signature stringlengths 29 44.1k | implementation stringlengths 0 85.2k |
|---|---|
def parse_phlat_file ( phlatfile , mhc_alleles ) :
"""Parse the input phlat file to pull out the alleles it contains
: param phlatfile : Open file descriptor for a phlat output sum file
: param mhc _ alleles : dictionary of alleles .""" | for line in phlatfile :
if line . startswith ( 'Locus' ) :
continue
line = line . strip ( ) . split ( )
if line [ 0 ] . startswith ( 'HLA_D' ) :
line [ 0 ] = line [ 0 ] [ : - 1 ]
# strip the last character
# Sometimes we get an error saying there was insufficient read
# conve... |
def consume ( self , expect_class = None ) :
"""Retrieve the current token , then advance the parser .
If an expected class is provided , it will assert that the current token
matches that class ( is an instance ) .
Note that when calling a token ' s nud ( ) or led ( ) functions , the " current "
token is t... | if expect_class and not isinstance ( self . current_token , expect_class ) :
raise InvalidTokenError ( "Unexpected token at %d: got %r, expected %s" % ( self . current_pos , self . current_token , expect_class . __name__ ) )
current_token = self . current_token
self . _forward ( )
return current_token |
def delete ( self , user ) :
"""Delete a resource""" | if user :
can_delete = yield self . can_delete ( user )
else :
can_delete = False
if not can_delete :
raise exceptions . Unauthorized ( 'User may not delete the resource' )
doc = { '_id' : self . id , '_deleted' : True }
try :
doc [ '_rev' ] = self . _rev
except AttributeError :
pass
db = self . db_... |
def get_resource ( resource_name ) :
"""Return a resource in current directory or in frozen package""" | resource_path = None
if hasattr ( sys , "frozen" ) :
resource_path = os . path . normpath ( os . path . join ( os . path . dirname ( sys . executable ) , resource_name ) )
elif not hasattr ( sys , "frozen" ) and pkg_resources . resource_exists ( "gns3server" , resource_name ) :
resource_path = pkg_resources . r... |
def get_climate ( self , device_label ) :
"""Get climate history
Args :
device _ label : device label of climate device""" | response = None
try :
response = requests . get ( urls . climate ( self . _giid ) , headers = { 'Accept' : 'application/json, text/javascript, */*; q=0.01' , 'Cookie' : 'vid={}' . format ( self . _vid ) } , params = { "deviceLabel" : device_label } )
except requests . exceptions . RequestException as ex :
raise... |
def make_dbsource ( ** kwargs ) :
"""Returns a mapnik PostGIS or SQLite Datasource .""" | if 'spatialite' in connection . settings_dict . get ( 'ENGINE' ) :
kwargs . setdefault ( 'file' , connection . settings_dict [ 'NAME' ] )
return mapnik . SQLite ( wkb_format = 'spatialite' , ** kwargs )
names = ( ( 'dbname' , 'NAME' ) , ( 'user' , 'USER' ) , ( 'password' , 'PASSWORD' ) , ( 'host' , 'HOST' ) , (... |
def from_code ( cls , environment , code , globals , uptodate = None ) :
"""Creates a template object from compiled code and the globals . This
is used by the loaders and environment to create a template object .""" | namespace = { 'environment' : environment , '__file__' : code . co_filename }
exec code in namespace
rv = cls . _from_namespace ( environment , namespace , globals )
rv . _uptodate = uptodate
return rv |
def add_options ( self ) :
"""Add program options .""" | self . add_bool_option ( "--reveal" , help = "show full announce URL including keys" )
self . add_bool_option ( "--raw" , help = "print the metafile's raw content in all detail" )
self . add_bool_option ( "-V" , "--skip-validation" , help = "show broken metafiles with an invalid structure" )
self . add_value_option ( "... |
def getURL ( self , size = 'Medium' , urlType = 'url' ) :
"""Retrieves a url for the photo . ( flickr . photos . getSizes )
urlType - ' url ' or ' source '
' url ' - flickr page of photo
' source ' - image file""" | method = 'flickr.photos.getSizes'
data = _doget ( method , photo_id = self . id )
for psize in data . rsp . sizes . size :
if psize . label == size :
return getattr ( psize , urlType )
raise FlickrError , "No URL found" |
def _remote_status ( session , service_id , uuid , url , interval = 3 ) :
"""Poll for remote command status .""" | _LOGGER . info ( 'polling for status' )
resp = session . get ( url , params = { 'remoteServiceRequestID' : service_id , 'uuid' : uuid } ) . json ( )
if resp [ 'status' ] == 'SUCCESS' :
return 'completed'
time . sleep ( interval )
return _remote_status ( session , service_id , uuid , url ) |
def resolve_election_tie ( self , candidates ) :
"""call callback to resolve a tie between candidates""" | sorted_candidate_ids = list ( sorted ( candidates , key = self . candidate_order_fn ) )
return sorted_candidate_ids [ self . election_tie_cb ( candidates ) ] |
def list ( path , filename = None , start = None , stop = None , recursive = False , directories = False ) :
"""List files specified by dataPath .
Datapath may include a single wildcard ( ' * ' ) in the filename specifier .
Returns sorted list of absolute path strings .""" | path = uri_to_path ( path )
if not filename and recursive :
return listrecursive ( path )
if filename :
if os . path . isdir ( path ) :
path = os . path . join ( path , filename )
else :
path = os . path . join ( os . path . dirname ( path ) , filename )
else :
if os . path . isdir ( pat... |
def uclust_fasta_sort_from_filepath ( fasta_filepath , output_filepath = None , tmp_dir = gettempdir ( ) , HALT_EXEC = False ) :
"""Generates sorted fasta file via uclust - - mergesort .""" | if not output_filepath :
_ , output_filepath = mkstemp ( dir = tmp_dir , prefix = 'uclust_fasta_sort' , suffix = '.fasta' )
app = Uclust ( params = { '--tmpdir' : tmp_dir } , TmpDir = tmp_dir , HALT_EXEC = HALT_EXEC )
app_result = app ( data = { '--mergesort' : fasta_filepath , '--output' : output_filepath } )
retu... |
def groupby ( self , by = None , axis = 0 , level = None , as_index = True , sort = True , group_keys = True , squeeze = False , observed = False , ** kwargs ) :
"""Group DataFrame or Series using a mapper or by a Series of columns .
A groupby operation involves some combination of splitting the
object , applyi... | from pandas . core . groupby . groupby import groupby
if level is None and by is None :
raise TypeError ( "You have to supply one of 'by' and 'level'" )
axis = self . _get_axis_number ( axis )
return groupby ( self , by = by , axis = axis , level = level , as_index = as_index , sort = sort , group_keys = group_keys... |
def ji_windows ( self , ij_win ) : # what can be given to ij _ win NOT intuitive / right name by now ! ! !
"""For a given specific window , i . e . an element of : attr : ` windows ` , get the windows of all resolutions .
Arguments :
ij _ win { int } - - The index specifying the window for which to return the r... | ji_windows = { }
transform_src = self . _layer_meta [ self . _res_indices [ self . _windows_res ] [ 0 ] ] [ "transform" ]
for res in self . _res_indices :
transform_dst = self . _layer_meta [ self . _res_indices [ res ] [ 0 ] ] [ "transform" ]
ji_windows [ res ] = window_from_window ( window_src = self . window... |
def buscar ( self , id_vlan ) :
"""Get VLAN by its identifier .
: param id _ vlan : VLAN identifier .
: return : Following dictionary :
{ ' vlan ' : { ' id ' : < id _ vlan > ,
' nome ' : < nome _ vlan > ,
' num _ vlan ' : < num _ vlan > ,
' id _ ambiente ' : < id _ ambiente > ,
' id _ tipo _ rede ' : ... | if not is_valid_int_param ( id_vlan ) :
raise InvalidParameterError ( u'Vlan id is invalid or was not informed.' )
url = 'vlan/' + str ( id_vlan ) + '/'
code , xml = self . submit ( None , 'GET' , url )
return self . response ( code , xml ) |
def _from_dict ( cls , _dict ) :
"""Initialize a Configuration object from a json dictionary .""" | args = { }
if 'configuration_id' in _dict :
args [ 'configuration_id' ] = _dict . get ( 'configuration_id' )
if 'name' in _dict :
args [ 'name' ] = _dict . get ( 'name' )
else :
raise ValueError ( 'Required property \'name\' not present in Configuration JSON' )
if 'created' in _dict :
args [ 'created' ]... |
def list_features ( self , dataset , reverse = False , start = None , limit = None ) :
"""Lists features in a dataset .
Parameters
dataset : str
The dataset id .
reverse : str , optional
List features in reverse order .
Possible value is " true " .
start : str , optional
The id of the feature after ... | uri = URITemplate ( self . baseuri + '/{owner}/{id}/features' ) . expand ( owner = self . username , id = dataset )
params = { }
if reverse :
params [ 'reverse' ] = 'true'
if start :
params [ 'start' ] = start
if limit :
params [ 'limit' ] = int ( limit )
return self . session . get ( uri , params = params ... |
def _apply_workspaces ( self , combination , mode ) :
"""Allows user to force move a comma separated list of workspaces to the
given output when it ' s activated .
Example :
- DP1 _ workspaces = " 1,2,3" """ | if len ( combination ) > 1 and mode == "extend" :
sleep ( 3 )
for output in combination :
workspaces = getattr ( self , "{}_workspaces" . format ( output ) , "" ) . split ( "," )
for workspace in workspaces :
if not workspace :
continue
# switch to workspa... |
def plot_run_nlive ( method_names , run_dict , ** kwargs ) :
"""Plot the allocations of live points as a function of logX for the input
sets of nested sampling runs of the type used in the dynamic nested
sampling paper ( Higson et al . 2019 ) .
Plots also include analytically calculated distributions of relat... | logx_given_logl = kwargs . pop ( 'logx_given_logl' , None )
logl_given_logx = kwargs . pop ( 'logl_given_logx' , None )
logx_min = kwargs . pop ( 'logx_min' , None )
ymax = kwargs . pop ( 'ymax' , None )
npoints = kwargs . pop ( 'npoints' , 100 )
figsize = kwargs . pop ( 'figsize' , ( 6.4 , 2 ) )
post_mass_norm = kwarg... |
def toeplitz ( vect ) :
"""Find the toeplitz matrix as a list of lists given its first line / column .""" | return [ [ vect [ abs ( i - j ) ] for i in xrange ( len ( vect ) ) ] for j in xrange ( len ( vect ) ) ] |
def removePlugin ( self , package ) :
"""Remove a plugin
: param package : The plugin package name .""" | res = dict ( code = 1 , msg = None )
if package and isinstance ( package , string_types ) :
path = os . path . join ( self . plugin_abspath , package )
if os . path . isdir ( path ) :
try :
shutil . rmtree ( path )
except Exception as e :
res . update ( msg = str ( e ) )
... |
def instantiateSong ( fileName ) :
"""Create an AudioSegment with the data from the given file""" | ext = detectFormat ( fileName )
if ( ext == "mp3" ) :
return pd . AudioSegment . from_mp3 ( fileName )
elif ( ext == "wav" ) :
return pd . AudioSegment . from_wav ( fileName )
elif ( ext == "ogg" ) :
return pd . AudioSegment . from_ogg ( fileName )
elif ( ext == "flv" ) :
return pd . AudioSegment . from... |
async def _wait_for_data ( self , current_command , number_of_bytes ) :
"""This is a private utility method .
This method accumulates the requested number of bytes and
then returns the full command
: param current _ command : command id
: param number _ of _ bytes : how many bytes to wait for
: returns : ... | while number_of_bytes :
next_command_byte = await self . read ( )
current_command . append ( next_command_byte )
number_of_bytes -= 1
return current_command |
def _speak_as_spell_out_inherit ( self , element ) :
"""Speak one letter at a time for each word for elements and descendants .
: param element : The element .
: type element : hatemile . util . html . htmldomelement . HTMLDOMElement""" | self . _reverse_speak_as ( element , 'spell-out' )
self . _isolate_text_node ( element )
self . _visit ( element , self . _speak_as_spell_out ) |
def generate_api_docs ( package , api_dir , clean = False , printlog = True ) :
"""Generate a module level API documentation of a python package .
Description
Generates markdown API files for each module in a Python package whereas
the structure is as follows :
` package / package . subpackage / package . s... | if printlog :
print ( '\n\nGenerating Module Files\n%s\n' % ( 50 * '=' ) )
prefix = package . __name__ + "."
# clear the previous version
if clean :
if os . path . isdir ( api_dir ) :
shutil . rmtree ( api_dir )
# get subpackages
api_docs = { }
for importer , pkg_name , is_pkg in pkgutil . iter_modules ... |
def remove_object_metadata_key ( self , container , obj , key , prefix = None ) :
"""Removes the specified key from the storage object ' s metadata . If the key
does not exist in the metadata , nothing is done .""" | self . set_object_metadata ( container , obj , { key : "" } , prefix = prefix ) |
def _split_lines ( self ) :
'''Creates the parsed _ lines dict which keeps all record data in document order indexed by the record type .''' | parsed_lines = { }
for rt in all_record_types :
parsed_lines [ rt ] = [ ]
parsed_lines [ 0 ] = [ ]
for line in self . lines :
linetype = line [ 0 : 6 ]
if linetype in all_record_types :
parsed_lines [ linetype ] . append ( line )
else :
parsed_lines [ 0 ] . append ( line )
self . parsed_... |
def get_one_optional ( self , locator ) :
"""Gets an optional component reference that matches specified locator .
: param locator : the locator to find references by .
: return : a matching component reference or null if nothing was found .""" | try :
components = self . find ( locator , False )
return components [ 0 ] if len ( components ) > 0 else None
except Exception as ex :
return None |
def add ( self , path , compress = None ) :
"""Add ` path ` to the MAR file .
If ` path ` is a file , it will be added directly .
If ` path ` is a directory , it will be traversed recursively and all
files inside will be added .
Args :
path ( str ) : path to file or directory on disk to add to this MAR
... | if os . path . isdir ( path ) :
self . add_dir ( path , compress )
else :
self . add_file ( path , compress ) |
def _print_cline ( self , buf , i , icol ) :
"""Print clines after multirow - blocks are finished""" | for cl in self . clinebuf :
if cl [ 0 ] == i :
buf . write ( '\\cline{{{cl:d}-{icol:d}}}\n' . format ( cl = cl [ 1 ] , icol = icol ) )
# remove entries that have been written to buffer
self . clinebuf = [ x for x in self . clinebuf if x [ 0 ] != i ] |
def _get_all_file_version_ids ( self , secure_data_path , limit = None ) :
"""Convenience function that returns a generator that will paginate over the file version ids
secure _ data _ path - - full path to the file in the safety deposit box
limit - - Default ( 100 ) , limits how many records to be returned fro... | offset = 0
# Prime the versions dictionary so that all the logic can happen in the loop
versions = { 'has_next' : True , 'next_offset' : 0 }
while ( versions [ 'has_next' ] ) :
offset = versions [ 'next_offset' ]
versions = self . get_file_versions ( secure_data_path , limit , offset )
for summary in versio... |
def get ( self , request , * args , ** kwargs ) :
"""Method for handling GET requests . Passes the
following arguments to the context :
* * * obj * * - The object to publish
* * * done _ url * * - The result of the ` get _ done _ url ` method""" | self . object = self . get_object ( )
return self . render ( request , obj = self . object , done_url = self . get_done_url ( ) ) |
def fastqIterator ( fn , verbose = False , allowNameMissmatch = False ) :
"""A generator function which yields FastqSequence objects read from a file or
stream . This is a general function which wraps fastqIteratorSimple . In
future releases , we may allow dynamic switching of which base iterator is
used .
... | it = fastqIteratorSimple ( fn , verbose = verbose , allowNameMissmatch = allowNameMissmatch )
for s in it :
yield s |
def decode_html_entities ( s ) :
"""Replaces html entities with the character they represent .
> > > print ( decode _ html _ entities ( " & lt ; 3 & amp ; " ) )""" | parser = HTMLParser . HTMLParser ( )
def unesc ( m ) :
return parser . unescape ( m . group ( ) )
return re . sub ( r'(&[^;]+;)' , unesc , ensure_unicode ( s ) ) |
def get_api_connector ( cls ) :
"""Initialize an api connector for future use .""" | if cls . _api is None : # pragma : no cover
cls . load_config ( )
cls . debug ( 'initialize connection to remote server' )
apihost = cls . get ( 'api.host' )
if not apihost :
raise MissingConfiguration ( )
apienv = cls . get ( 'api.env' )
if apienv and apienv in cls . apienvs :
a... |
def handle_send ( entity : BaseEntity , author_user : UserType , recipients : List [ Dict ] , parent_user : UserType = None , ) -> None :
"""Send an entity to remote servers .
Using this we will build a list of payloads per protocol . After that , each recipient will get the generated
protocol payload delivered... | payloads = [ ]
public_payloads = { "activitypub" : { "auth" : None , "payload" : None , "urls" : set ( ) , } , "diaspora" : { "auth" : None , "payload" : None , "urls" : set ( ) , } , }
# Flatten to unique recipients
unique_recipients = unique_everseen ( recipients )
# Generate payloads and collect urls
for recipient i... |
def updatePlayer ( name , settings ) :
"""update an existing PlayerRecord setting and save to disk file""" | player = delPlayer ( name )
# remove the existing record
_validate ( settings )
player . update ( settings )
player . save ( )
getKnownPlayers ( ) [ player . name ] = player
return player |
def _is_link ( fs , path ) :
"""Check that the given path is a symbolic link .
Note that unlike ` os . path . islink ` , we * do * propagate file system errors
other than a non - existent path or non - existent directory component .
E . g . , should EPERM or ELOOP be raised , an exception will bubble up .""" | try :
return stat . S_ISLNK ( fs . lstat ( path ) . st_mode )
except exceptions . FileNotFound :
return False |
def get_all ( self ) :
"""Gets all items in file .""" | logger . debug ( 'Fetching items. Path: {data_file}' . format ( data_file = self . data_file ) )
return load_file ( self . data_file ) |
def finalize ( self ) :
"""Disconnects signals and frees resources""" | self . model ( ) . sigItemChanged . disconnect ( self . repoTreeItemChanged )
selectionModel = self . selectionModel ( )
# need to store reference to prevent crash in PySide
selectionModel . currentChanged . disconnect ( self . currentItemChanged ) |
def approvewitness ( ctx , witnesses , account ) :
"""Approve witness ( es )""" | pprint ( ctx . peerplays . approvewitness ( witnesses , account = account ) ) |
def kill_running_submission ( self , submissionid , user_check = True ) :
"""Attempt to kill the remote job associated with this submission id .
: param submissionid :
: param user _ check : Check if the current user owns this submission
: return : True if the job was killed , False if an error occurred""" | submission = self . get_submission ( submissionid , user_check )
if not submission :
return False
if "jobid" not in submission :
return False
return self . _client . kill_job ( submission [ "jobid" ] ) |
def magicrun ( text , shell , prompt_template = "default" , aliases = None , envvars = None , extra_commands = None , speed = 1 , test_mode = False , commentecho = False , ) :
"""Echo out each character in ` ` text ` ` as keyboard characters are pressed ,
wait for a RETURN keypress , then run the ` ` text ` ` in ... | goto_regulartype = magictype ( text , prompt_template , speed )
if goto_regulartype :
return goto_regulartype
run_command ( text , shell , aliases = aliases , envvars = envvars , extra_commands = extra_commands , test_mode = test_mode , )
return goto_regulartype |
def kill ( self ) :
"""Shut down the socket immediately .""" | self . _socket . shutdown ( socket . SHUT_RDWR )
self . _socket . close ( ) |
def FieldDefinitionProtosFromTuples ( field_def_tuples ) :
"""Converts ( field - name , type ) tuples to MetricFieldDefinition protos .""" | # TODO : This needs fixing for Python 3.
field_def_protos = [ ]
for field_name , field_type in field_def_tuples :
if field_type in ( int , long ) :
field_type = rdf_stats . MetricFieldDefinition . FieldType . INT
elif issubclass ( field_type , Text ) :
field_type = rdf_stats . MetricFieldDefinit... |
async def load_field ( obj , elem_type , params = None , elem = None ) :
"""Loads a field from the reader , based on the field type specification . Demultiplexer .
: param obj :
: param elem _ type :
: param params :
: param elem :
: return :""" | if issubclass ( elem_type , x . UVarintType ) or issubclass ( elem_type , x . IntType ) or isinstance ( obj , ( int , bool ) ) :
return set_elem ( elem , obj )
elif issubclass ( elem_type , x . BlobType ) :
fvalue = await load_blob ( obj , elem_type )
return set_elem ( elem , fvalue )
elif issubclass ( elem... |
def raised_funds_by_project ( df ) :
"""Raised funds organized by project .""" | df [ 'CaptacaoReal' ] = df [ 'CaptacaoReal' ] . apply ( pd . to_numeric )
return ( df [ [ 'Pronac' , 'CaptacaoReal' ] ] . groupby ( [ 'Pronac' ] ) . sum ( ) ) |
def addDelay ( self , urlPattern = "" , delay = 0 , httpMethod = None ) :
"""Adds delays .""" | print ( "addDelay is deprecated please use delays instead" )
delay = { "urlPattern" : urlPattern , "delay" : delay }
if httpMethod :
delay [ "httpMethod" ] = httpMethod
return self . delays ( delays = { "data" : [ delay ] } ) |
def listen ( self , port : int , address : str = "" , ** kwargs : Any ) -> HTTPServer :
"""Starts an HTTP server for this application on the given port .
This is a convenience alias for creating an ` . HTTPServer `
object and calling its listen method . Keyword arguments not
supported by ` HTTPServer . listen... | server = HTTPServer ( self , ** kwargs )
server . listen ( port , address )
return server |
def add_menu ( self , menu ) :
'''add to the default popup menu''' | from MAVProxy . modules . mavproxy_map import mp_slipmap
self . default_popup . add ( menu )
self . map . add_object ( mp_slipmap . SlipDefaultPopup ( self . default_popup , combine = True ) ) |
def default_kms_key_name ( self , value ) :
"""Set default KMS encryption key for objects in the bucket .
: type value : str or None
: param value : new KMS key name ( None to clear any existing key ) .""" | encryption_config = self . _properties . get ( "encryption" , { } )
encryption_config [ "defaultKmsKeyName" ] = value
self . _patch_property ( "encryption" , encryption_config ) |
def out_name ( stem , timestep = None ) :
"""Return StagPy out file name .
Args :
stem ( str ) : short description of file content .
timestep ( int ) : timestep if relevant .
Returns :
str : the output file name .
Other Parameters :
conf . core . outname ( str ) : the generic name stem , defaults to
... | if timestep is not None :
stem = ( stem + INT_FMT ) . format ( timestep )
return conf . core . outname + '_' + stem |
def deprecate ( func ) :
"""A deprecation warning emmiter as a decorator .""" | @ wraps ( func )
def wrapper ( * args , ** kwargs ) :
warn ( "Deprecated, this will be removed in the future" , DeprecationWarning )
return func ( * args , ** kwargs )
wrapper . __doc__ = "Deprecated.\n" + ( wrapper . __doc__ or "" )
return wrapper |
def required_header ( header ) :
"""Function that verify if the header parameter is a essential header
: param header : A string represented a header
: returns : A boolean value that represent if the header is required""" | if header in IGNORE_HEADERS :
return False
if header . startswith ( 'HTTP_' ) or header == 'CONTENT_TYPE' :
return True
return False |
def jackknife_indexes ( data ) :
"""Given data points data , where axis 0 is considered to delineate points , return
a list of arrays where each array is a set of jackknife indexes .
For a given set of data Y , the jackknife sample J [ i ] is defined as the data set
Y with the ith data point deleted .""" | base = np . arange ( 0 , len ( data ) )
return ( np . delete ( base , i ) for i in base ) |
def mkconstraints ( ) :
"""Make constraint list for binary constraint problem .""" | constraints = [ ]
for j in range ( 1 , 10 ) :
vars = [ "%s%d" % ( i , j ) for i in uppercase [ : 9 ] ]
constraints . extend ( ( c , const_different ) for c in combinations ( vars , 2 ) )
for i in uppercase [ : 9 ] :
vars = [ "%s%d" % ( i , j ) for j in range ( 1 , 10 ) ]
constraints . extend ( ( c , con... |
def close ( self , name = None ) :
"""Closes the most recently opened element .
: name : if given , this value must match the name given for the most recently opened element . This
is primarily here for providing quick error checking for applications""" | tag = self . _open_elements . pop ( )
if name is not None and name != tag :
raise Exception ( "Tag closing mismatch" )
self . _pad ( )
self . _writer . endElement ( _normalize_name ( tag ) )
self . _newline ( ) |
def _process_service_check ( self , data , url , tag_by_host = False , services_incl_filter = None , services_excl_filter = None , custom_tags = None ) :
'''Report a service check , tagged by the service and the backend .
Statuses are defined in ` STATUS _ TO _ SERVICE _ CHECK ` mapping .''' | custom_tags = [ ] if custom_tags is None else custom_tags
service_name = data [ 'pxname' ]
status = data [ 'status' ]
haproxy_hostname = to_string ( self . hostname )
check_hostname = haproxy_hostname if tag_by_host else ''
if self . _is_service_excl_filtered ( service_name , services_incl_filter , services_excl_filter... |
def get_chinese_new_year ( self , year ) :
"""Compute Chinese New Year days . To return a list of holidays .
By default , it ' ll at least return the Chinese New Year holidays chosen
using the following options :
* ` ` include _ chinese _ new _ year _ eve ` `
* ` ` include _ chinese _ new _ year ` ` ( on by... | days = [ ]
lunar_first_day = ChineseNewYearCalendar . lunar ( year , 1 , 1 )
# Chinese new year ' s eve
if self . include_chinese_new_year_eve :
days . append ( ( lunar_first_day - timedelta ( days = 1 ) , self . chinese_new_year_eve_label ) )
# Chinese new year ( is included by default )
if self . include_chinese_... |
def write_config_file ( self , f , comments ) :
"""This method write a sample file , with attributes , descriptions ,
sample values , required flags , using the configuration object
properties .""" | if self . conf_hidden :
return False
if comments :
f . write ( "\n" )
f . write ( "# Attribute (" )
f . write ( str ( self . e_type . __name__ ) )
f . write ( ") : " )
f . write ( self . _name . upper ( ) )
f . write ( "\n" )
if self . _desc and self . _desc != argparse . SUPPRESS :
... |
def _summary ( self , name = None ) :
"""Return a summarized representation .
Parameters
name : str
name to use in the summary representation
Returns
String with a summarized representation of the index""" | if len ( self ) > 0 :
head = self [ 0 ]
if hasattr ( head , 'format' ) and not isinstance ( head , str ) :
head = head . format ( )
tail = self [ - 1 ]
if hasattr ( tail , 'format' ) and not isinstance ( tail , str ) :
tail = tail . format ( )
index_summary = ', %s to %s' % ( pprint_... |
def hex_to_int ( value ) :
"""Convert hex string like " \x0A \xE3 " to 2787.""" | if version_info . major >= 3 :
return int . from_bytes ( value , "big" )
return int ( value . encode ( "hex" ) , 16 ) |
def store_zonefiles ( self , zonefile_names , zonefiles , zonefile_txids , zonefile_block_heights , peer_zonefile_hashes , peer_hostport , path , con = None ) :
"""Store a list of RPC - fetched zonefiles ( but only ones in peer _ zonefile _ hashes ) from the given peer _ hostport
Return the list of zonefile hashe... | ret = [ ]
with AtlasDBOpen ( con = con , path = path ) as dbcon :
for fetched_zfhash , zonefile_txt in zonefiles . items ( ) :
if fetched_zfhash not in peer_zonefile_hashes or fetched_zfhash not in zonefile_block_heights : # unsolicited
log . warn ( "%s: Unsolicited zonefile %s" % ( self . hostp... |
def channels_add_all ( self , room_id , ** kwargs ) :
"""Adds all of the users of the Rocket . Chat server to the channel .""" | return self . __call_api_post ( 'channels.addAll' , roomId = room_id , kwargs = kwargs ) |
def _distributeCells ( numCellsPop ) :
'''distribute cells across compute nodes using round - robin''' | from . . import sim
hostCells = { }
for i in range ( sim . nhosts ) :
hostCells [ i ] = [ ]
for i in range ( numCellsPop ) :
hostCells [ sim . nextHost ] . append ( i )
sim . nextHost += 1
if sim . nextHost >= sim . nhosts :
sim . nextHost = 0
if sim . cfg . verbose :
print ( ( "Distributed ... |
def tau3_from_mass1_mass2 ( mass1 , mass2 , f_lower ) :
r"""Returns : math : ` \ tau _ 3 ` from the component masses and given frequency .""" | mtotal = mass1 + mass2
eta = eta_from_mass1_mass2 ( mass1 , mass2 )
return tau3_from_mtotal_eta ( mtotal , eta , f_lower ) |
def convert_sshkey ( cls , sshkey ) :
"""Return dict param with valid entries for vm / paas methods .""" | params = { }
if sshkey :
params [ 'keys' ] = [ ]
for ssh in sshkey :
if os . path . exists ( os . path . expanduser ( ssh ) ) :
if 'ssh_key' in params :
cls . echo ( "Can't have more than one sshkey file." )
continue
with open ( ssh ) as fdesc :
... |
def renew_session ( self ) :
"""Have to be called on user actions to check and renew session""" | if ( ( not 'user_uid' in self . cookieInterface . cookies ) or self . cookieInterface . cookies [ 'user_uid' ] != self . session_uid ) and ( not self . expired ) :
self . on_session_expired ( )
if self . expired :
self . session_uid = str ( random . randint ( 1 , 999999999 ) )
self . cookieInterface . set_cooki... |
def start ( self ) :
"""start command in background and does not wait for it .
: rtype : self""" | if self . is_started :
raise EasyProcessError ( self , 'process was started twice!' )
if self . use_temp_files :
self . _stdout_file = tempfile . TemporaryFile ( prefix = 'stdout_' )
self . _stderr_file = tempfile . TemporaryFile ( prefix = 'stderr_' )
stdout = self . _stdout_file
stderr = self . _s... |
def search ( self , term ) :
"""Search for a user by name .
: param str term : What to search for .
: return : The results as a SearchWrapper iterator or None if no results .
: rtype : SearchWrapper or None""" | r = requests . get ( self . apiurl + "/users" , params = { "filter[name]" : term } , headers = self . header )
if r . status_code != 200 :
raise ServerError
jsd = r . json ( )
if jsd [ 'meta' ] [ 'count' ] :
return SearchWrapper ( jsd [ 'data' ] , jsd [ 'links' ] [ 'next' ] if 'next' in jsd [ 'links' ] else Non... |
def _hm_form_message ( self , thermostat_id , protocol , source , function , start , payload ) :
"""Forms a message payload , excluding CRC""" | if protocol == constants . HMV3_ID :
start_low = ( start & constants . BYTEMASK )
start_high = ( start >> 8 ) & constants . BYTEMASK
if function == constants . FUNC_READ :
payload_length = 0
length_low = ( constants . RW_LENGTH_ALL & constants . BYTEMASK )
length_high = ( constants .... |
def docstr ( self , prefix = '' , include_label = True ) :
"""Returns a string summarizing the parameter . Format is :
< prefix > ` ` name ` ` : { ` ` default ` ` , ` ` dtype ` ` }
< prefix > ` ` description ` ` Label : ` ` label ` ` .""" | outstr = "%s%s : {%s, %s}\n" % ( prefix , self . name , str ( self . default ) , str ( self . dtype ) . replace ( "<type '" , '' ) . replace ( "'>" , '' ) ) + "%s %s" % ( prefix , self . description )
if include_label :
outstr += " Label: %s" % ( self . label )
return outstr |
def _pack_cwl ( unpacked_cwl ) :
"""Pack CWL into a single document for submission .""" | out_file = "%s-pack%s" % os . path . splitext ( unpacked_cwl )
cmd = "cwltool --pack {unpacked_cwl} > {out_file}"
_run_tool ( cmd . format ( ** locals ( ) ) )
return out_file |
def section ( self , ctx , optional = False ) :
"""Return section of the config for a specific context ( sub - command ) .
Parameters :
ctx ( Context ) : The Click context object .
optional ( bool ) : If ` ` True ` ` , return an empty config object when section is missing .
Returns :
Section : The configu... | values = self . load ( )
try :
return values [ ctx . info_name ]
except KeyError :
if optional :
return configobj . ConfigObj ( { } , ** self . DEFAULT_CONFIG_OPTS )
raise LoggedFailure ( "Configuration section '{}' not found!" . format ( ctx . info_name ) ) |
def dangling ( self , targets : sos_targets ) :
'''returns
1 . missing targets , which are missing from the DAG or from the provided targets
2 . existing targets of provided target list , not in DAG''' | existing = [ ]
missing = [ ]
if env . config [ 'trace_existing' ] :
for x in self . _all_depends_files . keys ( ) :
if x not in self . _all_output_files :
if x . target_exists ( ) :
existing . append ( x )
else :
missing . append ( x )
else :
missi... |
def enable_chimera_inline ( ) :
"""Enable IPython magic commands to run some Chimera actions
Currently supported :
- % chimera _ export _ 3D [ < model > ] :
Depicts the Chimera 3D canvas in a WebGL iframe . Requires
a headless Chimera build and a Notebook instance . SLOW .
- % chimera _ run < command > : ... | from IPython . display import IFrame
from IPython . core . magic import register_line_magic
import chimera
import Midas
@ register_line_magic
def chimera_export_3D ( line ) :
if chimera . viewer . __class__ . __name__ == 'NoGuiViewer' :
print ( 'This magic requires a headless Chimera build. ' 'Check http://... |
def log_once ( key ) :
"""Returns True if this is the " first " call for a given key .
Various logging settings can adjust the definition of " first " .
Example :
> > > if log _ once ( " some _ key " ) :
. . . logger . info ( " Some verbose logging statement " )""" | global _last_logged
if _disabled :
return False
elif key not in _logged :
_logged . add ( key )
_last_logged = time . time ( )
return True
elif _periodic_log and time . time ( ) - _last_logged > 60.0 :
_logged . clear ( )
_last_logged = time . time ( )
return False
else :
return False |
def clean_dict ( data ) :
"""Remove None - valued keys from a dictionary , recursively .""" | if is_mapping ( data ) :
out = { }
for k , v in data . items ( ) :
if v is not None :
out [ k ] = clean_dict ( v )
return out
elif is_sequence ( data ) :
return [ clean_dict ( d ) for d in data if d is not None ]
return data |
def get_music_library_information ( self , search_type , start = 0 , max_items = 100 , full_album_art_uri = False , search_term = None , subcategories = None , complete_result = False ) :
"""Retrieve music information objects from the music library .
This method is the main method to get music information items ,... | search = self . SEARCH_TRANSLATION [ search_type ]
# Add sub categories
if subcategories is not None :
for category in subcategories :
search += '/' + url_escape_path ( really_unicode ( category ) )
# Add fuzzy search
if search_term is not None :
search += ':' + url_escape_path ( really_unicode ( search... |
def _set_result_from_operation ( self ) :
"""Set the result or exception from the operation if it is complete .""" | # This must be done in a lock to prevent the polling thread
# and main thread from both executing the completion logic
# at the same time .
with self . _completion_lock : # If the operation isn ' t complete or if the result has already been
# set , do not call set _ result / set _ exception again .
# Note : self . _ re... |
def refresh ( self , force_cache = False ) :
"""Perform a system refresh .
: param force _ cache : Force an update of the camera cache""" | if self . check_if_ok_to_update ( ) or force_cache :
for sync_name , sync_module in self . sync . items ( ) :
_LOGGER . debug ( "Attempting refresh of sync %s" , sync_name )
sync_module . refresh ( force_cache = force_cache )
if not force_cache : # Prevents rapid clearing of motion detect proper... |
def encode_function_call ( self , function_name , args ) :
"""Return the encoded function call .
Args :
function _ name ( str ) : One of the existing functions described in the
contract interface .
args ( List [ object ] ) : The function arguments that wll be encoded and
used in the contract execution in ... | if function_name not in self . function_data :
raise ValueError ( 'Unkown function {}' . format ( function_name ) )
description = self . function_data [ function_name ]
function_selector = zpad ( encode_int ( description [ 'prefix' ] ) , 4 )
arguments = encode_abi ( description [ 'encode_types' ] , args )
return fu... |
async def unicode_type ( self , elem ) :
"""Unicode type
: param elem :
: return :""" | if self . writing :
await dump_uvarint ( self . iobj , len ( elem ) )
await self . iobj . awrite ( bytes ( elem , 'utf8' ) )
else :
ivalue = await load_uvarint ( self . iobj )
if ivalue == 0 :
return ''
fvalue = bytearray ( ivalue )
await self . iobj . areadinto ( fvalue )
return str... |
def payments ( self , virtual_account_id , data = { } , ** kwargs ) :
"""Fetch Payment for Virtual Account Id
Args :
virtual _ account _ id :
Id for which Virtual Account objects has to be retrieved
Returns :
Payment dict for given Virtual Account Id""" | url = "{}/{}/payments" . format ( self . base_url , virtual_account_id )
return self . get_url ( url , data , ** kwargs ) |
def ingest_flash ( self ) :
"""Process post - flash .""" | self . flash = extract_flash ( self . hdulist [ 0 ] . header , self . hdulist [ 1 ] )
# Set post - flash to zeros
if self . flash is None :
self . flash = np . zeros_like ( self . science )
return
# Apply the flash subtraction if necessary .
# Not applied to ERR , to be consistent with ingest _ dark ( )
if self... |
def parameter_list ( data ) :
"""Create a list of parameter objects from a dict .
: param data : Dictionary to convert to parameter list .
: type data : dict
: return : Parameter list .
: rtype : dict""" | items = [ ]
for item in data :
param = Parameter ( item [ 'name' ] , item [ 'value' ] )
if 'meta' in item :
param . meta = item [ 'meta' ]
items . append ( param )
return items |
def _strip_counters ( self , sub_line ) :
"""Find the codeline end by taking out the counters and durations .""" | try :
end = sub_line . rindex ( '}' )
except ValueError :
return sub_line
else :
return sub_line [ : ( end + 1 ) ] |
def connect ( self ) :
"""Get a connection to this peer .
If an connection to the peer already exists ( either incoming or
outgoing ) , that ' s returned . Otherwise , a new outgoing connection to
this peer is created .
: return :
A future containing a connection to this host .""" | # Prefer incoming connections over outgoing connections .
if self . connections : # First value is an incoming connection
future = gen . Future ( )
future . set_result ( self . connections [ 0 ] )
return future
if self . _connecting : # If we ' re in the process of connecting to the peer , just wait
# and r... |
def _summarize ( self ) :
"""Game summary implementation .""" | self . _achievements_summarized = True
data = None
if self . _postgame :
data = self . _postgame . action
game_type = 'DM' if self . _header . lobby . game_type == 'DM' else 'RM'
self . _summary = { 'players' : list ( self . players ( data , game_type ) ) , 'diplomacy' : self . _diplomacy , 'rec_owner_index' : self... |
def currentVersion ( self ) :
"""returns the current version of the site""" | if self . _currentVersion is None :
self . __init ( self . _url )
return self . _currentVersion |
def compute_chunk ( self , graph , dates , sids , initial_workspace ) :
"""Compute the Pipeline terms in the graph for the requested start and end
dates .
This is where we do the actual work of running a pipeline .
Parameters
graph : zipline . pipeline . graph . ExecutionPlan
Dependency graph of the terms... | self . _validate_compute_chunk_params ( graph , dates , sids , initial_workspace , )
get_loader = self . _get_loader
# Copy the supplied initial workspace so we don ' t mutate it in place .
workspace = initial_workspace . copy ( )
refcounts = graph . initial_refcounts ( workspace )
execution_order = graph . execution_o... |
def search ( self , template : str , first : bool = False ) -> _Result :
"""Search the : class : ` Element < Element > ` for the given parse
template .
: param template : The Parse template to use .""" | elements = [ r for r in findall ( template , self . xml ) ]
return _get_first_or_list ( elements , first ) |
def set_scene_config ( self , scene_id , config ) :
"""reconfigure a scene by scene ID""" | if not scene_id in self . state . scenes : # does that scene _ id exist ?
err_msg = "Requested to reconfigure scene {sceneNum}, which does not exist" . format ( sceneNum = scene_id )
logging . info ( err_msg )
return ( False , 0 , err_msg )
if scene_id == self . state . activeSceneId :
pass
# TODO :... |
def install_os ( name , ** kwargs ) :
'''Installs the given image on the device . After the installation is complete
the device is rebooted , if reboot = True is given as a keyworded argument .
. . code - block : : yaml
salt : / / images / junos _ image . tgz :
junos :
- install _ os
- timeout : 100
-... | ret = { 'name' : name , 'changes' : { } , 'result' : True , 'comment' : '' }
ret [ 'changes' ] = __salt__ [ 'junos.install_os' ] ( name , ** kwargs )
return ret |
def meaculpa ( nick , rest ) :
"Sincerely apologize" | if rest :
rest = rest . strip ( )
if rest :
return random . choice ( phrases . direct_apologies ) % dict ( a = nick , b = rest )
else :
return random . choice ( phrases . apologies ) % dict ( a = nick ) |
def file ( self , owner = None , ** kwargs ) :
"""Create the File TI object .
Args :
owner :
* * kwargs :
Return :""" | return File ( self . tcex , owner = owner , ** kwargs ) |
def f_measure ( reference_beats , estimated_beats , f_measure_threshold = 0.07 ) :
"""Compute the F - measure of correct vs incorrectly predicted beats .
" Correctness " is determined over a small window .
Examples
> > > reference _ beats = mir _ eval . io . load _ events ( ' reference . txt ' )
> > > refer... | validate ( reference_beats , estimated_beats )
# When estimated beats are empty , no beats are correct ; metric is 0
if estimated_beats . size == 0 or reference_beats . size == 0 :
return 0.
# Compute the best - case matching between reference and estimated locations
matching = util . match_events ( reference_beats... |
def _update_url_map ( self ) :
'''Assemble any dynamic or configurable URLs''' | if HAS_WEBSOCKETS :
self . url_map . update ( { 'ws' : WebsocketEndpoint , } )
# Allow the Webhook URL to be overridden from the conf .
self . url_map . update ( { self . apiopts . get ( 'webhook_url' , 'hook' ) . lstrip ( '/' ) : Webhook , } )
# Enable the single - page JS app URL .
self . url_map . update ( { sel... |
def addsshkey ( self , title , key ) :
"""Add a new ssh key for the current user
: param title : title of the new key
: param key : the key itself
: return : true if added , false if it didn ' t add it ( it could be because the name or key already exists )""" | data = { 'title' : title , 'key' : key }
request = requests . post ( self . keys_url , headers = self . headers , data = data , verify = self . verify_ssl , auth = self . auth , timeout = self . timeout )
if request . status_code == 201 :
return True
else :
return False |
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