signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def _loadData ( self , data ) :
"""Load attribute values from Plex XML response .""" | self . _setValue = None
self . id = data . attrib . get ( 'id' )
self . label = data . attrib . get ( 'label' )
self . summary = data . attrib . get ( 'summary' )
self . type = data . attrib . get ( 'type' )
self . default = self . _cast ( data . attrib . get ( 'default' ) )
self . value = self . _cast ( data . attrib ... |
def tsplit ( string , delimiters ) :
"""Behaves str . split but supports tuples of delimiters .""" | delimiters = tuple ( delimiters )
if len ( delimiters ) < 1 :
return [ string , ]
final_delimiter = delimiters [ 0 ]
for i in delimiters [ 1 : ] :
string = string . replace ( i , final_delimiter )
return string . split ( final_delimiter ) |
def get_topics ( self ) :
""": calls : ` GET / repos / : owner / : repo / topics < https : / / developer . github . com / v3 / repos / # list - all - topics - for - a - repository > ` _
: rtype : list of strings""" | headers , data = self . _requester . requestJsonAndCheck ( "GET" , self . url + "/topics" , headers = { 'Accept' : Consts . mediaTypeTopicsPreview } )
return data [ 'names' ] |
def _import_plugins ( self ) :
"""Internal function , ensure all plugin packages are imported .""" | if self . detected :
return
# In some cases , plugin scanning may start during a request .
# Make sure there is only one thread scanning for plugins .
self . scanLock . acquire ( )
if self . detected :
return
# previous threaded released + completed
try :
import_apps_submodule ( "content_plugins" )
self... |
def duplicates_removed ( it , already_seen = ( ) ) :
"""Returns a list with duplicates removed from the iterable ` it ` .
Order is preserved .""" | lst = [ ]
seen = set ( )
for i in it :
if i in seen or i in already_seen :
continue
lst . append ( i )
seen . add ( i )
return lst |
def do_verify ( marfile , keyfiles = None ) :
"""Verify the MAR file .""" | try :
with open ( marfile , 'rb' ) as f :
with MarReader ( f ) as m : # Check various parts of the mar file
# e . g . signature algorithms and additional block sections
errors = m . get_errors ( )
if errors :
print ( "File is not well formed: {}" . format ( er... |
def todict ( self ) :
"""Returns a dictionary fully representing the state of this object""" | return { 'index' : self . index , 'seed' : hb_encode ( self . seed ) , 'n' : self . n , 'root' : hb_encode ( self . root ) , 'hmac' : hb_encode ( self . hmac ) , 'timestamp' : self . timestamp } |
def get_private_rooms ( self , ** kwargs ) :
"""Get a listing of all private rooms with their names and IDs""" | return GetPrivateRooms ( settings = self . settings , ** kwargs ) . call ( ** kwargs ) |
def _delete_stale ( self ) :
"""Delete files left in self . _ stale _ files . Also delete their directories if empty .""" | for name , hash_ in self . _stale_files . items ( ) :
path = self . download_root . joinpath ( name )
if not path . exists ( ) :
continue
current_hash = self . _path_hash ( path )
if current_hash == hash_ :
progress_logger . info ( 'deleting: %s which is stale...' , name )
path .... |
def write_metadata ( self , symbol , metadata , prune_previous_version = True , ** kwargs ) :
"""Write ' metadata ' under the specified ' symbol ' name to this library .
The data will remain unchanged . A new version will be created .
If the symbol is missing , it causes a write with empty data ( None , pickled... | # Make a normal write with empty data and supplied metadata if symbol does not exist
try :
previous_version = self . _read_metadata ( symbol )
except NoDataFoundException :
return self . write ( symbol , data = None , metadata = metadata , prune_previous_version = prune_previous_version , ** kwargs )
# Reaching... |
def backoff ( max_tries = constants . BACKOFF_DEFAULT_MAXTRIES , delay = constants . BACKOFF_DEFAULT_DELAY , factor = constants . BACKOFF_DEFAULT_FACTOR , exceptions = None ) :
"""Implements an exponential backoff decorator which will retry decorated
function upon given exceptions . This implementation is based o... | if max_tries <= 0 :
raise ValueError ( 'Max tries must be greater than 0; got {!r}' . format ( max_tries ) )
if delay <= 0 :
raise ValueError ( 'Delay must be greater than 0; got {!r}' . format ( delay ) )
if factor <= 1 :
raise ValueError ( 'Backoff factor must be greater than 1; got {!r}' . format ( facto... |
def do_page_truncate ( self , args : List [ str ] ) :
"""Read in a text file and display its output in a pager , truncating long lines if they don ' t fit .
Truncated lines can still be accessed by scrolling to the right using the arrow keys .
Usage : page _ chop < file _ path >""" | if not args :
self . perror ( 'page_truncate requires a path to a file as an argument' , traceback_war = False )
return
self . page_file ( args [ 0 ] , chop = True ) |
def corr_flat_und ( a1 , a2 ) :
'''Returns the correlation coefficient between two flattened adjacency
matrices . Only the upper triangular part is used to avoid double counting
undirected matrices . Similarity metric for weighted matrices .
Parameters
A1 : NxN np . ndarray
undirected matrix 1
A2 : NxN ... | n = len ( a1 )
if len ( a2 ) != n :
raise BCTParamError ( "Cannot calculate flattened correlation on " "matrices of different size" )
triu_ix = np . where ( np . triu ( np . ones ( ( n , n ) ) , 1 ) )
return np . corrcoef ( a1 [ triu_ix ] . flat , a2 [ triu_ix ] . flat ) [ 0 ] [ 1 ] |
def norm ( self , order = 2 ) :
"""Find the vector norm , with the given order , of the values""" | return ( sum ( val ** order for val in abs ( self ) . values ( ) ) ) ** ( 1 / order ) |
def load_label ( self , idx ) :
"""Load label image as 1 x height x width integer array of label indices .
The leading singleton dimension is required by the loss .
The full 400 labels are translated to the 59 class task labels .""" | label_400 = scipy . io . loadmat ( '{}/trainval/{}.mat' . format ( self . context_dir , idx ) ) [ 'LabelMap' ]
label = np . zeros_like ( label_400 , dtype = np . uint8 )
for idx , l in enumerate ( self . labels_59 ) :
idx_400 = self . labels_400 . index ( l ) + 1
label [ label_400 == idx_400 ] = idx + 1
label =... |
def tweak ( environment , opts ) :
"""Commands operating on environment data
Usage :
datacats tweak - - install - postgis [ ENVIRONMENT ]
datacats tweak - - add - redis [ ENVIRONMENT ]
datacats tweak - - admin - password [ ENVIRONMENT ]
Options :
- - install - postgis Install postgis in ckan database
... | environment . require_data ( )
if opts [ '--install-postgis' ] :
print "Installing postgis"
environment . install_postgis_sql ( )
if opts [ '--add-redis' ] : # Let the user know if they are trying to add it and it is already there
print ( 'Adding redis extra container... Please note that you will have ' 'to... |
def mrca_matrix ( self ) :
'''Return a dictionary storing all pairwise MRCAs . ` ` M [ u ] [ v ] ` ` = MRCA of nodes ` ` u ` ` and ` ` v ` ` . Excludes ` ` M [ u ] [ u ] ` ` because MRCA of node and itself is itself
Returns :
` ` dict ` ` : ` ` M [ u ] [ v ] ` ` = MRCA of nodes ` ` u ` ` and ` ` v ` `''' | M = dict ( )
leaves_below = dict ( )
for node in self . traverse_postorder ( ) :
leaves_below [ node ] = list ( )
if node . is_leaf ( ) :
leaves_below [ node ] . append ( node ) ;
M [ node ] = dict ( )
else :
for i in range ( len ( node . children ) - 1 ) :
for l1 in leav... |
def get_class ( classname , all = False ) :
"""Retrieve a class from the registry .
: raises : marshmallow . exceptions . RegistryError if the class cannot be found
or if there are multiple entries for the given class name .""" | try :
classes = _registry [ classname ]
except KeyError :
raise RegistryError ( 'Class with name {!r} was not found. You may need ' 'to import the class.' . format ( classname ) )
if len ( classes ) > 1 :
if all :
return _registry [ classname ]
raise RegistryError ( 'Multiple classes with name {... |
def fetch_bookshelf ( start_url , output_dir ) :
"""Fetch all the books off of a gutenberg project bookshelf page
example bookshelf page ,
http : / / www . gutenberg . org / wiki / Children % 27s _ Fiction _ ( Bookshelf )""" | # make output directory
try :
os . mkdir ( OUTPUT_DIR + output_dir )
except OSError as e :
raise ( e )
# fetch page
r = requests . get ( start_url )
# extract links
soup = bs ( r . text , 'html.parser' )
book_links = soup . find_all ( class_ = re . compile ( "extiw" ) )
new_links = [ ]
for el in book_links :
... |
def env_to_statement ( env ) :
'''Return the abstraction description of an environment variable definition
into a statement for shell script .
> > > env _ to _ statement ( dict ( name = ' X ' , value = ' Y ' ) )
' X = " Y " ; export X '
> > > env _ to _ statement ( dict ( name = ' X ' , value = ' Y ' , raw ... | source_file = env . get ( 'file' , None )
if source_file :
return '. %s' % __escape ( source_file , env )
execute = env . get ( 'execute' , None )
if execute :
return execute
name = env [ 'name' ]
value = __escape ( env [ 'value' ] , env )
return '%s=%s; export %s' % ( name , value , name ) |
def remove_markup ( s ) :
"""Remove all < * > html markup tags from s .""" | mo = _markup_re . search ( s )
while mo :
s = s [ 0 : mo . start ( ) ] + s [ mo . end ( ) : ]
mo = _markup_re . search ( s )
return s |
def padding ( s , bs = AES . block_size ) :
"""Fills a bytes - like object with arbitrary symbols to make its length divisible by ` bs ` .""" | s = to_bytes ( s )
if len ( s ) % bs == 0 :
res = s + b'' . join ( map ( to_bytes , [ random . SystemRandom ( ) . choice ( string . ascii_lowercase + string . digits ) for _ in range ( bs - 1 ) ] ) ) + to_bytes ( chr ( 96 - bs ) )
elif len ( s ) % bs > 0 and len ( s ) > bs :
res = s + b'' . join ( map ( to_byte... |
def _resume_with_session_id ( self , server_info : ServerConnectivityInfo , ssl_version_to_use : OpenSslVersionEnum ) -> bool :
"""Perform one session resumption using Session IDs .""" | session1 = self . _resume_ssl_session ( server_info , ssl_version_to_use )
try : # Recover the session ID
session1_id = self . _extract_session_id ( session1 )
except IndexError : # Session ID not assigned
return False
if session1_id == '' : # Session ID empty
return False
# Try to resume that SSL session
s... |
def followers ( self ) :
"""获取关注此问题的用户
: return : 关注此问题的用户
: rtype : Author . Iterable
: 问题 : 要注意若执行过程中另外有人关注 , 可能造成重复获取到某些用户""" | self . _make_soup ( )
followers_url = self . url + 'followers'
for x in common_follower ( followers_url , self . xsrf , self . _session ) :
yield x |
def _patch_multiple ( target , spec = None , create = False , spec_set = None , autospec = None , new_callable = None , ** kwargs ) :
"""Perform multiple patches in a single call . It takes the object to be
patched ( either as an object or a string to fetch the object by importing )
and keyword arguments for th... | if type ( target ) in ( unicode , str ) :
getter = lambda : _importer ( target )
else :
getter = lambda : target
if not kwargs :
raise ValueError ( 'Must supply at least one keyword argument with patch.multiple' )
# need to wrap in a list for python 3 , where items is a view
items = list ( kwargs . items ( ... |
def set_server_handler ( self , handler_func , name = None , header_filter = None , alias = None , interval = 0.5 ) :
"""Sets an automatic handler for the type of message template currently loaded .
This feature allows users to set a python handler function which is called
automatically by the Rammbock message ... | msg_template = self . _get_message_template ( )
server , server_name = self . _servers . get_with_name ( name )
server . set_handler ( msg_template , handler_func , header_filter = header_filter , alias = alias , interval = interval ) |
def parse_text ( file_name ) :
"""Parse data from Ohio State University text mocap files ( http : / / accad . osu . edu / research / mocap / mocap _ data . htm ) .""" | # Read the header
fid = open ( file_name , 'r' )
point_names = np . array ( fid . readline ( ) . split ( ) ) [ 2 : - 1 : 3 ]
fid . close ( )
for i in range ( len ( point_names ) ) :
point_names [ i ] = point_names [ i ] [ 0 : - 2 ]
# Read the matrix data
S = np . loadtxt ( file_name , skiprows = 1 )
field = np . ui... |
def toProtocolElement ( self ) :
"""Returns the representation of this CallSet as the corresponding
ProtocolElement .""" | variantSet = self . getParentContainer ( )
gaCallSet = protocol . CallSet ( biosample_id = self . getBiosampleId ( ) )
if variantSet . getCreationTime ( ) :
gaCallSet . created = variantSet . getCreationTime ( )
if variantSet . getUpdatedTime ( ) :
gaCallSet . updated = variantSet . getUpdatedTime ( )
gaCallSet... |
def rescale_variables ( df , variables_include = [ ] , variables_exclude = [ ] ) :
"""Rescale variables in a DataFrame , excluding variables with NaNs and strings ,
excluding specified variables , and including specified variables .""" | variables_not_rescale = variables_exclude
variables_not_rescale . extend ( df . columns [ df . isna ( ) . any ( ) ] . tolist ( ) )
# variables with NaNs
variables_not_rescale . extend ( df . select_dtypes ( include = [ "object" , "datetime" , "timedelta" ] ) . columns )
# variables with strings
variables_rescale = list... |
def call_filter ( self , name , value , args = None , kwargs = None , context = None , eval_ctx = None ) :
"""Invokes a filter on a value the same way the compiler does it .
Note that on Python 3 this might return a coroutine in case the
filter is running from an environment in async mode and the filter
suppo... | func = self . filters . get ( name )
if func is None :
fail_for_missing_callable ( 'no filter named %r' , name )
args = [ value ] + list ( args or ( ) )
if getattr ( func , 'contextfilter' , False ) :
if context is None :
raise TemplateRuntimeError ( 'Attempted to invoke context ' 'filter without contex... |
def process_post ( self , post , render = True ) :
"""A high level view to create post processing .
: param post : Dictionary representing the post
: type post : dict
: param render : Choice if the markdown text has to be converted or not
: type render : bool
: return :""" | post_processor = self . post_processor
post_processor . process ( post , render )
try :
author = self . user_callback ( post [ "user_id" ] )
except Exception :
raise Exception ( "No user_loader has been installed for this " "BloggingEngine. Add one with the " "'BloggingEngine.user_loader' decorator." )
if autho... |
def fbresnet152 ( num_classes = 1000 , pretrained = 'imagenet' ) :
"""Constructs a ResNet - 152 model .
Args :
pretrained ( bool ) : If True , returns a model pre - trained on ImageNet""" | model = FBResNet ( Bottleneck , [ 3 , 8 , 36 , 3 ] , num_classes = num_classes )
if pretrained is not None :
settings = pretrained_settings [ 'fbresnet152' ] [ pretrained ]
assert num_classes == settings [ 'num_classes' ] , "num_classes should be {}, but is {}" . format ( settings [ 'num_classes' ] , num_classe... |
def set_nweight ( self , node_from , node_to , weight_there , weight_back ) :
r"""Set a single n - weight / edge - weight .
Parameters
node _ from : int
Node - id from the first node of the edge .
node _ to : int
Node - id from the second node of the edge .
weight _ there : float
Weight from first to ... | if node_from >= self . __nodes or node_from < 0 :
raise ValueError ( 'Invalid node id (node_from) of {}. Valid values are 0 to {}.' . format ( node_from , self . __nodes - 1 ) )
elif node_to >= self . __nodes or node_to < 0 :
raise ValueError ( 'Invalid node id (node_to) of {}. Valid values are 0 to {}.' . form... |
def help ( self , * args ) :
"""Can be overridden ( and for example _ Menu does ) .""" | if args :
self . messages . error ( self . messages . command_does_not_accept_arguments )
else :
print ( self . helpfull ) |
def _validate_header ( self , hed ) :
"""Validate the list that represents the table header .
: param hed : The list that represents the table header .
: type hed : list ( list ( hatemile . util . html . htmldomelement . HTMLDOMElement ) )
: return : True if the table header is valid or False if the table hea... | # pylint : disable = no - self - use
if not bool ( hed ) :
return False
length = - 1
for row in hed :
if not bool ( row ) :
return False
elif length == - 1 :
length = len ( row )
elif len ( row ) != length :
return False
return True |
def _GetShowID ( self , stringSearch , origStringSearch = None ) :
"""Search for given string as an existing entry in the database file name
table or , if no match is found , as a show name from the TV guide .
If an exact match is not found in the database the user can accept
or decline the best match from th... | showInfo = tvfile . ShowInfo ( )
if origStringSearch is None :
goodlogging . Log . Info ( "RENAMER" , "Looking up show ID for: {0}" . format ( stringSearch ) )
origStringSearch = stringSearch
goodlogging . Log . IncreaseIndent ( )
showInfo . showID = self . _db . SearchFileNameTable ( stringSearch )
if showInfo... |
def get_sampleV ( self , res , DV = None , resMode = 'abs' , ind = None , Out = '(X,Y,Z)' ) :
"""Sample , with resolution res , the volume defined by DV or ind""" | args = [ self . Poly , self . dgeom [ 'P1Min' ] [ 0 ] , self . dgeom [ 'P1Max' ] [ 0 ] , self . dgeom [ 'P2Min' ] [ 1 ] , self . dgeom [ 'P2Max' ] [ 1 ] , res ]
kwdargs = dict ( DV = DV , dVMode = resMode , ind = ind , VType = self . Id . Type , VLim = self . Lim , Out = Out , margin = 1.e-9 )
pts , dV , ind , reseff =... |
def truncate_to ( self , cert ) :
"""Remove all certificates in the path after the cert specified
: param cert :
An asn1crypto . x509 . Certificate object to find
: raises :
LookupError - when the certificate could not be found
: return :
The current ValidationPath object , for chaining""" | cert_index = None
for index , entry in enumerate ( self ) :
if entry . issuer_serial == cert . issuer_serial :
cert_index = index
break
if cert_index is None :
raise LookupError ( 'Unable to find the certificate specified' )
while len ( self ) > cert_index + 1 :
self . pop ( )
return self |
def check_user ( self , user_id ) :
"""Check whether this user can read this dataset""" | if self . hidden == 'N' :
return True
for owner in self . owners :
if int ( owner . user_id ) == int ( user_id ) :
if owner . view == 'Y' :
return True
return False |
def export ( self , class_name , method_name , export_data = False , export_dir = '.' , export_filename = 'data.json' , export_append_checksum = False , ** kwargs ) :
"""Port a trained estimator to the syntax of a chosen programming language .
Parameters
: param class _ name : string
The name of the class in ... | # Arguments :
self . class_name = class_name
self . method_name = method_name
# Estimator :
est = self . estimator
self . output_activation = est . out_activation_
self . hidden_activation = est . activation
self . n_layers = est . n_layers_
self . n_hidden_layers = est . n_layers_ - 2
self . n_inputs = len ( est . coe... |
def _authenticate ( ) :
'''Retrieve CSRF and API tickets for the Proxmox API''' | global url , port , ticket , csrf , verify_ssl
url = config . get_cloud_config_value ( 'url' , get_configured_provider ( ) , __opts__ , search_global = False )
port = config . get_cloud_config_value ( 'port' , get_configured_provider ( ) , __opts__ , default = 8006 , search_global = False )
username = config . get_clou... |
def move_images ( self , image_directory ) :
"""Moves png - files one directory up from path / image / * . png - > path / * . png""" | image_paths = glob ( image_directory + "/**/*.png" , recursive = True )
for image_path in image_paths :
destination = image_path . replace ( "\\image\\" , "\\" )
shutil . move ( image_path , destination )
image_folders = glob ( image_directory + "/**/image" , recursive = True )
for image_folder in image_folders... |
def GetMultipleTags ( tag_list , start_time , end_time , sampling_rate = None , fill_limit = 99999 , verify_time = False , desc_as_label = False , utc = False ) :
"""Retrieves raw data from eDNA history for multiple tags , merging them into
a single DataFrame , and resampling the data according to the specified
... | # Since we are pulling data from multiple tags , let ' s iterate over each
# one . For this case , we only want to pull data using the " raw " method ,
# which will obtain all data as it is actually stored in the historian .
dfs = [ ]
columns_names = [ ]
for tag in tag_list :
df = GetHist ( tag , start_time , end_t... |
def GET_getitemtypes ( self ) -> None :
"""Get the types of all current exchange items supposed to return
the values of | Parameter | or | Sequence | objects or the time series
of | IOSequence | objects .""" | for item in state . getitems :
type_ = self . _get_itemtype ( item )
for name , _ in item . yield_name2value ( ) :
self . _outputs [ name ] = type_ |
def phrase_strings ( self , phrase_type ) :
"""Returns strings corresponding all phrases matching a given phrase type
: param phrase _ type : POS such as " NP " , " VP " , " det " , etc .
: type phrase _ type : str
: return : a list of strings representing those phrases""" | return [ u" " . join ( subtree . leaves ( ) ) for subtree in self . subtrees_for_phrase ( phrase_type ) ] |
def _handle_create ( self , response , ignore_tombstone , auto_refresh ) :
'''Handles response from self . create ( )
Args :
response ( requests . models . Response ) : response object from self . create ( )
ignore _ tombstone ( bool ) : If True , will attempt creation , if tombstone exists ( 409 ) , will del... | # 201 , success , refresh
if response . status_code == 201 : # if not specifying uri , capture from response and append to object
self . uri = self . repo . parse_uri ( response . text )
# creation successful
if auto_refresh :
self . refresh ( )
elif auto_refresh == None :
if self . repo... |
def max_word_width ( myDict ) :
'''currd = { 0 : ' AutoPauseSpeed ' , 125 : ' HRLimitLow ' , 6 : ' Activity ' }
max _ wordwidth ( currd )''' | maxValueWidth = 0
for each in myDict :
eachValueWidth = myDict [ each ] . __len__ ( )
if ( eachValueWidth > maxValueWidth ) :
maxValueWidth = eachValueWidth
return ( maxValueWidth ) |
def find_outer_region ( im , r = 0 ) :
r"""Finds regions of the image that are outside of the solid matrix .
This function uses the rolling ball method to define where the outer region
ends and the void space begins .
This function is particularly useful for samples that do not fill the
entire rectangular i... | if r == 0 :
dt = spim . distance_transform_edt ( input = im )
r = int ( sp . amax ( dt ) ) * 2
im_padded = sp . pad ( array = im , pad_width = r , mode = 'constant' , constant_values = True )
dt = spim . distance_transform_edt ( input = im_padded )
seeds = ( dt >= r ) + get_border ( shape = im_padded . shape )
... |
def wait_for_task ( task_data , task_uri = '/tasks' ) :
"""Run task and check the result .
Args :
task _ data ( str ) : the task json to execute
Returns :
str : Task status .""" | taskid = post_task ( task_data , task_uri )
if isinstance ( task_data , str ) :
json_data = json . loads ( task_data )
else :
json_data = task_data
# inspect the task to see if a timeout is configured
job = json_data [ 'job' ] [ 0 ]
env = job . get ( 'credentials' )
task_type = job . get ( 'type' )
timeout = TA... |
def tt_comp ( self , sampled_topics ) :
"""Compute term - topic matrix from sampled _ topics .""" | samples = sampled_topics . shape [ 0 ]
tt = np . zeros ( ( self . V , self . K , samples ) )
for s in range ( samples ) :
tt [ : , : , s ] = samplers_lda . tt_comp ( self . tokens , sampled_topics [ s , : ] , self . N , self . V , self . K , self . beta )
return tt |
def unique_everseen ( iterable , key = None ) :
"""Yield unique elements , preserving order .
> > > list ( unique _ everseen ( ' AAAABBBCCDAABBB ' ) )
[ ' A ' , ' B ' , ' C ' , ' D ' ]
> > > list ( unique _ everseen ( ' ABBCcAD ' , str . lower ) )
[ ' A ' , ' B ' , ' C ' , ' D ' ]
Sequences with a mix of ... | seenset = set ( )
seenset_add = seenset . add
seenlist = [ ]
seenlist_add = seenlist . append
if key is None :
for element in iterable :
try :
if element not in seenset :
seenset_add ( element )
yield element
except TypeError :
if element not i... |
def get ( self , name , handler , request = None ) :
"""Begin Fetch of current value of a PV
: param name : A single name string or list of name strings
: param request : A : py : class : ` p4p . Value ` or string to qualify this request , or None to use a default .
: param callable handler : Completion notif... | chan = self . _channel ( name )
return _p4p . ClientOperation ( chan , handler = unwrapHandler ( handler , self . _nt ) , pvRequest = wrapRequest ( request ) , get = True , put = False ) |
def register_i18n_js ( self , * paths ) :
"""Register templates path translations files , like
` select2 / select2 _ locale _ { lang } . js ` .
Only existing files are registered .""" | languages = self . config [ "BABEL_ACCEPT_LANGUAGES" ]
assets = self . extensions [ "webassets" ]
for path in paths :
for lang in languages :
filename = path . format ( lang = lang )
try :
assets . resolver . search_for_source ( assets , filename )
except IOError :
pa... |
def resample_ann ( resampled_t , ann_sample ) :
"""Compute the new annotation indices
Parameters
resampled _ t : numpy array
Array of signal locations as returned by scipy . signal . resample
ann _ sample : numpy array
Array of annotation locations
Returns
resampled _ ann _ sample : numpy array
Arra... | tmp = np . zeros ( len ( resampled_t ) , dtype = 'int16' )
j = 0
tprec = resampled_t [ j ]
for i , v in enumerate ( ann_sample ) :
while True :
d = False
if v < tprec :
j -= 1
tprec = resampled_t [ j ]
if j + 1 == len ( resampled_t ) :
tmp [ j ] += 1
... |
def new_result ( self , data_mode = 'value' , time_mode = 'framewise' ) :
'''Create a new result
Attributes
data _ object : MetadataObject
id _ metadata : MetadataObject
audio _ metadata : MetadataObject
frame _ metadata : MetadataObject
label _ metadata : MetadataObject
parameters : dict''' | from datetime import datetime
result = AnalyzerResult ( data_mode = data_mode , time_mode = time_mode )
# Automatically write known metadata
result . id_metadata . date = datetime . now ( ) . replace ( microsecond = 0 ) . isoformat ( ' ' )
result . id_metadata . version = timeside . core . __version__
result . id_metad... |
def macronize_text ( self , text ) :
"""Return macronized form of text .
E . g . " Gallia est omnis divisa in partes tres , " - >
" galliā est omnis dīvīsa in partēs trēs , "
: param text : raw text
: return : macronized text
: rtype : str""" | macronized_words = [ entry [ 2 ] for entry in self . macronize_tags ( text ) ]
return " " . join ( macronized_words ) |
def partition_chem_env ( self , n_sphere = 4 , use_lookup = None ) :
"""This function partitions the molecule into subsets of the
same chemical environment .
A chemical environment is specified by the number of
surrounding atoms of a certain kind around an atom with a
certain atomic number represented by a ... | if use_lookup is None :
use_lookup = settings [ 'defaults' ] [ 'use_lookup' ]
def get_chem_env ( self , i , n_sphere ) :
env_index = self . get_coordination_sphere ( i , n_sphere = n_sphere , only_surface = False , give_only_index = True , use_lookup = use_lookup )
env_index . remove ( i )
atoms = self ... |
def present ( name , type , url , access = None , user = None , password = None , database = None , basic_auth = None , basic_auth_user = None , basic_auth_password = None , tls_auth = None , json_data = None , is_default = None , with_credentials = None , type_logo_url = None , orgname = None , profile = 'grafana' ) :... | if isinstance ( profile , string_types ) :
profile = __salt__ [ 'config.option' ] ( profile )
ret = { 'name' : name , 'result' : None , 'comment' : None , 'changes' : { } }
datasource = __salt__ [ 'grafana4.get_datasource' ] ( name , orgname , profile )
data = _get_json_data ( name = name , type = type , url = url ... |
def multi_interpolation_basis ( n_objectives = 6 , n_interp_steps = 5 , width = 128 , channels = 3 ) :
"""A paramaterization for interpolating between each pair of N objectives .
Sometimes you want to interpolate between optimizing a bunch of objectives ,
in a paramaterization that encourages images to align . ... | N , M , W , Ch = n_objectives , n_interp_steps , width , channels
const_term = sum ( [ lowres_tensor ( [ W , W , Ch ] , [ W // k , W // k , Ch ] ) for k in [ 1 , 2 , 4 , 8 ] ] )
const_term = tf . reshape ( const_term , [ 1 , 1 , 1 , W , W , Ch ] )
example_interps = [ sum ( [ lowres_tensor ( [ M , W , W , Ch ] , [ 2 , W... |
def validate ( self , fixerrors = True ) :
"""Validates that the geometry is correctly formatted according to the geometry type .
Parameters :
- * * fixerrors * * ( optional ) : Attempts to fix minor errors without raising exceptions ( defaults to True )
Returns :
- True if the geometry is valid .
Raises ... | # validate nullgeometry or has type and coordinates keys
if not self . _data : # null geometry , no further checking needed
return True
elif "type" not in self . _data or "coordinates" not in self . _data :
raise Exception ( "A geometry dictionary or instance must have the type and coordinates entries" )
# firs... |
def registrar_for_scope ( cls , goal ) :
"""Returns a subclass of this registrar suitable for registering on the specified goal .
Allows reuse of the same registrar for multiple goals , and also allows us to decouple task
code from knowing which goal ( s ) the task is to be registered in .""" | type_name = '{}_{}' . format ( cls . __name__ , goal )
if PY2 :
type_name = type_name . encode ( 'utf-8' )
return type ( type_name , ( cls , ) , { 'options_scope' : goal } ) |
def list ( self , ** params ) :
"""Retrieve all contacts
Returns all contacts available to the user according to the parameters provided
: calls : ` ` get / contacts ` `
: param dict params : ( optional ) Search options .
: return : List of dictionaries that support attriubte - style access , which represen... | _ , _ , contacts = self . http_client . get ( "/contacts" , params = params )
return contacts |
def get_idxs ( data , eid2idx ) :
"""Convert from event IDs to event indices .
: param data : an array with a field eid
: param eid2idx : a dictionary eid - > idx
: returns : the array of event indices""" | uniq , inv = numpy . unique ( data [ 'eid' ] , return_inverse = True )
idxs = numpy . array ( [ eid2idx [ eid ] for eid in uniq ] ) [ inv ]
return idxs |
def match_url ( self , request ) :
"""Match the request against a file in the adapter directory
: param request : The request
: type request : : class : ` requests . Request `
: return : Path to the file
: rtype : ` ` str ` `""" | parsed_url = urlparse ( request . path_url )
path_url = parsed_url . path
query_params = parsed_url . query
match = None
for path in self . paths :
for item in self . index :
target_path = os . path . join ( BASE_PATH , path , path_url [ 1 : ] )
query_path = target_path . lower ( ) + quote ( '?' + q... |
def _get_aria_autocomplete ( self , field ) :
"""Returns the appropriate value for attribute aria - autocomplete of field .
: param field : The field .
: type field : hatemile . util . html . htmldomelement . HTMLDOMElement
: return : The ARIA value of field .
: rtype : str""" | tag_name = field . get_tag_name ( )
input_type = None
if field . has_attribute ( 'type' ) :
input_type = field . get_attribute ( 'type' ) . lower ( )
if ( ( tag_name == 'TEXTAREA' ) or ( ( tag_name == 'INPUT' ) and ( not ( ( input_type == 'button' ) or ( input_type == 'submit' ) or ( input_type == 'reset' ) or ( in... |
def _aggregate_on_chunks ( x , f_agg , chunk_len ) :
"""Takes the time series x and constructs a lower sampled version of it by applying the aggregation function f _ agg on
consecutive chunks of length chunk _ len
: param x : the time series to calculate the aggregation of
: type x : numpy . ndarray
: param... | return [ getattr ( x [ i * chunk_len : ( i + 1 ) * chunk_len ] , f_agg ) ( ) for i in range ( int ( np . ceil ( len ( x ) / chunk_len ) ) ) ] |
def badgify_badges ( ** kwargs ) :
"""Returns all badges or only awarded badges for the given user .""" | User = get_user_model ( )
user = kwargs . get ( 'user' , None )
username = kwargs . get ( 'username' , None )
if username :
try :
user = User . objects . get ( username = username )
except User . DoesNotExist :
pass
if user :
awards = Award . objects . filter ( user = user ) . select_related... |
def room ( self , name , participantIdentity = None , ** kwargs ) :
"""Create a < Room > element
: param name : Room name
: param participantIdentity : Participant identity when connecting to the Room
: param kwargs : additional attributes
: returns : < Room > element""" | return self . nest ( Room ( name , participantIdentity = participantIdentity , ** kwargs ) ) |
def msg ( message ) :
"""Log a regular message
: param message : the message to be logged""" | to_stdout ( " --- {message}" . format ( message = message ) )
if _logger :
_logger . info ( message ) |
def remove ( self , rev , permanent = False ) :
"""Removes a revision from this changelist
: param rev : Revision to remove
: type rev : : class : ` . Revision `
: param permanent : Whether or not we need to set the changelist to default
: type permanent : bool""" | if not isinstance ( rev , Revision ) :
raise TypeError ( 'argument needs to be an instance of Revision' )
if rev not in self :
raise ValueError ( '{} not in changelist' . format ( rev ) )
self . _files . remove ( rev )
if not permanent :
rev . changelist = self . _connection . default |
def get_full_recirc_content ( self , published = True ) :
"""performs es search and gets all content objects""" | q = self . get_query ( )
search = custom_search_model ( Content , q , published = published , field_map = { "feature_type" : "feature_type.slug" , "tag" : "tags.slug" , "content-type" : "_type" } )
return search |
def wrap_io_os_err ( e ) :
'''Formats IO and OS error messages for wrapping in FSQExceptions''' | msg = ''
if e . strerror :
msg = e . strerror
if e . message :
msg = ' ' . join ( [ e . message , msg ] )
if e . filename :
msg = ': ' . join ( [ msg , e . filename ] )
return msg |
def extract_css_links ( bs4 ) :
"""Extracting css links from BeautifulSoup object
: param bs4 : ` BeautifulSoup `
: return : ` list ` List of links""" | links = extract_links ( bs4 )
real_css = [ anchor for anchor in links if anchor . endswith ( ( '.css' , '.CSS' ) ) ]
css_link_tags = [ anchor [ 'href' ] for anchor in bs4 . select ( 'link[type="text/css"]' ) if anchor . has_attr ( 'href' ) ]
return list ( set ( real_css + css_link_tags ) ) |
async def list_statuses ( self , request ) :
"""Fetches the committed status of batches by either a POST or GET .
Request :
body : A JSON array of one or more id strings ( if POST )
query :
- id : A comma separated list of up to 15 ids ( if GET )
- wait : Request should not return until all batches commit... | error_traps = [ error_handlers . StatusResponseMissing ]
# Parse batch ids from POST body , or query paramaters
if request . method == 'POST' :
if request . headers [ 'Content-Type' ] != 'application/json' :
LOGGER . debug ( 'Request headers had wrong Content-Type: %s' , request . headers [ 'Content-Type' ]... |
def fft_coefficient ( self , x , param = None ) :
"""As in tsfresh ` fft _ coefficient < https : / / github . com / blue - yonder / tsfresh / blob / master / tsfresh / feature _ extraction / feature _ calculators . py # L852 > ` _ Calculates the fourier coefficients of the one - dimensional discrete Fourier Transfo... | if param is None :
param = [ { 'attr' : 'abs' , 'coeff' : 44 } , { 'attr' : 'abs' , 'coeff' : 63 } , { 'attr' : 'abs' , 'coeff' : 0 } , { 'attr' : 'real' , 'coeff' : 0 } , { 'attr' : 'real' , 'coeff' : 23 } ]
_fft_coef = feature_calculators . fft_coefficient ( x , param )
logging . debug ( "fft coefficient by tsfre... |
def get_country_long ( self , ip ) :
'''Get country _ long''' | rec = self . get_all ( ip )
return rec and rec . country_long |
def is_jid ( jid ) :
'''Returns True if the passed in value is a job id''' | if not isinstance ( jid , six . string_types ) :
return False
if len ( jid ) != 20 and ( len ( jid ) <= 21 or jid [ 20 ] != '_' ) :
return False
try :
int ( jid [ : 20 ] )
return True
except ValueError :
return False |
def event ( self , event ) :
"""Allow GUI to be closed upon holding Shift""" | if event . type ( ) == QtCore . QEvent . Close :
modifiers = self . app . queryKeyboardModifiers ( )
shift_pressed = QtCore . Qt . ShiftModifier & modifiers
states = self . app . controller . states
if shift_pressed :
print ( "Force quitted.." )
self . app . controller . host . emit ( "p... |
def update ( self ) :
'''Update our object ' s data''' | self . _json = self . _request ( method = 'GET' , url = self . API ) . _json |
def validate ( self , input_parameters , context ) :
"""Runs all set type transformers / validators against the provided input parameters and returns any errors""" | errors = { }
for key , type_handler in self . input_transformations . items ( ) :
if self . raise_on_invalid :
if key in input_parameters :
input_parameters [ key ] = self . initialize_handler ( type_handler , input_parameters [ key ] , context = context )
else :
try :
if... |
def group_by_key_func ( iterable , key_func ) :
"""Create a dictionary from an iterable such that the keys are the result of evaluating a key function on elements
of the iterable and the values are lists of elements all of which correspond to the key .
> > > def si ( d ) : return sorted ( d . items ( ) )
> > ... | result = defaultdict ( list )
for item in iterable :
result [ key_func ( item ) ] . append ( item )
return result |
def read_config ( * args ) :
'''Read Traffic Server configuration variable definitions .
. . versionadded : : 2016.11.0
. . code - block : : bash
salt ' * ' trafficserver . read _ config proxy . config . http . keep _ alive _ post _ out''' | ret = { }
if _TRAFFICCTL :
cmd = _traffic_ctl ( 'config' , 'get' )
else :
cmd = _traffic_line ( '-r' )
try :
for arg in args :
log . debug ( 'Querying: %s' , arg )
ret [ arg ] = _subprocess ( cmd + [ arg ] )
except KeyError :
pass
return ret |
def end_at ( self , document_fields ) :
"""End query results at a particular document value .
The result set will * * include * * the document specified by
` ` document _ fields ` ` .
If the current query already has specified an end cursor - - either
via this method or
: meth : ` ~ . firestore _ v1beta1 ... | return self . _cursor_helper ( document_fields , before = False , start = False ) |
def _build ( self , parent_cache ) :
"""Build the initial cache from the parent .
Only include the | MICE | which are unaffected by the subsystem cut .
A | MICE | is affected if either the cut splits the mechanism
or splits the connections between the purview and mechanism""" | for key , mice in parent_cache . cache . items ( ) :
if not mice . damaged_by_cut ( self . subsystem ) :
self . cache [ key ] = mice |
def login_user ( server , login , password ) :
"""Get the login session .
: param server : The Geonode server URL .
: type server : basestring
: param login : The login to use on Geonode .
: type login : basestring
: param password : The password to use on Geonode .
: type password : basestring""" | login_url = urljoin ( server , login_url_prefix )
# Start the web session
session = requests . session ( )
result = session . get ( login_url )
# Check if the request ok
if not result . ok :
message = ( tr ( 'Request failed to {geonode_url}, got status code {status_code} ' 'and reason {request_reason}' ) . format (... |
def match_arr_lengths ( l ) :
"""Check that all the array lengths match so that a DataFrame can be created successfully .
: param list l : Nested arrays
: return bool : Valid or invalid""" | try : # length of first list . use as basis to check other list lengths against .
inner_len = len ( l [ 0 ] )
# check each nested list
for i in l : # if the length doesn ' t match the first list , then don ' t proceed .
if len ( i ) != inner_len :
return False
except IndexError : # could... |
def _is_en_passant_valid ( self , opponent_pawn_location , position ) :
"""Finds if their opponent ' s pawn is next to this pawn
: rtype : bool""" | try :
pawn = position . piece_at_square ( opponent_pawn_location )
return pawn is not None and isinstance ( pawn , Pawn ) and pawn . color != self . color and position . piece_at_square ( opponent_pawn_location ) . just_moved_two_steps
except IndexError :
return False |
def namedb_namespace_insert ( cur , input_namespace_rec ) :
"""Add a namespace to the database ,
if it doesn ' t exist already .
It must be a * revealed * namespace , not a ready namespace
( to mark a namespace as ready , you should use the namedb _ apply _ operation ( )
method ) .""" | namespace_rec = copy . deepcopy ( input_namespace_rec )
namedb_namespace_fields_check ( namespace_rec )
try :
query , values = namedb_insert_prepare ( cur , namespace_rec , "namespaces" )
except Exception , e :
log . exception ( e )
log . error ( "FATAL: Failed to insert revealed namespace '%s'" % namespace... |
def build ( ctx , max_revisions , targets , operators , archiver ) :
"""Build the wily cache .""" | config = ctx . obj [ "CONFIG" ]
from wily . commands . build import build
if max_revisions :
logger . debug ( f"Fixing revisions to {max_revisions}" )
config . max_revisions = max_revisions
if operators :
logger . debug ( f"Fixing operators to {operators}" )
config . operators = operators . strip ( ) . ... |
def list_items ( queue ) :
'''List contents of a queue''' | itemstuple = _list_items ( queue )
items = [ item [ 0 ] for item in itemstuple ]
return items |
def parse_fastp_log ( self , f ) :
"""Parse the JSON output from fastp and save the summary statistics""" | try :
parsed_json = json . load ( f [ 'f' ] )
except :
log . warn ( "Could not parse fastp JSON: '{}'" . format ( f [ 'fn' ] ) )
return None
# Fetch a sample name from the command
s_name = f [ 's_name' ]
cmd = parsed_json [ 'command' ] . split ( )
for i , v in enumerate ( cmd ) :
if v == '-i' :
... |
def transpose ( self , * axes ) :
"""Permute the dimensions of a Timeseries .""" | if self . ndim <= 1 :
return self
ar = np . asarray ( self ) . transpose ( * axes )
if axes [ 0 ] != 0 : # then axis 0 is unaffected by the transposition
newlabels = [ self . labels [ ax ] for ax in axes ]
return Timeseries ( ar , self . tspan , newlabels )
else :
return ar |
def init_app ( self , app , ** kwargs ) :
"""Initialize application object .
: param app : An instance of : class : ` ~ flask . Flask ` .""" | self . init_config ( app )
# Initialize extensions
self . menu_ext . init_app ( app )
self . menu = app . extensions [ 'menu' ]
self . breadcrumbs . init_app ( app )
# Register blueprint in order to register template and static folder .
app . register_blueprint ( Blueprint ( 'invenio_theme' , __name__ , template_folder... |
def write_ndef ( self , ndef , slot = 1 ) :
"""Write an NDEF tag configuration to the YubiKey NEO .""" | if not self . capabilities . have_nfc_ndef ( slot ) :
raise yubikey_base . YubiKeyVersionError ( "NDEF slot %i unsupported in %s" % ( slot , self ) )
return self . _device . _write_config ( ndef , _NDEF_SLOTS [ slot ] ) |
def pdb_downloader_and_metadata ( self , outdir = None , pdb_file_type = None , force_rerun = False ) :
"""Download ALL mapped experimental structures to the protein structures directory .
Args :
outdir ( str ) : Path to output directory , if protein structures directory not set or other output directory is
d... | if not outdir :
outdir = self . structure_dir
if not outdir :
raise ValueError ( 'Output directory must be specified' )
if not pdb_file_type :
pdb_file_type = self . pdb_file_type
# Check if we have any PDBs
if self . num_structures_experimental == 0 :
log . debug ( '{}: no structures available ... |
def _escape ( self , bits ) :
"""value : ' foobar { ' - > ' foobar { { '
value : ' x } ' - > ' x } } '""" | # for value , field _ name , format _ spec , conversion in bits :
while True :
try :
value , field_name , format_spec , conversion = next ( bits )
if value :
end = value [ - 1 ]
if end in ( u'{' , u'}' ) :
value += end
yield value , field_name , format... |
def setup_logging ( app , disable_existing_loggers = True ) :
"""Setup the logging using logging . yaml .
: param app : The app which setups the logging . Used for the log ' s filename and for the log ' s name .
: type app : str
: param disable _ existing _ loggers : If False , loggers which exist when this c... | conf = yaml . load ( open ( os . path . join ( os . path . dirname ( os . path . abspath ( __file__ ) ) , 'logging.yaml' ) , 'r' ) )
conf [ 'disable_existing_loggers' ] = disable_existing_loggers
conf [ 'loggers' ] [ app ] = conf [ 'loggers' ] . pop ( '__name__' )
logging . config . dictConfig ( conf ) |
def removeRnaQuantificationSet ( self ) :
"""Removes an rnaQuantificationSet from this repo""" | self . _openRepo ( )
dataset = self . _repo . getDatasetByName ( self . _args . datasetName )
rnaQuantSet = dataset . getRnaQuantificationSetByName ( self . _args . rnaQuantificationSetName )
def func ( ) :
self . _updateRepo ( self . _repo . removeRnaQuantificationSet , rnaQuantSet )
self . _confirmDelete ( "RnaQu... |
def procrustes ( a , b , reflection = True , translation = True , scale = True , return_cost = True ) :
"""Perform Procrustes ' analysis subject to constraints . Finds the
transformation T mapping a to b which minimizes the square sum
distances between Ta and b , also called the cost .
Parameters
a : ( n , ... | a = np . asanyarray ( a , dtype = np . float64 )
b = np . asanyarray ( b , dtype = np . float64 )
if not util . is_shape ( a , ( - 1 , 3 ) ) or not util . is_shape ( b , ( - 1 , 3 ) ) :
raise ValueError ( 'points must be (n,3)!' )
if len ( a ) != len ( b ) :
raise ValueError ( 'a and b must contain same number ... |
def fetch_starting_at_coord ( self , coord ) : # b2 = BAMFile ( self . path , blockStart = coord [ 0 ] , innerStart = coord [ 1 ] , index _ obj = self . index , reference = self . _ reference )
"""starting at a certain coordinate was supposed to make output
. . warning : : creates a new instance of a BAMFile obje... | b2 = BAMFile ( self . path , BAMFile . Options ( blockStart = coord [ 0 ] , innerStart = coord [ 1 ] , reference = self . reference ) )
return b2 |
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