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def getBody ( self ) : """Extract body json"""
data = None try : data = json . loads ( self . request . body ) except : data = json . loads ( urllib . unquote_plus ( self . request . body ) ) return data
def get_reference_template ( self , ref_type ) : """Return the reference template for the type as an ordered dictionary . Zotero . item _ template ( ) caches data after the first API call ."""
template = self . _zotero_lib . item_template ( ref_type ) return OrderedDict ( sorted ( template . items ( ) , key = lambda x : x [ 0 ] ) )
def power_on ( self ) : """Power on the set - top box ."""
if not self . is_powered_on ( ) : log . debug ( 'Powering on set-top box at %s:%s.' , self . ip , self . port ) self . send_key ( keys . POWER )
def get_checked ( self ) : """Return the list of checked items that do not have any child ."""
checked = [ ] def get_checked_children ( item ) : if not self . tag_has ( "unchecked" , item ) : ch = self . get_children ( item ) if not ch and self . tag_has ( "checked" , item ) : checked . append ( item ) else : for c in ch : get_checked_children (...
def get_all_tags ( self ) : """Return a tuple of lists ( [ common _ tags ] , [ anti _ tags ] , [ organisational _ tags ] ) all tags of all tasks of this course Since this is an heavy procedure , we use a cache to cache results . Cache should be updated when a task is modified ."""
if self . _all_tags_cache != None : return self . _all_tags_cache tag_list_common = set ( ) tag_list_misconception = set ( ) tag_list_org = set ( ) tasks = self . get_tasks ( ) for id , task in tasks . items ( ) : for tag in task . get_tags ( ) [ 0 ] : tag_list_common . add ( tag ) for tag in task ....
def find_file_structure ( self , body , params = None ) : """` < http : / / www . elastic . co / guide / en / elasticsearch / reference / current / ml - file - structure . html > ` _ : arg body : The contents of the file to be analyzed : arg charset : Optional parameter to specify the character set of the fil...
if body in SKIP_IN_PATH : raise ValueError ( "Empty value passed for a required argument 'body'." ) return self . transport . perform_request ( "POST" , "/_ml/find_file_structure" , params = params , body = self . _bulk_body ( body ) , )
def WriteClientStartupInfo ( self , client_id , startup_info , cursor = None ) : """Writes a new client startup record ."""
query = """ SET @now = NOW(6); INSERT INTO client_startup_history (client_id, timestamp, startup_info) VALUES (%(client_id)s, @now, %(startup_info)s); UPDATE clients SET last_startup_timestamp = @now WHERE client_id = %(client_id)s; """ params = { "client_id" : db_utils . ClientID...
def _netstat_sunos ( ) : '''Return netstat information for SunOS flavors'''
log . warning ( 'User and program not (yet) supported on SunOS' ) ret = [ ] for addr_family in ( 'inet' , 'inet6' ) : # Lookup TCP connections cmd = 'netstat -f {0} -P tcp -an | tail +5' . format ( addr_family ) out = __salt__ [ 'cmd.run' ] ( cmd , python_shell = True ) for line in out . splitlines ( ) : ...
def Back ( self , n = 1 , dl = 0 ) : """退格键n次"""
self . Delay ( dl ) self . keyboard . tap_key ( self . keyboard . backspace_key , n )
def check_for_lime ( self , pattern ) : """Check to see if LiME has loaded on the remote system : type pattern : str : param pattern : pattern to check output against : type listen _ port : int : param listen _ port : port LiME is listening for connections on"""
check = self . commands . lime_check . value lime_loaded = False result = self . shell . execute ( check ) stdout = self . shell . decode ( result [ 'stdout' ] ) connections = self . net_parser . parse ( stdout ) for conn in connections : local_addr , remote_addr = conn if local_addr == pattern : lime_l...
def rebin_spec ( spec , wavnew , oversamp = 100 , plot = False ) : """Rebin a spectrum to a new wavelength array while preserving the total flux Parameters spec : array - like The wavelength and flux to be binned wavenew : array - like The new wavelength array Returns np . ndarray The rebinned flu...
wave , flux = spec nlam = len ( wave ) x0 = np . arange ( nlam , dtype = float ) x0int = np . arange ( ( nlam - 1. ) * oversamp + 1. , dtype = float ) / oversamp w0int = np . interp ( x0int , x0 , wave ) spec0int = np . interp ( w0int , wave , flux ) / oversamp # Set up the bin edges for down - binning maxdiffw1 = np ....
def ensure_local_files ( ) : """Ensure that filesystem is setup / filled out in a valid way"""
if _file_permissions : if not os . path . isdir ( AUTH_DIR ) : os . mkdir ( AUTH_DIR ) for fn in [ CONFIG_FILE ] : contents = load_json_dict ( fn ) for key , val in list ( _FILE_CONTENT [ fn ] . items ( ) ) : if key not in contents : contents [ key ] = val ...
def flatten ( source , task_limit = None ) : """Given an asynchronous sequence of sequences , generate the elements of the sequences as soon as they ' re received . The sequences are awaited concurrently , although it ' s possible to limit the amount of running sequences using the ` task _ limit ` argument . ...
return base_combine . raw ( source , task_limit = task_limit , switch = False , ordered = False )
def _put_buffers ( state , buffer_paths , buffers ) : """The inverse of _ remove _ buffers , except here we modify the existing dict / lists . Modifying should be fine , since this is used when state comes from the wire ."""
for buffer_path , buffer in zip ( buffer_paths , buffers ) : # we ' d like to set say sync _ data [ ' x ' ] [ 0 ] [ ' y ' ] = buffer # where buffer _ path in this example would be [ ' x ' , 0 , ' y ' ] obj = state for key in buffer_path [ : - 1 ] : obj = obj [ key ] obj [ buffer_path [ - 1 ] ] = buf...
def expose_event ( self , widget , event ) : """When an area of the window is exposed , we just copy out of the server - side , off - screen surface to that area ."""
x , y , width , height = event . area self . logger . debug ( "surface is %s" % self . surface ) if self . surface is not None : win = widget . get_window ( ) cr = win . cairo_create ( ) # set clip area for exposed region cr . rectangle ( x , y , width , height ) cr . clip ( ) # Paint from off -...
def _start_http_session ( self ) : """Start a new requests HTTP session , clearing cookies and session data . : return : None"""
api_logger . debug ( "Starting new HTTP session..." ) self . session = requests . Session ( ) self . session . headers . update ( { "User-Agent" : self . user_agent } ) if self . username and self . password : api_logger . debug ( "Requests will use authorization." ) self . session . auth = HTTPBasicAuth ( self...
def read_table_pattern ( self , header_pattern , row_pattern , footer_pattern , postprocess = str , attribute_name = None , last_one_only = True ) : """Parse table - like data . A table composes of three parts : header , main body , footer . All the data matches " row pattern " in the main body will be returned...
with zopen ( self . filename , 'rt' ) as f : text = f . read ( ) table_pattern_text = header_pattern + r"\s*^(?P<table_body>(?:\s+" + row_pattern + r")+)\s+" + footer_pattern table_pattern = re . compile ( table_pattern_text , re . MULTILINE | re . DOTALL ) rp = re . compile ( row_pattern ) tables = [ ] for mt in t...
def show_namespace ( name , ** kwargs ) : '''Return information for a given namespace defined by the specified name CLI Examples : : salt ' * ' kubernetes . show _ namespace kube - system'''
cfg = _setup_conn ( ** kwargs ) try : api_instance = kubernetes . client . CoreV1Api ( ) api_response = api_instance . read_namespace ( name ) return api_response . to_dict ( ) except ( ApiException , HTTPError ) as exc : if isinstance ( exc , ApiException ) and exc . status == 404 : return None...
def set_work_request ( self , worker_name , sample_set , subkeys = None ) : """Make a work request for an existing stored sample ( or sample _ set ) . Args : worker _ name : ' strings ' , ' pe _ features ' , whatever sample _ set : the md5 of a sample _ set in the Workbench data store subkeys : just get a s...
# Does worker support sample _ set _ input ? if self . plugin_meta [ worker_name ] [ 'sample_set_input' ] : yield self . work_request ( worker_name , sample_set , subkeys ) # Loop through all the md5s and return a generator with yield else : md5_list = self . get_sample_set ( sample_set ) for md5 in md5_lis...
def fatal ( ftn , txt ) : """If can ' t continue ."""
msg = "{0}.{1}:FATAL:{2}\n" . format ( modname , ftn , txt ) raise SystemExit ( msg )
def setmonitor ( self , enable = True ) : """Alias for setmode ( ' monitor ' ) or setmode ( ' managed ' ) Only available with Npcap"""
# We must reset the monitor cache if enable : res = self . setmode ( 'monitor' ) else : res = self . setmode ( 'managed' ) if not res : log_runtime . error ( "Npcap WlanHelper returned with an error code !" ) self . cache_mode = None tmp = self . cache_mode = self . ismonitor ( ) return tmp if enable else (...
def attack_class ( self , x , target_y ) : """Run the attack on a specific target class . : param x : tf Tensor . The input example . : param target _ y : tf Tensor . The attacker ' s desired target class . Returns : A targeted adversarial example , intended to be classified as the target class ."""
adv = self . base_attacker . generate ( x , y_target = target_y , ** self . params ) return adv
def export_profile ( self ) : """Export minimum needs to a json file . This method will save the current state of the minimum needs setup . Then open a dialog allowing the user to browse to the desired destination location and allow the user to save the needs as a json file ."""
file_name_dialog = QFileDialog ( self ) file_name_dialog . setAcceptMode ( QFileDialog . AcceptSave ) file_name_dialog . setNameFilter ( self . tr ( 'JSON files (*.json *.JSON)' ) ) file_name_dialog . setDefaultSuffix ( 'json' ) file_name = None if file_name_dialog . exec_ ( ) : file_name = file_name_dialog . selec...
def console_set_default_background ( con : tcod . console . Console , col : Tuple [ int , int , int ] ) -> None : """Change the default background color for a console . Args : con ( Console ) : Any Console instance . col ( Union [ Tuple [ int , int , int ] , Sequence [ int ] ] ) : An ( r , g , b ) sequence ...
lib . TCOD_console_set_default_background ( _console ( con ) , col )
def debug ( self , key ) : """Returns True if the debug setting is enabled ."""
return ( not self . quiet and not self . debug_none and ( self . debug_all or getattr ( self , "debug_%s" % key ) ) )
def move_to_pat ( pat : str , offset : ( float , float ) = None , tolerance : int = 0 ) -> None : """See help for click _ on _ pat"""
with tempfile . NamedTemporaryFile ( ) as f : subprocess . call ( ''' xwd -root -silent -display :0 | convert xwd:- png:''' + f . name , shell = True ) loc = visgrep ( f . name , pat , tolerance ) pat_size = get_png_dim ( pat ) if offset is None : x , y = [ l + ps // 2 for l , ps in zip ( l...
def replace ( self , s , data , attrs = None ) : """Replace the attributes of the plotter data in a string % ( replace _ note ) s Parameters s : str String where the replacements shall be made data : InteractiveBase Data object from which to use the coordinates and insert the coordinate and attribute ...
# insert labels s = s . format ( ** self . rc [ 'labels' ] ) # replace attributes attrs = attrs or data . attrs if hasattr ( getattr ( data , 'psy' , None ) , 'arr_name' ) : attrs = attrs . copy ( ) attrs [ 'arr_name' ] = data . psy . arr_name s = safe_modulo ( s , attrs ) # replace datetime . datetime like tim...
def task_ref_role ( name , rawtext , text , lineno , inliner , options = None , content = None ) : """Process a role that references the target nodes created by the ` ` lsst - task ` ` directive . Parameters name The role name used in the document . rawtext The entire markup snippet , with role . text...
# app = inliner . document . settings . env . app node = pending_task_xref ( rawsource = text ) return [ node ] , [ ]
def update_req ( req ) : """Updates a given req object with the latest version ."""
if not req . name : return req , None info = get_package_info ( req . name ) if info [ 'info' ] . get ( '_pypi_hidden' ) : print ( '{} is hidden on PyPI and will not be updated.' . format ( req ) ) return req , None if _is_pinned ( req ) and _is_version_range ( req ) : print ( '{} is pinned to a range a...
def default_display ( value , with_module = True ) : """Default display for unknown objects ."""
object_type = type ( value ) try : name = object_type . __name__ module = object_type . __module__ if with_module : return name + ' object of ' + module + ' module' else : return name except : type_str = to_text_string ( object_type ) return type_str [ 1 : - 1 ]
def list_env ( self , saltenv = 'base' ) : '''Return a list of the files in the file server ' s specified environment'''
load = { 'saltenv' : saltenv , 'cmd' : '_file_list' } return salt . utils . data . decode ( self . channel . send ( load ) ) if six . PY2 else self . channel . send ( load )
def convert ( args ) : """% prog convert in . fastq illumina fastq quality encoding uses offset 64 , and sanger uses 33 . This script creates a new file with the correct encoding . Output gzipped file if input is also gzipped ."""
p = OptionParser ( convert . __doc__ ) p . set_phred ( ) opts , args = p . parse_args ( args ) if len ( args ) != 1 : sys . exit ( not p . print_help ( ) ) infastq , = args phred = opts . phred or str ( guessoffset ( [ infastq ] ) ) ophred = { "64" : "33" , "33" : "64" } [ phred ] gz = infastq . endswith ( ".gz" ) ...
def info_dialog ( self , title = "Information" , message = "" , ** kwargs ) : """Show an information dialog Usage : C { dialog . info _ dialog ( title = " Information " , message = " " , * * kwargs ) } @ param title : window title for the dialog @ param message : message displayed in the dialog @ return : a...
return self . _run_kdialog ( title , [ "--msgbox" , message ] , kwargs )
def snap_picture ( self ) : """Take a picture with camera to create a new thumbnail ."""
return api . request_new_image ( self . sync . blink , self . network_id , self . camera_id )
def enter_unlink_mode ( self ) : """Enter unlinking mode for a group"""
self . logger . info ( "enter_unlink_mode Group %s" , self . group_id ) self . scene_command ( '0A' ) # should send http : / / 0.0.0.0/0?0A01 = I = 0 # # TODO check return status status = self . hub . get_buffer_status ( ) return status
def insert ( self , row ) : """Add a row ( type : dict ) by inserting it into the table . Columns must exist . data = dict ( title = ' I am a banana ! ' ) table . insert ( data ) Returns the inserted row ' s primary key ."""
self . _check_dropped ( ) res = self . engine . execute ( self . table . insert ( row ) ) if len ( res . inserted_primary_key ) > 0 : return res . inserted_primary_key [ 0 ]
def ack ( self ) : """Acknowledge Message . : raises AMQPInvalidArgument : Invalid Parameters : raises AMQPChannelError : Raises if the channel encountered an error . : raises AMQPConnectionError : Raises if the connection encountered an error . : return :"""
if not self . _method : raise AMQPMessageError ( 'Message.ack only available on incoming messages' ) self . _channel . basic . ack ( delivery_tag = self . delivery_tag )
def read_value ( self , key , filepath = None , filename = None ) : """Tries to read the value of given key from JSON file filename . : param filepath : Path to file : param filename : Name of file : param key : Key to search for : return : Value corresponding to given key : raises OSError , EnvironmentEr...
path = filepath if filepath else self . filepath name = filename if filename else self . filename name = self . _ends_with ( name , ".json" ) path = self . _ends_with ( path , os . path . sep ) try : output = self . _read_json ( path , name ) if key not in output : raise KeyError ( "Key '{}' not found i...
def standardized_compound ( self ) : """Return the : class : ` ~ pubchempy . Compound ` that was produced when this Substance was standardized . Requires an extra request . Result is cached ."""
for c in self . record [ 'compound' ] : if c [ 'id' ] [ 'type' ] == CompoundIdType . STANDARDIZED : return Compound . from_cid ( c [ 'id' ] [ 'id' ] [ 'cid' ] )
def addPos ( self , dp_x = None , dy = None , dz = None ) : """Add vector to current actor position ."""
p = np . array ( self . GetPosition ( ) ) if dz is None : # assume dp _ x is of the form ( x , y , z ) self . SetPosition ( p + dp_x ) else : self . SetPosition ( p + [ dp_x , dy , dz ] ) if self . trail : self . updateTrail ( ) return self
def _save_namepaths_bids_derivatives ( self , f , tag , save_directory , suffix = None ) : """Creates output directory and output name Paramters f : str input files , includes the file bids _ suffix tag : str what should be added to f in the output file . save _ directory : str additional directory th...
file_name = f . split ( '/' ) [ - 1 ] . split ( '.' ) [ 0 ] if tag != '' : tag = '_' + tag if suffix : file_name , _ = drop_bids_suffix ( file_name ) save_name = file_name + tag save_name += '_' + suffix else : save_name = file_name + tag paths_post_pipeline = f . split ( self . pipeline ) if self ....
def get_default_config ( self ) : """Returns the default collector settings"""
config = super ( VarnishCollector , self ) . get_default_config ( ) config . update ( { 'path' : 'varnish' , 'bin' : '/usr/bin/varnishstat' , 'use_sudo' : False , 'sudo_cmd' : '/usr/bin/sudo' , } ) return config
def structure_results ( res ) : """Format Elasticsearch result as Python dictionary"""
out = { 'hits' : { 'hits' : [ ] } } keys = [ u'admin1_code' , u'admin2_code' , u'admin3_code' , u'admin4_code' , u'alternativenames' , u'asciiname' , u'cc2' , u'coordinates' , u'country_code2' , u'country_code3' , u'dem' , u'elevation' , u'feature_class' , u'feature_code' , u'geonameid' , u'modification_date' , u'name'...
def drop_callback_reference ( self , subscription ) : """Drop reference to the callback function after unsubscribing . Any future messages arriving for that subscription will result in exceptions being raised . : param subscription : Subscription ID to delete callback reference for ."""
if subscription not in self . __subscriptions : raise workflows . Error ( "Attempting to drop callback reference for unknown subscription" ) if not self . __subscriptions [ subscription ] [ "unsubscribed" ] : raise workflows . Error ( "Attempting to drop callback reference for live subscription" ) del self . __...
def download_next_song ( self , song ) : """Downloads the next song and starts playing it"""
dl_ydl_opts = dict ( ydl_opts ) dl_ydl_opts [ "progress_hooks" ] = [ self . ytdl_progress_hook ] dl_ydl_opts [ "outtmpl" ] = self . output_format # Move the songs from the next cache to the current cache self . move_next_cache ( ) self . state = 'ready' self . play_empty ( ) # Download the file and create the stream wi...
def item_frequency ( sa , xlabel = LABEL_DEFAULT , ylabel = LABEL_DEFAULT , title = LABEL_DEFAULT ) : """Plots an item frequency of the sarray provided as input , and returns the resulting Plot object . The function supports SArrays with dtype str . Parameters sa : SArray The data to get an item frequency...
if ( not isinstance ( sa , tc . data_structures . sarray . SArray ) or sa . dtype != str ) : raise ValueError ( "turicreate.visualization.item_frequency supports " + "SArrays of dtype str" ) title = _get_title ( title ) plt_ref = tc . extensions . plot_item_frequency ( sa , xlabel , ylabel , title ) return Plot ( p...
def open_remote_file ( dataset_key , file_name , profile = 'default' , mode = 'w' , ** kwargs ) : """Open a remote file object that can be used to write to or read from a file in a data . world dataset : param dataset _ key : Dataset identifier , in the form of owner / id : type dataset _ key : str : param ...
return _get_instance ( profile , ** kwargs ) . open_remote_file ( dataset_key , file_name , mode = mode , ** kwargs )
def _create_trial_info ( self , expr_dir ) : """Create information for given trial . Meta file will be loaded if exists , and the trial information will be saved in db backend . Args : expr _ dir ( str ) : Directory path of the experiment ."""
meta = self . _build_trial_meta ( expr_dir ) self . logger . debug ( "Create trial for %s" % meta ) trial_record = TrialRecord . from_json ( meta ) trial_record . save ( )
def _new ( self , dx_hash , close = False , ** kwargs ) : """: param dx _ hash : Standard hash populated in : func : ` dxpy . bindings . DXDataObject . new ( ) ` containing attributes common to all data object classes . : type dx _ hash : dict : param init _ from : Record from which to initialize the metadata ...
if "init_from" in kwargs : if kwargs [ "init_from" ] is not None : if not isinstance ( kwargs [ "init_from" ] , DXRecord ) : raise DXError ( "Expected instance of DXRecord to init_from" ) dx_hash [ "initializeFrom" ] = { "id" : kwargs [ "init_from" ] . get_id ( ) , "project" : kwargs [ "...
def guess_value ( text_value ) : # type : ( str ) - > str """Get string value for common strings . Method is far from complete but helping with odd arxml files . : param text _ value : value in text like " true " : return : string for value like " 1" """
if sys . version_info >= ( 3 , 0 ) : text_value = text_value . casefold ( ) else : text_value = text_value . lower ( ) if text_value in [ "false" , "off" ] : return "0" elif text_value in [ "true" , "on" ] : return "1" return text_value
def get_member_class ( resource ) : """Returns the registered member class for the given resource . : param resource : registered resource : type resource : class implementing or instance providing or subclass of a registered resource interface ."""
reg = get_current_registry ( ) if IInterface in provided_by ( resource ) : member_class = reg . getUtility ( resource , name = 'member-class' ) else : member_class = reg . getAdapter ( resource , IMemberResource , name = 'member-class' ) return member_class
def save_hdf ( self , filename , path = '' , overwrite = False , append = False ) : """Saves object data to HDF file ( only works if MCMC is run ) Samples are saved to / samples location under given path , : class : ` ObservationTree ` is saved to / obs location under given path . : param filename : Name of...
if os . path . exists ( filename ) : with pd . HDFStore ( filename ) as store : if path in store : if overwrite : os . remove ( filename ) elif not append : raise IOError ( '{} in {} exists. Set either overwrite or append option.' . format ( path , fi...
async def _string_data ( self , data ) : """This is a private message handler method . It is the message handler for String data messages that will be printed to the console . : param data : message : returns : None - message is sent to console"""
reply = '' data = data [ 1 : - 1 ] for x in data : reply_data = x if reply_data : reply += chr ( reply_data ) if self . log_output : logging . info ( reply ) else : print ( reply )
async def delCronJob ( self , iden ) : '''Delete a cron job Args : iden ( bytes ) : The iden of the cron job to be deleted'''
cron = self . cell . agenda . appts . get ( iden ) if cron is None : raise s_exc . NoSuchIden ( ) self . _trig_auth_check ( cron . useriden ) await self . cell . agenda . delete ( iden )
def rule_from_pattern ( pattern , base_path = None , source = None ) : """Take a . gitignore match pattern , such as " * . py [ cod ] " or " * * / * . bak " , and return an IgnoreRule suitable for matching against files and directories . Patterns which do not match files , such as comments and blank lines , w...
if base_path and base_path != abspath ( base_path ) : raise ValueError ( 'base_path must be absolute' ) # Store the exact pattern for our repr and string functions orig_pattern = pattern # Early returns follow # Discard comments and seperators if pattern . strip ( ) == '' or pattern [ 0 ] == '#' : return # Disc...
def interrogate ( self , platformIdentifier , configuration , libraries , libOverrides = { } ) : """Interrogates UnrealBuildTool about the build flags for the specified third - party libraries"""
# Determine which libraries need their modules parsed by UBT , and which are override - only libModules = list ( [ lib for lib in libraries if lib not in libOverrides ] ) # Check that we have at least one module to parse details = ThirdPartyLibraryDetails ( ) if len ( libModules ) > 0 : # Retrieve the list of third - p...
def get_resources ( self ) : """Gets a JSON mapping of server - side resource names to paths : rtype dict"""
status , _ , body = self . _request ( 'GET' , '/' , { 'Accept' : 'application/json' } ) if status == 200 : tmp , resources = json . loads ( bytes_to_str ( body ) ) , { } for k in tmp : # The keys and values returned by json . loads ( ) are unicode , # which will cause problems when passed into httplib later...
def _read_preference_for ( self , session ) : """Read only access to the read preference of this instance or session ."""
# Override this operation ' s read preference with the transaction ' s . if session : return session . _txn_read_preference ( ) or self . __read_preference return self . __read_preference
def from_archive ( archive_filename , py_interpreter = sys . executable ) : """extract metadata from a given sdist archive file : param archive _ filename : a sdist archive file : param py _ interpreter : The full path to the used python interpreter : returns : a json blob with metadata"""
with _extract_to_tempdir ( archive_filename ) as root_dir : data = _setup_py_run_from_dir ( root_dir , py_interpreter ) return data
def get_clients_groups ( self ) -> typing . Iterator [ 'Group' ] : """Gets all clients groups Returns : generator of Groups"""
for group in self . groups : if group . group_is_client_group : yield group
def iso_mesh_line ( vertices , tris , vertex_data , levels ) : """Generate an isocurve from vertex data in a surface mesh . Parameters vertices : ndarray , shape ( Nv , 3) Vertex coordinates . tris : ndarray , shape ( Nf , 3) Indices of triangular element into the vertices array . vertex _ data : ndarra...
lines = None connects = None vertex_level = None level_index = None if not all ( [ isinstance ( x , np . ndarray ) for x in ( vertices , tris , vertex_data , levels ) ] ) : raise ValueError ( 'all inputs must be numpy arrays' ) if vertices . shape [ 1 ] <= 3 : verts = vertices elif vertices . shape [ 1 ] == 4 :...
def send_cmd_recv_rsp ( self , cmd_code , cmd_data , timeout , send_idm = True , check_status = True ) : """Send a command and receive a response . This low level method sends an arbitrary command with the 8 - bit integer * cmd _ code * , followed by the captured tag identifier ( IDm ) if * send _ idm * is : ...
idm = self . idm if send_idm else bytearray ( ) cmd = chr ( 2 + len ( idm ) + len ( cmd_data ) ) + chr ( cmd_code ) + idm + cmd_data log . debug ( ">> {0:02x} {1:02x} {2} {3} ({4}s)" . format ( cmd [ 0 ] , cmd [ 1 ] , hexlify ( cmd [ 2 : 10 ] ) , hexlify ( cmd [ 10 : ] ) , timeout ) ) started = time . time ( ) for retr...
def create_new_csv ( samples , args ) : """create csv file that can be use with bcbio - w template"""
out_fn = os . path . splitext ( args . csv ) [ 0 ] + "-merged.csv" logger . info ( "Preparing new csv: %s" % out_fn ) with file_transaction ( out_fn ) as tx_out : with open ( tx_out , 'w' ) as handle : handle . write ( _header ( args . csv ) ) for s in samples : sample_name = s [ 'name' ...
def size ( self ) : """Returns the size of the cache in bytes ."""
total_size = 0 for dir_path , dir_names , filenames in os . walk ( self . dir ) : for f in filenames : fp = os . path . join ( dir_path , f ) total_size += os . path . getsize ( fp ) return total_size
def remove_unsupported_kwargs ( module_or_fn , all_kwargs_dict ) : """Removes any kwargs not supported by ` module _ or _ fn ` from ` all _ kwargs _ dict ` . A new dict is return with shallow copies of keys & values from ` all _ kwargs _ dict ` , as long as the key is accepted by module _ or _ fn . The return...
if all_kwargs_dict is None : all_kwargs_dict = { } if not isinstance ( all_kwargs_dict , dict ) : raise ValueError ( "all_kwargs_dict must be a dict with string keys." ) return { kwarg : value for kwarg , value in all_kwargs_dict . items ( ) if supports_kwargs ( module_or_fn , kwarg ) != NOT_SUPPORTED }
def all_schema_names ( self , cache = False , cache_timeout = None , force = False ) : """Parameters need to be passed as keyword arguments . For unused parameters , they are referenced in cache _ util . memoized _ func decorator . : param cache : whether cache is enabled for the function : type cache : boo...
return self . db_engine_spec . get_schema_names ( self . inspector )
def mx_page_trees ( self , mx_page ) : """return trees assigned to given MX Page"""
resp = dict ( ) for tree_name , tree in self . scheduler . timetable . trees . items ( ) : if tree . mx_page == mx_page : rest_tree = self . _get_tree_details ( tree_name ) resp [ tree . tree_name ] = rest_tree . document return resp
def _capture_original_object ( self ) : """Capture the original python object ."""
try : self . _doubles_target = getattr ( self . target , self . _name ) except AttributeError : raise VerifyingDoubleError ( self . target , self . _name )
def file_hash ( path , hash_type = "md5" , block_size = 65536 , hex_digest = True ) : """Hash a given file with md5 , or any other and return the hex digest . You can run ` hashlib . algorithms _ available ` to see which are available on your system unless you have an archaic python version , you poor soul ) . ...
hashed = hashlib . new ( hash_type ) with open ( path , "rb" ) as infile : buf = infile . read ( block_size ) while len ( buf ) > 0 : hashed . update ( buf ) buf = infile . read ( block_size ) return hashed . hexdigest ( ) if hex_digest else hashed . digest ( )
def _ttr ( self , k , dist , cache ) : """Three terms recursion coefficients ."""
a , b = evaluation . evaluate_recurrence_coefficients ( dist , k ) return - a , b
def fetch ( bank , key , cachedir ) : '''Fetch information from a file .'''
inkey = False key_file = os . path . join ( cachedir , os . path . normpath ( bank ) , '{0}.p' . format ( key ) ) if not os . path . isfile ( key_file ) : # The bank includes the full filename , and the key is inside the file key_file = os . path . join ( cachedir , os . path . normpath ( bank ) + '.p' ) inkey ...
async def addNodes ( self , nodedefs ) : '''Add / merge nodes in bulk . The addNodes API is designed for bulk adds which will also set properties and add tags to existing nodes . Nodes are specified as a list of the following tuples : ( ( form , valu ) , { ' props ' : { } , ' tags ' : { } } ) Args : nod...
for ( formname , formvalu ) , forminfo in nodedefs : props = forminfo . get ( 'props' ) # remove any universal created props . . . if props is not None : props . pop ( '.created' , None ) node = await self . addNode ( formname , formvalu , props = props ) if node is not None : tags =...
def build ( self , builder ) : """Build XML by appending to builder"""
params = dict ( Value = self . value , Status = self . status . value , ProtocolDeviationRepeatKey = self . repeat_key ) if self . code : params [ 'Code' ] = self . code if self . pdclass : params [ 'Class' ] = self . pdclass if self . transaction_type : params [ 'TransactionType' ] = self . transaction_typ...
def _merge_args ( qCmd , parsed_args , _extra_values , value_specs ) : """Merge arguments from _ extra _ values into parsed _ args . If an argument value are provided in both and it is a list , the values in _ extra _ values will be merged into parsed _ args . @ param parsed _ args : the parsed args from know...
temp_values = _extra_values . copy ( ) for key , value in six . iteritems ( temp_values ) : if hasattr ( parsed_args , key ) : arg_value = getattr ( parsed_args , key ) if arg_value is not None and value is not None : if isinstance ( arg_value , list ) : if value and isin...
def _resample_data ( self , gssha_var ) : """This function resamples the data to match the GSSHA grid IN TESTING MODE"""
self . data = self . data . lsm . resample ( gssha_var , self . gssha_grid )
def not_empty ( message = None ) -> Filter_T : """Validate any object to ensure it ' s not empty ( is None or has no elements ) ."""
def validate ( value ) : if value is None : _raise_failure ( message ) if hasattr ( value , '__len__' ) and value . __len__ ( ) == 0 : _raise_failure ( message ) return value return validate
def findCycle ( self , cycNum ) : '''Method that looks through the self . cycles and returns the nearest cycle : Parameters cycNum : int int of the cycle desired cycle .'''
cycNum = int ( cycNum ) i = 0 while i < len ( self . cycles ) : if cycNum < int ( self . cycles [ i ] ) : break i += 1 if i == 0 : return self . cycles [ i ] elif i == len ( self . cycles ) : return self . cycles [ i - 1 ] lower = int ( self . cycles [ i - 1 ] ) higher = int ( self . cycles [ i ...
def added ( self , context ) : """Ingredient method called before anything else . Here this method just builds the full command tree and stores it inside the context as the ` ` cmd _ tree ` ` attribute . The structure of the tree is explained by the : func : ` build _ cmd _ tree ( ) ` function ."""
context . cmd_tree = self . _build_cmd_tree ( self . command ) context . cmd_toplevel = context . cmd_tree . cmd_obj # Collect spices from the top - level command for spice in context . cmd_toplevel . get_cmd_spices ( ) : context . bowl . add_spice ( spice )
def connect ( self , host = 'localhost' ) : """Connect to the server and set everything up . Args : host : hostname to connect to"""
# Connect get_logger ( ) . info ( "Connecting to RabbitMQ server..." ) self . _conn = pika . BlockingConnection ( pika . ConnectionParameters ( host = host ) ) self . _channel = self . _conn . channel ( ) # Exchanger get_logger ( ) . info ( "Declaring topic exchanger {}..." . format ( self . exchange ) ) self . _channe...
def get ( self , key : str , default = None , as_type : type = None , binary_file = False ) : """Get a setting specified by key ` ` key ` ` . Normally , settings are strings , but if you put non - strings into the settings object , you can request unserialization by specifying ` ` as _ type ` ` . If the key doe...
if as_type is None and key in self . _h . defaults : as_type = self . _h . defaults [ key ] . type if key in self . _cache ( ) : value = self . _cache ( ) [ key ] else : value = None if self . _parent : value = getattr ( self . _parent , self . _h . attribute_name ) . get ( key , as_type = str )...
def connect ( self , uri , link_quality_callback , link_error_callback ) : """Connect the link driver to a specified URI of the format : radio : / / < dongle nbr > / < radio channel > / [ 250K , 1M , 2M ] The callback for linkQuality can be called at any moment from the driver to report back the link quality ...
# check if the URI is a radio URI if not re . search ( '^radio://' , uri ) : raise WrongUriType ( 'Not a radio URI' ) # Open the USB dongle if not re . search ( '^radio://([0-9a-fA-F]+)((/([0-9]+))' '((/(250K|1M|2M))?(/([A-F0-9]+))?)?)?$' , uri ) : raise WrongUriType ( 'Wrong radio URI format!' ) uri_data = re ...
def seen ( self , event , nickname ) : """Shows the amount of time since the given nickname was last seen in the channel ."""
try : self . joined [ nickname ] except KeyError : pass else : if nickname == self . get_nickname ( event ) : prefix = "you are" else : prefix = "%s is" % nickname return "%s here right now" % prefix try : seen = self . timesince ( self . quit [ nickname ] ) except KeyError : ...
def parse ( cls , request , default_start = 0 , default_end = 9 , max_end = 50 ) : '''Parse the range headers into a range object . When there are no range headers , check for a page ' pagina ' parameter , otherwise use the defaults defaults : param request : a request object : param default _ start : default...
settings = request . registry . settings page_param = settings . get ( 'oe.paging.page.queryparam' , 'pagina' ) if 'Range' in request . headers and request . headers [ 'Range' ] is not '' : match = re . match ( '^items=([0-9]+)-([0-9]+)$' , request . headers [ 'Range' ] ) if match : start = int ( match ...
def logplr ( self ) : """Returns the log of the prior - weighted likelihood ratio at the current parameter values . The logprior is calculated first . If the logprior returns ` ` - inf ` ` ( possibly indicating a non - physical point ) , then ` ` loglr ` ` is not called ."""
logp = self . logprior if logp == - numpy . inf : return logp else : return logp + self . loglr
def get_eidos_bayesian_scorer ( prior_counts = None ) : """Return a BayesianScorer based on Eidos curation counts ."""
table = load_eidos_curation_table ( ) subtype_counts = { 'eidos' : { r : [ c , i ] for r , c , i in zip ( table [ 'RULE' ] , table [ 'Num correct' ] , table [ 'Num incorrect' ] ) } } prior_counts = prior_counts if prior_counts else copy . deepcopy ( default_priors ) scorer = BayesianScorer ( prior_counts = prior_counts...
def ensure_dir ( path , parents = False ) : """Returns a boolean indicating whether the directory already existed . Will attempt to create parent directories if * parents * is True ."""
if parents : from os . path import dirname parent = dirname ( path ) if len ( parent ) and parent != path : ensure_dir ( parent , True ) try : os . mkdir ( path ) except OSError as e : if e . errno == 17 : # EEXIST return True raise return False
def skip_if ( self , condition : bool , default : Any = None ) -> 'Question' : """Skip the question if flag is set and return the default instead ."""
self . should_skip_question = condition self . default = default return self
def main ( ) : """NAME scalc _ magic . py DESCRIPTION calculates Sb from pmag _ results files SYNTAX scalc _ magic - h [ command line options ] INPUT takes magic formatted pmag _ results ( 2.5 ) or sites ( 3.0 ) table pmag _ result _ name ( 2.5 ) must start with " VGP : Site " must have average _ ...
coord , kappa , cutoff , n = 0 , 0 , 180. , 0 nb , anti , spin , v , boot = 1000 , 0 , 0 , 0 , 0 data_model = 3 rev = 0 if '-dm' in sys . argv : ind = sys . argv . index ( "-dm" ) data_model = int ( sys . argv [ ind + 1 ] ) if data_model == 2 : coord_key = 'tilt_correction' in_file = 'pmag_results.txt' ...
def batlab2sparkle ( experiment_data ) : """Sparkle expects meta data to have a certain heirarchial organization , reformat batlab experiment data to fit ."""
# This is mostly for convention . . attribute that matters most is samplerate , # since it is used in the GUI to calculate things like duration nsdata = { } for attr in [ 'computername' , 'pst_filename' , 'title' , 'who' , 'date' , 'program_date' ] : nsdata [ attr ] = experiment_data [ attr ] for itest , test in en...
def is_first ( self , value ) : """The is _ first property . Args : value ( string ) . the property value ."""
if value == self . _defaults [ 'ai.session.isFirst' ] and 'ai.session.isFirst' in self . _values : del self . _values [ 'ai.session.isFirst' ] else : self . _values [ 'ai.session.isFirst' ] = value
def getURL ( self , CorpNum , UserID , ToGo ) : """: param CorpNum : 팝빌회원 사업자번호 : param UserID : 팝빌회원 아이디 : param ToGo : [ PLUSFRIEND - 플러스친구계정관리 , SENDER - 발신번호관리 , TEMPLATE - 알림톡템플릿관리 , BOX - 카카오톡전송내용 ] : return : 팝빌 URL"""
if ToGo == None or ToGo == '' : raise PopbillException ( - 99999999 , "TOGO값이 입력되지 않았습니다." ) if ToGo == 'SENDER' : result = self . _httpget ( '/Message/?TG=' + ToGo , CorpNum , UserID ) else : result = self . _httpget ( '/KakaoTalk/?TG=' + ToGo , CorpNum , UserID ) return result . url
def discretize ( value , factor = 100 ) : """Discretize the given value , pre - multiplying by the given factor"""
if not isinstance ( value , Iterable ) : return int ( value * factor ) int_value = list ( deepcopy ( value ) ) for i in range ( len ( int_value ) ) : int_value [ i ] = int ( int_value [ i ] * factor ) return int_value
def reqMktData ( self , contract : Contract , genericTickList : str = '' , snapshot : bool = False , regulatorySnapshot : bool = False , mktDataOptions : List [ TagValue ] = None ) -> Ticker : """Subscribe to tick data or request a snapshot . Returns the Ticker that holds the market data . The ticker will initi...
reqId = self . client . getReqId ( ) ticker = self . wrapper . startTicker ( reqId , contract , 'mktData' ) self . client . reqMktData ( reqId , contract , genericTickList , snapshot , regulatorySnapshot , mktDataOptions ) return ticker
def serialize_date ( value ) : """Attempts to convert ` value ` into an ` ` xs : date ` ` string . If ` value ` is ` ` None ` ` , ` ` None ` ` will be returned . Args : value : A date value . This can be a string , datetime . date , or datetime . datetime object . Returns : An ` ` xs : date ` ` formatte...
if not value : return None elif isinstance ( value , datetime . datetime ) : return value . date ( ) . isoformat ( ) elif isinstance ( value , datetime . date ) : return value . isoformat ( ) else : return parse_date ( value ) . isoformat ( )
def transition_to_execute_complete ( self ) : """Transition to execute complate"""
assert self . state in [ AQStateMachineStates . execute ] self . state = AQStateMachineStates . execute_complete
def _should_wrap ( self , node , child , is_left ) : """Wrap child if : - it has lower precedence - same precedence with position opposite to associativity direction"""
node_precedence = node . op_precedence ( ) child_precedence = child . op_precedence ( ) if node_precedence > child_precedence : # 3 * ( 4 + 5) return True if ( node_precedence == child_precedence and is_left != node . op_left_associative ( ) ) : # 3 - ( 4 - 5) # (2 * * 3 ) * * 4 return True return False
def dict_merge ( base , addition , append_lists = False ) : """Merge one dictionary with another , recursively . Fields present in addition will be added to base if not present or merged if both values are dictionaries or lists ( with append _ lists = True ) . If the values are different data types , the valu...
if not isinstance ( base , dict ) or not isinstance ( addition , dict ) : raise TypeError ( "dict_merge only works with dicts." ) new_base = deepcopy ( base ) for key , value in addition . items ( ) : # Simplest case : Key not in base , so add value to base if key not in new_base . keys ( ) : new_base [...
def is_supported ( cls , desc ) : """Determines if the given label descriptor is supported . Args : desc ( : class : ` endpoints _ management . gen . servicemanagement _ v1 _ messages . LabelDescriptor ` ) : the label descriptor to test Return : ` True ` if desc is supported , otherwise ` False `"""
for l in cls : if l . matches ( desc ) : return True return False
def calculate_gamma_matrix ( magnetic_states , Omega = 1 ) : r"""Calculate the matrix of decay between states . This function calculates the matrix $ \ gamma _ { ij } $ of decay rates between states | i > and | j > ( in the units specified by the Omega argument ) . > > > g = State ( " Rb " , 87,5,0,1 / Intege...
Ne = len ( magnetic_states ) II = magnetic_states [ 0 ] . i gamma = [ [ 0.0 for j in range ( Ne ) ] for i in range ( Ne ) ] for i in range ( Ne ) : for j in range ( i ) : ei = magnetic_states [ i ] ej = magnetic_states [ j ] einsteinAij = Transition ( ei , ej ) . einsteinA if einstei...
def connect ( self , host , port ) : '''Connect to a host and port .'''
# Clear the connect state immediately since we ' re no longer connected # at this point . self . _connected = False # Only after the socket has connected do we clear this state ; closed # must be False so that writes can be buffered in writePacket ( ) . The # closed state might have been set to True due to a socket err...