signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def show ( config_file = False ) :
'''Return a list of sysctl parameters for this minion
CLI Example :
. . code - block : : bash
salt ' * ' sysctl . show''' | roots = ( 'kern' , 'vm' , 'vfs' , 'net' , 'hw' , 'machdep' , 'user' , 'ddb' , 'proc' , 'emul' , 'security' , 'init' )
cmd = 'sysctl -ae'
ret = { }
out = __salt__ [ 'cmd.run' ] ( cmd , output_loglevel = 'trace' )
comps = [ '' ]
for line in out . splitlines ( ) :
if any ( [ line . startswith ( '{0}.' . format ( root ... |
def _hash_task ( task ) :
"""Returns a unique hash for identify a task and its params""" | params = task . get ( "params" )
if params :
params = json . dumps ( sorted ( list ( task [ "params" ] . items ( ) ) , key = lambda x : x [ 0 ] ) )
# pylint : disable = no - member
full = [ str ( task . get ( x ) ) for x in [ "path" , "interval" , "dailytime" , "weekday" , "monthday" , "queue" ] ]
full . extend ( [... |
def display_message ( self , clear , beep , timeout , line1 , line2 ) :
"""Display a message on all of the keypads in this area .""" | self . _elk . send ( dm_encode ( self . _index , clear , beep , timeout , line1 , line2 ) ) |
def set_build_image ( self ) :
"""Overrides build _ image for worker , to be same as in orchestrator build""" | current_platform = platform . processor ( )
orchestrator_platform = current_platform or 'x86_64'
current_buildimage = self . get_current_buildimage ( )
for plat , build_image in self . build_image_override . items ( ) :
self . log . debug ( 'Overriding build image for %s platform to %s' , plat , build_image )
s... |
def parse_coach_ec_df ( infile ) :
"""Parse the EC . dat output file of COACH and return a dataframe of results
EC . dat contains the predicted EC number and active residues .
The columns are : PDB _ ID , TM - score , RMSD , Sequence identity ,
Coverage , Confidence score , EC number , and Active site residue... | ec_df = pd . read_table ( infile , delim_whitespace = True , names = [ 'pdb_template' , 'tm_score' , 'rmsd' , 'seq_ident' , 'seq_coverage' , 'c_score' , 'ec_number' , 'binding_residues' ] )
ec_df [ 'pdb_template_id' ] = ec_df [ 'pdb_template' ] . apply ( lambda x : x [ : 4 ] )
ec_df [ 'pdb_template_chain' ] = ec_df [ '... |
def noisy_moment ( self , moment : 'cirq.Moment' , system_qubits : Sequence [ 'cirq.Qid' ] ) -> 'cirq.OP_TREE' :
"""Adds noise to the operations from a moment .
Args :
moment : The moment to add noise to .
system _ qubits : A list of all qubits in the system .
Returns :
An OP _ TREE corresponding to the n... | if not hasattr ( self . noisy_moments , '_not_overridden' ) :
return self . noisy_moments ( [ moment ] , system_qubits )
if not hasattr ( self . noisy_operation , '_not_overridden' ) :
return [ self . noisy_operation ( op ) for op in moment ]
assert False , 'Should be unreachable.' |
def create_translate_dictionaries ( symbols ) :
u"""create translate dictionaries for text , google , docomo , kddi and softbank via ` symbols `
create dictionaries for translate emoji character to carrier from unicode ( forward ) or to unicode from carrier ( reverse ) .
method return dictionary instance which ... | unicode_to_text = { }
unicode_to_docomo_img = { }
unicode_to_kddi_img = { }
unicode_to_softbank_img = { }
unicode_to_google = { }
unicode_to_docomo = { }
unicode_to_kddi = { }
unicode_to_softbank = { }
google_to_unicode = { }
docomo_to_unicode = { }
kddi_to_unicode = { }
softbank_to_unicode = { }
for x in symbols :
... |
def timeit ( func ) :
"""Simple decorator to time functions
: param func : function to decorate
: type func : callable
: return : wrapped function
: rtype : callable""" | @ wraps ( func )
def _wrapper ( * args , ** kwargs ) :
start = time . time ( )
result = func ( * args , ** kwargs )
elapsed = time . time ( ) - start
LOGGER . info ( '%s took %s seconds to complete' , func . __name__ , round ( elapsed , 2 ) )
return result
return _wrapper |
def stop_executing_svc_checks ( self ) :
"""Disable service check execution ( globally )
Format of the line that triggers function call : :
STOP _ EXECUTING _ SVC _ CHECKS
: return : None""" | if self . my_conf . execute_service_checks :
self . my_conf . modified_attributes |= DICT_MODATTR [ "MODATTR_ACTIVE_CHECKS_ENABLED" ] . value
self . my_conf . execute_service_checks = False
self . my_conf . explode_global_conf ( )
self . daemon . update_program_status ( ) |
def use_file ( self , enabled = True , file_name = None , level = logging . WARNING , when = 'd' , interval = 1 , backup_count = 30 , delay = False , utc = False , at_time = None , log_format = None , date_format = None ) :
"""Handler for logging to a file , rotating the log file at certain timed intervals .""" | if enabled :
if not self . __file_handler :
assert file_name , 'File name is missing!'
# Create new TimedRotatingFileHandler instance
kwargs = { 'filename' : file_name , 'when' : when , 'interval' : interval , 'backupCount' : backup_count , 'encoding' : 'UTF-8' , 'delay' : delay , 'utc' : ut... |
import re
pattern = '^[a-z]$|^([a-z]).*\\1$'
def validate_string ( s ) :
"""Function to validate whether the input string begins and ends with the same character using regular expressions .
Example :
> > > validate _ string ( ' mom ' )
' Valid '
> > > validate _ string ( ' z ' )
' Valid '
> > > validate... | if re . match ( pattern , s ) :
return 'Valid'
else :
return 'Invalid' |
def _section_from_spec ( elf_file , spec ) :
'''Retrieve a section given a " spec " ( either number or name ) .
Return None if no such section exists in the file .''' | if isinstance ( spec , int ) :
num = int ( spec )
if num < elf_file . num_sections ( ) :
return elf_file . get_section ( num )
# Not a number . Must be a name then
if isinstance ( spec , str ) :
try :
return elf_file . get_section_by_name ( spec )
except AttributeError :
return N... |
def wait_time ( self , value ) :
"""Setter for * * self . _ _ wait _ time * * attribute .
: param value : Attribute value .
: type value : int or float""" | if value is not None :
assert type ( value ) in ( int , float ) , "'{0}' attribute: '{1}' type is not 'int' or 'float'!" . format ( "wait_time" , value )
assert value >= 0 , "'{0}' attribute: '{1}' need to be positive!" . format ( "wait_time" , value )
self . __wait_time = value |
def compute_radius ( wcs ) :
"""Compute the radius from the center to the furthest edge of the WCS .""" | ra , dec = wcs . wcs . crval
img_center = SkyCoord ( ra = ra * u . degree , dec = dec * u . degree )
wcs_foot = wcs . calc_footprint ( )
img_corners = SkyCoord ( ra = wcs_foot [ : , 0 ] * u . degree , dec = wcs_foot [ : , 1 ] * u . degree )
radius = img_center . separation ( img_corners ) . max ( ) . value
return radiu... |
def set_pixel ( self , x , y , state ) :
"""Set pixel at " x , y " to " state " where state can be one of " ON " , " OFF "
or " TOGGLE " """ | self . send_cmd ( "P" + str ( x + 1 ) + "," + str ( y + 1 ) + "," + state ) |
def map ( self , func : Callable [ [ Tuple [ Any , Log ] ] , Tuple [ Any , Log ] ] ) -> 'Writer' :
"""Map a function func over the Writer value .
Haskell :
fmap f m = Writer $ let ( a , w ) = runWriter m in ( f a , w )
Keyword arguments :
func - - Mapper function :""" | a , w = self . run ( )
b , _w = func ( ( a , w ) )
return Writer ( b , _w ) |
def match_function_pattern ( self , first , rest = None , least = 1 , offset = 0 ) :
"""Match each char sequentially from current SourceString position
until the pattern doesnt match and return all maches .
Integer argument least defines and minimum amount of chars that can
be matched .
This version takes f... | if not self . has_space ( offset = offset ) :
return ''
firstchar = self . string [ self . pos + offset ]
if not first ( firstchar ) :
return ''
output = [ firstchar ]
pattern = first if rest is None else rest
for char in self . string [ self . pos + offset + 1 : ] :
if pattern ( char ) :
output . a... |
def _resolve ( self , path , migration_file ) :
"""Resolve a migration instance from a file .
: param migration _ file : The migration file
: type migration _ file : str
: rtype : eloquent . migrations . migration . Migration""" | variables = { }
name = '_' . join ( migration_file . split ( '_' ) [ 4 : ] )
migration_file = os . path . join ( path , '%s.py' % migration_file )
with open ( migration_file ) as fh :
exec ( fh . read ( ) , { } , variables )
klass = variables [ inflection . camelize ( name ) ]
instance = klass ( )
instance . set_sc... |
def validate_get_dbs ( connection ) :
"""validates the connection object is capable of read access to rethink
should be at least one test database by default
: param connection : < rethinkdb . net . DefaultConnection >
: return : < set > list of databases
: raises : ReqlDriverError AssertionError""" | remote_dbs = set ( rethinkdb . db_list ( ) . run ( connection ) )
assert remote_dbs
return remote_dbs |
def componentSelection ( self , comp ) :
"""Toggles the selection of * comp * from the currently active parameter""" | # current row which is selected in auto parameters to all component selection to
indexes = self . selectedIndexes ( )
index = indexes [ 0 ]
self . model ( ) . toggleSelection ( index , comp ) |
def device_not_active ( self , addr ) :
"""Handle inactive devices .""" | self . aldb_device_handled ( addr )
for callback in self . _cb_device_not_active :
callback ( addr ) |
def _read_coord_h5 ( files , shapes , header , twod ) :
"""Read all coord hdf5 files of a snapshot .
Args :
files ( list of pathlib . Path ) : list of NodeCoordinates files of
a snapshot .
shapes ( list of ( int , int ) ) : shape of mesh grids .
header ( dict ) : geometry info .
twod ( str ) : ' XZ ' , ... | meshes = [ ]
for h5file , shape in zip ( files , shapes ) :
meshes . append ( { } )
with h5py . File ( h5file , 'r' ) as h5f :
for coord , mesh in h5f . items ( ) : # for some reason , the array is transposed !
meshes [ - 1 ] [ coord ] = mesh [ ( ) ] . reshape ( shape ) . T
meshe... |
def remove_align_qc_tools ( data ) :
"""Remove alignment based QC tools we don ' t need for data replicates .
When we do multiple variant calling on a sample file ( somatic / germline ) ,
avoid re - running QC .""" | align_qc = set ( [ "qsignature" , "coverage" , "picard" , "samtools" , "fastqc" ] )
data [ "config" ] [ "algorithm" ] [ "qc" ] = [ t for t in dd . get_algorithm_qc ( data ) if t not in align_qc ]
return data |
def _set_current_page ( self , current_page , last_page ) :
"""Get the current page for the request .
: param current _ page : The current page of results
: type current _ page : int
: param last _ page : The last page of results
: type last _ page : int
: rtype : int""" | if not current_page :
current_page = self . resolve_current_page ( )
if current_page > last_page :
if last_page > 0 :
return last_page
return 1
if not self . _is_valid_page_number ( current_page ) :
return 1
return current_page |
def run_hook ( self , app : FlaskUnchained , bundles : List [ Bundle ] ) :
"""Hook entry point . Override to disable standard behavior of iterating
over bundles to discover objects and processing them .""" | self . process_objects ( app , self . collect_from_bundles ( bundles ) ) |
def get_file_size ( path ) :
"""The the size of a file in bytes .
Parameters
path : str
The path of the file .
Returns
int
The size of the file in bytes .
Raises
IOError
If the file does not exist .
OSError
If a file system error occurs .""" | assert isinstance ( path , ( str , _oldstr ) )
if not os . path . isfile ( path ) :
raise IOError ( 'File "%s" does not exist.' , path )
return os . path . getsize ( path ) |
def to_positive_multiple_of_10 ( string ) :
"""Converts a string into its encoded positive integer ( greater zero ) or throws an exception .""" | try :
value = int ( string )
except ValueError :
msg = '"%r" is not a positive multiple of 10 (greater zero).' % string
raise argparse . ArgumentTypeError ( msg )
if value <= 0 or value % 10 != 0 :
msg = '"%r" is not a positive multiple of 10 (greater zero).' % string
raise argparse . ArgumentTypeEr... |
def get_proteins_from_psm ( line ) :
"""From a line , return list of proteins reported by Mzid2TSV . When unrolled
lines are given , this returns the single protein from the line .""" | proteins = line [ mzidtsvdata . HEADER_PROTEIN ] . split ( ';' )
outproteins = [ ]
for protein in proteins :
prepost_protein = re . sub ( '\(pre=.*post=.*\)' , '' , protein ) . strip ( )
outproteins . append ( prepost_protein )
return outproteins |
def dict ( self ) :
"""Returns dictionary of post fields and attributes""" | post_dict = { 'id' : self . id , 'link' : self . link , 'permalink' : self . permalink , 'content_type' : self . content_type , 'slug' : self . slug , 'updated' : self . updated , # . strftime ( conf . GOSCALE _ ATOM _ DATETIME _ FORMAT ) ,
'published' : self . published , # . strftime ( conf . GOSCALE _ ATOM _ DATETIM... |
def normalizeX ( value ) :
"""Normalizes x coordinate .
* * * value * * must be an : ref : ` type - int - float ` .
* Returned value is the same type as the input value .""" | if not isinstance ( value , ( int , float ) ) :
raise TypeError ( "X coordinates must be instances of " ":ref:`type-int-float`, not %s." % type ( value ) . __name__ )
return value |
def shutdown ( server , graceful = True ) :
"""Shut down the application .
If a graceful stop is requested , waits for all of the IO loop ' s
handlers to finish before shutting down the rest of the process .
We impose a 10 second timeout .
Based on http : / / tornadogists . org / 3428652/""" | ioloop = IOLoop . instance ( )
logging . info ( "Stopping server..." )
# Stop listening for new connections
server . stop ( )
def final_stop ( ) :
ioloop . stop ( )
logging . info ( "Stopped." )
sys . exit ( 0 )
def poll_stop ( counts = { 'remaining' : None , 'previous' : None } ) :
remaining = len ( io... |
def create ( cls , exiter , args , env , target_roots = None , daemon_graph_session = None , options_bootstrapper = None ) :
"""Creates a new LocalPantsRunner instance by parsing options .
: param Exiter exiter : The Exiter instance to use for this run .
: param list args : The arguments ( e . g . sys . argv ) ... | build_root = get_buildroot ( )
options , build_config , options_bootstrapper = cls . parse_options ( args , env , setup_logging = True , options_bootstrapper = options_bootstrapper , )
global_options = options . for_global_scope ( )
# Option values are usually computed lazily on demand ,
# but command line options are ... |
def _get_library_search_paths ( ) :
"""Returns a list of library search paths , considering of the current working
directory , default paths and paths from environment variables .""" | search_paths = [ '' , '/usr/lib64' , '/usr/local/lib64' , '/usr/lib' , '/usr/local/lib' , '/run/current-system/sw/lib' , '/usr/lib/x86_64-linux-gnu/' , os . path . abspath ( os . path . dirname ( __file__ ) ) ]
if sys . platform == 'darwin' :
path_environment_variable = 'DYLD_LIBRARY_PATH'
else :
path_environme... |
def emitResetAxisSignal ( self , axisNumber ) :
"""Emits the sigResetAxis with the axisNumber as parameter
axisNumber should be 0 for X , 1 for Y , and 2 for both axes .""" | assert axisNumber in ( VALID_AXES_NUMBERS ) , "Axis Nr should be one of {}, got {}" . format ( VALID_AXES_NUMBERS , axisNumber )
# Hide ' auto - scale ( A ) ' button
logger . debug ( "ArgosPgPlotItem.autoBtnClicked, mode:{}" . format ( self . autoBtn . mode ) )
if self . autoBtn . mode == 'auto' :
self . autoBtn . ... |
def add ( self , date_range , library_name ) :
"""Adds the library with the given date range to the underlying collection of libraries used by this store .
The underlying libraries should not overlap as the date ranges are assumed to be CLOSED _ CLOSED by this function
and the rest of the class .
Arguments : ... | # check that the library is valid
try :
self . _arctic_lib . arctic [ library_name ]
except Exception as e :
logger . error ( "Could not load library" )
raise e
assert date_range . start and date_range . end , "Date range should have start and end properties {}" . format ( date_range )
start = date_range . ... |
def _validate_iss ( claims , issuer = None ) :
"""Validates that the ' iss ' claim is valid .
The " iss " ( issuer ) claim identifies the principal that issued the
JWT . The processing of this claim is generally application specific .
The " iss " value is a case - sensitive string containing a StringOrURI
v... | if issuer is not None :
if isinstance ( issuer , string_types ) :
issuer = ( issuer , )
if claims . get ( 'iss' ) not in issuer :
raise JWTClaimsError ( 'Invalid issuer' ) |
def factory_reset ( self , ids , except_ids = False , except_baudrate_and_ids = False ) :
"""Reset all motors on the bus to their factory default settings .""" | mode = ( 0x02 if except_baudrate_and_ids else 0x01 if except_ids else 0xFF )
for id in ids :
try :
self . _send_packet ( self . _protocol . DxlResetPacket ( id , mode ) )
except ( DxlTimeoutError , DxlCommunicationError ) :
pass |
def get_user_by_auth_token ( token = None ) :
"""Return the AuthUser associated to the token , otherwise it will return None .
If token is not provided , it will pull it from the headers : Authorization
Exception :
Along with AuthError , it may
: param token :
: return : AuthUser""" | if not token :
token = request . get_auth_token ( )
secret_key = get_jwt_secret ( )
s = utils . unsign_jwt ( token = token , secret_key = secret_key , salt = get_jwt_salt ( ) )
if "id" not in s :
raise exceptions . AuthError ( "Invalid Authorization Bearer Token" )
return get_user_by_id ( int ( s [ "id" ] ) ) |
def dna ( self , dna ) :
"""Replace this chromosome ' s DNA with new DNA of equal length ,
assigning the new DNA to the chromosome ' s genes sequentially .
For example , if a chromosome contains these genes . . .
1 . 100100
2 . 011011
. . . and the new DNA is 1111100000 , the genes become :
1 . 11111
... | assert self . length == len ( dna )
i = 0
for gene in self . genes :
gene . dna = dna [ i : i + gene . length ]
i += gene . length |
def _parse_entry ( self , cols ) :
"""Parses an entry ' s row and adds the result to py : attr : ` entries ` .
Parameters
cols : : class : ` bs4 . ResultSet `
The list of columns for that entry .""" | rank , name , vocation , * values = [ c . text . replace ( '\xa0' , ' ' ) . strip ( ) for c in cols ]
rank = int ( rank )
if self . category == Category . EXPERIENCE or self . category == Category . LOYALTY_POINTS :
extra , value = values
else :
value , * extra = values
value = int ( value . replace ( ',' , '' ... |
def static2dplot_timeaveraged ( var , time ) :
"""If the static _ taverage option is set in tplot , and is supplied with a time range , then the spectrogram
plot ( s ) for which it is set will have another window pop up , where the displayed y and z values are
averaged by the number of seconds between the speci... | # Grab names of data loaded in as tplot variables .
names = list ( pytplot . data_quants . keys ( ) )
# Get data we ' ll actually work with here .
valid_variables = tplot_utilities . get_data ( names )
# Don ' t plot anything unless we have spectrograms with which to work .
if valid_variables : # Get z label
labels... |
def _close_remaining_channels ( self ) :
"""Forcefully close all open channels .
: return :""" | for channel_id in list ( self . _channels ) :
self . _channels [ channel_id ] . set_state ( Channel . CLOSED )
self . _channels [ channel_id ] . close ( )
self . _cleanup_channel ( channel_id ) |
def _adjust_offset ( self , real_wave_mfcc , algo_parameters ) :
"""OFFSET""" | self . log ( u"Called _adjust_offset" )
self . _apply_offset ( offset = algo_parameters [ 0 ] ) |
def autodiscover ( ) :
"""Taken from ` ` django . contrib . admin . autodiscover ` ` and used to run
any calls to the ` ` processor _ for ` ` decorator .""" | global LOADED
if LOADED :
return
LOADED = True
for app in get_app_name_list ( ) :
try :
module = import_module ( app )
except ImportError :
pass
else :
try :
import_module ( "%s.page_processors" % app )
except :
if module_has_submodule ( module , "... |
def get_initializer ( default_init_type : str , default_init_scale : float , default_init_xavier_rand_type : str , default_init_xavier_factor_type : str , embed_init_type : str , embed_init_sigma : float , rnn_init_type : str , extra_initializers : Optional [ List [ Tuple [ str , mx . initializer . Initializer ] ] ] = ... | # default initializer
if default_init_type == C . INIT_XAVIER :
default_init = [ ( C . DEFAULT_INIT_PATTERN , mx . init . Xavier ( rnd_type = default_init_xavier_rand_type , factor_type = default_init_xavier_factor_type , magnitude = default_init_scale ) ) ]
elif default_init_type == C . INIT_UNIFORM :
default_... |
def propinfo ( cls , value , prop , visitor ) :
"""Like : py : meth : ` normalize . visitor . VisitorPattern . apply ` , but takes a
property and returns a dict with some basic info . The default
implementation returns just the name of the property and the type in
here .""" | if not prop :
return { "name" : value . __name__ }
rv = { "name" : prop . name }
if prop . valuetype :
if isinstance ( prop . valuetype , tuple ) :
rv [ 'type' ] = [ typ . __name__ for typ in prop . valuetype ]
else :
rv [ 'type' ] = prop . valuetype . __name__
return rv |
def as_hdu ( self ) :
"Return a version of ourself as an astropy . io . fits . PrimaryHDU object" | from astropy . io import fits
# transfer header , preserving ordering
ahdr = self . get_header ( )
header = fits . Header ( ahdr . items ( ) )
data = self . get_mddata ( )
hdu = fits . PrimaryHDU ( data = data , header = header )
return hdu |
def det4D ( m ) :
'''det4D ( array ) yields the determinate of the given matrix array , which may have more than 2
dimensions , in which case the later dimensions are multiplied and added point - wise .''' | # I just solved this in Mathematica , copy - pasted , and replaced the string ' ] m ' with ' ] * m ' :
# Mathematica code : Det @ Table [ m [ i ] [ j ] , { i , 0 , 3 } , { j , 0 , 3 } ]
return ( m [ 0 ] [ 3 ] * m [ 1 ] [ 2 ] * m [ 2 ] [ 1 ] * m [ 3 ] [ 0 ] - m [ 0 ] [ 2 ] * m [ 1 ] [ 3 ] * m [ 2 ] [ 1 ] * m [ 3 ] [ 0 ]... |
def contains_rva ( self , rva ) :
"""Check whether the section contains the address provided .""" | # Check if the SizeOfRawData is realistic . If it ' s bigger than the size of
# the whole PE file minus the start address of the section it could be
# either truncated or the SizeOfRawData contains a misleading value .
# In either of those cases we take the VirtualSize
if len ( self . pe . __data__ ) - self . pe . adju... |
def add_source ( self , name , src_dict , free = None , save_source_maps = True , use_pylike = True , use_single_psf = False ) :
"""Add a new source to the model . Source properties
( spectrum , spatial model ) are set with the src _ dict argument .
Parameters
name : str
Source name .
src _ dict : dict or... | # if self . roi . has _ source ( name ) :
# msg = ' Source % s already exists . ' % name
# self . logger . error ( msg )
# raise Exception ( msg )
srcmap_utils . delete_source_map ( self . files [ 'srcmap' ] , name )
src = self . roi [ name ]
if self . config [ 'gtlike' ] [ 'expscale' ] is not None and name not in self... |
def update_groups_for_state ( self , state : State ) :
"""Update all the Group memberships for the users
who have State
: param state : State to update for
: return :""" | users = get_users_for_state ( state )
for config in self . filter ( states = state ) :
logger . debug ( "in state loop" )
for user in users :
logger . debug ( "in user loop for {}" . format ( user ) )
config . update_group_membership_for_user ( user ) |
def revocation_date ( self , value ) :
"""A datetime . datetime object of when the certificate was revoked , if the
status is not " good " or " unknown " .""" | if value is not None and not isinstance ( value , datetime ) :
raise TypeError ( _pretty_message ( '''
revocation_date must be an instance of datetime.datetime, not %s
''' , _type_name ( value ) ) )
self . _revocation_date = value |
def getISAStudy ( studyNum , pathToISATABFile , noAssays = True ) :
"""This function returns a Study object given the study number in an ISA file
Typically , you should use the exploreISA function to check the contents
of the ISA file and retrieve the study number you are interested in !
: param studyNum : Th... | from isatools import isatab
import copy
try :
isa = isatab . load ( pathToISATABFile , skip_load_tables = True )
st = copy . deepcopy ( isa . studies [ studyNum - 1 ] )
if noAssays :
st . assays = [ ]
return st
except FileNotFoundError as err :
raise err |
def camel_2_snake ( name ) :
"Converts CamelCase to camel _ case" | s1 = re . sub ( '(.)([A-Z][a-z]+)' , r'\1_\2' , name )
return re . sub ( '([a-z0-9])([A-Z])' , r'\1_\2' , s1 ) . lower ( ) |
def get_url_image_prediction ( self , model_id , picture_url , token = None , url = API_GET_PREDICTION_IMAGE_URL ) :
"""Gets a prediction from a supplied picture url based on a previously trained model .
: param model _ id : string , once you train a model you ' ll be given a model id to use .
: param picture _... | auth = 'Bearer ' + self . check_for_token ( token )
m = MultipartEncoder ( fields = { 'sampleLocation' : picture_url , 'modelId' : model_id } )
h = { 'Authorization' : auth , 'Cache-Control' : 'no-cache' , 'Content-Type' : m . content_type }
the_url = url
r = requests . post ( the_url , headers = h , data = m )
return ... |
def date_added ( self , date_added ) :
"""Updates the security labels date _ added
Args :
date _ added : Converted to % Y - % m - % dT % H : % M : % SZ date format""" | date_added = self . _utils . format_datetime ( date_added , date_format = '%Y-%m-%dT%H:%M:%SZ' )
self . _data [ 'dateAdded' ] = date_added
request = self . _base_request
request [ 'dateAdded' ] = date_added
return self . _tc_requests . update ( request , owner = self . owner ) |
def add_grant ( self , grant ) :
"""Adds a Grant that the provider should support .
: param grant : An instance of a class that extends
: class : ` oauth2 . grant . GrantHandlerFactory `
: type grant : oauth2 . grant . GrantHandlerFactory""" | if hasattr ( grant , "expires_in" ) :
self . token_generator . expires_in [ grant . grant_type ] = grant . expires_in
if hasattr ( grant , "refresh_expires_in" ) :
self . token_generator . refresh_expires_in = grant . refresh_expires_in
self . grant_types . append ( grant ) |
def Muller_Steinhagen_Heck ( m , x , rhol , rhog , mul , mug , D , roughness = 0 , L = 1 ) :
r'''Calculates two - phase pressure drop with the Muller - Steinhagen and Heck
(1986 ) correlation from [ 1 ] _ , also in [ 2 ] _ and [ 3 ] _ .
. . math : :
\ Delta P _ { tp } = G _ { MSH } ( 1 - x ) ^ { 1/3 } + \ Del... | # Liquid - only properties , for calculation of dP _ lo
v_lo = m / rhol / ( pi / 4 * D ** 2 )
Re_lo = Reynolds ( V = v_lo , rho = rhol , mu = mul , D = D )
fd_lo = friction_factor ( Re = Re_lo , eD = roughness / D )
dP_lo = fd_lo * L / D * ( 0.5 * rhol * v_lo ** 2 )
# Gas - only properties , for calculation of dP _ go
... |
def parse ( self ) :
"""Apply search template .""" | self . verbose = bool ( self . re_verbose )
self . unicode = bool ( self . re_unicode )
self . global_flag_swap = { "unicode" : ( ( self . re_unicode is not None ) if not _util . PY37 else False ) , "verbose" : False }
self . temp_global_flag_swap = { "unicode" : False , "verbose" : False }
self . ascii = self . re_uni... |
def classify_by_name ( names ) :
"""Classify a ( composite ) ligand by the HETID ( s )""" | if len ( names ) > 3 : # Polymer
if len ( set ( config . RNA ) . intersection ( set ( names ) ) ) != 0 :
ligtype = 'RNA'
elif len ( set ( config . DNA ) . intersection ( set ( names ) ) ) != 0 :
ligtype = 'DNA'
else :
ligtype = "POLYMER"
else :
ligtype = 'SMALLMOLECULE'
for name ... |
def strip_accents ( x ) :
u"""Strip accents in the input phrase X .
Strip accents in the input phrase X ( assumed in UTF - 8 ) by replacing
accented characters with their unaccented cousins ( e . g . é by e ) .
: param x : the input phrase to strip .
: type x : string
: return : Return such a stripped X ... | x = re_latex_lowercase_a . sub ( "a" , x )
x = re_latex_lowercase_ae . sub ( "ae" , x )
x = re_latex_lowercase_oe . sub ( "oe" , x )
x = re_latex_lowercase_e . sub ( "e" , x )
x = re_latex_lowercase_i . sub ( "i" , x )
x = re_latex_lowercase_o . sub ( "o" , x )
x = re_latex_lowercase_u . sub ( "u" , x )
x = re_latex_lo... |
def get_contained_extras ( marker ) :
"""Collect " extra = = . . . " operands from a marker .
Returns a list of str . Each str is a speficied extra in this marker .""" | if not marker :
return set ( )
marker = Marker ( str ( marker ) )
extras = set ( )
_markers_collect_extras ( marker . _markers , extras )
return extras |
def show ( self , ax : plt . Axes = None , figsize : tuple = ( 3 , 3 ) , title : Optional [ str ] = None , hide_axis : bool = True , cmap : str = 'tab20' , alpha : float = 0.5 , ** kwargs ) :
"Show the ` ImageSegment ` on ` ax ` ." | ax = show_image ( self , ax = ax , hide_axis = hide_axis , cmap = cmap , figsize = figsize , interpolation = 'nearest' , alpha = alpha , vmin = 0 )
if title :
ax . set_title ( title ) |
def parse_block ( self , contents , parent , module , depth ) :
"""Extracts all executable definitions from the specified string and adds
them to the specified parent .""" | for anexec in self . RE_EXEC . finditer ( contents ) :
x = self . _process_execs ( anexec , parent , module )
parent . executables [ x . name . lower ( ) ] = x
if isinstance ( parent , Module ) and "public" in x . modifiers :
parent . publics [ x . name . lower ( ) ] = 1
# To handle the embedded... |
def node_setup ( domain , master , ticket ) :
'''Setup the icinga2 node .
Returns : :
icinga2 node setup - - ticket TICKET _ ID - - endpoint master . domain . tld - - zone domain . tld - - master _ host master . domain . tld - - trustedcert / etc / icinga2 / pki / trusted - master . crt
CLI Example :
. . co... | result = __salt__ [ 'cmd.run_all' ] ( [ "icinga2" , "node" , "setup" , "--ticket" , ticket , "--endpoint" , master , "--zone" , domain , "--master_host" , master , "--trustedcert" , "{0}trusted-master.crt" . format ( get_certs_path ( ) ) ] , python_shell = False )
return result |
def fetch ( self , wait = 0 ) :
"""get the task result objects .
: param int wait : how many milliseconds to wait for a result
: return : an unsorted list of task objects""" | if self . started :
return fetch ( self . id , wait = wait , cached = self . cached ) |
def masked_local_attention_2d ( q , k , v , query_shape = ( 8 , 16 ) , memory_flange = ( 8 , 16 ) , name = None ) :
"""Strided block local self - attention .
Each position in a query block can attend to all the generated queries in
the query block , which are generated in raster scan , and positions that are
... | with tf . variable_scope ( name , default_name = "local_masked_self_attention_2d" , values = [ q , k , v ] ) :
v_shape = common_layers . shape_list ( v )
# Pad query to ensure multiple of corresponding lengths .
q = pad_to_multiple_2d ( q , query_shape )
# Set up query blocks .
q_indices = gather_in... |
def request ( self , method , uri , params = None , data = None , headers = None , auth = None , timeout = None , allow_redirects = False ) :
"""Make an HTTP request .""" | url = self . relative_uri ( uri )
return self . domain . request ( method , url , params = params , data = data , headers = headers , auth = auth , timeout = timeout , allow_redirects = allow_redirects ) |
def send_output ( self , value , stdout ) :
"""Write the output or value of the expression back to user .
> > > print ( ' cash rules everything around me ' )
cash rules everything around me""" | writer = self . writer
if value is not None :
writer . write ( '{!r}\n' . format ( value ) . encode ( 'utf8' ) )
if stdout :
writer . write ( stdout . encode ( 'utf8' ) )
yield from writer . drain ( ) |
def _parseParams ( self ) :
"""Parse parameters from their string HTML representation to dictionary .
Result is saved to the : attr : ` params ` property .""" | # check if there are any parameters
if " " not in self . _element or "=" not in self . _element :
return
# remove ' < ' & ' > '
params = self . _element . strip ( ) [ 1 : - 1 ] . strip ( )
# remove tagname
offset = params . find ( self . getTagName ( ) ) + len ( self . getTagName ( ) )
params = params [ offset : ] ... |
def mark_entities ( tokens , positions , markers = [ ] , style = "insert" ) :
"""Adds special markers around tokens at specific positions ( e . g . , entities )
Args :
tokens : A list of tokens ( the sentence )
positions :
1 ) A list of inclusive ranges ( tuples ) corresponding to the
token ranges of the ... | if markers and len ( markers ) != 2 * len ( positions ) :
msg = ( f"Expected len(markers) == 2 * len(positions), " f"but {len(markers)} != {2 * len(positions)}." )
raise ValueError ( msg )
toks = list ( tokens )
# markings will be of the form :
# [ ( position , entity _ idx ) , ( position , entity _ idx ) , . .... |
def generate ( self , secret , type = 'totp' , account = 'alex' , issuer = None , algo = 'sha1' , digits = 6 , init_counter = None ) :
"""https : / / github . com / google / google - authenticator / wiki / Key - Uri - Format""" | args = { }
uri = 'otpauth://{0}/{1}?{2}'
try : # converts the secret to a 16 cars string
a = binascii . unhexlify ( secret )
args [ SECRET ] = base64 . b32encode ( a ) . decode ( 'ascii' )
except binascii . Error as ex :
raise ValueError ( str ( ex ) )
except Exception as ex :
print ( ex )
raise Val... |
def osd_tree ( conn , cluster ) :
"""Check the status of an OSD . Make sure all are up and in
What good output would look like : :
" epoch " : 8,
" num _ osds " : 1,
" num _ up _ osds " : 1,
" num _ in _ osds " : " 1 " ,
" full " : " false " ,
" nearfull " : " false "
Note how the booleans are actua... | ceph_executable = system . executable_path ( conn , 'ceph' )
command = [ ceph_executable , '--cluster={cluster}' . format ( cluster = cluster ) , 'osd' , 'tree' , '--format=json' , ]
out , err , code = remoto . process . check ( conn , command , )
try :
loaded_json = json . loads ( b'' . join ( out ) . decode ( 'ut... |
def send_email_confirmation ( request , user , signup = False ) :
"""E - mail verification mails are sent :
a ) Explicitly : when a user signs up
b ) Implicitly : when a user attempts to log in using an unverified
e - mail while EMAIL _ VERIFICATION is mandatory .
Especially in case of b ) , we want to limi... | from . models import EmailAddress , EmailConfirmation
cooldown_period = timedelta ( seconds = app_settings . EMAIL_CONFIRMATION_COOLDOWN )
email = user_email ( user )
if email :
try :
email_address = EmailAddress . objects . get_for_user ( user , email )
if not email_address . verified :
... |
def find_one ( self , tname , where = None , where_not = None , columns = None , astype = None ) :
'''Find a single record in the provided table from the database . If multiple match , return
the first one based on the internal order of the records . If no records are found , return
empty dictionary , string or... | records = self . find ( tname , where = where , where_not = where_not , columns = columns , astype = 'dataframe' )
return self . _output ( records , single = True , astype = astype ) |
def pdu_to_function_code_or_raise_error ( resp_pdu ) :
"""Parse response PDU and return of : class : ` ModbusFunction ` or
raise error .
: param resp _ pdu : PDU of response .
: return : Subclass of : class : ` ModbusFunction ` matching the response .
: raises ModbusError : When response contains error code... | function_code = struct . unpack ( '>B' , resp_pdu [ 0 : 1 ] ) [ 0 ]
if function_code not in function_code_to_function_map . keys ( ) :
error_code = struct . unpack ( '>B' , resp_pdu [ 1 : 2 ] ) [ 0 ]
raise error_code_to_exception_map [ error_code ]
return function_code |
def handler ( event , context ) :
"""Historical { { cookiecutter . technology _ name } } event poller .
This poller is run at a set interval in order to ensure that changes do not go undetected by historical .
Historical pollers generate ` polling events ` which simulate changes . These polling events contain c... | log . debug ( 'Running poller. Configuration: {}' . format ( event ) )
for account in get_historical_accounts ( ) :
try : # TODO describe all items
# Example : :
# groups = describe _ security _ groups (
# account _ number = account [ ' id ' ] ,
# assume _ role = HISTORICAL _ ROLE ,
# region = C... |
def AddInstanceTags ( r , instance , tags , dry_run = False ) :
"""Adds tags to an instance .
@ type instance : str
@ param instance : instance to add tags to
@ type tags : list of str
@ param tags : tags to add to the instance
@ type dry _ run : bool
@ param dry _ run : whether to perform a dry run
@... | query = { "tag" : tags , "dry-run" : dry_run , }
return r . request ( "put" , "/2/instances/%s/tags" % instance , query = query ) |
def get_assessment_taken_admin_session ( self , proxy ) :
"""Gets the ` ` OsidSession ` ` associated with the assessment taken administration service .
arg : proxy ( osid . proxy . Proxy ) : a proxy
return : ( osid . assessment . AssessmentTakenAdminSession ) - an
` ` AssessmentTakenAdminSession ` `
raise :... | if not self . supports_assessment_taken_admin ( ) :
raise errors . Unimplemented ( )
# pylint : disable = no - member
return sessions . AssessmentTakenAdminSession ( proxy = proxy , runtime = self . _runtime ) |
def ptmsiReallocationComplete ( ) :
"""P - TMSI REALLOCATION COMPLETE Section 9.4.8""" | a = TpPd ( pd = 0x3 )
b = MessageType ( mesType = 0x11 )
# 00010001
packet = a / b
return packet |
def bm3_big_F ( p , v , v0 ) :
"""calculate big F for linearlized form
not fully tested
: param p :
: param f :
: return :""" | f = bm3_small_f ( v , v0 )
return cal_big_F ( p , f ) |
def get_sec2gos ( sortobj ) :
"""Initialize section _ name2goids .""" | sec_gos = [ ]
for section_name , nts in sortobj . get_desc2nts_fnc ( hdrgo_prt = True ) [ 'sections' ] :
sec_gos . append ( ( section_name , set ( nt . GO for nt in nts ) ) )
return cx . OrderedDict ( sec_gos ) |
def get_cognitive_process_metadata ( self ) :
"""Gets the metadata for a cognitive process .
return : ( osid . Metadata ) - metadata for the cognitive process
* compliance : mandatory - - This method must be implemented . *""" | # Implemented from template for osid . resource . ResourceForm . get _ group _ metadata _ template
metadata = dict ( self . _mdata [ 'cognitive_process' ] )
metadata . update ( { 'existing_id_values' : self . _my_map [ 'cognitiveProcessId' ] } )
return Metadata ( ** metadata ) |
def create_module ( self , spec ) :
"""Improve python2 semantics for module creation .""" | mod = super ( NamespaceLoader2 , self ) . create_module ( spec )
# Set a few properties required by PEP 302
# mod . _ _ file _ _ = [ p for p in self . path ]
# this will set mod . _ _ repr _ _ to not builtin . . . shouldnt break anything in py2 . . .
# CAREFUL : get _ filename present implies the module has ONE locatio... |
def get_requirements_information ( self , path : Path ) -> Tuple [ RequirementsOptions , Optional [ str ] ] :
"""Returns the information needed to install requirements for a repository - what kind is used and the hash
of contents of the defining file .""" | if self . pipfile_location is not None :
pipfile = path / self . pipfile_location / "Pipfile"
pipfile_lock = path / self . pipfile_location / "Pipfile.lock"
pipfile_exists = pipfile . exists ( )
pipfile_lock_exists = pipfile_lock . exists ( )
if pipfile_exists and pipfile_lock_exists :
optio... |
def setGridColor ( self , color ) :
"""Sets the color for the grid for this instance to the given color .
: param color | < QColor >""" | palette = self . palette ( )
palette . setColor ( palette . GridForeground , QColor ( color ) ) |
async def trigger_act ( self , addr ) :
"""Trigger agent in : attr : ` addr ` to act .
This method is quite inefficient if used repeatedly for a large number
of agents .
. . seealso : :
: py : meth : ` creamas . mp . MultiEnvironment . trigger _ all `""" | r_agent = await self . env . connect ( addr , timeout = TIMEOUT )
return await r_agent . act ( ) |
def close ( self ) :
"""Cleanly shutdown the connection to RabbitMQ
: raises : sprockets . mixins . amqp . ConnectionStateError""" | if not self . closable :
LOGGER . warning ( 'Closed called while %s' , self . state_description )
raise ConnectionStateError ( self . state_description )
self . state = self . STATE_CLOSING
LOGGER . info ( 'Closing RabbitMQ connection' )
self . connection . close ( ) |
def survey_change_name ( request , pk ) :
"""Works well with :
http : / / www . appelsiini . net / projects / jeditable""" | survey = get_object_or_404 ( Survey , pk = pk )
if not request . user . has_perm ( "formly.change_survey_name" , obj = survey ) :
raise PermissionDenied ( )
survey . name = request . POST . get ( "name" )
survey . save ( )
return JsonResponse ( { "status" : "OK" , "name" : survey . name } ) |
def _need_bib_run ( self , old_cite_counter ) :
'''Determine if you need to run " bibtex " .
1 . Check if * . bib exists .
2 . Check latex output for hints .
3 . Test if the numbers of citations changed
during first latex run .
4 . Examine * . bib for changes .''' | with open ( '%s.aux' % self . project_name ) as fobj :
match = BIB_PATTERN . search ( fobj . read ( ) )
if not match :
return False
else :
self . bib_file = match . group ( 1 )
if not os . path . isfile ( '%s.bib' % self . bib_file ) :
self . log . warning ( 'Could not find *.bib file.' ... |
def transformToNative ( obj ) :
"""Turn obj . value into a date or datetime .""" | if obj . isNative :
return obj
obj . isNative = True
if obj . value == '' :
return obj
obj . value = obj . value
obj . value = parseDtstart ( obj , allowSignatureMismatch = True )
if getattr ( obj , 'value_param' , 'DATE-TIME' ) . upper ( ) == 'DATE-TIME' :
if hasattr ( obj , 'tzid_param' ) : # Keep a copy ... |
def post ( self , request , * args , ** kwargs ) :
"""Method for handling POST requests .
Deletes the object . Successful deletes are logged .
Returns a ' render redirect ' to the result of the
` get _ done _ url ` method .
If a ProtectedError is raised , the ` render ` method
is called with message expla... | self . object = self . get_object ( )
msg = None
if request . POST . get ( 'delete' ) :
try :
with transaction . commit_on_success ( ) :
self . log_action ( self . object , CMSLog . DELETE )
msg = "%s deleted" % self . object
self . object . delete ( )
except Protecte... |
def getIdentifierForPoint ( self , point ) :
"""Create a unique identifier for and assign it to ` ` point ` ` .
If the point already has an identifier , the existing
identifier will be returned .
> > > contour . getIdentifierForPoint ( point )
' ILHGJlygfds '
` ` point ` ` must be a : class : ` BasePoint ... | point = normalizers . normalizePoint ( point )
return self . _getIdentifierforPoint ( point ) |
def to_array ( self ) :
"""Serializes this ChatActionMessage to a dictionary .
: return : dictionary representation of this object .
: rtype : dict""" | array = super ( ChatActionMessage , self ) . to_array ( )
array [ 'action' ] = u ( self . action )
# py2 : type unicode , py3 : type str
if self . receiver is not None :
if isinstance ( self . receiver , None ) :
array [ 'chat_id' ] = None ( self . receiver )
# type Noneelif isinstance ( self . rece... |
def model ( self ) :
"""Model of the spectrum with given redshift .""" | if self . z == 0 :
m = self . _model
else : # wavelength
if self . _internal_wave_unit . physical_type == 'length' :
rs = self . _redshift_model . inverse
# frequency or wavenumber
# NOTE : This will never execute as long as internal wavelength
# unit remains Angstrom .
else : # pragma :... |
def main ( ) :
"""Command - line entry point for running the view server .""" | import getopt
from . import __version__ as VERSION
try :
option_list , argument_list = getopt . gnu_getopt ( sys . argv [ 1 : ] , 'h' , [ 'version' , 'help' , 'json-module=' , 'debug' , 'log-file=' ] )
message = None
for option , value in option_list :
if option in ( '--version' ) :
mess... |
def queryAll ( self , * args , ** kwargs ) :
"""Returns a : class : ` Deferred ` object which will have its callback invoked
with a : class : ` BatchedView ` when the results are complete .
Parameters follow conventions of
: meth : ` ~ couchbase . bucket . Bucket . query ` .
Example : :
d = cb . queryAll ... | if not self . connected :
cb = lambda x : self . queryAll ( * args , ** kwargs )
return self . connect ( ) . addCallback ( cb )
kwargs [ 'itercls' ] = BatchedView
o = super ( RawBucket , self ) . query ( * args , ** kwargs )
o . start ( )
return o . _getDeferred ( ) |
async def set_position ( self , position , wait_for_completion = True ) :
"""Set window to desired position .
Parameters :
* position : Position object containing the target position .
* wait _ for _ completion : If set , function will return
after device has reached target position .""" | command_send = CommandSend ( pyvlx = self . pyvlx , wait_for_completion = wait_for_completion , node_id = self . node_id , parameter = position )
await command_send . do_api_call ( )
if not command_send . success :
raise PyVLXException ( "Unable to send command" )
await self . after_update ( ) |
def _get_handled_methods ( self , actions_map ) :
"""Get names of HTTP methods that can be used at requested URI .
Arguments :
: actions _ map : Map of actions . Must have the same structure as
self . _ item _ actions and self . _ collection _ actions""" | methods = ( 'OPTIONS' , )
defined_actions = [ ]
for action_name in actions_map . keys ( ) :
view_method = getattr ( self , action_name , None )
method_exists = view_method is not None
method_defined = view_method != self . not_allowed_action
if method_exists and method_defined :
defined_actions ... |
def get_volume_by_id ( self , id ) :
"""Get ScaleIO Volume object by its ID
: param name : ID of volume
: return : ScaleIO Volume object
: raise KeyError : No Volume with specified ID found
: rtype : ScaleIO Volume object""" | for vol in self . conn . volumes :
if vol . id == id :
return vol
raise KeyError ( "Volume with ID " + id + " not found" ) |
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