signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def slerp ( cls , q0 , q1 , amount = 0.5 ) :
"""Spherical Linear Interpolation between quaternions .
Implemented as described in https : / / en . wikipedia . org / wiki / Slerp
Find a valid quaternion rotation at a specified distance along the
minor arc of a great circle passing through any two existing quate... | # Ensure quaternion inputs are unit quaternions and 0 < = amount < = 1
q0 . _fast_normalise ( )
q1 . _fast_normalise ( )
amount = np . clip ( amount , 0 , 1 )
dot = np . dot ( q0 . q , q1 . q )
# If the dot product is negative , slerp won ' t take the shorter path .
# Note that v1 and - v1 are equivalent when the negat... |
def from_json ( payload ) :
"""Build a ` ` Place ` ` instance from the specified JSON object .
@ param payload : JSON representation of a place : :
" area _ id " : string ,
" address " : {
component _ type : string ,
" locale " : string ,
component _ type : string ,
" category " : string ,
" contact... | return payload and Place ( [ ( float ( lon ) , float ( lat ) , float ( alt ) ) for ( lon , lat , alt ) in payload [ 'boundaries' ] ] if payload . get ( 'boundaries' ) else GeoPoint . from_json ( payload [ 'location' ] ) , address = payload . get ( 'address' ) and ( Place . __parse_address__ ( payload [ 'address' ] ) if... |
def render ( element , level = 0 ) :
"""Renders the HTML builder ` element ` and it ' s children to a string .
Example : :
> > > print (
. . . render (
. . . html . form ( action = ' / search ' , name = ' f ' ) (
. . . html . input ( name = ' q ' ) ,
. . . html . input ( name = ' search _ button ' , typ... | if hasattr ( element , 'render' ) :
return element . render ( level )
elif isinstance ( element , basestring ) :
return _render_string ( element , level )
elif hasattr ( element , '__iter__' ) :
return _render_iteratable ( element , level )
elif element is None :
return ''
raise TypeError ( 'Cannot rend... |
def render ( self , horizontal_spacing : int = 1 , vertical_spacing : int = 1 , crossing_char : str = None , use_unicode_characters : bool = True ) -> str :
"""Outputs text containing the diagram .""" | block_diagram = BlockDiagramDrawer ( )
w = self . width ( )
h = self . height ( )
# Communicate padding into block diagram .
for x in range ( 0 , w - 1 ) :
block_diagram . set_col_min_width ( x * 2 + 1 , # Horizontal separation looks narrow , so partials round up .
int ( np . ceil ( self . horizontal_padding . ... |
def after_this_request ( func : Callable ) -> Callable :
"""Schedule the func to be called after the current request .
This is useful in situations whereby you want an after request
function for a specific route or circumstance only , for example ,
. . code - block : : python
def index ( ) :
@ after _ thi... | _request_ctx_stack . top . _after_request_functions . append ( func )
return func |
def _validate_dependencies_met ( ) :
"""Verifies that PyOpenSSL ' s package - level dependencies have been met .
Throws ` ImportError ` if they are not met .""" | # Method added in ` cryptography = = 1.1 ` ; not available in older versions
from cryptography . x509 . extensions import Extensions
if getattr ( Extensions , "get_extension_for_class" , None ) is None :
raise ImportError ( "'cryptography' module missing required functionality. " "Try upgrading to v1.3.4 or newer.... |
def copyCurrentLayout ( self , sourceViewSUID , targetViewSUID , body , verbose = None ) :
"""Copy one network view layout onto another , setting the node location and view scale to match . This makes visually comparing networks simple .
: param sourceViewSUID : Source network view SUID ( or " current " )
: par... | response = api ( url = self . ___url + 'apply/layouts/copycat/' + str ( sourceViewSUID ) + '/' + str ( targetViewSUID ) + '' , method = "PUT" , body = body , verbose = verbose )
return response |
def file_md5 ( filename ) :
"""Generate the md5 checksum for a file
Args :
filename ( Str ) : The file to be checksummed .
Returns :
( Str ) : The hex checksum
Notes :
If the file is gzipped , the md5 checksum returned is
for the uncompressed ASCII file .""" | with zopen ( filename , 'r' ) as f :
file_string = f . read ( )
try : # attempt to decode byte object
file_string = file_string . decode ( )
except AttributeError :
pass
return ( md5sum ( file_string ) ) |
def change_status ( self , status ) :
"""Change the user ' s status
: param user :
: param email :
: return :""" | def cb ( ) :
self . user . update ( status = status )
return status
return signals . user_update ( self , ACTIONS [ "STATUS" ] , cb , data = { "status" : self . status } ) |
def isconsistent ( self ) :
'''Check if the timeseries is consistent''' | for dt1 , dt0 in laggeddates ( self ) :
if dt1 <= dt0 :
return False
return True |
def create_record_sets ( self , record_set_dicts ) :
"""Accept list of record _ set dicts .
Return list of record _ set objects .""" | record_set_objects = [ ]
for record_set_dict in record_set_dicts : # pop removes the ' Enabled ' key and tests if True .
if record_set_dict . pop ( 'Enabled' , True ) :
record_set_objects . append ( self . create_record_set ( record_set_dict ) )
return record_set_objects |
def update ( self , request , datum ) :
"""Switches the action verbose name , if needed .""" | if getattr ( self , 'action_present' , False ) :
self . verbose_name = self . _get_action_name ( )
self . verbose_name_plural = self . _get_action_name ( 'plural' ) |
def makedbthreads ( self ) :
"""Setup and create threads for class""" | # Find all the target folders in the analysis and add them to the targetfolders set
for sample in self . metadata :
if sample [ self . analysistype ] . combinedtargets != 'NA' :
self . targetfolders . add ( sample [ self . analysistype ] . targetpath )
# Create and start threads for each fasta file in the l... |
def verify ( self , smessage , signature = None , encoder = encoding . RawEncoder ) :
"""Verifies the signature of a signed message , returning the message
if it has not been tampered with else raising
: class : ` ~ ValueError ` .
: param smessage : [ : class : ` bytes ` ] Either the original messaged or a
... | if signature is not None : # If we were given the message and signature separately , combine
# them .
smessage = signature + smessage
# Decode the signed message
smessage = encoder . decode ( smessage )
return libnacl . crypto_sign_open ( smessage , self . _key ) |
def _check_lsm_input ( self , data_var_map_array ) :
"""This function checks the input var map array
to ensure the required input variables exist""" | REQUIRED_HMET_VAR_LIST = [ 'Prcp' , 'Pres' , 'Temp' , 'Clod' , 'RlHm' , 'Drad' , 'Grad' , 'WndS' ]
# make sure all required variables exist
given_hmet_var_list = [ ]
for gssha_data_var , lsm_data_var in data_var_map_array :
gssha_data_hmet_name = self . netcdf_attributes [ gssha_data_var ] [ 'hmet_name' ]
if gs... |
def get_child_objective_banks ( self , objective_bank_id ) :
"""Gets the children of the given objective bank .
arg : objective _ bank _ id ( osid . id . Id ) : the ` ` Id ` ` to query
return : ( osid . learning . ObjectiveBankList ) - the children of the
objective bank
raise : NotFound - ` ` objective _ ba... | # Implemented from template for
# osid . resource . BinHierarchySession . get _ child _ bins
if self . _catalog_session is not None :
return self . _catalog_session . get_child_catalogs ( catalog_id = objective_bank_id )
return ObjectiveBankLookupSession ( self . _proxy , self . _runtime ) . get_objective_banks_by_... |
def _clean_files_only ( self , files ) :
'''if a user only wants to process one or more specific files , instead of a full sosreport''' | try :
if not ( os . path . exists ( self . origin_path ) ) :
self . logger . info ( "Creating Origin Path - %s" % self . origin_path )
os . makedirs ( self . origin_path )
# create the origin _ path directory
if not ( os . path . exists ( self . dir_path ) ) :
self . logger . inf... |
def create_config ( allow_insecure_config_file = False ) :
"""Create config based on / etc / ddsclient . conf and ~ / . ddsclient . conf ( $ DDSCLIENT _ CONF )
: param allow _ insecure _ config _ file : bool : when true we will not check ~ / . ddsclient permissions .
: return : Config with the configuration to ... | config = Config ( )
config . add_properties ( GLOBAL_CONFIG_FILENAME )
user_config_filename = get_user_config_filename ( )
if user_config_filename == LOCAL_CONFIG_FILENAME and not allow_insecure_config_file :
verify_file_private ( user_config_filename )
config . add_properties ( user_config_filename )
return config |
def CrearCertificacionCabecera ( self , pto_emision = 1 , nro_orden = None , tipo_certificado = None , nro_planta = None , nro_ing_bruto_depositario = None , titular_grano = None , cuit_depositante = None , nro_ing_bruto_depositante = None , cuit_corredor = None , cod_grano = None , campania = None , datos_adicionales ... | self . certificacion = { }
self . certificacion [ 'cabecera' ] = dict ( ptoEmision = pto_emision , nroOrden = nro_orden , tipoCertificado = tipo_certificado , nroPlanta = nro_planta or None , # opcional
nroIngBrutoDepositario = nro_ing_bruto_depositario , titularGrano = titular_grano , cuitDepositante = cuit_depositant... |
def get_first_non_null_value ( self , ind_name , col_name ) :
"""For a given index and column , find the first non - null value .
Parameters
self : MagicDataFrame
ind _ name : str
index name for indexing
col _ name : str
column name for indexing
Returns
single value of str , float , or int""" | short_df = self . df . loc [ ind_name , col_name ]
mask = pd . notnull ( short_df )
print ( short_df [ mask ] )
try :
val = short_df [ mask ] . unique ( ) [ 0 ]
except IndexError :
val = None
return val |
def filter_string ( self , word ) :
"""Return a string like the input but containing only legal IPA segments
Args :
word ( unicode ) : input string to be filtered
Returns :
unicode : string identical to ` word ` but with invalid IPA segments
absent""" | segs = [ m . group ( 0 ) for m in self . seg_regex . finditer ( word ) ]
return '' . join ( segs ) |
def get_dataset ( self , key , info ) :
"""Get the data from the files .""" | logger . debug ( "Getting raw data" )
res = super ( HRITGOESFileHandler , self ) . get_dataset ( key , info )
self . mda [ 'calibration_parameters' ] = self . _get_calibration_params ( )
res = self . calibrate ( res , key . calibration )
new_attrs = info . copy ( )
new_attrs . update ( res . attrs )
res . attrs = new_a... |
def _process_response ( self , response ) :
"""Parse response""" | forward_raw = False
content_type = response . headers [ 'Content-Type' ]
if content_type != 'application/json' :
logger . debug ( "headers: %s" , response . headers )
# API BUG : text / xml content - type with json payload
# http : / / forum . mediafiredev . com / showthread . php ? 136
if content_type ... |
def generate_combined_fasta ( self , genome_list , genome_dir ) :
'''Generate a combined fasta using the genbank files .
Args
genome _ list ( list )
genome _ dir ( string )''' | fasta = [ ]
for genome in genome_list :
full_path = genome_dir + genome
handle = open ( full_path , "rU" )
print 'making combined fasta for' , genome
try :
seq_record = SeqIO . read ( handle , 'genbank' )
org_accession = seq_record . name
except AssertionError , e :
print str... |
def _brentq_cdf ( self , value ) :
"""Helper function to compute percent _ point .
As scipy . stats . gaussian _ kde doesn ' t provide this functionality out of the box we need
to make a numerical approach :
- First we scalarize and bound cumulative _ distribution .
- Then we define a function ` f ( x ) = c... | # The decorator expects an instance method , but usually are decorated before being bounded
bound_cdf = partial ( scalarize ( GaussianKDE . cumulative_distribution ) , self )
def f ( x ) :
return bound_cdf ( x ) - value
return f |
def timezone ( zone ) :
"""Try to get timezone using pytz or python - dateutil
: param zone : timezone str
: return : timezone tzinfo or None""" | try :
import pytz
return pytz . timezone ( zone )
except ImportError :
pass
try :
from dateutil . tz import gettz
return gettz ( zone )
except ImportError :
return None |
def get_descriptor_for_layer ( self , layer ) :
"""Returns the standard JSON descriptor for the layer . There is a lot of
usefule information in there .""" | if not layer in self . _layer_descriptor_cache :
params = { 'f' : 'pjson' }
if self . token :
params [ 'token' ] = self . token
response = requests . get ( self . _build_request ( layer ) , params = params )
self . _layer_descriptor_cache [ layer ] = response . json ( )
return self . _layer_desc... |
def get ( self , specification , * args , ** kwargs ) :
"""A more convenient version of : py : meth : ` acquire ( ) ` for when you can
provide positional arguments in a right order .""" | arguments = dict ( enumerate ( args ) )
arguments . update ( kwargs )
return self . acquire ( specification , arguments = arguments ) |
async def delete ( self , key ) :
"""Deletes the Key
Parameters :
key ( str ) : Key to delete
Response :
bool : ` ` True ` ` on success""" | response = await self . _discard ( key )
return response . body is True |
def clear_info ( self ) :
"""Clear the device info .""" | self . _version_text = None
self . _inventory_text = None
self . _users_text = None
self . os_version = None
self . os_type = None
self . family = None
self . platform = None
self . udi = None
# self . is _ console = None
self . prompt = None
self . prompt_re = None |
def query ( self , query ) :
'''Returns a sequence of objects matching criteria expressed in ` query `''' | query = query . copy ( )
query . key = self . _transform ( query . key )
return self . child_datastore . query ( query ) |
def p_version_def ( t ) :
"""version _ def : VERSION ID LBRACE procedure _ def procedure _ def _ list RBRACE EQUALS constant SEMI""" | global name_dict
id = t [ 2 ]
value = t [ 8 ]
lineno = t . lineno ( 1 )
if id_unique ( id , 'version' , lineno ) :
name_dict [ id ] = const_info ( id , value , lineno ) |
def get_load ( jid ) :
'''Return the load data that marks a specified jid''' | log . debug ( 'sdstack_etcd returner <get_load> called jid: %s' , jid )
read_profile = __opts__ . get ( 'etcd.returner_read_profile' )
client , path = _get_conn ( __opts__ , read_profile )
return salt . utils . json . loads ( client . get ( '/' . join ( ( path , 'jobs' , jid , '.load.p' ) ) ) . value ) |
def get_user_configured_modules ( self ) :
"""Get a dict of all available and configured py3status modules
in the user ' s i3status . conf .""" | user_modules = { }
if not self . py3_modules :
return user_modules
for module_name , module_info in self . get_user_modules ( ) . items ( ) :
for module in self . py3_modules :
if module_name == module . split ( " " ) [ 0 ] :
include_path , f_name = module_info
user_modules [ mod... |
def _eval_model ( self ) :
"""Convenience method for evaluating the model with the current parameters
: return : named tuple with results""" | arguments = self . _x_grid . copy ( )
arguments . update ( { param : param . value for param in self . model . params } )
return self . model ( ** key2str ( arguments ) ) |
def get_or_create ( session , model , ** kwargs ) :
"""Get or create sqlalchemy instance .
Args :
session ( Sqlalchemy session ) :
model ( sqlalchemy model ) :
kwargs ( dict ) : kwargs to lookup or create instance .
Returns :
Tuple : first element is found or created instance , second is boolean - True ... | instance = session . query ( model ) . filter_by ( ** kwargs ) . first ( )
if instance :
return instance , False
else :
instance = model ( ** kwargs )
if 'dataset' in kwargs :
instance . update_sequence_id ( session , kwargs [ 'dataset' ] )
session . add ( instance )
session . commit ( )
... |
def set_widgets ( self ) :
"""Set widgets on the Exposure Layer From Browser tab .""" | self . tvBrowserExposure_selection_changed ( )
# Set icon
exposure = self . parent . step_fc_functions1 . selected_value ( layer_purpose_exposure [ 'key' ] )
icon_path = get_image_path ( exposure )
self . lblIconIFCWExposureFromBrowser . setPixmap ( QPixmap ( icon_path ) ) |
def fetch ( self ) :
"""Lazily trigger download of the data when requested .""" | if self . _file_path is not None :
return self . _file_path
temp_path = self . context . work_path
if self . _content_hash is not None :
self . _file_path = storage . load_file ( self . _content_hash , temp_path = temp_path )
return self . _file_path
if self . response is not None :
self . _file_path = ... |
def get_assignable_bin_ids ( self , bin_id ) :
"""Gets a list of bins including and under the given bin node in which any resource can be assigned .
arg : bin _ id ( osid . id . Id ) : the ` ` Id ` ` of the ` ` Bin ` `
return : ( osid . id . IdList ) - list of assignable bin ` ` Ids ` `
raise : NullArgument -... | # Implemented from template for
# osid . resource . ResourceBinAssignmentSession . get _ assignable _ bin _ ids
# This will likely be overridden by an authorization adapter
mgr = self . _get_provider_manager ( 'RESOURCE' , local = True )
lookup_session = mgr . get_bin_lookup_session ( proxy = self . _proxy )
bins = loo... |
def uniqify ( func ) :
"""Make sure that a method returns a unique name .""" | @ six . wraps ( func )
def unique ( self , * args , ** kwargs ) :
return self . unique ( func ( self , * args , ** kwargs ) )
return unique |
def _raise_connection_failure ( address , error ) :
"""Convert a socket . error to ConnectionFailure and raise it .""" | host , port = address
# If connecting to a Unix socket , port will be None .
if port is not None :
msg = '%s:%d: %s' % ( host , port , error )
else :
msg = '%s: %s' % ( host , error )
if isinstance ( error , socket . timeout ) :
raise NetworkTimeout ( msg )
elif isinstance ( error , SSLError ) and 'timed ou... |
def create ( self , name , plugin_data_dir , gzip = False ) :
"""Create a new plugin .
Args :
name ( string ) : The name of the plugin . The ` ` : latest ` ` tag is
optional , and is the default if omitted .
plugin _ data _ dir ( string ) : Path to the plugin data directory .
Plugin data directory must co... | self . client . api . create_plugin ( name , plugin_data_dir , gzip )
return self . get ( name ) |
def _gap_progenitor_setup ( self ) :
"""Setup an Orbit instance that ' s the progenitor integrated backwards""" | self . _gap_progenitor = self . _progenitor ( ) . flip ( )
# new orbit , flip velocities
# Make sure we do not use physical coordinates
self . _gap_progenitor . turn_physical_off ( )
# Now integrate backward in time until tdisrupt
ts = numpy . linspace ( 0. , self . _tdisrupt , 1001 )
self . _gap_progenitor . integrate... |
def hazard_class_style ( layer , classification , display_null = False ) :
"""Set colors to the layer according to the hazard .
: param layer : The layer to style .
: type layer : QgsVectorLayer
: param display _ null : If we should display the null hazard zone . Default to
False .
: type display _ null :... | categories = [ ]
# Conditional styling
attribute_table_styles = [ ]
for hazard_class , ( color , label ) in list ( classification . items ( ) ) :
if hazard_class == not_exposed_class [ 'key' ] and not display_null : # We don ' t want to display the null value ( not exposed ) .
# We skip it .
continue
... |
def generate_tokens ( lines , flags ) :
"""This is a rewrite of pypy . module . parser . pytokenize . generate _ tokens since
the original function is not RPYTHON ( uses yield )
It was also slightly modified to generate Token instances instead
of the original 5 - tuples - - it ' s now a 4 - tuple of
* the T... | token_list = [ ]
lnum = parenlev = continued = 0
namechars = NAMECHARS
numchars = NUMCHARS
contstr , needcont = '' , 0
contline = None
indents = [ 0 ]
altindents = [ 0 ]
last_comment = ''
parenlevstart = ( 0 , 0 , "" )
# make the annotator happy
endDFA = automata . DFA ( [ ] , [ ] )
# make the annotator happy
line = ''... |
def InputDNAQuantitySplines ( seq_length , n_bases = 10 , name = "DNASmoothPosition" , ** kwargs ) :
"""Convenience wrapper around keras . layers . Input :
` Input ( ( seq _ length , n _ bases ) , name = name , * * kwargs ) `""" | return Input ( ( seq_length , n_bases ) , name = name , ** kwargs ) |
def update_sql ( table , filter , updates ) :
'''> > > update _ sql ( ' tbl ' , { ' foo ' : ' a ' , ' bar ' : 1 } , { ' bar ' : 2 , ' baz ' : ' b ' } )
( ' UPDATE tbl SET bar = $ 1 , baz = $ 2 WHERE bar = $ 3 AND foo = $ 4 ' , [ 2 , ' b ' , 1 , ' a ' ] )''' | where_keys , where_vals = _split_dict ( filter )
up_keys , up_vals = _split_dict ( updates )
changes = _pairs ( up_keys , sep = ', ' )
where = _pairs ( where_keys , start = len ( up_keys ) + 1 )
sql = 'UPDATE {} SET {} WHERE {}' . format ( table , changes , where )
return sql , up_vals + where_vals |
def tokens ( self , instance ) :
"""Just display current acceptable TOTP tokens""" | if not instance . pk : # e . g . : Use will create a new TOTP entry
return "-"
totp = TOTP ( instance . bin_key , instance . step , instance . t0 , instance . digits )
tokens = [ ]
for offset in range ( - instance . tolerance , instance . tolerance + 1 ) :
totp . drift = instance . drift + offset
tokens . a... |
def Process ( self , path ) :
"""Processes a given path .
Args :
path : Path ( as a string ) to post - process .
Returns :
A list of paths with environment variables replaced with their
values . If the mapping had a list of values for a particular variable ,
instead of just one value , then all possible... | path = re . sub ( self . SYSTEMROOT_RE , r"%systemroot%" , path , count = 1 )
path = re . sub ( self . SYSTEM32_RE , r"%systemroot%\\system32" , path , count = 1 )
matches_iter = self . WIN_ENVIRON_REGEX . finditer ( path )
var_names = set ( m . group ( 1 ) . lower ( ) for m in matches_iter )
results = [ path ]
for var... |
def envvar_constructor ( loader , node ) :
"""Tag constructor to use environment variables in YAML files . Usage :
- ! TAG VARIABLE
raise while loading the document if variable does not exists
- ! TAG VARIABLE : = DEFAULT _ VALUE
For instance :
credentials :
user : ! env USER : = root
group : ! env GR... | value = loader . construct_python_unicode ( node )
data = value . split ( ':=' , 1 )
if len ( data ) == 2 :
var , default = data
return os . environ . get ( var , default )
else :
return os . environ [ value ] |
def get_transcript_format ( transcript_content ) :
"""Returns transcript format .
Arguments :
transcript _ content ( str ) : Transcript file content .""" | try :
sjson_obj = json . loads ( transcript_content )
except ValueError : # With error handling ( set to ' ERROR _ RAISE ' ) , we will be getting
# the exception if something went wrong in parsing the transcript .
srt_subs = SubRipFile . from_string ( transcript_content , error_handling = SubRipFile . ERROR_RAI... |
def parsePortSpec ( spec , separator = '-' ) :
'''Parses a port specification in two forms into the same form .
In the first form the specification is just an integer . In this case a
tuple is returned containing the same integer twice .
In the second form the specification is two numbers separated by a hyphe... | x = list ( map ( lambda x : x . strip ( ) , spec . split ( separator ) ) )
return tuple ( map ( int , x * ( 3 - len ( x ) ) ) ) |
def get_field_info ( self , field ) :
"""Given an instance of a serializer field , return a dictionary
of metadata about it .""" | field_info = collections . OrderedDict ( )
field_info [ 'type' ] = self . label_lookup [ field ]
field_info [ 'required' ] = getattr ( field , 'required' , False )
attrs = [ 'read_only' , 'label' , 'help_text' , 'allow_null' , 'min_length' , 'max_length' , 'min_value' , 'max_value' , ]
# Handle default attribute
defaul... |
def minmax_auto_scale ( img , as_uint16 ) :
"""Utility function for rescaling all pixel values of input image to fit the range of uint8.
Rescaling method is min - max , which is all pixel values are normalized to [ 0 , 1 ] by using img . min ( ) and img . max ( )
and then are scaled up by 255 times .
If the a... | if as_uint16 :
output_high = 65535
output_type = np . uint16
else :
output_high = 255
output_type = np . uint8
return rescale_pixel_intensity ( img , input_low = img . min ( ) , input_high = img . max ( ) , output_low = 0 , output_high = output_high , output_type = output_type ) |
def passthrough ( args ) :
"""% prog passthrough chrY . vcf chrY . new . vcf
Pass through Y and MT vcf .""" | p = OptionParser ( passthrough . __doc__ )
opts , args = p . parse_args ( args )
if len ( args ) != 2 :
sys . exit ( not p . print_help ( ) )
vcffile , newvcffile = args
fp = open ( vcffile )
fw = open ( newvcffile , "w" )
gg = [ "0/0" , "0/1" , "1/1" ]
for row in fp :
if row [ 0 ] == "#" :
print ( row ... |
def _add_vcf_header_sample_cl ( in_file , items , base_file ) :
"""Add phenotype information to a VCF header .
Encode tumor / normal relationships in VCF header .
Could also eventually handle more complicated pedigree information if useful .""" | paired = vcfutils . get_paired ( items )
if paired :
toadd = [ "##SAMPLE=<ID=%s,Genomes=Tumor>" % paired . tumor_name ]
if paired . normal_name :
toadd . append ( "##SAMPLE=<ID=%s,Genomes=Germline>" % paired . normal_name )
toadd . append ( "##PEDIGREE=<Derived=%s,Original=%s>" % ( paired . tumo... |
def create_data_types ( self ) :
"""Map of standard playbook variable types to create method .""" | return { 'Binary' : self . create_binary , 'BinaryArray' : self . create_binary_array , 'KeyValue' : self . create_key_value , 'KeyValueArray' : self . create_key_value_array , 'String' : self . create_string , 'StringArray' : self . create_string_array , 'TCEntity' : self . create_tc_entity , 'TCEntityArray' : self . ... |
def _remove_untraceable ( self ) :
"""Remove from the tracer those wires that CompiledSimulation cannot track .
Create _ probe _ mapping for wires only traceable via probes .""" | self . _probe_mapping = { }
wvs = { wv for wv in self . tracer . wires_to_track if self . _traceable ( wv ) }
self . tracer . wires_to_track = wvs
self . tracer . _wires = { wv . name : wv for wv in wvs }
self . tracer . trace . __init__ ( wvs ) |
def check_no_multiple_handlers ( self , resource ) :
'''The same verb cannot be repeated on several endpoints .''' | seen = [ ]
errors = [ ]
msg = 'HTTP verb "{}" associated to more than one endpoint in "{}".'
for method in resource . callbacks :
for op in getattr ( method , 'swagger_ops' ) :
if op in seen :
errors . append ( msg . format ( op , resource . __name__ ) )
else :
seen . append ... |
def insertFromMimeData ( self , data ) :
"""Paste the MIME data at the current cursor position .
This method also adds another undo - object to the undo - stack .""" | undoObj = UndoPaste ( self , data , self . pasteCnt )
self . pasteCnt += 1
self . qteUndoStack . push ( undoObj ) |
def main ( ) :
"""Entry point""" | client_1 = MessageBot ( "verne" , "Jules Verne" )
client_1 . start ( )
client_1 . connect ( "127.0.0.1" )
client_2 = MessageBot ( "adams" , "Douglas Adams" )
client_2 . start ( )
client_2 . connect ( "127.0.0.1" )
herald_1 = Herald ( client_1 )
herald_1 . start ( )
herald_2 = Herald ( client_2 )
herald_2 . start ( )
ha... |
def parse_response ( self , block = True , timeout = 0 ) :
"Parse the response from a publish / subscribe command" | connection = self . connection
if connection is None :
raise RuntimeError ( 'pubsub connection not set: ' 'did you forget to call subscribe() or psubscribe()?' )
if not block and not connection . can_read ( timeout = timeout ) :
return None
return self . _execute ( connection , connection . read_response ) |
def _new_instance ( cls , children = None , connector = None , negated = False ) :
"""Create a new instance of this class when new Nodes ( or subclasses ) are
needed in the internal code in this class . Normally , it just shadows
_ _ init _ _ ( ) . However , subclasses with an _ _ init _ _ signature that aren '... | obj = QBase ( children , connector , negated )
obj . __class__ = cls
return obj |
def run ( self , from_email , recipients , message ) :
"""This does the dirty work . Connects to Amazon SES via boto and fires
off the message .
: param str from _ email : The email address the message will show as
originating from .
: param list recipients : A list of email addresses to send the
message ... | self . _open_ses_conn ( )
try : # We use the send _ raw _ email func here because the Django
# EmailMessage object we got these values from constructs all of
# the headers and such .
self . connection . send_raw_email ( source = from_email , destinations = recipients , raw_message = dkim_sign ( message ) , )
except... |
def set_argsx ( self , arguments , * args ) :
"""Setup the command line arguments , the first item must be an ( absolute ) filename
to run . Variadic function , must be NULL terminated .""" | return lib . zproc_set_argsx ( self . _as_parameter_ , arguments , * args ) |
def validate_value_range ( self , value ) :
"""Args :
value : Throws DsdlException if this value cannot be represented by this type .""" | low , high = self . value_range
if not low <= value <= high :
error ( 'Value [%s] is out of range %s' , value , self . value_range ) |
def mpris ( self ) :
"""Get the current output format and return it .""" | if self . _kill :
raise KeyboardInterrupt
current_player_id = self . _player_details . get ( "id" )
cached_until = self . py3 . CACHE_FOREVER
if self . _player is None :
text = self . format_none
color = self . py3 . COLOR_BAD
composite = [ { "full_text" : text , "color" : color } ]
self . _data = {... |
def get_auth ( ) :
"""Return a tuple for authenticating a user
If not successful raise ` ` AgileError ` ` .""" | auth = get_auth_from_env ( )
if auth [ 0 ] and auth [ 1 ] :
return auth
home = os . path . expanduser ( "~" )
config = os . path . join ( home , '.gitconfig' )
if not os . path . isfile ( config ) :
raise GithubException ( 'No .gitconfig available' )
parser = configparser . ConfigParser ( )
parser . read ( conf... |
def rejectEdit ( self ) :
"""Cancels the edit for this label .""" | if self . _lineEdit :
self . _lineEdit . hide ( )
self . editingCancelled . emit ( ) |
def open_connection ( func ) :
"""Decorate a function to create a ` nds2 . connection ` if required""" | @ wraps ( func )
def wrapped_func ( * args , ** kwargs ) : # pylint : disable = missing - docstring
if kwargs . get ( 'connection' , None ) is None :
try :
host = kwargs . pop ( 'host' )
except KeyError :
raise TypeError ( "one of `connection` or `host` is required " "to quer... |
def inject ( self , other ) :
"""Add two compatible ` Series ` along their shared x - axis values .
Parameters
other : ` Series `
a ` Series ` whose xindex intersects with ` self . xindex `
Returns
out : ` Series `
the sum of ` self ` and ` other ` along their shared x - axis values
Raises
ValueErro... | # check Series compatibility
self . is_compatible ( other )
if ( self . xunit == second ) and ( other . xspan [ 0 ] < self . xspan [ 0 ] ) :
other = other . crop ( start = self . xspan [ 0 ] )
if ( self . xunit == second ) and ( other . xspan [ 1 ] > self . xspan [ 1 ] ) :
other = other . crop ( end = self . xs... |
def copy ( self ) :
"""Returns a copy of this UnionProducts .
Edits to the copy ' s mappings will not affect the product mappings in the original .
The copy is shallow though , so edits to the copy ' s product values will mutate the original ' s
product values .
: API : public
: rtype : : class : ` UnionP... | products_by_target = defaultdict ( OrderedSet )
for key , value in self . _products_by_target . items ( ) :
products_by_target [ key ] = OrderedSet ( value )
return UnionProducts ( products_by_target = products_by_target ) |
def GetMessages ( self , formatter_mediator , event ) :
"""Determines the formatted message strings for an event object .
Args :
formatter _ mediator ( FormatterMediator ) : mediates the interactions
between formatters and other components , such as storage and Windows
EventLog resources .
event ( EventOb... | event_values = event . CopyToDict ( )
# TODO : clean up the default formatter and add a test to make sure
# it is clear how it is intended to work .
text_pieces = [ ]
for key , value in event_values . items ( ) :
if key in definitions . RESERVED_VARIABLE_NAMES :
continue
text_pieces . append ( '{0:s}: {... |
def has_flag ( conf , atom , flag ) :
'''Verify if the given package or DEPEND atom has the given flag .
Warning : This only works if the configuration files tree is in the correct
format ( the one enforced by enforce _ nice _ config )
CLI Example :
. . code - block : : bash
salt ' * ' portage _ config . ... | if flag in get_flags_from_package_conf ( conf , atom ) :
return True
return False |
def generation ( self ) :
"""Returns the number of ancestors that are dictionaries""" | if not self . parent :
return 0
elif self . parent . is_dict :
return 1 + self . parent . generation
else :
return self . parent . generation |
def get_handler_stats ( self ) :
'''Return handler read statistics
Returns a dictionary of managed handler data read statistics . The
format is primarily controlled by the
: func : ` SocketStreamCapturer . dump _ all _ handler _ stats ` function : :
< capture address > : < list of handler capture statistics... | return { address : stream_capturer [ 0 ] . dump_all_handler_stats ( ) for address , stream_capturer in self . _stream_capturers . iteritems ( ) } |
def get_column ( column_name , node , context ) :
"""Get a column by name from the selectable .
Args :
column _ name : str , name of the column to retrieve .
node : SqlNode , the node the column is being retrieved for .
context : CompilationContext , compilation specific metadata .
Returns :
column , th... | column = try_get_column ( column_name , node , context )
if column is None :
selectable = get_node_selectable ( node , context )
raise AssertionError ( u'Column "{}" not found in selectable "{}". Columns present are {}. ' u'Context is {}.' . format ( column_name , selectable . original , [ col . name for col in... |
def sample_truncated_gaussian ( mu = 0 , sigma = 1 , lb = - np . Inf , ub = np . Inf ) :
"""Sample a truncated normal with the specified params . This
is not the most stable way but it works as long as the
truncation region is not too far from the mean .""" | # Broadcast arrays to be of the same shape
mu , sigma , lb , ub = np . broadcast_arrays ( mu , sigma , lb , ub )
shp = mu . shape
if np . allclose ( sigma , 0.0 ) :
return mu
cdflb = normal_cdf ( lb , mu , sigma )
cdfub = normal_cdf ( ub , mu , sigma )
# Sample uniformly from the CDF
cdfsamples = cdflb + np . rando... |
def write_moc_fits ( moc , filename , ** kwargs ) :
"""Write a MOC as a FITS file .
Any additional keyword arguments are passed to the
astropy . io . fits . HDUList . writeto method .""" | tbhdu = write_moc_fits_hdu ( moc )
prihdr = fits . Header ( )
prihdu = fits . PrimaryHDU ( header = prihdr )
hdulist = fits . HDUList ( [ prihdu , tbhdu ] )
hdulist . writeto ( filename , ** kwargs ) |
def generate_anchors ( base_size = 16 , ratios = [ 0.5 , 1 , 2 ] , scales = 2 ** np . arange ( 3 , 6 ) ) :
"""Generate anchor ( reference ) windows by enumerating aspect ratios X
scales wrt a reference ( 0 , 0 , 15 , 15 ) window .""" | base_anchor = np . array ( [ 1 , 1 , base_size , base_size ] , dtype = 'float32' ) - 1
ratio_anchors = _ratio_enum ( base_anchor , ratios )
anchors = np . vstack ( [ _scale_enum ( ratio_anchors [ i , : ] , scales ) for i in range ( ratio_anchors . shape [ 0 ] ) ] )
return anchors |
def get_user_agent ( ) :
"""Construct and informative user - agent string .
Includes OS version and docker version info
Not thread - safe
: return :""" | global user_agent_string
if user_agent_string is None : # get OS type
try :
sysinfo = subprocess . check_output ( 'lsb_release -i -r -s' . split ( ' ' ) )
dockerinfo = subprocess . check_output ( 'docker --version' . split ( ' ' ) )
user_agent_string = ' ' . join ( [ sysinfo . replace ( '\t'... |
def lint ( session ) :
"""Run linters .
Returns a failure if the linters find linting errors or sufficiently
serious code quality issues .""" | session . install ( 'flake8' , * LOCAL_DEPS )
session . install ( '-e' , '.' )
session . run ( 'flake8' , os . path . join ( 'google' , 'cloud' , 'bigquery_storage_v1beta1' ) )
session . run ( 'flake8' , 'tests' ) |
def xpathNextChild ( self , ctxt ) :
"""Traversal function for the " child " direction The child axis
contains the children of the context node in document order .""" | if ctxt is None :
ctxt__o = None
else :
ctxt__o = ctxt . _o
ret = libxml2mod . xmlXPathNextChild ( ctxt__o , self . _o )
if ret is None :
raise xpathError ( 'xmlXPathNextChild() failed' )
__tmp = xmlNode ( _obj = ret )
return __tmp |
def _process_data ( self , obj ) :
"""Processes command results .""" | assert len ( self . _waiters ) > 0 , ( type ( obj ) , obj )
waiter , encoding , cb = self . _waiters . popleft ( )
if isinstance ( obj , RedisError ) :
if isinstance ( obj , ReplyError ) :
if obj . args [ 0 ] . startswith ( 'READONLY' ) :
obj = ReadOnlyError ( obj . args [ 0 ] )
_set_excepti... |
def activate ( self , token ) :
"""Make a copy of the received token and call ` self . _ activate ` .""" | if watchers . worth ( 'MATCHER' , 'DEBUG' ) : # pragma : no cover
watchers . MATCHER . debug ( "Node <%s> activated with token %r" , self , token )
return self . _activate ( token . copy ( ) ) |
def get_group_id ( self , uuid = None ) :
"""Get group id based on uuid .
Args :
uuid ( str ) : optional uuid . defaults to self . cuuid
Raises :
PyLmodUnexpectedData : No group data was returned .
requests . RequestException : Exception connection error
Returns :
int : numeric group id""" | group_data = self . get_group ( uuid )
try :
return group_data [ 'response' ] [ 'docs' ] [ 0 ] [ 'id' ]
except ( KeyError , IndexError ) :
failure_message = ( 'Error in get_group response data - ' 'got {0}' . format ( group_data ) )
log . exception ( failure_message )
raise PyLmodUnexpectedData ( failur... |
def _is_chinese_char ( self , cp ) :
"""Checks whether CP is the codepoint of a CJK character .""" | # This defines a " chinese character " as anything in the CJK Unicode block :
# https : / / en . wikipedia . org / wiki / CJK _ Unified _ Ideographs _ ( Unicode _ block )
# Note that the CJK Unicode block is NOT all Japanese and Korean characters ,
# despite its name . The modern Korean Hangul alphabet is a different b... |
def _backlog ( self , data ) :
"""Find all the datagrepper messages between ' then ' and ' now ' .
Put those on our work queue .
Should be called in a thread so as not to block the hub at startup .""" | try :
data = json . loads ( data )
except ValueError as e :
self . log . info ( "Status contents are %r" % data )
self . log . exception ( e )
self . log . info ( "Skipping backlog retrieval." )
return
last = data [ 'message' ] [ 'body' ]
if isinstance ( last , str ) :
last = json . loads ( last... |
def to_import ( import_ ) :
"""Serializes import to id string
: param import _ : object to serialize
: return : string id""" | from sevenbridges . models . storage_import import Import
if not import_ :
raise SbgError ( 'Import is required!' )
elif isinstance ( import_ , Import ) :
return import_ . id
elif isinstance ( import_ , six . string_types ) :
return import_
else :
raise SbgError ( 'Invalid import parameter!' ) |
def initialize_callbacks ( self ) :
"""Initializes all callbacks and save the result in the
` ` callbacks _ ` ` attribute .
Both ` ` default _ callbacks ` ` and ` ` callbacks ` ` are used ( in that
order ) . Callbacks may either be initialized or not , and if
they don ' t have a name , the name is inferred ... | callbacks_ = [ ]
class Dummy : # We cannot use None as dummy value since None is a
# legitimate value to be set .
pass
for name , cb in self . _uniquely_named_callbacks ( ) : # check if callback itself is changed
param_callback = getattr ( self , 'callbacks__' + name , Dummy )
if param_callback is not Dummy... |
def _list_packages ( self , args ) :
'''List files for an installed package''' | packages = self . _pkgdb_fun ( 'list_packages' , self . db_conn )
for package in packages :
if self . opts [ 'verbose' ] :
status_msg = ',' . join ( package )
else :
status_msg = package [ 0 ]
self . ui . status ( status_msg ) |
def _qsturng ( p , r , v ) :
"""scalar version of qsturng""" | # # print ' q ' , p
# r is interpolated through the q to y here we only need to
# account for when p and / or v are not found in the table .
global A , p_keys , v_keys
if p < .1 or p > .999 :
raise ValueError ( 'p must be between .1 and .999' )
if p < .9 :
if v < 2 :
raise ValueError ( 'v must be > 2 wh... |
def run_has_samplesheet ( fc_dir , config , require_single = True ) :
"""Checks if there ' s a suitable SampleSheet . csv present for the run""" | fc_name , _ = flowcell . parse_dirname ( fc_dir )
sheet_dirs = config . get ( "samplesheet_directories" , [ ] )
fcid_sheet = { }
for ss_dir in ( s for s in sheet_dirs if os . path . exists ( s ) ) :
with utils . chdir ( ss_dir ) :
for ss in glob . glob ( "*.csv" ) :
fc_ids = _get_flowcell_id ( s... |
def create_partitions ( self , topic_partitions , timeout_ms = None , validate_only = False ) :
"""Create additional partitions for an existing topic .
: param topic _ partitions : A map of topic name strings to NewPartition objects .
: param timeout _ ms : Milliseconds to wait for new partitions to be
create... | version = self . _matching_api_version ( CreatePartitionsRequest )
timeout_ms = self . _validate_timeout ( timeout_ms )
if version == 0 :
request = CreatePartitionsRequest [ version ] ( topic_partitions = [ self . _convert_create_partitions_request ( topic_name , new_partitions ) for topic_name , new_partitions in ... |
def gff3_verifier ( entries , line = None ) :
"""Raises error if invalid GFF3 format detected
Args :
entries ( list ) : A list of GFF3Entry instances
line ( int ) : Line number of first entry
Raises :
FormatError : Error when GFF3 format incorrect with descriptive message""" | regex = r'^[a-zA-Z0-9.:^*$@!+_?-|]+\t.+\t.+\t\d+\t\d+\t' + r'\d*\.?\d*\t[+-.]\t[.0-2]\t.+{0}$' . format ( os . linesep )
delimiter = r'\t'
for entry in entries :
try :
entry_verifier ( [ entry . write ( ) ] , regex , delimiter )
except FormatError as error : # Format info on what entry error came from
... |
def as_dict ( self ) :
"""json friendly dict representation of Kpoints""" | d = { "comment" : self . comment , "nkpoints" : self . num_kpts , "generation_style" : self . style . name , "kpoints" : self . kpts , "usershift" : self . kpts_shift , "kpts_weights" : self . kpts_weights , "coord_type" : self . coord_type , "labels" : self . labels , "tet_number" : self . tet_number , "tet_weight" : ... |
def show ( self , notebook = notebook_display ) :
"""Display cluster properties and scaling relation parameters .""" | print ( "\nCluster Ensemble:" )
if notebook is True :
display ( self . _df )
elif notebook is False :
print ( self . _df )
self . massrich_parameters ( ) |
def next ( self ) :
"""A ` next ` that caches the returned results . Together with the
slightly different ` _ _ iter _ _ ` , these cursors can be iterated over
more than once .""" | if self . __tailable :
return PymongoCursor . next ( self )
try :
ret = PymongoCursor . next ( self )
except StopIteration :
self . __fullcache = True
raise
self . __itercache . append ( ret )
return ret |
def ordering_for ( self , term , view ) :
"""Return ordering ( model field chain ) for term ( serializer field chain )
or None if invalid
Raise ImproperlyConfigured if serializer _ class not set on view""" | if not self . _is_allowed_term ( term , view ) :
return None
serializer = self . _get_serializer_class ( view ) ( )
serializer_chain = term . split ( '.' )
model_chain = [ ]
for segment in serializer_chain [ : - 1 ] :
field = serializer . get_all_fields ( ) . get ( segment )
if not ( field and field . sourc... |
def participating_ec_states ( self ) :
'''The state of each execution context this component is participating
in .''' | with self . _mutex :
if not self . _participating_ec_states :
if self . participating_ecs :
states = [ ]
for ec in self . participating_ecs :
states . append ( self . _get_ec_state ( ec ) )
self . _participating_ec_states = states
else :
... |
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