idx int64 0 251k | question stringlengths 53 3.53k | target stringlengths 5 1.23k | len_question int64 20 893 | len_target int64 3 238 |
|---|---|---|---|---|
6,200 | def trim_sparse ( M , n_std = 3 , s_min = None , s_max = None ) : try : from scipy . sparse import coo_matrix except ImportError as e : print ( str ( e ) ) print ( "I am peforming dense normalization by default." ) return trim_dense ( M . todense ( ) ) r = M . tocoo ( ) sparsity = np . array ( r . sum ( axis = 1 ) ) . ... | Apply the trimming procedure to a sparse matrix . | 301 | 10 |
6,201 | def normalize_dense ( M , norm = "frag" , order = 1 , iterations = 3 ) : s = np . array ( M , np . float64 ) floatorder = np . float64 ( order ) if norm == "SCN" : for _ in range ( 0 , iterations ) : sumrows = s . sum ( axis = 1 ) maskrows = ( sumrows != 0 ) [ : , None ] * ( sumrows != 0 ) [ None , : ] sums_row = sumro... | Apply one of the many normalization types to input dense matrix . Will also apply any callable norms such as a user - made or a lambda function . | 572 | 31 |
6,202 | def normalize_sparse ( M , norm = "frag" , order = 1 , iterations = 3 ) : try : from scipy . sparse import csr_matrix except ImportError as e : print ( str ( e ) ) print ( "I am peforming dense normalization by default." ) return normalize_dense ( M . todense ( ) ) r = csr_matrix ( M ) if norm == "SCN" : for _ in range... | Applies a normalization type to a sparse matrix . | 316 | 11 |
6,203 | def GC_wide ( genome , window = 1000 ) : GC = [ ] from Bio import SeqIO with open ( genome ) as handle : sequence = "" . join ( [ str ( record . seq ) for record in SeqIO . parse ( handle , "fasta" ) ] ) n = len ( sequence ) for i in range ( 0 , n , window ) : portion = sequence [ i : min ( i + window , n ) ] GC . appe... | Compute GC across a window of given length . | 107 | 10 |
6,204 | def to_dade_matrix ( M , annotations = "" , filename = None ) : n , m = M . shape A = np . zeros ( ( n + 1 , m + 1 ) ) A [ 1 : , 1 : ] = M if not annotations : annotations = np . array ( [ "" for _ in n ] , dtype = str ) A [ 0 , : ] = annotations A [ : , 0 ] = annotations . T if filename : try : np . savetxt ( filename... | Returns a Dade matrix from input numpy matrix . Any annotations are added as header . If filename is provided and valid said matrix is also saved as text . | 165 | 32 |
6,205 | def largest_connected_component ( matrix ) : try : import scipy . sparse n , components = scipy . sparse . csgraph . connected_components ( matrix , directed = False ) print ( "I found " + str ( n ) + " connected components." ) component_dist = collections . Counter ( components ) print ( "Distribution of components: "... | Compute the adjacency matrix of the largest connected component of the graph whose input matrix is adjacent . | 172 | 21 |
6,206 | def to_structure ( matrix , alpha = 1 ) : connected = largest_connected_component ( matrix ) distances = to_distance ( connected , alpha ) n , m = connected . shape bary = np . sum ( np . triu ( distances , 1 ) ) / ( n ** 2 ) # barycenters d = np . array ( np . sum ( distances ** 2 , 0 ) / n - bary ) # distances to ori... | Compute best matching 3D genome structure from underlying input matrix using ShRec3D - derived method from Lesne et al . 2014 . | 344 | 28 |
6,207 | def get_missing_bins ( original , trimmed ) : original_diag = np . diag ( original ) trimmed_diag = np . diag ( trimmed ) index = [ ] m = min ( original . shape ) for j in range ( min ( trimmed . shape ) ) : k = 0 while original_diag [ j + k ] != trimmed_diag [ j ] and k < 2 * m : k += 1 index . append ( k + j ) return... | Retrieve indices of a trimmed matrix with respect to the original matrix . Fairly fast but is only correct if diagonal values are different which is always the case in practice . | 108 | 34 |
6,208 | def distance_to_contact ( D , alpha = 1 ) : if callable ( alpha ) : distance_function = alpha else : try : a = np . float64 ( alpha ) def distance_function ( x ) : return 1 / ( x ** ( 1 / a ) ) except TypeError : print ( "Alpha parameter must be callable or an array-like" ) raise except ZeroDivisionError : raise ValueE... | Compute contact matrix from input distance matrix . Distance values of zeroes are given the largest contact count otherwise inferred non - zero distance values . | 157 | 29 |
6,209 | def pdb_to_structure ( filename ) : try : from Bio . PDB import PDB except ImportError : print ( "I can't import Biopython which is needed to handle PDB files." ) raise p = PDB . PDBParser ( ) structure = p . get_structure ( 'S' , filename ) for _ in structure . get_chains ( ) : atoms = [ np . array ( atom . get_coord ... | Import a structure object from a PDB file . | 112 | 10 |
6,210 | def positions_to_contigs ( positions ) : if isinstance ( positions , np . ndarray ) : flattened_positions = positions . flatten ( ) else : try : flattened_positions = np . array ( [ pos for contig in positions for pos in contig ] ) except TypeError : flattened_positions = np . array ( positions ) if ( np . diff ( posit... | Flattens and converts a positions array to a contigs array if applicable . | 186 | 16 |
6,211 | def distance_diagonal_law ( matrix , positions = None ) : n = min ( matrix . shape ) if positions is None : return np . array ( [ np . average ( np . diagonal ( matrix , j ) ) for j in range ( n ) ] ) else : contigs = positions_to_contigs ( positions ) def is_intra ( i , j ) : return contigs [ i ] == contigs [ j ] max_... | Compute a distance law trend using the contact averages of equal distances . Specific positions can be supplied if needed . | 308 | 22 |
6,212 | def rippe_parameters ( matrix , positions , lengths = None , init = None , circ = False ) : n , _ = matrix . shape if lengths is None : lengths = np . abs ( np . diff ( positions ) ) measurements , bins = [ ] , [ ] for i in range ( n ) : for j in range ( 1 , i ) : mean_length = ( lengths [ i ] + lengths [ j ] ) / 2. if... | Estimate parameters from the model described in Rippe et al . 2001 . | 218 | 16 |
6,213 | def scalogram ( M , circ = False ) : # Sanity checks if not type ( M ) is np . ndarray : M = np . array ( M ) if M . shape [ 0 ] != M . shape [ 1 ] : raise ValueError ( "Matrix is not square." ) try : n = min ( M . shape ) except AttributeError : n = M . size N = np . zeros ( M . shape ) for i in range ( n ) : for j in... | Computes so - called scalograms used to easily visualize contacts at different distance scales . Edge cases have been painstakingly taken care of . | 315 | 28 |
6,214 | def asd ( M1 , M2 ) : from scipy . fftpack import fft2 spectra1 = np . abs ( fft2 ( M1 ) ) spectra2 = np . abs ( fft2 ( M2 ) ) return np . linalg . norm ( spectra2 - spectra1 ) | Compute a Fourier transform based distance between two matrices . | 72 | 13 |
6,215 | def remove_intra ( M , contigs ) : N = np . copy ( M ) n = len ( N ) assert n == len ( contigs ) # Naive implmentation for now for ( i , j ) in itertools . product ( range ( n ) , range ( n ) ) : if contigs [ i ] == contigs [ j ] : N [ i , j ] = 0 return N | Remove intrachromosomal contacts | 88 | 7 |
6,216 | def positions_to_contigs ( positions ) : contig_labels = np . zeros_like ( positions ) contig_index = 0 for i , p in enumerate ( positions ) : if p == 0 : contig_index += 1 contig_labels [ i ] = contig_index return contig_labels | Label contigs according to relative positions | 73 | 7 |
6,217 | def contigs_to_positions ( contigs , binning = 10000 ) : positions = np . zeros_like ( contigs ) index = 0 for _ , chunk in itertools . groubpy ( contigs ) : l = len ( chunk ) positions [ index : index + l ] = np . arange ( list ( chunk ) ) * binning index += l return positions | Build positions from contig labels | 83 | 6 |
6,218 | def split_matrix ( M , contigs ) : index = 0 for _ , chunk in itertools . groubpy ( contigs ) : l = len ( chunk ) yield M [ index : index + l , index : index + l ] index += l | Split multiple chromosome matrix | 56 | 4 |
6,219 | def find_nearest ( sorted_list , x ) : if x <= sorted_list [ 0 ] : return sorted_list [ 0 ] elif x >= sorted_list [ - 1 ] : return sorted_list [ - 1 ] else : lower = find_le ( sorted_list , x ) upper = find_ge ( sorted_list , x ) if ( x - lower ) > ( upper - x ) : return upper else : return lower | Find the nearest item of x from sorted array . | 95 | 10 |
6,220 | def format_x_tick ( axis , major_locator = None , major_formatter = None , minor_locator = None , minor_formatter = None ) : if major_locator : axis . xaxis . set_major_locator ( major_locator ) if major_formatter : axis . xaxis . set_major_formatter ( major_formatter ) if minor_locator : axis . xaxis . set_minor_locat... | Set x axis s format . | 197 | 6 |
6,221 | def set_legend ( axis , lines , legend ) : try : if legend : axis . legend ( lines , legend ) except Exception as e : raise ValueError ( "invalid 'legend', Error: %s" % e ) | Set line legend . | 50 | 4 |
6,222 | def get_max ( array ) : largest = - np . inf for i in array : try : if i > largest : largest = i except : pass if np . isinf ( largest ) : raise ValueError ( "there's no numeric value in array!" ) else : return largest | Get maximum value of an array . Automatically ignore invalid data . | 59 | 13 |
6,223 | def get_min ( array ) : smallest = np . inf for i in array : try : if i < smallest : smallest = i except : pass if np . isinf ( smallest ) : raise ValueError ( "there's no numeric value in array!" ) else : return smallest | Get minimum value of an array . Automatically ignore invalid data . | 58 | 13 |
6,224 | def get_yAxis_limit ( y , lower = 0.05 , upper = 0.2 ) : smallest = get_min ( y ) largest = get_max ( y ) gap = largest - smallest if gap >= 0.000001 : y_min = smallest - lower * gap y_max = largest + upper * gap else : y_min = smallest - lower * abs ( smallest ) y_max = largest + upper * abs ( largest ) return y_min ,... | Find optimal y_min and y_max that guarantee enough space for legend and plot . | 105 | 18 |
6,225 | def create_figure ( width = 20 , height = 10 ) : figure = plt . figure ( figsize = ( width , height ) ) axis = figure . add_subplot ( 1 , 1 , 1 ) return figure , axis | Create a figure instance . | 49 | 5 |
6,226 | def preprocess_x_y ( x , y ) : def is_iterable_slicable ( a ) : if hasattr ( a , "__iter__" ) and hasattr ( a , "__getitem__" ) : return True else : return False if is_iterable_slicable ( x ) : if is_iterable_slicable ( x [ 0 ] ) : return x , y else : return ( x , ) , ( y , ) else : raise ValueError ( "invalid input!" ... | Preprocess x y input data . Returns list of list style . | 115 | 13 |
6,227 | def execute ( input_params , engine , cwd = None ) : try : taskengine_exe = config . get ( 'engine' ) except NoConfigOptionError : raise TaskEngineNotFoundError ( "Task Engine config option not set." + "\nPlease verify the 'engine' configuration setting." ) if not os . path . exists ( taskengine_exe ) : raise TaskEngin... | Execute a task with the provided input parameters | 465 | 9 |
6,228 | def run ( self , wrappers = [ "" , "" ] ) : opened_file = open ( self . lyfile , 'w' ) lilystring = self . piece_obj . toLily ( ) opened_file . writelines ( wrappers [ 0 ] + "\\version \"2.18.2\" \n" + lilystring + wrappers [ 1 ] ) opened_file . close ( ) # subprocess.Popen(['sudo', self.lily_script," --output=" + # se... | run the lilypond script on the hierarchy class | 154 | 11 |
6,229 | def extract_fasta ( partition_file , fasta_file , output_dir , chunk_size = DEFAULT_CHUNK_SIZE , max_cores = DEFAULT_MAX_CORES , ) : genome = { record . id : record . seq for record in SeqIO . parse ( fasta_file , "fasta" ) } data_chunks = list ( zip ( * np . genfromtxt ( partition_file , usecols = ( 0 , 1 ) , dtype = ... | Extract sequences from bins | 362 | 5 |
6,230 | def merge_fasta ( fasta_file , output_dir ) : # First, define some functions for ordering chunks and detecting # consecutive chunk sequences def chunk_lexicographic_order ( chunk ) : """A quick callback to sort chunk ids lexicographically (first on original names alphabetically, then on relative position on the origina... | Merge chunks into complete FASTA bins | 706 | 9 |
6,231 | def monitor ( ) : log = logging . getLogger ( __name__ ) loop = asyncio . get_event_loop ( ) asyncio . ensure_future ( console ( loop , log ) ) loop . run_forever ( ) | Wrapper to call console with a loop . | 51 | 9 |
6,232 | def make_object ( cls , data ) : if issubclass ( cls , Object ) : self = object . __new__ ( cls ) self . _data = data else : self = data return self | Creates an API object of class cls setting its _data to data . Subclasses of Object are required to use this to build a new empty instance without using their constructor . | 46 | 36 |
6,233 | def String ( length = None , * * kwargs ) : return Property ( length = length , types = stringy_types , convert = to_string , * * kwargs ) | A string valued property with max . length . | 40 | 9 |
6,234 | def Datetime ( null = True , * * kwargs ) : return Property ( types = datetime . datetime , convert = util . local_timezone , load = dateutil . parser . parse , null = null , * * kwargs ) | A datetime property . | 54 | 5 |
6,235 | def InstanceOf ( cls , * * kwargs ) : return Property ( types = cls , load = cls . load , * * kwargs ) | A property that is an instance of cls . | 36 | 10 |
6,236 | def ListOf ( cls , * * kwargs ) : def _list_load ( value ) : return [ cls . load ( d ) for d in value ] return Property ( types = list , load = _list_load , default = list , * * kwargs ) | A property that is a list of cls . | 61 | 10 |
6,237 | def add_dimension ( self , name , data = None ) : self . dimensions . add ( name ) if data is None : valobj = self . __dimtype__ ( ) else : valobj = make_object ( self . __dimtype__ , data ) self . _data [ name ] = valobj setattr ( self , name , valobj ) return valobj | Add a named dimension to this entity . | 79 | 8 |
6,238 | def print_block ( self , section_key , f = sys . stdout , file_format = "mwtab" ) : if file_format == "mwtab" : for key , value in self [ section_key ] . items ( ) : if section_key == "METABOLOMICS WORKBENCH" and key not in ( "VERSION" , "CREATED_ON" ) : continue if key in ( "VERSION" , "CREATED_ON" ) : cw = 20 - len (... | Print mwtab section into a file or stdout . | 731 | 12 |
6,239 | def _is_mwtab ( string ) : if isinstance ( string , str ) : lines = string . split ( "\n" ) elif isinstance ( string , bytes ) : lines = string . decode ( "utf-8" ) . split ( "\n" ) else : raise TypeError ( "Expecting <class 'str'> or <class 'bytes'>, but {} was passed" . format ( type ( string ) ) ) lines = [ line for... | Test if input string is in mwtab format . | 142 | 11 |
6,240 | def getTraceIdsBySpanName ( self , service_name , span_name , end_ts , limit , order ) : self . send_getTraceIdsBySpanName ( service_name , span_name , end_ts , limit , order ) return self . recv_getTraceIdsBySpanName ( ) | Fetch trace ids by service and span name . Gets limit number of entries from before the end_ts . | 77 | 23 |
6,241 | def getTraceIdsByServiceName ( self , service_name , end_ts , limit , order ) : self . send_getTraceIdsByServiceName ( service_name , end_ts , limit , order ) return self . recv_getTraceIdsByServiceName ( ) | Fetch trace ids by service name . Gets limit number of entries from before the end_ts . | 66 | 21 |
6,242 | def getTraceIdsByAnnotation ( self , service_name , annotation , value , end_ts , limit , order ) : self . send_getTraceIdsByAnnotation ( service_name , annotation , value , end_ts , limit , order ) return self . recv_getTraceIdsByAnnotation ( ) | Fetch trace ids with a particular annotation . Gets limit number of entries from before the end_ts . | 74 | 22 |
6,243 | def getTracesByIds ( self , trace_ids , adjust ) : self . send_getTracesByIds ( trace_ids , adjust ) return self . recv_getTracesByIds ( ) | Get the full traces associated with the given trace ids . | 45 | 12 |
6,244 | def getTraceSummariesByIds ( self , trace_ids , adjust ) : self . send_getTraceSummariesByIds ( trace_ids , adjust ) return self . recv_getTraceSummariesByIds ( ) | Fetch trace summaries for the given trace ids . | 54 | 12 |
6,245 | def getTraceCombosByIds ( self , trace_ids , adjust ) : self . send_getTraceCombosByIds ( trace_ids , adjust ) return self . recv_getTraceCombosByIds ( ) | Not content with just one of traces summaries or timelines? Want it all? This is the method for you . | 51 | 23 |
6,246 | def setTraceTimeToLive ( self , trace_id , ttl_seconds ) : self . send_setTraceTimeToLive ( trace_id , ttl_seconds ) self . recv_setTraceTimeToLive ( ) | Change the TTL of a trace . If we find an interesting trace we want to keep around for further investigation . | 53 | 22 |
6,247 | def discover_datasource_columns ( datastore_str , datasource_id ) : datastore = DataStore ( datastore_str ) datasource = datastore . get_datasource ( datasource_id ) if datasource . type != "RASTER" : return datasource . list_columns ( ) else : return [ ] | Loop through the datastore s datasources to find the datasource identified by datasource_id return the matching datasource s columns . | 80 | 28 |
6,248 | def _get_column_type ( self , column ) : ctype = column . GetType ( ) if ctype in [ ogr . OFTInteger , ogr . OFTReal ] : return 'numeric' else : return 'string' | Return numeric if the column is of type integer or real otherwise return string . | 53 | 15 |
6,249 | def _get_default_mapfile_excerpt ( self ) : layerobj = self . _get_layer_stub ( ) classobj = mapscript . classObj ( ) layerobj . insertClass ( classobj ) styleobj = self . _get_default_style ( ) classobj . insertStyle ( styleobj ) return mapserializer . layerobj_to_dict ( layerobj , None ) | Given an OGR string an OGR connection and an OGR layer create and return a representation of a MapFile LAYER block . | 87 | 28 |
6,250 | def _get_layer_stub ( self ) : layerobj = mapscript . layerObj ( ) layerobj . name = self . name layerobj . status = mapscript . MS_ON projection = self . ogr_layer . GetSpatialRef ( ) featureIdColumn = self . _get_featureId_column ( ) if featureIdColumn is not None and featureIdColumn != '' : layerobj . metadata . set... | builds a minimal mapscript layerobj with no styling | 498 | 11 |
6,251 | def reelect_app ( self , request , app ) : # disconnect app explicitly to break possibly existing connection app . disconnect ( ) endpoints_size = len ( app . locator . endpoints ) # try x times, where x is the number of different endpoints in app locator. for _ in xrange ( 0 , endpoints_size + 1 ) : # last chance to t... | tries to connect to the same app on differnet host from dist - info | 540 | 17 |
6,252 | def RecordHelloWorld ( handler , t ) : url = "%s/receive_recording.py" % THIS_URL t . startRecording ( url ) t . say ( "Hello, World." ) t . stopRecording ( ) json = t . RenderJson ( ) logging . info ( "RecordHelloWorld json: %s" % json ) handler . response . out . write ( json ) | Demonstration of recording a message . | 87 | 7 |
6,253 | def RedirectDemo ( handler , t ) : # t.say ("One moment please.") t . redirect ( SIP_PHONE ) json = t . RenderJson ( ) logging . info ( "RedirectDemo json: %s" % json ) handler . response . out . write ( json ) | Demonstration of redirecting to another number . | 66 | 9 |
6,254 | def TransferDemo ( handler , t ) : t . say ( "One moment please." ) t . transfer ( MY_PHONE ) t . say ( "Hi. I am a robot" ) json = t . RenderJson ( ) logging . info ( "TransferDemo json: %s" % json ) handler . response . out . write ( json ) | Demonstration of transfering to another number | 77 | 8 |
6,255 | def retry ( ExceptionToCheck , tries = 4 , delay = 3 , backoff = 2 , status_codes = [ ] , logger = None ) : if backoff is None or backoff <= 0 : raise ValueError ( "backoff must be a number greater than 0" ) tries = math . floor ( tries ) if tries < 0 : raise ValueError ( "tries must be a number 0 or greater" ) if dela... | Decorator function for retrying the decorated function using an exponential or fixed backoff . | 279 | 18 |
6,256 | def _custom_response_edit ( self , method , url , headers , body , response ) : if self . get_implementation ( ) . is_mock ( ) : delay = self . get_setting ( "MOCKDATA_DELAY" , 0.0 ) time . sleep ( delay ) self . _edit_mock_response ( method , url , headers , body , response ) | This method allows a service to edit a response . | 86 | 10 |
6,257 | def postURL ( self , url , headers = { } , body = None ) : return self . _load_resource ( "POST" , url , headers , body ) | Request a URL using the HTTP method POST . | 36 | 9 |
6,258 | def putURL ( self , url , headers , body = None ) : return self . _load_resource ( "PUT" , url , headers , body ) | Request a URL using the HTTP method PUT . | 33 | 10 |
6,259 | def patchURL ( self , url , headers , body ) : return self . _load_resource ( "PATCH" , url , headers , body ) | Request a URL using the HTTP method PATCH . | 32 | 10 |
6,260 | def setup_dir ( f ) : setup_dir = os . path . dirname ( os . path . abspath ( __file__ ) ) def wrapped ( * args , * * kwargs ) : with chdir ( setup_dir ) : return f ( * args , * * kwargs ) return wrapped | Decorate f to run inside the directory where setup . py resides . | 67 | 14 |
6,261 | def feedback_form ( context ) : user = None url = None if context . get ( 'request' ) : url = context [ 'request' ] . path if context [ 'request' ] . user . is_authenticated ( ) : user = context [ 'request' ] . user return { 'form' : FeedbackForm ( url = url , user = user ) , 'background_color' : FEEDBACK_FORM_COLOR , ... | Template tag to render a feedback form . | 124 | 8 |
6,262 | def select ( self , * itms ) : if not itms : itms = [ '*' ] self . terms . append ( "select %s from %s" % ( ', ' . join ( itms ) , self . table ) ) return self | Joins the items to be selected and inserts the current table name | 55 | 13 |
6,263 | def _in ( self , * lst ) : self . terms . append ( 'in (%s)' % ', ' . join ( [ '"%s"' % x for x in lst ] ) ) return self | Build out the in clause . Using _in due to shadowing for in | 46 | 15 |
6,264 | def compile ( self ) : cs = "" for term in self . terms : if cs : cs += " " cs += term self . compiled_str = urllib . parse . quote ( cs ) return self | Take all of the parts components and build the complete query to be passed to Yahoo YQL | 44 | 18 |
6,265 | def read_files ( * sources , * * kwds ) : filenames = _generate_filenames ( sources ) filehandles = _generate_handles ( filenames ) for fh , source in filehandles : try : f = mwtab . MWTabFile ( source ) f . read ( fh ) if kwds . get ( 'validate' ) : validator . validate_file ( mwtabfile = f , section_schema_mapping = ... | Construct a generator that yields file instances . | 204 | 8 |
6,266 | def is_url ( path ) : try : parse_result = urlparse ( path ) return all ( ( parse_result . scheme , parse_result . netloc , parse_result . path ) ) except ValueError : return False | Test if path represents a valid URL . | 49 | 8 |
6,267 | def AuthMiddleware ( app ) : # url_for mustn't be used here because AuthMiddleware is built once at startup, # url path can be reconstructed only on http requests (based on environ) basic_redirect_form = BasicRedirectFormPlugin ( login_form_url = "/signin" , login_handler_path = "/login" , post_login_url = "/" , logout... | Add authentication and authorization middleware to the app . | 265 | 10 |
6,268 | def _get_full_path ( self , path , environ ) : if path . startswith ( '/' ) : path = environ . get ( 'SCRIPT_NAME' , '' ) + path return path | Return the full path to path by prepending the SCRIPT_NAME . If path is a URL do nothing . | 47 | 23 |
6,269 | def _replace_qs ( self , url , qs ) : url_parts = list ( urlparse ( url ) ) url_parts [ 4 ] = qs return urlunparse ( url_parts ) | Replace the query string of url with qs and return the new URL . | 44 | 16 |
6,270 | def write ( self ) : with open ( storage . config_file , 'w' ) as cfg : yaml . dump ( self . as_dict ( ) , cfg , default_flow_style = False ) storage . refresh ( ) | write the current settings to the config file | 52 | 8 |
6,271 | def process_bind_param ( self , value , dialect ) : if value is not None : value = simplejson . dumps ( value ) return value | convert value from python object to json | 31 | 8 |
6,272 | def process_result_value ( self , value , dialect ) : if value is not None : value = simplejson . loads ( value ) return value | convert value from json to a python object | 31 | 9 |
6,273 | def getBriefModuleInfoFromFile ( fileName ) : modInfo = BriefModuleInfo ( ) _cdmpyparser . getBriefModuleInfoFromFile ( modInfo , fileName ) modInfo . flush ( ) return modInfo | Builds the brief module info from file | 50 | 8 |
6,274 | def getBriefModuleInfoFromMemory ( content ) : modInfo = BriefModuleInfo ( ) _cdmpyparser . getBriefModuleInfoFromMemory ( modInfo , content ) modInfo . flush ( ) return modInfo | Builds the brief module info from memory | 48 | 8 |
6,275 | def getDisplayName ( self ) : if self . alias == "" : return self . name return self . name + " as " + self . alias | Provides a name for display purpose respecting the alias | 31 | 10 |
6,276 | def flush ( self ) : self . __flushLevel ( 0 ) if self . __lastImport is not None : self . imports . append ( self . __lastImport ) | Flushes the collected information | 36 | 5 |
6,277 | def __flushLevel ( self , level ) : objectsCount = len ( self . objectsStack ) while objectsCount > level : lastIndex = objectsCount - 1 if lastIndex == 0 : # We have exactly one element in the stack if self . objectsStack [ 0 ] . __class__ . __name__ == "Class" : self . classes . append ( self . objectsStack [ 0 ] ) e... | Merge the found objects to the required level | 199 | 9 |
6,278 | def _onEncoding ( self , encString , line , pos , absPosition ) : self . encoding = Encoding ( encString , line , pos , absPosition ) | Memorizes module encoding | 36 | 5 |
6,279 | def _onGlobal ( self , name , line , pos , absPosition , level ) : # level is ignored for item in self . globals : if item . name == name : return self . globals . append ( Global ( name , line , pos , absPosition ) ) | Memorizes a global variable | 58 | 6 |
6,280 | def _onClass ( self , name , line , pos , absPosition , keywordLine , keywordPos , colonLine , colonPos , level ) : self . __flushLevel ( level ) c = Class ( name , line , pos , absPosition , keywordLine , keywordPos , colonLine , colonPos ) if self . __lastDecorators is not None : c . decorators = self . __lastDecorat... | Memorizes a class | 106 | 5 |
6,281 | def _onWhat ( self , name , line , pos , absPosition ) : self . __lastImport . what . append ( ImportWhat ( name , line , pos , absPosition ) ) | Memorizes an imported item | 40 | 6 |
6,282 | def _onClassAttribute ( self , name , line , pos , absPosition , level ) : # A class must be on the top of the stack attributes = self . objectsStack [ level ] . classAttributes for item in attributes : if item . name == name : return attributes . append ( ClassAttribute ( name , line , pos , absPosition ) ) | Memorizes a class attribute | 73 | 6 |
6,283 | def _onInstanceAttribute ( self , name , line , pos , absPosition , level ) : # Instance attributes may appear in member functions only so we already # have a function on the stack of objects. To get the class object one # more step is required so we -1 here. attributes = self . objectsStack [ level - 1 ] . instanceAtt... | Memorizes a class instance attribute | 105 | 7 |
6,284 | def _onArgument ( self , name , annotation ) : self . objectsStack [ - 1 ] . arguments . append ( Argument ( name , annotation ) ) | Memorizes a function argument | 33 | 6 |
6,285 | def _onError ( self , message ) : self . isOK = False if message . strip ( ) != "" : self . errors . append ( message ) | Memorizies a parser error message | 33 | 8 |
6,286 | def _onLexerError ( self , message ) : self . isOK = False if message . strip ( ) != "" : self . lexerErrors . append ( message ) | Memorizes a lexer error message | 38 | 8 |
6,287 | def gen_mapname ( ) : filepath = None while ( filepath is None ) or ( os . path . exists ( os . path . join ( config [ 'mapfiles_dir' ] , filepath ) ) ) : filepath = '%s.map' % _gen_string ( ) return filepath | Generate a uniq mapfile pathname . | 68 | 10 |
6,288 | def config_content ( self , command , vars ) : settable_vars = [ var ( 'db_url' , 'Database url for sqlite, postgres or mysql' , default = 'sqlite:///%(here)s/studio.db' ) , var ( 'ms_url' , 'Url to the mapserv CGI' , default = 'http://localhost/cgi-bin/mapserv' ) , var ( 'admin_password' , 'Password for default admin ... | Called by self . write_config this returns the text content for the config file given the provided variables . | 258 | 22 |
6,289 | def _resolve_definitions ( self , schema , definitions ) : if not definitions : return schema if not isinstance ( schema , dict ) : return schema ref = schema . pop ( '$ref' , None ) if ref : path = ref . split ( '/' ) [ 2 : ] definition = definitions for component in path : definition = definitions [ component ] if de... | Interpolates definitions from the top - level definitions key into the schema . This is performed in a cut - down way similar to JSON schema . | 145 | 29 |
6,290 | def _get_serializer ( self , _type ) : if _type in _serializers : # _serializers is module level return _serializers [ _type ] # array and object are special types elif _type == 'array' : return self . _get_array_serializer ( ) elif _type == 'object' : return self . _get_object_serializer ( ) raise ValueError ( 'Unknow... | Gets a serializer for a particular type . For primitives returns the serializer from the module - level serializers . For arrays and objects uses the special _get_T_serializer methods to build the encoders and decoders . | 102 | 51 |
6,291 | def _get_array_serializer ( self ) : if not self . _items : raise ValueError ( 'Must specify \'items\' for \'array\' type' ) field = SchemaField ( self . _items ) def encode ( value , field = field ) : if not isinstance ( value , list ) : value = [ value ] return [ field . encode ( i ) for i in value ] def decode ( val... | Gets the encoder and decoder for an array . Uses the items key to build the encoders and decoders for the specified type . | 114 | 31 |
6,292 | def encode ( self , value ) : if value is None and self . _default is not None : value = self . _default for encoder in self . _encoders : try : return encoder ( value ) except ValueError as ex : pass raise ValueError ( 'Value \'{}\' is invalid. {}' . format ( value , ex . message ) ) | The encoder for this schema . Tries each encoder in order of the types specified for this schema . | 78 | 22 |
6,293 | def decode ( self , value ) : # Use the default value unless the field accepts None types has_null_encoder = bool ( encode_decode_null in self . _decoders ) if value is None and self . _default is not None and not has_null_encoder : value = self . _default for decoder in self . _decoders : try : return decoder ( value ... | The decoder for this schema . Tries each decoder in order of the types specified for this schema . | 120 | 22 |
6,294 | def _fail_early ( message , * * kwds ) : import json output = dict ( kwds ) output . update ( { 'msg' : message , 'failed' : True , } ) print ( json . dumps ( output ) ) sys . exit ( 1 ) | The module arguments are dynamically generated based on the Opsview version . This means that fail_json isn t available until after the module has been properly initialized and the schemas have been loaded . | 59 | 38 |
6,295 | def _compare_recursive ( old , new ) : if isinstance ( new , dict ) : for key in six . iterkeys ( new ) : try : if _compare_recursive ( old [ key ] , new [ key ] ) : return True except ( KeyError , TypeError ) : return True elif isinstance ( new , list ) or isinstance ( new , tuple ) : for i , item in enumerate ( new )... | Deep comparison between objects ; assumes that new contains user defined parameters so only keys which exist in new will be compared . Returns True if they differ . Else False . | 135 | 32 |
6,296 | def _requires_update ( self , old_object , new_object ) : old_encoded = self . manager . _encode ( old_object ) new_encoded = self . manager . _encode ( new_object ) return _compare_recursive ( old_encoded , new_encoded ) | Checks whether the old object and new object differ ; only checks keys which exist in the new object | 69 | 20 |
6,297 | def url2domain ( url ) : parsed_uri = urlparse . urlparse ( url ) domain = '{uri.netloc}' . format ( uri = parsed_uri ) domain = re . sub ( "^.+@" , "" , domain ) domain = re . sub ( ":.+$" , "" , domain ) return domain | extract domain from url | 76 | 5 |
6,298 | def init_model ( engine ) : if meta . Session is None : sm = orm . sessionmaker ( autoflush = True , autocommit = False , bind = engine ) meta . engine = engine meta . Session = orm . scoped_session ( sm ) | Call me before using any of the tables or classes in the model | 60 | 13 |
6,299 | def register_prop ( name , handler_get , handler_set ) : global props_get , props_set if handler_get : props_get [ name ] = handler_get if handler_set : props_set [ name ] = handler_set | register a property handler | 54 | 4 |
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