signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def to_lower ( cls ) : # NOQA
"""Return a list of all the fields that should be lowercased
This is done on fields with ` lower = True ` .""" | email = cls . get_fields_by_class ( EmailType )
lower = cls . get_fields_by_prop ( 'lower' , True ) + email
return list ( set ( email + lower ) ) |
def describe ( self , bucket , descriptor = None ) :
"""https : / / github . com / frictionlessdata / tableschema - pandas - py # storage""" | # Set descriptor
if descriptor is not None :
self . __descriptors [ bucket ] = descriptor
# Get descriptor
else :
descriptor = self . __descriptors . get ( bucket )
if descriptor is None :
dataframe = self . __dataframes [ bucket ]
descriptor = self . __mapper . restore_descriptor ( datafram... |
def addTask ( self , task ) :
"""Add a task to the task set .""" | with self . regcond :
self . taskset . append ( task )
task . add_callback ( 'resolved' , self . child_done , self . numtasks )
self . numtasks += 1
self . count += 1
task . initialize ( self )
task . start ( ) |
def get_realtime_alarm ( username , auth , url ) :
"""Takes in no param as input to fetch RealTime Alarms from HP IMC RESTFUL API
: param username OpeatorName , String type . Required . Default Value " admin " . Checks the operator
has the privileges to view the Real - Time Alarms .
: param auth : requests au... | f_url = url + "/imcrs/fault/faultRealTime?operatorName=" + username
response = requests . get ( f_url , auth = auth , headers = HEADERS )
try :
realtime_alarm_list = ( json . loads ( response . text ) )
return realtime_alarm_list [ 'faultRealTime' ] [ 'faultRealTimeList' ]
except requests . exceptions . Request... |
def from_array ( array ) :
"""Deserialize a new ShippingOption from a given dictionary .
: return : new ShippingOption instance .
: rtype : ShippingOption""" | if array is None or not array :
return None
# end if
assert_type_or_raise ( array , dict , parameter_name = "array" )
data = { }
data [ 'id' ] = u ( array . get ( 'id' ) )
data [ 'title' ] = u ( array . get ( 'title' ) )
data [ 'prices' ] = LabeledPrice . from_array_list ( array . get ( 'prices' ) , list_level = 1 ... |
def print_functions ( self , d ) :
"""Export all the functions to dot files""" | for c in self . contracts :
for f in c . functions :
f . cfg_to_dot ( os . path . join ( d , '{}.{}.dot' . format ( c . name , f . name ) ) ) |
def _read_state_variables ( self ) :
"""Reads the stateVariable information from the xml - file .
The information we like to extract are name and dataType so we
can assign them later on to FritzActionArgument - instances .
Returns a dictionary : key : value = name : dataType""" | nodes = self . root . iterfind ( './/ns:stateVariable' , namespaces = { 'ns' : self . namespace } )
for node in nodes :
key = node . find ( self . nodename ( 'name' ) ) . text
value = node . find ( self . nodename ( 'dataType' ) ) . text
self . state_variables [ key ] = value |
def update_policy_configuration ( self , configuration , project , configuration_id ) :
"""UpdatePolicyConfiguration .
Update a policy configuration by its ID .
: param : class : ` < PolicyConfiguration > < azure . devops . v5_0 . policy . models . PolicyConfiguration > ` configuration : The policy configuratio... | route_values = { }
if project is not None :
route_values [ 'project' ] = self . _serialize . url ( 'project' , project , 'str' )
if configuration_id is not None :
route_values [ 'configurationId' ] = self . _serialize . url ( 'configuration_id' , configuration_id , 'int' )
content = self . _serialize . body ( c... |
def checked_open ( filename , log = None , quiet = False ) :
"""Open and validate the given metafile .
Optionally provide diagnostics on the passed logger , for
invalid metafiles , which then just cause a warning but no exception .
" quiet " can supress that warning .""" | with open ( filename , "rb" ) as handle :
raw_data = handle . read ( )
data = bencode . bdecode ( raw_data )
try :
check_meta ( data )
if raw_data != bencode . bencode ( data ) :
raise ValueError ( "Bad bencoded data - dict keys out of order?" )
except ValueError as exc :
if log : # Warn about i... |
def sign_up ( self ) :
"""Signs up a participant for the experiment .
This is done using a POST request to the / participant / endpoint .""" | self . log ( "Bot player signing up." )
self . subscribe_to_quorum_channel ( )
while True :
url = ( "{host}/participant/{self.worker_id}/" "{self.hit_id}/{self.assignment_id}/" "debug?fingerprint_hash={hash}&recruiter=bots:{bot_name}" . format ( host = self . host , self = self , hash = uuid . uuid4 ( ) . hex , bot... |
def compose_all ( stream , Loader = Loader ) :
"""Parse all YAML documents in a stream
and produce corresponding representation trees .""" | loader = Loader ( stream )
try :
while loader . check_node ( ) :
yield loader . get_node ( )
finally :
loader . dispose ( ) |
def write ( self , obj , ** kwargs ) :
"""we are going to write this as a frame table""" | name = obj . name or 'values'
obj , self . levels = self . validate_multiindex ( obj )
cols = list ( self . levels )
cols . append ( name )
obj . columns = cols
return super ( ) . write ( obj = obj , ** kwargs ) |
def _calc_F_guess ( self , alpha , predictions , probabilities ) :
"""Calculate an estimate of the F - measure based on the scores""" | num = np . sum ( predictions . T * probabilities , axis = 1 )
den = np . sum ( ( 1 - alpha ) * probabilities + alpha * predictions . T , axis = 1 )
F_guess = num / den
# Ensure guess is not undefined
F_guess [ den == 0 ] = 0.5
return F_guess |
def advisory_lock ( dax , key , lock_mode = LockMode . wait , xact = False ) :
"""A context manager for obtaining a lock , executing code , and then releasing
the lock .
A boolean value is passed to the block indicating whether or not the lock was
obtained .
: dax : a DataAccess instance
: key : either a ... | if lock_mode == LockMode . wait :
obtain_lock ( dax , key , lock_mode , xact )
else :
got_lock = obtain_lock ( dax , key , lock_mode , xact )
if not got_lock :
if lock_mode == LockMode . error :
raise Exception ( "Unable to obtain advisory lock {}" . format ( key ) )
else : # loc... |
def add_tags_to_bookmark ( self , bookmark_id , tags ) :
"""Add tags to to a bookmark .
The identified bookmark must belong to the current user .
: param bookmark _ id : ID of the bookmark to delete .
: param tags : Comma separated tags to be applied .""" | url = self . _generate_url ( 'bookmarks/{0}/tags' . format ( bookmark_id ) )
params = dict ( tags = tags )
return self . post ( url , params ) |
def reconnect ( self , exc = None ) :
"""Schedule reconnect after connection has been unexpectedly lost .""" | # Reset protocol binding before starting reconnect
self . protocol = None
if not self . closing :
log . warning ( 'disconnected from Rflink, reconnecting' )
self . loop . create_task ( self . connect ( ) ) |
def sphere ( target , pore_diameter = 'pore.diameter' , throat_area = 'throat.area' ) :
r"""Calculates internal surface area of pore bodies assuming they are spherical
then subtracts the area of the neighboring throats in a crude way , by
simply considering the throat cross - sectional area , thus not accountin... | network = target . project . network
R = target [ pore_diameter ] / 2
Asurf = 4 * _np . pi * R ** 2
Tn = network . find_neighbor_throats ( pores = target . Ps , flatten = False )
Tsurf = _np . array ( [ _np . sum ( network [ throat_area ] [ Ts ] ) for Ts in Tn ] )
value = Asurf - Tsurf
return value |
def create_http_method ( logic : Callable , http_method : str , handle_http : Callable , before : Callable = None , after : Callable = None ) -> Callable :
"""Create a handler method to be used in a handler class .
: param callable logic : The underlying function to execute with the
parsed and validated paramet... | @ functools . wraps ( logic )
def fn ( handler , * args , ** kwargs ) :
if before is not None and callable ( before ) :
before ( )
result = handle_http ( handler , args , kwargs , logic )
if after is not None and callable ( after ) :
after ( result )
return result
return fn |
def protect ( self , password = None , read_protect = False , protect_from = 0 ) :
"""Protect a FeliCa Lite Tag .
A FeliCa Lite Tag can be provisioned with a custom password
( or the default manufacturer key if the password is an empty
string or bytearray ) to ensure that data retrieved by future
read opera... | return super ( FelicaLite , self ) . protect ( password , read_protect , protect_from ) |
def list_numbers ( self , ** kwargs ) : # noqa : E501
"""Get your numbers # noqa : E501
List all your purchased numbers # noqa : E501
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass async = True
> > > thread = api . list _ numbers ( async = True )... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async' ) :
return self . list_numbers_with_http_info ( ** kwargs )
# noqa : E501
else :
( data ) = self . list_numbers_with_http_info ( ** kwargs )
# noqa : E501
return data |
def extract ( src_vector : str , burn_attribute : str , src_raster : list , dst_names : list , dst_dir : str , src_raster_template : str = None , gdal_dtype : int = 4 , n_jobs : int = 1 ) :
"""Extract values from list of single band raster for pixels overlapping with a vector data .
The extracted data will be sto... | if src_raster_template is None :
src_raster_template = src_raster [ 0 ]
path_rasterized = os . path . join ( dst_dir , f"burn_attribute_rasterized_{burn_attribute}.tif" )
paths_extracted_aux = { ele : os . path . join ( dst_dir , f"{ele}.npy" ) for ele in [ f"aux_vector_{burn_attribute}" , "aux_coord_x" , "aux_coor... |
def add_next_tick_callback ( self , callback ) :
'''Add callback to be invoked once on the next tick of the event loop .
Args :
callback ( callable ) :
A callback function to execute on the next tick .
Returns :
NextTickCallback : can be used with ` ` remove _ next _ tick _ callback ` `
. . note : :
N... | from . . server . callbacks import NextTickCallback
cb = NextTickCallback ( self , None )
return self . _add_session_callback ( cb , callback , one_shot = True , originator = self . add_next_tick_callback ) |
def get_best_experiment_sets ( nets , expvars , num ) :
'''given the network and the experimental variables , and the bound on the size of an experiment set
returns the experiments as a ` ` TermSet ` ` object [ instance ] .''' | netsf = nets . to_file ( )
expvarsf = expvars . to_file ( )
best = - 1
best_solutions = [ ]
best_found = False
i = 0
while i < num and not best_found :
i += 1
num_exp = String2TermSet ( 'pexperiment(' + str ( i ) + ')' )
num_expf = num_exp . to_file ( )
prg = [ netsf , expvarsf , num_expf , find_best_ex... |
def symbols_to_prob ( symbols ) :
'''Return a dict mapping symbols to probability .
input :
symbols : iterable of hashable items
works well if symbols is a zip of iterables''' | myCounter = Counter ( symbols )
N = float ( len ( list ( symbols ) ) )
# symbols might be a zip object in python 3
for k in myCounter :
myCounter [ k ] /= N
return myCounter |
def get_utc_date ( entry ) :
"""Return datestamp converted to UTC""" | if entry [ 'numeric_date_stamp' ] == '0' :
entry [ 'numeric_date_stamp_utc' ] = '0'
return entry
else :
if '.' in entry [ 'numeric_date_stamp' ] :
t = datetime . strptime ( entry [ 'numeric_date_stamp' ] , '%Y%m%d%H%M%S.%f' )
else :
t = datetime . strptime ( entry [ 'numeric_date_stamp' ... |
def dict ( self ) :
"""Return this ` ` SoSOptions ` ` option values as a dictionary of
argument name to value mappings .
: returns : a name : value dictionary of option values .""" | odict = { }
for arg in _arg_names :
value = getattr ( self , arg )
# Do not attempt to store preset option values in presets
if arg in ( 'add_preset' , 'del_preset' , 'desc' , 'note' ) :
value = None
odict [ arg ] = value
return odict |
def _partition_operation_sql ( self , operation , settings = None , from_part = None ) :
"""Performs some operation over partition
: param db : Database object to execute operation on
: param operation : Operation to execute from SystemPart . OPERATIONS set
: param settings : Settings for executing request to... | operation = operation . upper ( )
assert operation in self . OPERATIONS , "operation must be in [%s]" % comma_join ( self . OPERATIONS )
sql = "ALTER TABLE `%s`.`%s` %s PARTITION %s" % ( self . _database . db_name , self . table , operation , self . partition )
if from_part is not None :
sql += " FROM %s" % from_pa... |
def _run_smoove ( full_bams , sr_bams , disc_bams , work_dir , items ) :
"""Run lumpy - sv using smoove .""" | batch = sshared . get_cur_batch ( items )
ext = "-%s-svs" % batch if batch else "-svs"
name = "%s%s" % ( dd . get_sample_name ( items [ 0 ] ) , ext )
out_file = os . path . join ( work_dir , "%s-smoove.genotyped.vcf.gz" % name )
sv_exclude_bed = sshared . prepare_exclude_file ( items , out_file )
old_out_file = os . pa... |
def post ( self , url , data ) :
"""Send a HTTP POST request to a URL and return the result .""" | headers = { "Content-type" : "application/x-www-form-urlencoded" , "Accept" : "text/json" }
self . conn . request ( "POST" , url , data , headers )
return self . _process_response ( ) |
def get_modifications ( self ) :
"""Extract INDRA Modification Statements from the BioPAX model .
To extract Modifications , this method reuses the structure of
BioPAX Pattern ' s
org . biopax . paxtools . pattern . PatternBox . constrolsStateChange pattern
with additional constraints to specify the type of... | for modtype , modclass in modtype_to_modclass . items ( ) : # TODO : we could possibly try to also extract generic
# modifications here
if modtype == 'modification' :
continue
stmts = self . _get_generic_modification ( modclass )
self . statements += stmts |
def _get_files ( self , folderId ) :
"""Retrieve the list of files contained in a folder""" | uri = '/' . join ( [ self . base_url , self . name , folderId , 'Files' ] )
return uri , { } , 'get' , None , None , False , None |
def get_fixture ( self , fixture_id , head2head = None ) :
"""Loads a single fixture .
Args :
* fixture _ id ( str ) : the id of the fixture
* head2head ( int , optional ) : load the previous n fixture of the two teams
Returns :
* : obj : json : the fixture - json""" | filters = [ ]
if head2head is not None and int ( head2head ) > 0 :
self . logger . debug ( f'Getting fixture {fixture_id}. head2head is {head2head}.' )
filters . append ( self . __createFilter ( 'head2head' , head2head ) )
else :
self . logger . debug ( f'Getting fixture {fixture_id}.' )
return self . _requ... |
def count_genes ( model ) :
"""Count the number of distinct genes in model reactions .""" | genes = set ( )
for reaction in model . reactions :
if reaction . genes is None :
continue
if isinstance ( reaction . genes , boolean . Expression ) :
genes . update ( v . symbol for v in reaction . genes . variables )
else :
genes . update ( reaction . genes )
return len ( genes ) |
def add_spaces ( self , spaces , ret = False ) :
"""Add ` ` pyny . Spaces ` ` to the current space . In other words , it
merges multiple ` ` pyny . Spaces ` ` in this instance .
: param places : ` ` pyny . Spaces ` ` to add .
: type places : list of pyny . Spaces
: param ret : If True , returns the whole up... | if type ( spaces ) != list :
spaces = [ spaces ]
Space . add_places ( self , sum ( [ space . places for space in spaces ] , [ ] ) )
if ret :
return self |
def generate_dc_xml ( dc_dict ) :
"""Generate a DC XML string .""" | # Define the root namespace .
root_namespace = '{%s}' % DC_NAMESPACES [ 'oai_dc' ]
# Set the elements namespace URL .
elements_namespace = '{%s}' % DC_NAMESPACES [ 'dc' ]
schema_location = ( 'http://www.openarchives.org/OAI/2.0/oai_dc/ ' 'http://www.openarchives.org/OAI/2.0/oai_dc.xsd' )
root_attributes = { '{%s}schema... |
def clustering_fields ( self ) :
"""Union [ List [ str ] , None ] : Fields defining clustering for the table
( Defaults to : data : ` None ` ) .
Clustering fields are immutable after table creation .
. . note : :
As of 2018-06-29 , clustering fields cannot be set on a table
which does not also have time p... | prop = self . _properties . get ( "clustering" )
if prop is not None :
return list ( prop . get ( "fields" , ( ) ) ) |
def process_pulls ( self , testpulls = None , testarchive = None , expected = None ) :
"""Runs self . find _ pulls ( ) * and * processes the pull requests unit tests ,
status updates and wiki page creations .
: arg expected : for unit testing the output results that would be returned
from running the tests in... | from datetime import datetime
pulls = self . find_pulls ( None if testpulls is None else testpulls . values ( ) )
for reponame in pulls :
for pull in pulls [ reponame ] :
try :
archive = self . archive [ pull . repokey ]
if pull . snumber in archive : # We pass the archive in so that... |
def coarse_tag_str ( pos_seq ) :
"""Convert POS sequence to our coarse system , formatted as a string .""" | global tag2coarse
tags = [ tag2coarse . get ( tag , 'O' ) for tag in pos_seq ]
return '' . join ( tags ) |
def get_all_network_interfaces ( self , filters = None ) :
"""Retrieve all of the Elastic Network Interfaces ( ENI ' s )
associated with your account .
: type filters : dict
: param filters : Optional filters that can be used to limit
the results returned . Filters are provided
in the form of a dictionary... | params = { }
if filters :
self . build_filter_params ( params , filters )
return self . get_list ( 'DescribeNetworkInterfaces' , params , [ ( 'item' , NetworkInterface ) ] , verb = 'POST' ) |
def parse_args ( args , default_server_definitions_path , default_profile_definitions_path ) :
"""Parse the command line arguments and return the args dictionary""" | prog = os . path . basename ( sys . argv [ 0 ] )
usage = '%(prog)s [options] server'
desc = """
Test script for testing get_central_instances method. This script executes
a number of tests and displays against a set of servers defined in the
test file
"""
epilog = """
Examples:
%s Fujitsu -v 3
%s -v 1`
""" % ( pr... |
def clear_samples ( self ) :
"""Clears the chain and blobs from memory .""" | # store the iteration that the clear is occuring on
self . _lastclear = self . niterations
self . _itercounter = 0
# now clear the chain
self . _sampler . reset ( ) |
def search_group_by_id ( self , groupID ) -> Group :
"""searches a group by given id
Args :
groupID ( str ) : groupID the group to search for
Returns
the group object or None if it couldn ' t find a group""" | for g in self . groups :
if g . id == groupID :
return g
return None |
def getUserAgent ( ) :
'''Generate a randomized user agent by permuting a large set of possible values .
The returned user agent should look like a valid , in - use brower , with a specified preferred language of english .
Return value is a list of tuples , where each tuple is one of the user - agent headers . ... | coding = random . choice ( ENCODINGS )
random . shuffle ( coding )
coding = random . choice ( ( ", " , "," ) ) . join ( coding )
accept_list = [ tmp for tmp in random . choice ( ACCEPT ) ]
accept_list . append ( random . choice ( ACCEPT_POSTFIX ) )
accept_str = random . choice ( ( ", " , "," ) ) . join ( accept_list )
... |
def auto_change_docstring ( app , what , name , obj , options , lines ) :
r"""Make some automatic changes to docstrings .
Things this function does are :
- Add a title to module docstrings
- Merge lines that end with a ' \ ' with the next line .""" | if what == 'module' and name . startswith ( 'pylatex' ) :
lines . insert ( 0 , len ( name ) * '=' )
lines . insert ( 0 , name )
hits = 0
for i , line in enumerate ( lines . copy ( ) ) :
if line . endswith ( '\\' ) :
lines [ i - hits ] += lines . pop ( i + 1 - hits )
hits += 1 |
def run ( self ) :
"""Run the plugin .""" | # Only run if the build was successful
if self . workflow . build_process_failed :
self . log . info ( "Not promoting failed build to koji" )
return
self . koji_session = get_koji_session ( self . workflow , self . koji_fallback )
koji_metadata , output_files = self . get_metadata ( )
try :
server_dir = sel... |
def calcSMA ( self ) :
"""Calculates the semi - major axis from Keplers Third Law""" | try :
return eq . KeplersThirdLaw ( None , self . star . M , self . P ) . a
except HierarchyError :
return np . nan |
def create_secgroup ( self , name , desc ) :
"""Creates a new server security group .
: param str name : The name of the security group to create .
: param str desc : A short description of the group .""" | self . nova . security_groups . create ( name , desc ) |
def _add_argument_register ( self , reg_offset ) :
"""Registers a register offset as being used as an argument to the function .
: param reg _ offset : The offset of the register to register .""" | if reg_offset in self . _function_manager . _arg_registers and reg_offset not in self . _argument_registers :
self . _argument_registers . append ( reg_offset ) |
def update_image ( self , container_name , image_name ) :
"""update a container ' s image ,
: param container _ name : ` class ` : ` str ` , container name
: param image _ name : ` class ` : ` str ` , the full image name , like alpine : 3.3
: return : ` class ` : ` bool ` , True if success , otherwise False .... | code , container = self . get_container ( container_name )
if code != httplib . OK :
self . logger . error ( "Container %s is not exists. error code %s, error message %s" , container_name , code , container )
return False
_ , old_image_name , _ = utils . parse_image_name ( container . image )
repository , name ... |
def reachableFrom ( self , id , hint = None , relationships = None , lbls = None , callback = None , output = 'application/json' ) :
"""Get all the nodes reachable from a starting point , traversing the provided edges . from : / graph / reachablefrom / { id }
Arguments :
id : The type of the edge
hint : A lab... | if id and id . startswith ( 'http:' ) :
id = parse . quote ( id , safe = '' )
kwargs = { 'id' : id , 'hint' : hint , 'relationships' : relationships , 'lbls' : lbls , 'callback' : callback }
kwargs = { k : dumps ( v ) if builtins . type ( v ) is dict else v for k , v in kwargs . items ( ) }
param_rest = self . _mak... |
def frequencies_plot ( self , xmin = 0 , xmax = 200 ) :
"""Generate the qualities plot""" | helptext = '''
A possible way to assess the complexity of a library even in
absence of a reference sequence is to look at the kmer profile of the reads.
The idea is to count all the kmers (_i.e._, sequence of length `k`) that occur
in the reads. In this way it is possible... |
def get_config ( cls , key , default = None ) :
"""Shortcut to access the application ' s config in your class
: param key : The key to access
: param default : The default value when None
: returns mixed :""" | return cls . _app . config . get ( key , default ) |
def _pull_query_results ( resultset ) :
'''Parses a ResultSet returned from InfluxDB into a dictionary of results ,
grouped by series names and optional JSON - encoded grouping tags .''' | _results = collections . defaultdict ( lambda : { } )
for _header , _values in resultset . items ( ) :
_header , _group_tags = _header
if _group_tags :
_results [ _header ] [ salt . utils . json . dumps ( _group_tags ) ] = [ _value for _value in _values ]
else :
_results [ _header ] = [ _val... |
def repeat_last_axis ( array , count ) :
"""Restride ` array ` to repeat ` count ` times along the last axis .
Parameters
array : np . array
The array to restride .
count : int
Number of times to repeat ` array ` .
Returns
result : array
Array of shape array . shape + ( count , ) composed of ` array... | return as_strided ( array , array . shape + ( count , ) , array . strides + ( 0 , ) ) |
def get_syllable_count ( self , syllables : List [ str ] ) -> int :
"""Counts the number of syllable groups that would occur after ellision .
Often we will want preserve the position and separation of syllables so that they
can be used to reconstitute a line , and apply stresses to the original word positions .... | tmp_syllables = copy . deepcopy ( syllables )
return len ( string_utils . remove_blank_spaces ( string_utils . move_consonant_right ( tmp_syllables , self . _find_solo_consonant ( tmp_syllables ) ) ) ) |
def get_modules ( modulename = None ) :
"""Return a list of modules and packages under modulename .
If modulename is not given , return a list of all top level modules
and packages .""" | modulename = compat . ensure_not_unicode ( modulename )
if not modulename :
try :
return ( [ modname for ( importer , modname , ispkg ) in iter_modules ( ) if not modname . startswith ( "_" ) ] + list ( sys . builtin_module_names ) )
except OSError : # Bug in Python 2.6 , see # 275
return list (... |
def get_sections ( self , s , base , sections = [ 'Parameters' , 'Other Parameters' ] ) :
"""Method that extracts the specified sections out of the given string if
( and only if ) the docstring follows the numpy documentation guidelines
[1 ] _ . Note that the section either must appear in the
: attr : ` param... | params = self . params
# Remove the summary and dedent the rest
s = self . _remove_summary ( s )
for section in sections :
key = '%s.%s' % ( base , section . lower ( ) . replace ( ' ' , '_' ) )
params [ key ] = self . _get_section ( s , section )
return s |
def _GetStatus ( self , two_factor = False ) :
"""Check whether OS Login is installed .
Args :
two _ factor : bool , True if two factor should be enabled .
Returns :
bool , True if OS Login is installed .""" | params = [ 'status' ]
if two_factor :
params += [ '--twofactor' ]
retcode = self . _RunOsLoginControl ( params )
if retcode is None :
if self . oslogin_installed :
self . logger . warning ( 'OS Login not installed.' )
self . oslogin_installed = False
return None
# Prevent log spam when OS Lo... |
def initialize ( app : Flask , app_config ) :
"""Initialize the module .
: param app : The Flask application .
: param app _ config : Application configuration dictionary . If ` http . serve _ on _ endpoint ` attribute
is specified ( e . g . / sacredboard / ) , the application will be hosted on that endpoint ... | sub_url = app_config [ "http.serve_on_endpoint" ]
if sub_url != "/" :
app . wsgi_app = ReverseProxied ( app . wsgi_app , script_name = sub_url ) |
def _validate_config ( self ) :
"""Ensure at least one switch is configured""" | if len ( cfg . CONF . ml2_arista . get ( 'switch_info' ) ) < 1 :
msg = _ ( 'Required option - when "sec_group_support" is enabled, ' 'at least one switch must be specified ' )
LOG . exception ( msg )
raise arista_exc . AristaConfigError ( msg = msg ) |
def fetch ( args ) :
"""% prog fetch " query "
OR
% prog fetch queries . txt
Please provide a UniProt compatible ` query ` to retrieve data . If ` query ` contains
spaces , please remember to " quote " it .
You can also specify a ` filename ` which contains queries , one per line .
Follow this syntax < ... | import re
import csv
p = OptionParser ( fetch . __doc__ )
p . add_option ( "--format" , default = "tab" , choices = valid_formats , help = "download format [default: %default]" )
p . add_option ( "--columns" , default = "entry name, protein names, genes,organism" , help = "columns to download, if --format is `tab` or `... |
def get_addition_score ( source_counts , prediction_counts , target_counts ) :
"""Compute the addition score ( Equation 4 in the paper ) .""" | added_to_prediction_counts = prediction_counts - source_counts
true_positives = sum ( ( added_to_prediction_counts & target_counts ) . values ( ) )
selected = sum ( added_to_prediction_counts . values ( ) )
# Note that in the paper the summation is done over all the ngrams in the
# output rather than the ngrams in the ... |
def DataRefreshRequired ( self , path = None , last = None ) :
"""True if we need to update this path from the client .
Args :
path : The path relative to the root to check freshness of .
last : An aff4 : last attribute to check freshness of .
At least one of path or last must be supplied .
Returns :
Tr... | # If we didn ' t get given a last attribute , use the path to get one from the
# object .
if last is None :
if path is None : # If we didn ' t get a path either , we can ' t do anything .
raise type_info . TypeValueError ( "Either 'path' or 'last' must" " be supplied as an argument." )
fd = aff4 . FACTO... |
def radial_density ( im , bins = 10 , voxel_size = 1 ) :
r"""Computes radial density function by analyzing the histogram of voxel
values in the distance transform . This function is defined by
Torquato [ 1 ] as :
. . math : :
\ int _ 0 ^ \ infty P ( r ) dr = 1.0
where * P ( r ) dr * is the probability of ... | if im . dtype == bool :
im = spim . distance_transform_edt ( im )
mask = find_dt_artifacts ( im ) == 0
im [ mask ] = 0
x = im [ im > 0 ] . flatten ( )
h = sp . histogram ( x , bins = bins , density = True )
h = _parse_histogram ( h = h , voxel_size = voxel_size )
rdf = namedtuple ( 'radial_density_function' , ( 'R'... |
def interface_by_macaddr ( self , macaddr ) :
'''Given a MAC address , return the interface that ' owns ' this address''' | macaddr = EthAddr ( macaddr )
for devname , iface in self . _devinfo . items ( ) :
if iface . ethaddr == macaddr :
return iface
raise KeyError ( "No device has MAC address {}" . format ( macaddr ) ) |
def name ( self ) :
"""The name for this window as it should be displayed in the status bar .""" | # Name , explicitely set for the window .
if self . chosen_name :
return self . chosen_name
else :
pane = self . active_pane
if pane :
return pane . name
return '' |
def all ( self ) :
"""Return all registered users
http : / / www . keycloak . org / docs - api / 3.4 / rest - api / index . html # _ users _ resource""" | return self . _client . get ( url = self . _client . get_full_url ( self . get_path ( 'collection' , realm = self . _realm_name ) ) ) |
def description ( self ) :
"""This read - only attribute is a sequence of 7 - item sequences .""" | if self . _closed :
return
description = [ ]
for col in self . _result [ "cols" ] :
description . append ( ( col , None , None , None , None , None , None ) )
return tuple ( description ) |
def advanced_search ( pattern ) :
"""Parse the grammar of a pattern and build a queryset with it .""" | query_parsed = QUERY . parseString ( pattern )
return Entry . published . filter ( query_parsed [ 0 ] ) . distinct ( ) |
def get ( self ) :
"""Get a task from the queue .""" | tasks = self . _get_avaliable_tasks ( )
if not tasks :
return None
name , data = tasks [ 0 ]
self . _client . kv . delete ( name )
return data |
def listext ( self , ext , stream = sys . stdout ) :
"""Print to the given ` stream ` a table with the list of the output files
with the given ` ext ` produced by the flow .""" | nodes_files = [ ]
for node in self . iflat_nodes ( ) :
filepath = node . outdir . has_abiext ( ext )
if filepath :
nodes_files . append ( ( node , File ( filepath ) ) )
if nodes_files :
print ( "Found %s files with extension `%s` produced by the flow" % ( len ( nodes_files ) , ext ) , file = stream ... |
def save_config ( config , logdir = None ) :
"""Save a new configuration by name .
If a logging directory is specified , is will be created and the configuration
will be stored there . Otherwise , a log message will be printed .
Args :
config : Configuration object .
logdir : Location for writing summarie... | if logdir :
with config . unlocked :
config . logdir = logdir
message = 'Start a new run and write summaries and checkpoints to {}.'
tf . logging . info ( message . format ( config . logdir ) )
tf . gfile . MakeDirs ( config . logdir )
config_path = os . path . join ( config . logdir , 'conf... |
def closed ( self , reason ) :
'''异步爬取本地化处理完成后 , 使用结果数据 , 进行输出文件的渲染 , 渲染完毕 ,
调用 : meth : ` . MobiSpider . generate _ mobi _ file ` 方法 , 生成目标 ` ` mobi ` ` 文件''' | # 拷贝封面 & 报头图片文件
utils . mkdirp ( os . path . join ( self . build_source_dir , 'images' ) )
self . _logger . info ( self . options )
shutil . copy ( self . options . get ( 'img_cover' ) , os . path . join ( self . build_source_dir , 'images' , 'cover.jpg' ) )
shutil . copy ( self . options . get ( 'img_masthead' ) , os ... |
def move_in_32 ( library , session , space , offset , length , extended = False ) :
"""Moves an 32 - bit block of data from the specified address space and offset to local memory .
Corresponds to viMoveIn32 * functions of the VISA library .
: param library : the visa library wrapped by ctypes .
: param sessio... | buffer_32 = ( ViUInt32 * length ) ( )
if extended :
ret = library . viMoveIn32Ex ( session , space , offset , length , buffer_32 )
else :
ret = library . viMoveIn32 ( session , space , offset , length , buffer_32 )
return list ( buffer_32 ) , ret |
def original_unescape ( self , s ) :
"""Since we need to use this sometimes""" | if isinstance ( s , basestring ) :
return unicode ( HTMLParser . unescape ( self , s ) )
elif isinstance ( s , list ) :
return [ unicode ( HTMLParser . unescape ( self , item ) ) for item in s ]
else :
return s |
def redim ( cls , dataset , dimensions ) :
"""Rename coords on the Cube .""" | new_dataset = dataset . data . copy ( )
for name , new_dim in dimensions . items ( ) :
if name == new_dataset . name ( ) :
new_dataset . rename ( new_dim . name )
for coord in new_dataset . dim_coords :
if name == coord . name ( ) :
coord . rename ( new_dim . name )
return new_datase... |
def sleep ( self , ms = 1 ) :
"""Pauses the current green thread for * ms * milliseconds : :
p = h . pipe ( )
@ h . spawn
def _ ( ) :
p . send ( ' 1 ' )
h . sleep ( 50)
p . send ( ' 2 ' )
p . recv ( ) # returns ' 1'
p . recv ( ) # returns ' 2 ' after 50 ms""" | self . scheduled . add ( ms , getcurrent ( ) )
self . loop . switch ( ) |
def envelop ( self , begin , end = None ) :
"""Returns the set of all intervals fully contained in the range
[ begin , end ) .
Completes in O ( m + k * log n ) time , where :
* n = size of the tree
* m = number of matches
* k = size of the search range
: rtype : set of Interval""" | root = self . top_node
if not root :
return set ( )
if end is None :
iv = begin
return self . envelop ( iv . begin , iv . end )
elif begin >= end :
return set ( )
result = root . search_point ( begin , set ( ) )
# bound _ begin might be greater
boundary_table = self . boundary_table
bound_begin = bounda... |
def build ( self , title , text , img_url ) :
""": param title : Title of the card
: param text : Description of the card
: param img _ url : Image of the card""" | super ( ImageCard , self ) . build ( )
self . title = Title ( id = self . id + "-title" , text = title , classname = "card-title" , size = 3 , parent = self )
self . block = Panel ( id = self . id + "-block" , classname = "card-block" , parent = self )
self . image = Image ( id = self . id + "-image" , img_url = img_ur... |
def detect_member ( row , key ) :
'''properly detects if a an attribute exists''' | ( target , tkey , tvalue ) = dict_crawl ( row , key )
if target :
return True
return False |
def compute ( self ) :
"""This is the main method of the : class : ` MUSX ` class . It computes a
set of soft clauses belonging to an MUS of the input formula .
First , the method checks whether the formula is satisfiable . If it
is , nothing else is done . Otherwise , an * unsatisfiable core * of the
formu... | # cheking whether or not the formula is unsatisfiable
if not self . oracle . solve ( assumptions = self . sels ) : # get an overapproximation of an MUS
approx = sorted ( self . oracle . get_core ( ) )
if self . verbose :
print ( 'c MUS approx:' , ' ' . join ( [ str ( self . vmap [ sel ] + 1 ) for sel in... |
def dim_dtau ( self , pars ) :
r""": math : Add formula""" | self . _set_parameters ( pars )
# term 1
num1 = - self . m * ( self . w ** self . c ) * self . c * ( self . tau ** ( self . c - 1 ) ) * np . sin ( self . ang )
term1 = self . sigmai * num1 / self . denom
# term 2
num2a = - self . m * self . otc * np . sin ( self . ang )
num2b = 2 * ( self . w ** 2.0 ) * self . c * ( se... |
def do_down ( self , arg ) :
"""d ( own ) [ count ]
Move the current frame count ( default one ) levels down in the
stack trace ( to a newer frame ) .""" | if self . curindex + 1 == len ( self . stack ) :
self . error ( 'Newest frame' )
return
try :
count = int ( arg or 1 )
except ValueError :
self . error ( 'Invalid frame count (%s)' % arg )
return
if count < 0 :
newframe = len ( self . stack ) - 1
else :
newframe = min ( len ( self . stack ) ... |
def print_mhc_peptide ( neoepitope_info , peptides , pepmap , outfile , netmhc = False ) :
"""Accept data about one neoepitope from merge _ mhc _ peptide _ calls and print it to outfile . This is
a generic module to reduce code redundancy .
: param pandas . core . frame neoepitope _ info : object containing wit... | if netmhc :
peptide_names = [ neoepitope_info . peptide_name ]
else :
peptide_names = [ x for x , y in peptides . items ( ) if neoepitope_info . pept in y ]
# Convert named tuple to dict so it can be modified
neoepitope_info = neoepitope_info . _asdict ( )
# Handle fusion peptides ( They are characterized by ha... |
def env ( self , current_scope ) :
"""Return an environment that will look up in current _ scope for keys in
this tuple , and the parent env otherwise .""" | return self . __env_cache . get ( current_scope . ident , framework . Environment , current_scope , names = self . keys ( ) , parent = framework . Environment ( { 'self' : current_scope } , parent = self . __parent_env ) ) |
def evdev_device ( self ) :
"""Return our corresponding evdev device object""" | devices = [ evdev . InputDevice ( fn ) for fn in evdev . list_devices ( ) ]
for device in devices :
if device . name == self . evdev_device_name :
return device
raise Exception ( "%s: could not find evdev device '%s'" % ( self , self . evdev_device_name ) ) |
def validate_config_must_have ( config , required_keys ) :
"""Validate a config dictionary to make sure it has all of the specified keys
Args :
config : the config to validate .
required _ keys : the list of possible keys that config must include .
Raises :
Exception if the config does not have any of the... | missing_keys = set ( required_keys ) - set ( config )
if len ( missing_keys ) > 0 :
raise Exception ( 'Invalid config with missing keys "%s"' % ', ' . join ( missing_keys ) ) |
def register_success ( self , upgrade ) :
"""Register a successful upgrade .""" | u = Upgrade ( upgrade = upgrade . name , applied = datetime . now ( ) )
db . session . add ( u )
db . session . commit ( ) |
def DOMDebugger_setXHRBreakpoint ( self , url ) :
"""Function path : DOMDebugger . setXHRBreakpoint
Domain : DOMDebugger
Method name : setXHRBreakpoint
Parameters :
Required arguments :
' url ' ( type : string ) - > Resource URL substring . All XHRs having this substring in the URL will get stopped upon .... | assert isinstance ( url , ( str , ) ) , "Argument 'url' must be of type '['str']'. Received type: '%s'" % type ( url )
subdom_funcs = self . synchronous_command ( 'DOMDebugger.setXHRBreakpoint' , url = url )
return subdom_funcs |
def support_autoupload_enable ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
support = ET . SubElement ( config , "support" , xmlns = "urn:brocade.com:mgmt:brocade-ras" )
autoupload = ET . SubElement ( support , "autoupload" )
enable = ET . SubElement ( autoupload , "enable" )
callback = kwargs . pop ( 'callback' , self . _callback )
return callback ( config ) |
def get_dict ( self , obj , state = None , base_name = 'View' ) :
"""The style dict for a view instance .""" | return self . get_dict_for_class ( class_name = obj . __class__ , state = obj . state , base_name = base_name ) |
def devices ( self ) :
"""Manages users enrolled u2f devices""" | self . verify_integrity ( )
if session . get ( 'u2f_device_management_authorized' , False ) :
if request . method == 'GET' :
return jsonify ( self . get_devices ( ) ) , 200
elif request . method == 'DELETE' :
response = self . remove_device ( request . json )
if response [ 'status' ] == ... |
def do_speak ( self , args : argparse . Namespace ) :
"""Repeats what you tell me to .""" | words = [ ]
for word in args . words :
if args . piglatin :
word = '%s%say' % ( word [ 1 : ] , word [ 0 ] )
if args . shout :
word = word . upper ( )
words . append ( word )
repetitions = args . repeat or 1
for i in range ( min ( repetitions , self . maxrepeats ) ) :
self . poutput ( ' '... |
def independentlinear60__ffnn ( ) :
"""4 - Layer Neural Network""" | from keras . models import Sequential
from keras . layers import Dense
model = Sequential ( )
model . add ( Dense ( 32 , activation = 'relu' , input_dim = 60 ) )
model . add ( Dense ( 20 , activation = 'relu' ) )
model . add ( Dense ( 20 , activation = 'relu' ) )
model . add ( Dense ( 1 ) )
model . compile ( optimizer ... |
def apply_empty_result ( self ) :
"""we have an empty result ; at least 1 axis is 0
we will try to apply the function to an empty
series in order to see if this is a reduction function""" | # we are not asked to reduce or infer reduction
# so just return a copy of the existing object
if self . result_type not in [ 'reduce' , None ] :
return self . obj . copy ( )
# we may need to infer
reduce = self . result_type == 'reduce'
from pandas import Series
if not reduce :
EMPTY_SERIES = Series ( [ ] )
... |
def _fail_early ( message , ** kwds ) :
"""The module arguments are dynamically generated based on the Opsview
version . This means that fail _ json isn ' t available until after the module
has been properly initialized and the schemas have been loaded .""" | import json
output = dict ( kwds )
output . update ( { 'msg' : message , 'failed' : True , } )
print ( json . dumps ( output ) )
sys . exit ( 1 ) |
def get_scopes_information ( self ) :
"""Return a list with the description of all the scopes requested .""" | scopes = StandardScopeClaims . get_scopes_info ( self . params [ 'scope' ] )
if settings . get ( 'OIDC_EXTRA_SCOPE_CLAIMS' ) :
scopes_extra = settings . get ( 'OIDC_EXTRA_SCOPE_CLAIMS' , import_str = True ) . get_scopes_info ( self . params [ 'scope' ] )
for index_extra , scope_extra in enumerate ( scopes_extra... |
def accept ( self ) :
"""Method invoked when OK button is clicked .""" | output_path = self . output_path_line_edit . text ( )
if not output_path :
display_warning_message_box ( self , tr ( 'Empty Output Path' ) , tr ( 'Output path can not be empty' ) )
return
try :
self . convert_metadata ( )
except MetadataConversionError as e :
display_warning_message_box ( self , tr ( 'M... |
def get_cursor ( cls ) :
"""Return a message list cursor that returns sqlite3 . Row objects""" | db = SqliteConnection . get ( )
db . row_factory = sqlite3 . Row
return db . cursor ( ) |
def explain_linear_regressor_weights ( reg , vec = None , top = _TOP , target_names = None , targets = None , feature_names = None , coef_scale = None , feature_re = None , feature_filter = None , ) :
"""Return an explanation of a linear regressor weights .
See : func : ` eli5 . explain _ weights ` for descriptio... | if isinstance ( reg , ( SVR , NuSVR ) ) and reg . kernel != 'linear' :
return explain_weights_sklearn_not_supported ( reg )
feature_names , coef_scale = handle_hashing_vec ( vec , feature_names , coef_scale )
feature_names , flt_indices = get_feature_names_filtered ( reg , vec , feature_names = feature_names , feat... |
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