signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def handle ( self , error , connection ) :
"""Handle any cleanup or similar activity related to an error
occurring on a pooled connection .""" | error_class = error . __class__
if error_class in ( ConnectionExpired , ServiceUnavailable , DatabaseUnavailableError ) :
self . deactivate ( connection . address )
elif error_class in ( NotALeaderError , ForbiddenOnReadOnlyDatabaseError ) :
self . remove_writer ( connection . address ) |
def refresh_hrefs ( self , request ) :
"""Refresh all the cached menu item HREFs in the database .""" | for item in treenav . MenuItem . objects . all ( ) :
item . save ( )
# refreshes the HREF
self . message_user ( request , _ ( 'Menu item HREFs refreshed successfully.' ) )
info = self . model . _meta . app_label , self . model . _meta . model_name
changelist_url = reverse ( 'admin:%s_%s_changelist' % info , cur... |
def values ( self ) :
"""Returns a list of all values in the dictionary .
Returns :
list of str : [ value1 , value2 , . . . , valueN ]""" | all_values = [ v . decode ( 'utf-8' ) for k , v in self . rdb . hgetall ( self . session_hash ) . items ( ) ]
return all_values |
def clean ( self , value ) :
"""Clean
Goes through each of the values in the list , cleans it , stores it , and
returns a new list
Arguments :
value { list } - - The value to clean
Returns :
list""" | # If the value is None and it ' s optional , return as is
if value is None and self . _optional :
return None
# If the value is not a list
if not isinstance ( value , list ) :
raise ValueError ( 'value' )
# Recurse and return it
return [ self . _node . clean ( m ) for m in value ] |
def cone ( cls , ** kwargs ) :
"""Returns a cone .
Kwargs :
start ( list ) : Start of cone , default [ 0 , - 1 , 0 ] .
end ( list ) : End of cone , default [ 0 , 1 , 0 ] .
radius ( float ) : Maximum radius of cone at start , default 1.0.
slices ( int ) : Number of slices , default 16.""" | s = kwargs . get ( 'start' , Vector ( 0.0 , - 1.0 , 0.0 ) )
e = kwargs . get ( 'end' , Vector ( 0.0 , 1.0 , 0.0 ) )
if isinstance ( s , list ) :
s = Vector ( * s )
if isinstance ( e , list ) :
e = Vector ( * e )
r = kwargs . get ( 'radius' , 1.0 )
slices = kwargs . get ( 'slices' , 16 )
ray = e . minus ( s )
ax... |
def changed ( self , filename = '.md5' , glob = None ) :
"""Are any of the files matched by ` ` glob ` ` changed ?""" | if glob is not None :
filename += '.glob-' + '' . join ( ch . lower ( ) for ch in glob if ch . isalpha ( ) )
return changed ( self , filename , glob = glob ) |
def later_than ( after , before ) :
"""True if then is later or equal to that""" | if isinstance ( after , str ) :
after = str_to_time ( after )
elif isinstance ( after , int ) :
after = time . gmtime ( after )
if isinstance ( before , str ) :
before = str_to_time ( before )
elif isinstance ( before , int ) :
before = time . gmtime ( before )
return after >= before |
def _hash ( self , iv , value ) :
"""Generate and hmac signature for this encrypted data
: param key :
: param iv :
: param value :
: return string :""" | return hmac . new ( self . key , msg = iv + value , digestmod = hashlib . sha256 ) . hexdigest ( ) |
def get_protein_id_list ( df , level = 0 ) :
"""Return a complete list of shortform IDs from a DataFrame
Extract all protein IDs from a dataframe from multiple rows containing
protein IDs in MaxQuant output format : e . g . P07830 ; P63267 ; Q54A44 ; P63268
Long names ( containing species information ) are el... | protein_list = [ ]
for s in df . index . get_level_values ( level ) :
protein_list . extend ( get_protein_ids ( s ) )
return list ( set ( protein_list ) ) |
def _push_tag_buffer ( self , data ) :
"""Write a pending tag attribute from * data * to the stack .""" | if data . context & data . CX_QUOTED :
self . _emit_first ( tokens . TagAttrQuote ( char = data . quoter ) )
self . _emit_all ( self . _pop ( ) )
buf = data . padding_buffer
self . _emit_first ( tokens . TagAttrStart ( pad_first = buf [ "first" ] , pad_before_eq = buf [ "before_eq" ] , pad_after_eq = buf [ "aft... |
def restore ( self ) :
"""Copy files from the backup folder to the sym - linked optimizer folder .""" | if os . path . exists ( self . backup_path ) :
for file in glob . glob ( self . backup_path + "/*" ) :
shutil . copy ( file , self . path ) |
def parameters ( self ) :
"""A property that returns all of the model ' s parameters .""" | parameters = [ ]
for hl in self . hidden_layers :
parameters . extend ( hl . parameters )
parameters . extend ( self . top_layer . parameters )
return parameters |
def add_typeattr ( typeattr , ** kwargs ) :
"""Add an typeattr to an existing type .""" | tmpltype = get_templatetype ( typeattr . type_id , user_id = kwargs . get ( 'user_id' ) )
ta = _set_typeattr ( typeattr )
tmpltype . typeattrs . append ( ta )
db . DBSession . flush ( )
return ta |
def plot_aqhist ( samples , file_type , ** plot_args ) :
"""Create line graph plot of histogram data for BBMap ' aqhist ' output .
The ' samples ' parameter could be from the bbmap mod _ data dictionary :
samples = bbmap . MultiqcModule . mod _ data [ file _ type ]""" | sumy = sum ( [ int ( samples [ sample ] [ 'data' ] [ x ] [ 0 ] ) for sample in samples for x in samples [ sample ] [ 'data' ] ] )
cutoff = sumy * 0.999
all_x = set ( )
for item in sorted ( chain ( * [ samples [ sample ] [ 'data' ] . items ( ) for sample in samples ] ) ) :
all_x . add ( item [ 0 ] )
cutoff -= it... |
def _get_response ( self , method , endpoint , data = None ) :
"""Helper method for wrapping API requests , mainly for catching errors
in one place .
: param method : valid HTTP method
: type method : str
: param endpoint : API endpoint
: type endpoint : str
: param data : extra parameters passed with t... | url = urljoin ( IVONA_REGION_ENDPOINTS [ self . region ] , endpoint )
response = getattr ( self . session , method ) ( url , json = data , )
if 'x-amzn-ErrorType' in response . headers :
raise IvonaAPIException ( response . headers [ 'x-amzn-ErrorType' ] )
if response . status_code != requests . codes . ok :
ra... |
def match_window ( in_data , offset ) :
'''Find the longest match for the string starting at offset in the preceeding data''' | window_start = max ( offset - WINDOW_MASK , 0 )
for n in range ( MAX_LEN , THRESHOLD - 1 , - 1 ) :
window_end = min ( offset + n , len ( in_data ) )
# we ' ve not got enough data left for a meaningful result
if window_end - offset < THRESHOLD :
return None
str_to_find = in_data [ offset : window... |
def _read_config ( self ) :
"""Read the configuration from the various places it may be read from .
: rtype : str
: raises : ValueError""" | if not self . _file_path :
return None
elif self . _file_path . startswith ( 's3://' ) :
return self . _read_s3_config ( )
elif self . _file_path . startswith ( 'http://' ) or self . _file_path . startswith ( 'https://' ) :
return self . _read_remote_config ( )
elif not path . exists ( self . _file_path ) :... |
async def addNodes ( self , nodes ) :
'''Add a list of packed nodes to the cortex .
Args :
nodes ( list ) : [ ( ( form , valu ) , { ' props ' : { } , ' tags ' : { } } ) , . . . ]
Yields :
( tuple ) : Packed node tuples ( ( form , valu ) , { ' props ' : { } , ' tags ' : { } } )''' | # First check that that user may add each form
done = { }
for node in nodes :
formname = node [ 0 ] [ 0 ]
if done . get ( formname ) :
continue
self . _reqUserAllowed ( 'node:add' , formname )
done [ formname ] = True
async with await self . cell . snap ( user = self . user ) as snap :
with ... |
def _compute_dk_dtau ( self , tau , n ) :
r"""Evaluate : math : ` dk / d \ tau ` at the specified locations with the specified derivatives .
Parameters
tau : : py : class : ` Matrix ` , ( ` M ` , ` D ` )
` M ` inputs with dimension ` D ` .
n : : py : class : ` Array ` , ( ` D ` , )
Degree of derivative wi... | # Construct the derivative pattern :
# For each dimension , this will contain the index of the dimension
# repeated a number of times equal to the order of derivative with
# respect to that dimension .
# Example : For d ^ 3 k ( x , y , z ) / dx ^ 2 dy , n would be [ 2 , 1 , 0 ] and
# deriv _ pattern should be [ 0 , 0 ,... |
def _postprocess_hover ( self , renderer , source ) :
"""Limit hover tool to annular wedges only .""" | if isinstance ( renderer . glyph , AnnularWedge ) :
super ( RadialHeatMapPlot , self ) . _postprocess_hover ( renderer , source ) |
def __objecthasfields ( bunchdt , data , commdct , idfobject , places = 7 , ** kwargs ) :
"""test if the idf object has the field values in kwargs""" | for key , value in list ( kwargs . items ( ) ) :
if not isfieldvalue ( bunchdt , data , commdct , idfobject , key , value , places = places ) :
return False
return True |
def make_market ( self , crypto , fiat , seperator = "_" ) :
"""Convert a crypto and fiat to a " market " string . All exchanges use their
own format for specifying markets . Subclasses can define their own
implementation .""" | return ( "%s%s%s" % ( self . fix_symbol ( crypto ) , seperator , self . fix_symbol ( fiat ) ) ) . lower ( ) |
def get_default_config ( self ) :
"""Returns the default collector settings""" | config = super ( NetworkCollector , self ) . get_default_config ( )
config . update ( { 'path' : 'network' , 'interfaces' : [ 'eth' , 'bond' , 'em' , 'p1p' , 'eno' , 'enp' , 'ens' , 'enx' ] , 'byte_unit' : [ 'bit' , 'byte' ] , 'greedy' : 'true' , } )
return config |
def rmi ( self , force = False , via_name = False ) :
"""remove this image
: param force : bool , force removal of the image
: param via _ name : bool , refer to the image via name , if false , refer via ID , not used now
: return : None""" | return os . remove ( self . local_location ) |
def login ( ctx ) :
"""Add an API key ( saved in ~ / . onecodex )""" | base_url = os . environ . get ( "ONE_CODEX_API_BASE" , "https://app.onecodex.com" )
if not ctx . obj [ "API_KEY" ] :
_login ( base_url )
else :
email = _login ( base_url , api_key = ctx . obj [ "API_KEY" ] )
ocx = Api ( api_key = ctx . obj [ "API_KEY" ] , telemetry = ctx . obj [ "TELEMETRY" ] )
# TODO :... |
def solar_noon_utc ( self , date , longitude ) :
"""Calculate solar noon time in the UTC timezone .
: param date : Date to calculate for .
: type date : : class : ` datetime . date `
: param longitude : Longitude - Eastern longitudes should be positive
: type longitude : float
: return : The UTC date and ... | jc = self . _jday_to_jcentury ( self . _julianday ( date ) )
eqtime = self . _eq_of_time ( jc )
timeUTC = ( 720.0 - ( 4 * longitude ) - eqtime ) / 60.0
hour = int ( timeUTC )
minute = int ( ( timeUTC - hour ) * 60 )
second = int ( ( ( ( timeUTC - hour ) * 60 ) - minute ) * 60 )
if second > 59 :
second -= 60
min... |
def _lookup ( self , p , directory , fsclass , create = 1 ) :
"""The generic entry point for Node lookup with user - supplied data .
This translates arbitrary input into a canonical Node . FS object
of the specified fsclass . The general approach for strings is
to turn it into a fully normalized absolute path... | if isinstance ( p , Base ) : # It ' s already a Node . FS object . Make sure it ' s the right
# class and return .
p . must_be_same ( fsclass )
return p
# str ( p ) in case it ' s something like a proxy object
p = str ( p )
if not os_sep_is_slash :
p = p . replace ( OS_SEP , '/' )
if p [ 0 : 1 ] == '#' : # ... |
def load_clubs ( self ) :
"""Fetches the MAL character clubs page and sets the current character ' s clubs attributes .
: rtype : : class : ` . Character `
: return : Current character object .""" | character = self . session . session . get ( u'http://myanimelist.net/character/' + str ( self . id ) + u'/' + utilities . urlencode ( self . name ) + u'/clubs' ) . text
self . set ( self . parse_clubs ( utilities . get_clean_dom ( character ) ) )
return self |
async def _send_sleep ( self , request : Request , stack : Stack ) :
"""Sleep for the amount of time specified in the Sleep layer""" | duration = stack . get_layer ( lyr . Sleep ) . duration
await sleep ( duration ) |
def copy_path_to_clipboard ( self ) :
"""Copies the file path to the clipboard""" | path = self . get_current_path ( )
QtWidgets . QApplication . clipboard ( ) . setText ( path )
debug ( 'path copied: %s' % path ) |
def activate ( request , activation_key , template_name = 'userena/activate_fail.html' , retry_template_name = 'userena/activate_retry.html' , success_url = None , extra_context = None ) :
"""Activate a user with an activation key .
The key is a SHA1 string . When the SHA1 is found with an
: class : ` UserenaSi... | try :
if ( not UserenaSignup . objects . check_expired_activation ( activation_key ) or not userena_settings . USERENA_ACTIVATION_RETRY ) :
user = UserenaSignup . objects . activate_user ( activation_key )
if user : # Sign the user in .
auth_user = authenticate ( identification = user . ... |
def open ( self , filepath , mode = 'w+b' ) :
"""Opens a file - will actually return a temporary file but replace the
original file when the context is closed .""" | # Check if the filepath can be accessed and is writable before creating
# the tempfile
if not _isFileAccessible ( filepath ) :
raise IOError ( 'File %s is not writable' % ( filepath , ) )
if filepath in self . _files :
with open ( self . _files [ filepath ] , mode = mode ) as tmpf :
yield tmpf
else :
... |
def agedepth ( self , d ) :
"""Get calendar age for a depth
Parameters
d : float
Sediment depth ( in cm ) .
Returns
Numeric giving true age at given depth .""" | # TODO ( brews ) : Function cannot handle hiatus
# See lines 77 - 100 of hist2 . cpp
x = self . mcmcfit . sediment_rate
theta0 = self . mcmcfit . headage
# Age abscissa ( in yrs ) . If array , dimension should be iterations or realizations of the sediment
deltac = self . thick
c0 = min ( self . depth )
# Uniform depth ... |
def separation ( sources , fs = 22050 , labels = None , alpha = 0.75 , ax = None , ** kwargs ) :
'''Source - separation visualization
Parameters
sources : np . ndarray , shape = ( nsrc , nsampl )
A list of waveform buffers corresponding to each source
fs : number > 0
The sampling rate
labels : list of s... | # Get the axes handle
ax , new_axes = __get_axes ( ax = ax )
# Make sure we have at least two dimensions
sources = np . atleast_2d ( sources )
if labels is None :
labels = [ 'Source {:d}' . format ( _ ) for _ in range ( len ( sources ) ) ]
kwargs . setdefault ( 'scaling' , 'spectrum' )
# The cumulative spectrogram ... |
def make_workspace ( measurement , channel = None , name = None , silence = False ) :
"""Create a workspace containing the model for a measurement
If ` channel ` is None then include all channels in the model
If ` silence ` is True , then silence HistFactory ' s output on
stdout and stderr .""" | context = silence_sout_serr if silence else do_nothing
with context ( ) :
hist2workspace = ROOT . RooStats . HistFactory . HistoToWorkspaceFactoryFast ( measurement )
if channel is not None :
workspace = hist2workspace . MakeSingleChannelModel ( measurement , channel )
else :
workspace = his... |
def convex_hull ( self ) :
"""Find the Convex Hull of the internal set of x , y points .
Returns
bnodes : array of ints
indices corresponding to points on the convex hull""" | bnodes , nb , na , nt = _tripack . bnodes ( self . lst , self . lptr , self . lend , self . npoints )
return self . _deshuffle_simplices ( bnodes [ : nb ] - 1 ) |
def initnew ( self , fname ) :
"""Use the current IDD and create a new empty IDF . If the IDD has not yet
been initialised then this is done first .
Parameters
fname : str , optional
Path to an IDF . This does not need to be set at this point .""" | iddfhandle = StringIO ( iddcurrent . iddtxt )
if self . getiddname ( ) == None :
self . setiddname ( iddfhandle )
idfhandle = StringIO ( '' )
self . idfname = idfhandle
self . read ( )
if fname :
self . idfname = fname |
def sign_jwt ( data , secret_key , expires_in , salt = None , ** kw ) :
"""To create a signed JWT
: param data :
: param secret _ key :
: param expires _ in :
: param salt :
: param kw :
: return : string""" | s = itsdangerous . TimedJSONWebSignatureSerializer ( secret_key = secret_key , expires_in = expires_in , salt = salt , ** kw )
return s . dumps ( data ) |
def integratedAutocorrelationTime ( A_n , B_n = None , fast = False , mintime = 3 ) :
"""Estimate the integrated autocorrelation time .
See Also
statisticalInefficiency""" | g = statisticalInefficiency ( A_n , B_n , fast , mintime )
tau = ( g - 1.0 ) / 2.0
return tau |
def after_epoch ( self , epoch_id : int , epoch_data : EpochData ) :
"""Check termination conditions .
: param epoch _ id : number of the processed epoch
: param epoch _ data : epoch data to be checked
: raise KeyError : if the stream of variable was not found in ` ` epoch _ data ` `
: raise TypeError : if ... | if self . _stream not in epoch_data :
raise KeyError ( 'The hook could not determine whether the threshold was exceeded as the stream `{}`' 'was not found in the epoch data' . format ( self . _stream ) )
if self . _variable not in epoch_data [ self . _stream ] :
raise KeyError ( 'The hook could not determine wh... |
def random_words_string ( count = 1 , maxchars = None , sep = '' ) :
"""Gets a""" | nouns = sep . join ( [ random_word ( ) for x in xrange ( 0 , count ) ] )
if maxchars is not None and nouns > maxchars :
nouns = nouns [ 0 : maxchars - 1 ]
return nouns |
def identify ( self , geometry , mapExtent , imageDisplay , tolerance , geometryType = "esriGeometryPoint" , sr = None , layerDefs = None , time = None , layerTimeOptions = None , layers = "top" , returnGeometry = True , maxAllowableOffset = None , geometryPrecision = None , dynamicLayers = None , returnZ = False , ret... | params = { 'f' : 'json' , 'geometry' : geometry , 'geometryType' : geometryType , 'tolerance' : tolerance , 'mapExtent' : mapExtent , 'imageDisplay' : imageDisplay }
if layerDefs is not None :
params [ 'layerDefs' ] = layerDefs
if layers is not None :
params [ 'layers' ] = layers
if sr is not None :
params ... |
def _resolve_deps ( self , depmap ) :
"""Given a map of gen - key = > target specs , resolves the target specs into references .""" | deps = defaultdict ( lambda : OrderedSet ( ) )
for category , depspecs in depmap . items ( ) :
dependencies = deps [ category ]
for depspec in depspecs :
dep_address = Address . parse ( depspec )
try :
self . context . build_graph . maybe_inject_address_closure ( dep_address )
... |
def boolean ( name , value , persist = False ) :
'''Set up an SELinux boolean
name
The name of the boolean to set
value
The value to set on the boolean
persist
Defaults to False , set persist to true to make the boolean apply on a
reboot''' | ret = { 'name' : name , 'result' : True , 'comment' : '' , 'changes' : { } }
bools = __salt__ [ 'selinux.list_sebool' ] ( )
if name not in bools :
ret [ 'comment' ] = 'Boolean {0} is not available' . format ( name )
ret [ 'result' ] = False
return ret
rvalue = _refine_value ( value )
if rvalue is None :
... |
def save ( self ) :
"""Save current state of config dictionary .""" | with open ( self . config_file , "w" ) as f :
f . write ( dump ( self . config , default_flow_style = False ) ) |
def run_checked ( cmd , ret_ok = ( 0 , ) , ** kwargs ) :
"""Run command and raise PatoolError on error .""" | retcode = run ( cmd , ** kwargs )
if retcode not in ret_ok :
msg = "Command `%s' returned non-zero exit status %d" % ( cmd , retcode )
raise PatoolError ( msg )
return retcode |
def commit ( cls , client = None ) :
"""Commit everything from datapoints via the client .
: param client : InfluxDBClient instance for writing points to InfluxDB .
: attention : any provided client will supersede the class client .
: return : result of client . write _ points .""" | if not client :
client = cls . _client
rtn = client . write_points ( cls . _json_body_ ( ) )
cls . _reset_ ( )
return rtn |
def get_gateway_id ( self ) :
"""Return a unique id for the gateway .""" | host , _ = self . server_address
try :
ip_address = ipaddress . ip_address ( host )
except ValueError : # Only hosts using ip address supports unique id .
return None
if ip_address . version == 6 :
mac = get_mac_address ( ip6 = host )
else :
mac = get_mac_address ( ip = host )
return mac |
def generate_report ( self , output_file ) :
"""See base class .
output _ file must be a file handler that takes in bytes !""" | if self . TEMPLATE_NAME is not None :
template = TEMPLATE_ENV . get_template ( self . TEMPLATE_NAME )
report = template . render ( self . _context ( ) )
if isinstance ( report , six . string_types ) :
report = report . encode ( 'utf-8' )
output_file . write ( report ) |
def format ( sql , args = None ) :
"""Resolve variable references in a query within an environment .
This computes and resolves the transitive dependencies in the query and raises an
exception if that fails due to either undefined or circular references .
Args :
sql : query to format .
args : a dictionary... | resolved_vars = { }
code = [ ]
SqlStatement . _find_recursive_dependencies ( sql , args , code = code , resolved_vars = resolved_vars )
# Rebuild the SQL string , substituting just ' $ ' for escaped $ occurrences ,
# variable references substituted with their values , or literal text copied
# over as - is .
parts = [ ]... |
def clear ( self ) :
"""Clears all the container for this query widget .""" | for i in range ( self . count ( ) ) :
widget = self . widget ( i )
if widget is not None :
widget . close ( )
widget . setParent ( None )
widget . deleteLater ( ) |
def save_data ( self , filename = None ) :
"""Save data""" | if filename is None :
filename = self . filename
if filename is None :
filename = getcwd_or_home ( )
filename , _selfilter = getsavefilename ( self , _ ( "Save data" ) , filename , iofunctions . save_filters )
if filename :
self . filename = filename
else :
return False
QAppl... |
def export_to_pypsa ( self , session , method = 'onthefly' ) :
"""Exports MVGridDing0 grid to PyPSA database tables
Peculiarities of MV grids are implemented here . Derive general export
method from this and adapt to needs of LVGridDing0
Parameters
session : : sqlalchemy : ` SQLAlchemy session object < orm ... | # definitions for temp _ resolution table
temp_id = 1
timesteps = 2
start_time = datetime ( 1970 , 1 , 1 , 00 , 00 , 0 )
resolution = 'H'
nodes = self . _graph . nodes ( )
edges = [ edge for edge in list ( self . graph_edges ( ) ) if ( edge [ 'adj_nodes' ] [ 0 ] in nodes and not isinstance ( edge [ 'adj_nodes' ] [ 0 ] ... |
def set_max_attempts ( self , value ) :
"""stub""" | if value is None :
raise InvalidArgument ( 'value must be an integer' )
if value is not None and not isinstance ( value , int ) :
raise InvalidArgument ( 'value is not an integer' )
if not self . my_osid_object_form . _is_valid_integer ( value , self . get_max_attempts_metadata ( ) ) :
raise InvalidArgument... |
def _to_dict ( self ) :
"""Return a json dictionary representing this model .""" | _dict = { }
if hasattr ( self , 'id' ) and self . id is not None :
_dict [ 'id' ] = self . id
return _dict |
def _ordered_iterator ( self ) :
"""Interleave the values of each QuerySet in order to handle the requested
ordering . Also adds the ' # ' property to each returned item .""" | # A list of tuples , each with :
# * The iterable
# * The QuerySet number
# * The next value
# ( Remember that each QuerySet is already sorted . )
iterables = [ ]
for i , qs in zip ( self . _queryset_idxs , self . _querysets ) :
it = iter ( qs )
try :
value = next ( it )
except StopIteration : # If ... |
def submit ( ctx_name , parent_id , name , url , func , * args , ** kwargs ) :
"""Submit through a context
Parameters
ctx _ name : str
The name of the context to submit through
parent _ id : str
The ID of the group that the job is a part of .
name : str
The name of the job
url : str
The handler th... | if isinstance ( ctx_name , Context ) :
ctx = ctx_name
else :
ctx = ctxs . get ( ctx_name , ctxs [ ctx_default ] )
return _submit ( ctx , parent_id , name , url , func , * args , ** kwargs ) |
def feed ( self , json_item ) :
'''Feeds a json item into the Kafka topic
@ param json _ item : The loaded json object''' | @ MethodTimer . timeout ( self . settings [ 'KAFKA_FEED_TIMEOUT' ] , False )
def _feed ( json_item ) :
producer = self . _create_producer ( )
topic = self . settings [ 'KAFKA_INCOMING_TOPIC' ]
if not self . logger . json :
self . logger . info ( 'Feeding JSON into {0}\n{1}' . format ( topic , json .... |
def get_level_value ( level ) :
"""Returns the logging value associated with a particular level name . The
argument must be present in LEVELS _ DICT or be an integer constant .
Otherwise None will be returned .""" | try : # integral constants also work : they are the level value
return int ( level )
except ValueError :
try :
return LEVELS_DICT [ level . upper ( ) ]
except KeyError :
logging . warning ( "level '%s' cannot be translated to a level value (not present in LEVELS_DICT)" % level )
retu... |
def validate ( self , r ) :
'''Called automatically by self . result .''' | if self . show_invalid :
r . valid = True
elif r . valid :
if not r . description :
r . valid = False
if r . size and ( r . size + r . offset ) > r . file . size :
r . valid = False
if r . jump and ( r . jump + r . offset ) > r . file . size :
r . valid = False
if hasattr ( r... |
def greenkhorn ( a , b , M , reg , numItermax = 10000 , stopThr = 1e-9 , verbose = False , log = False ) :
"""Solve the entropic regularization optimal transport problem and return the OT matrix
The algorithm used is based on the paper
Near - linear time approximation algorithms for optimal transport via Sinkho... | a = np . asarray ( a , dtype = np . float64 )
b = np . asarray ( b , dtype = np . float64 )
M = np . asarray ( M , dtype = np . float64 )
if len ( a ) == 0 :
a = np . ones ( ( M . shape [ 0 ] , ) , dtype = np . float64 ) / M . shape [ 0 ]
if len ( b ) == 0 :
b = np . ones ( ( M . shape [ 1 ] , ) , dtype = np . ... |
def find_sparse_mode ( self , core , additional , scaling , weights = { } ) :
"""Find a sparse mode containing reactions of the core subset .
Return an iterator of the support of a sparse mode that contains as
many reactions from core as possible , and as few reactions from
additional as possible ( approximat... | if len ( core ) == 0 :
return
self . lp7 ( core )
k = set ( )
for reaction_id in core :
flux = self . get_flux ( reaction_id )
if self . is_flipped ( reaction_id ) :
flux *= - 1
if flux >= self . _epsilon :
k . add ( reaction_id )
if len ( k ) == 0 :
return
self . lp10 ( k , addition... |
def construct_blastn_cmdline ( fname1 , fname2 , outdir , blastn_exe = pyani_config . BLASTN_DEFAULT ) :
"""Returns a single blastn command .
- filename - input filename
- blastn _ exe - path to BLASTN executable""" | fstem1 = os . path . splitext ( os . path . split ( fname1 ) [ - 1 ] ) [ 0 ]
fstem2 = os . path . splitext ( os . path . split ( fname2 ) [ - 1 ] ) [ 0 ]
fstem1 = fstem1 . replace ( "-fragments" , "" )
prefix = os . path . join ( outdir , "%s_vs_%s" % ( fstem1 , fstem2 ) )
cmd = ( "{0} -out {1}.blast_tab -query {2} -db... |
def ID_SDR_all_available ( SDR ) :
"""Return an array of inner diameters with a given SDR .
IDs available are those commonly used based on the ' Used ' column
in the pipedb .""" | ID = [ ]
ND = ND_all_available ( )
for i in range ( len ( ND ) ) :
ID . append ( ID_SDR ( ND [ i ] , SDR ) . magnitude )
return ID * u . inch |
def collect_gaps ( blast , use_subject = False ) :
"""Collect the gaps between adjacent HSPs in the BLAST file .""" | key = lambda x : x . sstart if use_subject else x . qstart
blast . sort ( key = key )
for a , b in zip ( blast , blast [ 1 : ] ) :
if use_subject :
if a . sstop < b . sstart :
yield b . sstart - a . sstop
else :
if a . qstop < b . qstart :
yield b . qstart - a . qstop |
def gpg_version ( ) :
"""Returns the GPG version""" | cmd = flatten ( [ gnupg_bin ( ) , "--version" ] )
output = stderr_output ( cmd )
output = output . split ( '\n' ) [ 0 ] . split ( " " ) [ 2 ] . split ( '.' )
return tuple ( [ int ( x ) for x in output ] ) |
def countok ( self ) :
"""Boolean array showing which stars pass all count constraints .
A " count constraint " is a constraint that affects the number of stars .""" | ok = np . ones ( len ( self . stars ) ) . astype ( bool )
for name in self . constraints :
c = self . constraints [ name ]
if c . name not in self . selectfrac_skip :
ok &= c . ok
return ok |
def has_access_api ( f ) :
"""Use this decorator to enable granular security permissions to your API methods .
Permissions will be associated to a role , and roles are associated to users .
By default the permission ' s name is the methods name .
this will return a message and HTTP 401 is case of unauthorized... | if hasattr ( f , '_permission_name' ) :
permission_str = f . _permission_name
else :
permission_str = f . __name__
def wraps ( self , * args , ** kwargs ) :
permission_str = PERMISSION_PREFIX + f . _permission_name
if self . appbuilder . sm . has_access ( permission_str , self . __class__ . __name__ ) :... |
def _set_extent ( ax , projection , extent , extrema ) :
"""Sets the plot extent .
Parameters
ax : cartopy . GeoAxesSubplot instance
The axis whose boundaries are being tweaked .
projection : None or geoplot . crs instance
The projection , if one is being used .
extent : None or ( xmin , xmax , ymin , y... | if extent :
xmin , xmax , ymin , ymax = extent
xmin , xmax , ymin , ymax = max ( xmin , - 180 ) , min ( xmax , 180 ) , max ( ymin , - 90 ) , min ( ymax , 90 )
if projection : # Input ` ` extent ` ` into set _ extent ( ) .
ax . set_extent ( ( xmin , xmax , ymin , ymax ) , crs = ccrs . PlateCarree ( )... |
def load_shapefile ( self , feature_type , base_path ) :
"""Load downloaded shape file to QGIS Main Window .
TODO : This is cut & paste from OSM - refactor to have one method
: param feature _ type : What kind of features should be downloaded .
Currently ' buildings ' , ' building - points ' or ' roads ' are ... | path = '%s.shp' % base_path
if not os . path . exists ( path ) :
message = self . tr ( '%s does not exist. The server does not have any data for ' 'this extent.' % path )
raise FileMissingError ( message )
self . iface . addVectorLayer ( path , feature_type , 'ogr' ) |
def convertforoutput ( self , outputfile ) :
"""Convert from one of the source formats into target format . Relevant if converters are used in OutputTemplates . Sourcefile is a CLAMOutputFile instance .""" | assert isinstance ( outputfile , CLAMOutputFile )
# metadata of the destination file ( file to be generated here )
if not outputfile . metadata . __class__ in self . acceptforoutput :
raise Exception ( "Convertor " + self . __class__ . __name__ + " can not convert input files to " + outputfile . metadata . __class_... |
def exists ( self ) :
"""Returns true if the job is still running or zero - os still knows about this job ID
After a job is finished , a job remains on zero - os for max of 5min where you still can read the job result
after the 5 min is gone , the job result is no more fetchable
: return : bool""" | r = self . _client . _redis
flag = '{}:flag' . format ( self . _queue )
return bool ( r . exists ( flag ) ) |
def write ( content , filename = 'cache' ) :
"""write data to cache file
parameters :
cache _ path - path to cache file
content - a data structure to save into cache file""" | cache_path = get_cache_path ( filename )
with open ( cache_path , 'w' ) as file :
if content is not None :
json . dump ( content , file , indent = 3 , sort_keys = True ) |
def get_markov_blanket ( self , node ) :
"""Returns a markov blanket for a random variable . In the case
of Bayesian Networks , the markov blanket is the set of
node ' s parents , its children and its children ' s other parents .
Returns
list ( blanket _ nodes ) : List of nodes contained in Markov Blanket
... | children = self . get_children ( node )
parents = self . get_parents ( node )
blanket_nodes = children + parents
for child_node in children :
blanket_nodes . extend ( self . get_parents ( child_node ) )
blanket_nodes = set ( blanket_nodes )
blanket_nodes . remove ( node )
return list ( blanket_nodes ) |
def get_extended_attrtext ( value ) :
"""attrtext = 1 * ( any non - ATTRIBUTE _ ENDS character plus ' % ' )
This is a special parsing routine so that we get a value that
includes % escapes as a single string ( which we decode as a single
string later ) .""" | m = _non_extended_attribute_end_matcher ( value )
if not m :
raise errors . HeaderParseError ( "expected extended attrtext but found {!r}" . format ( value ) )
attrtext = m . group ( )
value = value [ len ( attrtext ) : ]
attrtext = ValueTerminal ( attrtext , 'extended-attrtext' )
_validate_xtext ( attrtext )
retur... |
def get_user ( self , validated_token ) :
"""Returns a stateless user object which is backed by the given validated
token .""" | if api_settings . USER_ID_CLAIM not in validated_token : # The TokenUser class assumes tokens will have a recognizable user
# identifier claim .
raise InvalidToken ( _ ( 'Token contained no recognizable user identification' ) )
return TokenUser ( validated_token ) |
def brf ( path , f , t ) :
"""batch _ rename _ file | 批量重命名文件""" | from . tools . file import batch_rename_file
batch_rename_file ( path , f , t ) |
def _validate_number ( self , input_number , path_to_root , object_title = '' ) :
'''a helper method for validating properties of a number
: return : input _ number''' | rules_path_to_root = re . sub ( '\[\d+\]' , '[0]' , path_to_root )
input_criteria = self . keyMap [ rules_path_to_root ]
error_dict = { 'object_title' : object_title , 'model_schema' : self . schema , 'input_criteria' : input_criteria , 'failed_test' : 'value_datatype' , 'input_path' : path_to_root , 'error_value' : in... |
def set_sampling_interval ( self , interval ) :
"""This method sets the sampling interval for the Firmata loop method
: param interval : time in milliseconds
: returns : No return value""" | task = asyncio . ensure_future ( self . core . set_sampling_interval ( interval ) )
self . loop . run_until_complete ( task ) |
def handleMatch ( self , m ) :
username = self . unescape ( m . group ( 2 ) )
"""Makesure ` username ` is registered and actived .""" | if MARTOR_ENABLE_CONFIGS [ 'mention' ] == 'true' :
if username in [ u . username for u in User . objects . exclude ( is_active = False ) ] :
url = '{0}{1}/' . format ( MARTOR_MARKDOWN_BASE_MENTION_URL , username )
el = markdown . util . etree . Element ( 'a' )
el . set ( 'href' , url )
... |
def application_id ( self , app_id ) :
"""Validate request application id matches true application id .
Verifying the Application ID matches : https : / / goo . gl / qAdqe4.
Args :
app _ id : str . Request application _ id .
Returns :
bool : True if valid , False otherwise .""" | if self . app_id != app_id :
warnings . warn ( 'Application ID is invalid.' )
return False
return True |
def texkeys2marc ( self , key , value ) :
"""Populate the ` ` 035 ` ` MARC field .""" | result = [ ]
values = force_list ( value )
if values :
value = values [ 0 ]
result . append ( { '9' : 'INSPIRETeX' , 'a' : value , } )
for value in values [ 1 : ] :
result . append ( { '9' : 'INSPIRETeX' , 'z' : value , } )
return result |
def getgroupurl ( idgroup , * args , ** kwargs ) :
"""Request Groups URL .
If idgroup is set , you ' ll get a response adequate for a MambuGroup object .
If not set , you ' ll get a response adequate for a MambuGroups object .
See mambugroup module and pydoc for further information .
Currently implemented f... | getparams = [ ]
if kwargs :
try :
if kwargs [ "fullDetails" ] == True :
getparams . append ( "fullDetails=true" )
else :
getparams . append ( "fullDetails=false" )
except Exception as ex :
pass
try :
getparams . append ( "creditOfficerUsername=%s" % kw... |
def processEnded ( self , reason ) :
"""Connected process shut down""" | log_debug ( "{name} process exited" , name = self . name )
if self . deferred :
if reason . type == ProcessDone :
self . deferred . callback ( reason . value . exitCode )
elif reason . type == ProcessTerminated :
self . deferred . errback ( reason )
return self . deferred |
def parser_from_buffer ( cls , fp ) :
"""Construct YamlParser from a file pointer .""" | yaml = YAML ( typ = "safe" )
return cls ( yaml . load ( fp ) ) |
def render ( self , name , value , attrs = None ) :
'''Render the widget as HTML inputs for display on a form .
: param name : form field base name
: param value : date value
: param attrs : - unused
: returns : HTML text with three inputs for year / month / day''' | # expects a value in format YYYY - MM - DD or YYYY - MM or YYYY ( or empty / None )
year , month , day = 'YYYY' , 'MM' , 'DD'
if value : # use the regular expression to pull out year , month , and day values
# if regular expression does not match , inputs will be empty
match = W3C_DATE_RE . match ( value )
if m... |
def interval_offset_on_transcript ( start , end , transcript ) :
"""Given an interval [ start : end ] and a particular transcript ,
return the start offset of the interval relative to the
chromosomal positions of the transcript .""" | # ensure that start _ pos : end _ pos overlap with transcript positions
if start > end :
raise ValueError ( "start_pos %d shouldn't be greater than end_pos %d" % ( start , end ) )
if start > transcript . end :
raise ValueError ( "Range %d:%d starts after transcript %s (%d:%d)" % ( start , end , transcript , tra... |
def register_to_sys_with_admin_list ( class_inst , admin_list = None , is_normal_admin_needed = False ) :
""": param class _ inst : model class
: param admin _ list : admin class
: param is _ normal _ admin _ needed : is normal admin registration needed
: return :""" | if admin_list is None :
admin_class = get_valid_admin_class_with_list ( [ ] , class_inst )
else :
admin_class = get_valid_admin_class_with_list ( admin_list , class_inst )
if is_normal_admin_needed :
register_all_type_of_admin ( admin_class , class_inst )
else :
register_admin ( admin_class , class_inst... |
def handle_quit ( self , params ) :
"""Handle the client breaking off the connection with a QUIT command .""" | response = ':%s QUIT :%s' % ( self . client_ident ( ) , params . lstrip ( ':' ) )
# Send quit message to all clients in all channels user is in , and
# remove the user from the channels .
for channel in self . channels . values ( ) :
for client in channel . clients :
client . send_queue . append ( response ... |
def validate ( self , nonce ) :
"""Does the nonce exist and is it valid for the request ?""" | if self . debug :
print ( "Checking nonce " + str ( nonce ) , file = sys . stderr )
try :
opaque , ip , expiretime = self . get ( nonce )
# pylint : disable = unused - variable
if expiretime < time . time ( ) :
if self . debug :
print ( "Nonce expired" , file = sys . stderr )
... |
def release ( self , key , owner ) :
"""Release lock with given name .
` key ` - lock name
` owner ` - name of application / component / whatever which held a lock
Raises ` MongoLockException ` if no such a lock .""" | status = self . collection . find_and_modify ( { '_id' : key , 'owner' : owner } , { 'locked' : False , 'owner' : None , 'created' : None , 'expire' : None } ) |
def _init_date_range ( self , start_date = None , end_date = None ) :
"""Set date range defaults if no dates are passed""" | self . end_date = end_date
self . start_date = start_date
if self . end_date is None :
today = now_utc ( ) . date ( )
end_date = self . event . end_dt . date ( )
self . end_date = end_date if end_date < today else today
if self . start_date is None :
self . start_date = self . end_date - timedelta ( day... |
def _opt_to_args ( cls , opt , val ) :
"""Convert a named option and optional value to command line
argument notation , correctly handling options that take
no value or that have special representations ( e . g . verify
and verbose ) .""" | no_value = ( "alloptions" , "all-logs" , "batch" , "build" , "debug" , "experimental" , "list-plugins" , "list-presets" , "list-profiles" , "noreport" , "quiet" , "verify" )
count = ( "verbose" , )
if opt in no_value :
return [ "--%s" % opt ]
if opt in count :
return [ "--%s" % opt for d in range ( 0 , int ( va... |
def fielddefsql_from_fieldspeclist ( self , fieldspeclist : FIELDSPECLIST_TYPE ) -> str :
"""Returns list of field - defining SQL fragments .""" | return "," . join ( [ self . fielddefsql_from_fieldspec ( x ) for x in fieldspeclist ] ) |
def find ( self , limit = None , reverse = False , sort = None , exclude = None , duplicates = True , pretty = False , ** filters ) :
"""Using filters and sorts , this finds all hyperlinks
on a web page
: param limit : Crop results down to limit specified
: param reverse : Reverse the list of links , useful f... | if exclude is None :
exclude = [ ]
if 'href' not in filters :
filters [ 'href' ] = True
search = self . _soup . findAll ( 'a' , ** filters )
if reverse :
search . reverse ( )
links = [ ]
for anchor in search :
build_link = anchor . attrs
try :
build_link [ u'seo' ] = seoify_hyperlink ( ancho... |
def validate_port_range ( cls , port_range ) :
"""Validate port range for Nmap scan""" | ports = port_range . split ( "-" )
if all ( ports ) and int ( ports [ - 1 ] ) <= 65535 and not len ( ports ) != 2 :
return True
raise ScannerException ( "Invalid port range {}" . format ( port_range ) ) |
def revoke_token ( self , token , token_type = None ) :
"""Ask Reddit to revoke the provided token .
: param token : The access or refresh token to revoke .
: param token _ type : ( Optional ) When provided , hint to Reddit what the
token type is for a possible efficiency gain . The value can be
either ` ` ... | data = { "token" : token }
if token_type is not None :
data [ "token_type_hint" ] = token_type
url = self . _requestor . reddit_url + const . REVOKE_TOKEN_PATH
self . _post ( url , success_status = codes [ "no_content" ] , ** data ) |
def _create_key ( lang , instance ) :
"""Crea la clave única de la caché""" | model_name = instance . __class__ . __name__
return "{0}__{1}_{2}" . format ( lang , model_name , instance . id ) |
def _update_raster_info ( self , ** update_props ) :
"""Ensures complete removal of raster _ info given the two roots : < spdoinfo > and < spref >""" | xpath_map = self . _data_structures [ update_props [ 'prop' ] ]
return [ update_complex ( xpath_root = self . _data_map . get ( '_raster_info_root' ) , xpath_map = xpath_map , ** update_props ) , update_complex ( xpath_root = self . _data_map . get ( '__raster_res_root' ) , xpath_map = xpath_map , ** update_props ) ] |
def add_case ( self , case_obj ) :
"""Add a case obj with individuals to adapter
Args :
case _ obj ( puzzle . models . Case )""" | for ind_obj in case_obj . individuals :
self . _add_individual ( ind_obj )
logger . debug ( "Adding case {0} to plugin" . format ( case_obj . case_id ) )
self . case_objs . append ( case_obj ) |
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