signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def start ( self , local_port , remote_address , remote_port ) :
"""Start ssh tunnel
type : local _ port : int
param : local _ port : local tunnel endpoint ip binding
type : remote _ address : str
param : remote _ address : Remote tunnel endpoing ip binding
type : remote _ port : int
param : remote _ po... | self . local_port = local_port
self . remote_address = remote_address
self . remote_port = remote_port
logger . debug ( ( "Starting ssh tunnel {0}:{1}:{2} for " "{3}@{4}" . format ( local_port , remote_address , remote_port , self . username , self . address ) ) )
self . forward = Forward ( local_port , remote_address ... |
def get_gtf_db ( gtf , in_memory = False ) :
"""create a gffutils DB , in memory if we don ' t have write permissions""" | db_file = gtf + ".db"
if file_exists ( db_file ) :
return gffutils . FeatureDB ( db_file )
if not os . access ( os . path . dirname ( db_file ) , os . W_OK | os . X_OK ) :
in_memory = True
db_file = ":memory:" if in_memory else db_file
if in_memory or not file_exists ( db_file ) :
infer_extent = guess_infer... |
def _get_redirect_url ( self , request ) :
"""Next gathered from session , then GET , then POST ,
then users absolute url .""" | if 'next' in request . session :
next_url = request . session [ 'next' ]
del request . session [ 'next' ]
elif 'next' in request . GET :
next_url = request . GET . get ( 'next' )
elif 'next' in request . POST :
next_url = request . POST . get ( 'next' )
else :
next_url = request . user . get_absolut... |
def reverse ( self ) :
"""This is a delayed reversing function . All it really does is to invert the _ reversed property of this
StridedInterval object .
: return : None""" | if self . bits == 8 : # We cannot reverse a one - byte value
return self
si = self . copy ( )
si . _reversed = not si . _reversed
return si |
def lookup_rdap ( self , inc_raw = False , retry_count = 3 , depth = 0 , excluded_entities = None , bootstrap = False , rate_limit_timeout = 120 , asn_alts = None , extra_org_map = None , inc_nir = True , nir_field_list = None , asn_methods = None , get_asn_description = True ) :
"""The function for retrieving and ... | from . rdap import RDAP
# Create the return dictionary .
results = { 'nir' : None }
asn_data = None
response = None
if not bootstrap : # Retrieve the ASN information .
log . debug ( 'ASN lookup for {0}' . format ( self . address_str ) )
asn_data = self . ipasn . lookup ( inc_raw = inc_raw , retry_count = retry_... |
def _next_shape_id ( self ) :
"""Return a unique shape id suitable for use with a new shape .
The returned id is 1 greater than the maximum shape id used so far .
In practice , the minimum id is 2 because the spTree element is always
assigned id = " 1 " .""" | # - - - presence of cached - max - shape - id indicates turbo mode is on - - -
if self . _cached_max_shape_id is not None :
self . _cached_max_shape_id += 1
return self . _cached_max_shape_id
return self . _spTree . max_shape_id + 1 |
def make_big_empty_files ( self ) :
"""Write out a empty file so the workers can seek to where they should write and write their data .""" | for file_url in self . file_urls :
local_path = file_url . get_local_path ( self . dest_directory )
with open ( local_path , "wb" ) as outfile :
if file_url . size > 0 :
outfile . seek ( int ( file_url . size ) - 1 )
outfile . write ( b'\0' ) |
def load_object ( import_path ) :
"""Shamelessly stolen from https : / / github . com / ojii / django - load
Loads an object from an ' import _ path ' , like in MIDDLEWARE _ CLASSES and the
likes .
Import paths should be : " mypackage . mymodule . MyObject " . It then imports the
module up until the last do... | if '.' not in import_path :
raise TypeError ( "'import_path' argument to 'load_object' must " "contain at least one dot." )
module_name , object_name = import_path . rsplit ( '.' , 1 )
module = import_module ( module_name )
return getattr ( module , object_name ) |
def hash_args ( * args , ** kwargs ) :
"""Define a unique string for any set of representable args .""" | arg_string = '_' . join ( [ str ( arg ) for arg in args ] )
kwarg_string = '_' . join ( [ str ( key ) + '=' + str ( value ) for key , value in iteritems ( kwargs ) ] )
combined = ':' . join ( [ arg_string , kwarg_string ] )
hasher = md5 ( )
hasher . update ( b ( combined ) )
return hasher . hexdigest ( ) |
def modify_target ( self , to_state , to_key ) :
"""Set both to _ state and to _ key at the same time to modify data flow target
: param str to _ state : State id of the target state
: param int to _ key : Data port id of the target port
: raises exceptions . ValueError : If parameters have wrong types or the... | if not isinstance ( to_state , string_types ) :
raise ValueError ( "Invalid data flow target port: from_state must be a string" )
if not isinstance ( to_key , int ) :
raise ValueError ( "Invalid data flow target port: from_outcome must be of type int" )
old_to_state = self . to_state
old_to_key = self . to_key
... |
def create_like ( self , repository_id , pull_request_id , thread_id , comment_id , project = None ) :
"""CreateLike .
[ Preview API ] Add a like on a comment .
: param str repository _ id : The repository ID of the pull request ' s target branch .
: param int pull _ request _ id : ID of the pull request .
... | route_values = { }
if project is not None :
route_values [ 'project' ] = self . _serialize . url ( 'project' , project , 'str' )
if repository_id is not None :
route_values [ 'repositoryId' ] = self . _serialize . url ( 'repository_id' , repository_id , 'str' )
if pull_request_id is not None :
route_values ... |
def object_to_json ( obj , indent = 2 ) :
"""transform object to json""" | instance_json = json . dumps ( obj , indent = indent , ensure_ascii = False , cls = DjangoJSONEncoder )
return instance_json |
def append_position_to_token_list ( token_list ) :
"""Converts a list of Token into a list of Token , asuming size = = 1""" | return [ PositionToken ( value . content , value . gd , index , index + 1 ) for ( index , value ) in enumerate ( token_list ) ] |
def find_video_detail_by_id ( self , video_id , ext = None ) :
"""doc : http : / / cloud . youku . com / docs ? id = 46""" | url = 'https://api.youku.com/videos/show.json'
params = { 'client_id' : self . client_id , 'video_id' : video_id }
if ext :
params [ 'ext' ] = ext
r = requests . get ( url , params = params )
check_error ( r )
return r . json ( ) |
def _to_str ( uniq ) :
"""Serializes a MOC to the STRING format .
HEALPix cells are separated by a comma . The HEALPix cell at order 0 and number 10 is encoded
by the string : " 0/10 " , the first digit representing the depth and the second the HEALPix cell number
for this depth . HEALPix cells next to each o... | def write_cells ( serial , a , b , sep = '' ) :
if a == b :
serial += '{0}{1}' . format ( a , sep )
else :
serial += '{0}-{1}{2}' . format ( a , b , sep )
return serial
res = ''
if uniq . size == 0 :
return res
depth , ipixels = utils . uniq2orderipix ( uniq )
min_depth = np . min ( dept... |
def run ( ) :
"""This client pulls PCAP files for building report .
Returns :
A list with ` view _ pcap ` , ` meta ` and ` filename ` objects .""" | global WORKBENCH
# Grab grab _ server _ argsrver args
args = client_helper . grab_server_args ( )
# Start up workbench connection
WORKBENCH = zerorpc . Client ( timeout = 300 , heartbeat = 60 )
WORKBENCH . connect ( 'tcp://' + args [ 'server' ] + ':' + args [ 'port' ] )
data_path = os . path . join ( os . path . dirnam... |
def process_text ( text , out_format = 'json_ld' , save_json = 'eidos_output.json' , webservice = None ) :
"""Return an EidosProcessor by processing the given text .
This constructs a reader object via Java and extracts mentions
from the text . It then serializes the mentions into JSON and
processes the resul... | if not webservice :
if eidos_reader is None :
logger . error ( 'Eidos reader is not available.' )
return None
json_dict = eidos_reader . process_text ( text , out_format )
else :
res = requests . post ( '%s/process_text' % webservice , json = { 'text' : text } )
json_dict = res . json ( ... |
def elbv2_load_balancer_dns_name ( self , lookup , default = None ) :
"""Args :
lookup : the friendly name of the V2 elb to look up
default : value to return in case of no match
Returns :
The hosted zone ID of the ELB found with a name matching ' lookup ' .""" | try :
elb = self . _elbv2_load_balancer ( lookup )
return elb [ 'DNSName' ]
except ClientError :
return default |
def data ( self , index , role ) :
"""Show tooltip with full path only for the root directory""" | if role == Qt . ToolTipRole :
root_dir = self . path_list [ 0 ] . split ( osp . sep ) [ - 1 ]
if index . data ( ) == root_dir :
return osp . join ( self . root_path , root_dir )
return QSortFilterProxyModel . data ( self , index , role ) |
def list_persistent_volume_claim_for_all_namespaces ( self , ** kwargs ) :
"""list or watch objects of kind PersistentVolumeClaim
This method makes a synchronous HTTP request by default . To make an
asynchronous HTTP request , please pass async _ req = True
> > > thread = api . list _ persistent _ volume _ cl... | kwargs [ '_return_http_data_only' ] = True
if kwargs . get ( 'async_req' ) :
return self . list_persistent_volume_claim_for_all_namespaces_with_http_info ( ** kwargs )
else :
( data ) = self . list_persistent_volume_claim_for_all_namespaces_with_http_info ( ** kwargs )
return data |
def _setup ( self , lines ) :
'''setup required adding content from the host to the rootfs ,
so we try to capture with with ADD .''' | bot . warning ( 'SETUP is error prone, please check output.' )
for line in lines : # For all lines , replace rootfs with actual root /
line = re . sub ( '[$]{?SINGULARITY_ROOTFS}?' , '' , '$SINGULARITY_ROOTFS' )
# If we have nothing left , don ' t continue
if line in [ '' , None ] :
continue
# I... |
def get_setup_requires ( ) :
"""Return the list of packages required for this setup . py run""" | # don ' t force requirements if just asking for help
if { '--help' , '--help-commands' } . intersection ( sys . argv ) :
return list ( )
# otherwise collect all requirements for all known commands
reqlist = [ ]
for cmd , dependencies in SETUP_REQUIRES . items ( ) :
if cmd in sys . argv :
reqlist . exten... |
def cumulative_density_at_times ( self , times , label = None ) :
"""Return a Pandas series of the predicted cumulative density function ( 1 - survival function ) at specific times .
Parameters
times : iterable or float
values to return the survival function at .
label : string , optional
Rename the serie... | label = coalesce ( label , self . _label )
return pd . Series ( self . _cumulative_density ( self . _fitted_parameters_ , times ) , index = _to_array ( times ) , name = label ) |
def bounding_box ( obj ) :
'''Get the ( x , y , z ) bounding box of an object containing points
Returns :
2D numpy array of [ [ min _ x , min _ y , min _ z ] , [ max _ x , max _ y , max _ z ] ]''' | return np . array ( [ np . min ( obj . points [ : , 0 : 3 ] , axis = 0 ) , np . max ( obj . points [ : , 0 : 3 ] , axis = 0 ) ] ) |
def _load_metadata ( self ) :
"""( Re ) load metadata from store .""" | if self . _synchronizer is None :
self . _load_metadata_nosync ( )
else :
mkey = self . _key_prefix + array_meta_key
with self . _synchronizer [ mkey ] :
self . _load_metadata_nosync ( ) |
def validate_listeners ( self ) :
"""Validates that some listeners are actually registered""" | if self . exception : # pylint : disable = raising - bad - type
raise self . exception
listeners = self . __listeners_for_thread
if not sum ( len ( l ) for l in listeners ) :
raise ValueError ( "No active listeners" ) |
def add_limbs ( self , key = None ) :
'''Add a new section from the tree into the existing os environment
Parameters :
key ( str ) :
The section name to grab from the environment''' | self . branch_out ( limb = key )
self . add_paths_to_os ( key = key ) |
def update ( self , incr = 1 , force = False ) :
"""Args :
incr ( int ) : Amount to increment ` ` count ` ` ( Default : 1)
force ( bool ) : Force refresh even if ` ` min _ delta ` ` has not been reached
Increment progress bar and redraw
Progress bar is only redrawn if ` ` min _ delta ` ` seconds past since ... | self . count += incr
if self . enabled :
currentTime = time . time ( )
# Update if force , 100 % , or minimum delta has been reached
if force or self . count == self . total or currentTime - self . last_update >= self . min_delta :
self . last_update = currentTime
self . refresh ( elapsed = ... |
def from_yaml ( cls , yaml_path , filename = None ) :
"""Split a dictionary into parameters controllers parts blocks defines
Args :
yaml _ path ( str ) : File path to YAML file , or a file in the same dir
filename ( str ) : If give , use this filename as the last element in
the yaml _ path ( so yaml _ path ... | if filename : # different filename to support passing _ _ file _ _
yaml_path = os . path . join ( os . path . dirname ( yaml_path ) , filename )
assert yaml_path . endswith ( ".yaml" ) , "Expected a/path/to/<yamlname>.yaml, got %r" % yaml_path
yamlname = os . path . basename ( yaml_path ) [ : - 5 ]
log . debug ( "P... |
def mysql_pub ( mysql_dsn , tables = None , blocking = False , ** kwargs ) :
"""MySQL row - based binlog events pub .
* * General Usage * *
Listen and pub all tables events : :
mysql _ pub ( mysql _ dsn )
Listen and pub only some tables events : :
mysql _ pub ( mysql _ dsn , tables = [ " test " ] )
By d... | # parse mysql settings
parsed = urlparse ( mysql_dsn )
mysql_settings = { "host" : parsed . hostname , "port" : parsed . port or 3306 , "user" : parsed . username , "passwd" : parsed . password }
# connect to binlog stream
stream = pymysqlreplication . BinLogStreamReader ( mysql_settings , server_id = random . randint ... |
def write_conf ( self ) :
"""Write the config to file""" | f = open ( self . output_filename , 'w' )
print ( self . t . render ( prefixes = self . prefixes ) , file = f )
f . close ( ) |
def get_as_type_with_default ( self , index , value_type , default_value ) :
"""Converts array element into a value defined by specied typecode .
If conversion is not possible it returns default value .
: param index : an index of element to get .
: param value _ type : the TypeCode that defined the type of t... | value = self [ index ]
return TypeConverter . to_type_with_default ( value_type , value , default_value ) |
def process_result_value ( self , value : Optional [ str ] , dialect : Dialect ) -> List [ int ] :
"""Convert things on the way from the database to Python .""" | retval = self . _dbstr_to_intlist ( value )
return retval |
def put ( self , local_path , destination_s3_path , ** kwargs ) :
"""Put an object stored locally to an S3 path .
: param local _ path : Path to source local file
: param destination _ s3 _ path : URL for target S3 location
: param kwargs : Keyword arguments are passed to the boto function ` put _ object `""" | self . _check_deprecated_argument ( ** kwargs )
# put the file
self . put_multipart ( local_path , destination_s3_path , ** kwargs ) |
def set_user_profile_photo ( self , photo : str ) -> bool :
"""Use this method to set a new profile photo .
This method only works for Users .
Bots profile photos must be set using BotFather .
Args :
photo ( ` ` str ` ` ) :
Profile photo to set .
Pass a file path as string to upload a new photo that exi... | return bool ( self . send ( functions . photos . UploadProfilePhoto ( file = self . save_file ( photo ) ) ) ) |
def refresh ( self ) :
"""刷新 Answer object 的属性 .
例如赞同数增加了 , 先调用 ` ` refresh ( ) ` `
再访问 upvote _ num属性 , 可获得更新后的赞同数 .
: return : None""" | super ( ) . refresh ( )
self . _html = None
self . _upvote_num = None
self . _content = None
self . _collect_num = None
self . _comment_num = None |
def create_node ( hostname , username , password , name , address ) :
'''Create a new node if it does not already exist .
hostname
The host / address of the bigip device
username
The iControl REST username
password
The iControl REST password
name
The name of the node to create
address
The addres... | ret = { 'name' : name , 'changes' : { } , 'result' : False , 'comment' : '' }
if __opts__ [ 'test' ] :
return _test_output ( ret , 'create' , params = { 'hostname' : hostname , 'username' : username , 'password' : password , 'name' : name , 'address' : address } )
# is this node currently configured ?
existing = __... |
def create_bottleneck_file ( bottleneck_path , image_lists , label_name , index , image_dir , category , sess , jpeg_data_tensor , decoded_image_tensor , resized_input_tensor , bottleneck_tensor ) :
"""Create a single bottleneck file .""" | tf . logging . debug ( 'Creating bottleneck at ' + bottleneck_path )
image_path = get_image_path ( image_lists , label_name , index , image_dir , category )
if not tf . gfile . Exists ( image_path ) :
tf . logging . fatal ( 'File does not exist %s' , image_path )
image_data = tf . gfile . GFile ( image_path , 'rb' ... |
def open ( filename , flag = 'c' , protocol = None , writeback = False , maxsize = DEFAULT_MAXSIZE , timeout = DEFAULT_TIMEOUT ) :
"""Open a database file as a persistent dictionary .
The persistent dictionary file is opened using : func : ` dbm . open ` , so
performance will depend on which : mod : ` dbm ` mod... | import dbm
dict = dbm . open ( filename , flag )
if maxsize is None and timeout is None :
return Shelf ( dict , protocol , writeback )
elif maxsize is None :
return TimeoutShelf ( dict , protocol , writeback , timeout = timeout )
elif timeout is None :
return LRUShelf ( dict , protocol , writeback , maxsize... |
def Refresh ( ) :
"""looks up symbols within the inferior and caches their names / values .
If debugging information is only partial , this method does its best to
find as much information as it can , validation can be done using
IsSymbolFileSane .""" | try :
GdbCache . DICT = gdb . lookup_type ( 'PyDictObject' ) . pointer ( )
GdbCache . TYPE = gdb . lookup_type ( 'PyTypeObject' ) . pointer ( )
except gdb . error as err : # The symbol file we ' re using doesn ' t seem to provide type information .
pass
interp_head_name = GdbCache . FuzzySymbolLookup ( 'int... |
def enrichment_from_msp ( dfmsp , modification = "Phospho (STY)" ) :
"""Calculate relative enrichment of peptide modifications from modificationSpecificPeptides . txt .
Taking a modifiedsitepeptides ` ` DataFrame ` ` returns the relative enrichment of the specified
modification in the table .
The returned dat... | dfmsp [ 'Modifications' ] = np . array ( [ modification in m for m in dfmsp [ 'Modifications' ] ] )
dfmsp = dfmsp . set_index ( [ 'Modifications' ] )
dfmsp = dfmsp . filter ( regex = 'Intensity ' )
dfmsp [ dfmsp == 0 ] = np . nan
df_r = dfmsp . sum ( axis = 0 , level = 0 )
modified = df_r . loc [ True ] . values
total ... |
def _kmedoids_run ( X , n_clusters , distance , max_iter , tol , rng ) :
"""Run a single trial of k - medoids clustering
on dataset X , and given number of clusters""" | membs = np . empty ( shape = X . shape [ 0 ] , dtype = int )
centers = kmeans . _kmeans_init ( X , n_clusters , method = '' , rng = rng )
sse_last = 9999.9
n_iter = 0
for it in range ( 1 , max_iter ) :
membs = kmeans . _assign_clusters ( X , centers )
centers , sse_arr = _update_centers ( X , membs , n_clusters... |
def add_subcommands ( parser , commands ) :
"Add commands to a parser" | subps = parser . add_subparsers ( )
for cmd , cls in commands :
subp = subps . add_parser ( cmd , help = cls . __doc__ )
add_args = getattr ( cls , 'add_arguments' , None )
if add_args :
add_args ( subp )
handler = getattr ( cls , 'handle' , None )
if handler :
subp . set_defaults ( ... |
def select ( self , * args , ** kwargs ) :
'''Query this object and all of its references for objects that
match the given selector .
There are a few different ways to call the ` ` select ` ` method .
The most general is to supply a JSON - like query dictionary as the
single argument or as keyword arguments... | selector = _select_helper ( args , kwargs )
# Want to pass selector that is a dictionary
return _list_attr_splat ( find ( self . references ( ) , selector , { 'plot' : self } ) ) |
def _save_cookie ( cookie_name , cookie_value ) :
"""Save cookie""" | config = ConfigParser . SafeConfigParser ( )
config . read ( _config )
if not config . has_section ( 'cookies' ) :
config . add_section ( 'cookies' )
config . set ( 'cookies' , cookie_name , cookie_value )
with open ( _config , 'w' ) as ini :
config . write ( ini ) |
def _descend_namespace ( caller_globals , name ) :
"""Given a globals dictionary , and a name of the form " a . b . c . d " , recursively
walk the globals expanding caller _ globals [ ' a ' ] [ ' b ' ] [ ' c ' ] [ ' d ' ] returning
the result . Raises an exception ( IndexError ) on failure .""" | names = name . split ( '.' )
cur = caller_globals
for i in names :
if type ( cur ) is dict :
cur = cur [ i ]
else :
cur = getattr ( cur , i )
return cur |
def add_permission ( self , permission ) :
"""Add a permission to this Admin User . A role defines permissions that
can be enabled or disabled . Elements define the target for permission
operations and can be either Access Control Lists , Engines or Policy
elements . Domain specifies where the access is grant... | if 'permissions' not in self . data :
self . data [ 'superuser' ] = False
self . data [ 'permissions' ] = { 'permission' : [ ] }
for p in permission :
self . data [ 'permissions' ] [ 'permission' ] . append ( p . data )
self . update ( ) |
def _vec_alpha ( self , donor_catchments ) :
"""Return vector alpha which is the weights for donor model errors
Methodology source : Kjeldsen , Jones & Morris 2014 , eq 10
: param donor _ catchments : Catchments to use as donors
: type donor _ catchments : list of : class : ` Catchment `
: return : Vector o... | return np . dot ( linalg . inv ( self . _matrix_omega ( donor_catchments ) ) , self . _vec_b ( donor_catchments ) ) |
def load_object ( import_path ) :
"""Loads an object from an ' import _ path ' , like in MIDDLEWARE _ CLASSES and the
likes .
Import paths should be : " mypackage . mymodule . MyObject " . It then imports the
module up until the last dot and tries to get the attribute after that dot
from the imported module... | if not isinstance ( import_path , six . string_types ) :
return import_path
if '.' not in import_path :
raise TypeError ( "'import_path' argument to 'django_load.core.load_object' must " "contain at least one dot." )
module_name , object_name = import_path . rsplit ( '.' , 1 )
module = import_module ( module_na... |
def run ( items , background = None ) :
"""Detect copy number variations from batched set of samples using WHAM .""" | if not background :
background = [ ]
background_bams = [ ]
paired = vcfutils . get_paired_bams ( [ x [ "align_bam" ] for x in items ] , items )
if paired :
inputs = [ paired . tumor_data ]
if paired . normal_bam :
background = [ paired . normal_data ]
background_bams = [ paired . normal_bam ... |
def search_function ( root1 , q , s , f , l , o = 'g' ) :
"""function to get links""" | global links
links = search ( q , o , s , f , l )
root1 . destroy ( )
root1 . quit ( ) |
def parse_content_stream ( page_or_stream , operators = '' ) :
"""Parse a PDF content stream into a sequence of instructions .
A PDF content stream is list of instructions that describe where to render
the text and graphics in a PDF . This is the starting point for analyzing
PDFs .
If the input is a page an... | if not isinstance ( page_or_stream , Object ) :
raise TypeError ( "stream must a PDF object" )
if ( page_or_stream . _type_code != ObjectType . stream and page_or_stream . get ( '/Type' ) != '/Page' ) :
raise TypeError ( "parse_content_stream called on page or stream object" )
try :
if page_or_stream . get ... |
def is_json_file ( filename , show_warnings = False ) :
"""Check configuration file type is JSON
Return a boolean indicating wheather the file is JSON format or not""" | try :
config_dict = load_config ( filename , file_type = "json" )
is_json = True
except :
is_json = False
return ( is_json ) |
def retention_period ( self , value ) :
"""Set the retention period for items in the bucket .
: type value : int
: param value :
number of seconds to retain items after upload or release from
event - based lock .
: raises ValueError : if the bucket ' s retention policy is locked .""" | policy = self . _properties . setdefault ( "retentionPolicy" , { } )
if value is not None :
policy [ "retentionPeriod" ] = str ( value )
else :
policy = None
self . _patch_property ( "retentionPolicy" , policy ) |
def ply2gii ( in_file , metadata , out_file = None ) :
"""Convert from ply to GIfTI""" | from pathlib import Path
from numpy import eye
from nibabel . gifti import ( GiftiMetaData , GiftiCoordSystem , GiftiImage , GiftiDataArray , )
from pyntcloud import PyntCloud
in_file = Path ( in_file )
surf = PyntCloud . from_file ( str ( in_file ) )
# Update centroid metadata
metadata . update ( zip ( ( 'SurfaceCente... |
def update_domain_name ( self , domain_name , certificate_name = None , certificate_body = None , certificate_private_key = None , certificate_chain = None , certificate_arn = None , lambda_name = None , stage = None , route53 = True , base_path = None ) :
"""This updates your certificate information for an existin... | print ( "Updating domain name!" )
certificate_name = certificate_name + str ( time . time ( ) )
api_gateway_domain = self . apigateway_client . get_domain_name ( domainName = domain_name )
if not certificate_arn and certificate_body and certificate_private_key and certificate_chain :
acm_certificate = self . acm_cl... |
def _bson_to_dict ( data , opts ) :
"""Decode a BSON string to document _ class .""" | try :
obj_size = _UNPACK_INT ( data [ : 4 ] ) [ 0 ]
except struct . error as exc :
raise InvalidBSON ( str ( exc ) )
if obj_size != len ( data ) :
raise InvalidBSON ( "invalid object size" )
if data [ obj_size - 1 : obj_size ] != b"\x00" :
raise InvalidBSON ( "bad eoo" )
try :
return _elements_to_di... |
def get_plugin_folders ( ) :
"""Get linkchecker plugin folders . Default is ~ / . linkchecker / plugins / .""" | folders = [ ]
defaultfolder = normpath ( "~/.linkchecker/plugins" )
if not os . path . exists ( defaultfolder ) and not Portable :
try :
make_userdir ( defaultfolder )
except Exception as errmsg :
msg = _ ( "could not create plugin directory %(dirname)r: %(errmsg)r" )
args = dict ( dirna... |
def select ( self , fields = [ 'rowid' , '*' ] , offset = None , limit = None ) :
'''return SELECT SQL''' | # base SQL
SQL = 'SELECT %s FROM %s' % ( ',' . join ( fields ) , self . _table )
# selectors
if self . _selectors :
SQL = ' ' . join ( [ SQL , 'WHERE' , self . _selectors ] ) . strip ( )
# modifiers
if self . _modifiers :
SQL = ' ' . join ( [ SQL , self . _modifiers ] )
# limit
if limit is not None and isinstan... |
def sync_and_deploy_gateway ( collector ) :
"""Do a sync followed by deploying the gateway""" | configuration = collector . configuration
aws_syncr = configuration [ 'aws_syncr' ]
find_gateway ( aws_syncr , configuration )
artifact = aws_syncr . artifact
aws_syncr . artifact = ""
sync ( collector )
aws_syncr . artifact = artifact
deploy_gateway ( collector ) |
def dispatch_job_hook ( self , link , key , job_config , logfile , stream = sys . stdout ) :
"""Send a single job to be executed
Parameters
link : ` fermipy . jobs . chain . Link `
The link used to invoke the command we are running
key : str
A string that identifies this particular instance of the job
j... | full_sub_dict = job_config . copy ( )
full_command = "%s >& %s" % ( link . command_template ( ) . format ( ** full_sub_dict ) , logfile )
logdir = os . path . dirname ( logfile )
if self . _dry_run :
sys . stdout . write ( "%s\n" % full_command )
else :
try :
os . makedirs ( logdir )
except OSError ... |
def publish ( self , daap_server , preferred_database = None ) :
"""Publish a given ` DAAPServer ` instance .
The given instances should be fully configured , including the provider .
By default Zeroconf only advertises the first database , but the DAAP
protocol has support for multiple databases . Therefore ... | if daap_server in self . daap_servers :
self . unpublish ( daap_server )
# Zeroconf can advertise the information for one database only . Since
# the protocol supports multiple database , let the user decide which
# database to advertise . If none is specified , take the first one .
provider = daap_server . provide... |
def set_status ( self , trial , status ) :
"""Sets status and checkpoints metadata if needed .
Only checkpoints metadata if trial status is a terminal condition .
PENDING , PAUSED , and RUNNING switches have checkpoints taken care of
in the TrialRunner .
Args :
trial ( Trial ) : Trial to checkpoint .
st... | trial . status = status
if status in [ Trial . TERMINATED , Trial . ERROR ] :
self . try_checkpoint_metadata ( trial ) |
def _android_get_installed_platform_tools_version ( self ) :
"""Crudely parse out the installed platform - tools version""" | platform_tools_dir = os . path . join ( self . android_sdk_dir , 'platform-tools' )
if not os . path . exists ( platform_tools_dir ) :
return None
data_file = os . path . join ( platform_tools_dir , 'source.properties' )
if not os . path . exists ( data_file ) :
return None
with open ( data_file , 'r' ) as file... |
def _create_model ( self , X , Y ) :
"""Creates the model given some input data X and Y .""" | # - - - define kernel
self . input_dim = X . shape [ 1 ]
if self . kernel is None :
kern = GPy . kern . RBF ( self . input_dim , variance = 1. )
else :
kern = self . kernel
self . kernel = None
# - - - define model
noise_var = Y . var ( ) * 0.01 if self . noise_var is None else self . noise_var
self . model... |
def beacons ( opts , functions , context = None , proxy = None ) :
'''Load the beacon modules
: param dict opts : The Salt options dictionary
: param dict functions : A dictionary of minion modules , with module names as
keys and funcs as values .''' | return LazyLoader ( _module_dirs ( opts , 'beacons' ) , opts , tag = 'beacons' , pack = { '__context__' : context , '__salt__' : functions , '__proxy__' : proxy or { } } , virtual_funcs = [ ] , ) |
def make_k8s_lando_router ( config , obj , queue_name ) :
"""Makes MessageRouter which can listen to queue _ name sending messages to the k8s version of lando .
: param config : WorkerConfig / ServerConfig : settings for connecting to the queue
: param obj : object : implements lando specific methods
: param ... | return MessageRouter ( config , obj , queue_name , K8S_LANDO_INCOMING_MESSAGES , processor_constructor = WorkQueueProcessor ) |
def create_principal ( name , enctypes = None ) :
'''Create Principal
CLI Example :
. . code - block : : bash
salt ' kdc . example . com ' kerberos . create _ principal host / example . com''' | ret = { }
krb_cmd = 'addprinc -randkey'
if enctypes :
krb_cmd += ' -e {0}' . format ( enctypes )
krb_cmd += ' {0}' . format ( name )
cmd = __execute_kadmin ( krb_cmd )
if cmd [ 'retcode' ] != 0 or cmd [ 'stderr' ] :
if not cmd [ 'stderr' ] . splitlines ( ) [ - 1 ] . startswith ( 'WARNING:' ) :
ret [ 'co... |
def tree_view_keypress_callback ( self , widget , event ) :
"""General method to adapt widget view and controller behavior according the key press / release and
button release events
Here the scrollbar motion to follow key cursor motions in editable is already in .
: param Gtk . TreeView widget : The tree vie... | current_row_path , current_focused_column = self . tree_view . get_cursor ( )
# print ( current _ row _ path , current _ focused _ column )
if isinstance ( widget , Gtk . TreeView ) and not self . active_entry_widget : # avoid jumps for active entry widget
pass
# cursor motion / selection changes ( e . g . also... |
def parse_dict ( value ) :
"""Parse a dict value from the tox config .
. . code - block : ini
[ travis ]
python =
2.7 : py27 , docs
3.5 : py { 35,36}
With this config , the value of ` ` python ` ` would be parsed
by this function , and would return : :
'2.7 ' : ' py27 , docs ' ,
'3.5 ' : ' py { 35... | lines = [ line . strip ( ) for line in value . strip ( ) . splitlines ( ) ]
pairs = [ line . split ( ':' , 1 ) for line in lines if line ]
return dict ( ( k . strip ( ) , v . strip ( ) ) for k , v in pairs ) |
def SendReply ( self , response , tag = None ) :
"""Allows this flow to send a message to its parent flow .
If this flow does not have a parent , the message is ignored .
Args :
response : An RDFValue ( ) instance to be sent to the parent .
tag : If specified , tag the result with this tag .
Raises :
Va... | if not isinstance ( response , rdfvalue . RDFValue ) :
raise ValueError ( "SendReply can only send RDFValues" )
if self . rdf_flow . parent_flow_id :
response = rdf_flow_objects . FlowResponse ( client_id = self . rdf_flow . client_id , request_id = self . rdf_flow . parent_request_id , response_id = self . Get... |
def LatLngsToGoogleLink ( source , destination ) :
"""Return a string " < a . . . " for a trip at a random time .""" | dt = GetRandomDatetime ( )
return "<a href='%s'>from:%s to:%s on %s</a>" % ( LatLngsToGoogleUrl ( source , destination , dt ) , FormatLatLng ( source ) , FormatLatLng ( destination ) , dt . ctime ( ) ) |
def ocsp_no_check ( self , value ) :
"""A bool - if the certificate should have the OCSP no check extension .
Only applicable to certificates created for signing OCSP responses .
Such certificates should normally be issued for a very short period of
time since they are effectively whitelisted by clients .""" | if value is None :
self . _ocsp_no_check = None
else :
self . _ocsp_no_check = bool ( value ) |
def get_freesurfer_label ( annot_input , verbose = True ) :
"""Print freesurfer label names .""" | labels , color_table , names = nib . freesurfer . read_annot ( annot_input )
if verbose :
print ( names )
return names |
def edit_filename ( filename , prefix = '' , suffix = '' , new_ext = None ) :
"""Edit a file name by add a prefix , inserting a suffix in front of a file
name extension or replacing the extension .
Parameters
filename : str
The file name .
prefix : str
The prefix to be added .
suffix : str
The suffi... | base , ext = os . path . splitext ( filename )
if new_ext is None :
new_filename = base + suffix + ext
else :
new_filename = base + suffix + new_ext
return new_filename |
def _annotate_fn_args ( stack , fn_opname , nargs , nkw = - 1 , consume_fn_name = True ) :
"""Add commas and equals as appropriate to function argument lists in the stack .""" | kwarg_names = [ ]
if nkw == - 1 :
if sys . version_info [ 0 ] < 3 : # Compute nkw and nargs from nargs for python 2.7
nargs , nkw = ( nargs % 256 , 2 * nargs // 256 )
else :
if fn_opname == 'CALL_FUNCTION_KW' :
if qj . _DEBUG_QJ :
assert len ( stack ) and stack [ - 1 ... |
def is_all_field_none ( self ) :
""": rtype : bool""" | if self . _payment is not None :
return False
if self . _read_only is not None :
return False
if self . _draft_payment is not None :
return False
return True |
def map_services ( self ) :
"""Get full Vera device service info .""" | # the Vera rest API is a bit rough so we need to make 2 calls
# to get all the info e need
self . get_simple_devices_info ( )
j = self . data_request ( { 'id' : 'status' , 'output_format' : 'json' } ) . json ( )
service_map = { }
items = j . get ( 'devices' )
for item in items :
service_map [ item . get ( 'id' ) ] ... |
def get_tiles_list ( element ) :
"""Returns the list of all tile names from Product _ Organisation element
in metadata . xml""" | tiles = { }
for el in element :
g = ( el . findall ( './/Granules' ) or el . findall ( './/Granule' ) ) [ 0 ]
name = g . attrib [ 'granuleIdentifier' ]
name_parts = name . split ( '_' )
mgs = name_parts [ - 2 ]
tiles [ mgs ] = name
return tiles |
def table_enumerate ( self , columns , content ) :
"""Enumerate each table column .""" | columns . insert ( 0 , { 'label' : '#' , 'enumerated' : True } )
i = 0
for row in content :
i += 1
row . insert ( 0 , '{:d}' . format ( i ) )
return ( columns , content ) |
def set_legend_position ( self , legend_position ) :
"""Sets legend position . Default is ' r ' .
b - At the bottom of the chart , legend entries in a horizontal row .
bv - At the bottom of the chart , legend entries in a vertical column .
t - At the top of the chart , legend entries in a horizontal row .
t... | if legend_position :
self . legend_position = quote ( legend_position )
else :
self . legend_position = None |
def _valid_key ( self , key ) :
"""Return True if supplied key string serves as a valid attribute name : alphanumeric strings
beginning with a letter . Leading underscore not allowed . Also test for conflict with protected
attribute names ( e . g . dict class instance methods ) .""" | if not isinstance ( key , str ) :
return False
elif hasattr ( { } , key ) :
return False
elif key in self . _special_names :
return False
else :
return self . _valid_key_pattern . match ( key ) |
def simple_response ( self , status , msg = "" ) :
"""Write a simple response back to the client .""" | status = str ( status )
buf = [ self . server . protocol + " " + status + CRLF , "Content-Length: %s\r\n" % len ( msg ) , "Content-Type: text/plain\r\n" ]
if status [ : 3 ] in ( "413" , "414" ) : # Request Entity Too Large / Request - URI Too Long
self . close_connection = True
if self . response_protocol == 'H... |
def iter_links ( self ) :
"""An iterator over the working links in the machine .
Generates a series of ( x , y , link ) tuples .""" | for x in range ( self . width ) :
for y in range ( self . height ) :
for link in Links :
if ( x , y , link ) in self :
yield ( x , y , link ) |
def set_user_passwd ( self , userid , data ) :
"""Set user password""" | return self . api_call ( ENDPOINTS [ 'users' ] [ 'password' ] , dict ( userid = userid ) , body = data ) |
def get_assessment_offered ( self , assessment_offered_id ) :
"""Gets the ` ` AssessmentOffered ` ` specified by its ` ` Id ` ` .
In plenary mode , the exact ` ` Id ` ` is found or a ` ` NotFound ` `
results . Otherwise , the returned ` ` AssessmentOffered ` ` may have
a different ` ` Id ` ` than requested , ... | # Implemented from template for
# osid . resource . ResourceLookupSession . get _ resource
# NOTE : This implementation currently ignores plenary view
collection = JSONClientValidated ( 'assessment' , collection = 'AssessmentOffered' , runtime = self . _runtime )
result = collection . find_one ( dict ( { '_id' : Object... |
def sync_subscriber ( subscriber ) :
"""Sync a Customer with Stripe api data .""" | customer , _created = Customer . get_or_create ( subscriber = subscriber )
try :
customer . sync_from_stripe_data ( customer . api_retrieve ( ) )
customer . _sync_subscriptions ( )
customer . _sync_invoices ( )
customer . _sync_cards ( )
customer . _sync_charges ( )
except InvalidRequestError as e :... |
def execute ( self , action , parameters ) :
"""Execute a DynamoDB action with the given parameters . The method will
retry requests that failed due to OS level errors or when being
throttled by DynamoDB .
: param str action : DynamoDB action to invoke
: param dict parameters : parameters to send into the a... | measurements = collections . deque ( [ ] , self . _max_retries )
for attempt in range ( 1 , self . _max_retries + 1 ) :
try :
result = yield self . _execute ( action , parameters , attempt , measurements )
except ( exceptions . InternalServerError , exceptions . RequestException , exceptions . Throttlin... |
def print_locals ( * args , ** kwargs ) :
"""Prints local variables in function .
If no arguments all locals are printed .
Variables can be specified directly ( variable values passed in ) as varargs
or indirectly ( variable names passed in ) in kwargs by using keys and a list
of strings .""" | from utool import util_str
from utool import util_dbg
from utool import util_dict
locals_ = util_dbg . get_parent_frame ( ) . f_locals
keys = kwargs . get ( 'keys' , None if len ( args ) == 0 else [ ] )
to_print = { }
for arg in args :
varname = util_dbg . get_varname_from_locals ( arg , locals_ )
to_print [ va... |
def log_player_plays_road_builder ( self , player , location1 , location2 ) :
""": param player : catan . game . Player
: param location1 : string , see hexgrid . location ( )
: param location2 : string , see hexgrid . location ( )""" | self . _logln ( '{0} plays road builder, builds at {1} and {2}' . format ( player . color , location1 , location2 ) ) |
def _attributeStr ( self , name ) :
"""Return name = value for a single attribute""" | return "{}={}" . format ( _encodeAttr ( name ) , "," . join ( [ _encodeAttr ( v ) for v in self . attributes [ name ] ] ) ) |
def map_recursive ( function , iterable ) :
"""Apply function recursively to every item or value of iterable and returns a
new iterable object with the results .""" | if isiterable ( iterable ) :
dataOut = iterable . __class__ ( )
for i in iterable :
if isinstance ( dataOut , dict ) :
dataOut [ i ] = map_recursive ( function , iterable [ i ] )
else : # convert to list and append
if not isinstance ( dataOut , list ) :
da... |
def _complete_url ( self , text , tld_pos , tld ) :
"""Expand string in both sides to match whole URL .
: param str text : text where we want to find URL
: param int tld _ pos : position of TLD
: param str tld : matched TLD which should be in text
: return : returns URL
: rtype : str""" | left_ok = True
right_ok = True
max_len = len ( text ) - 1
end_pos = tld_pos
start_pos = tld_pos
while left_ok or right_ok :
if left_ok :
if start_pos <= 0 :
left_ok = False
else :
if text [ start_pos - 1 ] not in self . _stop_chars_left :
start_pos -= 1
... |
def _fill ( self , values ) :
"""Add extra values to fill the line""" | if not self . _previous_line :
self . _previous_line = values
return super ( StackedLine , self ) . _fill ( values )
new_values = values + list ( reversed ( self . _previous_line ) )
self . _previous_line = values
return new_values |
def compute_qu ( self ) :
"""Computes the mean and variance of q ( u ) , the variational distribution on
inducing outputs . SVGP with this q ( u ) should predict identically to
SGPR .
: return : mu , A""" | Kuf = features . Kuf ( self . feature , self . kern , self . X )
Kuu = features . Kuu ( self . feature , self . kern , jitter = settings . jitter )
Sig = Kuu + ( self . likelihood . variance ** - 1 ) * tf . matmul ( Kuf , Kuf , transpose_b = True )
Sig_sqrt = tf . cholesky ( Sig )
Sig_sqrt_Kuu = tf . matrix_triangular_... |
def _merge_skyline ( self , skylineq , segment ) :
"""Arguments :
skylineq ( collections . deque ) :
segment ( HSegment ) :""" | if len ( skylineq ) == 0 :
skylineq . append ( segment )
return
if skylineq [ - 1 ] . top == segment . top :
s = skylineq [ - 1 ]
skylineq [ - 1 ] = HSegment ( s . start , s . length + segment . length )
else :
skylineq . append ( segment ) |
def max ( self , axis = None , skipna = True ) :
"""Return the maximum value of the Index .
Parameters
axis : int , optional
For compatibility with NumPy . Only 0 or None are allowed .
skipna : bool , default True
Returns
scalar
Maximum value .
See Also
Index . min : Return the minimum value in an... | nv . validate_minmax_axis ( axis )
return nanops . nanmax ( self . _values , skipna = skipna ) |
def _combine_qc_samples ( samples ) :
"""Combine split QC analyses into single samples based on BAM files .""" | by_bam = collections . defaultdict ( list )
for data in [ utils . to_single_data ( x ) for x in samples ] :
batch = dd . get_batch ( data ) or dd . get_sample_name ( data )
if not isinstance ( batch , ( list , tuple ) ) :
batch = [ batch ]
batch = tuple ( batch )
by_bam [ ( dd . get_align_bam ( ... |
def get_model_path ( self , name ) :
"""Infer the path to the XML model name .""" | name , ext = os . path . splitext ( name )
ext = '.xml'
xmlfile = name + self . config [ 'file_suffix' ] + ext
xmlfile = utils . resolve_path ( xmlfile , workdir = self . config [ 'fileio' ] [ 'workdir' ] )
return xmlfile |
def safe_repr ( obj ) :
"""Try to get ` ` _ _ name _ _ ` ` first , ` ` _ _ class _ _ . _ _ name _ _ ` ` second
and finally , if we can ' t get anything acceptable , fallback
to user a ` ` repr ( ) ` ` call .""" | name = getattr ( obj , '__name__' , getattr ( obj . __class__ , '__name__' ) )
if name == 'ndict' :
name = 'dict'
return name or repr ( obj ) |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.