idx int64 0 63k | question stringlengths 53 5.28k | target stringlengths 5 805 |
|---|---|---|
5,700 | def _useChunk ( self , index ) -> None : if self . currentChunk is not None : if self . currentChunkIndex == index and not self . currentChunk . closed : return self . currentChunk . close ( ) self . currentChunk = self . _openChunk ( index ) self . currentChunkIndex = index self . itemNum = self . currentChunk . numKeys + 1 | Switch to specific chunk |
5,701 | def numKeys ( self ) -> int : chunks = self . _listChunks ( ) num_chunks = len ( chunks ) if num_chunks == 0 : return 0 count = ( num_chunks - 1 ) * self . chunkSize last_chunk = self . _openChunk ( chunks [ - 1 ] ) count += sum ( 1 for _ in last_chunk . _lines ( ) ) last_chunk . close ( ) return count | This will iterate only over the last chunk since the name of the last chunk indicates how many lines in total exist in all other chunks |
5,702 | def register ( self , subscriber ) : assert isinstance ( subscriber , RequestHandler ) logger . debug ( 'New subscriber' ) self . subscribers . add ( subscriber ) | Register a new subscriber . This method should be invoked by listeners to start receiving messages . |
5,703 | def deregister ( self , subscriber ) : try : logger . debug ( 'Subscriber left' ) self . subscribers . remove ( subscriber ) except KeyError : logger . debug ( 'Error removing subscriber: ' + str ( subscriber ) ) | Stop publishing to a subscriber . |
5,704 | def shutdown ( self ) : self . _done . set ( ) self . executor . shutdown ( wait = False ) | Stop the publishing loop . |
5,705 | def add_alignment ( self , ref_seq , annotation ) -> Annotation : seq_features = get_seqs ( ref_seq ) annoated_align = { } allele = ref_seq . description . split ( "," ) [ 0 ] locus = allele . split ( "*" ) [ 0 ] . split ( "-" ) [ 1 ] for feat in seq_features : if feat in annotation . annotation : if isinstance ( annotation . annotation [ feat ] , DBSeq ) : seq_len = len ( str ( annotation . annotation [ feat ] ) ) ref_len = len ( seq_features [ feat ] ) else : seq_len = len ( str ( annotation . annotation [ feat ] . seq ) ) ref_len = len ( seq_features [ feat ] ) if seq_len == ref_len : seq = list ( annotation . annotation [ feat ] . seq ) gaps = self . refdata . annoated_alignments [ locus ] [ allele ] [ feat ] [ 'Gaps' ] if self . verbose and self . verbosity > 0 : self . logger . info ( self . logname + " Lengths match for " + feat ) self . logger . info ( self . logname + " Gaps at " + feat ) self . logger . info ( self . logname + "-" . join ( [ "," . join ( [ str ( s ) for s in g ] ) for g in gaps ] ) ) for i in range ( 0 , len ( gaps ) ) : for j in gaps [ i ] : loc = j seq . insert ( loc , '-' ) nseq = '' . join ( seq ) annoated_align . update ( { feat : nseq } ) else : in_seq = str ( annotation . annotation [ feat ] . seq ) ref_seq = self . refdata . annoated_alignments [ locus ] [ allele ] [ feat ] [ 'Seq' ] alignment = pairwise2 . align . globalxx ( in_seq , ref_seq ) if self . verbose and self . verbosity > 0 : self . logger . info ( self . logname + " Align2 -> in_seq != ref_len " + feat ) self . logger . info ( self . logname + " " + str ( len ( in_seq ) ) + " == " + str ( ref_len ) ) annoated_align . update ( { feat : alignment [ 0 ] [ 0 ] } ) else : nseq = '' . join ( list ( repeat ( '-' , len ( seq_features [ feat ] ) ) ) ) annoated_align . update ( { feat : nseq } ) annotation . aligned = annoated_align return annotation | add_alignment - method for adding the alignment to an annotation |
5,706 | def object2xml ( self , data ) : r if not self . __options [ 'encoding' ] : self . set_options ( encoding = self . __encoding ) if self . __options [ 'header_declare' ] : self . __tree . append ( self . build_xml_header ( ) ) root = self . __options [ 'root' ] if not root : assert ( isinstance ( data , utils . DictTypes ) and len ( data ) == 1 ) , 'if root not specified, the data that dict object and length must be one required.' root , data = data . items ( ) [ 0 ] self . build_tree ( data , root ) xml = unicode ( '' . join ( self . __tree ) . strip ( ) ) if self . __options [ 'encoding' ] != self . __encoding : xml = xml . encode ( self . __options [ 'encoding' ] , errors = self . __options [ 'errors' ] ) return xml | r Convert python object to xml string . |
5,707 | def build_tree ( self , data , tagname , attrs = None , depth = 0 ) : r if data is None : data = '' indent = ( '\n%s' % ( self . __options [ 'indent' ] * depth ) ) if self . __options [ 'indent' ] else '' if isinstance ( data , utils . DictTypes ) : if self . __options [ 'hasattr' ] and self . check_structure ( data . keys ( ) ) : attrs , values = self . pickdata ( data ) self . build_tree ( values , tagname , attrs , depth ) else : self . __tree . append ( '%s%s' % ( indent , self . tag_start ( tagname , attrs ) ) ) iter = data . iteritems ( ) if self . __options [ 'ksort' ] : iter = sorted ( iter , key = lambda x : x [ 0 ] , reverse = self . __options [ 'reverse' ] ) for k , v in iter : attrs = { } if self . __options [ 'hasattr' ] and isinstance ( v , utils . DictTypes ) and self . check_structure ( v . keys ( ) ) : attrs , v = self . pickdata ( v ) self . build_tree ( v , k , attrs , depth + 1 ) self . __tree . append ( '%s%s' % ( indent , self . tag_end ( tagname ) ) ) elif utils . is_iterable ( data ) : for v in data : self . build_tree ( v , tagname , attrs , depth ) else : self . __tree . append ( indent ) data = self . safedata ( data , self . __options [ 'cdata' ] ) self . __tree . append ( self . build_tag ( tagname , data , attrs ) ) | r Build xml tree . |
5,708 | def check_structure ( self , keys ) : r return set ( keys ) <= set ( [ self . __options [ 'attrkey' ] , self . __options [ 'valuekey' ] ] ) | r Check structure availability by attrkey and valuekey option . |
5,709 | def pickdata ( self , data ) : r attrs = data . get ( self . __options [ 'attrkey' ] ) or { } values = data . get ( self . __options [ 'valuekey' ] ) or '' return ( attrs , values ) | r Pick data from attrkey and valuekey option . |
5,710 | def safedata ( self , data , cdata = True ) : r safe = ( '<![CDATA[%s]]>' % data ) if cdata else cgi . escape ( str ( data ) , True ) return safe | r Convert xml special chars to entities . |
5,711 | def build_tag ( self , tag , text = '' , attrs = None ) : r return '%s%s%s' % ( self . tag_start ( tag , attrs ) , text , self . tag_end ( tag ) ) | r Build tag full info include the attributes . |
5,712 | def build_attr ( self , attrs ) : r attrs = sorted ( attrs . iteritems ( ) , key = lambda x : x [ 0 ] ) return ' ' . join ( map ( lambda x : '%s="%s"' % x , attrs ) ) | r Build tag attributes . |
5,713 | def tag_start ( self , tag , attrs = None ) : r return '<%s %s>' % ( tag , self . build_attr ( attrs ) ) if attrs else '<%s>' % tag | r Build started tag info . |
5,714 | def open_file_dialog ( self ) : dialog = QtWidgets . QFileDialog sender = self . sender ( ) if sender == self . btn_open_source : textbox = self . source_path elif sender == self . btn_open_target : textbox = self . target_path folder = dialog . getExistingDirectory ( self , 'Select a file:' , textbox . text ( ) , options = QtWidgets . QFileDialog . ShowDirsOnly ) if str ( folder ) != '' : textbox . setText ( folder ) if sender == self . btn_open_source : self . reset_avaliable ( folder ) | Opens a file dialog to get the path to a file and put tha tpath in the correct textbox |
5,715 | def class_type_changed ( self ) : if self . source_path . text ( ) : self . reset_avaliable ( self . source_path . text ( ) ) | Forces a reset if the class type is changed from instruments to scripts or vice versa |
5,716 | def select_inputs ( self , address : str , amount : int ) -> dict : utxos = [ ] utxo_sum = Decimal ( 0 ) for tx in sorted ( self . listunspent ( address = address ) , key = itemgetter ( 'confirmations' ) ) : if tx [ "address" ] not in ( self . pa_parameters . P2TH_addr , self . pa_parameters . test_P2TH_addr ) : utxos . append ( MutableTxIn ( txid = tx [ 'txid' ] , txout = tx [ 'vout' ] , sequence = Sequence . max ( ) , script_sig = ScriptSig . empty ( ) ) ) utxo_sum += Decimal ( tx [ "amount" ] ) if utxo_sum >= amount : return { 'utxos' : utxos , 'total' : utxo_sum } if utxo_sum < amount : raise InsufficientFunds ( "Insufficient funds." ) raise Exception ( "undefined behavior :.(" ) | finds apropriate utxo s to include in rawtx while being careful to never spend old transactions with a lot of coin age . Argument is intiger returns list of apropriate UTXO s |
5,717 | def listunspent ( self , address : str = "" , minconf : int = 1 , maxconf : int = 999999 , ) -> list : if address : return self . req ( "listunspent" , [ minconf , maxconf , [ address ] ] ) return self . req ( "listunspent" , [ minconf , maxconf ] ) | list UTXOs modified version to allow filtering by address . |
5,718 | def rem2ics ( ) : from argparse import ArgumentParser , FileType from dateutil . parser import parse from sys import stdin , stdout parser = ArgumentParser ( description = 'Converter from Remind to iCalendar syntax.' ) parser . add_argument ( '-s' , '--startdate' , type = lambda s : parse ( s ) . date ( ) , default = date . today ( ) - timedelta ( weeks = 12 ) , help = 'Start offset for remind call (default: -12 weeks)' ) parser . add_argument ( '-m' , '--month' , type = int , default = 15 , help = 'Number of month to generate calendar beginning wit startdate (default: 15)' ) parser . add_argument ( '-a' , '--alarm' , type = int , default = - 10 , help = 'Trigger time for the alarm before the event in minutes (default: -10)' ) parser . add_argument ( '-z' , '--zone' , help = 'Timezone of Remind file (default: local timezone)' ) parser . add_argument ( 'infile' , nargs = '?' , default = expanduser ( '~/.reminders' ) , help = 'The Remind file to process (default: ~/.reminders)' ) parser . add_argument ( 'outfile' , nargs = '?' , type = FileType ( 'w' ) , default = stdout , help = 'Output iCalendar file (default: stdout)' ) args = parser . parse_args ( ) zone = timezone ( args . zone ) if args . zone else None if args . infile == '-' : remind = Remind ( args . infile , zone , args . startdate , args . month , timedelta ( minutes = args . alarm ) ) vobject = remind . stdin_to_vobject ( stdin . read ( ) ) if vobject : args . outfile . write ( vobject . serialize ( ) ) else : remind = Remind ( args . infile , zone , args . startdate , args . month , timedelta ( minutes = args . alarm ) ) args . outfile . write ( remind . to_vobject ( ) . serialize ( ) ) | Command line tool to convert from Remind to iCalendar |
5,719 | def ics2rem ( ) : from argparse import ArgumentParser , FileType from sys import stdin , stdout parser = ArgumentParser ( description = 'Converter from iCalendar to Remind syntax.' ) parser . add_argument ( '-l' , '--label' , help = 'Label for every Remind entry' ) parser . add_argument ( '-p' , '--priority' , type = int , help = 'Priority for every Remind entry (0..9999)' ) parser . add_argument ( '-t' , '--tag' , action = 'append' , help = 'Tag(s) for every Remind entry' ) parser . add_argument ( '--tail' , help = 'Text to append to every remind summary, following final %%"' ) parser . add_argument ( '--sep' , default = " " , help = 'String to separate summary (and tail) from description' ) parser . add_argument ( '--postdate' , help = 'String to follow the date in every Remind entry. ' 'Useful for entering "back" and "delta" fields (see man remind).' ) parser . add_argument ( '--posttime' , help = 'String to follow the time in every timed Remind entry. ' 'Useful for entering "tdelta" and "trepeat" fields (see man remind).' ) parser . add_argument ( '-z' , '--zone' , help = 'Timezone of Remind file (default: local timezone)' ) parser . add_argument ( 'infile' , nargs = '?' , type = FileType ( 'r' ) , default = stdin , help = 'Input iCalendar file (default: stdin)' ) parser . add_argument ( 'outfile' , nargs = '?' , type = FileType ( 'w' ) , default = stdout , help = 'Output Remind file (default: stdout)' ) args = parser . parse_args ( ) zone = timezone ( args . zone ) if args . zone else None vobject = readOne ( args . infile . read ( ) ) rem = Remind ( localtz = zone ) . to_reminders ( vobject , args . label , args . priority , args . tag , args . tail , args . sep , args . postdate , args . posttime ) args . outfile . write ( rem ) | Command line tool to convert from iCalendar to Remind |
5,720 | def _parse_remind ( self , filename , lines = '' ) : files = { } reminders = { } if lines : filename = '-' files [ filename ] = lines reminders [ filename ] = { } cmd = [ 'remind' , '-l' , '-s%d' % self . _month , '-b1' , '-y' , '-r' , filename , str ( self . _startdate ) ] try : rem = Popen ( cmd , stdin = PIPE , stdout = PIPE ) . communicate ( input = lines . encode ( 'utf-8' ) ) [ 0 ] . decode ( 'utf-8' ) except OSError : raise OSError ( 'Error running: %s' % ' ' . join ( cmd ) ) rem = rem . splitlines ( ) for ( fileinfo , line ) in zip ( rem [ : : 2 ] , rem [ 1 : : 2 ] ) : fileinfo = fileinfo . split ( ) src_filename = fileinfo [ 3 ] if src_filename not in files : files [ src_filename ] = open ( src_filename ) . readlines ( ) reminders [ src_filename ] = { } mtime = getmtime ( src_filename ) if mtime > self . _mtime : self . _mtime = mtime text = files [ src_filename ] [ int ( fileinfo [ 2 ] ) - 1 ] event = self . _parse_remind_line ( line , text ) if event [ 'uid' ] in reminders [ src_filename ] : reminders [ src_filename ] [ event [ 'uid' ] ] [ 'dtstart' ] += event [ 'dtstart' ] reminders [ src_filename ] [ event [ 'uid' ] ] [ 'line' ] += line else : reminders [ src_filename ] [ event [ 'uid' ] ] = event reminders [ src_filename ] [ event [ 'uid' ] ] [ 'line' ] = line for source in files . values ( ) : for line in source : if line . startswith ( 'include' ) : new_file = line . split ( ' ' ) [ 1 ] . strip ( ) if new_file not in reminders : reminders [ new_file ] = { } mtime = getmtime ( new_file ) if mtime > self . _mtime : self . _mtime = mtime return reminders | Calls remind and parses the output into a dict |
5,721 | def _parse_remind_line ( self , line , text ) : event = { } line = line . split ( None , 6 ) dat = [ int ( f ) for f in line [ 0 ] . split ( '/' ) ] if line [ 4 ] != '*' : start = divmod ( int ( line [ 4 ] ) , 60 ) event [ 'dtstart' ] = [ datetime ( dat [ 0 ] , dat [ 1 ] , dat [ 2 ] , start [ 0 ] , start [ 1 ] , tzinfo = self . _localtz ) ] if line [ 3 ] != '*' : event [ 'duration' ] = timedelta ( minutes = int ( line [ 3 ] ) ) else : event [ 'dtstart' ] = [ date ( dat [ 0 ] , dat [ 1 ] , dat [ 2 ] ) ] msg = ' ' . join ( line [ 5 : ] ) if line [ 4 ] == '*' else line [ 6 ] msg = msg . strip ( ) . replace ( '%_' , '\n' ) . replace ( '["["]' , '[' ) if ' at ' in msg : ( event [ 'msg' ] , event [ 'location' ] ) = msg . rsplit ( ' at ' , 1 ) else : event [ 'msg' ] = msg if '%"' in text : event [ 'description' ] = Remind . _gen_description ( text ) tags = line [ 2 ] . split ( ',' ) classes = [ 'PUBLIC' , 'PRIVATE' , 'CONFIDENTIAL' ] for tag in tags [ : - 1 ] : if tag in classes : event [ 'class' ] = tag event [ 'categories' ] = [ tag for tag in tags [ : - 1 ] if tag not in classes ] event [ 'uid' ] = '%s@%s' % ( tags [ - 1 ] [ 7 : ] , getfqdn ( ) ) return event | Parse a line of remind output into a dict |
5,722 | def _interval ( dates ) : interval = ( dates [ 1 ] - dates [ 0 ] ) . days last = dates [ 0 ] for dat in dates [ 1 : ] : if ( dat - last ) . days != interval : return 0 last = dat return interval | Return the distance between all dates and 0 if they are different |
5,723 | def _gen_dtend_rrule ( dtstarts , vevent ) : interval = Remind . _interval ( dtstarts ) if interval > 0 and interval % 7 == 0 : rset = rrule . rruleset ( ) rset . rrule ( rrule . rrule ( freq = rrule . WEEKLY , interval = interval // 7 , count = len ( dtstarts ) ) ) vevent . rruleset = rset elif interval > 1 : rset = rrule . rruleset ( ) rset . rrule ( rrule . rrule ( freq = rrule . DAILY , interval = interval , count = len ( dtstarts ) ) ) vevent . rruleset = rset elif interval > 0 : if isinstance ( dtstarts [ 0 ] , datetime ) : rset = rrule . rruleset ( ) rset . rrule ( rrule . rrule ( freq = rrule . DAILY , count = len ( dtstarts ) ) ) vevent . rruleset = rset else : vevent . add ( 'dtend' ) . value = dtstarts [ - 1 ] + timedelta ( days = 1 ) else : rset = rrule . rruleset ( ) if isinstance ( dtstarts [ 0 ] , datetime ) : for dat in dtstarts : rset . rdate ( dat ) else : for dat in dtstarts : rset . rdate ( datetime ( dat . year , dat . month , dat . day ) ) vevent . dtstart . value = dtstarts [ 0 ] - timedelta ( days = 1 ) vevent . rruleset = rset vevent . dtstart . value = dtstarts [ 0 ] if not isinstance ( dtstarts [ 0 ] , datetime ) : vevent . add ( 'dtend' ) . value = dtstarts [ 0 ] + timedelta ( days = 1 ) | Generate an rdate or rrule from a list of dates and add it to the vevent |
5,724 | def _gen_vevent ( self , event , vevent ) : vevent . add ( 'dtstart' ) . value = event [ 'dtstart' ] [ 0 ] vevent . add ( 'dtstamp' ) . value = datetime . fromtimestamp ( self . _mtime ) vevent . add ( 'summary' ) . value = event [ 'msg' ] vevent . add ( 'uid' ) . value = event [ 'uid' ] if 'class' in event : vevent . add ( 'class' ) . value = event [ 'class' ] if 'categories' in event and len ( event [ 'categories' ] ) > 0 : vevent . add ( 'categories' ) . value = event [ 'categories' ] if 'location' in event : vevent . add ( 'location' ) . value = event [ 'location' ] if 'description' in event : vevent . add ( 'description' ) . value = event [ 'description' ] if isinstance ( event [ 'dtstart' ] [ 0 ] , datetime ) : if self . _alarm != timedelta ( ) : valarm = vevent . add ( 'valarm' ) valarm . add ( 'trigger' ) . value = self . _alarm valarm . add ( 'action' ) . value = 'DISPLAY' valarm . add ( 'description' ) . value = event [ 'msg' ] if 'duration' in event : vevent . add ( 'duration' ) . value = event [ 'duration' ] else : vevent . add ( 'dtend' ) . value = event [ 'dtstart' ] [ 0 ] elif len ( event [ 'dtstart' ] ) == 1 : vevent . add ( 'dtend' ) . value = event [ 'dtstart' ] [ 0 ] + timedelta ( days = 1 ) if len ( event [ 'dtstart' ] ) > 1 : Remind . _gen_dtend_rrule ( event [ 'dtstart' ] , vevent ) | Generate vevent from given event |
5,725 | def _update ( self ) : update = not self . _reminders with self . _lock : for fname in self . _reminders : if getmtime ( fname ) > self . _mtime : update = True break if update : self . _reminders = self . _parse_remind ( self . _filename ) | Reload Remind files if the mtime is newer |
5,726 | def get_uids ( self , filename = None ) : self . _update ( ) if filename : if filename not in self . _reminders : return [ ] return self . _reminders [ filename ] . keys ( ) return [ uid for uids in self . _reminders . values ( ) for uid in uids ] | UIDs of all reminders in the file excluding included files If a filename is specified only it s UIDs are return otherwise all . |
5,727 | def to_vobjects ( self , filename , uids = None ) : self . _update ( ) if not uids : uids = self . _reminders [ filename ] items = [ ] for uid in uids : cal = iCalendar ( ) self . _gen_vevent ( self . _reminders [ filename ] [ uid ] , cal . add ( 'vevent' ) ) etag = md5 ( ) etag . update ( self . _reminders [ filename ] [ uid ] [ 'line' ] . encode ( "utf-8" ) ) items . append ( ( uid , cal , '"%s"' % etag . hexdigest ( ) ) ) return items | Return iCal objects and etags of all Remind entries in uids |
5,728 | def to_vobject ( self , filename = None , uid = None ) : self . _update ( ) cal = iCalendar ( ) if uid : self . _gen_vevent ( self . _reminders [ filename ] [ uid ] , cal . add ( 'vevent' ) ) elif filename : for event in self . _reminders [ filename ] . values ( ) : self . _gen_vevent ( event , cal . add ( 'vevent' ) ) else : for filename in self . _reminders : for event in self . _reminders [ filename ] . values ( ) : self . _gen_vevent ( event , cal . add ( 'vevent' ) ) return cal | Return iCal object of Remind lines If filename and UID are specified the vObject only contains that event . If only a filename is specified the vObject contains all events in the file . Otherwise the vObject contains all all objects of all files associated with the Remind object . |
5,729 | def stdin_to_vobject ( self , lines ) : cal = iCalendar ( ) for event in self . _parse_remind ( '-' , lines ) [ '-' ] . values ( ) : self . _gen_vevent ( event , cal . add ( 'vevent' ) ) return cal | Return iCal object of the Remind commands in lines |
5,730 | def _parse_rruleset ( rruleset ) : if rruleset . _rrule [ 0 ] . _freq == 0 : return [ ] rep = [ ] if rruleset . _rrule [ 0 ] . _byweekday and len ( rruleset . _rrule [ 0 ] . _byweekday ) > 1 : rep . append ( '*1' ) elif rruleset . _rrule [ 0 ] . _freq == rrule . DAILY : rep . append ( '*%d' % rruleset . _rrule [ 0 ] . _interval ) elif rruleset . _rrule [ 0 ] . _freq == rrule . WEEKLY : rep . append ( '*%d' % ( 7 * rruleset . _rrule [ 0 ] . _interval ) ) else : return Remind . _parse_rdate ( rruleset . _rrule [ 0 ] ) if rruleset . _rrule [ 0 ] . _byweekday and len ( rruleset . _rrule [ 0 ] . _byweekday ) > 1 : daynums = set ( range ( 7 ) ) - set ( rruleset . _rrule [ 0 ] . _byweekday ) weekdays = [ 'Mon' , 'Tue' , 'Wed' , 'Thu' , 'Fri' , 'Sat' , 'Sun' ] days = [ weekdays [ day ] for day in daynums ] rep . append ( 'SKIP OMIT %s' % ' ' . join ( days ) ) if rruleset . _rrule [ 0 ] . _until : rep . append ( rruleset . _rrule [ 0 ] . _until . strftime ( 'UNTIL %b %d %Y' ) . replace ( ' 0' , ' ' ) ) elif rruleset . _rrule [ 0 ] . _count : rep . append ( rruleset [ - 1 ] . strftime ( 'UNTIL %b %d %Y' ) . replace ( ' 0' , ' ' ) ) return rep | Convert from iCal rrule to Remind recurrence syntax |
5,731 | def _event_duration ( vevent ) : if hasattr ( vevent , 'dtend' ) : return vevent . dtend . value - vevent . dtstart . value elif hasattr ( vevent , 'duration' ) and vevent . duration . value : return vevent . duration . value return timedelta ( 0 ) | unify dtend and duration to the duration of the given vevent |
5,732 | def to_remind ( self , vevent , label = None , priority = None , tags = None , tail = None , sep = " " , postdate = None , posttime = None ) : remind = [ 'REM' ] trigdates = None if hasattr ( vevent , 'rrule' ) : trigdates = Remind . _parse_rruleset ( vevent . rruleset ) dtstart = vevent . dtstart . value if isinstance ( dtstart , datetime ) and dtstart . tzinfo : dtstart = dtstart . astimezone ( self . _localtz ) dtend = None if hasattr ( vevent , 'dtend' ) : dtend = vevent . dtend . value if isinstance ( dtend , datetime ) and dtend . tzinfo : dtend = dtend . astimezone ( self . _localtz ) if not hasattr ( vevent , 'rdate' ) and not isinstance ( trigdates , str ) : remind . append ( dtstart . strftime ( '%b %d %Y' ) . replace ( ' 0' , ' ' ) ) if postdate : remind . append ( postdate ) if priority : remind . append ( 'PRIORITY %s' % priority ) if isinstance ( trigdates , list ) : remind . extend ( trigdates ) duration = Remind . _event_duration ( vevent ) if type ( dtstart ) is date and duration . days > 1 : remind . append ( '*1' ) if dtend is not None : dtend -= timedelta ( days = 1 ) remind . append ( dtend . strftime ( 'UNTIL %b %d %Y' ) . replace ( ' 0' , ' ' ) ) if isinstance ( dtstart , datetime ) : remind . append ( dtstart . strftime ( 'AT %H:%M' ) . replace ( ' 0' , ' ' ) ) if posttime : remind . append ( posttime ) if duration . total_seconds ( ) > 0 : remind . append ( 'DURATION %d:%02d' % divmod ( duration . total_seconds ( ) / 60 , 60 ) ) if hasattr ( vevent , 'rdate' ) : remind . append ( Remind . _parse_rdate ( vevent . rdate . value ) ) elif isinstance ( trigdates , str ) : remind . append ( trigdates ) if hasattr ( vevent , 'class' ) : remind . append ( 'TAG %s' % Remind . _abbr_tag ( vevent . getChildValue ( 'class' ) ) ) if tags : remind . extend ( [ 'TAG %s' % Remind . _abbr_tag ( tag ) for tag in tags ] ) if hasattr ( vevent , 'categories_list' ) : for categories in vevent . categories_list : for category in categories . value : remind . append ( 'TAG %s' % Remind . _abbr_tag ( category ) ) remind . append ( Remind . _gen_msg ( vevent , label , tail , sep ) ) return ' ' . join ( remind ) + '\n' | Generate a Remind command from the given vevent |
5,733 | def to_reminders ( self , ical , label = None , priority = None , tags = None , tail = None , sep = " " , postdate = None , posttime = None ) : if not hasattr ( ical , 'vevent_list' ) : return '' reminders = [ self . to_remind ( vevent , label , priority , tags , tail , sep , postdate , posttime ) for vevent in ical . vevent_list ] return '' . join ( reminders ) | Return Remind commands for all events of a iCalendar |
5,734 | def append_vobject ( self , ical , filename = None ) : if not filename : filename = self . _filename elif filename not in self . _reminders : return with self . _lock : outdat = self . to_reminders ( ical ) open ( filename , 'a' ) . write ( outdat ) return Remind . _get_uid ( outdat ) | Append a Remind command generated from the iCalendar to the file |
5,735 | def remove ( self , uid , filename = None ) : if not filename : filename = self . _filename elif filename not in self . _reminders : return uid = uid . split ( '@' ) [ 0 ] with self . _lock : rem = open ( filename ) . readlines ( ) for ( index , line ) in enumerate ( rem ) : if uid == md5 ( line [ : - 1 ] . encode ( 'utf-8' ) ) . hexdigest ( ) : del rem [ index ] open ( filename , 'w' ) . writelines ( rem ) break | Remove the Remind command with the uid from the file |
5,736 | def move_vobject ( self , uid , from_file , to_file ) : if from_file not in self . _reminders or to_file not in self . _reminders : return uid = uid . split ( '@' ) [ 0 ] with self . _lock : rem = open ( from_file ) . readlines ( ) for ( index , line ) in enumerate ( rem ) : if uid == md5 ( line [ : - 1 ] . encode ( 'utf-8' ) ) . hexdigest ( ) : del rem [ index ] open ( from_file , 'w' ) . writelines ( rem ) open ( to_file , 'a' ) . write ( line ) break | Move the Remind command with the uid from from_file to to_file |
5,737 | def expand_include ( filename ) : open_files = set ( ) def _expand_include_rec ( filename ) : if filename in open_files : raise RuntimeError ( 'Recursive include statement detected for ' 'file: ' + filename ) else : open_files . add ( filename ) with open ( filename ) as open_file : for line in open_file : line_stripped = line . strip ( ) . replace ( "//" , "#" ) if line_stripped . startswith ( '@include ' ) : inc_to_clean = line_stripped . split ( None , 1 ) [ 1 ] inc_filename = inc_to_clean . replace ( '"' , " " ) . strip ( ) for included_line in _expand_include_rec ( inc_filename ) : yield included_line else : yield line open_files . remove ( filename ) try : lines = [ ] for line in _expand_include_rec ( filename ) : lines . append ( line ) return '' . join ( lines ) except RuntimeError : return None | Expand the content of a file into a string . |
5,738 | def to_json ( self ) : self . logger . debug ( "Returning json info" ) individual_info = { 'family_id' : self . family , 'id' : self . individual_id , 'sex' : str ( self . sex ) , 'phenotype' : str ( self . phenotype ) , 'mother' : self . mother , 'father' : self . father , 'extra_info' : self . extra_info } return individual_info | Return the individual info in a dictionary for json . |
5,739 | def to_madeline ( self ) : self . logger . debug ( "Returning madeline info" ) if self . sex == 1 : madeline_gender = 'M' elif self . sex == 2 : madeline_gender = 'F' else : madeline_gender = '.' if self . father == '0' : madeline_father = '.' else : madeline_father = self . father if self . mother == '0' : madeline_mother = '.' else : madeline_mother = self . mother if self . phenotype == 1 : madeline_phenotype = 'U' elif self . phenotype == 2 : madeline_phenotype = 'A' else : madeline_phenotype = '.' return "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}" . format ( self . family , self . individual_id , madeline_gender , madeline_father , madeline_mother , madeline_phenotype , self . proband , self . consultand , self . alive ) | Return the individual info in a madeline formated string |
5,740 | def module_name_from_path ( folder_name , verbose = False ) : folder_name = folder_name . split ( '.pyc' ) [ 0 ] folder_name = folder_name . split ( '.py' ) [ 0 ] folder_name = os . path . normpath ( folder_name ) path = folder_name + '/' package = get_python_package ( path ) module = [ ] if verbose : print ( ( 'folder_name' , folder_name ) ) while True : path = os . path . dirname ( path ) module . append ( os . path . basename ( path ) ) if os . path . basename ( path ) == package : path = os . path . dirname ( path ) break if os . path . dirname ( path ) == path : path , module = None , None break if verbose : print ( ( 'path' , path , os . path . dirname ( path ) ) ) if verbose : print ( ( 'module' , module ) ) if verbose : print ( ( 'module' , module ) ) module . reverse ( ) module = '.' . join ( module ) return module , path | takes in a path to a folder or file and return the module path and the path to the module |
5,741 | def explore_package ( module_name ) : packages = [ ] loader = pkgutil . get_loader ( module_name ) for sub_module in pkgutil . walk_packages ( [ os . path . dirname ( loader . get_filename ( ) ) ] , prefix = module_name + '.' ) : _ , sub_module_name , _ = sub_module packages . append ( sub_module_name ) return packages | returns all the packages in the module |
5,742 | def generate_from_directory ( cls , directory ) : files = [ os . path . join ( directory , f ) for f in os . listdir ( directory ) if os . path . isfile ( os . path . join ( directory , f ) ) ] return cls ( files ) | Create a parser by defining which input files it will read from . |
5,743 | def get_density ( self ) : strc = self . get_output_structure ( ) density = sum ( strc . get_masses ( ) ) / strc . get_volume ( ) * 1.660539040 return Property ( scalars = [ Scalar ( value = density ) ] , units = "g/(cm^3)" ) | Compute the density from the output structure |
5,744 | def get_number_of_atoms ( self ) : strc = self . get_output_structure ( ) if not strc : return None return Property ( scalars = [ Scalar ( value = len ( strc ) ) ] , units = "/unit cell" ) | Get the number of atoms in the calculated structure . |
5,745 | def load_b26_file ( file_name ) : assert os . path . exists ( file_name ) with open ( file_name , 'r' ) as infile : data = yaml . safe_load ( infile ) return data | loads a . b26 file into a dictionary |
5,746 | def recv_message ( self , debug = False ) : if debug : packet = self . sock . recv ( 1024 ) hexdump ( packet ) packet_length_data = self . sock . recv ( 4 ) if len ( packet_length_data ) < 4 : raise Exception ( "Nothing in the socket!" ) packet_length = struct . unpack ( "<I" , packet_length_data ) [ 0 ] packet = self . sock . recv ( packet_length - 4 ) if not crc32 ( packet_length_data + packet [ 0 : - 4 ] ) == struct . unpack ( '<I' , packet [ - 4 : ] ) [ 0 ] : raise Exception ( "CRC32 was not correct!" ) x = struct . unpack ( "<I" , packet [ : 4 ] ) auth_key_id = packet [ 4 : 12 ] if auth_key_id == b'\x00\x00\x00\x00\x00\x00\x00\x00' : ( message_id , message_length ) = struct . unpack ( "<QI" , packet [ 12 : 24 ] ) data = packet [ 24 : 24 + message_length ] elif auth_key_id == self . auth_key_id : pass message_key = packet [ 12 : 28 ] encrypted_data = packet [ 28 : - 4 ] aes_key , aes_iv = self . aes_calculate ( message_key , direction = "from server" ) decrypted_data = crypt . ige_decrypt ( encrypted_data , aes_key , aes_iv ) assert decrypted_data [ 0 : 8 ] == self . server_salt assert decrypted_data [ 8 : 16 ] == self . session_id message_id = decrypted_data [ 16 : 24 ] seq_no = struct . unpack ( "<I" , decrypted_data [ 24 : 28 ] ) [ 0 ] message_data_length = struct . unpack ( "<I" , decrypted_data [ 28 : 32 ] ) [ 0 ] data = decrypted_data [ 32 : 32 + message_data_length ] else : raise Exception ( "Got unknown auth_key id" ) return data | Reading socket and receiving message from server . Check the CRC32 . |
5,747 | def get_category_lists ( self , init_kwargs = None , additional_parents_aliases = None ) : if self . _category_editor is not None : return self . _category_editor . get_lists ( ) from . toolbox import get_category_lists init_kwargs = init_kwargs or { } catlist_kwargs = { } if self . _category_lists_init_kwargs is not None : catlist_kwargs . update ( self . _category_lists_init_kwargs ) catlist_kwargs . update ( init_kwargs ) lists = get_category_lists ( catlist_kwargs , additional_parents_aliases , obj = self ) return lists | Returns a list of CategoryList objects associated with this model instance . |
5,748 | def enable_category_lists_editor ( self , request , editor_init_kwargs = None , additional_parents_aliases = None , lists_init_kwargs = None , handler_init_kwargs = None ) : from . toolbox import CategoryRequestHandler additional_parents_aliases = additional_parents_aliases or [ ] lists_init_kwargs = lists_init_kwargs or { } editor_init_kwargs = editor_init_kwargs or { } handler_init_kwargs = handler_init_kwargs or { } handler = CategoryRequestHandler ( request , self , ** handler_init_kwargs ) lists = self . get_category_lists ( init_kwargs = lists_init_kwargs , additional_parents_aliases = additional_parents_aliases ) handler . register_lists ( lists , lists_init_kwargs = lists_init_kwargs , editor_init_kwargs = editor_init_kwargs ) self . _category_editor = handler return handler . listen ( ) | Enables editor functionality for categories of this object . |
5,749 | def add_to_category ( self , category , user ) : init_kwargs = { 'category' : category , 'creator' : user , 'linked_object' : self } tie = self . categories . model ( ** init_kwargs ) tie . save ( ) return tie | Add this model instance to a category . |
5,750 | def remove_from_category ( self , category ) : ctype = ContentType . objects . get_for_model ( self ) self . categories . model . objects . filter ( category = category , content_type = ctype , object_id = self . id ) . delete ( ) | Removes this object from a given category . |
5,751 | def get_ties_for_categories_qs ( cls , categories , user = None , status = None ) : if not isinstance ( categories , list ) : categories = [ categories ] category_ids = [ ] for category in categories : if isinstance ( category , models . Model ) : category_ids . append ( category . id ) else : category_ids . append ( category ) filter_kwargs = { 'content_type' : ContentType . objects . get_for_model ( cls , for_concrete_model = False ) , 'category_id__in' : category_ids } if user is not None : filter_kwargs [ 'creator' ] = user if status is not None : filter_kwargs [ 'status' ] = status ties = get_tie_model ( ) . objects . filter ( ** filter_kwargs ) return ties | Returns a QuerySet of Ties for the given categories . |
5,752 | def get_from_category_qs ( cls , category ) : ids = cls . get_ties_for_categories_qs ( category ) . values_list ( 'object_id' ) . distinct ( ) filter_kwargs = { 'id__in' : [ i [ 0 ] for i in ids ] } return cls . objects . filter ( ** filter_kwargs ) | Returns a QuerySet of objects of this type associated with the given category . |
5,753 | def main ( ) : parser = argparse . ArgumentParser ( ) parser . add_argument ( "-f" , "--file" , required = True , help = "input file" , type = str ) parser . add_argument ( "-l" , "--locus" , required = True , help = "Locus" , type = str ) parser . add_argument ( "-k" , "--kir" , help = "Option for running with KIR" , action = 'store_true' ) parser . add_argument ( "-s" , "--server" , help = "Option for running with a server" , action = 'store_true' ) parser . add_argument ( "-v" , "--verbose" , help = "Option for running in verbose" , action = 'store_true' ) args = parser . parse_args ( ) fastafile = args . file locus = args . locus verbose = False if args . verbose : verbose = True verbose = False if args . verbose : verbose = True kir = False if args . kir : kir = True serv = False if args . server : serv = True if verbose : logging . basicConfig ( format = '%(asctime)s - %(name)-35s - %(levelname)-5s - %(message)s' , datefmt = '%m/%d/%Y %I:%M:%S %p' , level = logging . INFO ) server = None if serv : server = BioSeqDatabase . open_database ( driver = "pymysql" , user = "root" , passwd = "" , host = "localhost" , db = "bioseqdb" ) seqann = BioSeqAnn ( verbose = True , kir = kir ) for seq in SeqIO . parse ( fastafile , "fasta" ) : ann = seqann . annotate ( seq , locus = locus ) print ( '{:*^20} {:^20} {:*^20}' . format ( "" , str ( seq . description ) , "" ) ) l = 0 for f in ann . annotation : if isinstance ( ann . annotation [ f ] , DBSeq ) : print ( f , ann . method , str ( ann . annotation [ f ] ) , sep = "\t" ) l += len ( ann . annotation [ f ] ) else : print ( f , ann . method , str ( ann . annotation [ f ] . seq ) , sep = "\t" ) l += len ( ann . annotation [ f ] . seq ) print ( "" ) if serv : server . close ( ) | This is run if file is directly executed but not if imported as module . Having this in a separate function allows importing the file into interactive python and still able to execute the function for testing |
5,754 | def _push_subtree ( self , leaves : List [ bytes ] ) : size = len ( leaves ) if count_bits_set ( size ) != 1 : raise ValueError ( "invalid subtree with size != 2^k: %s" % size ) subtree_h , mintree_h = lowest_bit_set ( size ) , self . __mintree_height if mintree_h > 0 and subtree_h > mintree_h : raise ValueError ( "subtree %s > current smallest subtree %s" % ( subtree_h , mintree_h ) ) root_hash , hashes = self . __hasher . _hash_full ( leaves , 0 , size ) assert hashes == ( root_hash , ) if self . hashStore : for h in hashes : self . hashStore . writeLeaf ( h ) new_node_hashes = self . __push_subtree_hash ( subtree_h , root_hash ) nodes = [ ( self . tree_size , height , h ) for h , height in new_node_hashes ] if self . hashStore : for node in nodes : self . hashStore . writeNode ( node ) | Extend with a full subtree < = the current minimum subtree . |
5,755 | def resolve ( obj , pointer , registry = None ) : registry = LocalRegistry ( obj , registry or { } ) local = DocumentPointer ( pointer ) if local . document : registry [ local . document ] = obj local . document = '<local>' return registry . resolve ( local ) | resolve a local object |
5,756 | def addUrlScheme ( self , url ) : if not isinstance ( url , str ) : raise TypeError ( 'url must be a string value' ) if not url in self . _urlSchemes : self . _urlSchemes [ url ] = OEmbedUrlScheme ( url ) | Add a url scheme to this endpoint . It takes a url string and create the OEmbedUrlScheme object internally . |
5,757 | def match ( self , url ) : try : urlSchemes = self . _urlSchemes . itervalues ( ) except AttributeError : urlSchemes = self . _urlSchemes . values ( ) for urlScheme in urlSchemes : if urlScheme . match ( url ) : return True return False | Try to find if url matches against any of the schemes within this endpoint . |
5,758 | def request ( self , url , ** opt ) : params = opt params [ 'url' ] = url urlApi = self . _urlApi if 'format' in params and self . _implicitFormat : urlApi = self . _urlApi . replace ( '{format}' , params [ 'format' ] ) del params [ 'format' ] if '?' in urlApi : return "%s&%s" % ( urlApi , urllib . urlencode ( params ) ) else : return "%s?%s" % ( urlApi , urllib . urlencode ( params ) ) | Format the input url and optional parameters and provides the final url where to get the given resource . |
5,759 | def get ( self , url , ** opt ) : return self . fetch ( self . request ( url , ** opt ) ) | Convert the resource url to a complete url and then fetch the data from it . |
5,760 | def fetch ( self , url ) : opener = self . _urllib . build_opener ( ) opener . addheaders = self . _requestHeaders . items ( ) response = opener . open ( url ) headers = response . info ( ) raw = response . read ( ) raw = raw . decode ( 'utf8' ) if not 'Content-Type' in headers : raise OEmbedError ( 'Missing mime-type in response' ) if headers [ 'Content-Type' ] . find ( 'application/xml' ) != - 1 or headers [ 'Content-Type' ] . find ( 'text/xml' ) != - 1 : response = OEmbedResponse . newFromXML ( raw ) elif headers [ 'Content-Type' ] . find ( 'application/json' ) != - 1 or headers [ 'Content-Type' ] . find ( 'text/javascript' ) != - 1 or headers [ 'Content-Type' ] . find ( 'text/json' ) != - 1 : response = OEmbedResponse . newFromJSON ( raw ) else : raise OEmbedError ( 'Invalid mime-type in response - %s' % headers [ 'Content-Type' ] ) return response | Fetch url and create a response object according to the mime - type . |
5,761 | def embed ( self , url , format = 'json' , ** opt ) : if format not in [ 'json' , 'xml' ] : raise OEmbedInvalidRequest ( 'Format must be json or xml' ) opt [ 'format' ] = format return self . _request ( url , ** opt ) | Get an OEmbedResponse from one of the providers configured in this consumer according to the resource url . |
5,762 | def connect ( portname , baudrate ) : global SERPORT try : SERPORT = serial . Serial ( portname , baudrate , timeout = 0.1 ) except : raise HerkulexError ( "could not open the serial port" ) | Connect to the Herkulex bus |
5,763 | def checksum1 ( data , stringlength ) : value_buffer = 0 for count in range ( 0 , stringlength ) : value_buffer = value_buffer ^ data [ count ] return value_buffer & 0xFE | Calculate Checksum 1 |
5,764 | def send_data ( data ) : datalength = len ( data ) csm1 = checksum1 ( data , datalength ) csm2 = checksum2 ( csm1 ) data . insert ( 0 , 0xFF ) data . insert ( 1 , 0xFF ) data . insert ( 5 , csm1 ) data . insert ( 6 , csm2 ) stringtosend = "" for i in range ( len ( data ) ) : byteformat = '%02X' % data [ i ] stringtosend = stringtosend + "\\x" + byteformat try : SERPORT . write ( stringtosend . decode ( 'string-escape' ) ) except : raise HerkulexError ( "could not communicate with motors" ) | Send data to herkulex |
5,765 | def clear_errors ( ) : data = [ ] data . append ( 0x0B ) data . append ( BROADCAST_ID ) data . append ( RAM_WRITE_REQ ) data . append ( STATUS_ERROR_RAM ) data . append ( BYTE2 ) data . append ( 0x00 ) data . append ( 0x00 ) send_data ( data ) | Clears the errors register of all Herkulex servos |
5,766 | def scale ( input_value , input_min , input_max , out_min , out_max ) : input_span = input_max - input_min output_span = out_max - out_min valuescaled = float ( input_value - input_min ) / float ( input_span ) return out_min + ( valuescaled * output_span ) | scale a value from one range to another |
5,767 | def scan_servos ( ) : servos = [ ] for servo_id in range ( 0x00 , 0xFE ) : model = get_model ( servo_id ) if model : servos += [ ( servo_id , model ) ] return servos | Scan for the herkulex servos connected |
5,768 | def get_model ( servoid ) : data = [ ] data . append ( 0x09 ) data . append ( servoid ) data . append ( EEP_READ_REQ ) data . append ( MODEL_NO1_EEP ) data . append ( BYTE1 ) send_data ( data ) rxdata = [ ] try : rxdata = SERPORT . read ( 12 ) return ord ( rxdata [ 9 ] ) & 0xFF except : raise HerkulexError ( "could not communicate with motors" ) | Get the servo model |
5,769 | def get_servo_status ( self ) : data = [ ] data . append ( 0x09 ) data . append ( self . servoid ) data . append ( RAM_READ_REQ ) data . append ( STATUS_ERROR_RAM ) data . append ( BYTE1 ) send_data ( data ) rxdata = [ ] try : rxdata = SERPORT . read ( 12 ) return ord ( rxdata [ 9 ] ) & 0xFF except : raise HerkulexError ( "could not communicate with motors" ) | Get the error status of servo |
5,770 | def get_servo_status_detail ( self ) : data = [ ] data . append ( 0x09 ) data . append ( self . servoid ) data . append ( RAM_READ_REQ ) data . append ( STATUS_DETAIL_RAM ) data . append ( BYTE1 ) send_data ( data ) rxdata = [ ] try : rxdata = SERPORT . read ( 12 ) return ord ( rxdata [ 9 ] ) & 0xFF except HerkulexError : raise HerkulexError ( "could not communicate with motors" ) | Get the detailed error status of servo |
5,771 | def set_led ( self , colorcode ) : data = [ ] data . append ( 0x0A ) data . append ( self . servoid ) data . append ( RAM_WRITE_REQ ) data . append ( LED_CONTROL_RAM ) data . append ( 0x01 ) data . append ( colorcode ) send_data ( data ) | Set the LED Color of Herkulex |
5,772 | def brake_on ( self ) : data = [ ] data . append ( 0x0A ) data . append ( self . servoid ) data . append ( RAM_WRITE_REQ ) data . append ( TORQUE_CONTROL_RAM ) data . append ( 0x01 ) data . append ( 0x40 ) send_data ( data ) | Set the Brakes of Herkulex |
5,773 | def torque_off ( self ) : data = [ ] data . append ( 0x0A ) data . append ( self . servoid ) data . append ( RAM_WRITE_REQ ) data . append ( TORQUE_CONTROL_RAM ) data . append ( 0x01 ) data . append ( 0x00 ) send_data ( data ) | Set the torques of Herkulex to zero |
5,774 | def torque_on ( self ) : data = [ ] data . append ( 0x0A ) data . append ( self . servoid ) data . append ( RAM_WRITE_REQ ) data . append ( TORQUE_CONTROL_RAM ) data . append ( 0x01 ) data . append ( 0x60 ) send_data ( data ) | Enable the torques of Herkulex |
5,775 | def get_torque_state ( self ) : data = [ ] data . append ( 0x09 ) data . append ( self . servoid ) data . append ( RAM_READ_REQ ) data . append ( TORQUE_CONTROL_RAM ) data . append ( BYTE2 ) send_data ( data ) rxdata = [ ] try : rxdata = SERPORT . read ( 13 ) return bool ( ord ( rxdata [ 9 ] ) ) except HerkulexError : raise HerkulexError ( "could not communicate with motors" ) | get the torque state of motor |
5,776 | def set_servo_position ( self , goalposition , goaltime , led ) : goalposition_msb = int ( goalposition ) >> 8 goalposition_lsb = int ( goalposition ) & 0xff data = [ ] data . append ( 0x0C ) data . append ( self . servoid ) data . append ( I_JOG_REQ ) data . append ( goalposition_lsb ) data . append ( goalposition_msb ) data . append ( led ) data . append ( self . servoid ) data . append ( goaltime ) send_data ( data ) | Set the position of Herkulex |
5,777 | def get_servo_position ( self ) : data = [ ] data . append ( 0x09 ) data . append ( self . servoid ) data . append ( RAM_READ_REQ ) data . append ( CALIBRATED_POSITION_RAM ) data . append ( BYTE2 ) send_data ( data ) rxdata = [ ] try : rxdata = SERPORT . read ( 13 ) if ( self . servomodel == 0x06 ) or ( self . servomodel == 0x04 ) : return ( ( ord ( rxdata [ 10 ] ) & 0xff ) << 8 ) | ( ord ( rxdata [ 9 ] ) & 0xFF ) else : return ( ( ord ( rxdata [ 10 ] ) & 0x03 ) << 8 ) | ( ord ( rxdata [ 9 ] ) & 0xFF ) except HerkulexError : print "Could not read from the servos. Check connection" | Gets the current position of Herkulex |
5,778 | def get_servo_temperature ( self ) : data = [ ] data . append ( 0x09 ) data . append ( self . servoid ) data . append ( RAM_READ_REQ ) data . append ( TEMPERATURE_RAM ) data . append ( BYTE2 ) send_data ( data ) rxdata = [ ] try : rxdata = SERPORT . read ( 13 ) return ord ( rxdata [ 9 ] ) except HerkulexError : raise HerkulexError ( "Could not communicate with motors" ) | Gets the current temperature of Herkulex |
5,779 | def get_servo_torque ( self ) : data = [ ] data . append ( 0x09 ) data . append ( self . servoid ) data . append ( RAM_READ_REQ ) data . append ( PWM_RAM ) data . append ( BYTE2 ) send_data ( data ) rxdata = [ ] try : rxdata = SERPORT . read ( 13 ) if ord ( rxdata [ 10 ] ) <= 127 : return ( ( ord ( rxdata [ 10 ] ) & 0x03 ) << 8 ) | ( ord ( rxdata [ 9 ] ) & 0xFF ) else : return ( ord ( rxdata [ 10 ] ) - 0xFF ) * 0xFF + ( ord ( rxdata [ 9 ] ) & 0xFF ) - 0xFF except HerkulexError : raise HerkulexError ( "could not communicate with motors" ) | Gets the current torque of Herkulex |
5,780 | def set_servo_speed ( self , goalspeed , led ) : if goalspeed > 0 : goalspeed_msb = ( int ( goalspeed ) & 0xFF00 ) >> 8 goalspeed_lsb = int ( goalspeed ) & 0xff elif goalspeed < 0 : goalspeed_msb = 64 + ( 255 - ( ( int ( goalspeed ) & 0xFF00 ) >> 8 ) ) goalspeed_lsb = ( abs ( goalspeed ) & 0xff ) data = [ ] data . append ( 0x0C ) data . append ( self . servoid ) data . append ( I_JOG_REQ ) data . append ( goalspeed_lsb ) data . append ( goalspeed_msb ) data . append ( 0x02 | led ) data . append ( self . servoid ) data . append ( 0x00 ) send_data ( data ) | Set the Herkulex in continuous rotation mode |
5,781 | def set_position_p ( self , pvalue ) : pvalue_msb = int ( pvalue ) >> 8 pvalue_lsb = int ( pvalue ) & 0xff data = [ ] data . append ( 0x0B ) data . append ( self . servoid ) data . append ( RAM_WRITE_REQ ) data . append ( POSITION_KP_RAM ) data . append ( BYTE2 ) data . append ( pvalue_lsb ) data . append ( pvalue_msb ) send_data ( data ) | Set the P gain of the position PID |
5,782 | def set_position_i ( self , ivalue ) : ivalue_msb = int ( ivalue ) >> 8 ivalue_lsb = int ( ivalue ) & 0xff data = [ ] data . append ( 0x0B ) data . append ( self . servoid ) data . append ( RAM_WRITE_REQ ) data . append ( POSITION_KI_RAM ) data . append ( BYTE2 ) data . append ( ivalue_lsb ) data . append ( ivalue_msb ) send_data ( data ) | Set the I gain of the position PID |
5,783 | def set_position_d ( self , dvalue ) : dvalue_msb = int ( dvalue ) >> 8 dvalue_lsb = int ( dvalue ) & 0xff data = [ ] data . append ( 0x0B ) data . append ( self . servoid ) data . append ( RAM_WRITE_REQ ) data . append ( POSITION_KD_RAM ) data . append ( BYTE2 ) data . append ( dvalue_lsb ) data . append ( dvalue_msb ) send_data ( data ) | Set the D gain of the PID |
5,784 | def get_position_p ( self ) : data = [ ] data . append ( 0x09 ) data . append ( self . servoid ) data . append ( RAM_READ_REQ ) data . append ( POSITION_KP_RAM ) data . append ( BYTE2 ) send_data ( data ) rxdata = [ ] try : rxdata = SERPORT . read ( 13 ) return ( ord ( rxdata [ 10 ] ) * 256 ) + ( ord ( rxdata [ 9 ] ) & 0xff ) except HerkulexError : raise HerkulexError ( "could not communicate with motors" ) | Get the P value of the current PID for position |
5,785 | def get_position_i ( self ) : data = [ ] data . append ( 0x09 ) data . append ( self . servoid ) data . append ( RAM_READ_REQ ) data . append ( POSITION_KI_RAM ) data . append ( BYTE2 ) send_data ( data ) rxdata = [ ] try : rxdata = SERPORT . read ( 13 ) return ( ord ( rxdata [ 10 ] ) * 256 ) + ( ord ( rxdata [ 9 ] ) & 0xff ) except HerkulexError : raise HerkulexError ( "Could not read from motors" ) | Get the I value of the current PID for position |
5,786 | def get_position_d ( self ) : data = [ ] data . append ( 0x09 ) data . append ( self . servoid ) data . append ( RAM_READ_REQ ) data . append ( POSITION_KD_RAM ) data . append ( BYTE2 ) send_data ( data ) rxdata = [ ] try : rxdata = SERPORT . read ( 13 ) return ( ord ( rxdata [ 10 ] ) * 256 ) + ( ord ( rxdata [ 9 ] ) & 0xff ) except HerkulexError : raise HerkulexError ( "could not communicate with motors" ) | Get the D value of the current PID for position |
5,787 | def save_pid_eeprom ( self ) : pval = self . get_position_p ( ) ival = self . get_position_i ( ) dval = self . get_position_d ( ) pvalue_msb = int ( pval ) >> 8 pvalue_lsb = int ( pval ) & 0xff data_p = [ ] data_p . append ( 0x0B ) data_p . append ( self . servoid ) data_p . append ( EEP_WRITE_REQ ) data_p . append ( POSITION_KP_EEP ) data_p . append ( BYTE2 ) data_p . append ( pvalue_lsb ) data_p . append ( pvalue_msb ) send_data ( data_p ) ivalue_msb = int ( ival ) >> 8 ivalue_lsb = int ( ival ) & 0xff data_i = [ ] data_i . append ( 0x0B ) data_i . append ( self . servoid ) data_i . append ( EEP_WRITE_REQ ) data_i . append ( POSITION_KI_EEP ) data_i . append ( BYTE2 ) data_i . append ( ivalue_lsb ) data_i . append ( ivalue_msb ) send_data ( data_i ) dvalue_msb = int ( dval ) >> 8 dvalue_lsb = int ( dval ) & 0xff data_d = [ ] data_d . append ( 0x0B ) data_d . append ( self . servoid ) data_d . append ( EEP_WRITE_REQ ) data_d . append ( POSITION_KD_EEP ) data_d . append ( BYTE2 ) data_d . append ( dvalue_lsb ) data_d . append ( dvalue_msb ) send_data ( data_d ) | saves the PID values from RAM to EEPROM |
5,788 | def get_servo_angle ( self ) : servoposition = self . get_servo_position ( ) if ( self . servomodel == 0x06 ) or ( self . servomodel == 0x04 ) : return scale ( servoposition , 10627 , 22129 , - 159.9 , 159.6 ) else : return scale ( servoposition , 21 , 1002 , - 150 , 150 ) | Gets the current angle of the servo in degrees |
5,789 | def disable_logging ( func ) : return func handler = logging . NullHandler ( ) @ wraps ( func ) def wrapper ( * args , ** kwargs ) : logger = logging . getLogger ( ) logger . addHandler ( handler ) resp = func ( * args , ** kwargs ) logger . removeHandler ( handler ) return resp return wrapper | Temporary disable logging . |
5,790 | def format_output ( func ) : return func @ wraps ( func ) def wrapper ( * args , ** kwargs ) : try : response = func ( * args , ** kwargs ) except Exception as error : print ( colored ( error , 'red' ) , file = sys . stderr ) sys . exit ( 1 ) else : print ( response ) sys . exit ( 0 ) return wrapper | Format output . |
5,791 | def start ( self , * args , ** kwargs ) : self . _stop = False super ( ReadProbes , self ) . start ( * args , ** kwargs ) | start the read_probe thread |
5,792 | def quit ( self , * args , ** kwargs ) : self . _stop = True super ( ReadProbes , self ) . quit ( * args , ** kwargs ) | quit the read_probe thread |
5,793 | def _set_current_subscript ( self , active ) : current_subscript = self . sender ( ) if active : for subscript_name in list ( self . _current_subscript_stage [ 'subscript_exec_count' ] . keys ( ) ) : if subscript_name == current_subscript . name : self . _current_subscript_stage [ 'subscript_exec_count' ] [ subscript_name ] += 1 self . _current_subscript_stage [ 'current_subscript' ] = current_subscript else : self . _current_subscript_stage [ 'current_subscript' ] = current_subscript for subscript_name in list ( self . _current_subscript_stage [ 'subscript_exec_count' ] . keys ( ) ) : if subscript_name == current_subscript . name : duration = current_subscript . end_time - current_subscript . start_time if subscript_name in self . _current_subscript_stage [ 'subscript_exec_duration' ] : duration_old = self . _current_subscript_stage [ 'subscript_exec_duration' ] [ subscript_name ] else : duration_old = datetime . timedelta ( 0 ) exec_count = self . _current_subscript_stage [ 'subscript_exec_count' ] [ subscript_name ] duration_new = ( duration_old * ( exec_count - 1 ) + duration ) self . _current_subscript_stage [ 'subscript_exec_duration' ] [ subscript_name ] = ( duration_old * ( exec_count - 1 ) + duration ) / exec_count | sets the current subscript and keeps a counter of how ofter a particular subscript has been executed this information is usefull when implementing a status update or plotting functions that depend on which subscript is being executed |
5,794 | def remaining_time ( self ) : elapsed_time = ( datetime . datetime . now ( ) - self . start_time ) . total_seconds ( ) if self . progress == 0 : self . progress = 1 estimated_total_time = 100. / self . progress * elapsed_time return datetime . timedelta ( seconds = max ( estimated_total_time - elapsed_time , 0 ) ) | estimates the time remaining until script is finished |
5,795 | def stop ( self ) : for subscript in list ( self . scripts . values ( ) ) : subscript . stop ( ) print ( ( '--- stopping: ' , self . name ) ) self . _abort = True | stops itself and all the subscript |
5,796 | def get_script_module ( script_information , package = 'pylabcontrol' , verbose = False ) : module , _ , _ , _ , _ , _ , _ = Script . get_script_information ( script_information = script_information , package = package , verbose = verbose ) return module | wrapper to get the module for a script |
5,797 | def duplicate ( self ) : class_of_script = self . __class__ script_name = self . name script_instruments = self . instruments sub_scripts = self . scripts script_settings = self . settings log_function = self . log_function data_path = self . data_path class_creation_string = '' if script_instruments != { } : class_creation_string += ', instruments = script_instruments' if sub_scripts != { } : class_creation_string += ', scripts = sub_scripts' if script_settings != { } : class_creation_string += ', settings = script_settings' if log_function is not None : class_creation_string += ', log_function = log_function' if data_path is not None : class_creation_string += ', data_path = data_path' class_creation_string = 'class_of_script(name=script_name{:s})' . format ( class_creation_string ) script_instance = eval ( class_creation_string ) script_instance . data = deepcopy ( self . data ) script_instance . start_time = self . start_time script_instance . end_time = self . end_time script_instance . is_running = self . is_running return script_instance | create an copy of the script |
5,798 | def plot_validate ( self , figure_list ) : axes_list = self . get_axes_layout_validate ( figure_list ) self . _plot_validate ( axes_list ) | plots the data contained in self . data which should be a dictionary or a deque of dictionaries for the latter use the last entry |
5,799 | def uniqueof20 ( k , rep = 10000 ) : alphabet = 'ACDEFGHIKLMNPQRSTVWY' reps = [ len ( set ( random . choice ( alphabet ) for i in range ( k ) ) ) for j in range ( rep ) ] return sum ( reps ) / len ( reps ) | Sample k times out of alphabet how many different? |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.