idx int64 0 63k | question stringlengths 61 4.03k | target stringlengths 6 1.23k |
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2,200 | def list_dynamodb ( region , filter_by_kwargs ) : conn = boto . dynamodb . connect_to_region ( region ) tables = conn . list_tables ( ) return lookup ( tables , filter_by = filter_by_kwargs ) | List all DynamoDB tables . |
2,201 | def comittoapi ( api ) : global USED_API assert USED_API is None , "committoapi called again!" check = [ "PyQt4" , "PyQt5" , "PySide" , "PySide2" ] assert api in [ QT_API_PYQT5 , QT_API_PYQT4 , QT_API_PYSIDE , QT_API_PYSIDE2 ] for name in check : if name . lower ( ) != api and name in sys . modules : raise RuntimeError... | Commit to the use of specified Qt api . |
2,202 | def get_metadata ( dist ) : if not dist . has_metadata ( 'PKG-INFO' ) : return msg = email . message_from_string ( dist . get_metadata ( 'PKG-INFO' ) ) metadata = { } for header in [ l for l in msg . _headers ] : metadata [ header [ 0 ] ] = header [ 1 ] return metadata | Return dictionary of metadata for given dist |
2,203 | def add_options ( self , parser ) : parser . add_option ( "--with-%s" % self . name , action = "store_true" , dest = self . enable_opt , help = "Enable plugin %s: %s" % ( self . __class__ . __name__ , self . help ( ) ) ) | Add command - line options for this plugin . |
2,204 | def configure ( self , options , conf ) : self . conf = conf if hasattr ( options , self . enable_opt ) : self . enabled = getattr ( options , self . enable_opt ) | Configure the plugin and system based on selected options . |
2,205 | def raise_for_status ( status : int , headers : MutableMapping , data : MutableMapping ) -> None : if status != 200 : if status == 429 : if isinstance ( data , str ) : error = data else : error = data . get ( "error" , "ratelimited" ) try : retry_after = int ( headers . get ( "Retry-After" , 1 ) ) except ValueError : r... | Check request response status |
2,206 | def raise_for_api_error ( headers : MutableMapping , data : MutableMapping ) -> None : if not data [ "ok" ] : raise exceptions . SlackAPIError ( data . get ( "error" , "unknow_error" ) , headers , data ) if "warning" in data : LOG . warning ( "Slack API WARNING: %s" , data [ "warning" ] ) | Check request response for Slack API error |
2,207 | def decode_body ( headers : MutableMapping , body : bytes ) -> dict : type_ , encoding = parse_content_type ( headers ) decoded_body = body . decode ( encoding ) if type_ == "application/json" : payload = json . loads ( decoded_body ) else : if decoded_body == "ok" : payload = { "ok" : True } else : payload = { "ok" : ... | Decode the response body |
2,208 | def parse_content_type ( headers : MutableMapping ) -> Tuple [ Optional [ str ] , str ] : content_type = headers . get ( "content-type" ) if not content_type : return None , "utf-8" else : type_ , parameters = cgi . parse_header ( content_type ) encoding = parameters . get ( "charset" , "utf-8" ) return type_ , encodin... | Find content - type and encoding of the response |
2,209 | def prepare_request ( url : Union [ str , methods ] , data : Optional [ MutableMapping ] , headers : Optional [ MutableMapping ] , global_headers : MutableMapping , token : str , as_json : Optional [ bool ] = None , ) -> Tuple [ str , Union [ str , MutableMapping ] , MutableMapping ] : if isinstance ( url , methods ) :... | Prepare outgoing request |
2,210 | def decode_response ( status : int , headers : MutableMapping , body : bytes ) -> dict : data = decode_body ( headers , body ) raise_for_status ( status , headers , data ) raise_for_api_error ( headers , data ) return data | Decode incoming response |
2,211 | def prepare_iter_request ( url : Union [ methods , str ] , data : MutableMapping , * , iterkey : Optional [ str ] = None , itermode : Optional [ str ] = None , limit : int = 200 , itervalue : Optional [ Union [ str , int ] ] = None , ) -> Tuple [ MutableMapping , str , str ] : itermode , iterkey = find_iteration ( url ... | Prepare outgoing iteration request |
2,212 | def decode_iter_request ( data : dict ) -> Optional [ Union [ str , int ] ] : if "response_metadata" in data : return data [ "response_metadata" ] . get ( "next_cursor" ) elif "paging" in data : current_page = int ( data [ "paging" ] . get ( "page" , 1 ) ) max_page = int ( data [ "paging" ] . get ( "pages" , 1 ) ) if c... | Decode incoming response from an iteration request |
2,213 | def discard_event ( event : events . Event , bot_id : str = None ) -> bool : if event [ "type" ] in SKIP_EVENTS : return True elif bot_id and isinstance ( event , events . Message ) : if event . get ( "bot_id" ) == bot_id : LOG . debug ( "Ignoring event: %s" , event ) return True elif "message" in event and event [ "me... | Check if the incoming event needs to be discarded |
2,214 | def validate_request_signature ( body : str , headers : MutableMapping , signing_secret : str ) -> None : request_timestamp = int ( headers [ "X-Slack-Request-Timestamp" ] ) if ( int ( time . time ( ) ) - request_timestamp ) > ( 60 * 5 ) : raise exceptions . InvalidTimestamp ( timestamp = request_timestamp ) slack_sign... | Validate incoming request signature using the application signing secret . |
2,215 | def get_backup_file_time_tag ( file_name , custom_prefix = "backup" ) : name_string = file_name [ len ( custom_prefix ) : ] time_tag = name_string . split ( "." , 1 ) [ 0 ] return datetime . strptime ( time_tag , DATETIME_FORMAT ) | Returns a datetime object computed from a file name string with formatting based on DATETIME_FORMAT . |
2,216 | def get_download_uri ( package_name , version , source , index_url = None ) : tmpdir = None force_scan = True develop_ok = False if not index_url : index_url = 'http://cheeseshop.python.org/pypi' if version : pkg_spec = "%s==%s" % ( package_name , version ) else : pkg_spec = package_name req = pkg_resources . Requireme... | Use setuptools to search for a package s URI |
2,217 | def get_pkglist ( ) : dists = Distributions ( ) projects = [ ] for ( dist , _active ) in dists . get_distributions ( "all" ) : if dist . project_name not in projects : projects . append ( dist . project_name ) return projects | Return list of all installed packages |
2,218 | def register ( self , command : str , handler : Any ) : if not command . startswith ( "/" ) : command = f"/{command}" LOG . info ( "Registering %s to %s" , command , handler ) self . _routes [ command ] . append ( handler ) | Register a new handler for a specific slash command |
2,219 | def setpreferredapi ( api ) : global __PREFERRED_API if __SELECTED_API is not None : raise RuntimeError ( "A Qt api {} was already selected" . format ( __SELECTED_API ) ) if api . lower ( ) not in { "pyqt4" , "pyqt5" , "pyside" , "pyside2" } : raise ValueError ( api ) __PREFERRED_API = api . lower ( ) | Set the preferred Qt API . |
2,220 | def selectapi ( api ) : global __SELECTED_API , USED_API if api . lower ( ) not in { "pyqt4" , "pyqt5" , "pyside" , "pyside2" } : raise ValueError ( api ) if __SELECTED_API is not None and __SELECTED_API . lower ( ) != api . lower ( ) : raise RuntimeError ( "A Qt API {} was already selected" . format ( __SELECTED_API )... | Select an Qt API to use . |
2,221 | def get_highest_version ( versions ) : sorted_versions = [ ] for ver in versions : sorted_versions . append ( ( pkg_resources . parse_version ( ver ) , ver ) ) sorted_versions = sorted ( sorted_versions ) sorted_versions . reverse ( ) return sorted_versions [ 0 ] [ 1 ] | Returns highest available version for a package in a list of versions Uses pkg_resources to parse the versions |
2,222 | def get_distributions ( self , show , pkg_name = "" , version = "" ) : for name , dist in self . get_alpha ( show , pkg_name , version ) : ver = dist . version for package in self . environment [ dist . project_name ] : if ver == package . version : if show == "nonactive" and dist not in self . working_set : yield ( di... | Yield installed packages |
2,223 | def get_alpha ( self , show , pkg_name = "" , version = "" ) : alpha_list = [ ] for dist in self . get_packages ( show ) : if pkg_name and dist . project_name != pkg_name : pass elif version and dist . version != version : pass else : alpha_list . append ( ( dist . project_name + dist . version , dist ) ) alpha_list . ... | Return list of alphabetized packages |
2,224 | def get_packages ( self , show ) : if show == 'nonactive' or show == "all" : all_packages = [ ] for package in self . environment : for i in range ( len ( self . environment [ package ] ) ) : if self . environment [ package ] [ i ] : all_packages . append ( self . environment [ package ] [ i ] ) return all_packages els... | Return list of Distributions filtered by active status or all |
2,225 | def case_sensitive_name ( self , package_name ) : if len ( self . environment [ package_name ] ) : return self . environment [ package_name ] [ 0 ] . project_name | Return case - sensitive package name given any - case package name |
2,226 | def cache_incr ( self , key ) : cache . set ( key , cache . get ( key , 0 ) + 1 , self . expire_after ( ) ) | Non - atomic cache increment operation . Not optimal but consistent across different cache backends . |
2,227 | def call_plugins ( plugins , method , * arg , ** kw ) : for plug in plugins : func = getattr ( plug , method , None ) if func is None : continue result = func ( * arg , ** kw ) if result is not None : return result return None | Call all method on plugins in list that define it with provided arguments . The first response that is not None is returned . |
2,228 | def load_plugins ( builtin = True , others = True ) : for entry_point in pkg_resources . iter_entry_points ( 'yolk.plugins' ) : try : plugin = entry_point . load ( ) except KeyboardInterrupt : raise except Exception as err_msg : warn ( "Unable to load plugin %s: %s" % ( entry_point , err_msg ) , RuntimeWarning ) contin... | Load plugins either builtin others or both . |
2,229 | def s3_connect ( bucket_name , s3_access_key_id , s3_secret_key ) : conn = connect_s3 ( s3_access_key_id , s3_secret_key ) try : return conn . get_bucket ( bucket_name ) except S3ResponseError as e : if e . status == 403 : raise Exception ( "Bad Amazon S3 credentials." ) raise | Returns a Boto connection to the provided S3 bucket . |
2,230 | def s3_list ( s3_bucket , s3_access_key_id , s3_secret_key , prefix = None ) : bucket = s3_connect ( s3_bucket , s3_access_key_id , s3_secret_key ) return sorted ( [ key . name for key in bucket . list ( ) if key . name . endswith ( ".tbz" ) and ( prefix is None or key . name . startswith ( prefix ) ) ] ) | Lists the contents of the S3 bucket that end in . tbz and match the passed prefix if any . |
2,231 | def s3_download ( output_file_path , s3_bucket , s3_access_key_id , s3_secret_key , s3_file_key = None , prefix = None ) : bucket = s3_connect ( s3_bucket , s3_access_key_id , s3_secret_key ) if not s3_file_key : keys = s3_list ( s3_bucket , s3_access_key_id , s3_secret_key , prefix ) if not keys : raise Exception ( "T... | Downloads the file matching the provided key in the provided bucket from Amazon S3 . If s3_file_key is none it downloads the last file from the provided bucket with the . tbz extension filtering by prefix if it is provided . |
2,232 | def s3_upload ( source_file_path , bucket_name , s3_access_key_id , s3_secret_key ) : key = s3_key ( bucket_name , s3_access_key_id , s3_secret_key ) file_name = source_file_path . split ( "/" ) [ - 1 ] key . key = file_name if key . exists ( ) : raise Exception ( "s3 key %s already exists for current period." % ( file... | Uploads the to Amazon S3 the contents of the provided file keyed with the name of the file . |
2,233 | def validate_pypi_opts ( opt_parser ) : ( options , remaining_args ) = opt_parser . parse_args ( ) options_pkg_specs = [ options . versions_available , options . query_metadata_pypi , options . show_download_links , options . browse_website , options . fetch , options . show_deps , ] for pkg_spec in options_pkg_specs :... | Check parse options that require pkg_spec |
2,234 | def write ( self , inline ) : frame = inspect . currentframe ( ) . f_back if frame : mod = frame . f_globals . get ( '__name__' ) else : mod = sys . _getframe ( 0 ) . f_globals . get ( '__name__' ) if not mod in self . modulenames : self . stdout . write ( inline ) | Write a line to stdout if it isn t in a blacklist |
2,235 | def get_plugin ( self , method ) : all_plugins = [ ] for entry_point in pkg_resources . iter_entry_points ( 'yolk.plugins' ) : plugin_obj = entry_point . load ( ) plugin = plugin_obj ( ) plugin . configure ( self . options , None ) if plugin . enabled : if not hasattr ( plugin , method ) : self . logger . warn ( "Error... | Return plugin object if CLI option is activated and method exists |
2,236 | def set_log_level ( self ) : if self . options . debug : self . logger . setLevel ( logging . DEBUG ) elif self . options . quiet : self . logger . setLevel ( logging . ERROR ) else : self . logger . setLevel ( logging . INFO ) self . logger . addHandler ( logging . StreamHandler ( ) ) return self . logger | Set log level according to command - line options |
2,237 | def run ( self ) : opt_parser = setup_opt_parser ( ) ( self . options , remaining_args ) = opt_parser . parse_args ( ) logger = self . set_log_level ( ) pkg_spec = validate_pypi_opts ( opt_parser ) if not pkg_spec : pkg_spec = remaining_args self . pkg_spec = pkg_spec if not self . options . pypi_search and ( len ( sys... | Perform actions based on CLI options |
2,238 | def show_updates ( self ) : dists = Distributions ( ) if self . project_name : pkg_list = [ self . project_name ] else : pkg_list = get_pkglist ( ) found = None for pkg in pkg_list : for ( dist , active ) in dists . get_distributions ( "all" , pkg , dists . get_highest_installed ( pkg ) ) : ( project_name , versions ) ... | Check installed packages for available updates on PyPI |
2,239 | def show_distributions ( self , show ) : show_metadata = self . options . metadata plugins = self . get_plugin ( "add_column" ) ignores = [ "/UNIONFS" , "/KNOPPIX.IMG" ] workingenv = os . environ . get ( 'WORKING_ENV' ) if workingenv : ignores . append ( workingenv ) dists = Distributions ( ) results = None for ( dist ... | Show list of installed activated OR non - activated packages |
2,240 | def show_pypi_changelog ( self ) : hours = self . options . show_pypi_changelog if not hours . isdigit ( ) : self . logger . error ( "Error: You must supply an integer." ) return 1 try : changelog = self . pypi . changelog ( int ( hours ) ) except XMLRPCFault as err_msg : self . logger . error ( err_msg ) self . logger... | Show detailed PyPI ChangeLog for the last hours |
2,241 | def show_pypi_releases ( self ) : try : hours = int ( self . options . show_pypi_releases ) except ValueError : self . logger . error ( "ERROR: You must supply an integer." ) return 1 try : latest_releases = self . pypi . updated_releases ( hours ) except XMLRPCFault as err_msg : self . logger . error ( err_msg ) self ... | Show PyPI releases for the last number of hours |
2,242 | def fetch ( self ) : source = True directory = "." if self . options . file_type == "svn" : version = "dev" svn_uri = get_download_uri ( self . project_name , "dev" , True ) if svn_uri : directory = self . project_name + "_svn" return self . fetch_svn ( svn_uri , directory ) else : self . logger . error ( "ERROR: No su... | Download a package |
2,243 | def fetch_uri ( self , directory , uri ) : filename = os . path . basename ( urlparse ( uri ) [ 2 ] ) if os . path . exists ( filename ) : self . logger . error ( "ERROR: File exists: " + filename ) return 1 try : downloaded_filename , headers = urlretrieve ( uri , filename ) self . logger . info ( "Downloaded ./" + fi... | Use urllib . urlretrieve to download package to file in sandbox dir . |
2,244 | def fetch_svn ( self , svn_uri , directory ) : if not command_successful ( "svn --version" ) : self . logger . error ( "ERROR: Do you have subversion installed?" ) return 1 if os . path . exists ( directory ) : self . logger . error ( "ERROR: Checkout directory exists - %s" % directory ) return 1 try : os . mkdir ( dir... | Fetch subversion repository |
2,245 | def browse_website ( self , browser = None ) : if len ( self . all_versions ) : metadata = self . pypi . release_data ( self . project_name , self . all_versions [ 0 ] ) self . logger . debug ( "DEBUG: browser: %s" % browser ) if metadata . has_key ( "home_page" ) : self . logger . info ( "Launching browser: %s" % meta... | Launch web browser at project s homepage |
2,246 | def query_metadata_pypi ( self ) : if self . version and self . version in self . all_versions : metadata = self . pypi . release_data ( self . project_name , self . version ) else : metadata = self . pypi . release_data ( self . project_name , self . all_versions [ 0 ] ) if metadata : for key in metadata . keys ( ) : ... | Show pkg metadata queried from PyPI |
2,247 | def versions_available ( self ) : if self . version : spec = "%s==%s" % ( self . project_name , self . version ) else : spec = self . project_name if self . all_versions and self . version in self . all_versions : print_pkg_versions ( self . project_name , [ self . version ] ) elif not self . version and self . all_ver... | Query PyPI for a particular version or all versions of a package |
2,248 | def show_entry_map ( self ) : pprinter = pprint . PrettyPrinter ( ) try : entry_map = pkg_resources . get_entry_map ( self . options . show_entry_map ) if entry_map : pprinter . pprint ( entry_map ) except pkg_resources . DistributionNotFound : self . logger . error ( "Distribution not found: %s" % self . options . sho... | Show entry map for a package |
2,249 | def show_entry_points ( self ) : found = False for entry_point in pkg_resources . iter_entry_points ( self . options . show_entry_points ) : found = True try : plugin = entry_point . load ( ) print ( plugin . __module__ ) print ( " %s" % entry_point ) if plugin . __doc__ : print ( plugin . __doc__ ) print except Impo... | Show entry points for a module |
2,250 | def parse_pkg_ver ( self , want_installed ) : all_versions = [ ] arg_str = ( "" ) . join ( self . pkg_spec ) if "==" not in arg_str : project_name = arg_str version = None else : ( project_name , version ) = arg_str . split ( "==" ) project_name = project_name . strip ( ) version = version . strip ( ) if want_installed... | Return tuple with project_name and version from CLI args If the user gave the wrong case for the project name this corrects it |
2,251 | def install_backport_hook ( api ) : if api == USED_API : raise ValueError sys . meta_path . insert ( 0 , ImportHookBackport ( api ) ) | Install a backport import hook for Qt4 api |
2,252 | def install_deny_hook ( api ) : if api == USED_API : raise ValueError sys . meta_path . insert ( 0 , ImportHookDeny ( api ) ) | Install a deny import hook for Qt api . |
2,253 | def run_command ( cmd , env = None , max_timeout = None ) : arglist = cmd . split ( ) output = os . tmpfile ( ) try : pipe = Popen ( arglist , stdout = output , stderr = STDOUT , env = env ) except Exception as errmsg : return 1 , errmsg if max_timeout : start = time . time ( ) while pipe . poll ( ) is None : time . sl... | Run command and return its return status code and its output |
2,254 | async def iter ( self , url : Union [ str , methods ] , data : Optional [ MutableMapping ] = None , headers : Optional [ MutableMapping ] = None , * , limit : int = 200 , iterkey : Optional [ str ] = None , itermode : Optional [ str ] = None , minimum_time : Optional [ int ] = None , as_json : Optional [ bool ] = None ... | Iterate over a slack API method supporting pagination |
2,255 | async def _incoming_from_rtm ( self , url : str , bot_id : str ) -> AsyncIterator [ events . Event ] : async for data in self . _rtm ( url ) : event = events . Event . from_rtm ( json . loads ( data ) ) if sansio . need_reconnect ( event ) : break elif sansio . discard_event ( event , bot_id ) : continue else : yield e... | Connect and discard incoming RTM event if necessary . |
2,256 | def package_manager_owns ( self , dist ) : if dist . location . lower ( ) == get_python_lib ( ) . lower ( ) : filename = os . path . join ( dist . location , dist . egg_name ( ) + ".egg-info" ) else : filename = dist . location status , output = getstatusoutput ( "/usr/bin/acmefile -q %s" % filename ) if status == 0 : ... | Returns True if package manager owns file Returns False if package manager does not own file |
2,257 | def filter_url ( pkg_type , url ) : bad_stuff = [ "?modtime" , "#md5=" ] for junk in bad_stuff : if junk in url : url = url . split ( junk ) [ 0 ] break if url . endswith ( "-dev" ) : url = url . split ( "#egg=" ) [ 0 ] if pkg_type == "all" : return url elif pkg_type == "source" : valid_source_types = [ ".tgz" , ".tar.... | Returns URL of specified file type source egg or all |
2,258 | def request ( self , host , handler , request_body , verbose ) : self . verbose = verbose url = 'http://' + host + handler request = urllib2 . Request ( url ) request . add_data ( request_body ) request . add_header ( 'User-Agent' , self . user_agent ) request . add_header ( 'Content-Type' , 'text/xml' ) proxy_handler ... | Send xml - rpc request using proxy |
2,259 | def get_cache ( self ) : if self . no_cache : self . pkg_list = self . list_packages ( ) return if not os . path . exists ( self . yolk_dir ) : os . mkdir ( self . yolk_dir ) if os . path . exists ( self . pkg_cache_file ) : self . pkg_list = self . query_cached_package_list ( ) else : self . logger . debug ( "DEBUG: F... | Get a package name list from disk cache or PyPI |
2,260 | def get_xmlrpc_server ( self ) : check_proxy_setting ( ) if os . environ . has_key ( 'XMLRPC_DEBUG' ) : debug = 1 else : debug = 0 try : return xmlrpclib . Server ( XML_RPC_SERVER , transport = ProxyTransport ( ) , verbose = debug ) except IOError : self . logger ( "ERROR: Can't connect to XML-RPC server: %s" % XML_RPC... | Returns PyPI s XML - RPC server instance |
2,261 | def query_versions_pypi ( self , package_name ) : if not package_name in self . pkg_list : self . logger . debug ( "Package %s not in cache, querying PyPI..." % package_name ) self . fetch_pkg_list ( ) versions = [ ] for pypi_pkg in self . pkg_list : if pypi_pkg . lower ( ) == package_name . lower ( ) : if self . debug... | Fetch list of available versions for a package from The CheeseShop |
2,262 | def query_cached_package_list ( self ) : if self . debug : self . logger . debug ( "DEBUG: reading pickled cache file" ) return cPickle . load ( open ( self . pkg_cache_file , "r" ) ) | Return list of pickled package names from PYPI |
2,263 | def fetch_pkg_list ( self ) : self . logger . debug ( "DEBUG: Fetching package name list from PyPI" ) package_list = self . list_packages ( ) cPickle . dump ( package_list , open ( self . pkg_cache_file , "w" ) ) self . pkg_list = package_list | Fetch and cache master list of package names from PYPI |
2,264 | def search ( self , spec , operator ) : return self . xmlrpc . search ( spec , operator . lower ( ) ) | Query PYPI via XMLRPC interface using search spec |
2,265 | def release_data ( self , package_name , version ) : try : return self . xmlrpc . release_data ( package_name , version ) except xmlrpclib . Fault : return | Query PYPI via XMLRPC interface for a pkg s metadata |
2,266 | def package_releases ( self , package_name ) : if self . debug : self . logger . debug ( "DEBUG: querying PyPI for versions of " + package_name ) return self . xmlrpc . package_releases ( package_name ) | Query PYPI via XMLRPC interface for a pkg s available versions |
2,267 | def clone ( self ) -> "Event" : return self . __class__ ( copy . deepcopy ( self . event ) , copy . deepcopy ( self . metadata ) ) | Clone the event |
2,268 | def from_rtm ( cls , raw_event : MutableMapping ) -> "Event" : if raw_event [ "type" ] . startswith ( "message" ) : return Message ( raw_event ) else : return Event ( raw_event ) | Create an event with data coming from the RTM API . |
2,269 | def from_http ( cls , raw_body : MutableMapping , verification_token : Optional [ str ] = None , team_id : Optional [ str ] = None , ) -> "Event" : if verification_token and raw_body [ "token" ] != verification_token : raise exceptions . FailedVerification ( raw_body [ "token" ] , raw_body [ "team_id" ] ) if team_id an... | Create an event with data coming from the HTTP Event API . |
2,270 | def response ( self , in_thread : Optional [ bool ] = None ) -> "Message" : data = { "channel" : self [ "channel" ] } if in_thread : if "message" in self : data [ "thread_ts" ] = ( self [ "message" ] . get ( "thread_ts" ) or self [ "message" ] [ "ts" ] ) else : data [ "thread_ts" ] = self . get ( "thread_ts" ) or self ... | Create a response message . |
2,271 | def serialize ( self ) -> dict : data = { ** self } if "attachments" in self : data [ "attachments" ] = json . dumps ( self [ "attachments" ] ) return data | Serialize the message for sending to slack API |
2,272 | def query ( self , url : Union [ str , methods ] , data : Optional [ MutableMapping ] = None , headers : Optional [ MutableMapping ] = None , as_json : Optional [ bool ] = None , ) -> dict : url , body , headers = sansio . prepare_request ( url = url , data = data , headers = headers , global_headers = self . _headers ... | Query the slack API |
2,273 | def rtm ( self , url : Optional [ str ] = None , bot_id : Optional [ str ] = None ) -> Iterator [ events . Event ] : while True : bot_id = bot_id or self . _find_bot_id ( ) url = url or self . _find_rtm_url ( ) for event in self . _incoming_from_rtm ( url , bot_id ) : yield event url = None | Iterate over event from the RTM API |
2,274 | def get_config ( config_file ) : def load ( fp ) : try : return yaml . safe_load ( fp ) except yaml . YAMLError as e : sys . stderr . write ( text_type ( e ) ) sys . exit ( 1 ) if config_file == '-' : return load ( sys . stdin ) if not os . path . exists ( config_file ) : sys . stderr . write ( 'ERROR: Must either run ... | Get configuration from a file . |
2,275 | def get_options ( config_options , local_options , cli_options ) : options = DEFAULT_OPTIONS . copy ( ) if config_options is not None : options . update ( config_options ) if local_options is not None : options . update ( local_options ) if cli_options is not None : options . update ( cli_options ) return options | Figure out what options to use based on the four places it can come from . |
2,276 | def output_results ( results , metric , options ) : formatter = options [ 'Formatter' ] context = metric . copy ( ) try : context [ 'dimension' ] = list ( metric [ 'Dimensions' ] . values ( ) ) [ 0 ] except AttributeError : context [ 'dimension' ] = '' for result in results : stat_keys = metric [ 'Statistics' ] if not ... | Output the results to stdout . |
2,277 | def download_to_path ( self , gsuri , localpath , binary_mode = False , tmpdir = None ) : bucket_name , gs_rel_path = self . parse_uri ( gsuri ) bucket = self . _client . get_bucket ( bucket_name ) ablob = bucket . get_blob ( gs_rel_path ) if not ablob : raise GoogleStorageIOError ( "No such file on Google Storage: '{}... | This method is analogous to gsutil cp gsuri localpath but in a programatically accesible way . The only difference is that we have to make a guess about the encoding of the file to not upset downstream file operations . If you are downloading a VCF then False is great . If this is a BAM file you are asking for you shou... |
2,278 | def full_name ( self ) : formatted_user = [ ] if self . user . first_name is not None : formatted_user . append ( self . user . first_name ) if self . user . last_name is not None : formatted_user . append ( self . user . last_name ) return " " . join ( formatted_user ) | Returns the first and last name of the user separated by a space . |
2,279 | def use_defaults ( func ) : @ wraps ( func ) def wrapper ( row , cohort , filter_fn = None , normalized_per_mb = None , ** kwargs ) : filter_fn = first_not_none_param ( [ filter_fn , cohort . filter_fn ] , no_filter ) normalized_per_mb = first_not_none_param ( [ normalized_per_mb , cohort . normalized_per_mb ] , False ... | Decorator for functions that should automatically fall back to the Cohort - default filter_fn and normalized_per_mb if not specified . |
2,280 | def count_variants_function_builder ( function_name , filterable_variant_function = None ) : @ count_function def count ( row , cohort , filter_fn , normalized_per_mb , ** kwargs ) : def count_filter_fn ( filterable_variant , ** kwargs ) : assert filter_fn is not None , "filter_fn should never be None, but it is." retu... | Creates a function that counts variants that are filtered by the provided filterable_variant_function . The filterable_variant_function is a function that takes a filterable_variant and returns True or False . |
2,281 | def count_effects_function_builder ( function_name , only_nonsynonymous , filterable_effect_function = None ) : @ count_function def count ( row , cohort , filter_fn , normalized_per_mb , ** kwargs ) : def count_filter_fn ( filterable_effect , ** kwargs ) : assert filter_fn is not None , "filter_fn should never be None... | Create a function that counts effects that are filtered by the provided filterable_effect_function . The filterable_effect_function is a function that takes a filterable_effect and returns True or False . |
2,282 | def bootstrap_auc ( df , col , pred_col , n_bootstrap = 1000 ) : scores = np . zeros ( n_bootstrap ) old_len = len ( df ) df . dropna ( subset = [ col ] , inplace = True ) new_len = len ( df ) if new_len < old_len : logger . info ( "Dropping NaN values in %s to go from %d to %d rows" % ( col , old_len , new_len ) ) pre... | Calculate the boostrapped AUC for a given col trying to predict a pred_col . |
2,283 | def new_worker ( self , name : str ) : if not self . running : return self . immediate_worker worker = self . _new_worker ( name ) self . _start_worker ( worker ) return worker | Creates a new Worker and start a new Thread with it . Returns the Worker . |
2,284 | def new_worker_pool ( self , name : str , min_workers : int = 0 , max_workers : int = 1 , max_seconds_idle : int = DEFAULT_WORKER_POOL_MAX_SECONDS_IDLE ) : if not self . running : return self . immediate_worker worker = self . _new_worker_pool ( name , min_workers , max_workers , max_seconds_idle ) self . _start_worker... | Creates a new worker pool and starts it . Returns the Worker that schedules works to the pool . |
2,285 | def as_dataframe ( self , on = None , join_with = None , join_how = None , return_cols = False , rename_cols = False , keep_paren_contents = True , ** kwargs ) : df = self . _as_dataframe_unmodified ( join_with = join_with , join_how = join_how ) if on is None : return DataFrameHolder . return_obj ( None , df , return_... | Return this Cohort as a DataFrame and optionally include additional columns using on . |
2,286 | def load_dataframe ( self , df_loader_name ) : logger . debug ( "loading dataframe: {}" . format ( df_loader_name ) ) df_loaders = [ df_loader for df_loader in self . df_loaders if df_loader . name == df_loader_name ] if len ( df_loaders ) == 0 : raise ValueError ( "No DataFrameLoader with name %s" % df_loader_name ) i... | Instead of joining a DataFrameJoiner with the Cohort in as_dataframe sometimes we may want to just directly load a particular DataFrame . |
2,287 | def _get_function_name ( self , fn , default = "None" ) : if fn is None : fn_name = default else : fn_name = fn . __name__ return fn_name | Return name of function using default value if function not defined |
2,288 | def load_variants ( self , patients = None , filter_fn = None , ** kwargs ) : filter_fn = first_not_none_param ( [ filter_fn , self . filter_fn ] , no_filter ) filter_fn_name = self . _get_function_name ( filter_fn ) logger . debug ( "loading variants with filter_fn: {}" . format ( filter_fn_name ) ) patient_variants =... | Load a dictionary of patient_id to varcode . VariantCollection |
2,289 | def _hash_filter_fn ( self , filter_fn , ** kwargs ) : filter_fn_name = self . _get_function_name ( filter_fn , default = "filter-none" ) logger . debug ( "Computing hash for filter_fn: {} with kwargs {}" . format ( filter_fn_name , str ( dict ( ** kwargs ) ) ) ) fn_source = str ( dill . source . getsource ( filter_fn ... | Construct string representing state of filter_fn Used to cache filtered variants or effects uniquely depending on filter fn values |
2,290 | def _load_single_patient_variants ( self , patient , filter_fn , use_cache = True , ** kwargs ) : if filter_fn is None : use_filtered_cache = False else : filter_fn_name = self . _get_function_name ( filter_fn ) logger . debug ( "loading variants for patient {} with filter_fn {}" . format ( patient . id , filter_fn_nam... | Load filtered merged variants for a single patient optionally using cache |
2,291 | def _load_single_patient_merged_variants ( self , patient , use_cache = True ) : logger . debug ( "loading merged variants for patient {}" . format ( patient . id ) ) no_variants = False try : if use_cache : variant_cache_file_name = "%s-variants.pkl" % ( self . merge_type ) merged_variants = self . load_from_cache ( s... | Load merged variants for a single patient optionally using cache |
2,292 | def load_polyphen_annotations ( self , as_dataframe = False , filter_fn = None ) : filter_fn = first_not_none_param ( [ filter_fn , self . filter_fn ] , no_filter ) patient_annotations = { } for patient in self : annotations = self . _load_single_patient_polyphen ( patient , filter_fn = filter_fn ) if annotations is no... | Load a dataframe containing polyphen2 annotations for all variants |
2,293 | def load_effects ( self , patients = None , only_nonsynonymous = False , all_effects = False , filter_fn = None , ** kwargs ) : filter_fn = first_not_none_param ( [ filter_fn , self . filter_fn ] , no_filter ) filter_fn_name = self . _get_function_name ( filter_fn ) logger . debug ( "loading effects with filter_fn {}" ... | Load a dictionary of patient_id to varcode . EffectCollection |
2,294 | def load_kallisto ( self ) : kallisto_data = pd . concat ( [ self . _load_single_patient_kallisto ( patient ) for patient in self ] , copy = False ) if self . kallisto_ensembl_version is None : raise ValueError ( "Required a kallisto_ensembl_version but none was specified" ) ensembl_release = cached_release ( self . ka... | Load Kallisto transcript quantification data for a cohort |
2,295 | def _load_single_patient_kallisto ( self , patient ) : data = pd . read_csv ( patient . tumor_sample . kallisto_path , sep = "\t" ) data [ "patient_id" ] = patient . id return data | Load Kallisto gene quantification given a patient |
2,296 | def load_cufflinks ( self , filter_ok = True ) : return pd . concat ( [ self . _load_single_patient_cufflinks ( patient , filter_ok ) for patient in self ] , copy = False ) | Load a Cufflinks gene expression data for a cohort |
2,297 | def _load_single_patient_cufflinks ( self , patient , filter_ok ) : data = pd . read_csv ( patient . tumor_sample . cufflinks_path , sep = "\t" ) data [ "patient_id" ] = patient . id if filter_ok : data = data [ data [ "FPKM_status" ] == "OK" ] return data | Load Cufflinks gene quantification given a patient |
2,298 | def get_filtered_isovar_epitopes ( self , epitopes , ic50_cutoff ) : mutant_binding_predictions = [ ] for binding_prediction in epitopes : peptide = binding_prediction . peptide peptide_offset = binding_prediction . offset isovar_row = dict ( binding_prediction . source_sequence_key ) is_mutant = contains_mutant_residu... | Mostly replicates topiary . build_epitope_collection_from_binding_predictions |
2,299 | def plot_roc_curve ( self , on , bootstrap_samples = 100 , ax = None , ** kwargs ) : plot_col , df = self . as_dataframe ( on , return_cols = True , ** kwargs ) df = filter_not_null ( df , "benefit" ) df = filter_not_null ( df , plot_col ) df . benefit = df . benefit . astype ( bool ) return roc_curve_plot ( df , plot_... | Plot an ROC curve for benefit and a given variable |
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