idx int64 0 63k | question stringlengths 53 5.28k | target stringlengths 5 805 |
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55,600 | def _addProteins ( self , proteinIds , containerNames ) : proteinIds = AUX . toList ( proteinIds ) for containerName in containerNames : proteinContainer = getattr ( self , containerName ) proteinContainer . update ( proteinIds ) | Add one or multiple proteinIds to the respective container . |
55,601 | def satisfies ( self , other ) : if other . isnocare : return True if self . isnocare : return False if self . arbitrary : return True if self . constant and not other . arbitrary : return True if self . value is other . value and not other . arbitrary and not other . constant : return True return False | Check if the capabilities of a primitive are enough to satisfy a requirement . |
55,602 | def _list ( self , foldername = "INBOX" , reverse = False , since = None ) : folder = self . folder if foldername == "INBOX" else self . _getfolder ( foldername ) def sortcmp ( d ) : try : return d [ 1 ] . date except : return - 1 lst = folder . items ( ) if not since else folder . items_since ( since ) sorted_lst = sorted ( lst , key = sortcmp , reverse = 1 if reverse else 0 ) itemlist = [ ( folder , key , msg ) for key , msg in sorted_lst ] return itemlist | Do structured list output . |
55,603 | def ls ( self , foldername = "INBOX" , reverse = False , since = None , grep = None , field = None , stream = sys . stdout ) : if foldername == "" : foldername = "INBOX" msg_list = self . _list ( foldername , reverse , since ) for folder , mk , m in msg_list : try : output_items = ( "%s%s%s" % ( folder . folder or foldername or "INBOX" , SEPERATOR , mk ) , m . date , m . get_from ( ) [ 0 : 50 ] if m . get_from ( ) else "" , m . get_flags ( ) , re . sub ( "\n" , "" , m . get_subject ( ) or "" ) ) output_string = "% -20s % 20s % 50s [%s] %s" % output_items if not grep or ( grep and grep in output_string ) : if field : print ( output_items [ int ( field ) ] , file = stream ) else : print ( output_string , file = stream ) except IOError as e : if e . errno == errno . EPIPE : return self . logger . exception ( "whoops!" ) except Exception as e : self . logger . exception ( "whoops!" ) | Do standard text list of the folder to the stream . |
55,604 | def lisp ( self , foldername = "INBOX" , reverse = False , since = None , stream = sys . stdout ) : def fromval ( hdr ) : if hdr : return parseaddr ( hdr ) for folder , mk , m in self . _list ( foldername , reverse , since ) : try : print ( json . dumps ( { 'folder' : folder . folder or foldername or "INBOX" , 'key' : "%s%s%s" % ( folder . folder or foldername or "INBOX" , SEPERATOR , mk ) , 'date' : str ( m . date ) , "flags" : m . get_flags ( ) , 'from' : fromval ( m . get_from ( ) ) , 'subject' : re . sub ( "\n|\'|\"" , _escape , m . get_subject ( ) or "" ) } ) , file = stream ) except IOError as e : if e . errno == errno . EPIPE : return self . logger . exception ( "whoops!" ) except Exception as e : self . logger . exception ( "whoops!" ) | Do JSON list of the folder to the stream . |
55,605 | def lsfolders ( self , stream = sys . stdout ) : for f in self . folder . folders ( ) : print ( f . folder . strip ( "." ) , file = stream ) | List the subfolders |
55,606 | def _get ( self , msgid ) : foldername , msgkey = msgid . split ( SEPERATOR ) folder = self . folder if foldername == "INBOX" else self . _getfolder ( foldername ) msg = folder [ msgkey ] msg . is_seen = True hdr = list ( msg . items ( ) ) for p in msg . walk ( ) : yield hdr , p return | Yields the message header against each part from the message . |
55,607 | def gettext ( self , msgid , stream = sys . stdout , splitter = "--text follows this line--\n" ) : for hdr , part in self . _get ( msgid ) : if part . get_content_type ( ) == "text/plain" : for name , val in hdr : if name . lower ( ) == "content-type" : val = part [ "content-type" ] val = " " . join ( [ l . strip ( ) for l in val . split ( "\n" ) ] ) print ( "%s: %s" % ( name , val ) , file = stream ) print ( splitter , file = stream ) payload = part . get_payload ( decode = True ) chartype = part . get_charset ( ) or _get_charset ( part . get ( "Content-Type" , "" ) ) or "us-ascii" print ( payload . decode ( chartype ) , file = stream ) break | Get the first text part we can find and print it as a message . |
55,608 | def getrawpart ( self , msgid , stream = sys . stdout ) : for hdr , part in self . _get ( msgid ) : pl = part . get_payload ( decode = True ) if pl != None : print ( pl , file = stream ) break | Get the first part from the message and print it raw . |
55,609 | def getrawpartid ( self , msgid , partid , stream = sys . stdout ) : parts = [ part for hdr , part in self . _get ( msgid ) ] part = parts [ int ( partid ) ] pl = part . get_payload ( decode = True ) if pl != None : print ( pl , file = stream ) | Get a specific part from the message and print it raw . |
55,610 | def getraw ( self , msgid , stream = sys . stdout ) : foldername , msgkey = msgid . split ( SEPERATOR ) folder = self . folder if foldername == "INBOX" else self . _getfolder ( foldername ) msg = folder [ msgkey ] print ( msg . content ) | Get the whole message and print it . |
55,611 | def getstruct ( self , msgid , as_json = False , stream = sys . stdout ) : parts = [ part . get_content_type ( ) for hdr , part in self . _get ( msgid ) ] if as_json : print ( json . dumps ( parts ) , file = stream ) else : for c in parts : print ( c , file = stream ) | Get and print the whole message . |
55,612 | def _extract_alphabet ( self , grammar ) : alphabet = set ( [ ] ) for terminal in grammar . Terminals : alphabet |= set ( [ x for x in terminal ] ) self . alphabet = list ( alphabet ) | Extract an alphabet from the given grammar . |
55,613 | def action ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_ACTION' , column , value , ** kwargs ) | The underlying GICS table provides codes and descriptions identifying the current status or disposition of a grant project . |
55,614 | def applicant ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_APPLICANT' , column , value , ** kwargs ) | Find the applicant information for a grant . |
55,615 | def authority ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_AUTHORITY' , column , value , ** kwargs ) | Provides codes and associated authorizing statutes . |
55,616 | def construction ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_CONSTRUCTION' , column , value , ** kwargs ) | Identifies monetary descriptive and milestone information for Wastewater Treatment construction grants . |
55,617 | def eligible_cost ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_ELIGIBLE_COST' , column , value , ** kwargs ) | The assistance dollar amounts by eligible cost category . |
55,618 | def grant ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_GRANT' , column , value , ** kwargs ) | Provides various award project and grant personnel information . |
55,619 | def grant_assistance ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_GRANT_ASST_PGM' , column , value , ** kwargs ) | Many - to - many table connecting grants and assistance . |
55,620 | def grant_authority ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_GRANT_AUTH' , column , value , ** kwargs ) | Many - to - many table connecting grants and authority . |
55,621 | def lab_office ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_LAB_OFFICE' , column , value , ** kwargs ) | Abbreviations names and locations of labratories and offices . |
55,622 | def milestone ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_MILESTONE' , column , value , ** kwargs ) | Status codes and related dates of certain grants |
55,623 | def record_type ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_RECORD_TYPE' , column , value , ** kwargs ) | Codes and descriptions indicating whether an award is for a new project or for the continuation of a currently funded one . |
55,624 | def srf_cap ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_SRF_CAP' , column , value , ** kwargs ) | Fiscal dollar amounts for State Revolving Fund Capitalization Grants . |
55,625 | def status ( self , column = None , value = None , ** kwargs ) : return self . _resolve_call ( 'GIC_STATUS' , column , value , ** kwargs ) | Provides codes and descriptions of project milestones . |
55,626 | def recRemoveTreeFormating ( element ) : children = element . getchildren ( ) if len ( children ) > 0 : for child in children : recRemoveTreeFormating ( child ) if element . text is not None : if len ( element . text . strip ( ) ) == 0 : element . text = None else : element . text = element . text . strip ( ) if element . tail is not None : if len ( element . tail . strip ( ) ) == 0 : element . tail = None else : element . tail = element . tail . strip ( ) | Removes whitespace characters which are leftovers from previous xml formatting . |
55,627 | def recCopyElement ( oldelement ) : newelement = ETREE . Element ( oldelement . tag , oldelement . attrib ) if len ( oldelement . getchildren ( ) ) > 0 : for childelement in oldelement . getchildren ( ) : newelement . append ( recCopyElement ( childelement ) ) return newelement | Generates a copy of an xml element and recursively of all child elements . |
55,628 | def getParam ( xmlelement ) : elementTag = clearTag ( xmlelement . tag ) if elementTag in [ 'userParam' , 'cvParam' , 'referenceableParamGroupRef' ] : if elementTag == 'cvParam' : param = cvParamFromDict ( xmlelement . attrib ) elif elementTag == 'userParam' : param = userParamFromDict ( xmlelement . attrib ) else : param = refParamGroupFromDict ( xmlelement . attrib ) else : param = False return param | Converts an mzML xml element to a param tuple . |
55,629 | def xmlAddParams ( parentelement , params ) : if not params : return None for param in params : if len ( param ) == 3 : cvAttrib = { 'cvRef' : param [ 0 ] . split ( ':' ) [ 0 ] , 'accession' : param [ 0 ] , 'name' : oboTranslator . getNameWithId ( param [ 0 ] ) } if param [ 1 ] : cvAttrib . update ( { 'value' : param [ 1 ] } ) else : cvAttrib . update ( { 'value' : '' } ) if param [ 2 ] : unitName = oboTranslator . getNameWithId ( param [ 2 ] ) cvAttrib . update ( { 'unitAccession' : param [ 2 ] , 'unitCvRef' : param [ 2 ] . split ( ':' ) [ 0 ] , 'unitName' : unitName } ) paramElement = ETREE . Element ( 'cvParam' , ** cvAttrib ) elif len ( param ) == 4 : userAttrib = { 'name' : param [ 0 ] } if param [ 1 ] : userAttrib . update ( { 'value' : param [ 1 ] } ) else : userAttrib . update ( { 'value' : '' } ) if param [ 2 ] : userAttrib . update ( { 'unitAccession' : param [ 2 ] , 'unitCvRef' : param [ 2 ] . split ( ':' ) [ 0 ] } ) if param [ 3 ] : userAttrib . update ( { 'type' : param [ 3 ] } ) paramElement = ETREE . Element ( 'userParam' , ** userAttrib ) elif param [ 0 ] == 'ref' : refAttrib = { 'ref' : param [ 1 ] } paramElement = ETREE . Element ( 'referenceableParamGroupRef' , ** refAttrib ) parentelement . append ( paramElement ) | Generates new mzML parameter xml elements and adds them to the parentelement as xml children elements . |
55,630 | def interpretBitEncoding ( bitEncoding ) : if bitEncoding == '64' : floattype = 'd' numpyType = numpy . float64 elif bitEncoding == '32' : floattype = 'f' numpyType = numpy . float32 else : errorText = '' . join ( [ 'bitEncoding \'' , bitEncoding , '\' not defined. ' , 'Must be \'64\' or \'32\'' ] ) raise TypeError ( errorText ) return ( floattype , numpyType ) | Returns a floattype string and a numpy array type . |
55,631 | def calc_partition_function ( mass , omega_array , temperature_array ) : Kappa_t = mass * omega_array ** 2 return _np . sqrt ( 4 * _np . pi ** 2 * _scipy . constants . Boltzmann ** 2 * temperature_array ** 2 / ( mass * Kappa_t ) ) | Calculates the partition function of your system at each point in time . |
55,632 | def calc_mean_and_variance_of_variances ( self , NumberOfOscillations ) : SplittedArraySize = int ( self . SampleFreq / self . FTrap . n ) * NumberOfOscillations VoltageArraySize = len ( self . voltage ) SnippetsVariances = _np . var ( self . voltage [ : VoltageArraySize - _np . mod ( VoltageArraySize , SplittedArraySize ) ] . reshape ( - 1 , SplittedArraySize ) , axis = 1 ) return _np . mean ( SnippetsVariances ) , _np . var ( SnippetsVariances ) | Calculates the mean and variance of a set of varainces . This set is obtained by splitting the timetrace into chunks of points with a length of NumberOfOscillations oscillations . |
55,633 | def register_template_directory ( kb_app : kb , sphinx_app : Sphinx , sphinx_env : BuildEnvironment , docnames = List [ str ] , ) : template_bridge = sphinx_app . builder . templates actions = ResourceAction . get_callbacks ( kb_app ) for action in actions : f = os . path . dirname ( inspect . getfile ( action ) ) template_bridge . loaders . append ( SphinxFileSystemLoader ( f ) ) | Add this resource s templates dir to template paths |
55,634 | def add_directives ( kb_app : kb , sphinx_app : Sphinx , sphinx_env : BuildEnvironment , docnames = List [ str ] , ) : for k , v in list ( kb_app . config . resources . items ( ) ) : sphinx_app . add_directive ( k , ResourceDirective ) | For each resource type register a new Sphinx directive |
55,635 | def stamp_title ( kb_app : kb , sphinx_app : Sphinx , doctree : doctree ) : resources = sphinx_app . env . resources confdir = sphinx_app . confdir source = PurePath ( doctree . attributes [ 'source' ] ) docname = str ( source . relative_to ( confdir ) ) . split ( '.rst' ) [ 0 ] resource = resources . get ( docname ) if resource : title = get_rst_title ( doctree ) resource . title = title | Walk the tree and extra RST title into resource . title |
55,636 | def handle_exception ( error ) : response = jsonify ( error . to_dict ( ) ) response . status_code = error . status_code return response | Simple method for handling exceptions raised by PyBankID . |
55,637 | def create_from_pybankid_exception ( cls , exception ) : return cls ( "{0}: {1}" . format ( exception . __class__ . __name__ , str ( exception ) ) , _exception_class_to_status_code . get ( exception . __class__ ) , ) | Class method for initiating from a PyBankID exception . |
55,638 | def to_dict ( self ) : rv = dict ( self . payload or ( ) ) rv [ "message" ] = self . message return rv | Create a dict representation of this exception . |
55,639 | def integers ( num , minimum , maximum , base = 10 ) : function = 'integers' num , minimum , maximum = list ( map ( int , [ num , minimum , maximum ] ) ) if ( 1 <= num <= 10 ** 4 ) is False : print ( 'ERROR: %s is out of range' % num ) return if ( - 10 ** 9 <= minimum <= 10 ** 9 ) is False : print ( 'ERROR: %s is out of range' % minimum ) return if ( - 10 ** 9 <= maximum <= 10 ** 9 ) is False : print ( 'ERROR: %s is out of range' % maximum ) return if maximum < minimum : print ( 'ERROR: %s is less than %s' % ( maximum , minimum ) ) return base = int ( base ) if base not in [ 2 , 8 , 10 , 16 ] : raise Exception ( 'Base not in range!' ) opts = { 'num' : num , 'min' : minimum , 'max' : maximum , 'col' : 1 , 'base' : base , 'format' : 'plain' , 'rnd' : 'new' } integers = get_http ( RANDOM_URL , function , opts ) integers_arr = str_to_arr ( integers ) return integers_arr | Random integers within specified interval . |
55,640 | def sequence ( minimum , maximum ) : function = 'sequences' opts = { 'min' : minimum , 'max' : maximum , 'col' : 1 , 'format' : 'plain' , 'rnd' : 'new' } deal = get_http ( RANDOM_URL , function , opts ) deal_arr = str_to_arr ( deal ) return deal_arr | Randomize a sequence of integers . |
55,641 | def string ( num , length , digits = False , upper = True , lower = True , unique = False ) : function = 'strings' digits = convert ( digits ) upper = convert ( upper ) lower = convert ( lower ) unique = convert ( unique ) opts = { 'num' : num , 'len' : length , 'digits' : digits , 'upperalpha' : upper , 'loweralpha' : lower , 'format' : 'plain' , 'rnd' : 'new' } seq = get_http ( RANDOM_URL , function , opts ) seq = seq . strip ( ) . split ( '\n' ) return seq | Random strings . |
55,642 | def quota ( ip = None ) : url = 'http://www.random.org/quota/?format=plain' data = urlopen ( url ) credit = int ( data . read ( ) . strip ( ) ) if data . code == 200 : return credit else : return "ERROR: Server responded with code %s" % data . code | Check your quota . |
55,643 | def get_http ( base_url , function , opts ) : url = ( os . path . join ( base_url , function ) + '/?' + urlencode ( opts ) ) data = urlopen ( url ) if data . code != 200 : raise ValueError ( "Random.rg returned server code: " + str ( data . code ) ) return data . read ( ) | HTTP request generator . |
55,644 | def read ( * p ) : with open ( os . path . join ( * p ) , 'r' ) as fi : return fi . read ( ) | Build a file path from paths and return the contents . |
55,645 | def execute ( self , processProtocol , command , env = { } , path = None , uid = None , gid = None , usePTY = 0 , childFDs = None ) : raise NotImplementedError ( ) | Form a command and start a process in the desired environment . |
55,646 | def run ( self , command , env = { } , path = None , uid = None , gid = None , usePTY = 0 , childFDs = None ) : deferred = defer . Deferred ( ) processProtocol = _SummaryProcessProtocol ( deferred ) d = defer . maybeDeferred ( self . execute , processProtocol , command , env , path , uid , gid , usePTY , childFDs ) d . addErrback ( deferred . errback ) return deferred | Execute a command and return the results of the completed run . |
55,647 | def getOutput ( self , command , env = { } , path = None , uid = None , gid = None , usePTY = 0 , childFDs = None ) : deferred = defer . Deferred ( ) processProtocol = _SummaryProcessProtocol ( deferred ) self . execute ( processProtocol , command , env , path , uid , gid , usePTY , childFDs ) @ deferred . addCallback def getStdOut ( tuple_ ) : stdout , _stderr , _returnCode = tuple_ return stdout return deferred | Execute a command and get the output of the finished process . |
55,648 | def getExitCode ( self , command , env = { } , path = None , uid = None , gid = None , usePTY = 0 , childFDs = None ) : deferred = defer . Deferred ( ) processProtocol = _SummaryProcessProtocol ( deferred ) self . execute ( processProtocol , command , env , path , uid , gid , usePTY , childFDs ) @ deferred . addCallback def getStdOut ( tuple_ ) : _stdout , _stderr , exitCode = tuple_ return exitCode return deferred | Execute a command and get the return code of the finished process . |
55,649 | def validate_task ( original_task ) : task = original_task . _asdict ( ) if 'inputs' not in task or task [ 'inputs' ] is None : task [ 'inputs' ] = [ '*' ] if ( 'outputs' not in task or task [ 'outputs' ] is None or len ( task [ 'outputs' ] ) == 0 ) : task [ 'outputs' ] = [ '*' ] if not hasattr ( task [ 'inputs' ] , '__iter__' ) or isinstance ( task [ 'inputs' ] , str ) : task [ 'inputs' ] = ( task [ 'inputs' ] , ) else : task [ 'inputs' ] = tuple ( task [ 'inputs' ] ) if not hasattr ( task [ 'outputs' ] , '__iter__' ) or isinstance ( task [ 'outputs' ] , str ) : task [ 'outputs' ] = ( task [ 'outputs' ] , ) else : task [ 'outputs' ] = tuple ( task [ 'outputs' ] ) if not callable ( task [ 'fn' ] ) : raise TypeError ( 'Task function must be a callable object' ) if ( len ( task [ 'outputs' ] ) > 1 and not inspect . isgeneratorfunction ( task [ 'fn' ] ) ) : raise TypeError ( 'Multiple outputs are only supported with \ generator functions' ) if inspect . isgeneratorfunction ( task [ 'fn' ] ) : if task [ 'outputs' ] [ 0 ] == '*' : raise TypeError ( 'Generator functions cannot be used for tasks with \ output specification "*"' ) return Task ( ** task ) | Validates task and adds default values for missing options using the following steps . |
55,650 | def run_task ( task , workspace ) : data = copy . copy ( workspace ) task = validate_task ( task ) inputs = [ input_parser ( key , data ) for key in task . inputs ] if inspect . isgeneratorfunction ( task . fn ) : data . update ( zip ( task . outputs , task . fn ( * inputs ) ) ) else : results = task . fn ( * inputs ) if task . outputs [ 0 ] != '*' : results = { task . outputs [ 0 ] : results } elif not isinstance ( results , dict ) : raise TypeError ( 'Result should be a dict for output type *' ) data . update ( results ) return data | Runs the task and updates the workspace with results . |
55,651 | def run_hook ( name , workspace , hooks ) : data = copy . copy ( workspace ) for hook_listener in hooks . get ( name , [ ] ) : hook_listener ( data ) return data | Runs all hooks added under the give name . |
55,652 | def add_task ( self , fn , inputs = None , outputs = None ) : self . tasks . append ( Task ( fn , inputs , outputs ) ) return self | Adds a task to the workflow . |
55,653 | def add_hook ( self , name , function ) : if not callable ( function ) : return ValueError ( 'Hook function should be callable' ) if name not in self . hooks : self . hooks [ name ] = [ ] self . hooks [ name ] . append ( function ) return self | Adds a function to be called for hook of a given name . |
55,654 | def dns ( self ) : dns = { 'elb' : self . dns_elb ( ) , 'elb_region' : self . dns_elb_region ( ) , 'global' : self . dns_global ( ) , 'region' : self . dns_region ( ) , 'instance' : self . dns_instance ( ) , } return dns | DNS details . |
55,655 | def s3_app_bucket ( self , include_region = False ) : if include_region : s3_app_bucket = self . format [ 's3_app_region_bucket' ] . format ( ** self . data ) else : s3_app_bucket = self . format [ 's3_app_bucket' ] . format ( ** self . data ) return s3_app_bucket | Generate s3 application bucket name . |
55,656 | def shared_s3_app_bucket ( self , include_region = False ) : if include_region : shared_s3_app_bucket = self . format [ 'shared_s3_app_region_bucket' ] . format ( ** self . data ) else : shared_s3_app_bucket = self . format [ 'shared_s3_app_bucket' ] . format ( ** self . data ) return shared_s3_app_bucket | Generate shared s3 application bucket name . |
55,657 | def iam ( self ) : iam = { 'group' : self . format [ 'iam_group' ] . format ( ** self . data ) , 'lambda_role' : self . format [ 'iam_lambda_role' ] . format ( ** self . data ) , 'policy' : self . format [ 'iam_policy' ] . format ( ** self . data ) , 'profile' : self . format [ 'iam_profile' ] . format ( ** self . data ) , 'role' : self . format [ 'iam_role' ] . format ( ** self . data ) , 'user' : self . format [ 'iam_user' ] . format ( ** self . data ) , 'base' : self . format [ 'iam_base' ] . format ( ** self . data ) , } return iam | Generate iam details . |
55,658 | def archaius ( self ) : bucket = self . format [ 's3_bucket' ] . format ( ** self . data ) path = self . format [ 's3_bucket_path' ] . format ( ** self . data ) archaius_name = self . format [ 's3_archaius_name' ] . format ( ** self . data ) archaius = { 's3' : archaius_name , 'bucket' : bucket , 'path' : path } return archaius | Generate archaius bucket path . |
55,659 | def jenkins ( self ) : job_name = self . format [ 'jenkins_job_name' ] . format ( ** self . data ) job = { 'name' : job_name } return job | Generate jenkins job details . |
55,660 | def gitlab ( self ) : main_name = self . format [ 'git_repo' ] . format ( ** self . data ) qe_name = self . format [ 'git_repo_qe' ] . format ( ** self . data ) config_name = self . format [ 'git_repo_configs' ] . format ( ** self . data ) git = { 'config' : config_name , 'main' : main_name , 'qe' : qe_name , } return git | Generate gitlab details . |
55,661 | def get_value_matched_by_regex ( field_name , regex_matches , string ) : try : value = regex_matches . group ( field_name ) if value is not None : return value except IndexError : pass raise MissingFieldError ( string , field_name ) | Ensure value stored in regex group exists . |
55,662 | def positive_int ( val ) : if isinstance ( val , float ) : raise ValueError ( '"{}" must not be a float' . format ( val ) ) val = int ( val ) if val >= 0 : return val raise ValueError ( '"{}" must be positive' . format ( val ) ) | Parse val into a positive integer . |
55,663 | def strictly_positive_int_or_none ( val ) : val = positive_int_or_none ( val ) if val is None or val > 0 : return val raise ValueError ( '"{}" must be strictly positive' . format ( val ) ) | Parse val into either None or a strictly positive integer . |
55,664 | def _attributeLinesToDict ( attributeLines ) : attributes = dict ( ) for line in attributeLines : attributeId , attributeValue = line . split ( ':' , 1 ) attributes [ attributeId . strip ( ) ] = attributeValue . strip ( ) return attributes | Converts a list of obo Term lines to a dictionary . |
55,665 | def _termIsObsolete ( oboTerm ) : isObsolete = False if u'is_obsolete' in oboTerm : if oboTerm [ u'is_obsolete' ] . lower ( ) == u'true' : isObsolete = True return isObsolete | Determine wheter an obo Term entry is marked as obsolete . |
55,666 | def discover_handler_classes ( handlers_package ) : if handlers_package is None : return sys . path . insert ( 0 , os . getcwd ( ) ) package = import_module ( handlers_package ) if hasattr ( package , '__path__' ) : for _ , modname , _ in pkgutil . iter_modules ( package . __path__ ) : import_module ( '{package}.{module}' . format ( package = package . __name__ , module = modname ) ) return registered_handlers | Looks for handler classes within handler path module . |
55,667 | def get_multi_word_keywords ( features ) : keys = { 'is not' : Token ( TokenTypes . NOT_EQUAL , 'is not' ) , } return OrderedDict ( sorted ( list ( keys . items ( ) ) , key = lambda t : len ( t [ 0 ] ) , reverse = True ) ) | This returns an OrderedDict containing the multi word keywords in order of length . This is so the tokenizer will match the longer matches before the shorter matches |
55,668 | def inside_try ( func , options = { } ) : if six . PY2 : name = func . func_name else : name = func . __name__ @ wraps ( func ) def silenceit ( * args , ** kwargs ) : excpt = None try : return func ( * args , ** kwargs ) except Exception as excpt : if 'ctx' in kwargs : ctx = kwargs [ 'ctx' ] else : ctx = get_try_option ( None , 'ctx' ) if not ctx : ctx = Bubble ( 'Inside Try' ) head = name + ': silenced function inside_try:Error:' if get_try_option ( ctx , 'count_it' ) : ctx . gbc . cry ( head + 'counting' ) if get_try_option ( ctx , 'print_it' ) : ctx . gbc . cry ( head + 'printing:' + str ( excpt ) ) if get_try_option ( ctx , 'print_args' ) : ctx . gbc . cry ( head + 'printing ak:' + str ( excpt ) ) ctx . gbc . cry ( 'args' , stuff = args ) ctx . gbc . cry ( 'kwargs' , stuff = kwargs ) if get_try_option ( ctx , 'inspect_it' ) : ctx . gbc . cry ( head + 'inspecting:' , stuff = excpt ) for s in inspect . stack ( ) : ctx . gbc . cry ( head + ':stack:' , stuff = s ) if get_try_option ( ctx , 'log_it' ) : ctx . gbc . cry ( head + 'logging' ) for s in inspect . stack ( ) : ctx . gbc . cry ( head + ':stack:' , stuff = s ) if get_try_option ( ctx , 'reraise_it' ) : ctx . gbc . cry ( head + 'reraising' ) raise excpt return { 'error' : str ( excpt ) , 'silenced' : name , 'args' : args , 'kwargs' : kwargs } return silenceit | decorator to silence exceptions for logging we want a safe fail of the functions |
55,669 | def start ( self ) : Server ( ) . start ( self . options , self . handler_function , self . __class__ . component_type ) | Start the server and run forever . |
55,670 | def sort_entries ( self ) : return sorted ( self . data , key = self . sort_func , reverse = self . get_reverse ( ) ) | Get whether reverse is True or False . Return the sorted data . |
55,671 | def visible_fields ( self ) : form_visible_fields = self . form . visible_fields ( ) if self . render_fields : fields = self . render_fields else : fields = [ field . name for field in form_visible_fields ] filtered_fields = [ field for field in fields if field not in self . exclude_fields ] return [ field for field in form_visible_fields if field . name in filtered_fields ] | Returns the reduced set of visible fields to output from the form . |
55,672 | def get_fieldsets ( self , fieldsets = None ) : fieldsets = fieldsets or self . fieldsets if not fieldsets : raise StopIteration has_primary = any ( fieldset . get ( 'primary' ) for fieldset in fieldsets ) for fieldset_kwargs in fieldsets : fieldset_kwargs = copy . deepcopy ( fieldset_kwargs ) fieldset_kwargs [ 'form' ] = self if not has_primary : fieldset_kwargs [ 'primary' ] = True has_primary = True yield self . get_fieldset ( ** fieldset_kwargs ) | This method returns a generator which yields fieldset instances . |
55,673 | def get_chunks ( Array , Chunksize ) : for i in range ( 0 , len ( Array ) , Chunksize ) : yield Array [ i : i + Chunksize ] | Generator that yields chunks of size ChunkSize |
55,674 | def read_data_from_bin_file ( fileName ) : with open ( fileName , mode = 'rb' ) as file : fileContent = file . read ( ) ( ChannelData , LenOf1Channel , NumOfChannels , SampleTime ) = read_data_from_bytes ( fileContent ) return ChannelData , LenOf1Channel , NumOfChannels , SampleTime | Loads the binary data stored in the a binary file and extracts the data for each channel that was saved along with the sample rate and length of the data array . |
55,675 | def read_data_from_bytes ( fileContent ) : TotalDataLen = struct . unpack ( 'Q' , fileContent [ : 8 ] ) [ 0 ] NumOfChannels = struct . unpack ( 'I' , fileContent [ 8 : 12 ] ) [ 0 ] SampleTime = struct . unpack ( 'd' , fileContent [ 12 : 20 ] ) [ 0 ] AllChannelData = struct . unpack ( "f" * ( ( len ( fileContent ) - 20 ) // 4 ) , fileContent [ 20 : ] ) LenOf1Channel = int ( TotalDataLen / NumOfChannels ) ChannelData = list ( get_chunks ( AllChannelData , LenOf1Channel ) ) return ChannelData , LenOf1Channel , NumOfChannels , SampleTime | Takes the binary data stored in the binary string provided and extracts the data for each channel that was saved along with the sample rate and length of the data array . |
55,676 | def get_coord_box ( centre_x , centre_y , distance ) : return { 'top_left' : ( centre_x - distance , centre_y + distance ) , 'top_right' : ( centre_x + distance , centre_y + distance ) , 'bottom_left' : ( centre_x - distance , centre_y - distance ) , 'bottom_right' : ( centre_x + distance , centre_y - distance ) , } | Get the square boundary coordinates for a given centre and distance |
55,677 | def fleet_ttb ( unit_type , quantity , factories , is_techno = False , is_dict = False , stasis_enabled = False ) : unit_weights = { UNIT_SCOUT : 1 , UNIT_DESTROYER : 13 , UNIT_BOMBER : 10 , UNIT_CRUISER : 85 , UNIT_STARBASE : 1 , } govt_weight = 80 if is_dict else 100 prod_weight = 85 if is_techno else 100 weighted_qty = unit_weights [ unit_type ] * quantity ttb = ( weighted_qty * govt_weight * prod_weight ) * ( 2 * factories ) return ttb + ( ttb * 0.66 ) if stasis_enabled else ttb | Calculate the time taken to construct a given fleet |
55,678 | def parse_fasta ( data ) : name , seq = None , [ ] for line in data : line = line . rstrip ( ) if line . startswith ( '>' ) : if name : yield Sequence ( name , '' . join ( seq ) ) name , seq = line , [ ] else : seq . append ( line ) if name : yield Sequence ( name , '' . join ( seq ) ) | Load sequences in Fasta format . |
55,679 | def _reset ( self ) : self . records = list ( ) self . featsbyid = dict ( ) self . featsbyparent = dict ( ) self . countsbytype = dict ( ) | Clear internal data structure . |
55,680 | def get_by_label ( self , label ) : return next ( ( x for x in self if x . label == label ) , None ) | Return the first item with a specific label or None . |
55,681 | def getGenericAnswers ( self , name , instruction , prompts ) : responses = [ ] for prompt , _echo in prompts : password = self . getPassword ( prompt ) responses . append ( password ) return defer . succeed ( responses ) | Called when the server requests keyboard interactive authentication |
55,682 | def pairwise ( iterable ) : iterator = iter ( iterable ) try : first = next ( iterator ) except StopIteration : return for element in iterator : yield first , element first = element | Generate consecutive pairs of elements from the given iterable . |
55,683 | def https_policy_from_config ( config ) : server = config . cluster [ "server" ] base_url = URL . fromText ( native_string_to_unicode ( server ) ) ca_certs = pem . parse ( config . cluster [ "certificate-authority" ] . bytes ( ) ) if not ca_certs : raise ValueError ( "No certificate authority certificate found." ) ca_cert = ca_certs [ 0 ] try : ssl . Certificate . load ( ca_cert . as_bytes ( ) , FILETYPE_PEM ) except OpenSSLError as e : raise ValueError ( "Invalid certificate authority certificate found." , str ( e ) , ) netloc = NetLocation ( host = base_url . host , port = base_url . port ) policy = ClientCertificatePolicyForHTTPS ( credentials = { } , trust_roots = { netloc : ca_cert , } , ) return policy | Create an IPolicyForHTTPS which can authenticate a Kubernetes API server . |
55,684 | def authenticate_with_certificate_chain ( reactor , base_url , client_chain , client_key , ca_cert ) : if base_url . scheme != u"https" : raise ValueError ( "authenticate_with_certificate() makes sense for HTTPS, not {!r}" . format ( base_url . scheme ) , ) netloc = NetLocation ( host = base_url . host , port = base_url . port ) policy = ClientCertificatePolicyForHTTPS ( credentials = { netloc : TLSCredentials ( chain = Chain ( certificates = Certificates ( client_chain ) ) , key = client_key , ) , } , trust_roots = { netloc : ca_cert , } , ) return Agent ( reactor , contextFactory = policy ) | Create an IAgent which can issue authenticated requests to a particular Kubernetes server using a client certificate . |
55,685 | def authenticate_with_certificate ( reactor , base_url , client_cert , client_key , ca_cert ) : return authenticate_with_certificate_chain ( reactor , base_url , [ client_cert ] , client_key , ca_cert , ) | See authenticate_with_certificate_chain . |
55,686 | def authenticate_with_serviceaccount ( reactor , ** kw ) : config = KubeConfig . from_service_account ( ** kw ) policy = https_policy_from_config ( config ) token = config . user [ "token" ] agent = HeaderInjectingAgent ( _to_inject = Headers ( { u"authorization" : [ u"Bearer {}" . format ( token ) ] } ) , _agent = Agent ( reactor , contextFactory = policy ) , ) return agent | Create an IAgent which can issue authenticated requests to a particular Kubernetes server using a service account token . |
55,687 | def first_time_setup ( self ) : if not self . _auto_unlock_key_position ( ) : pw = password . create_passwords ( ) [ 0 ] attrs = { 'application' : self . keyring } gkr . item_create_sync ( self . default_keyring , gkr . ITEM_GENERIC_SECRET , self . keyring , attrs , pw , True ) found_pos = self . _auto_unlock_key_position ( ) item_info = gkr . item_get_info_sync ( self . default_keyring , found_pos ) gkr . create_sync ( self . keyring , item_info . get_secret ( ) ) | First time running Open Sesame? Create keyring and an auto - unlock key in default keyring . Make sure these things don t already exist . |
55,688 | def _auto_unlock_key_position ( self ) : found_pos = None default_keyring_ids = gkr . list_item_ids_sync ( self . default_keyring ) for pos in default_keyring_ids : item_attrs = gkr . item_get_attributes_sync ( self . default_keyring , pos ) app = 'application' if item_attrs . has_key ( app ) and item_attrs [ app ] == "opensesame" : found_pos = pos break return found_pos | Find the open sesame password in the default keyring |
55,689 | def get_position_searchable ( self ) : ids = gkr . list_item_ids_sync ( self . keyring ) position_searchable = { } for i in ids : item_attrs = gkr . item_get_attributes_sync ( self . keyring , i ) position_searchable [ i ] = item_attrs [ 'searchable' ] return position_searchable | Return dict of the position and corrasponding searchable str |
55,690 | def _match_exists ( self , searchable ) : position_searchable = self . get_position_searchable ( ) for pos , val in position_searchable . iteritems ( ) : if val == searchable : return pos return False | Make sure the searchable description doesn t already exist |
55,691 | def save_password ( self , password , ** attrs ) : pos_of_match = self . _match_exists ( attrs [ 'searchable' ] ) if pos_of_match : old_password = self . get_password ( pos_of_match ) . get_secret ( ) gkr . item_delete_sync ( self . keyring , pos_of_match ) desc = str ( int ( time . time ( ) ) ) + "_" + attrs [ 'searchable' ] gkr . item_create_sync ( self . keyring , gkr . ITEM_GENERIC_SECRET , desc , { } , old_password , True ) desc = attrs [ 'searchable' ] pos = gkr . item_create_sync ( self . keyring , gkr . ITEM_GENERIC_SECRET , desc , attrs , password , True ) return pos | Save the new password save the old password with the date prepended |
55,692 | def get_descriptor_for_idcode ( idcode ) : idcode = idcode & 0x0fffffff id_str = "XXXX" + bin ( idcode ) [ 2 : ] . zfill ( 28 ) descr_file_path = _check_cache_for_idcode ( id_str ) if descr_file_path : with open ( descr_file_path , 'r' ) as f : dat = json . load ( f ) if dat . get ( "_file_version" , - 1 ) == JTAGDeviceDescription . version : return JTAGDeviceDescription ( dat . get ( 'idcode' ) , dat . get ( 'name' ) , dat . get ( 'ir_length' ) , dat . get ( 'instruction_opcodes' ) , dat . get ( 'registers' ) , dat . get ( 'instruction_register_map' ) ) print ( " Device detected (" + id_str + "). Fetching missing descriptor..." ) sid = get_sid ( id_str ) details = get_details ( sid ) attribs = decode_bsdl ( sid ) instruction_length = 0 if attribs . get ( 'INSTRUCTION_LENGTH' ) == details . get ( 'INSTRUCTION_LENGTH' ) : instruction_length = attribs . get ( 'INSTRUCTION_LENGTH' ) elif attribs . get ( 'INSTRUCTION_LENGTH' ) and details . get ( 'INSTRUCTION_LENGTH' ) : raise Exception ( "INSTRUCTION_LENGTH can not be determined" ) elif attribs . get ( 'INSTRUCTION_LENGTH' ) : instruction_length = attribs . get ( 'INSTRUCTION_LENGTH' ) else : instruction_length = details . get ( 'INSTRUCTION_LENGTH' ) for instruction_name in details . get ( 'instructions' ) : if instruction_name not in attribs . get ( 'INSTRUCTION_OPCODE' , [ ] ) : raise Exception ( "INSTRUCTION_OPCODE sources do not match" ) descr = JTAGDeviceDescription ( attribs [ 'IDCODE_REGISTER' ] . upper ( ) , details [ 'name' ] , instruction_length , attribs [ 'INSTRUCTION_OPCODE' ] , attribs [ 'REGISTERS' ] , attribs [ 'INSTRUCTION_TO_REGISTER' ] ) if not os . path . isdir ( base_descr_dir ) : os . makedirs ( base_descr_dir ) descr_file_path = os . path . join ( base_descr_dir , attribs [ 'IDCODE_REGISTER' ] . upper ( ) + '.json' ) with open ( descr_file_path , 'w' ) as f : json . dump ( descr . _dump ( ) , f ) return descr | Use this method to find bsdl descriptions for devices . The caching on this method drastically lower the execution time when there are a lot of bsdl files and more than one device . May move it into a metaclass to make it more transparent . |
55,693 | def _fetch_dimensions ( self , dataset ) : yield Dimension ( u"school" ) yield Dimension ( u"year" , datatype = "year" ) yield Dimension ( u"semester" , datatype = "academic_term" , dialect = "swedish" ) yield Dimension ( u"municipality" , datatype = "year" , domain = "sweden/municipalities" ) | Iterate through semesters counties and municipalities . |
55,694 | def _merge_configs ( configs ) : result = { u"contexts" : [ ] , u"users" : [ ] , u"clusters" : [ ] , u"current-context" : None , } for config in configs : for k in { u"contexts" , u"users" , u"clusters" } : try : values = config . doc [ k ] except KeyError : pass else : result [ k ] . extend ( values ) if result [ u"current-context" ] is None : try : result [ u"current-context" ] = config . doc [ u"current-context" ] except KeyError : pass return KubeConfig ( result ) | Merge one or more KubeConfig objects . |
55,695 | def _merge_configs_from_env ( kubeconfigs ) : paths = list ( FilePath ( p ) for p in kubeconfigs . split ( pathsep ) if p ) config = _merge_configs ( list ( KubeConfig . from_file ( p . path ) for p in paths ) ) return config | Merge configuration files from a KUBECONFIG environment variable . |
55,696 | def network_kubernetes_from_context ( reactor , context = None , path = None , environ = None , default_config_path = FilePath ( expanduser ( u"~/.kube/config" ) ) , ) : if path is None : if environ is None : from os import environ try : kubeconfigs = environ [ u"KUBECONFIG" ] except KeyError : config = KubeConfig . from_file ( default_config_path . path ) else : config = _merge_configs_from_env ( kubeconfigs ) else : config = KubeConfig . from_file ( path . path ) if context is None : context = config . doc [ u"current-context" ] context = config . contexts [ context ] cluster = config . clusters [ context [ u"cluster" ] ] user = config . users [ context [ u"user" ] ] if isinstance ( cluster [ u"server" ] , bytes ) : base_url = URL . fromText ( cluster [ u"server" ] . decode ( "ascii" ) ) else : base_url = URL . fromText ( cluster [ u"server" ] ) [ ca_cert ] = parse ( cluster [ u"certificate-authority" ] . bytes ( ) ) client_chain = parse ( user [ u"client-certificate" ] . bytes ( ) ) [ client_key ] = parse ( user [ u"client-key" ] . bytes ( ) ) agent = authenticate_with_certificate_chain ( reactor , base_url , client_chain , client_key , ca_cert , ) return network_kubernetes ( base_url = base_url , agent = agent , ) | Create a new IKubernetes provider based on a kube config file . |
55,697 | def collection_location ( obj ) : kind = obj . kind apiVersion = obj . apiVersion prefix = version_to_segments [ apiVersion ] collection = kind . lower ( ) + u"s" if IObject . providedBy ( obj ) : namespace = obj . metadata . namespace else : namespace = None if namespace is None : return prefix + ( collection , ) return prefix + ( u"namespaces" , namespace , collection ) | Get the URL for the collection of objects like obj . |
55,698 | async def execute ( ctx ) : tail_depth = len ( ctx . stack ( ) ) - 1 story_part = ctx . get_current_story_part ( ) logger . debug ( '# going to call: {}' . format ( story_part . __name__ ) ) waiting_for = story_part ( ctx . message ) if inspect . iscoroutinefunction ( story_part ) : waiting_for = await waiting_for logger . debug ( '# got result {}' . format ( waiting_for ) ) if isinstance ( waiting_for , story_context . StoryContext ) : ctx = waiting_for . clone ( ) ctx . waiting_for = callable . WaitForReturn ( ) else : ctx = ctx . clone ( ) ctx . waiting_for = waiting_for tail_data = ctx . message [ 'session' ] [ 'stack' ] [ tail_depth ] [ 'data' ] tail_step = ctx . message [ 'session' ] [ 'stack' ] [ tail_depth ] [ 'step' ] if ctx . is_waiting_for_input ( ) : if isinstance ( ctx . waiting_for , callable . EndOfStory ) : if isinstance ( ctx . waiting_for . data , dict ) : new_data = { ** ctx . get_user_data ( ) , ** ctx . waiting_for . data } else : new_data = ctx . waiting_for . data ctx . message = { ** ctx . message , 'session' : { ** ctx . message [ 'session' ] , 'data' : new_data , } , } tail_step += 1 elif isinstance ( ctx . waiting_for , loop . ScopeMatcher ) : tail_data = matchers . serialize ( ctx . waiting_for ) elif isinstance ( ctx . waiting_for , loop . BreakLoop ) : tail_step += 1 else : tail_data = matchers . serialize ( matchers . get_validator ( ctx . waiting_for ) ) tail_step += 1 ctx . message = modify_stack_in_message ( ctx . message , lambda stack : stack [ : tail_depth ] + [ { 'data' : tail_data , 'step' : tail_step , 'topic' : stack [ tail_depth ] [ 'topic' ] , } ] + stack [ tail_depth + 1 : ] ) logger . debug ( '# mutated ctx after execute' ) logger . debug ( ctx ) return ctx | execute story part at the current context and make one step further |
55,699 | def iterate_storyline ( ctx ) : logger . debug ( '# start iterate' ) compiled_story = ctx . compiled_story ( ) if not compiled_story : return for step in range ( ctx . current_step ( ) , len ( compiled_story . story_line ) ) : ctx = ctx . clone ( ) tail = ctx . stack_tail ( ) ctx . message = modify_stack_in_message ( ctx . message , lambda stack : stack [ : - 1 ] + [ { 'data' : tail [ 'data' ] , 'step' : step , 'topic' : tail [ 'topic' ] , } ] ) logger . debug ( '# [{}] iterate' . format ( step ) ) logger . debug ( ctx ) ctx = yield ctx | iterate the last storyline from the last visited story part |
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