signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def get_all_importing_namespace_hashes ( self ) :
"""Get the set of all preordered and revealed namespace hashes that have not expired .""" | cur = self . db . cursor ( )
namespace_hashes = namedb_get_all_importing_namespace_hashes ( cur , self . lastblock )
return namespace_hashes |
def BytesIO ( * args , ** kwargs ) :
"""BytesIO constructor shim for the async wrapper .""" | raw = sync_io . BytesIO ( * args , ** kwargs )
return AsyncBytesIOWrapper ( raw ) |
def generate ( env ) :
"""Add Builders and construction variables for tar to an Environment .""" | try :
bld = env [ 'BUILDERS' ] [ 'Tar' ]
except KeyError :
bld = TarBuilder
env [ 'BUILDERS' ] [ 'Tar' ] = bld
env [ 'TAR' ] = env . Detect ( tars ) or 'gtar'
env [ 'TARFLAGS' ] = SCons . Util . CLVar ( '-c' )
env [ 'TARCOM' ] = '$TAR $TARFLAGS -f $TARGET $SOURCES'
env [ 'TARSUFFIX' ] = '.tar' |
def _dep_map ( self ) :
"""A map of extra to its list of ( direct ) requirements
for this distribution , including the null extra .""" | try :
return self . __dep_map
except AttributeError :
self . __dep_map = self . _filter_extras ( self . _build_dep_map ( ) )
return self . __dep_map |
def process_flat_files ( id_mappings_file , complexes_file = None , ptm_file = None , ppi_file = None , seq_file = None , motif_window = 7 ) :
"""Get INDRA Statements from HPRD data .
Of the arguments , ` id _ mappings _ file ` is required , and at least one of
` complexes _ file ` , ` ptm _ file ` , and ` ppi ... | id_df = pd . read_csv ( id_mappings_file , delimiter = '\t' , names = _hprd_id_cols , dtype = 'str' )
id_df = id_df . set_index ( 'HPRD_ID' )
if complexes_file is None and ptm_file is None and ppi_file is None :
raise ValueError ( 'At least one of complexes_file, ptm_file, or ' 'ppi_file must be given.' )
if ptm_fi... |
def notifications ( self ) :
"""Access the notifications
: returns : twilio . rest . api . v2010 . account . notification . NotificationList
: rtype : twilio . rest . api . v2010 . account . notification . NotificationList""" | if self . _notifications is None :
self . _notifications = NotificationList ( self . _version , account_sid = self . _solution [ 'sid' ] , )
return self . _notifications |
def measure_string ( self , text , fontname , fontsize , encoding = 0 ) :
"""Measure length of a string for a Base14 font .""" | return _fitz . Tools_measure_string ( self , text , fontname , fontsize , encoding ) |
def remove ( self , branch , turn , tick ) :
"""Delete all data from a specific tick""" | time_entity , parents , branches , keys , settings , presettings , remove_keycache , send = self . _remove_stuff
parent , entity , key = time_entity [ branch , turn , tick ]
branchkey = parent + ( entity , key )
keykey = parent + ( entity , )
if parent in parents :
parentt = parents [ parent ]
if entity in pare... |
def patch_with_options ( request , options , parent_queue_item = None ) :
"""Patch the given request with the given options ( e . g . user agent ) .
Args :
request ( : class : ` nyawc . http . Request ` ) : The request to patch .
options ( : class : ` nyawc . Options ` ) : The options to patch the request wit... | request . auth = copy . deepcopy ( options . identity . auth )
request . cookies = copy . deepcopy ( options . identity . cookies )
request . headers = copy . deepcopy ( options . identity . headers )
request . proxies = copy . deepcopy ( options . identity . proxies )
request . timeout = copy . copy ( options . perfor... |
def add_variables_from ( self , linear , vartype = None ) :
"""Add variables and / or linear biases to a binary quadratic model .
Args :
linear ( dict [ variable , bias ] / iterable [ ( variable , bias ) ] ) :
A collection of variables and their linear biases to add to the model .
If a dict , keys are varia... | if isinstance ( linear , abc . Mapping ) :
for v , bias in iteritems ( linear ) :
self . add_variable ( v , bias , vartype = vartype )
else :
try :
for v , bias in linear :
self . add_variable ( v , bias , vartype = vartype )
except TypeError :
raise TypeError ( "expected... |
def load_mo ( self , state , page_idx ) :
"""Loads a memory object from memory .
: param page _ idx : the index into the page
: returns : a tuple of the object""" | mo = self . _storage [ page_idx - self . _page_addr ]
return self . _sinkhole if mo is None else mo |
def configure_visual_baseline ( self ) :
"""Configure baseline directory""" | # Get baseline name
baseline_name = self . config . get_optional ( 'VisualTests' , 'baseline_name' , '{Driver_type}' )
for section in self . config . sections ( ) :
for option in self . config . options ( section ) :
option_value = self . config . get ( section , option )
baseline_name = baseline_na... |
def runner ( fun , arg = None , timeout = 5 ) :
'''Execute a runner on the master and return the data from the runner
function
CLI Example :
. . code - block : : bash
salt publish . runner manage . down''' | arg = _parse_args ( arg )
if 'master_uri' not in __opts__ :
return 'No access to master. If using salt-call with --local, please remove.'
log . info ( 'Publishing runner \'%s\' to %s' , fun , __opts__ [ 'master_uri' ] )
auth = salt . crypt . SAuth ( __opts__ )
tok = auth . gen_token ( b'salt' )
load = { 'cmd' : 'mi... |
def to_excel ( self , filename , recommended_only = False , include_io = True ) :
"""Return an Excel file for each model and dataset .
Parameters
filename : str or ExcelWriter object
Either the file name ( string ) or an ExcelWriter object .
recommended _ only : bool , optional
If True , only recommended ... | df = self . to_df ( recommended_only , include_io )
if isinstance ( filename , string_types ) :
filename = os . path . expanduser ( filename )
df . to_excel ( filename , index = False ) |
def _get_contents_between ( string , opener , closer ) :
"""Get the contents of a string between two characters""" | opener_location = string . index ( opener )
closer_location = string . index ( closer )
content = string [ opener_location + 1 : closer_location ]
return content |
def delete_ipv4 ( self , ipv4_id ) :
"""Delete ipv4""" | uri = 'api/ipv4/%s/' % ( ipv4_id )
return super ( ApiNetworkIPv4 , self ) . delete ( uri ) |
def system ( session ) :
"""Run the system test suite .""" | system_test_path = os . path . join ( "tests" , "system.py" )
system_test_folder_path = os . path . join ( "tests" , "system" )
# Sanity check : Only run tests if the environment variable is set .
if not os . environ . get ( "GOOGLE_APPLICATION_CREDENTIALS" , "" ) :
session . skip ( "Credentials must be set via env... |
def _vector ( x , type = 'row' ) :
"""Convert an object to a row or column vector .""" | if isinstance ( x , ( list , tuple ) ) :
x = np . array ( x , dtype = np . float32 )
elif not isinstance ( x , np . ndarray ) :
x = np . array ( [ x ] , dtype = np . float32 )
assert x . ndim == 1
if type == 'column' :
x = x [ : , None ]
return x |
def get_symbol ( x ) :
"""Retrieve recorded computation history as ` Symbol ` .
Parameters
x : NDArray
Array representing the head of computation graph .
Returns
Symbol
The retrieved Symbol .""" | hdl = SymbolHandle ( )
check_call ( _LIB . MXAutogradGetSymbol ( x . handle , ctypes . byref ( hdl ) ) )
return Symbol ( hdl ) |
def get_net_size ( mask ) :
'''Turns an IPv4 netmask into it ' s corresponding prefix length
(255.255.255.0 - > 24 as in 192.168.1.10/24 ) .''' | binary_str = ''
for octet in mask . split ( '.' ) :
binary_str += bin ( int ( octet ) ) [ 2 : ] . zfill ( 8 )
return len ( binary_str . rstrip ( '0' ) ) |
def file ( cls , uri_or_path ) :
"""Given either a URI like s3 : / / bucket / path . txt or a path like / path . txt ,
return a file object for it .""" | uri = urlparse ( uri_or_path )
if not uri . scheme : # Just a normal path
return open ( uri_or_path , 'rb' )
else :
it = cls ( uri_or_path ) . download_iter ( uri . path . lstrip ( '/' ) , skip_hash = True )
if not it :
raise ValueError ( '{0} not found' . format ( uri_or_path ) )
tmp = tempfile... |
def decrement ( self , column , amount = 1 , extras = None ) :
"""Decrement a column ' s value by a given amount
: param column : The column to increment
: type column : str
: param amount : The amount by which to increment
: type amount : int
: param extras : Extra columns
: type extras : dict
: retu... | if extras is None :
extras = { }
extras = self . _add_updated_at_column ( extras )
return self . to_base ( ) . decrement ( column , amount , extras ) |
def get_plink_version ( ) :
"""Gets the Plink version from the binary .
: returns : the version of the Plink software
: rtype : str
This function uses : py : class : ` subprocess . Popen ` to gather the version of
the Plink binary . Since executing the software to gather the version
creates an output file... | # Running the command
tmp_fn = None
with tempfile . NamedTemporaryFile ( delete = False ) as tmpfile :
tmp_fn = tmpfile . name + "_pyGenClean"
# The command to run
command = [ "plink" , "--noweb" , "--out" , tmp_fn ]
output = None
try :
proc = Popen ( command , stdout = PIPE , stderr = PIPE )
output = proc ... |
def get_controller ( self ) :
"""Gets the configured OpenFlow controller address .
This method is corresponding to the following ovs - vsctl command : :
$ ovs - vsctl get - controller < bridge >""" | command = ovs_vsctl . VSCtlCommand ( 'get-controller' , [ self . br_name ] )
self . run_command ( [ command ] )
result = command . result
return result [ 0 ] if len ( result ) == 1 else result |
def change_group_name ( self , group_jid : str , new_name : str ) :
"""Changes the a group ' s name to something new
: param group _ jid : The JID of the group whose name should be changed
: param new _ name : The new name to give to the group""" | log . info ( "[+] Requesting a group name change for JID {} to '{}'" . format ( group_jid , new_name ) )
return self . _send_xmpp_element ( group_adminship . ChangeGroupNameRequest ( group_jid , new_name ) ) |
def start ( self , ** kwargs ) :
"""Present the PTY of the container inside the current process .
This will take over the current process ' TTY until the container ' s PTY
is closed .""" | pty_stdin , pty_stdout , pty_stderr = self . sockets ( )
pumps = [ ]
if pty_stdin and self . interactive :
pumps . append ( io . Pump ( io . Stream ( self . stdin ) , pty_stdin , wait_for_output = False ) )
if pty_stdout :
pumps . append ( io . Pump ( pty_stdout , io . Stream ( self . stdout ) , propagate_close... |
def monitor_session_span_command_dest_vlan_val ( self , ** kwargs ) :
"""Auto Generated Code""" | config = ET . Element ( "config" )
monitor = ET . SubElement ( config , "monitor" , xmlns = "urn:brocade.com:mgmt:brocade-span" )
session = ET . SubElement ( monitor , "session" )
session_number_key = ET . SubElement ( session , "session-number" )
session_number_key . text = kwargs . pop ( 'session_number' )
span_comma... |
def _ParseAccountsData ( self , account_data ) :
"""Parse the SSH key data into a user map .
Args :
account _ data : string , the metadata server SSH key attributes data .
Returns :
dict , a mapping of the form : { ' username ' : [ ' sshkey1 , ' sshkey2 ' , . . . ] } .""" | if not account_data :
return { }
lines = [ line for line in account_data . splitlines ( ) if line ]
user_map = { }
for line in lines :
if not all ( ord ( c ) < 128 for c in line ) :
self . logger . info ( 'SSH key contains non-ascii character: %s.' , line )
continue
split_line = line . split... |
def MySend ( request_path , payload = None , content_type = "application/octet-stream" , timeout = None , force_auth = True , ** kwargs ) :
"""Run MySend1 maybe twice , because Rietveld is unreliable .""" | try :
return MySend1 ( request_path , payload , content_type , timeout , force_auth , ** kwargs )
except Exception , e :
if type ( e ) != urllib2 . HTTPError or e . code != 500 : # only retry on HTTP 500 error
raise
print >> sys . stderr , "Loading " + request_path + ": " + ExceptionDetail ( ) + "; ... |
def v_lift_valve_Crane ( rho , D1 = None , D2 = None , style = 'swing check angled' ) :
r'''Calculates the approximate minimum velocity required to lift the disk
or other controlling element of a check valve to a fully open , stable ,
position according to the Crane method [ 1 ] _ .
. . math : :
v _ { min }... | specific_volume = 1. / rho
if D1 is not None and D2 is not None :
beta = D1 / D2
beta2 = beta * beta
if style == 'swing check angled' :
return 45.0 * specific_volume ** 0.5
elif style == 'swing check straight' :
return 75.0 * specific_volume ** 0.5
elif style == 'swing check UL' :
return 120.0 * spe... |
def _printUUID ( uuid , detail = 'word' ) :
"""Return friendly abbreviated string for uuid .""" | if not isinstance ( detail , int ) :
detail = detailNum [ detail ]
if detail > detailNum [ 'word' ] :
return uuid
if uuid is None :
return None
return "%s...%s" % ( uuid [ : 4 ] , uuid [ - 4 : ] ) |
def SerializeFaultDetail ( self , val , info ) :
"""Serialize an object""" | self . _SerializeDataObject ( val , info , ' xsi:typ="{1}"' . format ( val . _wsdlName ) , self . defaultNS ) |
def operate_on_bulb ( self , method , params = None ) :
"""Build socket and send command to the bulb through it
: param method : method you want to use
: param params : parameters needed for this method ( can be a string if ony one parameter is needed )
: type method : str
: type params : list of str""" | # Get the message
self . command = YeelightCommand ( self . next_cmd_id ( ) , method , params )
# Send with socket
tcp_socket = socket . socket ( socket . AF_INET , socket . SOCK_STREAM )
tcp_socket . connect ( ( self . ip , int ( self . port ) ) )
tcp_socket . send ( self . command . get_message ( ) . encode ( ) )
dat... |
def losing_name ( self ) :
"""Returns a ` ` string ` ` of the losing team ' s name , such as ' Indiana '
Hoosiers ' .""" | if self . winner == HOME :
if 'cbb/schools' not in str ( self . _away_name ) :
return str ( self . _away_name )
return self . _away_name . text ( )
if 'cbb/schools' not in str ( self . _home_name ) :
return str ( self . _home_name )
return self . _home_name . text ( ) |
def isSigned ( self , ns_uri , ns_key ) :
"""Return whether a particular key is signed , regardless of
its namespace alias""" | return self . message . getKey ( ns_uri , ns_key ) in self . signed_fields |
def close ( self ) :
"""Closes the serial port .""" | if self . pyb and self . pyb . serial :
self . pyb . serial . close ( )
self . pyb = None |
def generate_url_map ( yaml_path = TOC_PATH ) -> dict :
"""Generates mapping from each URL to its previous and next URLs in the
textbook . The dictionary looks like :
' ch / 10 / some _ page . html ' : {
' prev ' : ' ch / 09 / foo . html ' ,
' next ' : ' ch / 10 / bar . html ' ,""" | with open ( yaml_path ) as f :
data = yaml . load ( f )
pipeline = [ t . remove ( _not_internal_link ) , flatmap ( _flatten_sections ) , t . map ( t . get ( 'url' ) ) , list , _sliding_three , t . map ( _adj_pages ) , t . merge ( ) ]
return t . pipe ( data , * pipeline ) |
def get_file_versions ( self , secure_data_path , limit = None , offset = None ) :
"""Get versions of a particular file
This is just a shim to get _ secret _ versions
secure _ data _ path - - full path to the file in the safety deposit box
limit - - Default ( 100 ) , limits how many records to be returned fro... | return self . get_secret_versions ( secure_data_path , limit , offset ) |
def sender ( self , body , stamp , url , sig ) :
"""Validate request is from Alexa .
Verifying that the Request was Sent by Alexa : https : / / goo . gl / AcrzB5.
Checking the Signature of the Request : https : / / goo . gl / FDkjBN .
Checking the Timestamp of the Request : https : / / goo . gl / Z5JhqZ
Arg... | if not timestamp ( stamp ) :
return False
if self . url != url :
if not signature_cert_chain_url ( url ) :
return False
certs = retrieve ( url )
if not certs :
return False
if not cert_chain ( certs ) :
return False
self . url = url
self . cert = certs [ 0 ]
if not si... |
def get_vpn ( self , vpn_name ) :
"""Returns a specific VPN name details from CPNR server .""" | request_url = self . _build_url ( [ 'VPN' , vpn_name ] )
return self . _do_request ( 'GET' , request_url ) |
def oop ( aa ) :
"""For cmd output .""" | return ( '%s %s %s %.2f %+.2f %s %s %s %s %+.2f %s %s %.2f %.4f %.4f' % ( aa . stock_no , aa . stock_name , aa . data_date [ - 1 ] , aa . raw_data [ - 1 ] , aa . range_per , aa . MAC ( 3 ) , aa . MAC ( 6 ) , aa . MAC ( 18 ) , aa . MAO ( 3 , 6 ) [ 1 ] , aa . MAO ( 3 , 6 ) [ 0 ] [ 1 ] [ - 1 ] , aa . MAO ( 3 , 6 ) [ 0 ] [... |
def _parse_env_var_file ( data ) :
"""Parses a basic VAR = " value data " file contents into a dict
: param data :
A unicode string of the file data
: return :
A dict of parsed name / value data""" | output = { }
for line in data . splitlines ( ) :
line = line . strip ( )
if not line or '=' not in line :
continue
parts = line . split ( '=' )
if len ( parts ) != 2 :
continue
name = parts [ 0 ]
value = parts [ 1 ]
if len ( value ) > 1 :
if value [ 0 ] == '"' and val... |
def circle_line_intersection ( center , r , a , b ) :
'''Computes two intersection points between the circle centered at < center > and radius < r > and a line given by two points a and b .
If no intersection exists , or if a = = b , None is returned . If one intersection exists , it is repeated in the answer .
... | s = b - a
# Quadratic eqn coefs
A = np . linalg . norm ( s ) ** 2
if abs ( A ) < tol :
return None
B = 2 * np . dot ( a - center , s )
C = np . linalg . norm ( a - center ) ** 2 - r ** 2
disc = B ** 2 - 4 * A * C
if disc < 0.0 :
return None
t1 = ( - B + np . sqrt ( disc ) ) / 2.0 / A
t2 = ( - B - np . sqrt ( di... |
def create ( name , allocated_storage , db_instance_class , engine , master_username , master_user_password , db_name = None , db_security_groups = None , vpc_security_group_ids = None , vpc_security_groups = None , availability_zone = None , db_subnet_group_name = None , preferred_maintenance_window = None , db_parame... | if not allocated_storage :
raise SaltInvocationError ( 'allocated_storage is required' )
if not db_instance_class :
raise SaltInvocationError ( 'db_instance_class is required' )
if not engine :
raise SaltInvocationError ( 'engine is required' )
if not master_username :
raise SaltInvocationError ( 'maste... |
def plot ( data , xcats , ycats = None , pconfig = None ) :
"""Plot a 2D heatmap .
: param data : List of lists , each a representing a row of values .
: param xcats : Labels for x axis
: param ycats : Labels for y axis . Defaults to same as x .
: param pconfig : optional dict with config key : value pairs ... | if pconfig is None :
pconfig = { }
# Allow user to overwrite any given config for this plot
if 'id' in pconfig and pconfig [ 'id' ] and pconfig [ 'id' ] in config . custom_plot_config :
for k , v in config . custom_plot_config [ pconfig [ 'id' ] ] . items ( ) :
pconfig [ k ] = v
if ycats is None :
y... |
def department_create ( self , data , ** kwargs ) :
"https : / / developer . zendesk . com / rest _ api / docs / chat / departments # create - department" | api_path = "/api/v2/departments"
return self . call ( api_path , method = "POST" , data = data , ** kwargs ) |
def manage_permission_for ( brain_or_object , permission , roles , acquire = 0 ) :
"""Change the settings for the given permission .
Code extracted from ` IRoleManager . manage _ permission `
: param brain _ or _ object : Catalog brain or object
: param permission : The permission to be granted
: param role... | obj = api . get_object ( brain_or_object )
if isinstance ( roles , basestring ) :
roles = [ roles ]
for item in obj . ac_inherited_permissions ( 1 ) :
name , value = item [ : 2 ]
if name == permission :
permission = Permission ( name , value , obj )
if acquire :
roles = list ( ro... |
def compute_normals ( self , cell_normals = True , point_normals = True , split_vertices = False , flip_normals = False , consistent_normals = True , auto_orient_normals = False , non_manifold_traversal = True , feature_angle = 30.0 , inplace = False ) :
"""Compute point and / or cell normals for a mesh .
The fil... | normal = vtk . vtkPolyDataNormals ( )
normal . SetComputeCellNormals ( cell_normals )
normal . SetComputePointNormals ( point_normals )
normal . SetSplitting ( split_vertices )
normal . SetFlipNormals ( flip_normals )
normal . SetConsistency ( consistent_normals )
normal . SetAutoOrientNormals ( auto_orient_normals )
n... |
def _get_languages ( cls ) -> set :
"""Get supported languages ( by querying the server ) .""" | if not cls . _server_is_alive ( ) :
cls . _start_server_on_free_port ( )
url = urllib . parse . urljoin ( cls . _url , 'Languages' )
languages = set ( )
for e in cls . _get_root ( url , num_tries = 1 ) :
languages . add ( e . get ( 'abbr' ) )
languages . add ( e . get ( 'abbrWithVariant' ) )
return language... |
def deconstruct ( self ) :
"""FK to version always points to a version table""" | name , path , args , kwargs = super ( FKToVersion , self ) . deconstruct ( )
if not kwargs [ 'to' ] . endswith ( '_version' ) :
kwargs [ 'to' ] = '{0}_version' . format ( kwargs [ 'to' ] )
return name , path , args , kwargs |
async def add_user ( self , username , password = None , display_name = None ) :
"""Add a user to this controller .
: param str username : Username
: param str password : Password
: param str display _ name : Display name
: returns : A : class : ` ~ juju . user . User ` instance""" | if not display_name :
display_name = username
user_facade = client . UserManagerFacade . from_connection ( self . connection ( ) )
users = [ client . AddUser ( display_name = display_name , username = username , password = password ) ]
results = await user_facade . AddUser ( users )
secret_key = results . results [... |
def acknowledge ( self , size , msg ) :
"""Acknowledge bytes received by a transfer target , scheduling new chunks
to keep the window full . This should be called for every chunk received
by the target .""" | stream = self . router . stream_by_id ( msg . src_id )
state = self . _state_by_stream [ stream ]
state . lock . acquire ( )
try :
if state . unacked < size :
LOG . error ( '%r.acknowledge(src_id %d): unacked=%d < size %d' , self , msg . src_id , state . unacked , size )
state . unacked -= min ( state .... |
def visit_Name ( self , node ) :
"""Turn global variable used not shadows to function call .
We check it is a name from an assignment as import or functions use
should not be turn into call .""" | if ( isinstance ( node . ctx , ast . Load ) and node . id not in self . local_decl and node . id in self . to_expand ) :
self . update = True
return ast . Call ( func = node , args = [ ] , keywords = [ ] )
return node |
def get_encoding_from_reponse ( r ) :
"""获取requests库get或post返回的对象编码
Args :
r : requests库get或post返回的对象
Returns :
对象编码""" | encoding = requests . utils . get_encodings_from_content ( r . text )
return encoding [ 0 ] if encoding else requests . utils . get_encoding_from_headers ( r . headers ) |
def tag_alert ( self , id , tags ) :
"""Append tags to tag list . Don ' t add same tag more than once .""" | response = self . get_db ( ) . alerts . update_one ( { '_id' : { '$regex' : '^' + id } } , { '$addToSet' : { 'tags' : { '$each' : tags } } } )
return response . matched_count > 0 |
def feature ( self , type_ = None , identifier = None , description = None , entry_name = None , limit = None , as_df = False ) :
"""Method to query : class : ` . models . Feature ` objects in database
Check available features types with ` ` pyuniprot . query ( ) . feature _ types ` `
: param type _ : type ( s ... | q = self . session . query ( models . Feature )
model_queries_config = ( ( type_ , models . Feature . type_ ) , ( identifier , models . Feature . identifier ) , ( description , models . Feature . description ) )
q = self . get_model_queries ( q , model_queries_config )
q = self . get_one_to_many_queries ( q , ( ( entry... |
def _get_registries ( self ) :
"""Return a list of registries that this build updated
For orchestrator it should attempt to filter out non - pulp registries , on worker - return
all registries""" | if self . workflow . buildstep_result . get ( PLUGIN_BUILD_ORCHESTRATE_KEY ) :
registries = self . workflow . push_conf . pulp_registries
if not registries :
registries = self . workflow . push_conf . all_registries
return registries
else :
return self . workflow . push_conf . all_registries |
def generate_expand_search_database_from_contigs ( self , contig_files , output_database_file , search_method ) :
'''Given a collection of search _ hmm _ files , search the contigs in
contig _ files , and generate an HMM from the resulting hits , outputting
it as output _ database _ file .
Parameters
contig... | ss = SequenceSearcher ( self . search_hmm_files )
seqio = SequenceIO ( )
if search_method == self . DIAMOND_SEARCH_METHOD :
if self . diamond_database == None or self . unaligned_sequence_database == None :
logging . warning ( "Cannot expand_search continue with no diamond database or unaligned sequences." ... |
def _get_partition_info ( storage_system , device_path ) :
'''Returns partition informations for a device path , of type
vim . HostDiskPartitionInfo''' | try :
partition_infos = storage_system . RetrieveDiskPartitionInfo ( devicePath = [ device_path ] )
except vim . fault . NoPermission as exc :
log . exception ( exc )
raise salt . exceptions . VMwareApiError ( 'Not enough permissions. Required privilege: ' '{0}' . format ( exc . privilegeId ) )
except vim .... |
def serialize ( self , value , ** kwargs ) :
"""Serialize the attribute of the input data .
Gets the attribute value with accessor and converts it using the
type serialization . Schema will place this serialized value into
corresponding compartment of the HAL structure with the name of the
attribute as a ke... | if types . Type . is_type ( self . attr_type ) :
try :
value = self . accessor . get ( value , ** kwargs )
except ( AttributeError , KeyError ) :
if not hasattr ( self , "default" ) and self . required :
raise
value = self . default ( ) if callable ( self . default ) else sel... |
def serialzeValueToTCL ( self , val , do_eval = False ) -> Tuple [ str , str , bool ] :
"""Serialize value to TCL
: return : tuple ( serialized value , serialized evaluated value of value , value is constant flag )""" | return str ( val ) , str ( val ) , True |
def getStorageEngines ( self ) :
"""Returns list of supported storage engines .
@ return : List of storage engine names .""" | cur = self . _conn . cursor ( )
cur . execute ( """SHOW STORAGE ENGINES;""" )
rows = cur . fetchall ( )
if rows :
return [ row [ 0 ] . lower ( ) for row in rows if row [ 1 ] in [ 'YES' , 'DEFAULT' ] ]
else :
return [ ] |
def WriteGoogleTransitFeed ( self , file ) :
"""Output this schedule as a Google Transit Feed in file _ name .
Args :
file : path of new feed file ( a string ) or a file - like object
Returns :
None""" | # Compression type given when adding each file
archive = zipfile . ZipFile ( file , 'w' )
if 'agency' in self . _table_columns :
agency_string = StringIO . StringIO ( )
writer = util . CsvUnicodeWriter ( agency_string )
columns = self . GetTableColumns ( 'agency' )
writer . writerow ( columns )
for ... |
def generate_nb_state_data ( means , weights , R ) :
"""Generates data according to the Negative Binomial Convex Mixture Model .
Args :
means ( array ) : Cell types - genes x clusters
weights ( array ) : Cell cluster assignments - clusters x cells
R ( array ) : dispersion parameter - 1 x genes
Returns :
... | cells = weights . shape [ 1 ]
# x _ true = true means
x_true = np . dot ( means , weights )
# convert means into P
R_ = np . tile ( R , ( cells , 1 ) ) . T
P_true = x_true / ( R_ + x_true )
sample = np . random . negative_binomial ( np . tile ( R , ( cells , 1 ) ) . T , P_true )
return sample . astype ( float ) |
def execute ( self , input_data ) :
'''Execute method''' | # Grab the raw bytes of the sample
raw_bytes = input_data [ 'sample' ] [ 'raw_bytes' ]
# Spin up the rekall session and render components
session = MemSession ( raw_bytes )
renderer = WorkbenchRenderer ( session = session )
# Run the plugin
session . RunPlugin ( self . plugin_name , renderer = renderer )
return rendere... |
def load_window_settings ( self , prefix , default = False , section = 'main' ) :
"""Load window layout settings from userconfig - based configuration
with * prefix * , under * section *
default : if True , do not restore inner layout""" | get_func = CONF . get_default if default else CONF . get
window_size = get_func ( section , prefix + 'size' )
prefs_dialog_size = get_func ( section , prefix + 'prefs_dialog_size' )
if default :
hexstate = None
else :
hexstate = get_func ( section , prefix + 'state' , None )
pos = get_func ( section , prefix + ... |
def classattribute ( func ) :
"""Wrap a function as a class attribute .
This differs from attribute by identifying attributes explicitly listed
in a class definition rather than those only defined on instances of
a class .""" | attr = abc . abstractmethod ( func )
attr . __iclassattribute__ = True
attr = _property ( attr )
return attr |
def add_interim_values ( module , input , output ) :
"""The forward hook used to save interim tensors , detached
from the graph . Used to calculate the multipliers""" | try :
del module . x
except AttributeError :
pass
try :
del module . y
except AttributeError :
pass
module_type = module . __class__ . __name__
if module_type in op_handler :
func_name = op_handler [ module_type ] . __name__
# First , check for cases where we don ' t need to save the x and y ten... |
def VerifyStructure ( self , parser_mediator , line ) :
"""Verify that this file is a Sophos Anti - Virus log file .
Args :
parser _ mediator ( ParserMediator ) : mediates interactions between parsers
and other components , such as storage and dfVFS .
line ( str ) : line from a text file .
Returns :
boo... | try :
structure = self . _LOG_LINE . parseString ( line )
except pyparsing . ParseException :
logger . debug ( 'Not a Sophos Anti-Virus log file' )
return False
# Expect spaces at position 9 and 16.
if ' ' not in ( line [ 8 ] , line [ 15 ] ) :
logger . debug ( 'Not a Sophos Anti-Virus log file' )
re... |
def dot_solve ( self , y ) :
r"""Compute the inner product of a vector with the inverse of the
covariance matrix applied to itself :
. . math : :
y \ , K ^ { - 1 } \ , y
Args :
y ( ndarray [ nsamples ] ) : The vector : math : ` y ` .""" | return np . dot ( y . T , cho_solve ( self . _factor , y ) ) |
def split_channels ( image ) :
"""Split channels of a multi - channel ANTsImage into a collection
of scalar ANTsImage types
Arguments
image : ANTsImage
multi - channel image to split
Returns
list of ANTsImage types
Example
> > > import ants
> > > image = ants . image _ read ( ants . get _ ants _ d... | inpixeltype = image . pixeltype
dimension = image . dimension
components = 1
libfn = utils . get_lib_fn ( 'splitChannels%s' % image . _libsuffix )
itkimages = libfn ( image . pointer )
antsimages = [ iio . ANTsImage ( pixeltype = inpixeltype , dimension = dimension , components = components , pointer = itkimage ) for i... |
def set_logging ( cfg_obj ) :
"""Enable or disable logging per config object parameter""" | log_status = cfg_obj [ 'LOGGING' ] [ 'ENABLE_LOGGING' ]
if log_status :
logger . disabled = False
elif not log_status :
logger . info ( '%s: Logging disabled per local configuration file (%s) parameters.' % ( inspect . stack ( ) [ 0 ] [ 3 ] , cfg_obj [ 'PROJECT' ] [ 'CONFIG_PATH' ] ) )
logger . disabled = T... |
def btc_is_p2wpkh_address ( address ) :
"""Is the given address a p2wpkh address ?""" | wver , whash = segwit_addr_decode ( address )
if whash is None :
return False
if len ( whash ) != 20 :
return False
return True |
def set_edge_label ( self , edge , label ) :
"""Set the label of an edge .
@ type edge : edge
@ param edge : One edge .
@ type label : string
@ param label : Edge label .""" | self . set_edge_properties ( edge , label = label )
if not self . DIRECTED :
self . set_edge_properties ( ( edge [ 1 ] , edge [ 0 ] ) , label = label ) |
def custom_str ( self , sc_expr_str_fn ) :
"""Works like Symbol . _ _ str _ _ ( ) , but allows a custom format to be used for
all symbol / choice references . See expr _ str ( ) .""" | return "\n\n" . join ( node . custom_str ( sc_expr_str_fn ) for node in self . nodes ) |
def _transform ( self , value ) :
"""Applies any defined transformation to the given value""" | if self . transform :
try :
value = self . transform ( value )
except :
import sys
exc_type , exc_obj , exc_tb = sys . exc_info ( )
raise AssertionError ( 'Error applying transformation <{0}>: {2}: {3}' . format ( self . transform . __name__ , value , exc_type . __name__ , exc_ob... |
def permute_outputs ( Y , X ) :
"""Permute the output according to one of the inputs as in [ _ 2]
References
. . [ 2 ] Elmar Plischke ( 2010 ) " An effective algorithm for computing global
sensitivity indices ( EASI ) Reliability Engineering & System Safety " ,
95:4 , 354-360 . doi : 10.1016 / j . ress . 20... | permutation_index = np . argsort ( X )
permutation_index = np . concatenate ( [ permutation_index [ : : 2 ] , permutation_index [ 1 : : 2 ] [ : : - 1 ] ] )
return Y [ permutation_index ] |
def sql ( self , query ) :
"""Perform a SQL query and create a L { DataFrame } of the result .
The SQL query is run using Spark SQL . This is not intended for
querying arbitrary databases , but rather querying Spark SQL tables .
Parameters
query : string
The SQL query to pass to Spark SQL to execute .
R... | return DataFrame . from_spark_rdd ( self . sql_ctx . sql ( query ) , self . sql_ctx ) |
def calculate_oobatake_dH ( seq , temp ) :
"""Get dH using Oobatake method in units cal / mol .
Args :
seq ( str , Seq , SeqRecord ) : Amino acid sequence
temp ( float ) : Temperature in degrees C
Returns :
float : dH in units cal / mol""" | seq = ssbio . protein . sequence . utils . cast_to_str ( seq )
dH = 0
temp += 273.15
T0 = 298.15
for aa in seq :
H0 = oobatake_dictionary [ aa ] [ 'dH' ] * 1000
dH += H0
return dH + _sum_of_dCp ( seq ) * ( temp - T0 ) |
def generate ( passphrase , trees = [ 'primary' ] ) :
"""Generate a seed for the primary tree of a Gem wallet .
You may choose to store the passphrase for a user so the user doesn ' t have
to type it in every time . This is okay ( although the security risks should
be obvious ) but Gem strongly discourages st... | seeds , multi_wallet = MultiWallet . generate ( trees , entropy = True )
result = { }
for tree in trees :
result [ tree ] = dict ( private_seed = seeds [ tree ] , public_seed = multi_wallet . public_wif ( tree ) , encrypted_seed = PassphraseBox . encrypt ( passphrase , seeds [ tree ] ) )
return result |
def scalac_classpath_entries ( self ) :
"""Returns classpath entries for the scalac classpath .""" | return ScalaPlatform . global_instance ( ) . compiler_classpath_entries ( self . context . products , self . context . _scheduler ) |
def pair ( p , q ) :
"""Computes the bilinear pairing e ( p , q ) . @ p must be a G1Element and @ q must
be a G2Element .
@ returns a GtElement""" | # Check types
assertType ( p , G1Element )
assertType ( q , G2Element )
result = GtElement ( )
librelic . pc_map_abi ( byref ( result ) , byref ( p ) , byref ( q ) )
return result |
def on_disconnect_request ( self , py_db , request ) :
''': param DisconnectRequest request :''' | self . api . set_enable_thread_notifications ( py_db , False )
self . api . remove_all_breakpoints ( py_db , filename = '*' )
self . api . remove_all_exception_breakpoints ( py_db )
self . api . request_resume_thread ( thread_id = '*' )
response = pydevd_base_schema . build_response ( request )
return NetCommand ( CMD_... |
def load ( fin , dtype = np . float32 , max_vocab = None ) :
"""Load word embedding file .
Args :
fin ( File ) : File object to read . File should be open for reading ascii .
dtype ( numpy . dtype ) : Element data type to use for the array .
max _ vocab ( int ) : Number of vocabulary to read .
Returns :
... | vocab = { }
arr = None
i = 0
for line in fin :
if max_vocab is not None and i >= max_vocab :
break
try :
token , v = _parse_line ( line , dtype )
except ( ValueError , IndexError ) :
raise ParseError ( b'Parsing error in line: ' + line )
if token in vocab :
parse_warn ( b... |
def _ParseLogLine ( self , parser_mediator , structure , key ) :
"""Parse a single log line and produce an event object .
Args :
parser _ mediator ( ParserMediator ) : mediates interactions between parsers
and other components , such as storage and dfvfs .
key ( str ) : identifier of the structure of tokens... | time_elements_tuple = self . _GetTimeElementsTuple ( structure )
try :
date_time = dfdatetime_time_elements . TimeElements ( time_elements_tuple = time_elements_tuple )
except ValueError :
parser_mediator . ProduceExtractionWarning ( 'invalid date time value: {0!s}' . format ( structure . date_time ) )
retu... |
def methods ( self ) :
"""Returns all documented methods as ` pydoc . Function ` objects in
the class , sorted alphabetically with ` _ _ init _ _ ` always coming
first .
Unfortunately , this also includes class methods .""" | p = lambda o : ( isinstance ( o , Function ) and o . method and self . module . _docfilter ( o ) )
return filter ( p , self . doc . values ( ) ) |
def get_tensor_device ( self , tensor_name ) :
"""The device of a tensor .
Note that only tf tensors have device assignments .
Args :
tensor _ name : a string , name of a tensor in the graph .
Returns :
a string or None , representing the device name .""" | tensor = self . _name_to_tensor ( tensor_name )
if isinstance ( tensor , tf . Tensor ) :
return tensor . device
else : # mtf . Tensor
return None |
def mk_dropdown_tree ( cls , model , root_node , for_node = None ) :
'''Override of ` ` treebeard ` ` method to enforce the same root .''' | options = [ ]
# The difference is that we only generate the subtree for the current root .
logger . debug ( "Using root node pk of %s" % root_node . pk )
cls . add_subtree ( for_node , root_node , options )
return options [ 1 : ] |
def set ( self , uri , content ) :
"""Cache node content for uri .
No return .""" | key , value = self . _prepare_node ( uri , content )
self . _set ( key , value ) |
def start ( self ) :
"""Start the ssh client and connect to the host .
It will wait until the ssh service is available during 90 seconds .
If it doesn ' t succed to connect then the function will raise
an SSHException .""" | if self . via_ip :
connect_to = self . via_ip
self . description = '[%s@%s via %s]' % ( self . _user , self . _hostname , self . via_ip )
else :
connect_to = self . _hostname
self . description = '[%s@%s]' % ( self . _user , self . _hostname )
exception = None
for i in range ( 60 ) :
try :
s... |
def _none_rejecter ( validation_callable # type : Callable
) : # type : ( . . . ) - > Callable
"""Wraps the given validation callable to reject None values . When a None value is received by the wrapper ,
it is not passed to the validation _ callable and instead this function will raise a WrappingFailure . When a... | # option ( a ) use the ` decorate ( ) ` helper method to preserve name and signature of the inner object
# = = > NO , we want to support also non - function callable objects
# option ( b ) simply create a wrapper manually
def reject_none ( x ) :
if x is not None :
return validation_callable ( x )
else :... |
def delete_password ( self , service , username ) :
"""Delete the password for the username of the service .""" | service = escape_for_ini ( service )
username = escape_for_ini ( username )
config = configparser . RawConfigParser ( )
if os . path . exists ( self . file_path ) :
config . read ( self . file_path )
try :
if not config . remove_option ( service , username ) :
raise PasswordDeleteError ( "Password not f... |
def make_map ( ) :
"""Create , configure and return the routes Mapper""" | map = Mapper ( directory = config [ 'pylons.paths' ] [ 'controllers' ] , always_scan = config [ 'debug' ] )
# The ErrorController route ( handles 404/500 error pages ) ; it should
# likely stay at the top , ensuring it can always be resolved
map . connect ( 'error/:action/:id' , controller = 'error' )
# CUSTOM ROUTES H... |
def add_training_sample ( self , text = u'' , lang = '' ) :
"""Initial step for adding new sample to training data .
You need to call ` save _ training _ samples ( ) ` afterwards .
: param text : Sample text to be added .
: param lang : Language label for the input text .""" | self . trainer . add ( text = text , lang = lang ) |
def get_satellites_list ( self , sat_type ) :
"""Get a sorted satellite list : master then spare
: param sat _ type : type of the required satellites ( arbiters , schedulers , . . . )
: type sat _ type : str
: return : sorted satellites list
: rtype : list [ alignak . objects . satellitelink . SatelliteLink... | satellites_list = [ ]
if sat_type in [ 'arbiters' , 'schedulers' , 'reactionners' , 'brokers' , 'receivers' , 'pollers' ] :
for satellite in getattr ( self , sat_type ) :
satellites_list . append ( satellite )
satellites_list = master_then_spare ( satellites_list )
return satellites_list |
def _declare_namespace ( self , package_name ) :
'''Mock for # pkg _ resources . declare _ namespace ( ) which calls
# pkgutil . extend _ path ( ) afterwards as the original implementation doesn ' t
seem to properly find all available namespace paths .''' | self . state [ 'declare_namespace' ] ( package_name )
mod = sys . modules [ package_name ]
mod . __path__ = pkgutil . extend_path ( mod . __path__ , package_name ) |
def _get_netmiko_args ( optional_args ) :
'''Check for Netmiko arguments that were passed in as NAPALM optional arguments .
Return a dictionary of these optional args that will be passed into the
Netmiko ConnectHandler call .
. . note : :
This is a port of the NAPALM helper for backwards compatibility with ... | if HAS_NETMIKO_HELPERS :
return napalm . base . netmiko_helpers . netmiko_args ( optional_args )
# Older version don ' t have the netmiko _ helpers module , the following code is
# simply a port from the NAPALM code base , for backwards compatibility :
# https : / / github . com / napalm - automation / napalm / blo... |
def list_members ( self , list_id = None , slug = None , owner_screen_name = None , owner_id = None ) :
"""Returns the members of a list .
List id or ( slug and ( owner _ screen _ name or owner _ id ) ) are required""" | assert list_id or ( slug and ( owner_screen_name or owner_id ) )
url = 'https://api.twitter.com/1.1/lists/members.json'
params = { 'cursor' : - 1 }
if list_id :
params [ 'list_id' ] = list_id
else :
params [ 'slug' ] = slug
if owner_screen_name :
params [ 'owner_screen_name' ] = owner_screen_name
... |
def add_spectroscopy ( self , label = '0_0' , ** props ) :
"""Adds spectroscopic measurement to particular star ( s ) ( corresponding to individual model node )
Default 0_0 should be primary star
legal inputs are ' Teff ' , ' logg ' , ' feh ' , and in form ( val , err )""" | if label not in self . leaf_labels :
raise ValueError ( 'No model node named {} (must be in {}). Maybe define models first?' . format ( label , self . leaf_labels ) )
for k , v in props . items ( ) :
if k not in self . spec_props :
raise ValueError ( 'Illegal property {} (only {} allowed).' . format ( k... |
def matches_extension ( path , extension ) :
"""Returns True if path has the given extension , or if
the last path component matches the extension . Supports
Unix glob matching .
> > > matches _ extension ( " . / www / profile . php " , " php " )
True
> > > matches _ extension ( " . / scripts / menu . js ... | _ , ext = os . path . splitext ( path )
if ext == '' : # If there is no extension , grab the file name and
# compare it to the given extension .
return os . path . basename ( path ) == extension
else : # If the is an extension , drop the leading period and
# compare it to the extension .
return fnmatch . fnmatc... |
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