptions . FileNotFound : return False | Check that the given path is a directory . |
5,008 | def _is_file ( fs , path ) : try : return stat . S_ISREG ( fs . stat ( path ) . st_mode ) except exceptions . FileNotFound : return False | Check that the given path is a file . |
5,009 | def _is_link ( fs , path ) : try : return stat . S_ISLNK ( fs . lstat ( path ) . st_mode ) except exceptions . FileNotFound : return False | Check that the given path is a symbolic link . |
5,010 | def list ( self , ** kwargs ) : return ModelList ( self . ghost . execute_get ( '%s/' % self . _type_name , ** kwargs ) , self . _type_name , self , kwargs , model_type = self . _model_type ) | Fetch a list of resources from the API . |
5,011 | def get ( self , id = None , slug = None , ** kwargs ) : if id : items = self . ghost . execute_get ( '%s/%s/' % ( self . _type_name , id ) , ** kwargs ) elif slug : items = self . ghost . execute_get ( '%s/slug/%s/' % ( self . _type_name , slug ) , ** kwargs ) else : raise GhostException ( 500 , 'Either the ID or the ... | Fetch a resource from the API . Either the id or the slug has to be present . |
5,012 | def create ( self , ** kwargs ) : response = self . ghost . execute_post ( '%s/' % self . _type_name , json = { self . _type_name : [ kwargs ] } ) return self . _model_type ( response . get ( self . _type_name ) [ 0 ] ) | Creates a new resource . |
5,013 | def create ( self , ** kwargs ) : return super ( PostController , self ) . create ( ** self . _with_markdown ( kwargs ) ) | Creates a new post . When the markdown property is present it will be automatically converted to mobiledoc on v1 . + of the server . |
5,014 | def update ( self , id , ** kwargs ) : return super ( PostController , self ) . update ( id , ** self . _with_markdown ( kwargs ) ) | Updates an existing post . When the markdown property is present it will be automatically converted to mobiledoc on v1 . + of the server . |
5,015 | def define_residues_for_plotting_traj ( self , analysis_cutoff ) : self . residue_counts_fraction = { } for traj in self . residue_counts : self . residue_counts_fraction [ traj ] = { residue : float ( values ) / len ( self . contacts_per_timeframe [ traj ] ) for residue , values in self . residue_counts [ traj ] . ite... | Since plotting all residues that have made contact with the ligand over a lenghty simulation is not always feasible or desirable . Therefore only the residues that have been in contact with ligand for a long amount of time will be plotted in the final image . |
5,016 | def detect_aromatic_rings_in_ligand ( self ) : self . ligrings = { } try : ring_info = self . topology_data . mol . GetRingInfo ( ) self . ligand_ring_num = ring_info . NumRings ( ) except Exception as e : m = Chem . MolFromPDBFile ( "lig.pdb" ) ring_info = m . GetRingInfo ( ) self . ligand_ring_num = ring_info . NumRi... | Using rdkit to detect aromatic rings in ligand - size 4 - 6 atoms and all atoms are part of the ring . Saves this data in self . ligrings . |
5,017 | def define_all_protein_rings ( self ) : self . protein_rings = { } i = 0 for residue in self . topology_data . dict_of_plotted_res : for ring in self . rings : if ring [ 0 ] == residue [ 0 ] : atom_names = "" for atom in self . rings [ ring ] : atom_names = atom_names + " " + atom self . protein_rings [ i ] = self . to... | Make MDAnalysis atom selections for rings in protein residues that will be plotted in the final figure - since they are the only ones that should be analysed . Saves the rings in self . protein_rings dictionary . |
5,018 | def count_by_type ( self ) : pistack = defaultdict ( int ) for contact in self . timeseries : pkey = ( contact . ligandring , contact . type , contact . resid , contact . resname , contact . segid ) pistack [ pkey ] += 1 dtype = [ ( "ligand_ring_ids" , list ) , ( "type" , "|U4" ) , ( "resid" , int ) , ( "resname" , "|U... | Count how many times each individual pi - pi interaction occured throughout the simulation . Returns numpy array . |
5,019 | def main ( master_dsn , slave_dsn , tables , blocking = False ) : assert master_dsn . startswith ( "mysql" ) logger = logging . getLogger ( __name__ ) logger . info ( "replicating tables: %s" % ", " . join ( tables ) ) repl_db_sub ( master_dsn , slave_dsn , tables ) mysql_pub ( master_dsn , blocking = blocking ) | DB Replication app . |
5,020 | def get_text_position_in_ax_coord ( ax , pos , scale = default_text_relative_padding ) : ratio = get_axes_ratio ( ax ) x , y = scale , scale if ratio > 1 : y /= ratio elif 0 < ratio : x *= ratio pos = pos . lower ( ) if pos == 'nw' : y = 1 - y elif pos == 'ne' : x , y = 1 - x , 1 - y elif pos == 'sw' : pass elif pos ==... | Return text position corresponding to given pos . The text alignment in the bounding box should be set accordingly in order to have a good - looking layout . This corresponding text alignment can be obtained by get_text_alignment or get_text_position_and_inner_alignment function . |
5,021 | def get_text_position_and_inner_alignment ( ax , pos , scale = default_text_relative_padding , with_transAxes_kwargs = True ) : xy = get_text_position_in_ax_coord ( ax , pos , scale = scale ) alignment_fontdict = get_text_alignment ( pos ) if with_transAxes_kwargs : alignment_fontdict = { ** alignment_fontdict , ** { '... | Return text position and its alignment in its bounding box . The returned position is given in Axes coordinate as defined in matplotlib documentation on transformation . |
5,022 | def get_text_position ( fig , ax , ha = 'left' , va = 'top' , pad_scale = 1.0 ) : try : pad_scale = float ( pad_scale ) except : raise TypeError ( "'pad_scale should be of type 'float'" ) for arg in [ va , ha ] : assert type ( arg ) is str arg = arg . lower ( ) ax_height , ax_width = get_ax_size_in_inch ( fig , ax ) le... | Return text position inside of the given axis |
5,023 | def create_app ( config = None , config_obj = None ) : app = Flask ( __name__ ) configure_app ( app , config = config , config_obj = config_obj ) register_blueprints ( app ) bind_extensions ( app ) return app | Flask app factory function . |
5,024 | def configure_app ( app , config = None , config_obj = None ) : app . config . from_object ( config_obj or BaseConfig ) if config is not None : app . config . from_pyfile ( config ) | Configure application instance . |
5,025 | def bind_extensions ( app ) : app . db = app . config [ 'PUZZLE_BACKEND' ] app . db . init_app ( app ) bootstrap . init_app ( app ) markdown ( app ) @ app . template_filter ( 'islist' ) def islist ( object ) : return isinstance ( object , ( tuple , list ) ) | Configure extensions . |
5,026 | def find_donors_and_acceptors_in_ligand ( self ) : atom_names = [ x . name for x in self . topology_data . universe . ligand ] try : for atom in self . topology_data . mol . GetSubstructMatches ( self . HDonorSmarts , uniquify = 1 ) : self . donors . append ( atom_names [ atom [ 0 ] ] ) for atom in self . topology_data... | Since MDAnalysis a pre - set list for acceptor and donor atoms for proteins and solvents from specific forcefields it is necessary to find donor and acceptor atoms for the ligand molecule . This function uses RDKit and searches through ligand atoms to find matches for pre - set list of possible donor and acceptor atoms... |
5,027 | def count_by_type ( self , table , timesteps ) : hbonds = defaultdict ( int ) for contact in table : pkey = ( contact . donor_idx , contact . acceptor_idx , contact . donor_atom , contact . acceptor_atom , contact . donor_resnm , contact . donor_resid , contact . acceptor_resnm , contact . acceptor_resid ) hbonds [ pke... | Count how many times each individual hydrogen bonds occured throughout the simulation . Returns numpy array . |
5,028 | def determine_hbonds_for_drawing ( self , analysis_cutoff ) : self . frequency = defaultdict ( int ) for traj in self . hbonds_by_type : for bond in self . hbonds_by_type [ traj ] : if bond [ "donor_resnm" ] != "LIG" : self . frequency [ ( bond [ "donor_idx" ] , bond [ "acceptor_atom" ] , bond [ "donor_atom" ] , bond [... | Since plotting all hydrogen bonds could lead to a messy plot a cutoff has to be imple - mented . In this function the frequency of each hydrogen bond is summated and the total compared against analysis cutoff - a fraction multiplied by trajectory count . Those hydrogen bonds that are present for longer than analysis cu... |
5,029 | def convert2dbus ( value , signature ) : if len ( signature ) == 2 and signature . startswith ( 'a' ) : return dbus . Array ( value , signature = signature [ - 1 ] ) dbus_string_type = dbus . String if PY3 else dbus . UTF8String type_map = { 'b' : dbus . Boolean , 'y' : dbus . Byte , 'n' : dbus . Int16 , 'i' : dbus . I... | Converts value type from python to dbus according signature . |
5,030 | def convert ( dbus_obj ) : _isinstance = partial ( isinstance , dbus_obj ) ConvertType = namedtuple ( 'ConvertType' , 'pytype dbustypes' ) pyint = ConvertType ( int , ( dbus . Byte , dbus . Int16 , dbus . Int32 , dbus . Int64 , dbus . UInt16 , dbus . UInt32 , dbus . UInt64 ) ) pybool = ConvertType ( bool , ( dbus . Boo... | Converts dbus_obj from dbus type to python type . |
5,031 | def converter ( f ) : @ wraps ( f ) def wrapper ( * args , ** kwds ) : return convert ( f ( * args , ** kwds ) ) return wrapper | Decorator to convert value from dbus type to python type . |
5,032 | def exception_wrapper ( f ) : @ wraps ( f ) def wrapper ( * args , ** kwds ) : try : return f ( * args , ** kwds ) except dbus . exceptions . DBusException as err : _args = err . args raise PyMPRISException ( * _args ) return wrapper | Decorator to convert dbus exception to pympris exception . |
5,033 | def available_players ( ) : bus = dbus . SessionBus ( ) players = set ( ) for name in filter ( lambda item : item . startswith ( MPRIS_NAME_PREFIX ) , bus . list_names ( ) ) : owner_name = bus . get_name_owner ( name ) players . add ( convert ( owner_name ) ) return players | Searchs and returns set of unique names of objects which implements MPRIS2 interfaces . |
5,034 | def signal_wrapper ( f ) : @ wraps ( f ) def wrapper ( * args , ** kwds ) : args = map ( convert , args ) kwds = { convert ( k ) : convert ( v ) for k , v in kwds . items ( ) } return f ( * args , ** kwds ) return wrapper | Decorator converts function s arguments from dbus types to python . |
5,035 | def filter_properties_signals ( f , signal_iface_name ) : @ wraps ( f ) def wrapper ( iface , changed_props , invalidated_props , * args , ** kwargs ) : if iface == signal_iface_name : f ( changed_props , invalidated_props ) return wrapper | Filters signals by iface name . |
5,036 | def distance_function_match ( l1 , l2 , thresh , dist_fn , norm_funcs = [ ] ) : common = [ ] l1 = list ( enumerate ( l1 ) ) l2 = list ( enumerate ( l2 ) ) for norm_fn in norm_funcs : new_common , l1 , l2 = _match_by_norm_func ( l1 , l2 , lambda a : norm_fn ( a [ 1 ] ) , lambda a1 , a2 : dist_fn ( a1 [ 1 ] , a2 [ 1 ] ) ... | Returns pairs of matching indices from l1 and l2 . |
5,037 | def _match_by_norm_func ( l1 , l2 , norm_fn , dist_fn , thresh ) : common = [ ] l1_only_idx = set ( range ( len ( l1 ) ) ) l2_only_idx = set ( range ( len ( l2 ) ) ) buckets_l1 = _group_by_fn ( enumerate ( l1 ) , lambda x : norm_fn ( x [ 1 ] ) ) buckets_l2 = _group_by_fn ( enumerate ( l2 ) , lambda x : norm_fn ( x [ 1 ... | Matches elements in l1 and l2 using normalization functions . |
5,038 | def _match_munkres ( l1 , l2 , dist_matrix , thresh ) : equal_dist_matches = set ( ) m = Munkres ( ) indices = m . compute ( dist_matrix ) for l1_idx , l2_idx in indices : dst = dist_matrix [ l1_idx ] [ l2_idx ] if dst > thresh : continue for eq_l2_idx , eq_val in enumerate ( dist_matrix [ l1_idx ] ) : if abs ( dst - e... | Matches two lists using the Munkres algorithm . |
5,039 | def add_suspect ( self , case_obj , variant_obj ) : new_suspect = Suspect ( case = case_obj , variant_id = variant_obj . variant_id , name = variant_obj . display_name ) self . session . add ( new_suspect ) self . save ( ) return new_suspect | Link a suspect to a case . |
5,040 | def delete_suspect ( self , suspect_id ) : suspect_obj = self . suspect ( suspect_id ) logger . debug ( "Deleting suspect {0}" . format ( suspect_obj . name ) ) self . session . delete ( suspect_obj ) self . save ( ) | De - link a suspect from a case . |
5,041 | def configure_stream ( level = 'WARNING' ) : root_logger = logging . getLogger ( ) root_logger . setLevel ( level ) template = "[%(asctime)s] %(name)-25s %(levelname)-8s %(message)s" formatter = logging . Formatter ( template ) console = logging . StreamHandler ( ) console . setLevel ( level ) console . setFormatter ( ... | Configure root logger using a standard stream handler . |
5,042 | def _is_same_type_as_root ( self , obj ) : if not self . ALLOWS_SAME_TYPE_AS_ROOT_COLLECT : obj_model = get_model_from_instance ( obj ) obj_key = get_key_from_instance ( obj ) is_same_type_as_root = obj_model == self . root_obj_model and obj_key != self . root_obj_key if is_same_type_as_root : self . emit_event ( type ... | Testing if we try to collect an object of the same type as root . This is not really a good sign because it means that we are going to collect a whole new tree that will maybe collect a new tree that will ... |
5,043 | def initialize ( self , data ) : for item in data : if hasattr ( self , item ) : setattr ( self , item , data [ item ] ) | initialize variable from loaded data |
5,044 | def _add_transcripts ( self , variant_obj , info_dict ) : vep_string = info_dict . get ( 'CSQ' ) snpeff_string = info_dict . get ( 'ANN' ) if vep_string : vep_info = get_vep_info ( vep_string = vep_string , vep_header = self . vep_header ) for transcript_info in vep_info : transcript = self . _get_vep_transcript ( tran... | Return all transcripts sound in the vcf file |
5,045 | def _get_vep_transcript ( self , transcript_info ) : transcript = Transcript ( hgnc_symbol = transcript_info . get ( 'SYMBOL' ) , transcript_id = transcript_info . get ( 'Feature' ) , ensembl_id = transcript_info . get ( 'Gene' ) , biotype = transcript_info . get ( 'BIOTYPE' ) , consequence = transcript_info . get ( 'C... | Create a Transcript based on the vep annotation |
5,046 | def _get_snpeff_transcript ( self , transcript_info ) : transcript = Transcript ( hgnc_symbol = transcript_info . get ( 'Gene_Name' ) , transcript_id = transcript_info . get ( 'Feature' ) , ensembl_id = transcript_info . get ( 'Gene_ID' ) , biotype = transcript_info . get ( 'Transcript_BioType' ) , consequence = transc... | Create a transcript based on the snpeff annotation |
5,047 | def _makes_clone ( _func , * args , ** kw ) : self = args [ 0 ] . _clone ( ) _func ( self , * args [ 1 : ] , ** kw ) return self | A decorator that returns a clone of the current object so that we can re - use the object for similar requests . |
5,048 | def _handle_response ( self , response , data ) : if data and response . get ( 'content-type' , '' ) . split ( ';' ) [ 0 ] in ( 'application/json' , 'application/x-javascript' , 'text/javascript' , 'text/x-javascript' , 'text/x-json' ) : return json . loads ( data ) else : return data | Deserializes JSON if the content - type matches otherwise returns the response body as is . |
5,049 | def get_url ( self , * paths , ** params ) : path_stack = self . _attribute_stack [ : ] if paths : path_stack . extend ( paths ) u = self . _stack_collapser ( path_stack ) url = self . _url_template % { "domain" : self . _api_url , "generated_url" : u , } if self . _params or params : internal_params = self . _params .... | Returns the URL for this request . |
5,050 | def _clone ( self ) : cls = self . __class__ q = cls . __new__ ( cls ) q . __dict__ = self . __dict__ . copy ( ) q . _params = self . _params . copy ( ) q . _headers = self . _headers . copy ( ) q . _attribute_stack = self . _attribute_stack [ : ] return q | Clones the state of the current operation . |
5,051 | def delete ( ctx , family_id , individual_id , root ) : root = root or ctx . obj . get ( 'root' ) or os . path . expanduser ( "~/.puzzle" ) if os . path . isfile ( root ) : logger . error ( "'root' can't be a file" ) ctx . abort ( ) logger . info ( "Root directory is: {}" . format ( root ) ) db_path = os . path . join ... | Delete a case or individual from the database . |
5,052 | def variants ( case_id ) : filters = parse_filters ( ) values = [ value for key , value in iteritems ( filters ) if not isinstance ( value , dict ) and key != 'skip' ] is_active = any ( values ) variants , nr_of_variants = app . db . variants ( case_id , skip = filters [ 'skip' ] , filters = { 'gene_ids' : filters [ 'g... | Show all variants for a case . |
5,053 | def variant ( case_id , variant_id ) : case_obj = app . db . case ( case_id ) variant = app . db . variant ( case_id , variant_id ) if variant is None : return abort ( 404 , "variant not found" ) comments = app . db . comments ( variant_id = variant . md5 ) template = 'sv_variant.html' if app . db . variant_type == 'sv... | Show a single variant . |
5,054 | def parse_filters ( ) : genes_str = request . args . get ( 'gene_symbol' ) filters = { } for key in ( 'frequency' , 'cadd' , 'sv_len' ) : try : filters [ key ] = float ( request . args . get ( key ) ) except ( ValueError , TypeError ) : pass filters [ 'gene_symbols' ] = genes_str . split ( ',' ) if genes_str else None ... | Parse variant filters from the request object . |
5,055 | def suspects ( case_id , variant_id ) : case_obj = app . db . case ( case_id ) variant_obj = app . db . variant ( case_id , variant_id ) app . db . add_suspect ( case_obj , variant_obj ) return redirect ( request . referrer ) | Pin a variant as a suspect for a given case . |
5,056 | def queries ( ) : query = request . form [ 'query' ] name = request . form . get ( 'name' ) app . db . add_gemini_query ( name , query ) return redirect ( request . referrer ) | Store a new GEMINI query . |
5,057 | def load ( fp , object_pairs_hook = dict ) : return object_pairs_hook ( ( k , v ) for k , v , _ in parse ( fp ) if k is not None ) | Parse the contents of the ~io . IOBase . readline - supporting file - like object fp as a simple line - oriented . properties file and return a dict of the key - value pairs . |
5,058 | def loads ( s , object_pairs_hook = dict ) : fp = BytesIO ( s ) if isinstance ( s , binary_type ) else StringIO ( s ) return load ( fp , object_pairs_hook = object_pairs_hook ) | Parse the contents of the string s as a simple line - oriented . properties file and return a dict of the key - value pairs . |
5,059 | def _extractClipData ( self , audioClipSpec , showLogs = False ) : command = [ self . _ffmpegPath ] if not showLogs : command += [ '-nostats' , '-loglevel' , '0' ] command += [ '-i' , self . _audioFilePath , '-ss' , '%.3f' % audioClipSpec . start , '-t' , '%.3f' % audioClipSpec . duration ( ) , '-c' , 'copy' , '-map' ,... | Extracts a single clip according to audioClipSpec . |
5,060 | def add_phenotype ( self , ind_obj , phenotype_id ) : if phenotype_id . startswith ( 'HP:' ) or len ( phenotype_id ) == 7 : logger . debug ( 'querying on HPO term' ) hpo_results = phizz . query_hpo ( [ phenotype_id ] ) else : logger . debug ( 'querying on OMIM term' ) hpo_results = phizz . query_disease ( [ phenotype_i... | Add a phenotype term to the case . |
5,061 | def update_hpolist ( self , case_obj ) : hpo_list = self . case_genelist ( case_obj ) hpo_results = hpo_genes ( case_obj . phenotype_ids ( ) , * self . phenomizer_auth ) if hpo_results is None : pass else : gene_ids = [ result [ 'gene_id' ] for result in hpo_results if result [ 'gene_id' ] ] hpo_list . gene_ids = gene_... | Update the HPO gene list for a case based on current terms . |
5,062 | def remove_phenotype ( self , ind_obj , phenotypes = None ) : if phenotypes is None : logger . info ( "delete all phenotypes related to %s" , ind_obj . ind_id ) self . query ( PhenotypeTerm ) . filter_by ( ind_id = ind_obj . id ) . delete ( ) else : for term in ind_obj . phenotypes : if term . phenotype_id in phenotype... | Remove multiple phenotypes from an individual . |
5,063 | def match ( mode_lst : list , obj : 'object that has __destruct__ method' ) : try : structure = obj . __destruct__ ( ) except AttributeError : return False n = len ( mode_lst ) if n > len ( structure ) : return False for i in range ( n ) : mode = mode_lst [ i ] elem = obj [ i ] if isinstance ( mode , PatternList ) : if... | >>> from Redy . ADT . Core import match data P >>> from Redy . ADT . traits import ConsInd Discrete >>> |
5,064 | def gemini_query ( self , query_id ) : logger . debug ( "Looking for query with id {0}" . format ( query_id ) ) return self . query ( GeminiQuery ) . filter_by ( id = query_id ) . first ( ) | Return a gemini query |
5,065 | def add_gemini_query ( self , name , query ) : logger . info ( "Adding query {0} with text {1}" . format ( name , query ) ) new_query = GeminiQuery ( name = name , query = query ) self . session . add ( new_query ) self . save ( ) return new_query | Add a user defined gemini query |
5,066 | def delete_gemini_query ( self , query_id ) : query_obj = self . gemini_query ( query_id ) logger . debug ( "Delete query: {0}" . format ( query_obj . name_query ) ) self . session . delete ( query_obj ) self . save ( ) | Delete a gemini query |
5,067 | def distance_to ( self , point , unit = 'km' ) : assert isinstance ( point , GeoPoint ) , ( 'Other point should also be a Point instance.' ) if self == point : return 0.0 coefficient = 69.09 theta = self . longitude - point . longitude unit = unit . lower ( ) if unit else None distance = math . degrees ( math . acos ( ... | Calculate distance in miles or kilometers between current and other passed point . |
5,068 | def rad_latitude ( self ) : if self . _rad_latitude is None : self . _rad_latitude = math . radians ( self . latitude ) return self . _rad_latitude | Lazy conversion degrees latitude to radians . |
5,069 | def rad_longitude ( self ) : if self . _rad_longitude is None : self . _rad_longitude = math . radians ( self . longitude ) return self . _rad_longitude | Lazy conversion degrees longitude to radians . |
5,070 | def send ( term , stream ) : payload = erlang . term_to_binary ( term ) header = struct . pack ( '!I' , len ( payload ) ) stream . write ( header ) stream . write ( payload ) stream . flush ( ) | Write an Erlang term to an output stream . |
5,071 | def recv ( stream ) : header = stream . read ( 4 ) if len ( header ) != 4 : return None ( length , ) = struct . unpack ( '!I' , header ) payload = stream . read ( length ) if len ( payload ) != length : return None term = erlang . binary_to_term ( payload ) return term | Read an Erlang term from an input stream . |
5,072 | def recv_loop ( stream ) : message = recv ( stream ) while message : yield message message = recv ( stream ) | Yield Erlang terms from an input stream . |
5,073 | def _add_genotype_calls ( self , variant_obj , variant_line , case_obj ) : variant_line = variant_line . split ( '\t' ) if len ( variant_line ) > 8 : gt_format = variant_line [ 8 ] . split ( ':' ) for individual in case_obj . individuals : sample_id = individual . ind_id index = individual . ind_index gt_call = variant... | Add the genotype calls for the variant |
5,074 | def with_prefix ( self , root_path ) : return Conflict ( self . conflict_type , root_path + self . path , self . body ) | Returns a new conflict with a prepended prefix as a path . |
5,075 | def to_json ( self ) : path = self . path if self . conflict_type in ( 'REORDER' , 'SET_FIELD' ) : op = 'replace' elif self . conflict_type in ( 'MANUAL_MERGE' , 'ADD_BACK_TO_HEAD' ) : op = 'add' path += ( '-' , ) elif self . conflict_type == 'REMOVE_FIELD' : op = 'remove' else : raise ValueError ( 'Conflict Type %s ca... | Deserializes conflict to a JSON object . |
5,076 | def dump ( props , fp , separator = '=' , comments = None , timestamp = True , sort_keys = False ) : if comments is not None : print ( to_comment ( comments ) , file = fp ) if timestamp is not None and timestamp is not False : print ( to_comment ( java_timestamp ( timestamp ) ) , file = fp ) for k , v in itemize ( prop... | Write a series of key - value pairs to a file in simple line - oriented . properties format . |
5,077 | def dumps ( props , separator = '=' , comments = None , timestamp = True , sort_keys = False ) : s = StringIO ( ) dump ( props , s , separator = separator , comments = comments , timestamp = timestamp , sort_keys = sort_keys ) return s . getvalue ( ) | Convert a series of key - value pairs to a text string in simple line - oriented . properties format . |
5,078 | def join_key_value ( key , value , separator = '=' ) : r return escape ( key ) + separator + re . sub ( r'^ +' , lambda m : r'\ ' * m . end ( ) , _base_escape ( value ) ) | r Join a key and value together into a single line suitable for adding to a simple line - oriented . properties file . No trailing newline is added . |
5,079 | def GetPlaylists ( self , start , max_count , order , reversed ) : cv = convert2dbus return self . iface . GetPlaylists ( cv ( start , 'u' ) , cv ( max_count , 'u' ) , cv ( order , 's' ) , cv ( reversed , 'b' ) ) | Gets a set of playlists . |
5,080 | def init_app ( self , app ) : self . algorithm = app . config . get ( 'HASHING_METHOD' , 'sha256' ) if self . algorithm not in algs : raise ValueError ( '{} not one of {}' . format ( self . algorithm , algs ) ) self . rounds = app . config . get ( 'HASHING_ROUNDS' , 1 ) if not isinstance ( self . rounds , int ) : raise... | Initializes the Flask application with this extension . It grabs the necessary configuration values from app . config those being HASHING_METHOD and HASHING_ROUNDS . HASHING_METHOD defaults to sha256 but can be any one of hashlib . algorithms . HASHING_ROUNDS specifies the number of times to hash the input with the spe... |
5,081 | def hash_value ( self , value , salt = '' ) : def hashit ( value , salt ) : h = hashlib . new ( self . algorithm ) tgt = salt + value h . update ( tgt ) return h . hexdigest ( ) def fix_unicode ( value ) : if VER < 3 and isinstance ( value , unicode ) : value = str ( value ) elif VER >= 3 and isinstance ( value , str )... | Hashes the specified value combined with the specified salt . The hash is done HASHING_ROUNDS times as specified by the application configuration . |
5,082 | def check_value ( self , value_hash , value , salt = '' ) : h = self . hash_value ( value , salt = salt ) return h == value_hash | Checks the specified hash value against the hash of the provided salt and value . |
5,083 | def AddTrack ( self , uri , after_track , set_as_current ) : self . iface . AddTrack ( uri , convert2dbus ( after_track , 'o' ) , convert2dbus ( set_as_current , 'b' ) ) | Adds a URI in the TrackList . |
5,084 | def delete_gene ( self , * gene_ids ) : self . gene_ids = [ gene_id for gene_id in self . gene_ids if gene_id not in gene_ids ] | Delete one or more gene ids form the list . |
5,085 | def healthy_update_timer ( self ) : state = None if self . update_status_timer and self . update_status_timer . is_alive ( ) : _LOGGER . debug ( "Timer: healthy" ) state = True else : _LOGGER . debug ( "Timer: not healthy" ) state = False return state | Check state of update timer . |
5,086 | def initialize ( self ) : self . network_status = self . get_network_status ( ) self . name = self . network_status . get ( 'network_name' , 'Unknown' ) self . location_info = self . get_location_info ( ) self . device_info = self . get_device_info ( ) self . device_id = ( self . device_info . get ( 'device_id' ) if se... | initialize the object |
5,087 | def initialize_socket ( self ) : try : _LOGGER . debug ( "Trying to open socket." ) self . _socket = socket . socket ( socket . AF_INET , socket . SOCK_DGRAM ) self . _socket . bind ( ( '' , self . _udp_port ) ) except socket . error as err : raise err else : _LOGGER . debug ( "Socket open." ) socket_thread = threading... | initialize the socket |
5,088 | def initialize_worker ( self ) : worker_thread = threading . Thread ( name = "WorkerThread" , target = message_worker , args = ( self , ) ) worker_thread . setDaemon ( True ) worker_thread . start ( ) | initialize the worker thread |
5,089 | def initialize_zones ( self ) : zone_list = self . location_info . get ( 'zone_list' , { 'main' : True } ) for zone_id in zone_list : if zone_list [ zone_id ] : self . zones [ zone_id ] = Zone ( self , zone_id = zone_id ) else : _LOGGER . debug ( "Ignoring zone: %s" , zone_id ) | initialize receiver zones |
5,090 | def handle_status ( self ) : status = self . get_status ( ) if status : self . zones [ 'main' ] . update_status ( status ) | Handle status from device |
5,091 | def handle_netusb ( self , message ) : needs_update = 0 if self . _yamaha : if 'play_info_updated' in message : play_info = self . get_play_info ( ) if play_info : new_media_status = MediaStatus ( play_info , self . _ip_address ) if self . _yamaha . media_status != new_media_status : self . _yamaha . new_media_status (... | Handles netusb in message |
5,092 | def handle_features ( self , device_features ) : self . device_features = device_features if device_features and 'zone' in device_features : for zone in device_features [ 'zone' ] : zone_id = zone . get ( 'id' ) if zone_id in self . zones : _LOGGER . debug ( "handle_features: %s" , zone_id ) input_list = zone . get ( '... | Handles features of the device |
5,093 | def handle_event ( self , message ) : needs_update = 0 for zone in self . zones : if zone in message : _LOGGER . debug ( "Received message for zone: %s" , zone ) self . zones [ zone ] . update_status ( message [ zone ] ) if 'netusb' in message : needs_update += self . handle_netusb ( message [ 'netusb' ] ) if needs_upd... | Dispatch all event messages |
5,094 | def update_status ( self , reset = False ) : if self . healthy_update_timer and not reset : return if not self . device_features : self . handle_features ( self . get_features ( ) ) self . handle_status ( ) self . setup_update_timer ( ) | Update device status . |
5,095 | def setup_update_timer ( self , reset = False ) : _LOGGER . debug ( "Timer: firing again in %d seconds" , self . _interval ) self . update_status_timer = threading . Timer ( self . _interval , self . update_status , [ True ] ) self . update_status_timer . setDaemon ( True ) self . update_status_timer . start ( ) | Schedule a Timer Thread . |
5,096 | def set_playback ( self , playback ) : req_url = ENDPOINTS [ "setPlayback" ] . format ( self . _ip_address ) params = { "playback" : playback } return request ( req_url , params = params ) | Send Playback command . |
5,097 | def build_gemini_query ( self , query , extra_info ) : if 'WHERE' in query : return "{0} AND {1}" . format ( query , extra_info ) else : return "{0} WHERE {1}" . format ( query , extra_info ) | Append sql to a gemini query |
5,098 | def variants ( self , case_id , skip = 0 , count = 1000 , filters = None ) : filters = filters or { } logger . debug ( "Looking for variants in {0}" . format ( case_id ) ) limit = count + skip gemini_query = filters . get ( 'gemini_query' ) or "SELECT * from variants v" any_filter = False if filters . get ( 'frequency'... | Return count variants for a case . |
5,099 | def _variants ( self , case_id , gemini_query ) : individuals = [ ] case_obj = self . case ( case_id ) for individual in case_obj . individuals : individuals . append ( individual ) self . db = case_obj . variant_source self . variant_type = case_obj . variant_type gq = GeminiQuery ( self . db ) gq . run ( gemini_query... | Return variants found in the gemini database |
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