idx int64 0 63k | question stringlengths 53 5.28k | target stringlengths 5 805 |
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17,200 | def validation_statuses ( self , area_uuid ) : path = "/area/{uuid}/validations" . format ( uuid = area_uuid ) result = self . _make_request ( 'get' , path ) return result . json ( ) | Get count of validation statuses for all files in upload_area |
17,201 | def language_name ( self , text : str ) -> str : values = extract ( text ) input_fn = _to_func ( ( [ values ] , [ ] ) ) pos : int = next ( self . _classifier . predict_classes ( input_fn = input_fn ) ) LOGGER . debug ( "Predicted language position %s" , pos ) return sorted ( self . languages ) [ pos ] | Predict the programming language name of the given source code . |
17,202 | def scores ( self , text : str ) -> Dict [ str , float ] : values = extract ( text ) input_fn = _to_func ( ( [ values ] , [ ] ) ) prediction = self . _classifier . predict_proba ( input_fn = input_fn ) probabilities = next ( prediction ) . tolist ( ) sorted_languages = sorted ( self . languages ) return dict ( zip ( so... | A score for each language corresponding to the probability that the text is written in the given language . The score is a float value between 0 . 0 and 1 . 0 |
17,203 | def probable_languages ( self , text : str , max_languages : int = 3 ) -> Tuple [ str , ... ] : scores = self . scores ( text ) sorted_scores = sorted ( scores . items ( ) , key = itemgetter ( 1 ) , reverse = True ) languages , probabilities = list ( zip ( * sorted_scores ) ) rescaled_probabilities = [ log ( proba ) fo... | List of most probable programming languages the list is ordered from the most probable to the least probable one . |
17,204 | def learn ( self , input_dir : str ) -> float : if self . is_default : LOGGER . error ( "Cannot learn using default model" ) raise GuesslangError ( 'Cannot learn using default "readonly" model' ) languages = self . languages LOGGER . info ( "Extract training data" ) extensions = [ ext for exts in languages . values ( )... | Learn languages features from source files . |
17,205 | def main ( ) : parser = argparse . ArgumentParser ( description = __doc__ ) parser . add_argument ( 'reportfile' , type = argparse . FileType ( 'r' ) , help = "test report file generated by `guesslang --test TESTDIR`" ) parser . add_argument ( '-d' , '--debug' , default = False , action = 'store_true' , help = "show de... | Report graph creator command line |
17,206 | def search_files ( source : str , extensions : List [ str ] ) -> List [ Path ] : files = [ path for path in Path ( source ) . glob ( '**/*' ) if path . is_file ( ) and path . suffix . lstrip ( '.' ) in extensions ] nb_files = len ( files ) LOGGER . debug ( "Total files found: %d" , nb_files ) if nb_files < NB_FILES_MIN... | Retrieve files located the source directory and its subdirectories whose extension match one of the listed extensions . |
17,207 | def extract_from_files ( files : List [ Path ] , languages : Dict [ str , List [ str ] ] ) -> DataSet : enumerator = enumerate ( sorted ( languages . items ( ) ) ) rank_map = { ext : rank for rank , ( _ , exts ) in enumerator for ext in exts } with multiprocessing . Pool ( initializer = _process_init ) as pool : file_i... | Extract arrays of features from the given files . |
17,208 | def safe_read_file ( file_path : Path ) -> str : for encoding in FILE_ENCODINGS : try : return file_path . read_text ( encoding = encoding ) except UnicodeError : pass raise GuesslangError ( 'Encoding not supported for {!s}' . format ( file_path ) ) | Read a text file . Several text encodings are tried until the file content is correctly decoded . |
17,209 | def config_logging ( debug : bool = False ) -> None : if debug : level = 'DEBUG' tf_level = tf . logging . INFO else : level = 'INFO' tf_level = tf . logging . ERROR logging_config = config_dict ( 'logging.json' ) for logger in logging_config [ 'loggers' ] . values ( ) : logger [ 'level' ] = level logging . config . di... | Set - up application and tensorflow logging . |
17,210 | def config_dict ( name : str ) -> Dict [ str , Any ] : try : content = resource_string ( PACKAGE , DATADIR . format ( name ) ) . decode ( ) except DistributionNotFound as error : LOGGER . warning ( "Cannot load %s from packages: %s" , name , error ) content = DATA_FALLBACK . joinpath ( name ) . read_text ( ) return cas... | Load a JSON configuration dict from Guesslang config directory . |
17,211 | def model_info ( model_dir : Optional [ str ] = None ) -> Tuple [ str , bool ] : if model_dir is None : try : model_dir = resource_filename ( PACKAGE , DATADIR . format ( 'model' ) ) except DistributionNotFound as error : LOGGER . warning ( "Cannot load model from packages: %s" , error ) model_dir = str ( DATA_FALLBACK... | Retrieve Guesslang model directory name and tells if it is the default model . |
17,212 | def format ( self , record : logging . LogRecord ) -> str : if platform . system ( ) != 'Linux' : return super ( ) . format ( record ) record . msg = ( self . STYLE [ record . levelname ] + record . msg + self . STYLE [ 'END' ] ) record . levelname = ( self . STYLE [ 'LEVEL' ] + record . levelname + self . STYLE [ 'END... | Format log records to produce colored messages . |
17,213 | def main ( ) : parser = argparse . ArgumentParser ( description = __doc__ ) parser . add_argument ( 'githubtoken' , help = "Github OAuth token, see https://developer.github.com/v3/oauth/" ) parser . add_argument ( 'destination' , help = "location of the downloaded repos" ) parser . add_argument ( '-n' , '--nbrepo' , he... | Github repositories downloaded command line |
17,214 | def retry ( default = None ) : def decorator ( func ) : @ functools . wraps ( func ) def _wrapper ( * args , ** kw ) : for pos in range ( 1 , MAX_RETRIES ) : try : return func ( * args , ** kw ) except ( RuntimeError , requests . ConnectionError ) as error : LOGGER . warning ( "Failed: %s, %s" , type ( error ) , error ... | Retry functions after failures |
17,215 | def main ( ) : parser = argparse . ArgumentParser ( description = __doc__ ) parser . add_argument ( 'learn' , help = "learning source codes directory" ) parser . add_argument ( 'keywords' , help = "output keywords file, JSON" ) parser . add_argument ( '-n' , '--nbkeywords' , type = int , default = 10000 , help = "the n... | Keywords generator command line |
17,216 | def main ( ) -> None : try : _real_main ( ) except GuesslangError as error : LOGGER . critical ( "Failed: %s" , error ) sys . exit ( - 1 ) except KeyboardInterrupt : LOGGER . critical ( "Cancelled!" ) sys . exit ( - 2 ) | Run command line |
17,217 | def split ( text : str ) -> List [ str ] : return [ word for word in SEPARATOR . split ( text ) if word . strip ( ' \t' ) ] | Split a text into a list of tokens . |
17,218 | def main ( ) : parser = argparse . ArgumentParser ( description = __doc__ , formatter_class = argparse . RawDescriptionHelpFormatter ) parser . add_argument ( 'source' , help = "location of the downloaded repos" ) parser . add_argument ( 'destination' , help = "location of the extracted files" ) parser . add_argument (... | Files extractor command line |
17,219 | def combine_slices ( slice_datasets , rescale = None ) : if len ( slice_datasets ) == 0 : raise DicomImportException ( "Must provide at least one DICOM dataset" ) _validate_slices_form_uniform_grid ( slice_datasets ) voxels = _merge_slice_pixel_arrays ( slice_datasets , rescale ) transform = _ijk_to_patient_xyz_transfo... | Given a list of pydicom datasets for an image series stitch them together into a three - dimensional numpy array . Also calculate a 4x4 affine transformation matrix that converts the ijk - pixel - indices into the xyz - coordinates in the DICOM patient s coordinate system . |
17,220 | def _validate_slices_form_uniform_grid ( slice_datasets ) : invariant_properties = [ 'Modality' , 'SOPClassUID' , 'SeriesInstanceUID' , 'Rows' , 'Columns' , 'PixelSpacing' , 'PixelRepresentation' , 'BitsAllocated' , 'BitsStored' , 'HighBit' , ] for property_name in invariant_properties : _slice_attribute_equal ( slice_... | Perform various data checks to ensure that the list of slices form a evenly - spaced grid of data . Some of these checks are probably not required if the data follows the DICOM specification however it seems pertinent to check anyway . |
17,221 | def parse_url ( cls , string ) : match = cls . URL_RE . match ( string ) if not match : raise InvalidKeyError ( cls , string ) return match . groupdict ( ) | If it can be parsed as a version_guid with no preceding org + offering returns a dict with key version_guid and the value |
17,222 | def offering ( self ) : warnings . warn ( "Offering is no longer a supported property of Locator. Please use the course and run properties." , DeprecationWarning , stacklevel = 2 ) if not self . course and not self . run : return None elif not self . run and self . course : return self . course return "/" . join ( [ se... | Deprecated . Use course and run independently . |
17,223 | def make_usage_key_from_deprecated_string ( self , location_url ) : warnings . warn ( "make_usage_key_from_deprecated_string is deprecated! Please use make_usage_key" , DeprecationWarning , stacklevel = 2 ) return BlockUsageLocator . from_string ( location_url ) . replace ( run = self . run ) | Deprecated mechanism for creating a UsageKey given a CourseKey and a serialized Location . |
17,224 | def _from_string ( cls , serialized ) : course_key = CourseLocator . _from_string ( serialized ) parsed_parts = cls . parse_url ( serialized ) block_id = parsed_parts . get ( 'block_id' , None ) if block_id is None : raise InvalidKeyError ( cls , serialized ) return cls ( course_key , parsed_parts . get ( 'block_type' ... | Requests CourseLocator to deserialize its part and then adds the local deserialization of block |
17,225 | def _parse_block_ref ( cls , block_ref , deprecated = False ) : if deprecated and block_ref is None : return None if isinstance ( block_ref , LocalId ) : return block_ref is_valid_deprecated = deprecated and cls . DEPRECATED_ALLOWED_ID_RE . match ( block_ref ) is_valid = cls . ALLOWED_ID_RE . match ( block_ref ) if is_... | Given block_ref tries to parse it into a valid block reference . |
17,226 | def html_id ( self ) : if self . deprecated : id_fields = [ self . DEPRECATED_TAG , self . org , self . course , self . block_type , self . block_id , self . version_guid ] id_string = u"-" . join ( [ v for v in id_fields if v is not None ] ) return self . clean_for_html ( id_string ) else : return self . block_id | Return an id which can be used on an html page as an id attr of an html element . It is currently also persisted by some clients to identify blocks . |
17,227 | def to_deprecated_son ( self , prefix = '' , tag = 'i4x' ) : son = SON ( { prefix + 'tag' : tag } ) for field_name in ( 'org' , 'course' ) : son [ prefix + field_name ] = getattr ( self . course_key , field_name ) for ( dep_field_name , field_name ) in [ ( 'category' , 'block_type' ) , ( 'name' , 'block_id' ) ] : son [... | Returns a SON object that represents this location |
17,228 | def _from_deprecated_son ( cls , id_dict , run ) : course_key = CourseLocator ( id_dict [ 'org' ] , id_dict [ 'course' ] , run , id_dict [ 'revision' ] , deprecated = True , ) return cls ( course_key , id_dict [ 'category' ] , id_dict [ 'name' ] , deprecated = True ) | Return the Location decoding this id_dict and run |
17,229 | def _from_string ( cls , serialized ) : library_key = LibraryLocator . _from_string ( serialized ) parsed_parts = LibraryLocator . parse_url ( serialized ) block_id = parsed_parts . get ( 'block_id' , None ) if block_id is None : raise InvalidKeyError ( cls , serialized ) block_type = parsed_parts . get ( 'block_type' ... | Requests LibraryLocator to deserialize its part and then adds the local deserialization of block |
17,230 | def for_branch ( self , branch ) : return self . replace ( library_key = self . library_key . for_branch ( branch ) ) | Return a UsageLocator for the same block in a different branch of the library . |
17,231 | def for_version ( self , version_guid ) : return self . replace ( library_key = self . library_key . for_version ( version_guid ) ) | Return a UsageLocator for the same block in a different version of the library . |
17,232 | def _strip_object ( key ) : if hasattr ( key , 'version_agnostic' ) and hasattr ( key , 'for_branch' ) : return key . for_branch ( None ) . version_agnostic ( ) else : return key | Strips branch and version info if the given key supports those attributes . |
17,233 | def _strip_value ( value , lookup = 'exact' ) : if lookup == 'in' : stripped_value = [ _strip_object ( el ) for el in value ] else : stripped_value = _strip_object ( value ) return stripped_value | Helper function to remove the branch and version information from the given value which could be a single object or a list . |
17,234 | def _deprecation_warning ( cls ) : if issubclass ( cls , Location ) : warnings . warn ( "Location is deprecated! Please use locator.BlockUsageLocator" , DeprecationWarning , stacklevel = 3 ) elif issubclass ( cls , AssetLocation ) : warnings . warn ( "AssetLocation is deprecated! Please use locator.AssetLocator" , Depr... | Display a deprecation warning for the given cls |
17,235 | def _check_location_part ( cls , val , regexp ) : cls . _deprecation_warning ( ) return CourseLocator . _check_location_part ( val , regexp ) | Deprecated . See CourseLocator . _check_location_part |
17,236 | def _clean ( cls , value , invalid ) : cls . _deprecation_warning ( ) return BlockUsageLocator . _clean ( value , invalid ) | Deprecated . See BlockUsageLocator . _clean |
17,237 | def _join_keys_v1 ( left , right ) : if left . endswith ( ':' ) or '::' in left : raise ValueError ( "Can't join a left string ending in ':' or containing '::'" ) return u"{}::{}" . format ( _encode_v1 ( left ) , _encode_v1 ( right ) ) | Join two keys into a format separable by using _split_keys_v1 . |
17,238 | def _split_keys_v1 ( joined ) : left , _ , right = joined . partition ( '::' ) return _decode_v1 ( left ) , _decode_v1 ( right ) | Split two keys out a string created by _join_keys_v1 . |
17,239 | def _split_keys_v2 ( joined ) : left , _ , right = joined . rpartition ( '::' ) return _decode_v2 ( left ) , _decode_v2 ( right ) | Split two keys out a string created by _join_keys_v2 . |
17,240 | def refresher ( name , refreshers = CompletionRefresher . refreshers ) : def wrapper ( wrapped ) : refreshers [ name ] = wrapped return wrapped return wrapper | Decorator to add the decorated function to the dictionary of refreshers . Any function decorated with a |
17,241 | def refresh ( self , executor , callbacks , completer_options = None ) : if completer_options is None : completer_options = { } if self . is_refreshing ( ) : self . _restart_refresh . set ( ) return [ ( None , None , None , 'Auto-completion refresh restarted.' ) ] else : self . _completer_thread = threading . Thread ( ... | Creates a SQLCompleter object and populates it with the relevant completion suggestions in a background thread . |
17,242 | def handle_cd_command ( arg ) : CD_CMD = 'cd' tokens = arg . split ( CD_CMD + ' ' ) directory = tokens [ - 1 ] if len ( tokens ) > 1 else None if not directory : return False , "No folder name was provided." try : os . chdir ( directory ) subprocess . call ( [ 'pwd' ] ) return True , None except OSError as e : return F... | Handles a cd shell command by calling python s os . chdir . |
17,243 | def get_editor_query ( sql ) : sql = sql . strip ( ) pattern = re . compile ( '(^\\\e|\\\e$)' ) while pattern . search ( sql ) : sql = pattern . sub ( '' , sql ) return sql | Get the query part of an editor command . |
17,244 | def delete_favorite_query ( arg , ** _ ) : usage = 'Syntax: \\fd name.\n\n' + favoritequeries . usage if not arg : return [ ( None , None , None , usage ) ] status = favoritequeries . delete ( arg ) return [ ( None , None , None , status ) ] | Delete an existing favorite query . |
17,245 | def execute_system_command ( arg , ** _ ) : usage = "Syntax: system [command].\n" if not arg : return [ ( None , None , None , usage ) ] try : command = arg . strip ( ) if command . startswith ( 'cd' ) : ok , error_message = handle_cd_command ( arg ) if not ok : return [ ( None , None , None , error_message ) ] return ... | Execute a system shell command . |
17,246 | def need_completion_refresh ( queries ) : tokens = { 'use' , '\\u' , 'create' , 'drop' } for query in sqlparse . split ( queries ) : try : first_token = query . split ( ) [ 0 ] if first_token . lower ( ) in tokens : return True except Exception : return False | Determines if the completion needs a refresh by checking if the sql statement is an alter create drop or change db . |
17,247 | def is_mutating ( status ) : if not status : return False mutating = set ( [ 'insert' , 'update' , 'delete' , 'alter' , 'create' , 'drop' , 'replace' , 'truncate' , 'load' ] ) return status . split ( None , 1 ) [ 0 ] . lower ( ) in mutating | Determines if the statement is mutating based on the status . |
17,248 | def change_prompt_format ( self , arg , ** _ ) : if not arg : message = 'Missing required argument, format.' return [ ( None , None , None , message ) ] self . prompt = self . get_prompt ( arg ) return [ ( None , None , None , "Changed prompt format to %s" % arg ) ] | Change the prompt format . |
17,249 | def get_output_margin ( self , status = None ) : margin = self . get_reserved_space ( ) + self . get_prompt ( self . prompt ) . count ( '\n' ) + 1 if special . is_timing_enabled ( ) : margin += 1 if status : margin += 1 + status . count ( '\n' ) return margin | Get the output margin ( number of rows for the prompt footer and timing message . |
17,250 | def output ( self , output , status = None ) : if output : size = self . cli . output . get_size ( ) margin = self . get_output_margin ( status ) fits = True buf = [ ] output_via_pager = self . explicit_pager and special . is_pager_enabled ( ) for i , line in enumerate ( output , 1 ) : special . write_tee ( line ) spec... | Output text to stdout or a pager command . The status text is not outputted to pager or files . The message will be logged in the audit log if enabled . The message will be written to the tee file if enabled . The message will be written to the output file if enabled . |
17,251 | def _on_completions_refreshed ( self , new_completer ) : with self . _completer_lock : self . completer = new_completer if self . cli : self . cli . current_buffer . completer = new_completer if self . cli : self . cli . request_redraw ( ) | Swap the completer object in cli with the newly created completer . |
17,252 | def get_reserved_space ( self ) : reserved_space_ratio = .45 max_reserved_space = 8 _ , height = click . get_terminal_size ( ) return min ( int ( round ( height * reserved_space_ratio ) ) , max_reserved_space ) | Get the number of lines to reserve for the completion menu . |
17,253 | def find_matches ( text , collection , start_only = False , fuzzy = True , casing = None ) : last = last_word ( text , include = 'most_punctuations' ) text = last . lower ( ) completions = [ ] if fuzzy : regex = '.*?' . join ( map ( escape , text ) ) pat = compile ( '(%s)' % regex ) for item in sorted ( collection ) : ... | Find completion matches for the given text . Given the user s input text and a collection of available completions find completions matching the last word of the text . If start_only is True the text will match an available completion only at the beginning . Otherwise a completion is considered a match if the text appe... |
17,254 | def log ( logger , level , message ) : if logger . parent . name != 'root' : logger . log ( level , message ) else : print ( message , file = sys . stderr ) | Logs message to stderr if logging isn t initialized . |
17,255 | def read_config_file ( f ) : if isinstance ( f , basestring ) : f = os . path . expanduser ( f ) try : config = ConfigObj ( f , interpolation = False , encoding = 'utf8' ) except ConfigObjError as e : log ( LOGGER , logging . ERROR , "Unable to parse line {0} of config file " "'{1}'." . format ( e . line_number , f ) )... | Read a config file . |
17,256 | def read_config_files ( files ) : config = ConfigObj ( ) for _file in files : _config = read_config_file ( _file ) if bool ( _config ) is True : config . merge ( _config ) config . filename = _config . filename return config | Read and merge a list of config files . |
17,257 | def cli_bindings ( ) : key_binding_manager = KeyBindingManager ( enable_open_in_editor = True , enable_system_bindings = True , enable_auto_suggest_bindings = True , enable_search = True , enable_abort_and_exit_bindings = True ) @ key_binding_manager . registry . add_binding ( Keys . F2 ) def _ ( event ) : _logger . de... | Custom key bindings for cli . |
17,258 | def prompt ( * args , ** kwargs ) : try : return click . prompt ( * args , ** kwargs ) except click . Abort : return False | Prompt the user for input and handle any abort exceptions . |
17,259 | def run ( self , statement ) : statement = statement . strip ( ) if not statement : yield ( None , None , None , None ) components = sqlparse . split ( statement ) for sql in components : sql = sql . rstrip ( ';' ) if sql . endswith ( '\\G' ) : special . set_expanded_output ( True ) sql = sql [ : - 2 ] . strip ( ) cur ... | Execute the sql in the database and return the results . |
17,260 | def get_result ( self , cursor ) : title = headers = None if cursor . description is not None : headers = [ x [ 0 ] for x in cursor . description ] rows = cursor . fetchall ( ) status = '%d row%s in set' % ( len ( rows ) , '' if len ( rows ) == 1 else 's' ) else : logger . debug ( 'No rows in result.' ) rows = None sta... | Get the current result s data from the cursor . |
17,261 | def tables ( self ) : with self . conn . cursor ( ) as cur : cur . execute ( self . TABLES_QUERY ) for row in cur : yield row | Yields table names . |
17,262 | def table_columns ( self ) : with self . conn . cursor ( ) as cur : cur . execute ( self . TABLE_COLUMNS_QUERY % self . database ) for row in cur : yield row | Yields column names . |
17,263 | def create_toolbar_tokens_func ( get_is_refreshing , show_fish_help ) : token = Token . Toolbar def get_toolbar_tokens ( cli ) : result = [ ] result . append ( ( token , ' ' ) ) if cli . buffers [ DEFAULT_BUFFER ] . always_multiline : result . append ( ( token . On , '[F3] Multiline: ON ' ) ) else : result . append ( ... | Return a function that generates the toolbar tokens . |
17,264 | def _get_vi_mode ( cli ) : return { InputMode . INSERT : 'I' , InputMode . NAVIGATION : 'N' , InputMode . REPLACE : 'R' , InputMode . INSERT_MULTIPLE : 'M' } [ cli . vi_state . input_mode ] | Get the current vi mode for display . |
17,265 | def export ( defn ) : globals ( ) [ defn . __name__ ] = defn __all__ . append ( defn . __name__ ) return defn | Decorator to explicitly mark functions that are exposed in a lib . |
17,266 | def execute ( cur , sql ) : command , verbose , arg = parse_special_command ( sql ) if ( command not in COMMANDS ) and ( command . lower ( ) not in COMMANDS ) : raise CommandNotFound try : special_cmd = COMMANDS [ command ] except KeyError : special_cmd = COMMANDS [ command . lower ( ) ] if special_cmd . case_sensitive... | Execute a special command and return the results . If the special command is not supported a KeyError will be raised . |
17,267 | def find_prev_keyword ( sql ) : if not sql . strip ( ) : return None , '' parsed = sqlparse . parse ( sql ) [ 0 ] flattened = list ( parsed . flatten ( ) ) logical_operators = ( 'AND' , 'OR' , 'NOT' , 'BETWEEN' ) for t in reversed ( flattened ) : if t . value == '(' or ( t . is_keyword and ( t . value . upper ( ) not i... | Find the last sql keyword in an SQL statement Returns the value of the last keyword and the text of the query with everything after the last keyword stripped |
17,268 | def _get_thumbnail_options ( self , context , instance ) : width , height = None , None subject_location = False placeholder_width = context . get ( 'width' , None ) placeholder_height = context . get ( 'height' , None ) if instance . use_autoscale and placeholder_width : width = int ( placeholder_width ) if instance .... | Return the size and options of the thumbnail that should be inserted |
17,269 | def create_image_plugin ( filename , image , parent_plugin , ** kwargs ) : from cmsplugin_filer_image . models import FilerImage from filer . models import Image image_plugin = FilerImage ( ) image_plugin . placeholder = parent_plugin . placeholder image_plugin . parent = CMSPlugin . objects . get ( pk = parent_plugin ... | Used for drag - n - drop image insertion with djangocms - text - ckeditor . Set TEXT_SAVE_IMAGE_FUNCTION = cmsplugin_filer_image . integrations . ckeditor . create_image_plugin to enable . |
17,270 | def rename_tables ( db , table_mapping , reverse = False ) : from django . db import connection if reverse : table_mapping = [ ( dst , src ) for src , dst in table_mapping ] table_names = connection . introspection . table_names ( ) for source , destination in table_mapping : if source in table_names and destination in... | renames tables from source to destination name if the source exists and the destination does not exist yet . |
17,271 | def group_and_sort_statements ( stmt_list , ev_totals = None ) : def _count ( stmt ) : if ev_totals is None : return len ( stmt . evidence ) else : return ev_totals [ stmt . get_hash ( ) ] stmt_rows = defaultdict ( list ) stmt_counts = defaultdict ( lambda : 0 ) arg_counts = defaultdict ( lambda : 0 ) for key , s in _g... | Group statements by type and arguments and sort by prevalence . |
17,272 | def make_stmt_from_sort_key ( key , verb ) : def make_agent ( name ) : if name == 'None' or name is None : return None return Agent ( name ) StmtClass = get_statement_by_name ( verb ) inps = list ( key [ 1 ] ) if verb == 'Complex' : stmt = StmtClass ( [ make_agent ( name ) for name in inps ] ) elif verb == 'Conversion'... | Make a Statement from the sort key . |
17,273 | def get_ecs_cluster_for_queue ( queue_name , batch_client = None ) : if batch_client is None : batch_client = boto3 . client ( 'batch' ) queue_resp = batch_client . describe_job_queues ( jobQueues = [ queue_name ] ) if len ( queue_resp [ 'jobQueues' ] ) == 1 : queue = queue_resp [ 'jobQueues' ] [ 0 ] else : raise Batch... | Get the name of the ecs cluster using the batch client . |
17,274 | def tag_instances_on_cluster ( cluster_name , project = 'cwc' ) : ecs = boto3 . client ( 'ecs' ) task_arns = ecs . list_tasks ( cluster = cluster_name ) [ 'taskArns' ] if not task_arns : return tasks = ecs . describe_tasks ( cluster = cluster_name , tasks = task_arns ) [ 'tasks' ] container_instances = ecs . describe_c... | Adds project tag to untagged instances in a given cluster . |
17,275 | def submit_reading ( basename , pmid_list_filename , readers , start_ix = None , end_ix = None , pmids_per_job = 3000 , num_tries = 2 , force_read = False , force_fulltext = False , project_name = None ) : sub = PmidSubmitter ( basename , readers , project_name ) sub . set_options ( force_read , force_fulltext ) sub . ... | Submit an old - style pmid - centered no - database s3 only reading job . |
17,276 | def submit_combine ( basename , readers , job_ids = None , project_name = None ) : sub = PmidSubmitter ( basename , readers , project_name ) sub . job_list = job_ids sub . submit_combine ( ) return sub | Submit a batch job to combine the outputs of a reading job . |
17,277 | def submit_reading ( self , input_fname , start_ix , end_ix , ids_per_job , num_tries = 1 , stagger = 0 ) : self . ids_per_job = ids_per_job id_list_key = 'reading_results/%s/%s' % ( self . basename , self . _s3_input_name ) s3_client = boto3 . client ( 's3' ) s3_client . upload_file ( input_fname , bucket_name , id_li... | Submit a batch of reading jobs |
17,278 | def watch_and_wait ( self , poll_interval = 10 , idle_log_timeout = None , kill_on_timeout = False , stash_log_method = None , tag_instances = False , ** kwargs ) : return wait_for_complete ( self . _job_queue , job_list = self . job_list , job_name_prefix = self . basename , poll_interval = poll_interval , idle_log_ti... | This provides shortcut access to the wait_for_complete_function . |
17,279 | def run ( self , input_fname , ids_per_job , stagger = 0 , ** wait_params ) : submit_thread = Thread ( target = self . submit_reading , args = ( input_fname , 0 , None , ids_per_job ) , kwargs = { 'stagger' : stagger } , daemon = True ) submit_thread . start ( ) self . watch_and_wait ( ** wait_params ) submit_thread . ... | Run this submission all the way . |
17,280 | def set_options ( self , force_read = False , force_fulltext = False ) : self . options [ 'force_read' ] = force_read self . options [ 'force_fulltext' ] = force_fulltext return | Set the options for this run . |
17,281 | def get_chebi_name_from_id ( chebi_id , offline = False ) : chebi_name = chebi_id_to_name . get ( chebi_id ) if chebi_name is None and not offline : chebi_name = get_chebi_name_from_id_web ( chebi_id ) return chebi_name | Return a ChEBI name corresponding to the given ChEBI ID . |
17,282 | def get_chebi_name_from_id_web ( chebi_id ) : url_base = 'http://www.ebi.ac.uk/webservices/chebi/2.0/test/' url_fmt = url_base + 'getCompleteEntity?chebiId=%s' resp = requests . get ( url_fmt % chebi_id ) if resp . status_code != 200 : logger . warning ( "Got bad code form CHEBI client: %s" % resp . status_code ) retur... | Return a ChEBI mame corresponding to a given ChEBI ID using a REST API . |
17,283 | def get_subnetwork ( statements , nodes , relevance_network = None , relevance_node_lim = 10 ) : if relevance_network is not None : relevant_nodes = _find_relevant_nodes ( nodes , relevance_network , relevance_node_lim ) all_nodes = nodes + relevant_nodes else : all_nodes = nodes filtered_statements = _filter_statement... | Return a PySB model based on a subset of given INDRA Statements . |
17,284 | def _filter_statements ( statements , agents ) : filtered_statements = [ ] for s in stmts : if all ( [ a is not None for a in s . agent_list ( ) ] ) and all ( [ a . name in agents for a in s . agent_list ( ) ] ) : filtered_statements . append ( s ) return filtered_statements | Return INDRA Statements which have Agents in the given list . |
17,285 | def _find_relevant_nodes ( query_nodes , relevance_network , relevance_node_lim ) : all_nodes = relevance_client . get_relevant_nodes ( relevance_network , query_nodes ) nodes = [ n [ 0 ] for n in all_nodes [ : relevance_node_lim ] ] return nodes | Return a list of nodes that are relevant for the query . |
17,286 | def process_jsonld_file ( fname ) : with open ( fname , 'r' ) as fh : json_dict = json . load ( fh ) return process_jsonld ( json_dict ) | Process a JSON - LD file in the new format to extract Statements . |
17,287 | def tag_instance ( instance_id , ** tags ) : logger . debug ( "Got request to add tags %s to instance %s." % ( str ( tags ) , instance_id ) ) ec2 = boto3 . resource ( 'ec2' ) instance = ec2 . Instance ( instance_id ) filtered_tags = { k : v for k , v in tags . items ( ) if v and k } if instance . tags is not None : exi... | Tag a single ec2 instance . |
17,288 | def tag_myself ( project = 'cwc' , ** other_tags ) : base_url = "http://169.254.169.254" try : resp = requests . get ( base_url + "/latest/meta-data/instance-id" ) except requests . exceptions . ConnectionError : logger . warning ( "Could not connect to service. Note this should only " "be run from within a batch job."... | Function run when indra is used in an EC2 instance to apply tags . |
17,289 | def get_batch_command ( command_list , project = None , purpose = None ) : command_str = ' ' . join ( command_list ) ret = [ 'python' , '-m' , 'indra.util.aws' , 'run_in_batch' , command_str ] if not project and has_config ( 'DEFAULT_AWS_PROJECT' ) : project = get_config ( 'DEFAULT_AWS_PROJECT' ) if project : ret += [ ... | Get the command appropriate for running something on batch . |
17,290 | def get_jobs ( job_queue = 'run_reach_queue' , job_status = 'RUNNING' ) : batch = boto3 . client ( 'batch' ) jobs = batch . list_jobs ( jobQueue = job_queue , jobStatus = job_status ) return jobs . get ( 'jobSummaryList' ) | Returns a list of dicts with jobName and jobId for each job with the given status . |
17,291 | def get_job_log ( job_info , log_group_name = '/aws/batch/job' , write_file = True , verbose = False ) : job_name = job_info [ 'jobName' ] job_id = job_info [ 'jobId' ] logs = boto3 . client ( 'logs' ) batch = boto3 . client ( 'batch' ) resp = batch . describe_jobs ( jobs = [ job_id ] ) job_desc = resp [ 'jobs' ] [ 0 ]... | Gets the Cloudwatch log associated with the given job . |
17,292 | def get_log_by_name ( log_group_name , log_stream_name , out_file = None , verbose = True ) : logs = boto3 . client ( 'logs' ) kwargs = { 'logGroupName' : log_group_name , 'logStreamName' : log_stream_name , 'startFromHead' : True } lines = [ ] while True : response = logs . get_log_events ( ** kwargs ) if response . g... | Download a log given the log s group and stream name . |
17,293 | def dump_logs ( job_queue = 'run_reach_queue' , job_status = 'RUNNING' ) : jobs = get_jobs ( job_queue , job_status ) for job in jobs : get_job_log ( job , write_file = True ) | Write logs for all jobs with given the status to files . |
17,294 | def get_s3_file_tree ( s3 , bucket , prefix ) : def get_some_keys ( keys , marker = None ) : if marker : relevant_files = s3 . list_objects ( Bucket = bucket , Prefix = prefix , Marker = marker ) else : relevant_files = s3 . list_objects ( Bucket = bucket , Prefix = prefix ) keys . extend ( [ entry [ 'Key' ] for entry ... | Overcome s3 response limit and return NestedDict tree of paths . |
17,295 | def print_model ( self , include_unsigned_edges = False ) : sif_str = '' for edge in self . graph . edges ( data = True ) : n1 = edge [ 0 ] n2 = edge [ 1 ] data = edge [ 2 ] polarity = data . get ( 'polarity' ) if polarity == 'negative' : rel = '-1' elif polarity == 'positive' : rel = '1' elif include_unsigned_edges : ... | Return a SIF string of the assembled model . |
17,296 | def save_model ( self , fname , include_unsigned_edges = False ) : sif_str = self . print_model ( include_unsigned_edges ) with open ( fname , 'wb' ) as fh : fh . write ( sif_str . encode ( 'utf-8' ) ) | Save the assembled model s SIF string into a file . |
17,297 | def print_boolean_net ( self , out_file = None ) : init_str = '' for node_key in self . graph . nodes ( ) : node_name = self . graph . node [ node_key ] [ 'name' ] init_str += '%s = False\n' % node_name rule_str = '' for node_key in self . graph . nodes ( ) : node_name = self . graph . node [ node_key ] [ 'name' ] in_e... | Return a Boolean network from the assembled graph . |
17,298 | def _ensure_api_keys ( task_desc , failure_ret = None ) : def check_func_wrapper ( func ) : @ wraps ( func ) def check_api_keys ( * args , ** kwargs ) : global ELSEVIER_KEYS if ELSEVIER_KEYS is None : ELSEVIER_KEYS = { } if not has_config ( INST_KEY_ENV_NAME ) : logger . warning ( 'Institution API key %s not found in c... | Wrap Elsevier methods which directly use the API keys . |
17,299 | def check_entitlement ( doi ) : if doi . lower ( ) . startswith ( 'doi:' ) : doi = doi [ 4 : ] url = '%s/%s' % ( elsevier_entitlement_url , doi ) params = { 'httpAccept' : 'text/xml' } res = requests . get ( url , params , headers = ELSEVIER_KEYS ) if not res . status_code == 200 : logger . error ( 'Could not check ent... | Check whether IP and credentials enable access to content for a doi . |
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