idx int64 0 63k | question stringlengths 53 5.28k | target stringlengths 5 805 |
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49,100 | def iterconfig ( config , scan_type ) : if scan_type in config : for modality , scans in iter ( config [ scan_type ] . items ( ) ) : for scan in scans : scan . update ( { 'type' : scan_type , 'modality' : modality } ) yield scan | Iterate over BIDS configuration file |
49,101 | def rename_fmapm ( bids_base , basename ) : files = dict ( ) for ext in [ 'nii.gz' , 'json' ] : for echo in [ 1 , 2 ] : fname = '{0}_e{1}.{2}' . format ( basename , echo , ext ) src = os . path . join ( bids_base , 'fmap' , fname ) if os . path . exists ( src ) : dst = src . replace ( 'magnitude_e{0}' . format ( echo ) , 'magnitude{0}' . format ( echo ) ) logger . debug ( 'renaming %s to %s' , src , dst ) os . rename ( src , dst ) files [ ext ] = dst return files | Rename magnitude fieldmap file to BIDS specification |
49,102 | def convert ( input , output ) : dirname = os . path . dirname ( output ) if not os . path . exists ( dirname ) : os . makedirs ( dirname ) basename = os . path . basename ( output ) basename = re . sub ( '.nii(.gz)?' , '' , basename ) dcm2niix = commons . which ( 'dcm2niix' ) cmd = [ 'dcm2niix' , '-s' , 'y' , '-b' , 'y' , '-z' , 'y' , '-f' , basename , '-o' , dirname , input ] logger . debug ( cmd ) sp . check_output ( cmd ) | Run dcm2niix on input file |
49,103 | def DispatchSpout ( * a , ** kw ) : spout_class_name = get_config ( ) [ 'Spout' ] spout_class = import_name ( spout_class_name , default_ns = 'birding.spout' ) return spout_class ( * a , ** kw ) | Factory to dispatch spout class based on config . |
49,104 | def which ( x ) : for p in os . environ . get ( 'PATH' ) . split ( os . pathsep ) : p = os . path . join ( p , x ) if os . path . exists ( p ) : return os . path . abspath ( p ) return None | Same as which command on Linux |
49,105 | def serve ( context : Context , port = 8000 , browsersync_port = 3000 , browsersync_ui_port = 3030 ) : try : from watchdog . observers import Observer except ImportError : context . pip_command ( 'install' , 'watchdog>0.8,<0.9' ) from watchdog . observers import Observer from watchdog . events import PatternMatchingEventHandler class RebuildHandler ( PatternMatchingEventHandler ) : def __init__ ( self , * args , ** kwargs ) : super ( ) . __init__ ( * args , ** kwargs ) self . _patterns = [ '*.js' , '*.scss' , '*.html' ] self . _ignore_directories = True self . builder = None self . rebuild_javascript = threading . Event ( ) self . rebuild_stylesheets = threading . Event ( ) def on_any_event ( self , event ) : if self . builder : self . builder . cancel ( ) extension = event . src_path . rsplit ( '.' , 1 ) [ - 1 ] . lower ( ) if extension == 'js' : self . rebuild_javascript . set ( ) elif extension == 'scss' : self . rebuild_stylesheets . set ( ) self . builder = threading . Timer ( 3 , self . rebuild ) self . builder . start ( ) def rebuild ( self ) : if self . rebuild_javascript . is_set ( ) : self . rebuild_javascript . clear ( ) context . debug ( 'Triggering javascript build' ) bundle_javascript ( context ) if self . rebuild_stylesheets . is_set ( ) : self . rebuild_stylesheets . clear ( ) context . debug ( 'Triggering stylesheet build' ) bundle_stylesheets ( context ) context . debug ( 'Reloading browsers' ) context . node_tool ( 'browser-sync' , 'reload' , '--port=%s' % browsersync_port ) context . info ( 'Watching sources' ) observer = Observer ( ) paths = [ context . app . common_asset_source_path , context . app . asset_source_path , context . app . common_templates_path , context . app . templates_path , ] handler = RebuildHandler ( ) for path in paths : observer . schedule ( handler , path , recursive = True ) observer . setDaemon ( True ) observer . start ( ) context . info ( 'Starting browser sync' ) browsersync_args = [ 'start' , '--host=localhost' , '--no-open' , '--logLevel' , { 0 : 'silent' , 1 : 'info' , 2 : 'debug' } [ context . verbosity ] , '--port=%s' % browsersync_port , '--proxy=localhost:%s' % port , '--ui-port=%s' % browsersync_ui_port ] browsersync = functools . partial ( context . node_tool , 'browser-sync' , * browsersync_args ) threading . Thread ( target = browsersync , daemon = True ) . start ( ) context . info ( 'Starting web server' ) return start ( context , port = port ) | Starts a development server with auto - building and live - reload |
49,106 | def create_build_paths ( context : Context ) : paths = [ context . app . asset_build_path , context . app . screenshots_build_path , context . app . collected_assets_path ] for path in filter ( None , paths ) : os . makedirs ( path , exist_ok = True ) | Creates directories needed for build outputs |
49,107 | def node_dependencies ( context : Context ) : args = [ '--loglevel' , { 0 : 'silent' , 1 : 'warn' , 2 : 'info' } [ context . verbosity ] ] if not context . use_colour : args . append ( '--color false' ) args . append ( 'install' ) return context . shell ( 'npm' , * args ) | Updates node . js dependencies |
49,108 | def local_docker ( context : Context ) : output = io . StringIO ( ) with contextlib . redirect_stdout ( output ) : context . shell ( 'docker-machine' , 'ip' , 'default' ) host_machine_ip = output . getvalue ( ) . strip ( ) or socket . gethostbyname ( socket . gethostname ( ) ) args = ( ) if context . verbosity > 1 : args += ( '--verbose' , ) args += ( 'up' , '--build' , '--remove-orphans' ) if not context . use_colour : args += ( '--no-color' , ) context . shell ( 'docker-compose' , * args , environment = { 'HOST_MACHINE_IP' : host_machine_ip } ) | Runs the app in a docker container ; for local development only! Once performed docker - compose up can be used directly |
49,109 | def lint_javascript ( context : Context ) : args = [ '--config' , os . path . join ( context . app . common_templates_path , 'mtp_common' , 'build_tasks' , 'eslintrc.json' ) , '--format' , 'stylish' , ] if context . verbosity == 0 : args . append ( '--quiet' ) if not context . use_colour : args . append ( '--no-color' ) args . append ( context . app . javascript_source_path ) return context . node_tool ( 'eslint' , * args ) | Tests javascript for code and style errors |
49,110 | def lint_stylesheets ( context : Context ) : args = [ '--config' , os . path . join ( context . app . common_templates_path , 'mtp_common' , 'build_tasks' , 'sass-lint.yml' ) , '--format' , 'stylish' , '--syntax' , 'scss' , ] if context . verbosity > 1 : args . append ( '--verbose' ) args . append ( os . path . join ( context . app . scss_source_path , '**' , '*.scss' ) ) return context . node_tool ( 'sass-lint' , * args ) | Tests stylesheets for code and style errors |
49,111 | def govuk_template ( context : Context , version = '0.23.0' , replace_fonts = True ) : if FileSet ( os . path . join ( context . app . govuk_templates_path , 'base.html' ) ) : return url = 'https://github.com/alphagov/govuk_template/releases' '/download/v{0}/django_govuk_template-{0}.tgz' . format ( version ) try : context . shell ( 'curl --location %(silent)s --output govuk_template.tgz %(url)s' % { 'silent' : '--silent' if context . verbosity == 0 else '' , 'url' : url , } ) context . shell ( 'tar xzf govuk_template.tgz ./govuk_template' ) rsync_flags = '-avz' if context . verbosity == 2 else '-az' context . shell ( 'rsync %s govuk_template/static/ %s/' % ( rsync_flags , context . app . asset_build_path ) ) context . shell ( 'rsync %s govuk_template/templates/ %s/' % ( rsync_flags , context . app . templates_path ) ) finally : context . shell ( 'rm -rf govuk_template.tgz ./govuk_template' ) if replace_fonts : context . shell ( 'rm -rf %s/stylesheets/fonts-ie8.css' ' %s/stylesheets/fonts/' % ( context . app . asset_build_path , context . app . asset_build_path ) ) | Installs GOV . UK template |
49,112 | def additional_assets ( context : Context ) : rsync_flags = '-avz' if context . verbosity == 2 else '-az' for path in context . app . additional_asset_paths : context . shell ( 'rsync %s %s %s/' % ( rsync_flags , path , context . app . asset_build_path ) ) | Collects assets from GOV . UK frontend toolkit |
49,113 | def precompile_python_code ( context : Context ) : from compileall import compile_dir kwargs = { } if context . verbosity < 2 : kwargs [ 'quiet' ] = True compile_dir ( context . app . django_app_name , ** kwargs ) | Pre - compiles python modules |
49,114 | def make_messages ( context : Context , javascript = False , fuzzy = False ) : kwargs = { 'all' : True , 'keep_pot' : True , 'no_wrap' : True , } if fuzzy : kwargs [ 'allow_fuzzy' ] = True if javascript : kwargs . update ( domain = 'djangojs' , ignore_patterns = [ '*.bundle.js' ] ) with in_dir ( context . app . django_app_name ) : return context . management_command ( 'makemessages' , ** kwargs ) | Collects text into translation source files |
49,115 | def classify_format ( f ) : l0 , l1 = _get_two_lines ( f ) if loader . glove . check_valid ( l0 , l1 ) : return _glove elif loader . word2vec_text . check_valid ( l0 , l1 ) : return _word2vec_text elif loader . word2vec_bin . check_valid ( l0 , l1 ) : return _word2vec_bin else : raise OSError ( b"Invalid format" ) | Determine the format of word embedding file by their content . This operation only looks at the first two lines and does not check the sanity of input file . |
49,116 | def load ( cls , path , vocab = None , dtype = np . float32 , max_vocab = None , format = None , binary = False ) : freqs = None if vocab is not None : with open ( vocab , mode = 'rb' ) as f : freqs = loader . vocab . load_vocab ( f ) vocab = { k : i for i , ( k , v ) in enumerate ( sorted ( six . iteritems ( freqs ) , key = lambda k_v : k_v [ 1 ] , reverse = True ) [ : max_vocab ] ) } with open ( path , mode = 'rb' ) as f : if format is None : mod = classify_format ( f ) else : mod = _select_module ( format , binary ) with open ( path , mode = 'rb' ) as f : if vocab is not None : arr = mod . loader . load_with_vocab ( f , vocab , dtype = dtype ) v = vocab else : arr , v = mod . loader . load ( f , max_vocab = max_vocab , dtype = dtype ) obj = cls ( arr , v , freqs ) obj . _load_cond = mod return obj | Load pretrained word embedding from a file . |
49,117 | def paths_for_shell ( paths , separator = ' ' ) : paths = filter ( None , paths ) paths = map ( shlex . quote , paths ) if separator is None : return paths return separator . join ( paths ) | Converts a list of paths for use in shell commands |
49,118 | def register ( self , * dependencies , default = False , hidden = False , ignore_return_code = False ) : def outer ( func ) : task = Task ( func , * dependencies , default = default , hidden = hidden , ignore_return_code = ignore_return_code ) overidden_task = self . _tasks . pop ( task . name , None ) if overidden_task : self . _overidden_tasks [ task . name ] . append ( overidden_task ) self [ task . name ] = task return task return outer | Decorates a callable to turn it into a task |
49,119 | def lookup_task ( self , task ) : if isinstance ( task , str ) : try : return self [ task ] except KeyError : pass raise TaskError ( 'Unknown task %s' % task ) | Looks up a task by name or by callable |
49,120 | def get_default_task ( self ) : default_tasks = list ( filter ( lambda task : task . default , self . values ( ) ) ) if len ( default_tasks ) == 1 : return default_tasks [ 0 ] | Returns the default task if there is only one |
49,121 | def from_callable ( cls , func , ignored_parameters = set ( ) ) : group = cls ( ) signature = inspect . signature ( func ) for parameter in signature . parameters . values ( ) : if parameter . name . startswith ( '_' ) or parameter . name in ignored_parameters : continue parameter = Parameter . from_callable_parameter ( parameter ) group [ parameter . name ] = parameter return group | Reads a function or method signature to produce a set of parameters |
49,122 | def from_mapping ( cls , mapping ) : group = cls ( ) for name , value in mapping . items ( ) : if name . startswith ( '_' ) : continue group [ name ] = Parameter ( name = name , value = value , constraint = Parameter . constraint_from_type ( value ) , ) return group | Produces a set of parameters from a mapping |
49,123 | def to_dict ( self ) : return dict ( ( parameter . name , parameter . value ) for parameter in self . values ( ) ) | Converts the set of parameters into a dict |
49,124 | def consume_arguments ( self , argument_list ) : while True : argument_count = len ( argument_list ) for parameter in self . values ( ) : argument_list = parameter . consume_arguments ( argument_list ) if len ( argument_list ) == argument_count : return argument_list | Takes arguments from a list while there are parameters that can accept them |
49,125 | def update_from ( self , mapping ) : for key , value in mapping . items ( ) : if key in self : if isinstance ( value , Parameter ) : value = value . value self [ key ] . value = value | Updates the set of parameters from a mapping for keys that already exist |
49,126 | def from_callable_parameter ( cls , parameter ) : if parameter . kind == parameter . KEYWORD_ONLY or parameter . kind == parameter . POSITIONAL_OR_KEYWORD and parameter . default is not parameter . empty : if parameter . annotation is not parameter . empty : constraint = parameter . annotation else : constraint = Parameter . constraint_from_type ( parameter . default ) return cls ( name = parameter . name , value = parameter . default , constraint = constraint , ) else : raise ParameterError ( 'Only keyword parameters are supported' ) | Produces a parameter from a function or method |
49,127 | def constraint_from_type ( cls , value ) : if value is None : return None value_type = type ( value ) if value_type in ( str , int , bool ) : return value_type raise ParameterError ( 'Parameter type cannot be %s' % value_type ) | Returns the constraint callable given a value |
49,128 | def constraint_from_choices ( cls , value_type : type , choices : collections . Sequence ) : choices_str = ', ' . join ( map ( str , choices ) ) def constraint ( value ) : value = value_type ( value ) if value not in choices : raise ParameterError ( 'Argument must be one of %s' % choices_str ) return value constraint . __name__ = 'choices_%s' % value_type . __name__ constraint . __doc__ = 'choice of %s' % choices_str return constraint | Returns a constraint callable based on choices of a given type |
49,129 | def arg_name ( self ) : if self . constraint is bool and self . value : return '--no-%s' % self . name . replace ( '_' , '-' ) return '--%s' % self . name . replace ( '_' , '-' ) | Returns the name of the parameter as a command line flag |
49,130 | def consume_arguments ( self , argument_list ) : if len ( argument_list ) == 0 : return [ ] if argument_list [ 0 ] == self . arg_name : argument_list = argument_list [ 1 : ] if self . constraint is bool : self . value = not self . value else : try : value = argument_list . pop ( 0 ) except IndexError : raise ParameterError ( 'Argument %s expects a value' % self . arg_name ) self . value = value return argument_list | Takes arguments from a list while this parameter can accept them |
49,131 | def pip_command ( self , command , * args ) : try : from pip . _internal import main as pip_main except ImportError : from pip import main as pip_main args = [ command ] + list ( args ) if self . verbosity == 0 : args . insert ( 0 , '--quiet' ) elif self . verbosity == 2 : args . insert ( 0 , '--verbose' ) return pip_main ( args ) | Runs a pip command |
49,132 | def shell ( self , command , * args , environment = None ) : command += ' ' + ' ' . join ( args ) command = command . strip ( ) self . debug ( self . yellow_style ( '$ %s' % command ) ) env = self . env . copy ( ) env . update ( environment or { } ) return subprocess . call ( command , shell = True , env = env ) | Runs a shell command |
49,133 | def management_command ( self , command , * args , ** kwargs ) : self . setup_django ( ) if 'verbosity' not in kwargs : kwargs [ 'verbosity' ] = self . verbosity if not self . use_colour : kwargs [ 'no_color' ] = False self . debug ( self . yellow_style ( '$ manage.py %s' % command ) ) return call_command ( command , * args , ** kwargs ) | Runs a Django management command |
49,134 | def login ( request , user ) : session_auth_hash = '' if user is None : user = request . user if hasattr ( user , 'get_session_auth_hash' ) : session_auth_hash = user . get_session_auth_hash ( ) if SESSION_KEY in request . session : session_key = request . session [ SESSION_KEY ] if session_key != user . pk or ( session_auth_hash and request . session . get ( HASH_SESSION_KEY ) != session_auth_hash ) : request . session . flush ( ) else : request . session . cycle_key ( ) request . session [ SESSION_KEY ] = user . pk request . session [ BACKEND_SESSION_KEY ] = user . backend request . session [ USER_DATA_SESSION_KEY ] = user . user_data request . session [ HASH_SESSION_KEY ] = session_auth_hash update_token_in_session ( request . session , user . token ) if hasattr ( request , 'user' ) : request . user = user rotate_token ( request ) user_logged_in . send ( sender = user . __class__ , request = request , user = user ) | Persist a user id and a backend in the request . This way a user doesn t have to reauthenticate on every request . Note that data set during the anonymous session is retained when the user logs in . |
49,135 | def get_user ( request ) : user = None try : user_id = request . session [ SESSION_KEY ] token = request . session [ AUTH_TOKEN_SESSION_KEY ] user_data = request . session [ USER_DATA_SESSION_KEY ] backend_path = request . session [ BACKEND_SESSION_KEY ] except KeyError : pass else : if backend_path in settings . AUTHENTICATION_BACKENDS : backend = load_backend ( backend_path ) user = backend . get_user ( user_id , token , user_data ) if hasattr ( user , 'get_session_auth_hash' ) : session_hash = request . session . get ( HASH_SESSION_KEY ) session_hash_verified = session_hash and constant_time_compare ( session_hash , user . get_session_auth_hash ( ) ) if not session_hash_verified : request . session . flush ( ) user = None return user or MojAnonymousUser ( ) | Returns the user model instance associated with the given request session . If no user is retrieved an instance of MojAnonymousUser is returned . |
49,136 | def logout ( request ) : user = getattr ( request , 'user' , None ) if hasattr ( user , 'is_authenticated' ) and not user . is_authenticated : user = None user_logged_out . send ( sender = user . __class__ , request = request , user = user ) language = request . session . get ( LANGUAGE_SESSION_KEY ) request . session . flush ( ) if language is not None : request . session [ LANGUAGE_SESSION_KEY ] = language if hasattr ( request , 'user' ) : request . user = MojAnonymousUser ( ) | Removes the authenticated user s ID from the request and flushes their session data . |
49,137 | def fields ( self ) : return { k : getattr ( self , k , None ) for k in self . schema . fields } | return all the fields and their raw values for this Orm instance . This property returns a dict with the field names and their current values |
49,138 | def create ( cls , fields = None , ** fields_kwargs ) : instance = cls ( fields , ** fields_kwargs ) instance . save ( ) return instance | create an instance of cls with the passed in fields and set it into the db |
49,139 | def populate ( self , fields = None , ** fields_kwargs ) : pop_fields = { } fields = self . make_dict ( fields , fields_kwargs ) for k in self . schema . fields . keys ( ) : pop_fields [ k ] = fields . get ( k , None ) self . _populate ( pop_fields ) | take the passed in fields combine them with missing fields that should be there and then run all those through appropriate methods to hydrate this orm . |
49,140 | def _populate ( self , fields ) : schema = self . schema for k , v in fields . items ( ) : fields [ k ] = schema . fields [ k ] . iget ( self , v ) self . modify ( fields ) self . reset_modified ( ) | this runs all the fields through their iget methods to mimic them freshly coming out of the db then resets modified |
49,141 | def depopulate ( self , is_update ) : fields = { } schema = self . schema for k , field in schema . fields . items ( ) : is_modified = k in self . modified_fields orig_v = getattr ( self , k ) v = field . iset ( self , orig_v , is_update = is_update , is_modified = is_modified ) if is_modified or v is not None : if is_update and field . is_pk ( ) and v == orig_v : continue else : fields [ k ] = v if not is_update : for field_name in schema . required_fields . keys ( ) : if field_name not in fields : raise KeyError ( "Missing required field {}" . format ( field_name ) ) return fields | Get all the fields that need to be saved |
49,142 | def insert ( self ) : ret = True schema = self . schema fields = self . depopulate ( False ) q = self . query q . set_fields ( fields ) pk = q . insert ( ) if pk : fields = q . fields fields [ schema . pk . name ] = pk self . _populate ( fields ) else : ret = False return ret | persist the field values of this orm |
49,143 | def update ( self ) : ret = True fields = self . depopulate ( True ) q = self . query q . set_fields ( fields ) pk = self . pk if pk : q . is_field ( self . schema . pk . name , pk ) else : raise ValueError ( "You cannot update without a primary key" ) if q . update ( ) : fields = q . fields self . _populate ( fields ) else : ret = False return ret | re - persist the updated field values of this orm that has a primary key |
49,144 | def save ( self ) : ret = False pk = None if self . schema . pk . name not in self . modified_fields : pk = self . pk if pk : ret = self . update ( ) else : ret = self . insert ( ) return ret | persist the fields in this object into the db this will update if _id is set otherwise it will insert |
49,145 | def delete ( self ) : ret = False q = self . query pk = self . pk if pk : pk_name = self . schema . pk . name self . query . is_field ( pk_name , pk ) . delete ( ) setattr ( self , pk_name , None ) self . reset_modified ( ) for field_name in self . schema . fields : if getattr ( self , field_name , None ) != None : self . modified_fields . add ( field_name ) ret = True return ret | delete the object from the db if pk is set |
49,146 | def reset_modified ( self ) : self . modified_fields = set ( ) for field_name , field in self . schema . normal_fields . items ( ) : if isinstance ( field , ObjectField ) : self . modified_fields . add ( field_name ) | reset field modification tracking |
49,147 | def modify ( self , fields = None , ** fields_kwargs ) : modified_fields = set ( ) fields = self . make_dict ( fields , fields_kwargs ) fields = self . _modify ( fields ) for field_name , field_val in fields . items ( ) : in_schema = field_name in self . schema . fields if in_schema : setattr ( self , field_name , field_val ) modified_fields . add ( field_name ) return modified_fields | update the fields of this instance with the values in dict fields |
49,148 | def jsonable ( self , * args , ** options ) : d = { } for field_name , field in self . schema . normal_fields . items ( ) : field_val = getattr ( self , field_name , None ) field_val = field . jsonable ( self , field_val ) if field_val is not None : d [ field_name ] = field_val return d | return a public version of this instance that can be jsonified |
49,149 | def merge2images ( hdu1 , hdu2 , debugplot ) : image_header = hdu1 [ 0 ] . header image_header_ = hdu2 [ 0 ] . header naxis = image_header [ 'naxis' ] naxis_ = image_header_ [ 'naxis' ] if naxis != naxis_ : raise ValueError ( 'Incompatible NAXIS values: {}, {}' . format ( naxis , naxis_ ) ) naxis1 = image_header [ 'naxis1' ] naxis1_ = image_header_ [ 'naxis1' ] if naxis1 != naxis1_ : raise ValueError ( 'Incompatible NAXIS1 values: {}, {}' . format ( naxis1 , naxis1_ ) ) if naxis == 1 : naxis2 = 1 elif naxis == 2 : naxis2 = image_header [ 'naxis2' ] naxis2_ = image_header_ [ 'naxis2' ] if naxis2 != naxis2_ : raise ValueError ( 'Incompatible NAXIS2 values: {}, {}' . format ( naxis2 , naxis2_ ) ) else : raise ValueError ( 'Unexpected NAXIS value: {}' . format ( naxis ) ) image2d_merged = np . zeros ( ( naxis2 , naxis1 ) ) data1 = hdu1 [ 0 ] . data data2 = hdu2 [ 0 ] . data for i in range ( naxis2 ) : sp1 = data1 [ i , : ] sp2 = data2 [ i , : ] jmin1 , jmax1 = find_pix_borders ( sp1 , sought_value = 0 ) jmin2 , jmax2 = find_pix_borders ( sp2 , sought_value = 0 ) image2d_merged [ i , : ] = sp1 + sp2 useful1 = ( jmin1 != - 1 ) and ( jmax1 != naxis1 ) useful2 = ( jmin2 != - 1 ) and ( jmax2 != naxis1 ) if useful1 and useful2 : jmineff = max ( jmin1 , jmin2 ) jmaxeff = min ( jmax1 , jmax2 ) image2d_merged [ i , jmineff : ( jmaxeff + 1 ) ] /= 2 image_merged = fits . PrimaryHDU ( data = image2d_merged . astype ( np . float32 ) , header = image_header ) return image_merged | Merge 2 EMIR images averaging the common region . |
49,150 | def configure_environ ( dsn_env_name = 'PROM_DSN' , connection_class = DsnConnection ) : inters = [ ] cs = dsnparse . parse_environs ( dsn_env_name , parse_class = connection_class ) for c in cs : inter = c . interface set_interface ( inter , c . name ) inters . append ( inter ) return inters | configure interfaces based on environment variables |
49,151 | def configure ( dsn , connection_class = DsnConnection ) : c = dsnparse . parse ( dsn , parse_class = connection_class ) inter = c . interface set_interface ( inter , c . name ) return inter | configure an interface to be used to query a backend |
49,152 | def set_interface ( interface , name = '' ) : global interfaces if not interface : raise ValueError ( 'interface is empty' ) if name in interfaces : interfaces [ name ] . close ( ) interfaces [ name ] = interface | don t want to bother with a dsn? Use this method to make an interface available |
49,153 | async def open_websocket_server ( sock , filter = None ) : ws = await create_websocket_server ( sock , filter = filter ) try : yield ws finally : await ws . close ( ) | A context manager which serves this websocket . |
49,154 | async def create_websocket_server ( sock , filter = None ) : ws = Websocket ( ) await ws . start_server ( sock , filter = filter ) return ws | A more low - level form of open_websocket_server . You are responsible for closing this websocket . |
49,155 | def magic_fields ( self ) : return { f : v for f , v in self . fields . items ( ) if f . startswith ( '_' ) } | the magic fields for the schema |
49,156 | def set_index ( self , index_name , index ) : if not index_name : raise ValueError ( "index_name must have a value" ) if index_name in self . indexes : raise ValueError ( "index_name {} has already been defined on {}" . format ( index_name , str ( self . indexes [ index_name ] . fields ) ) ) if not isinstance ( index , Index ) : raise ValueError ( "{} is not an Index instance" . format ( type ( index ) ) ) index . name = index_name self . indexes [ index_name ] = index return self | add an index to the schema |
49,157 | def schema ( self ) : if not hasattr ( self , "_schema" ) : ret = None o = self . _type if isinstance ( o , type ) : ret = getattr ( o , "schema" , None ) elif isinstance ( o , Schema ) : ret = o else : module , klass = utils . get_objects ( o ) ret = klass . schema self . _schema = ret return self . _schema | return the schema instance if this is reference to another table |
49,158 | def fval ( self , instance ) : try : val = instance . __dict__ [ self . instance_field_name ] except KeyError as e : val = None return val | return the raw value that this property is holding internally for instance |
49,159 | def set_default_reference ( self , method , reference ) : if method not in self . _available_methods : raise ValueError ( 'Unknown method: {0}' . format ( method ) ) self . _default_references [ method ] = reference | Set the default reference for a method . |
49,160 | def get_default_reference ( self , method ) : if method not in self . _available_methods : raise ValueError ( 'Unknown method: {0}' . format ( method ) ) return self . _default_references . get ( method ) | Returns the default reference for a method . |
49,161 | def print_element_xray_transitions ( self , element , file = sys . stdout , tabulate_kwargs = None ) : header = [ 'IUPAC' , 'Siegbahn' , 'Energy (eV)' , 'Probability' ] rows = [ ] for xraytransition in self . element_xray_transitions ( element ) : try : iupac = self . xray_transition_notation ( xraytransition , 'iupac' ) except : iupac = '' try : siegbahn = self . xray_transition_notation ( xraytransition , 'siegbahn' ) except : siegbahn = '' try : energy_eV = self . xray_transition_energy_eV ( element , xraytransition ) except : energy_eV = '' try : probability = self . xray_transition_probability ( element , xraytransition ) except : probability = '' rows . append ( [ iupac , siegbahn , energy_eV , probability ] ) rows . sort ( key = operator . itemgetter ( 2 ) ) if tabulate_kwargs is None : tabulate_kwargs = { } file . write ( tabulate . tabulate ( rows , header , ** tabulate_kwargs ) ) | Prints all x - ray transitions for an element with their different notations and energy . |
49,162 | def get_subclasses ( modulepath , parent_class ) : if isinstance ( modulepath , ModuleType ) : modules = get_modules ( modulepath . __name__ ) else : modules = get_modules ( modulepath ) ret = set ( ) for m in modules : cs = inspect . getmembers ( m , lambda v : inspect . isclass ( v ) and issubclass ( v , parent_class ) ) for class_name , klass in cs : ret . add ( klass ) return ret | given a module return all the parent_class subclasses that are found in that module and any submodules . |
49,163 | def build_dump_order ( orm_class , orm_classes ) : if orm_class in orm_classes : return for field_name , field_val in orm_class . schema . fields . items ( ) : if field_val . is_ref ( ) : build_dump_order ( field_val . schema . orm_class , orm_classes ) if orm_class not in orm_classes : orm_classes . append ( orm_class ) | pass in an array when you encounter a ref call this method again with the array when something has no more refs then it gets appended to the array and returns each time something gets through the list they are added but before they are added to the list it is checked to see if it is already in the listt |
49,164 | def main_dump ( paths , directory , dry_run ) : table_map = get_table_map ( paths ) for conn_name , conn_info in table_map . items ( ) : inter = conn_info [ "interface" ] conn = inter . connection_config table_names = conn_info [ "table_names" ] cmd = get_base_cmd ( "backup" , inter , directory ) cmd . extend ( table_names ) if dry_run : echo . out ( " " . join ( cmd ) ) else : run_cmd ( cmd ) | dump all or part of the prom data currently only works on Postgres databases |
49,165 | def main_restore ( directory , conn_name ) : inter = get_interface ( conn_name ) conn = inter . connection_config cmd = get_base_cmd ( "restore" , inter , directory ) run_cmd ( cmd ) | Restore your database dumped with the dump command |
49,166 | def _get_fields ( self , table_name , ** kwargs ) : ret = { } query_str = [ ] query_args = [ 'f' , table_name ] query_str . append ( 'SELECT' ) query_str . append ( ', ' . join ( [ 'a.attnum' , 'a.attname' , 'a.attnotnull' , 't.typname' , 'i.indisprimary' , 'c.relname AS confrelname' , ] ) ) query_str . append ( 'FROM' ) query_str . append ( ' pg_attribute a' ) query_str . append ( 'JOIN pg_type t ON a.atttypid = t.oid' ) query_str . append ( 'LEFT JOIN pg_index i ON a.attrelid = i.indrelid' ) query_str . append ( ' AND a.attnum = any(i.indkey)' ) query_str . append ( 'LEFT JOIN pg_constraint s ON a.attrelid = s.conrelid' ) query_str . append ( ' AND s.contype = {} AND a.attnum = any(s.conkey)' . format ( self . val_placeholder ) ) query_str . append ( 'LEFT JOIN pg_class c ON s.confrelid = c.oid' ) query_str . append ( 'WHERE' ) query_str . append ( ' a.attrelid = {}::regclass' . format ( self . val_placeholder ) ) query_str . append ( ' AND a.attisdropped = False' ) query_str . append ( ' AND a.attnum > 0' ) query_str . append ( 'ORDER BY a.attnum ASC' ) query_str = os . linesep . join ( query_str ) fields = self . query ( query_str , * query_args , ** kwargs ) pg_types = { "float8" : float , "timestamp" : datetime . datetime , "int2" : int , "int4" : int , "int8" : long , "numeric" : decimal . Decimal , "text" : str , "bpchar" : str , "varchar" : str , "bool" : bool , "date" : datetime . date , "blob" : bytearray , } for row in fields : field = { "name" : row [ "attname" ] , "field_type" : pg_types [ row [ "typname" ] ] , "field_required" : row [ "attnotnull" ] , "pk" : bool ( row [ "indisprimary" ] ) , } if row [ "confrelname" ] : field [ "schema_table_name" ] = row [ "confrelname" ] field [ "ref_table_name" ] = row [ "confrelname" ] ret [ field [ "name" ] ] = field return ret | return all the fields for the given schema |
49,167 | def client_authentication ( self , request , auth = None , ** kwargs ) : try : auth_info = verify_client ( self . endpoint_context , request , auth ) except Exception as err : msg = "Failed to verify client due to: {}" . format ( err ) logger . error ( msg ) return self . error_cls ( error = "unauthorized_client" , error_description = msg ) else : if 'client_id' not in auth_info : logger . error ( 'No client_id, authentication failed' ) return self . error_cls ( error = "unauthorized_client" , error_description = 'unknown client' ) return auth_info | Deal with client authentication |
49,168 | def _post_parse_request ( self , request , client_id = '' , ** kwargs ) : if 'state' in request : try : sinfo = self . endpoint_context . sdb [ request [ 'code' ] ] except KeyError : logger . error ( 'Code not present in SessionDB' ) return self . error_cls ( error = "unauthorized_client" ) else : state = sinfo [ 'authn_req' ] [ 'state' ] if state != request [ 'state' ] : logger . error ( 'State value mismatch' ) return self . error_cls ( error = "unauthorized_client" ) if "client_id" not in request : request [ "client_id" ] = client_id logger . debug ( "%s: %s" % ( request . __class__ . __name__ , sanitize ( request ) ) ) return request | This is where clients come to get their access tokens |
49,169 | def register ( self , new_outputs , * args , ** kwargs ) : kwargs . update ( zip ( self . meta_names , args ) ) super ( OutputRegistry , self ) . register ( new_outputs , ** kwargs ) | Register outputs and metadata . |
49,170 | def initial_classification ( self , obresult , target_is_sky = False ) : with obresult . frames [ 0 ] . open ( ) as baseimg : has_bpm_ext = 'BPM' in baseimg self . logger . debug ( 'images have BPM extension: %s' , has_bpm_ext ) images_info = [ ] for f in obresult . frames : with f . open ( ) as img : hdr = img [ 0 ] . header iinfo = ImageInfo ( f ) finfo = { } iinfo . metadata = finfo finfo [ 'uuid' ] = hdr [ 'UUID' ] finfo [ 'exposure' ] = hdr [ 'EXPTIME' ] finfo [ 'airmass' ] = hdr [ 'airmass' ] finfo [ 'mjd' ] = hdr [ 'tstamp' ] iinfo . label = 'result_image_{}' . format ( finfo [ 'uuid' ] ) iinfo . mask = nfcom . Extension ( "BPM" ) iinfo . objmask_data = None iinfo . valid_target = False iinfo . valid_sky = False iinfo . itype = 'TARGET' if iinfo . itype == 'TARGET' : iinfo . valid_target = True if target_is_sky : iinfo . valid_sky = True if iinfo . itype == 'SKY' : iinfo . valid_sky = True images_info . append ( iinfo ) return images_info | Classify input frames |
49,171 | def update_or_create ( self , * args , ** kwargs ) : obj , created = super ( ) . update_or_create ( * args , ** kwargs ) if not created : return self . with_signal ( result = ( obj , created ) ) return obj , created | Only sent when not created since default implementation will call self . create when creating which triggers our signal already . |
49,172 | def update ( self , duration ) : if duration >= 0 : self . histogram . update ( duration ) self . meter . mark ( ) | Add a recorded duration . |
49,173 | def _build_g5k_conf ( vmong5k_conf ) : clusters = [ m . cluster for m in vmong5k_conf . machines ] sites = g5k_api_utils . get_clusters_sites ( clusters ) site_names = set ( sites . values ( ) ) if len ( site_names ) > 1 : raise Exception ( "Multisite deployment not supported yet" ) site = site_names . pop ( ) return _do_build_g5k_conf ( vmong5k_conf , site ) | Build the conf of the g5k provider from the vmong5k conf . |
49,174 | def copy_model_instance ( obj ) : meta = getattr ( obj , '_meta' ) return { f . name : getattr ( obj , f . name ) for f in meta . get_fields ( include_parents = False ) if not f . auto_created } | Copy Django model instance as a dictionary excluding automatically created fields like an auto - generated sequence as a primary key or an auto - created many - to - one reverse relation . |
49,175 | def load_data ( self , * args , ** kwargs ) : argpos = { v [ 'extras' ] [ 'argpos' ] : k for k , v in self . parameters . iteritems ( ) if 'argpos' in v [ 'extras' ] } data = dict ( { argpos [ n ] : a for n , a in enumerate ( args ) } , ** kwargs ) return self . apply_units_to_cache ( data ) | Collects positional and keyword arguments into data and applies units . |
49,176 | def grid_reload_from_name ( job_name ) : gk = get_api_client ( ) sites = get_all_sites_obj ( ) jobs = [ ] for site in [ s for s in sites if s . uid not in gk . excluded_site ] : logger . info ( "Reloading %s from %s" % ( job_name , site . uid ) ) _jobs = site . jobs . list ( name = job_name , state = "waiting,launching,running" ) if len ( _jobs ) == 1 : logger . info ( "Reloading %s from %s" % ( _jobs [ 0 ] . uid , site . uid ) ) jobs . append ( _jobs [ 0 ] ) elif len ( _jobs ) > 1 : raise EnosG5kDuplicateJobsError ( site , job_name ) return jobs | Reload all running or pending jobs of Grid 5000 with a given name . |
49,177 | def grid_reload_from_ids ( oargrid_jobids ) : gk = get_api_client ( ) jobs = [ ] for site , job_id in oargrid_jobids : jobs . append ( gk . sites [ site ] . jobs [ job_id ] ) return jobs | Reload all running or pending jobs of Grid 5000 from their ids |
49,178 | def grid_destroy_from_name ( job_name ) : jobs = grid_reload_from_name ( job_name ) for job in jobs : job . delete ( ) logger . info ( "Killing the job (%s, %s)" % ( job . site , job . uid ) ) | Destroy all the jobs with a given name . |
49,179 | def grid_destroy_from_ids ( oargrid_jobids ) : jobs = grid_reload_from_ids ( oargrid_jobids ) for job in jobs : job . delete ( ) logger . info ( "Killing the jobs %s" % oargrid_jobids ) | Destroy all the jobs with corresponding ids |
49,180 | def wait_for_jobs ( jobs ) : all_running = False while not all_running : all_running = True time . sleep ( 5 ) for job in jobs : job . refresh ( ) scheduled = getattr ( job , "scheduled_at" , None ) if scheduled is not None : logger . info ( "Waiting for %s on %s [%s]" % ( job . uid , job . site , _date2h ( scheduled ) ) ) all_running = all_running and job . state == "running" if job . state == "error" : raise Exception ( "The job %s is in error state" % job ) logger . info ( "All jobs are Running !" ) | Waits for all the jobs to be runnning . |
49,181 | def grid_deploy ( site , nodes , options ) : gk = get_api_client ( ) environment = options . pop ( "env_name" ) options . update ( environment = environment ) options . update ( nodes = nodes ) key_path = DEFAULT_SSH_KEYFILE options . update ( key = key_path . read_text ( ) ) logger . info ( "Deploying %s with options %s" % ( nodes , options ) ) deployment = gk . sites [ site ] . deployments . create ( options ) while deployment . status not in [ "terminated" , "error" ] : deployment . refresh ( ) print ( "Waiting for the end of deployment [%s]" % deployment . uid ) time . sleep ( 10 ) deploy = [ ] undeploy = [ ] if deployment . status == "terminated" : deploy = [ node for node , v in deployment . result . items ( ) if v [ "state" ] == "OK" ] undeploy = [ node for node , v in deployment . result . items ( ) if v [ "state" ] == "KO" ] elif deployment . status == "error" : undeploy = nodes return deploy , undeploy | Deploy and wait for the deployment to be finished . |
49,182 | def set_nodes_vlan ( site , nodes , interface , vlan_id ) : def _to_network_address ( host ) : splitted = host . split ( '.' ) splitted [ 0 ] = splitted [ 0 ] + "-" + interface return "." . join ( splitted ) gk = get_api_client ( ) network_addresses = [ _to_network_address ( n ) for n in nodes ] gk . sites [ site ] . vlans [ str ( vlan_id ) ] . submit ( { "nodes" : network_addresses } ) | Set the interface of the nodes in a specific vlan . |
49,183 | def clusters_sites_obj ( clusters ) : result = { } all_clusters = get_all_clusters_sites ( ) clusters_sites = { c : s for ( c , s ) in all_clusters . items ( ) if c in clusters } for cluster , site in clusters_sites . items ( ) : result . update ( { cluster : get_site_obj ( site ) } ) return result | Get all the corresponding sites of the passed clusters . |
49,184 | def get_all_clusters_sites ( ) : result = { } gk = get_api_client ( ) sites = gk . sites . list ( ) for site in sites : clusters = site . clusters . list ( ) result . update ( { c . uid : site . uid for c in clusters } ) return result | Get all the cluster of all the sites . |
49,185 | def get_nodes ( cluster ) : gk = get_api_client ( ) site = get_cluster_site ( cluster ) return gk . sites [ site ] . clusters [ cluster ] . nodes . list ( ) | Get all the nodes of a given cluster . |
49,186 | def get_cluster_interfaces ( cluster , extra_cond = lambda nic : True ) : nics = get_nics ( cluster ) nics = [ ( nic [ 'device' ] , nic [ 'name' ] ) for nic in nics if nic [ 'mountable' ] and nic [ 'interface' ] == 'Ethernet' and not nic [ 'management' ] and extra_cond ( nic ) ] nics = sorted ( nics ) return nics | Get the network interfaces names corresponding to a criteria . |
49,187 | def get_clusters_interfaces ( clusters , extra_cond = lambda nic : True ) : interfaces = { } for cluster in clusters : nics = get_cluster_interfaces ( cluster , extra_cond = extra_cond ) interfaces . setdefault ( cluster , nics ) return interfaces | Returns for each cluster the available cluster interfaces |
49,188 | def _do_synchronise_jobs ( walltime , machines ) : offset = SYNCHRONISATION_OFFSET start = time . time ( ) + offset _t = time . strptime ( walltime , "%H:%M:%S" ) _walltime = _t . tm_hour * 3600 + _t . tm_min * 60 + _t . tm_sec demands = defaultdict ( int ) for machine in machines : cluster = machine [ "cluster" ] demands [ cluster ] += machine [ "nodes" ] if len ( list ( demands . keys ( ) ) ) <= 1 : logger . debug ( "Only one cluster detected: no synchronisation needed" ) return None clusters = clusters_sites_obj ( list ( demands . keys ( ) ) ) sites = set ( list ( clusters . values ( ) ) ) if len ( sites ) <= 1 : logger . debug ( "Only one site detected: no synchronisation needed" ) return None ok = True for cluster , nodes in demands . items ( ) : cluster_status = clusters [ cluster ] . status . list ( ) ok = ok and can_start_on_cluster ( cluster_status . nodes , nodes , start , _walltime ) if not ok : break if ok : logger . info ( "Reservation_date=%s (%s)" % ( _date2h ( start ) , sites ) ) return start if start is None : raise EnosG5kSynchronisationError ( sites ) | This returns a common reservation date for all the jobs . |
49,189 | def add_data ( self , rawdata ) : for data in rawdata : try : item = data [ 0 ] if item [ 0 ] == 2 : continue if item [ 0 ] != 0 : warnings . warn ( f"Unknown message type '{item[0]}'" , Warning ) continue item = item [ 1 ] target = str ( item [ 0 ] ) try : data = item [ 1 ] except IndexError : data = dict ( ) try : method = getattr ( self , self . __head + target ) method ( data ) except AttributeError : self . _handle_unhandled ( target , data ) except IndexError : LOGGER . warning ( "Wrongly constructed message received: %r" , data ) self . conn . process_queues ( ) | Add data to given room s state |
49,190 | def register_callback ( self ) : cid = str ( self . __cid ) self . __cid += 1 event = queue . Queue ( ) self . __callbacks [ cid ] = event return cid , event | Register callback that we will have to wait for |
49,191 | def _handle_callback ( self , data ) : cb_id = data . get ( "id" ) args = data . get ( "args" ) event = self . __callbacks . pop ( cb_id , None ) if not event : return if not args : event . put ( args ) return err , info = args if err is None : event . put ( info ) else : LOGGER . warning ( "Callback returned error of %s" , str ( err ) ) event . put ( err ) | Handle lain s callback . Only used with getFileinfo so far |
49,192 | def _handle_userCount ( self , data ) : self . room . user_count = data self . conn . enqueue_data ( "user_count" , self . room . user_count ) | Handle user count changes |
49,193 | def _handle_userInfo ( self , data ) : for k , v in data . items ( ) : if k == "nick" : if v == "None" : v = "Volaphile" setattr ( self . room . user , k , v ) self . conn . enqueue_data ( k , self . room . user . nick ) elif k != "profile" : if not hasattr ( self . room , k ) : warnings . warn ( f"Skipping unset property {k}" , ResourceWarning ) continue setattr ( self . room , k , v ) self . conn . enqueue_data ( k , getattr ( self . room , k ) ) self . room . user_info = k , v self . conn . enqueue_data ( "user_info" , self . room . user_info ) | Handle user information |
49,194 | def _handle_config ( self , data ) : self . room . config . update ( data ) self . conn . enqueue_data ( "config" , data ) | Handle initial config push and config changes |
49,195 | def _handle_files ( self , data ) : initial = data . get ( "set" , False ) files = data [ "files" ] for f in files : try : fobj = File ( self . room , self . conn , f [ 0 ] , f [ 1 ] , type = f [ 2 ] , size = f [ 3 ] , expire_time = int ( f [ 4 ] ) / 1000 , uploader = f [ 6 ] . get ( "nick" ) or f [ 6 ] . get ( "user" ) , ) self . room . filedict = fobj . fid , fobj if not initial : self . conn . enqueue_data ( "file" , fobj ) except Exception : import pprint LOGGER . exception ( "bad file" ) pprint . pprint ( f ) if initial : self . conn . enqueue_data ( "initial_files" , self . room . files ) | Handle new files being uploaded |
49,196 | def _handle_delete_file ( self , data ) : file = self . room . filedict . get ( data ) if file : self . room . filedict = data , None self . conn . enqueue_data ( "delete_file" , file ) | Handle files being removed |
49,197 | def _handle_chat ( self , data ) : self . conn . enqueue_data ( "chat" , ChatMessage . from_data ( self . room , self . conn , data ) ) | Handle chat messages |
49,198 | def _handle_changed_config ( self , change ) : key , value = change . get ( "key" ) , change . get ( "value" ) self . room . config . update ( { key : value } ) self . conn . enqueue_data ( "config" , self . room . config ) | Handle configuration changes |
49,199 | def _handle_chat_name ( self , data ) : self . room . user . nick = data self . conn . enqueue_data ( "user" , self . room . user ) | Handle user name changes |
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