idx int64 0 63k | question stringlengths 61 4.03k | target stringlengths 6 1.23k |
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3,600 | def get_form ( self , request , obj = None , ** kwargs ) : if obj is None : kwargs [ 'form' ] = SlotAdminAddForm return super ( SlotAdmin , self ) . get_form ( request , obj , ** kwargs ) | Change the form depending on whether we re adding or editing the slot . |
3,601 | def get_cached_menus ( ) : items = cache . get ( CACHE_KEY ) if items is None : menu = generate_menu ( ) cache . set ( CACHE_KEY , menu . items ) else : menu = Menu ( items ) return menu | Return the menus from the cache or generate them if needed . |
3,602 | def maybe_obj ( str_or_obj ) : if not isinstance ( str_or_obj , six . string_types ) : return str_or_obj parts = str_or_obj . split ( "." ) mod , modname = None , None for p in parts : modname = p if modname is None else "%s.%s" % ( modname , p ) try : mod = __import__ ( modname ) except ImportError : if mod is None : ... | If argument is not a string return it . |
3,603 | def generate_menu ( ) : root_menu = Menu ( list ( copy . deepcopy ( settings . WAFER_MENUS ) ) ) for dynamic_menu_func in settings . WAFER_DYNAMIC_MENUS : dynamic_menu_func = maybe_obj ( dynamic_menu_func ) dynamic_menu_func ( root_menu ) return root_menu | Generate a new list of menus . |
3,604 | def lock ( self ) : self . __fd = open ( self . __lockfile , "w" ) if self . __locktype == "wait" : fcntl . flock ( self . __fd . fileno ( ) , fcntl . LOCK_EX ) elif self . __locktype == "lock" : try : fcntl . flock ( self . __fd . fileno ( ) , fcntl . LOCK_EX | fcntl . LOCK_NB ) except IOError : raise AlreadyLocked ( ... | Try to get locked the file - the function will wait until the file is unlocked if wait was defined as locktype - the funciton will raise AlreadyLocked exception if lock was defined as locktype |
3,605 | def _make_handler ( state_token , done_function ) : class LocalServerHandler ( BaseHTTPServer . BaseHTTPRequestHandler ) : def error_response ( self , msg ) : logging . warn ( 'Error response: %(msg)s. %(path)s' , msg = msg , path = self . path ) self . send_response ( 400 ) self . send_header ( 'Content-type' , 'text/... | Makes a a handler class to use inside the basic python HTTP server . |
3,606 | def configuration ( ) : 'Loads configuration from the file system.' defaults = cfg = ConfigParser . SafeConfigParser ( ) cfg . readfp ( io . BytesIO ( defaults ) ) cfg . read ( [ '/etc/coursera/courseraoauth2client.cfg' , os . path . expanduser ( '~/.coursera/courseraoauth2client.cfg' ) , 'courseraoauth2client.cfg' , ]... | Loads configuration from the file system . |
3,607 | def _load_token_cache ( self ) : 'Reads the local fs cache for pre-authorized access tokens' try : logging . debug ( 'About to read from local file cache file %s' , self . token_cache_file ) with open ( self . token_cache_file , 'rb' ) as f : fs_cached = cPickle . load ( f ) if self . _check_token_cache_type ( fs_cache... | Reads the local fs cache for pre - authorized access tokens |
3,608 | def _save_token_cache ( self , new_cache ) : 'Write out to the filesystem a cache of the OAuth2 information.' logging . debug ( 'Looking to write to local authentication cache...' ) if not self . _check_token_cache_type ( new_cache ) : logging . error ( 'Attempt to save a bad value: %s' , new_cache ) return try : loggi... | Write out to the filesystem a cache of the OAuth2 information . |
3,609 | def _check_token_cache_type ( self , cache_value ) : def check_string_value ( name ) : return ( isinstance ( cache_value [ name ] , str ) or isinstance ( cache_value [ name ] , unicode ) ) def check_refresh_token ( ) : if 'refresh' in cache_value : return check_string_value ( 'refresh' ) else : return True return ( isi... | Checks the cache_value for appropriate type correctness . |
3,610 | def _authorize_new_tokens ( self ) : logging . info ( 'About to request new OAuth2 tokens from Coursera.' ) state_token = uuid . uuid4 ( ) . hex authorization_url = self . _build_authorizaton_url ( state_token ) sys . stdout . write ( 'Please visit the following URL to authorize this app:\n' ) sys . stdout . write ( '\... | Stands up a new localhost http server and retrieves new OAuth2 access tokens from the Coursera OAuth2 server . |
3,611 | def _exchange_refresh_tokens ( self ) : 'Exchanges a refresh token for an access token' if self . token_cache is not None and 'refresh' in self . token_cache : refresh_form = { 'grant_type' : 'refresh_token' , 'refresh_token' : self . token_cache [ 'refresh' ] , 'client_id' : self . client_id , 'client_secret' : self .... | Exchanges a refresh token for an access token |
3,612 | def foreignkey ( element , exceptions ) : label = element . field . __dict__ [ 'label' ] try : label = unicode ( label ) except NameError : pass if ( not label ) or ( label in exceptions ) : return False else : return "_queryset" in element . field . __dict__ | function to determine if each select field needs a create button or not |
3,613 | def deserialize_by_field ( value , field ) : if isinstance ( field , forms . DateTimeField ) : value = parse_datetime ( value ) elif isinstance ( field , forms . DateField ) : value = parse_date ( value ) elif isinstance ( field , forms . TimeField ) : value = parse_time ( value ) return value | Some types get serialized to JSON as strings . If we know what they are supposed to be we can deserialize them |
3,614 | def main ( ) : "Boots up the command line tool" logging . captureWarnings ( True ) args = build_parser ( ) . parse_args ( ) args . setup_logging ( args ) try : return args . func ( args ) except SystemExit : raise except : logging . exception ( 'Problem when running command. Sorry!' ) sys . exit ( 1 ) | Boots up the command line tool |
3,615 | def objectatrib ( instance , atrib ) : atrib = atrib . replace ( "__" , "." ) atribs = [ ] atribs = atrib . split ( "." ) obj = instance for atrib in atribs : if type ( obj ) == dict : result = obj [ atrib ] else : try : result = getattr ( obj , atrib ) ( ) except Exception : result = getattr ( obj , atrib ) obj = resu... | this filter is going to be useful to execute an object method or get an object attribute dynamically . this method is going to take into account the atrib param can contains underscores |
3,616 | def upload_path ( instance , filename ) : path_separator = "/" date_separator = "-" ext_separator = "." empty_string = "" model_name = model_inspect ( instance ) [ 'modelname' ] date = datetime . now ( ) . strftime ( "%Y-%m-%d" ) . split ( date_separator ) curr_day = date [ 2 ] curr_month = date [ 1 ] curr_year = date ... | This method is created to return the path to upload files . This path must be different from any other to avoid problems . |
3,617 | def remove_getdisplay ( field_name ) : str_ini = 'get_' str_end = '_display' if str_ini == field_name [ 0 : len ( str_ini ) ] and str_end == field_name [ ( - 1 ) * len ( str_end ) : ] : field_name = field_name [ len ( str_ini ) : ( - 1 ) * len ( str_end ) ] return field_name | for string get_FIELD_NAME_display return FIELD_NAME |
3,618 | def append ( self , filename_in_zip , file_contents ) : self . in_memory_zip . seek ( - 1 , io . SEEK_END ) zf = zipfile . ZipFile ( self . in_memory_zip , "a" , zipfile . ZIP_DEFLATED , False ) zf . writestr ( filename_in_zip , file_contents ) for zfile in zf . filelist : zfile . create_system = 0 zf . close ( ) self ... | Appends a file with name filename_in_zip and contents of file_contents to the in - memory zip . |
3,619 | def writetofile ( self , filename ) : f = open ( filename , "w" ) f . write ( self . read ( ) ) f . close ( ) | Writes the in - memory zip to a file . |
3,620 | def sponsor_image_url ( sponsor , name ) : if sponsor . files . filter ( name = name ) . exists ( ) : return sponsor . files . filter ( name = name ) . first ( ) . item . url return '' | Returns the corresponding url from the sponsors images |
3,621 | def sponsor_tagged_image ( sponsor , tag ) : if sponsor . files . filter ( tag_name = tag ) . exists ( ) : return sponsor . files . filter ( tag_name = tag ) . first ( ) . tagged_file . item . url return '' | returns the corresponding url from the tagged image list . |
3,622 | def ifusergroup ( parser , token ) : try : tokensp = token . split_contents ( ) groups = [ ] groups += tokensp [ 1 : ] except ValueError : raise template . TemplateSyntaxError ( "Tag 'ifusergroup' requires at least 1 argument." ) nodelist_true = parser . parse ( ( 'else' , 'endifusergroup' ) ) token = parser . next_tok... | Check to see if the currently logged in user belongs to a specific group . Requires the Django authentication contrib app and middleware . |
3,623 | def OpenHandle ( self ) : if hasattr ( self , 'handle' ) : return self . handle else : handle = c_void_p ( ) ret = vmGuestLib . VMGuestLib_OpenHandle ( byref ( handle ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return handle | Gets a handle for use with other vSphere Guest API functions . The guest library handle provides a context for accessing information about the virtual machine . |
3,624 | def CloseHandle ( self ) : if hasattr ( self , 'handle' ) : ret = vmGuestLib . VMGuestLib_CloseHandle ( self . handle . value ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) del ( self . handle ) | Releases a handle acquired with VMGuestLib_OpenHandle |
3,625 | def UpdateInfo ( self ) : ret = vmGuestLib . VMGuestLib_UpdateInfo ( self . handle . value ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) | Updates information about the virtual machine . This information is associated with the VMGuestLibHandle . |
3,626 | def GetSessionId ( self ) : sid = c_void_p ( ) ret = vmGuestLib . VMGuestLib_GetSessionId ( self . handle . value , byref ( sid ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return sid | Retrieves the VMSessionID for the current session . Call this function after calling VMGuestLib_UpdateInfo . If VMGuestLib_UpdateInfo has never been called VMGuestLib_GetSessionId returns VMGUESTLIB_ERROR_NO_INFO . |
3,627 | def GetCpuLimitMHz ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetCpuLimitMHz ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the upperlimit of processor use in MHz available to the virtual machine . For information about setting the CPU limit see Limits and Reservations on page 14 . |
3,628 | def GetCpuReservationMHz ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetCpuReservationMHz ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the minimum processing power in MHz reserved for the virtual machine . For information about setting a CPU reservation see Limits and Reservations on page 14 . |
3,629 | def GetCpuShares ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetCpuShares ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the number of CPU shares allocated to the virtual machine . For information about how an ESX server uses CPU shares to manage virtual machine priority see the vSphere Resource Management Guide . |
3,630 | def GetElapsedMs ( self ) : counter = c_uint64 ( ) ret = vmGuestLib . VMGuestLib_GetElapsedMs ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the number of milliseconds that have passed in the virtual machine since it last started running on the server . The count of elapsed time restarts each time the virtual machine is powered on resumed or migrated using VMotion . This value counts milliseconds regardless of whether the virtual machine is using ... |
3,631 | def GetHostProcessorSpeed ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetHostProcessorSpeed ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the speed of the ESX system s physical CPU in MHz . |
3,632 | def GetMemActiveMB ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetMemActiveMB ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the amount of memory the virtual machine is actively using its estimated working set size . |
3,633 | def GetMemLimitMB ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetMemLimitMB ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the upper limit of memory that is available to the virtual machine . For information about setting a memory limit see Limits and Reservations on page 14 . |
3,634 | def GetMemMappedMB ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetMemMappedMB ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the amount of memory that is allocated to the virtual machine . Memory that is ballooned swapped or has never been accessed is excluded . |
3,635 | def GetMemOverheadMB ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetMemOverheadMB ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the amount of overhead memory associated with this virtual machine that is currently consumed on the host system . Overhead memory is additional memory that is reserved for data structures required by the virtualization layer . |
3,636 | def GetMemReservationMB ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetMemReservationMB ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the minimum amount of memory that is reserved for the virtual machine . For information about setting a memory reservation see Limits and Reservations on page 14 . |
3,637 | def GetMemShares ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetMemShares ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the number of memory shares allocated to the virtual machine . For information about how an ESX server uses memory shares to manage virtual machine priority see the vSphere Resource Management Guide . |
3,638 | def GetMemSwappedMB ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetMemSwappedMB ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the amount of memory that has been reclaimed from this virtual machine by transparently swapping guest memory to disk . |
3,639 | def GetMemTargetSizeMB ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetMemTargetSizeMB ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the size of the target memory allocation for this virtual machine . |
3,640 | def GetMemUsedMB ( self ) : counter = c_uint ( ) ret = vmGuestLib . VMGuestLib_GetMemUsedMB ( self . handle . value , byref ( counter ) ) if ret != VMGUESTLIB_ERROR_SUCCESS : raise VMGuestLibException ( ret ) return counter . value | Retrieves the estimated amount of physical host memory currently consumed for this virtual machine s physical memory . |
3,641 | def wafer_form_helper ( context , helper_name ) : request = context . request module , class_name = helper_name . rsplit ( '.' , 1 ) if module not in sys . modules : __import__ ( module ) mod = sys . modules [ module ] class_ = getattr ( mod , class_name ) return class_ ( request = request ) | Find the specified Crispy FormHelper and instantiate it . Handy when you are crispyifying other apps forms . |
3,642 | def page_menus ( root_menu ) : for page in Page . objects . filter ( include_in_menu = True ) : path = page . get_path ( ) menu = path [ 0 ] if len ( path ) > 1 else None try : root_menu . add_item ( page . name , page . get_absolute_url ( ) , menu = menu ) except MenuError as e : logger . error ( "Bad menu item %r for... | Add page menus . |
3,643 | def redirect_profile ( request ) : if request . user . is_authenticated : return HttpResponseRedirect ( reverse ( 'wafer_user_profile' , args = ( request . user . username , ) ) ) else : return redirect_to_login ( next = reverse ( redirect_profile ) ) | The default destination from logging in redirect to the actual profile URL |
3,644 | def reviewed_badge ( user , talk ) : context = { 'reviewed' : False , } review = None if user and not user . is_anonymous ( ) : review = talk . reviews . filter ( reviewer = user ) . first ( ) if review : context [ 'reviewed' ] = True context [ 'review_is_current' ] = review . is_current ( ) return context | Returns a badge for the user s reviews of the talk |
3,645 | def form_valid ( self , form , forms ) : if self . object : form . save ( ) for ( formobj , linkerfield ) in forms : if form != formobj : formobj . save ( ) else : self . object = form . save ( ) for ( formobj , linkerfield ) in forms : if form != formobj : setattr ( formobj . instance , linkerfield , self . object ) f... | Called if all forms are valid . Creates a Recipe instance along with associated Ingredients and Instructions and then redirects to a success page . |
3,646 | def form_invalid ( self , form , forms , open_tabs , position_form_default ) : return self . render_to_response ( self . get_context_data ( form = form , forms = forms , open_tabs = open_tabs , position_form_default = position_form_default ) ) | Called if a form is invalid . Re - renders the context data with the data - filled forms and errors . |
3,647 | def univariate_envelope_plot ( x , mean , std , ax = None , base_alpha = 0.375 , envelopes = [ 1 , 3 ] , lb = None , ub = None , expansion = 10 , ** kwargs ) : if ax is None : f = plt . figure ( ) ax = f . add_subplot ( 1 , 1 , 1 ) elif ax == 'gca' : ax = plt . gca ( ) mean = scipy . asarray ( mean , dtype = float ) . ... | Make a plot of a mean curve with uncertainty envelopes . |
3,648 | def fetch_token ( self ) : grant_type = 'client_credentials' channel = yield self . _tvm . ticket_full ( self . _client_id , self . _client_secret , grant_type , { } ) ticket = yield channel . rx . get ( ) raise gen . Return ( self . _make_token ( ticket ) ) | Gains token from secure backend service . |
3,649 | def process_summary ( summaryfile , ** kwargs ) : logging . info ( "Nanoget: Collecting metrics from summary file {} for {} sequencing" . format ( summaryfile , kwargs [ "readtype" ] ) ) ut . check_existance ( summaryfile ) if kwargs [ "readtype" ] == "1D" : cols = [ "read_id" , "run_id" , "channel" , "start_time" , "d... | Extracting information from an albacore summary file . |
3,650 | def check_bam ( bam , samtype = "bam" ) : ut . check_existance ( bam ) samfile = pysam . AlignmentFile ( bam , "rb" ) if not samfile . has_index ( ) : pysam . index ( bam ) samfile = pysam . AlignmentFile ( bam , "rb" ) logging . info ( "Nanoget: No index for bam file could be found, created index." ) if not samfile . ... | Check if bam file is valid . |
3,651 | def process_ubam ( bam , ** kwargs ) : logging . info ( "Nanoget: Starting to collect statistics from ubam file {}." . format ( bam ) ) samfile = pysam . AlignmentFile ( bam , "rb" , check_sq = False ) if not samfile . has_index ( ) : pysam . index ( bam ) samfile = pysam . AlignmentFile ( bam , "rb" ) logging . info (... | Extracting metrics from unaligned bam format Extracting lengths |
3,652 | def process_bam ( bam , ** kwargs ) : logging . info ( "Nanoget: Starting to collect statistics from bam file {}." . format ( bam ) ) samfile = check_bam ( bam ) chromosomes = samfile . references params = zip ( [ bam ] * len ( chromosomes ) , chromosomes ) with cfutures . ProcessPoolExecutor ( ) as executor : datadf =... | Combines metrics from bam after extraction . |
3,653 | def extract_from_bam ( params ) : bam , chromosome = params samfile = pysam . AlignmentFile ( bam , "rb" ) return [ ( read . query_name , nanomath . ave_qual ( read . query_qualities ) , nanomath . ave_qual ( read . query_alignment_qualities ) , read . query_length , read . query_alignment_length , read . mapping_quali... | Extracts metrics from bam . |
3,654 | def get_pID ( read ) : try : return 100 * ( 1 - read . get_tag ( "NM" ) / read . query_alignment_length ) except KeyError : try : return 100 * ( 1 - ( parse_MD ( read . get_tag ( "MD" ) ) + parse_CIGAR ( read . cigartuples ) ) / read . query_alignment_length ) except KeyError : return None except ZeroDivisionError : re... | Return the percent identity of a read . |
3,655 | def handle_compressed_input ( inputfq , file_type = "fastq" ) : ut . check_existance ( inputfq ) if inputfq . endswith ( ( '.gz' , 'bgz' ) ) : import gzip logging . info ( "Nanoget: Decompressing gzipped {} {}" . format ( file_type , inputfq ) ) return gzip . open ( inputfq , 'rt' ) elif inputfq . endswith ( '.bz2' ) :... | Return handles from compressed files according to extension . |
3,656 | def process_fasta ( fasta , ** kwargs ) : logging . info ( "Nanoget: Starting to collect statistics from a fasta file." ) inputfasta = handle_compressed_input ( fasta , file_type = "fasta" ) return ut . reduce_memory_usage ( pd . DataFrame ( data = [ len ( rec ) for rec in SeqIO . parse ( inputfasta , "fasta" ) ] , col... | Combine metrics extracted from a fasta file . |
3,657 | def process_fastq_plain ( fastq , ** kwargs ) : logging . info ( "Nanoget: Starting to collect statistics from plain fastq file." ) inputfastq = handle_compressed_input ( fastq ) return ut . reduce_memory_usage ( pd . DataFrame ( data = [ res for res in extract_from_fastq ( inputfastq ) if res ] , columns = [ "quals" ,... | Combine metrics extracted from a fastq file . |
3,658 | def stream_fastq_full ( fastq , threads ) : logging . info ( "Nanoget: Starting to collect full metrics from plain fastq file." ) inputfastq = handle_compressed_input ( fastq ) with cfutures . ProcessPoolExecutor ( max_workers = threads ) as executor : for results in executor . map ( extract_all_from_fastq , SeqIO . pa... | Generator for returning metrics extracted from fastq . |
3,659 | def process_fastq_rich ( fastq , ** kwargs ) : logging . info ( "Nanoget: Starting to collect statistics from rich fastq file." ) inputfastq = handle_compressed_input ( fastq ) res = [ ] for record in SeqIO . parse ( inputfastq , "fastq" ) : try : read_info = info_to_dict ( record . description ) res . append ( ( nanom... | Extract metrics from a richer fastq file . |
3,660 | def fq_minimal ( fq ) : try : while True : time = next ( fq ) [ 1 : ] . split ( " " ) [ 4 ] [ 11 : - 1 ] length = len ( next ( fq ) ) next ( fq ) next ( fq ) yield time , length except StopIteration : yield None | Minimal fastq metrics extractor . |
3,661 | def _get_piece ( string , index ) : piece = string [ index ] . strip ( ) piece = piece . upper ( ) piece_dict = { 'R' : Rook , 'P' : Pawn , 'B' : Bishop , 'N' : Knight , 'Q' : Queen , 'K' : King } try : return piece_dict [ piece ] except KeyError : raise ValueError ( "Piece {} is invalid" . format ( piece ) ) | Returns Piece subclass given index of piece . |
3,662 | def short_alg ( algebraic_string , input_color , position ) : return make_legal ( incomplete_alg ( algebraic_string , input_color , position ) , position ) | Converts a string written in short algebraic form the color of the side whose turn it is and the corresponding position into a complete move that can be played . If no moves match None is returned . |
3,663 | def implicify_hydrogens ( self ) : explicit = defaultdict ( list ) c = 0 for n , atom in self . atoms ( ) : if atom . element == 'H' : for m in self . neighbors ( n ) : if self . _node [ m ] . element != 'H' : explicit [ m ] . append ( n ) for n , h in explicit . items ( ) : atom = self . _node [ n ] len_h = len ( h ) ... | remove explicit hydrogen if possible |
3,664 | def explicify_hydrogens ( self ) : tmp = [ ] for n , atom in self . atoms ( ) : if atom . element != 'H' : for _ in range ( atom . get_implicit_h ( [ x . order for x in self . _adj [ n ] . values ( ) ] ) ) : tmp . append ( n ) for n in tmp : self . add_bond ( n , self . add_atom ( H ) , Bond ( ) ) self . flush_cache ( ... | add explicit hydrogens to atoms |
3,665 | def check_valence ( self ) : return [ x for x , atom in self . atoms ( ) if not atom . check_valence ( self . environment ( x ) ) ] | check valences of all atoms |
3,666 | def _matcher ( self , other ) : if isinstance ( other , ( self . _get_subclass ( 'CGRContainer' ) , MoleculeContainer ) ) : return GraphMatcher ( other , self , lambda x , y : x == y , lambda x , y : x == y ) raise TypeError ( 'only cgr-cgr possible' ) | return VF2 GraphMatcher |
3,667 | def to_datetime ( date ) : return datetime . datetime . combine ( date , datetime . datetime . min . time ( ) ) | Turn a date into a datetime at midnight . |
3,668 | def iter_size_changes ( self , issue ) : try : size_changes = list ( filter ( lambda h : h . field == 'Story Points' , itertools . chain . from_iterable ( [ c . items for c in issue . changelog . histories ] ) ) ) except AttributeError : return try : current_size = issue . fields . __dict__ [ self . fields [ 'StoryPoin... | Yield an IssueSnapshot for each time the issue size changed |
3,669 | def iter_changes ( self , issue , include_resolution_changes = True ) : is_resolved = False try : status_changes = list ( filter ( lambda h : h . field == 'status' , itertools . chain . from_iterable ( [ c . items for c in issue . changelog . histories ] ) ) ) except AttributeError : return last_status = status_changes... | Yield an IssueSnapshot for each time the issue changed status or resolution |
3,670 | def find_issues ( self , criteria = { } , jql = None , order = 'KEY ASC' , verbose = False , changelog = True ) : query = [ ] if criteria . get ( 'project' , False ) : query . append ( 'project IN (%s)' % ', ' . join ( [ '"%s"' % p for p in criteria [ 'project' ] ] ) ) if criteria . get ( 'issue_types' , False ) : quer... | Return a list of issues with changelog metadata . |
3,671 | def list_catalogs ( self ) : _form = CatalogSelectForm ( current = self . current ) _form . set_choices_of ( 'catalog' , [ ( i , i ) for i in fixture_bucket . get_keys ( ) ] ) self . form_out ( _form ) | Lists existing catalogs respect to ui view template format |
3,672 | def get_catalog ( self ) : catalog_data = fixture_bucket . get ( self . input [ 'form' ] [ 'catalog' ] ) add_or_edit = "Edit" if catalog_data . exists else "Add" catalog_edit_form = CatalogEditForm ( current = self . current , title = '%s: %s' % ( add_or_edit , self . input [ 'form' ] [ 'catalog' ] ) ) if catalog_data ... | Get existing catalog and fill the form with the model data . If given key not found as catalog it generates an empty catalog data form . |
3,673 | def save_catalog ( self ) : if self . input [ "cmd" ] == 'save_catalog' : try : edited_object = dict ( ) for i in self . input [ "form" ] [ "CatalogDatas" ] : edited_object [ i [ "catalog_key" ] ] = { "en" : i [ "en" ] , "tr" : i [ "tr" ] } newobj = fixture_bucket . get ( self . input [ "object_key" ] ) newobj . data =... | Saves the catalog data to given key Cancels if the cmd is cancel Notifies user with the process . |
3,674 | def merge_truthy ( * dicts ) : merged = { } for d in dicts : for k , v in d . items ( ) : merged [ k ] = v or merged . get ( k , v ) return merged | Merge multiple dictionaries keeping the truthy values in case of key collisions . |
3,675 | def perform ( self ) : db_versions = self . table . versions ( ) version = self . version if ( version . is_processed ( db_versions ) and not self . config . force_version == self . version . number ) : self . log ( u'version {} is already installed' . format ( version . number ) ) return self . start ( ) try : self . ... | Perform the version upgrade on the database . |
3,676 | def _perform_version ( self , version ) : if version . is_noop ( ) : self . log ( u'version {} is a noop' . format ( version . number ) ) else : self . log ( u'execute base pre-operations' ) for operation in version . pre_operations ( ) : operation . execute ( self . log ) if self . config . mode : self . log ( u'execu... | Inner method for version upgrade . |
3,677 | def _do_upgrade ( self ) : self . current . output [ 'cmd' ] = 'upgrade' self . current . output [ 'user_id' ] = self . current . user_id self . terminate_existing_login ( ) self . current . user . bind_private_channel ( self . current . session . sess_id ) user_sess = UserSessionID ( self . current . user_id ) user_se... | open websocket connection |
3,678 | def do_view ( self ) : self . current . output [ 'login_process' ] = True self . current . task_data [ 'login_successful' ] = False if self . current . is_auth : self . _do_upgrade ( ) else : try : auth_result = self . current . auth . authenticate ( self . current . input [ 'username' ] , self . current . input [ 'pas... | Authenticate user with given credentials . Connects user s queue and exchange |
3,679 | def __get_mapping ( self , structures ) : for c in permutations ( structures , len ( self . __patterns ) ) : for m in product ( * ( x . get_substructure_mapping ( y , limit = 0 ) for x , y in zip ( self . __patterns , c ) ) ) : mapping = { } for i in m : mapping . update ( i ) if mapping : yield mapping | match each pattern to each molecule . if all patterns matches with all molecules return generator of all possible mapping . |
3,680 | def get ( self , default = None ) : d = cache . get ( self . key ) return ( ( json . loads ( d . decode ( 'utf-8' ) ) if self . serialize else d ) if d is not None else default ) | return the cached value or default if it can t be found |
3,681 | def set ( self , val , lifetime = None ) : cache . set ( self . key , ( json . dumps ( val ) if self . serialize else val ) , lifetime or settings . DEFAULT_CACHE_EXPIRE_TIME ) return val | set cache value |
3,682 | def get_all ( self ) : result = cache . lrange ( self . key , 0 , - 1 ) return ( json . loads ( item . decode ( 'utf-8' ) ) for item in result if item ) if self . serialize else result | Get all list items . |
3,683 | def remove_item ( self , val ) : return cache . lrem ( self . key , json . dumps ( val ) ) | Removes given item from the list . |
3,684 | def flush ( cls , * args ) : return _remove_keys ( [ ] , [ ( cls . _make_key ( args ) if args else cls . PREFIX ) + '*' ] ) | Removes all keys of this namespace Without args clears all keys starting with cls . PREFIX if called with args clears keys starting with given cls . PREFIX + args |
3,685 | def update_or_expire_session ( self ) : if not hasattr ( self , 'key' ) : return now = time . time ( ) timestamp = float ( self . get ( ) or 0 ) or now sess_id = self . sess_id or UserSessionID ( self . user_id ) . get ( ) if sess_id and now - timestamp > self . SESSION_EXPIRE_TIME : Session ( sess_id ) . delete ( ) re... | Deletes session if keepalive request expired otherwise updates the keepalive timestamp value |
3,686 | def send_message_for_lane_change ( sender , ** kwargs ) : current = kwargs [ 'current' ] owners = kwargs [ 'possible_owners' ] if 'lane_change_invite' in current . task_data : msg_context = current . task_data . pop ( 'lane_change_invite' ) else : msg_context = DEFAULT_LANE_CHANGE_INVITE_MSG wfi = WFCache ( current ) .... | Sends a message to possible owners of the current workflows next lane . |
3,687 | def set_password ( sender , ** kwargs ) : if sender . model_class . __name__ == 'User' : usr = kwargs [ 'object' ] if not usr . password . startswith ( '$pbkdf2' ) : usr . set_password ( usr . password ) usr . save ( ) | Encrypts password of the user . |
3,688 | def channel_list ( self ) : if self . current . task_data . get ( 'msg' , False ) : if self . current . task_data . get ( 'target_channel_key' , False ) : self . current . output [ 'msgbox' ] = { 'type' : 'info' , "title" : _ ( u"Successful Operation" ) , "msg" : self . current . task_data [ 'msg' ] } del self . curren... | Main screen for channel management . Channels listed and operations can be chosen on the screen . If there is an error message like non - choice it is shown here . |
3,689 | def channel_choice_control ( self ) : self . current . task_data [ 'control' ] , self . current . task_data [ 'msg' ] = self . selection_error_control ( self . input [ 'form' ] ) if self . current . task_data [ 'control' ] : self . current . task_data [ 'option' ] = self . input [ 'cmd' ] self . current . task_data [ '... | It controls errors . If there is an error returns channel list screen with error message . |
3,690 | def create_new_channel ( self ) : self . current . task_data [ 'new_channel' ] = True _form = NewChannelForm ( Channel ( ) , current = self . current ) _form . title = _ ( u"Specify Features of New Channel to Create" ) _form . forward = fields . Button ( _ ( u"Create" ) , flow = "find_target_channel" ) self . form_out ... | Features of new channel are specified like channel s name owner etc . |
3,691 | def save_new_channel ( self ) : form_info = self . input [ 'form' ] channel = Channel ( typ = 15 , name = form_info [ 'name' ] , description = form_info [ 'description' ] , owner_id = form_info [ 'owner_id' ] ) channel . blocking_save ( ) self . current . task_data [ 'target_channel_key' ] = channel . key | It saves new channel according to specified channel features . |
3,692 | def choose_existing_channel ( self ) : if self . current . task_data . get ( 'msg' , False ) : self . show_warning_messages ( ) _form = ChannelListForm ( ) _form . title = _ ( u"Choose a Channel Which Will Be Merged With Chosen Channels" ) for channel in Channel . objects . filter ( typ = 15 ) . exclude ( key__in = sel... | It is a channel choice list and chosen channels at previous step shouldn t be on the screen . |
3,693 | def existing_choice_control ( self ) : self . current . task_data [ 'existing' ] = False self . current . task_data [ 'msg' ] = _ ( u"You should choose just one channel to do operation." ) keys , names = self . return_selected_form_items ( self . input [ 'form' ] [ 'ChannelList' ] ) if len ( keys ) == 1 : self . curren... | It controls errors . It generates an error message if zero or more than one channels are selected . |
3,694 | def split_channel ( self ) : if self . current . task_data . get ( 'msg' , False ) : self . show_warning_messages ( ) self . current . task_data [ 'split_operation' ] = True channel = Channel . objects . get ( self . current . task_data [ 'chosen_channels' ] [ 0 ] ) _form = SubscriberListForm ( title = _ ( u'Choose Sub... | A channel can be splitted to new channel or other existing channel . It creates subscribers list as selectable to moved . |
3,695 | def subscriber_choice_control ( self ) : self . current . task_data [ 'option' ] = None self . current . task_data [ 'chosen_subscribers' ] , names = self . return_selected_form_items ( self . input [ 'form' ] [ 'SubscriberList' ] ) self . current . task_data [ 'msg' ] = "You should choose at least one subscriber for m... | It controls subscribers choice and generates error message if there is a non - choice . |
3,696 | def move_complete_channel ( self ) : to_channel = Channel . objects . get ( self . current . task_data [ 'target_channel_key' ] ) chosen_channels = self . current . task_data [ 'chosen_channels' ] chosen_channels_names = self . current . task_data [ 'chosen_channels_names' ] with BlockSave ( Subscriber , query_dict = {... | Channels and theirs subscribers are moved completely to new channel or existing channel . |
3,697 | def move_chosen_subscribers ( self ) : from_channel = Channel . objects . get ( self . current . task_data [ 'chosen_channels' ] [ 0 ] ) to_channel = Channel . objects . get ( self . current . task_data [ 'target_channel_key' ] ) with BlockSave ( Subscriber , query_dict = { 'channel_id' : to_channel . key } ) : for sub... | After splitting operation only chosen subscribers are moved to new channel or existing channel . |
3,698 | def copy_and_move_messages ( from_channel , to_channel ) : with BlockSave ( Message , query_dict = { 'channel_id' : to_channel . key } ) : for message in Message . objects . filter ( channel = from_channel , typ = 15 ) : message . key = '' message . channel = to_channel message . save ( ) | While splitting channel and moving chosen subscribers to new channel old channel s messages are copied and moved to new channel . |
3,699 | def show_warning_messages ( self , title = _ ( u"Incorrect Operation" ) , box_type = 'warning' ) : msg = self . current . task_data [ 'msg' ] self . current . output [ 'msgbox' ] = { 'type' : box_type , "title" : title , "msg" : msg } del self . current . task_data [ 'msg' ] | It shows incorrect operations or successful operation messages . |
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