signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def get_sqlserver_product_version ( engine : "Engine" ) -> Tuple [ int ] :
"""Gets SQL Server version information .
Attempted to use ` ` dialect . server _ version _ info ` ` :
. . code - block : : python
from sqlalchemy import create _ engine
url = " mssql + pyodbc : / / USER : PASSWORD @ ODBC _ NAME "
e... | assert is_sqlserver ( engine ) , ( "Only call get_sqlserver_product_version() for Microsoft SQL Server " "instances." )
sql = "SELECT CAST(SERVERPROPERTY('ProductVersion') AS VARCHAR)"
rp = engine . execute ( sql )
# type : ResultProxy
row = rp . fetchone ( )
dotted_version = row [ 0 ]
# type : str # e . g . ' 12.0.520... |
def dump_service ( self , sc ) :
"""Read all data blocks of a given service .
: meth : ` dump _ service ` reads all data blocks from the service
with service code * sc * and returns a list of strings suitable
for printing . The number of strings returned does not
necessarily reflect the number of data block... | def lprint ( fmt , data , index ) :
ispchr = lambda x : x >= 32 and x <= 126
# noqa : E731
def print_bytes ( octets ) :
return ' ' . join ( [ '%02x' % x for x in octets ] )
def print_chars ( octets ) :
return '' . join ( [ chr ( x ) if ispchr ( x ) else '.' for x in octets ] )
return... |
def hook_output ( module : nn . Module , detach : bool = True , grad : bool = False ) -> Hook :
"Return a ` Hook ` that stores activations of ` module ` in ` self . stored `" | return Hook ( module , _hook_inner , detach = detach , is_forward = not grad ) |
def set_components ( self , params ) :
"""Set the value of exogenous model elements .
Element values can be passed as keyword = value pairs in the function call .
Values can be numeric type or pandas Series .
Series will be interpolated by integrator .
Examples
> > > model . set _ components ( { ' birth _... | # It might make sense to allow the params argument to take a pandas series , where
# the indices of the series are variable names . This would make it easier to
# do a Pandas apply on a DataFrame of parameter values . However , this may conflict
# with a pandas series being passed in as a dictionary element .
for key ,... |
def write_config ( filename , config , mode = "w" ) :
'''use configparser to write a config object to filename''' | with open ( filename , mode ) as filey :
config . write ( filey )
return filename |
def _get_phi ( self , C , mag ) :
"""Returns the magnitude dependent intra - event standard deviation ( phi )
( equation 15)""" | if mag < 5.5 :
return C [ "phi1" ]
elif mag < 5.75 :
return C [ "phi1" ] + ( C [ "phi2" ] - C [ "phi1" ] ) * ( ( mag - 5.5 ) / 0.25 )
else :
return C [ "phi2" ] |
def combined ( cls , code , path = None , extra_args = None ) :
"""Compile combined - json with abi , bin , devdoc , userdoc .
@ param code : literal solidity code as a string .
@ param path : absolute path to solidity - file . Note : code & path are
mutually exclusive !
@ param extra _ args : Either a spac... | if code and path :
raise ValueError ( 'sourcecode and path are mutually exclusive.' )
if path :
contracts = compile_file ( path , extra_args = extra_args )
with open ( path ) as handler :
code = handler . read ( )
elif code :
contracts = compile_code ( code , extra_args = extra_args )
else :
... |
def get_series_by_name ( self , name ) :
"""Returns the first : py : class : ` . Series ` of a given name , or ` ` None ` ` .
: param str name : The name to search by .""" | if not isinstance ( name , str ) :
raise TypeError ( "Can only search series by str name, not '%s'" % str ( name ) )
for series in self . all_series ( ) :
if series . name ( ) == name :
return series |
def get_content ( self ) :
"""performs es search and gets content objects""" | if "query" in self . query :
q = self . query [ "query" ]
else :
q = self . query
search = custom_search_model ( Content , q , field_map = { "feature-type" : "feature_type.slug" , "tag" : "tags.slug" , "content-type" : "_type" , } )
return search |
def detect ( ) :
"""Detect available plugins and return enabled / configured stats
Yields tuples of the form ( section , statsgroup ) sorted by the
default StatsGroup order which maybe overriden in the config
file . The ' section ' is the name of the configuration section
as well as the option used to enabl... | # Load plugins and config
plugins = load ( )
config = Config ( )
# Make sure that all sections have a valid plugin type defined
for section in config . sections ( ) :
if section == 'general' :
continue
try :
type_ = config . item ( section , 'type' )
except ConfigError :
raise Config... |
def integrate_converge ( self , crit = 1e-4 , verbose = True ) :
"""Integrates the model until model states are converging .
: param crit : exit criteria for difference of iterated
solutions [ default : 0.0001]
: type crit : float
: param bool verbose : information whether total elapsed time
should be pri... | # implemented by m - kreuzer
for varname , value in self . state . items ( ) :
value_old = copy . deepcopy ( value )
self . integrate_years ( 1 , verbose = False )
while np . max ( np . abs ( value_old - value ) ) > crit :
value_old = copy . deepcopy ( value )
self . integrate_years ( 1 , ve... |
def join ( cls , root , subkey ) :
"""Rebuild a full declaration name from its components .
for every string x , we have ` join ( split ( x ) ) = = x ` .""" | if subkey is None :
return root
return enums . SPLITTER . join ( ( root , subkey ) ) |
def nl_family ( self , value ) :
"""Family setter .""" | self . bytearray [ self . _get_slicers ( 0 ) ] = bytearray ( c_uint ( value or 0 ) ) |
def all ( self , query , ** kwargs ) :
"""https : / / api . slack . com / methods / search . all""" | self . url = 'https://slack.com/api/search.all'
return super ( Search , self ) . search_from_url ( query , ** kwargs ) |
def _parse_and_sort_accept_header ( accept_header ) :
"""Parse and sort the accept header items .
> > > _ parse _ and _ sort _ accept _ header ( ' application / json ; q = 0.5 , text / * ' )
[ ( ' text / * ' , 1.0 ) , ( ' application / json ' , 0.5 ) ]""" | return sorted ( [ _split_into_mimetype_and_priority ( x ) for x in accept_header . split ( ',' ) ] , key = lambda x : x [ 1 ] , reverse = True ) |
def via ( self , * args ) :
"""Creates an empty error to record in the stack
trace""" | error = None
if len ( self . errors ) > 0 :
error = self . _err ( "via" , * args )
return error |
def _scons_user_error ( e ) :
"""Handle user errors . Print out a message and a description of the
error , along with the line number and routine where it occured .
The file and line number will be the deepest stack frame that is
not part of SCons itself .""" | global print_stacktrace
etype , value , tb = sys . exc_info ( )
if print_stacktrace :
traceback . print_exception ( etype , value , tb )
filename , lineno , routine , dummy = find_deepest_user_frame ( traceback . extract_tb ( tb ) )
sys . stderr . write ( "\nscons: *** %s\n" % value )
sys . stderr . write ( 'File "... |
def is_valid_coll ( self , coll ) :
"""Determines if the collection name for a request is valid ( exists )
: param str coll : The name of the collection to check
: return : True if the collection is valid , false otherwise
: rtype : bool""" | # if coll = = self . all _ coll :
# return True
return ( coll in self . warcserver . list_fixed_routes ( ) or coll in self . warcserver . list_dynamic_routes ( ) ) |
def rowgroupmap ( table , key , mapper , header = None , presorted = False , buffersize = None , tempdir = None , cache = True ) :
"""Group rows under the given key then apply ` mapper ` to yield zero or more
output rows for each input group of rows .""" | return RowGroupMapView ( table , key , mapper , header = header , presorted = presorted , buffersize = buffersize , tempdir = tempdir , cache = cache ) |
def from_array ( array ) :
"""Deserialize a new Message from a given dictionary .
: return : new Message instance .
: rtype : Message""" | if array is None or not array :
return None
# end if
assert_type_or_raise ( array , dict , parameter_name = "array" )
from . . receivable . peer import User , Chat
from . . receivable . media import Animation , Audio , Contact , Document , Game , Location , MessageEntity , PhotoSize
from . . receivable . media impo... |
def debug_option ( f ) :
"""Configures - - debug option for CLI
: param f : Callback Function to be passed to Click""" | def callback ( ctx , param , value ) :
state = ctx . ensure_object ( Context )
state . debug = value
return value
return click . option ( '--debug' , expose_value = False , is_flag = True , envvar = "SAM_DEBUG" , help = 'Turn on debug logging to print debug message generated by SAM CLI.' , callback = callba... |
def _delete ( self , ** kwargs ) :
"""wrapped with delete , override that in a subclass to customize""" | requests_params = self . _handle_requests_params ( kwargs )
delete_uri = self . _meta_data [ 'uri' ]
session = self . _meta_data [ 'bigip' ] . _meta_data [ 'icr_session' ]
# Check the generation for match before delete
force = self . _check_force_arg ( kwargs . pop ( 'force' , True ) )
if not force :
self . _check_... |
def pop ( self , index = - 1 ) :
"""Retrieve the value at * index * , remove it from the collection , and
return it .""" | if index == 0 :
return self . _pop_left ( )
elif index == - 1 :
return self . _pop_right ( )
else :
return self . _pop_middle ( index ) |
def _quantize_symbol ( sym , excluded_symbols = None , offline_params = None , quantized_dtype = 'int8' ) :
"""Given a symbol object representing a neural network of data type FP32,
quantize it into a INT8 network .
Parameters
sym : Symbol
FP32 neural network symbol .
excluded _ sym _ names : list of stri... | num_excluded_symbols = 0
if excluded_symbols is not None :
assert isinstance ( excluded_symbols , list )
num_excluded_symbols = len ( excluded_symbols )
else :
excluded_symbols = [ ]
num_offline = 0
offline = [ ]
if offline_params is not None :
num_offline = len ( offline_params )
for k in offline_p... |
def handle_annotation_list ( self , line : str , position : int , tokens : ParseResults ) -> ParseResults :
"""Handle statements like ` ` DEFINE ANNOTATION X AS LIST { " Y " , " Z " , . . . } ` ` .
: raises : RedefinedAnnotationError""" | annotation = tokens [ 'name' ]
self . raise_for_redefined_annotation ( line , position , annotation )
self . annotation_to_local [ annotation ] = set ( tokens [ 'values' ] )
return tokens |
def convert_separable_convolution ( builder , layer , input_names , output_names , keras_layer ) :
"""Convert separable convolution layer from keras to coreml .
Parameters
keras _ layer : layer
A keras layer object .
builder : NeuralNetworkBuilder
A neural network builder object .""" | _check_data_format ( keras_layer )
# Get input and output names
input_name , output_name = ( input_names [ 0 ] , output_names [ 0 ] )
has_bias = keras_layer . use_bias
# Get the weights from _ keras .
weight_list = keras_layer . get_weights ( )
output_blob_shape = list ( filter ( None , keras_layer . output_shape ) )
o... |
def WriteFileHeader ( self , arcname = None , compress_type = None , st = None ) :
"""Writes a file header .""" | if not self . _stream :
raise ArchiveAlreadyClosedError ( "Attempting to write to a ZIP archive that was already closed." )
self . cur_zinfo = self . _GenerateZipInfo ( arcname = arcname , compress_type = compress_type , st = st )
self . cur_file_size = 0
self . cur_compress_size = 0
if self . cur_zinfo . compress_... |
def add_service ( service , zone = None , permanent = True ) :
'''Add a service for zone . If zone is omitted , default zone will be used .
CLI Example :
. . code - block : : bash
salt ' * ' firewalld . add _ service ssh
To assign a service to a specific zone :
. . code - block : : bash
salt ' * ' firew... | if zone :
cmd = '--zone={0} --add-service={1}' . format ( zone , service )
else :
cmd = '--add-service={0}' . format ( service )
if permanent :
cmd += ' --permanent'
return __firewall_cmd ( cmd ) |
def string_to_version ( verstring ) :
"""Return a tuple of ( epoch , version , release ) from a version string
This function replaces rpmUtils . miscutils . stringToVersion , see
https : / / bugzilla . redhat . com / 1364504""" | # is there an epoch ?
components = verstring . split ( ':' )
if len ( components ) > 1 :
epoch = components [ 0 ]
else :
epoch = 0
remaining = components [ : 2 ] [ 0 ] . split ( '-' )
version = remaining [ 0 ]
release = remaining [ 1 ]
return ( epoch , version , release ) |
def transformChildrenFromNative ( self , clearBehavior = True ) :
"""Recursively transform native children to vanilla representations .""" | for childArray in self . contents . values ( ) :
for child in childArray :
child = child . transformFromNative ( )
child . transformChildrenFromNative ( clearBehavior )
if clearBehavior :
child . behavior = None
child . parentBehavior = None |
def predict ( self , pairs ) :
"""Predicts the learned metric between input pairs . ( For now it just
calls decision function ) .
Returns the learned metric value between samples in every pair . It should
ideally be low for similar samples and high for dissimilar samples .
Parameters
pairs : array - like ... | check_is_fitted ( self , [ 'threshold_' , 'transformer_' ] )
return 2 * ( - self . decision_function ( pairs ) <= self . threshold_ ) - 1 |
def _compile_type ( self , schema ) :
"""Compile type schema : plain type matching""" | # Prepare self
self . compiled_type = const . COMPILED_TYPE . TYPE
self . name = get_type_name ( schema )
# Error partials
err_type = self . Invalid ( _ ( u'Wrong type' ) , self . name )
# Type check function
if six . PY2 and schema is basestring : # Relaxed rule for Python2 basestring
typecheck = lambda v : isinst... |
def grant_winsta_and_desktop ( th ) :
'''Grant the token ' s user access to the current process ' s window station and
desktop .''' | current_sid = win32security . GetTokenInformation ( th , win32security . TokenUser ) [ 0 ]
# Add permissions for the sid to the current windows station and thread id .
# This prevents windows error 0xC0000142.
winsta = win32process . GetProcessWindowStation ( )
set_user_perm ( winsta , WINSTA_ALL , current_sid )
deskto... |
def _read_track ( chunk ) :
"""Retuns a list of midi events and tempo change events""" | TEMPO , MIDI = range ( 2 )
# Deviations : The running status should be reset on non midi events , but
# some files contain meta events inbetween .
# TODO : Offset and time signature are not considered .
tempos = [ ]
events = [ ]
chunk = bytearray ( chunk )
deltasum = 0
status = 0
off = 0
while off < len ( chunk ) :
... |
def rg ( self ) :
"""Brazilian RG , return plain numbers .
Check : https : / / www . ngmatematica . com / 2014/02 / como - determinar - o - digito - verificador - do . html""" | digits = self . generator . random . sample ( range ( 0 , 9 ) , 8 )
checksum = sum ( i * digits [ i - 2 ] for i in range ( 2 , 10 ) )
last_digit = 11 - ( checksum % 11 )
if last_digit == 10 :
digits . append ( 'X' )
elif last_digit == 11 :
digits . append ( 0 )
else :
digits . append ( last_digit )
return '... |
def get_margin_requirement ( self ) :
"""Get margin requirements for intrument ( futures only )
: Retruns :
margin : dict
margin requirements for instrument
( all values are ` ` None ` ` for non - futures instruments )""" | contract = self . get_contract ( )
if contract . m_secType == "FUT" :
return futures . get_ib_futures ( contract . m_symbol , contract . m_exchange )
# else . . .
return { "exchange" : None , "symbol" : None , "description" : None , "class" : None , "intraday_initial" : None , "intraday_maintenance" : None , "overn... |
def count ( self ) :
"""Counts the number of rows of the main dataframe""" | try :
num = len ( self . df . index )
except Exception as e :
self . err ( e , "Can not count data" )
return
self . ok ( "Found" , num , "rows in the dataframe" ) |
def unjoin_domain ( username = None , password = None , domain = None , workgroup = 'WORKGROUP' , disable = False , restart = False ) : # pylint : disable = anomalous - backslash - in - string
'''Unjoin a computer from an Active Directory Domain . Requires a restart .
Args :
username ( str ) :
Username of an ... | # pylint : enable = anomalous - backslash - in - string
if six . PY2 :
username = _to_unicode ( username )
password = _to_unicode ( password )
domain = _to_unicode ( domain )
status = get_domain_workgroup ( )
if 'Workgroup' in status :
if status [ 'Workgroup' ] == workgroup :
return 'Already joi... |
def dataset_filepath ( filename , dataset_name = None , task = None , ** kwargs ) :
"""Get the path of the corresponding dataset file .
Parameters
filename : str
The name of the file .
dataset _ name : str , optional
The name of the dataset . Used to define a sub - directory to contain all
instances of ... | dataset_dir_path = dataset_dirpath ( dataset_name = dataset_name , task = task , ** kwargs )
return os . path . join ( dataset_dir_path , filename ) |
def notblocked ( page ) :
"""Determine if given url is a page that should be in sitemap .""" | for blocked in PAGES_TO_BLOCK :
if blocked [ 0 ] != '*' :
blocked = '*' + blocked
rx = re . compile ( blocked . replace ( '*' , '[^$]*' ) )
if rx . match ( page ) :
return False
return True |
def enable_backups ( self ) :
"""Enable Backups for this Instance . When enabled , we will automatically
backup your Instance ' s data so that it can be restored at a later date .
For more information on Instance ' s Backups service and pricing , see our
` Backups Page ` _
. . _ Backups Page : https : / / w... | self . _client . post ( "{}/backups/enable" . format ( Instance . api_endpoint ) , model = self )
self . invalidate ( )
return True |
def coombs_winners ( self , profile ) :
"""Returns an integer list that represents all possible winners of a profile under Coombs rule .
: ivar Profile profile : A Profile object that represents an election profile .""" | elecType = profile . getElecType ( )
if elecType == "soc" or elecType == "csv" :
return self . coombssoc_winners ( profile )
elif elecType == "toc" :
return self . coombstoc_winners ( profile )
else :
print ( "ERROR: unsupported profile type" )
exit ( ) |
def get_all ( ) :
'''Return all available boot services
CLI Example :
. . code - block : : bash
salt ' * ' service . get _ all''' | ret = set ( )
lines = glob . glob ( '/etc/init.d/*' )
for line in lines :
service = line . split ( '/etc/init.d/' ) [ 1 ]
# Remove README . If it ' s an enabled service , it will be added back in .
if service != 'README' :
ret . add ( service )
return sorted ( ret | set ( get_enabled ( ) ) ) |
def copy_file ( self , filepath ) :
"""Returns flag which says to copy rather than link a file .""" | copy_file = False
try :
copy_file = self . data [ filepath ] [ 'copy' ]
except KeyError :
return False
return copy_file |
def close ( self ) :
'''Releasing hardware resources .''' | try :
self . dut . close ( )
except Exception :
logging . warning ( 'Closing DUT was not successful' )
else :
logging . debug ( 'Closed DUT' ) |
def cmd_link_attributes ( self , args ) :
'''change optional link attributes''' | link = args [ 0 ]
attributes = args [ 1 ]
print ( "Setting link %s attributes (%s)" % ( link , attributes ) )
self . link_attributes ( link , attributes ) |
def plot_sampler ( sampler , suptitle = None , labels = None , bins = 50 , plot_samples = False , plot_hist = True , plot_chains = True , burn = 0 , chain_mask = None , temp_idx = 0 , weights = None , cutoff_weight = None , cmap = 'gray_r' , hist_color = 'k' , chain_alpha = 0.1 , points = None , covs = None , colors = ... | masked_weights = None
if points is not None :
points = scipy . atleast_2d ( points )
if covs is not None and len ( covs ) != len ( points ) :
raise ValueError ( "If covariance matrices are provided, len(covs) must equal len(points)!" )
elif covs is None :
covs = [ None , ] * len ( points )
... |
def remove_fact ( self , fact_id ) :
"""Remove fact from storage by it ' s ID""" | self . start_transaction ( )
fact = self . __get_fact ( fact_id )
if fact :
self . __remove_fact ( fact_id )
self . facts_changed ( )
self . end_transaction ( ) |
def inherited_labels ( cls ) :
"""Return list of labels from nodes class hierarchy .
: return : list""" | return [ scls . __label__ for scls in cls . mro ( ) if hasattr ( scls , '__label__' ) and not hasattr ( scls , '__abstract_node__' ) ] |
def get_translated_file ( fapi , file_uri , locale , retrieval_type , include_original_strings , use_cache , cache_dir = None ) :
"""Returns a translated file from smartling""" | file_data = None
cache_name = str ( file_uri ) + "." + str ( locale ) + "." + str ( retrieval_type ) + "." + str ( include_original_strings )
cache_file = os . path . join ( cache_dir , sha1 ( cache_name ) ) if cache_dir else None
if use_cache and os . path . exists ( cache_file ) :
print ( "Using cache file %s for... |
def insertRow ( self , row , item , parent ) :
"""Insert a single item before the given row in the child items of the parent specified .
: param row : the index where the rows get inserted
: type row : int
: param item : the item to insert . When creating the item , make sure it ' s parent is None .
If not ... | item . set_model ( self )
if parent . isValid ( ) :
parentitem = parent . internalPointer ( )
else :
parentitem = self . _root
self . beginInsertRows ( parent , row , row )
item . _parent = parentitem
if parentitem :
parentitem . childItems . insert ( row , item )
self . endInsertRows ( )
return True |
def get_specific_nodes ( self , node , names ) :
"""Given a node and a sequence of strings in ` names ` , return a
dictionary containing the names as keys and child
` ELEMENT _ NODEs ` , that have a ` tagName ` equal to the name .""" | nodes = [ ( x . tagName , x ) for x in node . childNodes if x . nodeType == x . ELEMENT_NODE and x . tagName in names ]
return dict ( nodes ) |
def remove_access ( self , ** kwargs ) : # noqa : E501
"""Removes the specified ids from the given dashboards ' ACL # noqa : E501
# noqa : E501
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass async _ req = True
> > > thread = api . remove _ access... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async_req' ) :
return self . remove_access_with_http_info ( ** kwargs )
# noqa : E501
else :
( data ) = self . remove_access_with_http_info ( ** kwargs )
# noqa : E501
return data |
def universe ( self ) :
"""Data universe available at the current time .
Universe contains the data passed in when creating a Backtest .
Use this data to determine strategy logic .""" | # avoid windowing every time
# if calling and on same date return
# cached value
if self . now == self . _last_chk :
return self . _funiverse
else :
self . _last_chk = self . now
self . _funiverse = self . _universe . loc [ : self . now ]
return self . _funiverse |
def get_attribute ( self , obj , attribute ) :
"""Returns single object attribute .
: param obj : requested object .
: param attribute : requested attribute to query .
: returns : returned value .
: rtype : str""" | raw_return = self . send_command_return ( obj , attribute , '?' )
if len ( raw_return ) > 2 and raw_return [ 0 ] == '"' and raw_return [ - 1 ] == '"' :
return raw_return [ 1 : - 1 ]
return raw_return |
def run_role ( self , name , options = None , content = None ) :
"""Generate a role node .
options : dict
key value arguments .
content : content
content of the directive
Returns
node : docutil Node
Node generated by the arguments .""" | if options is None :
options = { }
if content is None :
content = [ ]
role_fn , _ = role ( name , self . language , self . node . line , self . reporter )
vec , _ = role_fn ( name , rawtext = str ( content ) , text = str ( content ) , lineno = self . node . line , inliner = self . memo . inliner , options = opt... |
def set_topic_partitions ( self , * topics ) :
"""Set the topic / partitions to consume
Optionally specify offsets to start from
Accepts types :
* str ( utf - 8 ) : topic name ( will consume all available partitions )
* tuple : ( topic , partition )
* dict :
- { topic : partition }
- { topic : [ parti... | self . _topics = [ ]
self . _client . load_metadata_for_topics ( )
# Setup offsets
self . _offsets = OffsetsStruct ( fetch = dict ( ) , commit = dict ( ) , highwater = dict ( ) , task_done = dict ( ) )
# Handle different topic types
for arg in topics : # Topic name str - - all partitions
if isinstance ( arg , ( six... |
def query_starts_with ( query , prefixes ) :
"""Check if the query starts with any item from * prefixes * .""" | prefixes = [ prefix . lower ( ) for prefix in prefixes ]
formatted_sql = sqlparse . format ( query . lower ( ) , strip_comments = True )
return bool ( formatted_sql ) and formatted_sql . split ( ) [ 0 ] in prefixes |
def make_splice_junction_df ( fn , type = 'gene' ) :
"""Read the Gencode gtf file and make a pandas dataframe describing the
splice junctions
Parameters
filename : str of filename
Filename of the Gencode gtf file
Returns
df : pandas . DataFrame
Dataframe of splice junctions with the following columns ... | import itertools as it
import HTSeq
import numpy as np
# GFF _ Reader has an option for end _ included . However , I think it is
# backwards . So if your gtf is end - inclusive , you want the default
# ( end _ included = False ) . With this , one will NOT be subtracted from the end
# coordinate .
gffI = it . islice ( H... |
def upstream ( self , f , n = 1 ) :
"""find n upstream features where upstream is determined by
the strand of the query Feature f
Overlapping features are not considered .
f : a Feature object
n : the number of features to return""" | if f . strand == - 1 :
return self . right ( f , n )
return self . left ( f , n ) |
def combine_hex ( data ) :
'''Combine list of integer values to one big integer''' | output = 0x00
for i , value in enumerate ( reversed ( data ) ) :
output |= ( value << i * 8 )
return output |
def getfield ( self , pkt , s ) :
"""If the decryption of the content did not fail with a CipherError ,
we begin a loop on the clear content in order to get as much messages
as possible , of the type advertised in the record header . This is
notably important for several TLS handshake implementations , which ... | tmp_len = self . length_from ( pkt )
lst = [ ]
ret = b""
remain = s
if tmp_len is not None :
remain , ret = s [ : tmp_len ] , s [ tmp_len : ]
if remain == b"" :
if ( ( ( pkt . tls_session . tls_version or 0x0303 ) > 0x0200 ) and hasattr ( pkt , "type" ) and pkt . type == 23 ) :
return ret , [ TLSApplica... |
def process_app_config_section ( config , app_config ) :
"""Processes the app section from a configuration data dict .
: param config : The config reference of the object that will hold the
configuration data from the config _ data .
: param app _ config : App section from a config data dict .""" | if 'addresses' in app_config :
config . app [ 'addresses' ] = app_config [ 'addresses' ]
if 'component' in app_config :
config . app [ 'component' ] = app_config [ 'component' ]
if 'data' in app_config :
if 'sources' in app_config [ 'data' ] :
config . app [ 'data' ] [ 'sources' ] = app_config [ 'da... |
def getAllReadGroups ( self ) :
"""Get all read groups in a read group set""" | for dataset in self . getAllDatasets ( ) :
iterator = self . _client . search_read_group_sets ( dataset_id = dataset . id )
for readGroupSet in iterator :
readGroupSet = self . _client . get_read_group_set ( readGroupSet . id )
for readGroup in readGroupSet . read_groups :
yield read... |
def make_driveritem_deviceitem_devicename ( device_name , condition = 'is' , negate = False , preserve_case = False ) :
"""Create a node for DriverItem / DeviceItem / DeviceName
: return : A IndicatorItem represented as an Element node""" | document = 'DriverItem'
search = 'DriverItem/DeviceItem/DeviceName'
content_type = 'string'
content = device_name
ii_node = ioc_api . make_indicatoritem_node ( condition , document , search , content_type , content , negate = negate , preserve_case = preserve_case )
return ii_node |
def _setup_schema ( Base , session ) :
"""Create a function which adds ` _ _ marshmallow _ _ ` attribute to all signal models .""" | def create_schema_class ( m ) :
if hasattr ( m , 'send_signalbus_message' ) : # Signal models should not use the SQLAlchemy session .
class Meta ( object ) :
model = m
else :
class Meta ( object ) :
model = m
sqla_session = session
schema_class_name = '%sS... |
def create_job ( self , phases , name = None , input = None ) :
"""CreateJob
https : / / apidocs . joyent . com / manta / api . html # CreateJob""" | log . debug ( 'CreateJob' )
path = '/%s/jobs' % self . account
body = { "phases" : phases }
if name :
body [ "name" ] = name
if input :
body [ "input" ] = input
headers = { "Content-Type" : "application/json" }
res , content = self . _request ( path , "POST" , body = json . dumps ( body ) , headers = headers )
... |
def remap_file_lines ( from_path , to_path , line_map_list ) :
"""Adds line _ map list to the list of association of from _ file to
to to _ file""" | from_path = pyc2py ( from_path )
cache_file ( to_path )
remap_entry = file2file_remap_lines . get ( to_path )
if remap_entry :
new_list = list ( remap_entry . from_to_pairs ) + list ( line_map_list )
else :
new_list = line_map_list
# FIXME : look for duplicates ?
file2file_remap_lines [ to_path ] = RemapLineEnt... |
def write_tile_if_changed ( store , tile_data , coord , format ) :
"""Only write tile data if different from existing .
Try to read the tile data from the store first . If the existing
data matches , don ' t write . Returns whether the tile was written .""" | existing_data = store . read_tile ( coord , format )
if not existing_data or not tiles_are_equal ( existing_data , tile_data , format ) :
store . write_tile ( tile_data , coord , format )
return True
else :
return False |
def from_json ( cls , json_info ) :
"""Build a Result instance from a json string .""" | if json_info is None :
return None
return ResultRecord ( trial_id = json_info [ "trial_id" ] , timesteps_total = json_info [ "timesteps_total" ] , done = json_info . get ( "done" , None ) , episode_reward_mean = json_info . get ( "episode_reward_mean" , None ) , mean_accuracy = json_info . get ( "mean_accuracy" , N... |
def connect ( self , cback , subscribers = None , instance = None ) :
"""Add a function or a method as an handler of this signal .
Any handler added can be a coroutine .
: param cback : the callback ( or * handler * ) to be added to the set
: returns : ` ` None ` ` or the value returned by the corresponding w... | if subscribers is None :
subscribers = self . subscribers
# wrapper
if self . _fconnect is not None :
def _connect ( cback ) :
self . _connect ( subscribers , cback )
notify = partial ( self . _notify_one , instance )
if instance is not None :
result = self . _fconnect ( instance , cback... |
def _evaluate ( self , R , phi = 0. , t = 0. ) :
"""NAME :
_ evaluate
PURPOSE :
evaluate the potential at R , phi , t
INPUT :
R - Galactocentric cylindrical radius
phi - azimuth
t - time
OUTPUT :
Phi ( R , phi , t )
HISTORY :
2011-03-27 - Started - Bovy ( NYU )""" | return self . _A * math . exp ( - ( t - self . _to ) ** 2. / 2. / self . _sigma2 ) / self . _alpha * math . cos ( self . _alpha * math . log ( R ) - self . _m * ( phi - self . _omegas * t - self . _gamma ) ) |
def add_slot_ports ( self , slot ) :
"""Add the ports to be added for a adapter card
: param str slot : Slot name""" | slot_nb = int ( slot [ 4 ] )
# slot _ adapter = None
# if slot in self . node [ ' properties ' ] :
# slot _ adapter = self . node [ ' properties ' ] [ slot ]
# elif self . device _ info [ ' model ' ] = = ' c7200 ' :
# if self . device _ info [ ' npe ' ] = = ' npe - g2 ' :
# slot _ adapter = ' C7200 - IO - GE - E '
# el... |
def populate_from_trace_graph ( self , graph : TraceGraph ) -> None :
"""Populates this graph from the given one based on affected _ files""" | # Track which trace frames have been visited as we populate the full
# traces of the graph .
self . _visited_trace_frame_ids : Set [ int ] = set ( )
self . _populate_affected_issues ( graph )
if not self . _affected_issues_only : # Finds issues from the conditions and saves them .
# Also saves traces that have been tri... |
def update_properties ( self , new_properties ) :
"""Update config properties values
Property name must be equal to ' Section _ option ' of config property
: param new _ properties : dict with new properties values""" | [ self . _update_property_from_dict ( section , option , new_properties ) for section in self . sections ( ) for option in self . options ( section ) ] |
def signed_token_generator ( private_pem , ** kwargs ) :
""": param private _ pem :""" | def signed_token_generator ( request ) :
request . claims = kwargs
return common . generate_signed_token ( private_pem , request )
return signed_token_generator |
def get_blob_hash ( self , h = hashlib . md5 ) :
"""get hash instance of blob content
: param h : callable hash generator
: type h : builtin _ function _ or _ method
: rtype : _ hashlib . HASH
: return : hash instance""" | assert callable ( h )
return h ( self . get_blob_data ( ) ) |
def role_update ( self , role_id , data , ** kwargs ) :
"https : / / developer . zendesk . com / rest _ api / docs / chat / roles # update - role" | api_path = "/api/v2/roles/{role_id}"
api_path = api_path . format ( role_id = role_id )
return self . call ( api_path , method = "PUT" , data = data , ** kwargs ) |
def _validate_monotonic ( self ) :
"""Validate on is _ monotonic .""" | if not self . _on . is_monotonic :
formatted = self . on or 'index'
raise ValueError ( "{0} must be " "monotonic" . format ( formatted ) ) |
def _normalize_subplot_ids ( fig ) :
"""Make sure a layout subplot property is initialized for every subplot that
is referenced by a trace in the figure .
For example , if a figure contains a ` scatterpolar ` trace with the ` subplot `
property set to ` polar3 ` , this function will make sure the figure ' s l... | layout = fig . setdefault ( 'layout' , { } )
for trace in fig . get ( 'data' , None ) :
trace_type = trace . get ( 'type' , 'scatter' )
subplot_types = _trace_to_subplot . get ( trace_type , [ ] )
for subplot_type in subplot_types :
subplot_prop_name = _get_subplot_prop_name ( subplot_type )
... |
def items ( self ) :
"""Returns a depth - first flat list of all items in the document""" | l = [ ]
for e in self . data :
l += e . items ( )
return l |
def field_values ( self ) :
"""Access the field _ values
: returns : twilio . rest . autopilot . v1 . assistant . field _ type . field _ value . FieldValueList
: rtype : twilio . rest . autopilot . v1 . assistant . field _ type . field _ value . FieldValueList""" | if self . _field_values is None :
self . _field_values = FieldValueList ( self . _version , assistant_sid = self . _solution [ 'assistant_sid' ] , field_type_sid = self . _solution [ 'sid' ] , )
return self . _field_values |
def construct_url ( self ) :
"""Construct a full plex request URI , with ` params ` .""" | path = [ self . path ]
path . extend ( [ str ( x ) for x in self . params ] )
url = self . client . base_url + '/' . join ( x for x in path if x )
query = self . kwargs . get ( 'query' )
if query : # Dict - > List
if type ( query ) is dict :
query = query . items ( )
# Remove items with ` None ` value
... |
def _html_image ( page ) :
"""returns HTML img tag""" | source = _image ( page )
if not source :
return
alt = page . data . get ( 'label' ) or page . data . get ( 'title' )
img = "<img src=\"%s\"" % source
img += " alt=\"%s\" title=\"%s\" " % ( alt , alt )
img += "align=\"right\" width=\"240\">"
return img |
def has_item ( self , hash_key , range_key = None , consistent_read = False ) :
"""Checks the table to see if the Item with the specified ` ` hash _ key ` `
exists . This may save a tiny bit of time / bandwidth over a
straight : py : meth : ` get _ item ` if you have no intention to touch
the data that is ret... | try : # Attempt to get the key . If it can ' t be found , it ' ll raise
# an exception .
self . get_item ( hash_key , range_key = range_key , # This minimizes the size of the response body .
attributes_to_get = [ hash_key ] , consistent_read = consistent_read )
except dynamodb_exceptions . DynamoDBKeyNotFoundEr... |
def configure ( name , host , port , auth , current ) :
'''Configure is used to add various ES ports you are working on .
The user can add as many es ports as the one wants ,
but one will remain active at one point .''' | Config = ConfigParser . ConfigParser ( )
if not os . path . exists ( os . path . dirname ( filename ) ) :
try :
os . makedirs ( os . path . dirname ( filename ) )
except Exception as e :
click . echo ( e )
return
section_name = None
if ( current . lower ( ) == 'y' ) :
section_name = ... |
def read_rows ( self , read_position , retry = google . api_core . gapic_v1 . method . DEFAULT , timeout = google . api_core . gapic_v1 . method . DEFAULT , metadata = None , ) :
"""Reads rows from the table in the format prescribed by the read session .
Each response contains one or more table rows , up to a max... | # Wrap the transport method to add retry and timeout logic .
if "read_rows" not in self . _inner_api_calls :
self . _inner_api_calls [ "read_rows" ] = google . api_core . gapic_v1 . method . wrap_method ( self . transport . read_rows , default_retry = self . _method_configs [ "ReadRows" ] . retry , default_timeout ... |
def _construct_jbor ( job_id , field_name_and_maybe_index ) :
''': param job _ id : Job ID
: type job _ id : string
: param field _ name _ and _ maybe _ index : Field name , plus possibly " . N " where N is an array index
: type field _ name _ and _ maybe _ index : string
: returns : dict of JBOR''' | link = { "$dnanexus_link" : { "job" : job_id } }
if '.' in field_name_and_maybe_index :
split_by_dot = field_name_and_maybe_index . rsplit ( '.' , 1 )
link [ "$dnanexus_link" ] [ "field" ] = split_by_dot [ 0 ]
link [ "$dnanexus_link" ] [ "index" ] = int ( split_by_dot [ 1 ] )
else :
link [ "$dnanexus_li... |
async def _send_sack ( self ) :
"""Build and send a selective acknowledgement ( SACK ) chunk .""" | gaps = [ ]
gap_next = None
for tsn in sorted ( self . _sack_misordered ) :
pos = ( tsn - self . _last_received_tsn ) % SCTP_TSN_MODULO
if tsn == gap_next :
gaps [ - 1 ] [ 1 ] = pos
else :
gaps . append ( [ pos , pos ] )
gap_next = tsn_plus_one ( tsn )
sack = SackChunk ( )
sack . cumulati... |
def focusOutEvent ( self , event ) :
"""Overloads the focus out event to cancel editing when the widget loses
focus .
: param event | < QFocusEvent >""" | super ( XNavigationEdit , self ) . focusOutEvent ( event )
self . cancelEdit ( ) |
def setImportDataInterface ( self , values ) :
"""Return the current list of import data interfaces""" | exims = self . getImportDataInterfacesList ( )
new_values = [ value for value in values if value in exims ]
if len ( new_values ) < len ( values ) :
logger . warn ( "Some Interfaces weren't added..." )
self . Schema ( ) . getField ( 'ImportDataInterface' ) . set ( self , new_values ) |
def post ( self , path = '' , retry = 0 , ** data ) :
"""Post an item to the Graph API .
: param path : A string describing the path to the item .
: param retry : An integer describing how many times the request may be retried .
: param data : Graph API parameters such as ' message ' or ' source ' .
See ` F... | response = self . _query ( method = 'POST' , path = path , data = data , retry = retry )
if response is False :
raise FacebookError ( 'Could not post to "%s"' % path )
return response |
def Parse ( self , stat , file_object , knowledge_base ) :
"""Parse the sshd configuration .
Process each of the lines in the configuration file .
Assembes an sshd _ config file into a dictionary with the configuration
keyword as the key , and the configuration settings as value ( s ) .
Args :
stat : unus... | _ , _ = stat , knowledge_base
# Clean out any residual state .
self . _field_parser . Flush ( )
lines = [ l . strip ( ) for l in utils . ReadFileBytesAsUnicode ( file_object ) . splitlines ( ) ]
for line in lines : # Remove comments ( will break if it includes a quoted / escaped # )
line = line . split ( "#" ) [ 0 ... |
def tile_to_quadkey ( tile , level ) :
"""Transform tile coordinates to a quadkey""" | tile_x = tile [ 0 ]
tile_y = tile [ 1 ]
quadkey = ""
for i in xrange ( level ) :
bit = level - i
digit = ord ( '0' )
mask = 1 << ( bit - 1 )
# if ( bit - 1 ) > 0 else 1 > > ( bit - 1)
if ( tile_x & mask ) is not 0 :
digit += 1
if ( tile_y & mask ) is not 0 :
digit += 2
quadke... |
def upTo ( self , key ) :
"""Returns the urn up to given level using URN Constants
: param key : Identifier of the wished resource using URN constants
: type key : int
: returns : String representation of the partial URN requested
: rtype : str
: Example :
> > > a = URN ( urn = " urn : cts : latinLit : ... | middle = [ component for component in [ self . __parsed [ "textgroup" ] , self . __parsed [ "work" ] , self . __parsed [ "version" ] ] if component is not None ]
if key == URN . COMPLETE :
return self . __str__ ( )
elif key == URN . NAMESPACE :
return ":" . join ( [ "urn" , self . __parsed [ "urn_namespace" ] ,... |
def post ( self , resource ) :
"""Creates a new instance of the resource .
Args :
resource - gophish . models . Model - The resource instance""" | response = self . api . execute ( "POST" , self . endpoint , json = ( resource . as_dict ( ) ) )
if not response . ok :
raise Error . parse ( response . json ( ) )
return self . _cls . parse ( response . json ( ) ) |
def generate_barcodes ( nIds , codeLen = 12 ) :
"""Given a list of sample IDs generate unique n - base barcodes for each .
Note that only 4 ^ n unique barcodes are possible .""" | def next_code ( b , c , i ) :
return c [ : i ] + b + ( c [ i + 1 : ] if i < - 1 else '' )
def rand_base ( ) :
return random . choice ( [ 'A' , 'T' , 'C' , 'G' ] )
def rand_seq ( n ) :
return '' . join ( [ rand_base ( ) for _ in range ( n ) ] )
# homopolymer filter regex : match if 4 identical bases in a row... |
def next ( self ) :
"""Return the next page .
The page label is defined in ` ` settings . NEXT _ LABEL ` ` .
Return an empty string if current page is the last .""" | if self . _page . has_next ( ) :
return self . _endless_page ( self . _page . next_page_number ( ) , label = settings . NEXT_LABEL )
return '' |
def run ( items ) :
"""Run MetaSV if we have enough supported callers , adding output to the set of calls .""" | assert len ( items ) == 1 , "Expect one input to MetaSV ensemble calling"
data = items [ 0 ]
work_dir = _sv_workdir ( data )
out_file = os . path . join ( work_dir , "variants.vcf.gz" )
cmd = _get_cmd ( ) + [ "--sample" , dd . get_sample_name ( data ) , "--reference" , dd . get_ref_file ( data ) , "--bam" , dd . get_al... |
def flip ( self ) :
"""This will switch major / minor around , regardless of frequency truth .
This is intended for forcing one of two populations to relate correctly
to the same genotype definitions . When flipped , Ps and Qs will be
backward , and the maf will no longer relate to the " minor " allele
freq... | maj_count = self . maj_allele_count
self . maj_allele_count = self . min_allele_count
self . min_allele_count = maj_count
alleles = self . alleles
self . alleles = [ alleles [ 1 ] , alleles [ 0 ] ] |
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