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KaiLv
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UDR_Python

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def rem2ics ( ) : # pylint: disable=maybe-no-member 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
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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
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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 : # There is a race condition with the remind call above here. # This could be solved by parsing the remind -de output, # but I don't see an easy way to do that. 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 # Find included files without reminders and add them to the file list 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
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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
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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
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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 ) ) # temporary set dtstart to a different date, so it's not # removed from rset by python-vobject works around bug in # Android: # https://github.com/rfc2822/davdroid/issues/340 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
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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
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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
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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 .
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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
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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 .
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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
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def _parse_rruleset ( rruleset ) : # pylint: disable=protected-access 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
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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
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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 we don't get timezone information, handle it as a naive datetime. # See https://github.com/jspricke/python-remind/issues/2 for reference. 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
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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
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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
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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
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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
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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 .
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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 .
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def to_madeline ( self ) : #Convert sex to madeleine type self . logger . debug ( "Returning madeline info" ) if self . sex == 1 : madeline_gender = 'M' elif self . sex == 2 : madeline_gender = 'F' else : madeline_gender = '.' #Convert father to madeleine type if self . father == '0' : madeline_father = '.' else : madeline_father = self . father #Convert mother to madeleine type if self . mother == '0' : madeline_mother = '.' else : madeline_mother = self . mother #Convert phenotype to madeleine type 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
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def module_name_from_path ( folder_name , verbose = False ) : # strip off endings 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 ) # path = folder_name module = [ ] if verbose : print ( ( 'folder_name' , folder_name ) ) # os_sys_path = os.sys.path # # if os.path.normpath(path) in os_sys_path: # if verbose: # print('warning: path in sys.path!') # os_sys_path.remove(os.path.normpath(path)) # # # if verbose: # for elem in os_sys_path: # # print('os.sys.path', elem) 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 # failed to identify the module if os . path . dirname ( path ) == path : path , module = None , None break if verbose : print ( ( 'path' , path , os . path . dirname ( path ) ) ) # if path == os.path.dirname(path): # if verbose: # print('break -- os.path.dirname(path)', os.path.dirname(path)) # # path, module = None, None # break # if verbose : print ( ( 'module' , module ) ) # OLD START # while path not in os_sys_path: # path = os.path.dirname(path) # # if verbose: # print('path', path, os.path.dirname(path)) # # if path == os.path.dirname(path): # if verbose: # print('break -- os.path.dirname(path)', os.path.dirname(path)) # # path, module = None, None # break # module.append(os.path.basename(path)) # # if verbose: # print('module', module) # OLD END if verbose : print ( ( 'module' , module ) ) # module = module[:-1] # print('mod', module) # from the list construct the path like b26_toolkit.pylabcontrol.scripts and load it 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
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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
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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 .
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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
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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 .
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def load_b26_file ( file_name ) : # file_name = "Z:\Lab\Cantilever\Measurements\\tmp_\\a" 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
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def recv_message ( self , debug = False ) : if debug : packet = self . sock . recv ( 1024 ) # reads how many bytes to read hexdump ( packet ) packet_length_data = self . sock . recv ( 4 ) # reads how many bytes to read 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 ) # read the rest of bytes from socket # check the CRC32 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' : # No encryption - Plain text ( 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 .
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def get_category_lists ( self , init_kwargs = None , additional_parents_aliases = None ) : if self . _category_editor is not None : # Return editor lists instead of plain lists if it's enabled. 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 .
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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 # Set link to handler to mutate get_category_lists() behaviour. return handler . listen ( )
Enables editor functionality for categories of this object .
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def add_to_category ( self , category , user ) : init_kwargs = { 'category' : category , 'creator' : user , 'linked_object' : self } tie = self . categories . model ( * * init_kwargs ) # That's a model of Tie. tie . save ( ) return tie
Add this model instance to a category .
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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 .
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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 .
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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 .
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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
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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 ) # in general we want the highest bit, but here it's also the lowest bit # so just reuse that code instead of writing a new highest_bit_set() 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 .
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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
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def addUrlScheme ( self , url ) : #@TODO: validate invalid url format according to http://oembed.com/ 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 .
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def match ( self , url ) : try : urlSchemes = self . _urlSchemes . itervalues ( ) # Python 2 except AttributeError : urlSchemes = self . _urlSchemes . values ( ) # Python 3 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 .
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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 .
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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 .
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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 .
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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 .
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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
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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
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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' ) ) #print stringtosend except : raise HerkulexError ( "could not communicate with motors" )
Send data to herkulex
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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
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def scale ( input_value , input_min , input_max , out_min , out_max ) : # Figure out how 'wide' each range is input_span = input_max - input_min output_span = out_max - out_min # Convert the left range into a 0-1 range (float) valuescaled = float ( input_value - input_min ) / float ( input_span ) # Convert the 0-1 range into a value in the right range. return out_min + ( valuescaled * output_span )
scale a value from one range to another
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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def get_servo_position ( self ) : #global SERPORT 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 : #print ord(rxdata[9]),ord(rxdata[10]) 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
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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
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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
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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 ) #print goalspeed_msb,goalspeed_lsb 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
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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
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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
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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
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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
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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
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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
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def save_pid_eeprom ( self ) : pval = self . get_position_p ( ) ival = self . get_position_i ( ) dval = self . get_position_d ( ) #write P value 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 ) # write I value 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 ) # write D value 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
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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
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5,771
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 .
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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 .
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def start ( self , * args , * * kwargs ) : self . _stop = False super ( ReadProbes , self ) . start ( * args , * * kwargs )
start the read_probe thread
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def quit ( self , * args , * * kwargs ) : # real signature unknown self . _stop = True super ( ReadProbes , self ) . quit ( * args , * * kwargs )
quit the read_probe thread
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5,775
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 ( ) ) : # calculate the average duration to execute the subscript 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
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def remaining_time ( self ) : elapsed_time = ( datetime . datetime . now ( ) - self . start_time ) . total_seconds ( ) # safety to avoid devision by zero 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
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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
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5,778
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
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def duplicate ( self ) : # get settings of script 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 #create a new instance of same script type 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 ) # create instance script_instance = eval ( class_creation_string ) # copy some other properties that might be checked later for the duplicated script 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
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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
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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?
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def extract ( obj , pointer , bypass_ref = False ) : return Pointer ( pointer ) . extract ( obj , bypass_ref )
Extract member or element of obj according to pointer .
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def aa_counts ( aln , weights = None , gap_chars = '-.' ) : if weights is None : counts = Counter ( ) for rec in aln : seq_counts = Counter ( str ( rec . seq ) ) counts . update ( seq_counts ) else : if weights == True : # For convenience weights = sequence_weights ( aln ) else : assert len ( weights ) == len ( aln ) , ( "Length mismatch: weights = %d, alignment = %d" % ( len ( weights ) , len ( aln ) ) ) counts = defaultdict ( float ) for col in zip ( * aln ) : for aa , wt in zip ( col , weights ) : counts [ aa ] += wt # Don't count gaps for gap_char in gap_chars : if gap_char in counts : del counts [ gap_char ] return counts
Calculate the amino acid frequencies in a set of SeqRecords .
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def aa_frequencies ( aln , weights = None , gap_chars = '-.' ) : counts = aa_counts ( aln , weights , gap_chars ) # Reduce to frequencies scale = 1.0 / sum ( counts . values ( ) ) return dict ( ( aa , cnt * scale ) for aa , cnt in counts . iteritems ( ) )
Frequency of each residue type in an alignment .
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def blocks ( aln , threshold = 0.5 , weights = None ) : assert len ( aln ) if weights == False : def pct_nongaps ( col ) : return 1 - ( float ( col . count ( '-' ) ) / len ( col ) ) else : if weights in ( None , True ) : weights = sequence_weights ( aln , 'avg1' ) def pct_nongaps ( col ) : assert len ( col ) == len ( weights ) ngaps = sum ( wt * ( c == '-' ) for wt , c in zip ( weights , col ) ) return 1 - ( ngaps / len ( col ) ) seqstrs = [ str ( rec . seq ) for rec in aln ] clean_cols = [ col for col in zip ( * seqstrs ) if pct_nongaps ( col ) >= threshold ] alphabet = aln [ 0 ] . seq . alphabet clean_seqs = [ Seq ( '' . join ( row ) , alphabet ) for row in zip ( * clean_cols ) ] clean_recs = [ ] for rec , seq in zip ( aln , clean_seqs ) : newrec = deepcopy ( rec ) newrec . seq = seq clean_recs . append ( newrec ) return MultipleSeqAlignment ( clean_recs , alphabet = alphabet )
Remove gappy columns from an alignment .
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def col_counts ( col , weights = None , gap_chars = '-.' ) : cnt = defaultdict ( float ) for aa , wt in zip ( col , weights ) : if aa not in gap_chars : cnt [ aa ] += wt return cnt
Absolute counts of each residue type in a single column .
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def remove_empty_cols ( records ) : # In case it's a generator, turn it into a list records = list ( records ) seqstrs = [ str ( rec . seq ) for rec in records ] clean_cols = [ col for col in zip ( * seqstrs ) if not all ( c == '-' for c in col ) ] clean_seqs = [ '' . join ( row ) for row in zip ( * clean_cols ) ] for rec , clean_seq in zip ( records , clean_seqs ) : yield SeqRecord ( Seq ( clean_seq , rec . seq . alphabet ) , id = rec . id , name = rec . name , description = rec . description , dbxrefs = rec . dbxrefs , features = rec . features , annotations = rec . annotations , letter_annotations = rec . letter_annotations )
Remove all - gap columns from aligned SeqRecords .
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def to_graph ( alnfname , weight_func ) : import networkx G = networkx . Graph ( ) aln = AlignIO . read ( alnfname , 'fasta' ) for i , arec in enumerate ( aln ) : for brec in aln [ i + 1 : ] : ident = weight_func ( str ( arec . seq ) , str ( brec . seq ) ) G . add_edge ( arec . id , brec . id , weight = ident ) return G
Create a NetworkX graph from a sequence alignment .
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def guidance_UV ( index ) : if 0 < index < 3 : guidance = "Low exposure. No protection required. You can safely stay outside" elif 2 < index < 6 : guidance = "Moderate exposure. Seek shade during midday hours, cover up and wear sunscreen" elif 5 < index < 8 : guidance = "High exposure. Seek shade during midday hours, cover up and wear sunscreen" elif 7 < index < 11 : guidance = "Very high. Avoid being outside during midday hours. Shirt, sunscreen and hat are essential" elif index > 10 : guidance = "Extreme. Avoid being outside during midday hours. Shirt, sunscreen and hat essential." else : guidance = None return guidance
Return Met Office guidance regarding UV exposure based on UV index
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def parse_sitelist ( sitelist ) : sites = [ ] for site in sitelist [ "Locations" ] [ "Location" ] : try : ident = site [ "id" ] name = site [ "name" ] except KeyError : ident = site [ "@id" ] # Difference between loc-spec and text for some reason name = site [ "@name" ] if "latitude" in site : lat = float ( site [ "latitude" ] ) lon = float ( site [ "longitude" ] ) else : lat = lon = None s = Site ( ident , name , lat , lon ) sites . append ( s ) return sites
Return list of Site instances from retrieved sitelist data
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def _query ( self , data_category , resource_category , field , request , step , isotime = None ) : rest_url = "/" . join ( [ HOST , data_category , resource_category , field , DATA_TYPE , request ] ) query_string = "?" + "&" . join ( [ "res=" + step , "time=" + isotime if isotime is not None else "" , "key=" + self . key ] ) url = rest_url + query_string page = url_lib . urlopen ( url ) pg = page . read ( ) return pg
Request and return data from DataPoint RESTful API .
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def stand_alone_imagery ( self ) : return json . loads ( self . _query ( IMAGE , FORECAST , SURFACE_PRESSURE , CAPABILITIES , "" ) . decode ( errors = "replace" ) )
Returns capabilities data for stand alone imagery and includes URIs for the images .
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def map_overlay_forecast ( self ) : return json . loads ( self . _query ( LAYER , FORECAST , ALL , CAPABILITIES , "" ) . decode ( errors = "replace" ) )
Returns capabilities data for forecast map overlays .
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def map_overlay_obs ( self ) : return json . loads ( self . _query ( LAYER , OBSERVATIONS , ALL , CAPABILITIES , "" ) . decode ( errors = "replace" ) )
Returns capabilities data for observation map overlays .
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def load_and_append ( instrument_dict , instruments = None , raise_errors = False ) : if instruments is None : instruments = { } updated_instruments = { } updated_instruments . update ( instruments ) loaded_failed = { } for instrument_name , instrument_class_name in instrument_dict . items ( ) : instrument_settings = None module = None # check if instrument already exists if instrument_name in list ( instruments . keys ( ) ) and instrument_class_name == instruments [ instrument_name ] . __name__ : print ( ( 'WARNING: instrument {:s} already exists. Did not load!' . format ( instrument_name ) ) ) loaded_failed [ instrument_name ] = instrument_name else : instrument_instance = None if isinstance ( instrument_class_name , dict ) : if 'settings' in instrument_class_name : instrument_settings = instrument_class_name [ 'settings' ] instrument_filepath = str ( instrument_class_name [ 'filepath' ] ) instrument_class_name = str ( instrument_class_name [ 'class' ] ) path_to_module , _ = module_name_from_path ( instrument_filepath ) module = import_module ( path_to_module ) class_of_instrument = getattr ( module , instrument_class_name ) try : if instrument_settings is None : # this creates an instance of the class with default settings instrument_instance = class_of_instrument ( name = instrument_name ) else : # this creates an instance of the class with custom settings instrument_instance = class_of_instrument ( name = instrument_name , settings = instrument_settings ) except Exception as e : loaded_failed [ instrument_name ] = e if raise_errors : raise e continue elif isinstance ( instrument_class_name , Instrument ) : instrument_class_name = instrument_class_name . __class__ instrument_filepath = os . path . dirname ( inspect . getfile ( instrument_class_name ) ) # here we should also create an instrument instance at some point as in the other cases... # instrument_instance = raise NotImplementedError elif issubclass ( instrument_class_name , Instrument ) : class_of_instrument = instrument_class_name if instrument_settings is None : # this creates an instance of the class with default settings instrument_instance = class_of_instrument ( name = instrument_name ) else : # this creates an instance of the class with custom settings instrument_instance = class_of_instrument ( name = instrument_name , settings = instrument_settings ) updated_instruments [ instrument_name ] = instrument_instance return updated_instruments , loaded_failed
load instrument from instrument_dict and append to instruments
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def fail ( self , reason , obj , pointer = None ) : pointer = pointer_join ( pointer ) err = ValidationError ( reason , obj , pointer ) if self . fail_fast : raise err else : self . errors . append ( err ) return err
Called when validation fails .
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def get_locus ( sequences , kir = False , verbose = False , refdata = None , evalue = 10 ) : if not refdata : refdata = ReferenceData ( ) file_id = str ( randomid ( ) ) input_fasta = file_id + ".fasta" output_xml = file_id + ".xml" SeqIO . write ( sequences , input_fasta , "fasta" ) blastn_cline = NcbiblastnCommandline ( query = input_fasta , db = refdata . blastdb , evalue = evalue , outfmt = 5 , reward = 1 , penalty = - 3 , gapopen = 5 , gapextend = 2 , dust = 'yes' , out = output_xml ) stdout , stderr = blastn_cline ( ) blast_qresult = SearchIO . read ( output_xml , 'blast-xml' ) # Delete files cleanup ( file_id ) if len ( blast_qresult . hits ) == 0 : return '' loci = [ ] for i in range ( 0 , 3 ) : if kir : loci . append ( blast_qresult [ i ] . id . split ( "*" ) [ 0 ] ) else : loci . append ( blast_qresult [ i ] . id . split ( "*" ) [ 0 ] ) locus = set ( loci ) if len ( locus ) == 1 : if has_hla ( loci [ 0 ] ) or kir : return loci [ 0 ] else : return "HLA-" + loci [ 0 ] else : return ''
Gets the locus of the sequence by running blastn
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def address ( self ) -> str : return str ( self . _public_key . to_address ( net_query ( self . network ) ) )
generate an address from pubkey
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def sign_transaction ( self , txins : Union [ TxOut ] , tx : MutableTransaction ) -> MutableTransaction : solver = P2pkhSolver ( self . _private_key ) return tx . spend ( txins , [ solver for i in txins ] )
sign the parent txn outputs P2PKH
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