signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def get_paths ( scheme = _get_default_scheme ( ) , vars = None , expand = True ) :
"""Return a mapping containing an install scheme .
` ` scheme ` ` is the install scheme name . If not provided , it will
return the default scheme for the current platform .""" | _ensure_cfg_read ( )
if expand :
return _expand_vars ( scheme , vars )
else :
return dict ( _SCHEMES . items ( scheme ) ) |
def load_de_novos ( path , exclude_indels = True ) :
"""load mutations into dict indexed by HGNC ID .
Args :
path : path to file containing de novo data . This should have five tab -
separated columns e . g .
hgnc chr pos consequence var _ type
CTC1 17 8139190 missense _ variant snv
CTC1 17 8139191 fram... | genes = { }
with open ( path , "r" ) as handle :
header = handle . readline ( ) . strip ( ) . split ( "\t" )
for line in handle :
line = line . rstrip ( ) . split ( "\t" )
gene = line [ 0 ]
position = int ( line [ 2 ] ) - 1
consequence = line [ 3 ]
var_type = line [ 4 ]
... |
def on_reset_button ( self , _ ) :
"""Reset graph data and display empty graph""" | for graph in self . visible_graphs . values ( ) :
graph . reset ( )
for graph in self . graphs . values ( ) :
try :
graph . source . reset ( )
except NotImplementedError :
pass
# Reset clock
self . clock_view . set_text ( ZERO_TIME )
self . update_displayed_information ( ) |
def reference_year ( self , index ) :
"""Return the reference publication year .""" | # TODO Use meta : parsedDate field instead ?
ref_date = self . reference_date ( index )
try : # NB : datetime . year returns an int .
return parse ( ref_date ) . year
except ValueError :
matched = re . search ( r"\d{4}" , ref_date )
if matched :
return int ( matched . group ( ) )
else :
... |
def players ( game_id ) :
"""Gets player / coach / umpire information for the game with matching id .""" | # get data
data = mlbgame . data . get_players ( game_id )
# parse data
parsed = etree . parse ( data )
root = parsed . getroot ( )
output = { }
output [ 'game_id' ] = game_id
# get player / coach data
for team in root . findall ( 'team' ) :
type = team . attrib [ 'type' ] + "_team"
# the type is either home _ ... |
def strip_accents ( s ) :
"""Strip accents to prepare for slugification .""" | nfkd = unicodedata . normalize ( 'NFKD' , unicode ( s ) )
return u'' . join ( ch for ch in nfkd if not unicodedata . combining ( ch ) ) |
def cmd_snap_fence ( self , args ) :
'''snap fence to KML''' | threshold = 10.0
if len ( args ) > 0 :
threshold = float ( args [ 0 ] )
fencemod = self . module ( 'fence' )
loader = fencemod . fenceloader
changed = False
for i in range ( 0 , loader . count ( ) ) :
fp = loader . point ( i )
lat = fp . lat
lon = fp . lng
best = None
best_dist = ( threshold + 1... |
def _module_info_to_proto ( module_info , export_scope = None ) :
"""Serializes ` module _ into ` .
Args :
module _ info : An instance of ` ModuleInfo ` .
export _ scope : Optional ` string ` . Name scope to remove .
Returns :
An instance of ` module _ pb2 . SonnetModule ` .""" | def strip_name_scope ( name_scope ) :
return ops . strip_name_scope ( name_scope , export_scope )
def process_leafs ( value ) :
return strip_name_scope ( _graph_element_to_path ( value ) )
module_info_def = module_pb2 . SonnetModule ( module_name = module_info . module_name , scope_name = strip_name_scope ( mod... |
def get_def_conf ( ) :
'''return default configurations as simple dict''' | ret = dict ( )
for k , v in defConf . items ( ) :
ret [ k ] = v [ 0 ]
return ret |
def connection_from_url ( url , ** kw ) :
"""Given a url , return an : class : ` . ConnectionPool ` instance of its host .
This is a shortcut for not having to parse out the scheme , host , and port
of the url before creating an : class : ` . ConnectionPool ` instance .
: param url :
Absolute URL string tha... | scheme , host , port = get_host ( url )
if scheme == 'https' :
return HTTPSConnectionPool ( host , port = port , ** kw )
else :
return HTTPConnectionPool ( host , port = port , ** kw ) |
def export ( self , filename , offset = 0 , length = None ) :
"""Exports byte array to specified destination
Args :
filename ( str ) : destination to output file
offset ( int ) : byte offset ( default : 0)""" | self . __validate_offset ( filename = filename , offset = offset , length = length )
with open ( filename , 'w' ) as f :
if length is None :
length = len ( self . data ) - offset
if offset > 0 :
output = self . data [ offset : length ]
else :
output = self . data [ : length ]
f .... |
def revoke_api_key ( ) :
"""Form submission handler for revoking API keys .""" | build = g . build
form = forms . RevokeApiKeyForm ( )
if form . validate_on_submit ( ) :
api_key = models . ApiKey . query . get ( form . id . data )
if api_key . build_id != build . id :
logging . debug ( 'User does not have access to API key=%r' , api_key . id )
abort ( 403 )
api_key . act... |
async def ask_opinion ( self , addr , artifact ) :
"""Ask an agent ' s opinion about an artifact .
: param str addr : Address of the agent which opinion is asked
: type addr : : py : class : ` ~ creamas . core . agent . CreativeAgent `
: param object artifact : artifact to be evaluated
: returns : agent ' s... | remote_agent = await self . env . connect ( addr )
return await remote_agent . evaluate ( artifact ) |
def _get_post_data ( cls , args ) :
'''Return the post data .''' | if args . post_data :
return args . post_data
elif args . post_file :
return args . post_file . read ( ) |
async def close ( self , wait_for_completion = True ) :
"""Close window .
Parameters :
* wait _ for _ completion : If set , function will return
after device has reached target position .""" | await self . set_position ( position = Position ( position_percent = 100 ) , wait_for_completion = wait_for_completion ) |
def base ( self ) :
"""Returns properties that are neither incidental nor free .""" | result = [ p for p in self . lazy_properties if not ( p . feature . incidental or p . feature . free ) ]
result . extend ( self . base_ )
return result |
def get_report ( self , report_type , qs = None ) :
"""Get data from the report endpoint""" | if qs is None :
qs = { }
url = self . api_url + "/company/{0}/reports/{1}" . format ( self . company_id , report_type )
result = self . get ( url , params = qs )
return result |
def read ( self , tid , length , offset , fh ) :
"""Read from a file . Data is obtained from ` ` YTStor ` ` object ( which is kept under ` fh ` descriptor ) using its
` ` read ` ` method .
Parameters
tid : str
Path to file . Original ` path ` argument is converted to tuple identifier by ` ` _ pathdec ` ` de... | try :
return self . fds [ fh ] . read ( offset , length , fh )
except AttributeError : # control file
if tid [ 1 ] not in ( " next" , " prev" ) :
raise FuseOSError ( errno . EINVAL )
return self . __sh_script [ offset : offset + length ]
except KeyError : # descriptor does not exist .
raise Fuse... |
def remove ( self , link_type , product , linked_product , identifierType = None ) :
"""Remove a product link
: param link _ type : type of link , one of ' cross _ sell ' , ' up _ sell ' ,
' related ' or ' grouped '
: param product : ID or SKU of product
: param linked _ product : ID or SKU of linked produc... | return bool ( self . call ( 'catalog_product_link.remove' , [ link_type , product , linked_product , identifierType ] ) ) |
def reverse_params ( url_name , params = None , ** kwargs ) :
"""compute the reverse url of ` ` url _ name ` ` and add to it parameters from ` ` params ` `
as querystring
: param unicode url _ name : a URL pattern name
: param params : Some parameter to append to the reversed URL
: type params : : obj : ` d... | url = reverse ( url_name , ** kwargs )
params = urlencode ( params if params else { } )
if params :
return u"%s?%s" % ( url , params )
else :
return url |
def _scan_response ( self ) :
"""Create scan response data .""" | voltage = struct . pack ( "<H" , int ( self . voltage * 256 ) )
reading = struct . pack ( "<HLLL" , 0xFFFF , 0 , 0 , 0 )
response = voltage + reading
return response |
def bound_weights ( weights , minimum = None , maximum = None ) :
"""Bound a weight list so that all outcomes fit within specified bounds .
The probability distribution within the ` ` minimum ` ` and ` ` maximum ` `
values remains the same . Weights in the list with outcomes outside of
` ` minimum ` ` and ` `... | # Copy weights to avoid side - effects
bounded_weights = weights [ : ]
# Remove weights outside of minimum and maximum
if minimum is not None and maximum is not None :
if maximum < minimum :
raise ValueError
bounded_weights = [ bw for bw in bounded_weights if minimum <= bw [ 0 ] <= maximum ]
elif minimu... |
def chain_list ( self ) :
"""GET / chain
Use the Chain API to retrieve the current state of the blockchain .
The returned BlockchainInfo message is defined inside fabric . proto .
message BlockchainInfo {
uint64 height = 1;
bytes currentBlockHash = 2;
bytes previousBlockHash = 3;
: return : json body ... | res = self . _get ( self . _url ( "/chain" ) )
return self . _result ( res , True ) |
def __execute_bisz ( self , instr ) :
"""Execute BISZ instruction .""" | op0_val = self . read_operand ( instr . operands [ 0 ] )
op2_val = 1 if op0_val == 0 else 0
self . write_operand ( instr . operands [ 2 ] , op2_val )
return None |
def get_assessment_part_form_for_update ( self , assessment_part_id ) :
"""Gets the assessment part form for updating an existing assessment part .
A new assessment part form should be requested for each update
transaction .
arg : assessment _ part _ id ( osid . id . Id ) : the ` ` Id ` ` of the
` ` Assessm... | collection = JSONClientValidated ( 'assessment_authoring' , collection = 'AssessmentPart' , runtime = self . _runtime )
if not isinstance ( assessment_part_id , ABCId ) :
raise errors . InvalidArgument ( 'the argument is not a valid OSID Id' )
if ( assessment_part_id . get_identifier_namespace ( ) != 'assessment_au... |
def can_delete_assets ( self ) :
"""Tests if this user can delete ` ` Assets ` ` .
A return of true does not guarantee successful authorization . A
return of false indicates that it is known deleting an ` ` Asset ` `
will result in a ` ` PermissionDenied ` ` . This is intended as a
hint to an application th... | url_path = construct_url ( 'authorization' , bank_id = self . _catalog_idstr )
return self . _get_request ( url_path ) [ 'assetHints' ] [ 'canDelete' ] |
def ready ( self ) :
"""Sets up the application after startup .""" | self . log ( 'Got' , len ( schemastore ) , 'data and' , len ( configschemastore ) , 'component schemata.' , lvl = debug ) |
def sessions_info ( self , hosts ) :
"""Returns ClientInfo per session .
: param hosts : comma separated lists of members of the ZK ensemble .
: returns : A dictionary of ( session _ id , ClientInfo ) .""" | info_by_id = { }
for server_endpoint , dump in self . dump_by_server ( hosts ) . items ( ) :
server_ip , server_port = server_endpoint
for line in dump . split ( "\n" ) :
mat = self . IP_PORT_REGEX . match ( line )
if mat is None :
continue
ip , port , sid = mat . groups ( )
... |
def _init_metadata ( self ) :
"""stub""" | self . _min_string_length = None
self . _max_string_length = None
self . _solution_metadata = { 'element_id' : Id ( self . my_osid_object_form . _authority , self . my_osid_object_form . _namespace , 'solution' ) , 'element_label' : 'Solution' , 'required' : False , 'read_only' : False , 'linked' : False , 'array' : Fa... |
def _merge_states ( self , states ) :
"""Merges a list of states .
: param states : the states to merge
: returns SimState : the resulting state""" | if self . _hierarchy :
optimal , common_history , others = self . _hierarchy . most_mergeable ( states )
else :
optimal , common_history , others = states , None , [ ]
if len ( optimal ) >= 2 : # We found optimal states ( states that share a common ancestor ) to merge .
# Compute constraints for each state star... |
def assignMgtKey ( self , CorpNum , MgtKeyType , ItemKey , MgtKey , UserID = None ) :
"""관리번호할당
args
CorpNum : 팝빌회원 사업자번호
MgtKeyType : 세금계산서 유형 , SELL - 매출 , BUY - 매입 , TRUSTEE - 위수탁
ItemKey : 아이템키 ( Search API로 조회 가능 )
MgtKey : 세금계산서에 할당ᄒ... | if MgtKeyType == None or MgtKeyType == '' :
raise PopbillException ( - 99999999 , "세금계산서 발행유형이 입력되지 않았습니다." )
if ItemKey == None or ItemKey == '' :
raise PopbillException ( - 99999999 , "아이템키가 입력되지 않았습니다." )
if MgtKey == None or MgtKey == '' :
raise PopbillException ( - 99999999 , "관리번호가 입력되지 않았습니다." )
post... |
def exec_after_request_actions ( actions , response , ** kwargs ) :
"""Executes actions of the " after " and " after _ METHOD " groups .
A " response " var will be injected in the current context .""" | current_context [ "response" ] = response
groups = ( "after_" + flask . request . method . lower ( ) , "after" )
try :
rv = execute_actions ( actions , limit_groups = groups , ** kwargs )
except ReturnValueException as e :
rv = e . value
if rv :
return rv
return response |
def to_csv ( self , filename , stimuli = None , inhibitors = None , prepend = "" ) :
"""Writes the list of clampings to a CSV file
Parameters
filename : str
Absolute path where to write the CSV file
stimuli : Optional [ list [ str ] ]
List of stimuli names . If given , stimuli are converted to { 0,1 } ins... | self . to_dataframe ( stimuli , inhibitors , prepend ) . to_csv ( filename , index = False ) |
def NextToken ( self ) :
"""Fetch the next token by trying to match any of the regexes in order .""" | # Nothing in the input stream - no token can match .
if not self . buffer :
return
current_state = self . state
for token in self . _tokens : # Does the rule apply to us ?
if token . state_regex and not token . state_regex . match ( current_state ) :
continue
if self . verbose :
logging . de... |
def times ( filenames , tolerance = 2 ) :
"""For the given file ( s ) , return the time ranges available . Tolerance
sets the number of seconds between time ranges . Any gaps larger
than tolerance seconds will result in a new time range .
: param filenames : Single filename ( string ) or list of filenames
:... | times = { }
delta = datetime . timedelta ( seconds = tolerance )
if isinstance ( filenames , str ) :
filenames = [ filenames ]
for filename in filenames :
with open ( filename , 'r' ) as stream :
times [ filename ] = list ( )
header , packet = stream . read ( )
start , stop = header . ti... |
def hibernate ( app ) :
"""Pause an experiment and remove costly resources .""" | log ( "The database backup URL is..." )
backup_url = data . backup ( app )
log ( backup_url )
log ( "Scaling down the web servers..." )
heroku_app = HerokuApp ( app )
heroku_app . scale_down_dynos ( )
log ( "Removing addons..." )
addons = [ "heroku-postgresql" , # " papertrail " ,
"heroku-redis" , ]
for addon in addons... |
def size ( self , width = None , height = None ) :
u'''Set / get window size .''' | sc = System . Console
if width is not None and height is not None :
sc . BufferWidth , sc . BufferHeight = width , height
else :
return sc . BufferWidth , sc . BufferHeight
if width is not None and height is not None :
sc . WindowWidth , sc . WindowHeight = width , height
else :
return sc . WindowWidth ... |
def read_fits_bintable ( self , hdu = 1 , drop_nonscalar_ok = True , ** kwargs ) :
"""Open as a FITS file , read in a binary table , and return it as a
: class : ` pandas . DataFrame ` , converted with
: func : ` pkwit . numutil . fits _ recarray _ to _ data _ frame ` . The * hdu * argument
specifies which HD... | from astropy . io import fits
from . numutil import fits_recarray_to_data_frame as frtdf
with fits . open ( text_type ( self ) , mode = 'readonly' , ** kwargs ) as hdulist :
return frtdf ( hdulist [ hdu ] . data , drop_nonscalar_ok = drop_nonscalar_ok ) |
def linkify_one_command_with_commands ( self , commands , prop ) :
"""Link a command
: param commands : object commands
: type commands : object
: param prop : property name
: type prop : str
: return : None""" | if not hasattr ( self , prop ) :
return
command = getattr ( self , prop ) . strip ( )
if not command :
setattr ( self , prop , None )
return
data = { "commands" : commands , "call" : command }
if hasattr ( self , 'poller_tag' ) :
data . update ( { "poller_tag" : self . poller_tag } )
if hasattr ( self ,... |
def _updateRepo ( self , func , * args , ** kwargs ) :
"""Runs the specified function that updates the repo with the specified
arguments . This method ensures that all updates are transactional ,
so that if any part of the update fails no changes are made to the
repo .""" | # TODO how do we make this properly transactional ?
self . _repo . open ( datarepo . MODE_WRITE )
try :
func ( * args , ** kwargs )
self . _repo . commit ( )
finally :
self . _repo . close ( ) |
def order_by ( self , field_path , direction = ASCENDING ) :
"""Modify the query to add an order clause on a specific field .
See : meth : ` ~ . firestore _ v1beta1 . client . Client . field _ path ` for
more information on * * field paths * * .
Successive : meth : ` ~ . firestore _ v1beta1 . query . Query . ... | field_path_module . split_field_path ( field_path )
# raises
order_pb = self . _make_order ( field_path , direction )
new_orders = self . _orders + ( order_pb , )
return self . __class__ ( self . _parent , projection = self . _projection , field_filters = self . _field_filters , orders = new_orders , limit = self . _li... |
def deserialize_date ( attr ) :
"""Deserialize ISO - 8601 formatted string into Date object .
: param str attr : response string to be deserialized .
: rtype : Date
: raises : DeserializationError if string format invalid .""" | if isinstance ( attr , ET . Element ) :
attr = attr . text
if re . search ( r"[^\W\d_]" , attr , re . I + re . U ) :
raise DeserializationError ( "Date must have only digits and -. Received: %s" % attr )
# This must NOT use defaultmonth / defaultday . Using None ensure this raises an exception .
return isodate ... |
def redirect ( to , headers = None , status = 302 , content_type = "text/html; charset=utf-8" ) :
"""Abort execution and cause a 302 redirect ( by default ) .
: param to : path or fully qualified URL to redirect to
: param headers : optional dict of headers to include in the new request
: param status : statu... | headers = headers or { }
# URL Quote the URL before redirecting
safe_to = quote_plus ( to , safe = ":/%#?&=@[]!$&'()*+,;" )
# According to RFC 7231 , a relative URI is now permitted .
headers [ "Location" ] = safe_to
return HTTPResponse ( status = status , headers = headers , content_type = content_type ) |
def assign_comments ( self , tree , comments ) :
"""Capture any comments in the tree
header _ comments stores comments preceding a node""" | comments = list ( comments )
comments . sort ( key = lambda c : c . line )
idx_by_line = { 0 : 0 }
# { line _ no : comment _ idx }
for i , c in enumerate ( comments ) :
if c . line not in idx_by_line :
idx_by_line [ c . line ] = i
idx = [ ]
# convert comment tokens to strings , and remove any line breaks
se... |
def add_output_variable ( self , var ) :
"""Adds the argument variable as one of the output variable""" | assert ( isinstance ( var , Variable ) )
self . output_variable_list . append ( var ) |
def from_data ( data ) :
"""Construct a Prettytable from list of rows .""" | if len ( data ) == 0 : # pragma : no cover
return None
else :
ptable = PrettyTable ( )
ptable . field_names = data [ 0 ] . keys ( )
for row in data :
ptable . add_row ( row )
return ptable |
def dict ( self ) :
"""A dict that holds key / values for all of the properties in the
object .
: return :""" | from collections import OrderedDict
SKIP_KEYS = ( )
return OrderedDict ( ( p . key , getattr ( self , p . key ) ) for p in self . __mapper__ . attrs if p . key not in SKIP_KEYS ) |
def risk ( self , domain , ** kwargs ) :
"""Returns back the risk score for a given domain""" | return self . _results ( 'risk' , '/v1/risk' , items_path = ( 'components' , ) , domain = domain , cls = Reputation , ** kwargs ) |
def update_network ( network , name , profile = None ) :
'''Updates a network
CLI Example :
. . code - block : : bash
salt ' * ' neutron . update _ network network - name new - network - name
: param network : ID or name of network to update
: param name : Name of this network
: param profile : Profile ... | conn = _auth ( profile )
return conn . update_network ( network , name ) |
def nla_next ( nla , remaining ) :
"""Return next attribute in a stream of attributes .
https : / / github . com / thom311 / libnl / blob / libnl3_2_25 / lib / attr . c # L171
Calculates the offset to the next attribute based on the attribute given . The attribute provided is assumed to be
accessible , the ca... | totlen = int ( NLA_ALIGN ( nla . nla_len ) )
remaining . value -= totlen
return nlattr ( bytearray_ptr ( nla . bytearray , totlen ) ) |
def copy ( self ) :
"""Return a copy of ourself .""" | new_dict = IDict ( std = self . _std )
new_dict . update ( self . store )
return new_dict |
def to_file ( self , f ) :
"""Write vocab to a file .
: param ( file ) f : a file object , e . g . as returned by calling ` open `
File format :
word0 < TAB > count0
word1 < TAB > count1
word with index 0 is on the 0th line and so on . . .""" | for word in self . _index2word :
count = self . _counts [ word ]
f . write ( u'{}\t{}\n' . format ( word , count ) . encode ( 'utf-8' ) ) |
def point_line_distance ( point , start , end ) :
"""Distance from a point to a line , formed by two points
Args :
point ( : obj : ` Point ` )
start ( : obj : ` Point ` ) : line point
end ( : obj : ` Point ` ) : line point
Returns :
float : distance to line , in degrees""" | if start == end :
return distance ( point , start )
else :
un_dist = abs ( ( end . lat - start . lat ) * ( start . lon - point . lon ) - ( start . lat - point . lat ) * ( end . lon - start . lon ) )
n_dist = sqrt ( ( end . lat - start . lat ) ** 2 + ( end . lon - start . lon ) ** 2 )
if n_dist == 0 :
... |
def _get_argname_value ( self , argname ) :
'''Return the argname value looking up on all possible attributes''' | # Let ' s see if there ' s a private function to get the value
argvalue = getattr ( self , '__get_{0}__' . format ( argname ) , None )
if argvalue is not None and callable ( argvalue ) :
argvalue = argvalue ( )
if argvalue is None : # Let ' s see if the value is defined as a public class variable
argvalue = get... |
def _add_fluent_indexes ( self ) :
"""Add the index commands fluently specified on columns :""" | for column in self . _columns :
for index in [ 'primary' , 'unique' , 'index' ] :
column_index = column . get ( index )
if column_index is True :
getattr ( self , index ) ( column . name )
break
elif column_index :
getattr ( self , index ) ( column . name ... |
def _setContent ( self ) :
'''create string representation of doc / lit message container . If
message element is simple ( primitive ) , use python type as base class .''' | try :
simple = self . _simple
except AttributeError :
raise RuntimeError , 'call setUp first'
# TODO : Hidden contract . Must set self . ns before getNSAlias . . .
# File " / usr / local / python / lib / python2.4 / site - packages / ZSI / generate / containers . py " , line 625 , in _ setContent
# kw [ ' messa... |
def dataframe2sasdata ( self , df : 'pd.DataFrame' , table : str = '_df' , libref : str = '' , results : str = '' , keep_outer_quotes : bool = False ) -> 'SASdata' :
"""This method imports a Pandas Data Frame to a SAS Data Set , returning the SASdata object for the new Data Set .
: param df : Pandas Data Frame to... | if libref != '' :
if libref . upper ( ) not in self . assigned_librefs ( ) :
print ( "The libref specified is not assigned in this SAS Session." )
return None
if results == '' :
results = self . results
if self . nosub :
print ( "too complicated to show the code, read the source :), sorry." ... |
def load_cPkl ( fpath , verbose = None , n = None ) :
"""Loads a pickled file with optional verbosity .
Aims for compatibility between python2 and python3.
TestPickleExtentsSimple :
> > > def makedata _ simple ( ) :
> > > data = np . empty ( ( 500 , 2 * * 20 ) , dtype = np . uint8 ) + 1
> > > return data ... | verbose = _rectify_verb_read ( verbose )
if verbose :
print ( '[util_io] * load_cPkl(%r)' % ( util_path . tail ( fpath , n = n ) , ) )
try :
with open ( fpath , 'rb' ) as file_ :
data = pickle . load ( file_ )
except UnicodeDecodeError :
if six . PY3 : # try to open python2 pickle
with open ... |
def match_variant_sequence_to_reference_context ( variant_sequence , reference_context , min_transcript_prefix_length , max_transcript_mismatches , include_mismatches_after_variant = False , max_trimming_attempts = 2 ) :
"""Iteratively trim low - coverage subsequences of a variant sequence
until it either matches... | variant_sequence_in_reading_frame = None
# if we can ' t get the variant sequence to match this reference
# context then keep trimming it by coverage until either
for i in range ( max_trimming_attempts + 1 ) : # check the reverse - complemented prefix if the reference context is
# on the negative strand since variant s... |
def send_sms ( self , frm , to , text ) :
"""Sends a simple text message .
Example usage : :
> > > msg = " Cherie , n ' oublie pas les gauffres ! "
> > > nexmo . send _ sms ( ' + 33123456780 ' , ' + 33987654321 ' , msg )
: arg frm : The ` from ` field , a phone number ( international format with
or withou... | frm = re . sub ( '[^\d]' , '' , frm )
to = re . sub ( '[^\d]' , '' , to )
api_url = '%s/sms/json' % API_ENDPOINT
params = { 'api_key' : self . api_key , 'api_secret' : self . api_secret , 'from' : frm , 'to' : to , 'text' : text , }
return self . send_request ( api_url , params , method = 'POST' ) |
def close ( self , title , matchClass = False ) :
"""Close the specified window gracefully
Usage : C { window . close ( title , matchClass = False ) }
@ param title : window title to match against ( as case - insensitive substring match )
@ param matchClass : if True , match on the window class instead of the... | if matchClass :
self . _run_wmctrl ( [ "-c" , title , "-x" ] )
else :
self . _run_wmctrl ( [ "-c" , title ] ) |
def _parent_foreign_key_mappings ( cls ) :
"""Get a mapping of foreign name to the local name of foreign keys""" | parent_rel = cls . __mapper__ . relationships . get ( cls . export_parent )
if parent_rel :
return { l . name : r . name for ( l , r ) in parent_rel . local_remote_pairs }
return { } |
def a_star_search ( start , successors , state_value , is_goal ) :
"""This is a searching function of A *""" | if is_goal ( start ) :
return [ start ]
explored = [ ]
g = 1
h = state_value ( start )
f = g + h
p = [ start ]
frontier = [ ( f , g , h , p ) ]
while frontier :
f , g , h , path = frontier . pop ( 0 )
s = path [ - 1 ]
for ( action , state ) in successors ( s , path_actions ( path ) [ - 1 ] if len ( path... |
def callback ( msg , _ ) :
"""Callback function called by libnl upon receiving messages from the kernel .
Positional arguments :
msg - - nl _ msg class instance containing the data sent by the kernel .
Returns :
An integer , value of NL _ OK . It tells libnl to proceed with processing the next kernel messag... | # First convert ` msg ` into something more manageable .
nlh = nlmsg_hdr ( msg )
iface = ifinfomsg ( nlmsg_data ( nlh ) )
hdr = IFLA_RTA ( iface )
remaining = ctypes . c_int ( nlh . nlmsg_len - NLMSG_LENGTH ( iface . SIZEOF ) )
# Now iterate through each rtattr stored in ` iface ` .
while RTA_OK ( hdr , remaining ) : #... |
def _get_loggers ( ) :
"""Return list of Logger classes .""" | from . . import loader
modules = loader . get_package_modules ( 'logger' )
return list ( loader . get_plugins ( modules , [ _Logger ] ) ) |
def trail ( self ) :
"""Get all visitors by IP and then list the pages they visited in order .""" | inner = ( self . get_query ( ) . select ( PageView . ip , PageView . url ) . order_by ( PageView . timestamp ) )
return ( PageView . select ( PageView . ip , fn . array_agg ( PageView . url ) . alias ( 'urls' ) ) . from_ ( inner . alias ( 't1' ) ) . group_by ( PageView . ip ) ) |
def import_locations ( self , cells_file ) :
"""Parse OpenCellID . org data files .
` ` import _ locations ( ) ` ` returns a dictionary with keys containing the
OpenCellID . org _ database identifier , and values consisting of
a ` ` Cell ` ` objects .
It expects cell files in the following format : :
2274... | self . _cells_file = cells_file
field_names = ( 'ident' , 'latitude' , 'longitude' , 'mcc' , 'mnc' , 'lac' , 'cellid' , 'crange' , 'samples' , 'created' , 'updated' )
parse_date = lambda s : datetime . datetime . strptime ( s , '%Y-%m-%d %H:%M:%S' )
field_parsers = ( int , float , float , int , int , int , int , int , ... |
def nginx_web_ssl_config ( self ) :
"""Nginx web ssl config""" | dt = [ self . nginx_web_dir , self . nginx_ssl_dir ]
return nginx_conf_string . simple_ssl_web_conf . format ( dt = dt ) |
def register_module ( module_name , module_class ) :
""": return : None""" | assert isinstance ( module_name , str )
assert isinstance ( module_class , type )
if module_name not in ModuleRegistry :
ModuleRegistry [ module_name ] = module_class
else :
raise Exception ( "double registration in module registry" ) |
def instruments ( self , accountID , ** kwargs ) :
"""Get the list of tradeable instruments for the given Account . The list
of tradeable instruments is dependent on the regulatory division that
the Account is located in , thus should be the same for all Accounts
owned by a single user .
Args :
accountID ... | request = Request ( 'GET' , '/v3/accounts/{accountID}/instruments' )
request . set_path_param ( 'accountID' , accountID )
request . set_param ( 'instruments' , kwargs . get ( 'instruments' ) )
response = self . ctx . request ( request )
if response . content_type is None :
return response
if not response . content_... |
def get_path ( * args , module = a99 ) :
"""Returns full path to specified module
Args :
* args : are added at the end of module path with os . path . join ( )
module : Python module , defaults to a99
Returns : path string
> > > get _ path ( )""" | p = os . path . abspath ( os . path . join ( os . path . split ( module . __file__ ) [ 0 ] , * args ) )
return p |
def document ( self , document_tree , backend = None ) :
"""Create a : class : ` DocumentTemplate ` object based on the given
document tree and this template configuration
Args :
document _ tree ( DocumentTree ) : tree of the document ' s contents
backend : the backend to use when rendering the document""" | return self . template ( document_tree , configuration = self , backend = backend ) |
def merge_vertices ( self , digits = None , textured = True ) :
"""If a mesh has vertices that are closer than
trimesh . constants . tol . merge reindex faces to reference
the same index for both vertices .
Parameters
digits : int
If specified overrides tol . merge
textured : bool
If True avoids mergi... | grouping . merge_vertices ( self , digits = digits , textured = textured ) |
def dispatch ( self , * args , ** kwargs ) :
"""This decorator sets this view to have restricted permissions .""" | return super ( AnimalYearArchive , self ) . dispatch ( * args , ** kwargs ) |
def extra_action ( self , names , provider , action , ** kwargs ) :
'''Perform actions with block storage devices
Example :
. . code - block : : python
client . extra _ action ( names = [ ' myblock ' ] , action = ' volume _ create ' ,
provider = ' my - nova ' , kwargs = { ' voltype ' : ' SSD ' , ' size ' : ... | mapper = salt . cloud . Map ( self . _opts_defaults ( ) )
providers = mapper . map_providers_parallel ( )
if provider in providers :
provider += ':{0}' . format ( next ( six . iterkeys ( providers [ provider ] ) ) )
else :
return False
if isinstance ( names , six . string_types ) :
names = names . split ( '... |
def _rest_patch ( self , suburi , request_headers , request_body ) :
"""REST PATCH operation .
HTTP response codes could be 500 , 404 , 202 etc .""" | return self . _rest_op ( 'PATCH' , suburi , request_headers , request_body ) |
def add_scoped_variable ( self , name , data_type = None , default_value = None , scoped_variable_id = None ) :
"""Adds a scoped variable to the container state
: param name : The name of the scoped variable
: param data _ type : An optional data type of the scoped variable
: param default _ value : An option... | if scoped_variable_id is None : # All data port ids have to passed to the id generation as the data port id has to be unique inside a state
scoped_variable_id = generate_data_port_id ( self . get_data_port_ids ( ) )
self . _scoped_variables [ scoped_variable_id ] = ScopedVariable ( name , data_type , default_value ... |
def logout ( self ) :
"""Log out the user .
> > > odoo . logout ( )
True
* Python 2 : *
: return : ` True ` if the operation succeed , ` False ` if no user was logged
: raise : : class : ` odoorpc . error . RPCError `
: raise : ` urllib2 . URLError ` ( connection error )
* Python 3 : *
: return : ` ... | if not self . _env :
return False
self . json ( '/web/session/destroy' , { } )
self . _env = None
self . _login = None
self . _password = None
return True |
def _pvals_from_chi_squared ( self , pairwise_chisq ) :
"""return statistical significance for props ' columns .
* pairwise _ chisq * ( ndarray ) Matrix of chi - squared values ( bases for Wishart CDF )""" | return self . _intersperse_insertion_rows_and_columns ( 1.0 - WishartCDF ( pairwise_chisq , self . _n_min , self . _n_max ) . values ) |
def random_sent ( self , index ) :
"""Get one sample from corpus consisting of two sentences . With prob . 50 % these are two subsequent sentences
from one doc . With 50 % the second sentence will be a random one from another doc .
: param index : int , index of sample .
: return : ( str , str , int ) , sente... | t1 , t2 = self . get_corpus_line ( index )
if random . random ( ) > 0.5 :
label = 0
else :
t2 = self . get_random_line ( )
label = 1
assert len ( t1 ) > 0
assert len ( t2 ) > 0
return t1 , t2 , label |
def _run ( self ) : # type : ( Downloader ) - > None
"""Execute Downloader
: param Downloader self : this""" | # mark start
self . _start_time = blobxfer . util . datetime_now ( )
logger . info ( 'blobxfer start time: {0}' . format ( self . _start_time ) )
# ensure destination path
blobxfer . operations . download . Downloader . ensure_local_destination ( self . _creds , self . _spec , self . _general_options . dry_run )
logger... |
def createDocument ( self , initDict = None ) :
"""create and returns a document populated with the defaults or with the values in initDict""" | if initDict is not None :
return self . createDocument_ ( initDict )
else :
if self . _validation [ "on_load" ] :
self . _validation [ "on_load" ] = False
return self . createDocument_ ( self . defaultDocument )
self . _validation [ "on_load" ] = True
else :
return self . cre... |
def _refreshNodeFromTarget ( self ) :
"""Updates the config settings""" | for key , value in self . viewBox . state . items ( ) :
if key != "limits" :
childItem = self . childByNodeName ( key )
childItem . data = value
else : # limits contains a dictionary as well
for limitKey , limitValue in value . items ( ) :
limitChildItem = self . limitsItem .... |
def add_event_callback ( channel , callback , bouncetime = None ) :
""": param channel : the channel based on the numbering system you have specified
( : py : attr : ` GPIO . BOARD ` , : py : attr : ` GPIO . BCM ` or : py : attr : ` GPIO . SUNXI ` ) .
: param callback : TODO
: param bouncetime : ( optional ) ... | _check_configured ( channel , direction = IN )
if bouncetime is not None :
if _gpio_warnings :
warnings . warn ( "bouncetime is not (yet) fully supported, continuing anyway. Use GPIO.setwarnings(False) to disable warnings." , stacklevel = 2 )
pin = get_gpio_pin ( _mode , channel )
event . add_edge_callback ... |
def initialize_hashes ( self ) :
"""Create new hashlib objects for each hash we are going to calculate .""" | if ( 'md5' in self . hashes ) :
self . md5_calc = hashlib . md5 ( )
if ( 'sha-1' in self . hashes ) :
self . sha1_calc = hashlib . sha1 ( )
if ( 'sha-256' in self . hashes ) :
self . sha256_calc = hashlib . sha256 ( ) |
def delete_file ( self , path , prefixed_path , source_storage ) :
"""Checks if the target file should be deleted if it already exists""" | if isinstance ( self . storage , CumulusStorage ) :
if self . storage . exists ( prefixed_path ) :
try :
etag = self . storage . _get_object ( prefixed_path ) . etag
digest = "{0}" . format ( hashlib . md5 ( source_storage . open ( path ) . read ( ) ) . hexdigest ( ) )
if... |
def require_session_started ( func ) :
"""Check if API sessions are started and start them if not""" | @ functools . wraps ( func )
def inner_func ( self , * pargs , ** kwargs ) :
if not self . session_started :
logger . info ( 'Starting session for required meta method' )
self . start_session ( )
return func ( self , * pargs , ** kwargs )
return inner_func |
def to_cloudformation ( self , ** kwargs ) :
"""Returns the Lambda layer to which this SAM Layer corresponds .
: param dict kwargs : already - converted resources that may need to be modified when converting this macro to pure CloudFormation
: returns : a list of vanilla CloudFormation Resources , to which this... | resources = [ ]
# Append any CFN resources :
intrinsics_resolver = kwargs [ "intrinsics_resolver" ]
resources . append ( self . _construct_lambda_layer ( intrinsics_resolver ) )
return resources |
def get_subdomain_resolver ( name , db_path = None , zonefiles_dir = None ) :
"""Static method for determining the last - known resolver for a domain name .
Returns the resolver URL on success
Returns None on error""" | opts = get_blockstack_opts ( )
if not is_subdomains_enabled ( opts ) :
log . warn ( "Subdomain support is disabled" )
return None
if db_path is None :
db_path = opts [ 'subdomaindb_path' ]
if zonefiles_dir is None :
zonefiles_dir = opts [ 'zonefiles' ]
db = SubdomainDB ( db_path , zonefiles_dir )
resolv... |
def close ( self , timeout : int = 5 ) -> None :
"""Stop a ffmpeg instance .
Return a coroutine""" | if self . _read_task is not None and not self . _read_task . cancelled ( ) :
self . _read_task . cancel ( )
return super ( ) . close ( timeout ) |
def create ( self , date_at = None , minutes = 0 , note = '' , user_id = None , project_id = None , service_id = None ) :
"""date _ at - date of time entry . Format YYYY - MM - DD . default : today
minutes - default : 0
note - default : ' ' ( empty string )
user _ id - default : actual user id ( only admin us... | keywords = { 'date_at' : date_at , 'minutes' : minutes , 'note' : note , 'user_id' : user_id , 'project_id' : project_id , 'service_id' : service_id , }
foo = dict ( )
foo [ 'time_entry' ] = keywords
path = partial ( _path , self . adapter )
path = _path ( self . adapter )
return self . _post ( path , ** foo ) |
def auth_token ( self , apikey = None , secret = None , email = None , password = None ) :
"""Get authentication token . Uses POST to / auth interface .
: Returns : ( str ) Authentication JWT""" | if ( apikey and secret ) or ( self . _apikey and self . _secret ) :
body = { "key_id" : apikey or self . _apikey , "secret" : secret or self . _secret }
elif ( email and password ) or ( self . _email and self . _password ) :
body = { "user" : email or self . _email , "password" : password or self . _password }
... |
def _is_target_valid ( self , cfg , target ) : # pylint : disable = no - self - use
"""Check if the resolved target is valid .
: param cfg : The CFG analysis object .
: param int target : The target to check .
: return : True if the target is valid . False otherwise .
: rtype : bool""" | if self . base_state is not None :
try :
if self . base_state . solver . is_true ( ( self . base_state . memory . permissions ( target ) & 4 ) == 4 ) :
return True
except SimMemoryError :
pass
return False
if cfg . _addr_in_exec_memory_regions ( target ) : # the jump target is ex... |
def update ( cls , session , record ) :
"""Update a record .
Args :
session ( requests . sessions . Session ) : Authenticated session .
record ( helpscout . BaseModel ) : The record to
be updated .
Returns :
helpscout . BaseModel : Freshly updated record .""" | cls . _check_implements ( 'update' )
data = record . to_api ( )
del data [ 'id' ]
data [ 'reload' ] = True
return cls ( '/%s/%s.json' % ( cls . __endpoint__ , record . id ) , data = data , request_type = RequestPaginator . PUT , singleton = True , session = session , ) |
def _make_f_expectation ( self , expr ) :
"""Calculates : math : ` < F > ` in eq . 12 ( see Ale et al . 2013 ) to calculate : math : ` < F > ` for EACH VARIABLE combination .
: param expr : an expression
: return : a column vector . Each row correspond to an element of counter .
: rtype : : class : ` sympy . ... | # compute derivatives for EACH ENTRY in COUNTER
derives = sp . Matrix ( [ derive_expr_from_counter_entry ( expr , self . __species , tuple ( c . n_vector ) ) for c in self . __n_counter ] )
# Computes the factorial terms for EACH entry in COUNTER
factorial_terms = sp . Matrix ( [ get_one_over_n_factorial ( tuple ( c . ... |
def clamped_interpolation ( skimage_range , sinogram ) :
"""Interpolate in a possibly smaller space .
Sets all points that would be outside the domain to match the
boundary values .""" | min_x = skimage_range . domain . min ( ) [ 1 ]
max_x = skimage_range . domain . max ( ) [ 1 ]
def interpolation_wrapper ( x ) :
x = ( x [ 0 ] , np . maximum ( min_x , np . minimum ( max_x , x [ 1 ] ) ) )
return sinogram . interpolation ( x )
return interpolation_wrapper |
def unregisterContextEngineId ( self , contextEngineId , pduTypes ) :
"""Unregister application with dispatcher""" | # 4.3.4
if contextEngineId is None : # Default to local snmpEngineId
contextEngineId , = self . mibInstrumController . mibBuilder . importSymbols ( '__SNMP-FRAMEWORK-MIB' , 'snmpEngineID' )
for pduType in pduTypes :
k = contextEngineId , pduType
if k in self . _appsRegistration :
del self . _appsReg... |
async def handle_request ( self , request , write_callback , stream_callback ) :
"""Take a request from the HTTP Server and return a response object
to be sent back The HTTP Server only expects a response object , so
exception handling must be done here
: param request : HTTP Request object
: param write _ ... | # Define ` response ` var here to remove warnings about
# allocation before assignment below .
response = None
cancelled = False
try : # Request Middleware
response = await self . _run_request_middleware ( request )
# No middleware results
if not response : # Execute Handler
# Fetch handler from router
... |
def set_window ( self , windowC , windowW ) :
"""Sets visualization window
: param windowC : window center
: param windowW : window width
: return :""" | if not ( windowW and windowC ) :
windowW = np . max ( self . img ) - np . min ( self . img )
windowC = ( np . max ( self . img ) + np . min ( self . img ) ) / 2.0
self . imgmax = windowC + ( windowW / 2 )
self . imgmin = windowC - ( windowW / 2 )
self . windowC = windowC
self . windowW = windowW |
def cancel_entrust ( self , entrust_no ) :
"""对未成交的调仓进行伪撤单
: param entrust _ no :
: return :""" | xq_entrust_list = self . _get_xq_history ( )
is_have = False
for xq_entrusts in xq_entrust_list :
status = xq_entrusts [ "status" ]
# 调仓状态
for entrust in xq_entrusts [ "rebalancing_histories" ] :
if entrust [ "id" ] == entrust_no and status == "pending" :
is_have = True
buy_o... |
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