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def loads_with_timestamp ( value , salt ) : try : signing . loads ( value , salt = salt , max_age = - 999999 ) except signing . SignatureExpired as e : age = float ( str ( e ) . split ( 'Signature age ' ) [ 1 ] . split ( ' >' ) [ 0 ] ) timestamp = timezone . now ( ) - datetime . timedelta ( seconds = age ) return times...
Returns the unsigned value along with its timestamp the time when it got dumped .
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def set_keepalive ( sock , after_idle_sec = 1 , interval_sec = 3 , max_fails = 5 ) : if hasattr ( socket , "SO_KEEPALIVE" ) : sock . setsockopt ( socket . SOL_SOCKET , socket . SO_KEEPALIVE , 1 ) if hasattr ( socket , "TCP_KEEPIDLE" ) : sock . setsockopt ( socket . IPPROTO_TCP , socket . TCP_KEEPIDLE , after_idle_sec )...
Set TCP keepalive on an open socket .
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def _create_dictionary_of_veron ( self ) : self . log . debug ( 'starting the ``_create_dictionary_of_veron`` method' ) dictList = [ ] lines = string . split ( self . catData , '\n' ) totalCount = len ( lines ) count = 0 switch = 0 for line in lines : if ( len ( line ) == 0 or line [ 0 ] in [ "#" , " " ] ) and switch =...
create a list of dictionaries containing all the rows in the veron catalogue
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def display ( self , display_before = False ) : try : copy = self . image . copy ( ) except AttributeError : raise Exception ( "You need to set the Filter.image attribute for displaying" ) copy = BrightnessProcessor ( brightness = 0.6 ) . process ( copy ) s , g = self . _input , self . good_segments_indexes draw_segmen...
shows the effect of this filter
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def parse_mip_analysis ( mip_config_raw : dict , qcmetrics_raw : dict , sampleinfo_raw : dict ) -> dict : outdata = _define_output_dict ( ) _config ( mip_config_raw , outdata ) _qc_metrics ( outdata , qcmetrics_raw ) _qc_sample_info ( outdata , sampleinfo_raw ) return outdata
Parse the output analysis files from MIP for adding info to trend database
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def _updated_row_counts_in_tcs_helper_catalogue_tables_info ( self ) : self . log . debug ( 'starting the ``_updated_row_counts_in_tcs_helper_catalogue_tables_info`` method' ) sqlQuery = u % locals ( ) rows = readquery ( log = self . log , sqlQuery = sqlQuery , dbConn = self . cataloguesDbConn , quiet = False ) for row...
updated row counts in tcs catalogue tables
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def restart_listener ( self , topics ) : if self . listener is not None : if self . listener . running : self . stop ( ) self . __init__ ( topics = topics )
Restart listener after configuration update .
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def stop ( self ) : self . logger . debug ( "Stopping listener." ) self . listener . stop ( ) if self . thread is not None : self . thread . join ( ) self . thread = None self . logger . debug ( "Listener stopped." )
Stop listener .
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def create_subscriber ( self ) : if self . subscriber is None : if self . topics : self . subscriber = NSSubscriber ( self . services , self . topics , addr_listener = True , addresses = self . addresses , nameserver = self . nameserver ) self . recv = self . subscriber . start ( ) . recv
Create a subscriber instance using specified addresses and message types .
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def stop ( self ) : self . running = False time . sleep ( 1 ) if self . subscriber is not None : self . subscriber . stop ( ) self . subscriber = None
Stop subscriber and delete the instance
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def get_current_semver ( data ) : known = { key : data . get ( alias ) for key , alias in config . _forward_aliases . items ( ) if data . get ( alias ) is not None } potentials = [ known . pop ( Constants . VERSION_STRICT_FIELD , None ) , known . pop ( Constants . VERSION_FIELD , None ) , ] from_components = [ known . ...
Given a dictionary of all version data available determine the current version
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def make_new_semver ( current_semver , all_triggers , ** overrides ) : new_semver = { } bumped = False for sig_fig in SemVerSigFig : value = getattr ( current_semver , sig_fig ) override = overrides . get ( sig_fig ) if override is not None : new_semver [ sig_fig ] = override if int ( override ) > int ( value ) : bumpe...
Defines how to increment semver based on which significant figure is triggered
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def loads ( data ) : data += "\n_EOS_" match_dest = RE_HEADER . search ( data ) dest_name = match_dest . group ( 1 ) dest_ip = match_dest . group ( 2 ) traceroute = Traceroute ( dest_name , dest_ip ) matches_hop = RE_HOP . findall ( data ) for match_hop in matches_hop : idx = int ( match_hop [ 0 ] ) if match_hop [ 1 ] ...
Parser entry point . Parses the output of a traceroute execution
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def add_probe ( self , probe ) : if self . probes : probe_last = self . probes [ - 1 ] if not probe . ip : probe . ip = probe_last . ip probe . name = probe_last . name self . probes . append ( probe )
Adds a Probe instance to this hop s results .
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def synchronized ( func , * args , ** kwargs ) : if not ( args and hasattr ( args [ 0 ] , '_lock' ) ) : return func ( * args , ** kwargs ) with args [ 0 ] . _lock : return func ( * args , ** kwargs )
Function decorator to make function synchronized on self . _lock .
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def normalize_job_id ( job_id ) : if not isinstance ( job_id , uuid . UUID ) : job_id = uuid . UUID ( job_id ) return job_id
Convert a value to a job id .
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def start ( self ) : if self . _thread_running . is_set ( ) : raise RuntimeError ( 'the JobManager has already been started' ) self . _thread . start ( ) self . _thread_running . wait ( ) return
Start the JobManager thread .
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def stop ( self ) : self . logger . debug ( 'stopping the job manager' ) self . _thread_running . clear ( ) self . _thread_shutdown . wait ( ) self . _job_lock . acquire ( ) self . logger . debug ( 'waiting on ' + str ( len ( self . _jobs ) ) + ' job threads' ) for job_desc in self . _jobs . values ( ) : if job_desc [ ...
Stop the JobManager thread .
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def job_run ( self , callback , parameters = None ) : if not self . _thread_running . is_set ( ) : raise RuntimeError ( 'the JobManager is not running' ) parameters = ( parameters or ( ) ) if not isinstance ( parameters , ( list , tuple ) ) : parameters = ( parameters , ) job_desc = { } job_desc [ 'job' ] = JobRun ( ca...
Add a job and run it once immediately .
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def job_add ( self , callback , parameters = None , hours = 0 , minutes = 0 , seconds = 0 , tolerate_exceptions = True , expiration = None ) : if not self . _thread_running . is_set ( ) : raise RuntimeError ( 'the JobManager is not running' ) parameters = ( parameters or ( ) ) if not isinstance ( parameters , ( list , ...
Add a job to the job manager .
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def job_count_enabled ( self ) : enabled = 0 for job_desc in self . _jobs . values ( ) : if job_desc [ 'enabled' ] : enabled += 1 return enabled
Return the number of enabled jobs .
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def job_enable ( self , job_id ) : job_id = normalize_job_id ( job_id ) with self . _job_lock : job_desc = self . _jobs [ job_id ] job_desc [ 'enabled' ] = True
Enable a job .
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def job_disable ( self , job_id ) : job_id = normalize_job_id ( job_id ) with self . _job_lock : job_desc = self . _jobs [ job_id ] job_desc [ 'enabled' ] = False
Disable a job . Disabled jobs will not be executed .
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def job_delete ( self , job_id , wait = True ) : job_id = normalize_job_id ( job_id ) self . logger . info ( 'deleting job with id: ' + str ( job_id ) + ' and callback function: ' + self . _jobs [ job_id ] [ 'callback' ] . __name__ ) job_desc = self . _jobs [ job_id ] with self . _job_lock : job_desc [ 'enabled' ] = Fa...
Delete a job .
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def job_is_enabled ( self , job_id ) : job_id = normalize_job_id ( job_id ) job_desc = self . _jobs [ job_id ] return job_desc [ 'enabled' ]
Check if a job is enabled .
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def job_is_running ( self , job_id ) : job_id = normalize_job_id ( job_id ) if job_id not in self . _jobs : return False job_desc = self . _jobs [ job_id ] if job_desc [ 'job' ] : return job_desc [ 'job' ] . is_alive ( ) return False
Check if a job is currently running . False is returned if the job does not exist .
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def bin_b64_type ( arg ) : try : arg = base64 . standard_b64decode ( arg ) except ( binascii . Error , TypeError ) : raise argparse . ArgumentTypeError ( "{0} is invalid base64 data" . format ( repr ( arg ) ) ) return arg
An argparse type representing binary data encoded in base64 .
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def bin_hex_type ( arg ) : if re . match ( r'^[a-f0-9]{2}(:[a-f0-9]{2})+$' , arg , re . I ) : arg = arg . replace ( ':' , '' ) elif re . match ( r'^(\\x[a-f0-9]{2})+$' , arg , re . I ) : arg = arg . replace ( '\\x' , '' ) try : arg = binascii . a2b_hex ( arg ) except ( binascii . Error , TypeError ) : raise argparse . ...
An argparse type representing binary data encoded in hex .
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def dir_type ( arg ) : if not os . path . isdir ( arg ) : raise argparse . ArgumentTypeError ( "{0} is not a valid directory" . format ( repr ( arg ) ) ) return arg
An argparse type representing a valid directory .
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def email_type ( arg ) : if not is_valid_email_address ( arg ) : raise argparse . ArgumentTypeError ( "{0} is not a valid email address" . format ( repr ( arg ) ) ) return arg
An argparse type representing an email address .
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def log_level_type ( arg ) : if not arg . upper ( ) in ( 'NOTSET' , 'DEBUG' , 'INFO' , 'WARNING' , 'ERROR' , 'CRITICAL' ) : raise argparse . ArgumentTypeError ( "{0} is not a valid log level" . format ( repr ( arg ) ) ) return getattr ( logging , arg . upper ( ) )
An argparse type representing a logging level .
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def port_type ( arg ) : error_msg = "{0} is not a valid port" . format ( repr ( arg ) ) try : arg = ast . literal_eval ( arg ) except ValueError : raise argparse . ArgumentTypeError ( error_msg ) if arg < 0 or arg > 65535 : raise argparse . ArgumentTypeError ( error_msg ) return arg
An argparse type representing a tcp or udp port number .
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def timespan_type ( arg ) : try : arg = parse_timespan ( arg ) except ValueError : raise argparse . ArgumentTypeError ( "{0} is not a valid time span" . format ( repr ( arg ) ) ) return arg
An argparse type representing a timespan such as 6h for 6 hours .
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def get_own_ip ( ) : sock = socket . socket ( socket . AF_INET , socket . SOCK_DGRAM ) try : sock . connect ( ( "8.8.8.8" , 80 ) ) except socket . gaierror : ip_ = "127.0.0.1" else : ip_ = sock . getsockname ( ) [ 0 ] finally : sock . close ( ) return ip_
Get the host s ip number .
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def send ( self , msg ) : with self . _pub_lock : self . publish . send_string ( msg ) return self
Send the given message .
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def start ( self ) : pub_addr = "tcp://*:" + str ( self . _port ) self . _publisher = self . _publisher_class ( pub_addr , self . _name ) LOGGER . debug ( "entering publish %s" , str ( self . _publisher . destination ) ) addr = ( "tcp://" + str ( get_own_ip ( ) ) + ":" + str ( self . _publisher . port_number ) ) self ....
Start the publisher .
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def configure_stream_logger ( logger = '' , level = None , formatter = '%(levelname)-8s %(message)s' ) : level = level or logging . WARNING if isinstance ( level , str ) : level = getattr ( logging , level , None ) if level is None : raise ValueError ( 'invalid log level: ' + level ) root_logger = logging . getLogger (...
Configure the default stream handler for logging messages to the console remove other logging handlers and enable capturing warnings .
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def format_bytes_size ( val ) : if not val : return '0 bytes' for sz_name in [ 'bytes' , 'KB' , 'MB' , 'GB' , 'TB' , 'PB' , 'EB' ] : if val < 1024.0 : return "{0:.2f} {1}" . format ( val , sz_name ) val /= 1024.0 raise OverflowError ( )
Take a number of bytes and convert it to a human readable number .
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def grep ( expression , file , flags = 0 , invert = False ) : if isinstance ( file , str ) : file = open ( file ) lines = [ ] for line in file : if bool ( re . search ( expression , line , flags = flags ) ) ^ invert : lines . append ( line ) return lines
Search a file and return a list of all lines that match a regular expression .
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def parse_case_snake_to_camel ( snake , upper_first = True ) : snake = snake . split ( '_' ) first_part = snake [ 0 ] if upper_first : first_part = first_part . title ( ) return first_part + '' . join ( word . title ( ) for word in snake [ 1 : ] )
Convert a string from snake_case to CamelCase .
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def parse_to_slug ( words , maxlen = 24 ) : slug = '' maxlen = min ( maxlen , len ( words ) ) for c in words : if len ( slug ) == maxlen : break c = ord ( c ) if c == 0x27 : continue elif c >= 0x30 and c <= 0x39 : slug += chr ( c ) elif c >= 0x41 and c <= 0x5a : slug += chr ( c + 0x20 ) elif c >= 0x61 and c <= 0x7a : s...
Parse a string into a slug format suitable for use in URLs and other character restricted applications . Only utf - 8 strings are supported at this time .
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def selection_collision ( selections , poolsize ) : probability = 100.0 poolsize = float ( poolsize ) for i in range ( selections ) : probability = probability * ( poolsize - i ) / poolsize probability = ( 100.0 - probability ) return probability
Calculate the probability that two random values selected from an arbitrary sized pool of unique values will be equal . This is commonly known as the Birthday Problem .
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def unique ( seq , key = None ) : if key is None : key = lambda x : x preserved_type = type ( seq ) if preserved_type not in ( list , tuple ) : raise TypeError ( "unique argument 1 must be list or tuple, not {0}" . format ( preserved_type . __name__ ) ) seen = [ ] result = [ ] for item in seq : marker = key ( item ) if...
Create a unique list or tuple from a provided list or tuple and preserve the order .
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def xfrange ( start , stop = None , step = 1 ) : if stop is None : stop = start start = 0.0 start = float ( start ) while start < stop : yield start start += step
Iterate through an arithmetic progression .
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def set ( self , option , value ) : self . config_parser . set ( self . section_name , option , value )
Set an option to an arbitrary value .
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def reformat_exception ( cls , message , err , * format_args , ** format_kwds ) : final_message = message . format ( * format_args , ** format_kwds ) final_message = "{} -- {}: {}" . format ( final_message , type ( err ) . __name__ , str ( err ) , ) final_message = cls . sanitize_errstr ( final_message ) return final_m...
Reformats an exception by adding a message to it and reporting the original exception name and message
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def require_condition ( cls , expr , message , * format_args , ** format_kwds ) : if not expr : raise cls ( message , * format_args , ** format_kwds )
used to assert a certain state . If the expression renders a false value an exception will be raised with the supplied message
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def visit_html ( self , node ) : parentClsNode = node . parent . parent assert parentClsNode . attributes [ 'objtype' ] == 'class' assert parentClsNode . attributes [ 'domain' ] == 'py' sign = node . parent . parent . children [ 0 ] assert isinstance ( sign , desc_signature ) absolute_name = sign . attributes [ 'ids' ]...
Generate html elements and schematic json
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def run ( self ) : has_npm = npm_installation_check ( ) if has_npm : run_npm_install ( ) else : print ( "Warning: npm not installed using prebuilded js files!" , file = sys . stderr ) for js in JS_FILES : downloaded_js_name = os . path . join ( TOP_DIR , js ) installed_js_name = os . path . join ( TOP_DIR , "sphinx_hwt...
Download npm packages required by package . json and extract required files from them
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def density ( self ) : r = self . radius * _Rsun m = self . mass * _Msun return 0.75 * m / ( np . pi * r * r * r )
Stellar density in CGS units
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def get_context ( ) : pid = os . getpid ( ) if pid not in context : context [ pid ] = zmq . Context ( ) logger . debug ( 'renewed context for PID %d' , pid ) return context [ pid ]
Provide the context to use .
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def strp_isoformat ( strg ) : if isinstance ( strg , datetime ) : return strg if len ( strg ) < 19 or len ( strg ) > 26 : if len ( strg ) > 30 : strg = strg [ : 30 ] + '...' raise ValueError ( "Invalid ISO formatted time string '%s'" % strg ) if strg . find ( "." ) == - 1 : strg += '.000000' if sys . version [ 0 : 3 ] ...
Decode an ISO formatted string to a datetime object . Allow a time - string without microseconds .
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def find_analysis ( self , family , started_at , status ) : query = self . Analysis . query . filter_by ( family = family , started_at = started_at , status = status , ) return query . first ( )
Find a single analysis .
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def analyses ( self , * , family : str = None , query : str = None , status : str = None , deleted : bool = None , temp : bool = False , before : dt . datetime = None , is_visible : bool = None ) : analysis_query = self . Analysis . query if family : analysis_query = analysis_query . filter_by ( family = family ) elif ...
Fetch analyses form the database .
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def analysis ( self , analysis_id : int ) -> models . Analysis : return self . Analysis . query . get ( analysis_id )
Get a single analysis .
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def track_update ( self ) : metadata = self . info ( ) metadata . updated_at = dt . datetime . now ( ) self . commit ( )
Update the lastest updated date in the database .
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def add_pending ( self , family : str , email : str = None ) -> models . Analysis : started_at = dt . datetime . now ( ) new_log = self . Analysis ( family = family , status = 'pending' , started_at = started_at ) new_log . user = self . user ( email ) if email else None self . add_commit ( new_log ) return new_log
Add pending entry for an analysis .
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def add_user ( self , name : str , email : str ) -> models . User : new_user = self . User ( name = name , email = email ) self . add_commit ( new_user ) return new_user
Add a new user to the database .
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def user ( self , email : str ) -> models . User : return self . User . query . filter_by ( email = email ) . first ( )
Fetch a user from the database .
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def start ( self ) : if not self . _is_running : self . _do_run = True self . _thread . start ( ) return self
Start the receiver .
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def _check_age ( self , pub , min_interval = timedelta ( seconds = 0 ) ) : now = datetime . utcnow ( ) if ( now - self . _last_age_check ) <= min_interval : return LOGGER . debug ( "%s - checking addresses" , str ( datetime . utcnow ( ) ) ) self . _last_age_check = now to_del = [ ] with self . _address_lock : for addr ...
Check the age of the receiver .
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def _run ( self ) : port = broadcast_port nameservers = [ ] if self . _multicast_enabled : recv = MulticastReceiver ( port ) . settimeout ( 2. ) while True : try : recv = MulticastReceiver ( port ) . settimeout ( 2. ) LOGGER . info ( "Receiver initialized." ) break except IOError as err : if err . errno == errno . ENOD...
Run the receiver .
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def _add ( self , adr , metadata ) : with self . _address_lock : metadata [ "receive_time" ] = datetime . utcnow ( ) self . _addresses [ adr ] = metadata
Add an address .
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def get_console_width ( ) : if os . name == 'nt' : STD_INPUT_HANDLE = - 10 STD_OUTPUT_HANDLE = - 11 STD_ERROR_HANDLE = - 12 from ctypes import windll , Structure , byref try : from ctypes . wintypes import SHORT , WORD , DWORD except ImportError : from ctypes import ( c_short as SHORT , c_ushort as WORD , c_ulong as DW...
Return width of available window area . Autodetection works for Windows and POSIX platforms . Returns 80 for others
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def report_bar ( bytes_so_far , total_size , speed , eta ) : percent = int ( bytes_so_far * 100 / total_size ) current = approximate_size ( bytes_so_far ) . center ( 9 ) total = approximate_size ( total_size ) . center ( 9 ) shaded = int ( float ( bytes_so_far ) / total_size * AVAIL_WIDTH ) sys . stdout . write ( " {0}...
This callback for the download function is used to print the download bar
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def report_unknown ( bytes_so_far , total_size , speed , eta ) : sys . stdout . write ( "Downloading: {0} / Unknown - {1}/s " . format ( approximate_size ( bytes_so_far ) , approximate_size ( speed ) ) ) sys . stdout . write ( "\r" ) sys . stdout . flush ( )
This callback for the download function is used when the total size is unknown
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def report_onlysize ( bytes_so_far , total_size , speed , eta ) : percent = int ( bytes_so_far * 100 / total_size ) current = approximate_size ( bytes_so_far ) . center ( 10 ) total = approximate_size ( total_size ) . center ( 10 ) sys . stdout . write ( 'D: {0}% -{1}/{2}' . format ( percent , current , total ) + "eta ...
This callback for the download function is used when console width is not enough to print the bar . It prints only the sizes
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def ls_cmd ( context , before , status ) : runs = context . obj [ 'store' ] . analyses ( status = status , deleted = False , before = parse_date ( before ) if before else None , ) . limit ( 30 ) for run_obj in runs : if run_obj . status == 'pending' : message = f"{run_obj.id} | {run_obj.family} [{run_obj.status.upper()...
Display recent logs for analyses .
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def analytics ( account = None , * args , ** kwargs ) : if not account : try : account = settings . GOOGLE_ANALYTICS_ACCOUNT except : raise template . TemplateSyntaxError ( "Analytics account could not found either " "in tag parameters or settings" ) return { 'account' : account , 'params' : kwargs }
Simple Google Analytics integration .
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def analyses ( ) : per_page = int ( request . args . get ( 'per_page' , 50 ) ) page = int ( request . args . get ( 'page' , 1 ) ) query = store . analyses ( status = request . args . get ( 'status' ) , query = request . args . get ( 'query' ) , is_visible = request . args . get ( 'is_visible' ) == 'true' or None ) quer...
Display analyses .
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def analysis ( analysis_id ) : analysis_obj = store . analysis ( analysis_id ) if analysis_obj is None : return abort ( 404 ) if request . method == 'PUT' : analysis_obj . update ( request . json ) store . commit ( ) data = analysis_obj . to_dict ( ) data [ 'failed_jobs' ] = [ job_obj . to_dict ( ) for job_obj in analy...
Display a single analysis .
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def get_datetime_now ( ) : try : from django . utils import timezone return timezone . now ( ) except ImportError : return datetime . datetime . now ( )
Returns datetime object with current point in time .
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def is_valid_data ( obj ) : if obj : try : tmp = json . dumps ( obj , default = datetime_encoder ) del tmp except ( TypeError , UnicodeDecodeError ) : return False return True
Check if data is JSON serializable .
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def datetime_decoder ( dct ) : if isinstance ( dct , list ) : pairs = enumerate ( dct ) elif isinstance ( dct , dict ) : pairs = dct . items ( ) result = [ ] for key , val in pairs : if isinstance ( val , six . string_types ) : try : val = strp_isoformat ( val ) except ValueError : pass elif isinstance ( val , ( dict ,...
Decode datetimes to python objects .
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def _decode ( rawstr ) : try : rawstr = rawstr . decode ( 'utf-8' ) except ( AttributeError , UnicodeEncodeError ) : pass except ( UnicodeDecodeError ) : try : rawstr = rawstr . decode ( 'iso-8859-1' ) except ( UnicodeDecodeError ) : rawstr = rawstr . decode ( 'utf-8' , 'ignore' ) if not rawstr . startswith ( _MAGICK )...
Convert a raw string to a Message .
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def _encode ( msg , head = False , binary = False ) : rawstr = str ( _MAGICK ) + u"{0:s} {1:s} {2:s} {3:s} {4:s}" . format ( msg . subject , msg . type , msg . sender , msg . time . isoformat ( ) , msg . version ) if not head and msg . data : if not binary and isinstance ( msg . data , six . string_types ) : return ( r...
Convert a Message to a raw string .
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def _getsender ( ) : import os import pwd import socket host = socket . gethostname ( ) user = pwd . getpwuid ( os . getuid ( ) ) [ 0 ] return "%s@%s" % ( user , host )
Return local sender . Don t use the getpass module it looks at various environment variables and is unreliable .
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def _validate ( self ) : if not is_valid_subject ( self . subject ) : raise MessageError ( "Invalid subject: '%s'" % self . subject ) if not is_valid_type ( self . type ) : raise MessageError ( "Invalid type: '%s'" % self . type ) if not is_valid_sender ( self . sender ) : raise MessageError ( "Invalid sender: '%s'" % ...
Validate a messages attributes .
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def __generateSPK ( self ) : key = self . __KeyPair . generate ( ) key_serialized = self . __PublicKeyEncoder . encodePublicKey ( key . pub , self . __curve ) signature = self . __XEdDSA ( mont_priv = self . __ik . priv ) . sign ( key_serialized ) self . __spk = { "key" : key , "signature" : signature , "timestamp" : t...
Generate a new PK and sign its public key using the IK add the timestamp aswell to allow for periodic rotations .
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def __generateOTPKs ( self , num_otpks = None ) : if num_otpks == None : num_otpks = self . __max_num_otpks otpks = [ ] for _ in range ( num_otpks ) : otpks . append ( self . __KeyPair . generate ( ) ) try : self . __otpks . extend ( otpks ) except AttributeError : self . __otpks = otpks
Generate the given amount of OTPKs .
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def __checkSPKTimestamp ( self ) : if time . time ( ) - self . __spk [ "timestamp" ] > self . __spk_timeout : self . __generateSPK ( )
Check whether the SPK is too old and generate a new one in that case .
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def __refillOTPKs ( self ) : remainingOTPKs = len ( self . __otpks ) if remainingOTPKs < self . __min_num_otpks : self . __generateOTPKs ( self . __max_num_otpks - remainingOTPKs )
If the amount of available OTPKs fell under the minimum refills the OTPKs up to the maximum limit again .
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def hideFromPublicBundle ( self , otpk_pub ) : self . __checkSPKTimestamp ( ) for otpk in self . __otpks : if otpk . pub == otpk_pub : self . __otpks . remove ( otpk ) self . __hidden_otpks . append ( otpk ) self . __refillOTPKs ( )
Hide a one - time pre key from the public bundle .
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def deleteOTPK ( self , otpk_pub ) : self . __checkSPKTimestamp ( ) for otpk in self . __otpks : if otpk . pub == otpk_pub : self . __otpks . remove ( otpk ) for otpk in self . __hidden_otpks : if otpk . pub == otpk_pub : self . __hidden_otpks . remove ( otpk ) self . __refillOTPKs ( )
Delete a one - time pre key either publicly visible or hidden .
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def getPublicBundle ( self ) : self . __checkSPKTimestamp ( ) ik_pub = self . __ik . pub spk_pub = self . __spk [ "key" ] . pub spk_sig = self . __spk [ "signature" ] otpk_pubs = [ otpk . pub for otpk in self . __otpks ] return PublicBundle ( ik_pub , spk_pub , spk_sig , otpk_pubs )
Fill a PublicBundle object with the public bundle data of this State .
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def getSharedSecretActive ( self , other_public_bundle , allow_zero_otpks = False ) : self . __checkSPKTimestamp ( ) other_ik = self . __KeyPair ( pub = other_public_bundle . ik ) other_spk = { "key" : self . __KeyPair ( pub = other_public_bundle . spk ) , "signature" : other_public_bundle . spk_signature } other_otpks...
Do the key exchange as the active party . This involves selecting keys from the passive parties public bundle .
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def getSharedSecretPassive ( self , passive_exchange_data , allow_no_otpk = False , keep_otpk = False ) : self . __checkSPKTimestamp ( ) other_ik = self . __KeyPair ( pub = passive_exchange_data [ "ik" ] ) other_ek = self . __KeyPair ( pub = passive_exchange_data [ "ek" ] ) if self . __spk [ "key" ] . pub != passive_ex...
Do the key exchange as the passive party . This involves retrieving data about the key exchange from the active party .
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def save ( self , mode = 0o600 ) : if self . _parent is not None : self . _parent . save ( mode = mode ) else : config_dir = os . path . dirname ( os . path . abspath ( self . config_files [ - 1 ] ) ) try : os . makedirs ( config_dir ) except OSError as e : if not ( e . errno == errno . EEXIST and os . path . isdir ( c...
Serialize the config data to the user home directory .
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def getChemicalPotential ( self , solution ) : if isinstance ( solution , Solution ) : solution = solution . getSolution ( ) self . mu = self . solver . chemicalPotential ( solution ) return self . mu
Call solver in order to calculate chemical potential .
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def getDampingIntegral ( self ) : reservoir = self . getReservoir ( ) density = self . getDensity ( ) length = self . model . getSpatialStep ( ) if self . solution . ndim == 1 : nodes = self . model . getNumberOfNodes ( ) radius = linspace ( 0 , nodes * self . model . getSpatialStep ( ) , nodes ) integral = 2 * pi * su...
Calculate integral of damping terms of hamiltonian using rectangular method .
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def fmt_val ( val , shorten = True ) : val = repr ( val ) max = 50 if shorten : if len ( val ) > max : close = val [ - 1 ] val = val [ 0 : max - 4 ] + "..." if close in ( ">" , "'" , '"' , ']' , '}' , ')' ) : val = val + close return val
Format a value for inclusion in an informative text string .
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def fmt_dict_vals ( dict_vals , shorten = True ) : items = dict_vals . items ( ) if not items : return [ fmt_val ( None , shorten = shorten ) ] return [ "%s=%s" % ( k , fmt_val ( v , shorten = shorten ) ) for k , v in items ]
Returns list of key = val pairs formatted for inclusion in an informative text string .
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def build_command ( self , config , ** kwargs ) : command = [ 'perl' , self . script , CLI_OPTIONS [ 'config' ] [ 'option' ] , config ] for key , value in kwargs . items ( ) : if value : command . append ( CLI_OPTIONS [ key ] [ 'option' ] ) if value is True : command . append ( CLI_OPTIONS [ key ] . get ( 'default' , '...
Builds the command to execute MIP .
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def execute ( self , command ) : process = subprocess . Popen ( command , preexec_fn = lambda : signal . signal ( signal . SIGPIPE , signal . SIG_DFL ) ) return process
Start a new MIP run .
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def update ( self ) : self . log . debug ( 'starting the ``update`` method' ) if "sherlock wiki root" not in self . settings : print "Sherlock wiki settings not found in settings file" return staticTableInfo = self . _get_table_infos ( ) viewInfo = self . _get_view_infos ( ) streamedTableInfo = self . _get_stream_view_...
Update wiki pages
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def _get_table_infos ( self , trimmed = False ) : self . log . debug ( 'starting the ``_get_table_infos`` method' ) sqlQuery = u % locals ( ) tableInfo = readquery ( log = self . log , sqlQuery = sqlQuery , dbConn = self . cataloguesDbConn , quiet = False ) if trimmed : cleanTable = [ ] for r in tableInfo : orow = coll...
query the sherlock - catalogues database table metadata
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def _get_view_infos ( self , trimmed = False ) : self . log . debug ( 'starting the ``_get_view_infos`` method' ) sqlQuery = u % locals ( ) viewInfo = readquery ( log = self . log , sqlQuery = sqlQuery , dbConn = self . cataloguesDbConn , quiet = False ) if trimmed : cleanTable = [ ] for r in viewInfo : orow = collecti...
query the sherlock - catalogues database view metadata
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def _get_stream_view_infos ( self , trimmed = False ) : self . log . debug ( 'starting the ``_get_stream_view_infos`` method' ) sqlQuery = u % locals ( ) streamInfo = readquery ( log = self . log , sqlQuery = sqlQuery , dbConn = self . cataloguesDbConn , quiet = False ) if trimmed : cleanTable = [ ] for r in streamInfo...
query the sherlock - catalogues database streamed data tables metadata
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def email_user ( self , subject , message , from_email = settings . DEFAULT_FROM_EMAIL , ** kwargs ) : receiver = self . email if settings . EMAIL_OVERRIDE_ADDRESS : receiver = settings . EMAIL_OVERRIDE_ADDRESS send_mail ( subject , message , from_email , [ receiver ] , ** kwargs )
Sends an email to this User . If settings . EMAIL_OVERRIDE_ADDRESS is set this mail will be redirected to the alternate mail address .
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def clean ( context , days_ago , yes ) : number_of_days_ago = dt . datetime . now ( ) - dt . timedelta ( days = days_ago ) analyses = context . obj [ 'store' ] . analyses ( status = 'completed' , before = number_of_days_ago , deleted = False , ) for analysis_obj in analyses : LOG . debug ( f"checking analysis: {analysi...
Clean up files from old analyses runs .