Datasets:
Denis641
/
AdvTestNegatives

Dataset card Data Studio Files
xet
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1
query
stringlengths
5
1.23k
positive
stringlengths
53
15.2k
id_
int64
0
252k
task_name
stringlengths
87
242
negative
listlengths
20
553
Apply filters to the pileup elements and return a new Pileup with the filtered elements removed .
def filter ( self , filters ) : new_elements = [ e for e in self . elements if all ( function ( e ) for function in filters ) ] return Pileup ( self . locus , new_elements )
10,200
https://github.com/openvax/varlens/blob/715d3ede5893757b2fcba4117515621bca7b1e5d/varlens/read_evidence/pileup.py#L72-L86
[ "async", "def", "create_lease_if_not_exists_async", "(", "self", ",", "partition_id", ")", ":", "return_lease", "=", "None", "try", ":", "return_lease", "=", "AzureBlobLease", "(", ")", "return_lease", ".", "partition_id", "=", "partition_id", "serializable_lease", "=", "return_lease", ".", "serializable", "(", ")", "json_lease", "=", "json", ".", "dumps", "(", "serializable_lease", ")", "_logger", ".", "info", "(", "\"Creating Lease %r %r %r\"", ",", "self", ".", "lease_container_name", ",", "partition_id", ",", "json", ".", "dumps", "(", "{", "k", ":", "v", "for", "k", ",", "v", "in", "serializable_lease", ".", "items", "(", ")", "if", "k", "!=", "'event_processor_context'", "}", ")", ")", "await", "self", ".", "host", ".", "loop", ".", "run_in_executor", "(", "self", ".", "executor", ",", "functools", ".", "partial", "(", "self", ".", "storage_client", ".", "create_blob_from_text", ",", "self", ".", "lease_container_name", ",", "partition_id", ",", "json_lease", ")", ")", "except", "Exception", ":", "# pylint: disable=broad-except", "try", ":", "return_lease", "=", "await", "self", ".", "get_lease_async", "(", "partition_id", ")", "except", "Exception", "as", "err", ":", "# pylint: disable=broad-except", "_logger", ".", "error", "(", "\"Failed to create lease %r\"", ",", "err", ")", "raise", "err", "return", "return_lease" ]
Runs the decorated function in a new task
def new_task ( func ) : @ wraps ( func ) async def wrapper ( self , * args , * * kwargs ) : loop = get_event_loop ( ) loop . create_task ( func ( self , * args , * * kwargs ) ) return wrapper
10,201
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/analytics/base.py#L65-L74
[ "def", "GetAttachmentIdFromMediaId", "(", "media_id", ")", ":", "altchars", "=", "'+-'", "if", "not", "six", ".", "PY2", ":", "altchars", "=", "altchars", ".", "encode", "(", "'utf-8'", ")", "# altchars for '+' and '/'. We keep '+' but replace '/' with '-'", "buffer", "=", "base64", ".", "b64decode", "(", "str", "(", "media_id", ")", ",", "altchars", ")", "resoure_id_length", "=", "20", "attachment_id", "=", "''", "if", "len", "(", "buffer", ")", ">", "resoure_id_length", ":", "# We are cutting off the storage index.", "attachment_id", "=", "base64", ".", "b64encode", "(", "buffer", "[", "0", ":", "resoure_id_length", "]", ",", "altchars", ")", "if", "not", "six", ".", "PY2", ":", "attachment_id", "=", "attachment_id", ".", "decode", "(", "'utf-8'", ")", "else", ":", "attachment_id", "=", "media_id", "return", "attachment_id" ]
Iterates over all instances of analytics provider found in configuration
async def providers ( ) : for provider in settings . ANALYTICS_PROVIDERS : cls : BaseAnalytics = import_class ( provider [ 'class' ] ) yield await cls . instance ( * provider [ 'args' ] )
10,202
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/analytics/base.py#L77-L84
[ "def", "unshare", "(", "flags", ")", ":", "res", "=", "lib", ".", "unshare", "(", "flags", ")", "if", "res", "!=", "0", ":", "_check_error", "(", "ffi", ".", "errno", ")" ]
Track the view of a page
async def page_view ( self , url : str , title : str , user_id : str , user_lang : str = '' ) -> None : raise NotImplementedError
10,203
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/analytics/base.py#L37-L46
[ "def", "convert_to_experiment_list", "(", "experiments", ")", ":", "exp_list", "=", "experiments", "# Transform list if necessary", "if", "experiments", "is", "None", ":", "exp_list", "=", "[", "]", "elif", "isinstance", "(", "experiments", ",", "Experiment", ")", ":", "exp_list", "=", "[", "experiments", "]", "elif", "type", "(", "experiments", ")", "is", "dict", ":", "exp_list", "=", "[", "Experiment", ".", "from_json", "(", "name", ",", "spec", ")", "for", "name", ",", "spec", "in", "experiments", ".", "items", "(", ")", "]", "# Validate exp_list", "if", "(", "type", "(", "exp_list", ")", "is", "list", "and", "all", "(", "isinstance", "(", "exp", ",", "Experiment", ")", "for", "exp", "in", "exp_list", ")", ")", ":", "if", "len", "(", "exp_list", ")", ">", "1", ":", "logger", ".", "warning", "(", "\"All experiments will be \"", "\"using the same SearchAlgorithm.\"", ")", "else", ":", "raise", "TuneError", "(", "\"Invalid argument: {}\"", ".", "format", "(", "experiments", ")", ")", "return", "exp_list" ]
As per the law anonymize user identifier before sending it .
def hash_user_id ( self , user_id : str ) -> str : h = sha256 ( ) h . update ( user_id . encode ( ) ) return h . hexdigest ( )
10,204
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/analytics/base.py#L48-L55
[ "def", "_match_directories", "(", "self", ",", "entries", ",", "root", ",", "regex_string", ")", ":", "self", ".", "log", "(", "u\"Matching directory names in paged hierarchy\"", ")", "self", ".", "log", "(", "[", "u\"Matching within '%s'\"", ",", "root", "]", ")", "self", ".", "log", "(", "[", "u\"Matching regex '%s'\"", ",", "regex_string", "]", ")", "regex", "=", "re", ".", "compile", "(", "r\"\"", "+", "regex_string", ")", "directories", "=", "set", "(", ")", "root_len", "=", "len", "(", "root", ")", "for", "entry", "in", "entries", ":", "# look only inside root dir", "if", "entry", ".", "startswith", "(", "root", ")", ":", "self", ".", "log", "(", "[", "u\"Examining '%s'\"", ",", "entry", "]", ")", "# remove common prefix root/", "entry", "=", "entry", "[", "root_len", "+", "1", ":", "]", "# split path", "entry_splitted", "=", "entry", ".", "split", "(", "os", ".", "sep", ")", "# match regex", "if", "(", "(", "len", "(", "entry_splitted", ")", ">=", "2", ")", "and", "(", "re", ".", "match", "(", "regex", ",", "entry_splitted", "[", "0", "]", ")", "is", "not", "None", ")", ")", ":", "directories", ".", "add", "(", "entry_splitted", "[", "0", "]", ")", "self", ".", "log", "(", "[", "u\"Match: '%s'\"", ",", "entry_splitted", "[", "0", "]", "]", ")", "else", ":", "self", ".", "log", "(", "[", "u\"No match: '%s'\"", ",", "entry", "]", ")", "return", "sorted", "(", "directories", ")" ]
Delete a workflow .
def delete ( cls , uuid ) : to_delete = Workflow . query . get ( uuid ) db . session . delete ( to_delete )
10,205
https://github.com/inveniosoftware-contrib/invenio-workflows/blob/9c09fd29509a3db975ac2aba337e6760d8cfd3c2/invenio_workflows/models.py#L96-L99
[ "def", "unload", "(", "self", ")", ":", "unloaded", "=", "False", "if", "self", ".", "_lib", "is", "not", "None", ":", "if", "self", ".", "_winlib", "is", "not", "None", ":", "# ctypes passes integers as 32-bit C integer types, which will", "# truncate the value of a 64-bit pointer in 64-bit python, so", "# we have to change the FreeLibrary method to take a pointer", "# instead of an integer handle.", "ctypes", ".", "windll", ".", "kernel32", ".", "FreeLibrary", ".", "argtypes", "=", "(", "ctypes", ".", "c_void_p", ",", ")", "# On Windows we must free both loaded libraries before the", "# temporary file can be cleaned up.", "ctypes", ".", "windll", ".", "kernel32", ".", "FreeLibrary", "(", "self", ".", "_lib", ".", "_handle", ")", "ctypes", ".", "windll", ".", "kernel32", ".", "FreeLibrary", "(", "self", ".", "_winlib", ".", "_handle", ")", "self", ".", "_lib", "=", "None", "self", ".", "_winlib", "=", "None", "unloaded", "=", "True", "else", ":", "# On OSX and Linux, just release the library; it's not safe", "# to close a dll that ctypes is using.", "del", "self", ".", "_lib", "self", ".", "_lib", "=", "None", "unloaded", "=", "True", "if", "self", ".", "_temp", "is", "not", "None", ":", "os", ".", "remove", "(", "self", ".", "_temp", ".", "name", ")", "self", ".", "_temp", "=", "None", "return", "unloaded" ]
Run a workflow by name with list of data objects .
def run_worker ( wname , data , engine_uuid_hex = None , * * kwargs ) : if 'stop_on_halt' not in kwargs : kwargs [ 'stop_on_halt' ] = False if engine_uuid_hex : engine_uuid = uuid . UUID ( hex = engine_uuid_hex ) engine = WorkflowEngine . from_uuid ( uuid = engine_uuid , * * kwargs ) else : engine = WorkflowEngine . with_name ( wname , * * kwargs ) engine . save ( ) objects = get_workflow_object_instances ( data , engine ) db . session . commit ( ) engine . process ( objects , * * kwargs ) return engine
10,206
https://github.com/inveniosoftware-contrib/invenio-workflows/blob/9c09fd29509a3db975ac2aba337e6760d8cfd3c2/invenio_workflows/worker_engine.py#L30-L62
[ "def", "breakpoint_set", "(", "self", ",", "addr", ",", "thumb", "=", "False", ",", "arm", "=", "False", ")", ":", "flags", "=", "enums", ".", "JLinkBreakpoint", ".", "ANY", "if", "thumb", ":", "flags", "=", "flags", "|", "enums", ".", "JLinkBreakpoint", ".", "THUMB", "elif", "arm", ":", "flags", "=", "flags", "|", "enums", ".", "JLinkBreakpoint", ".", "ARM", "handle", "=", "self", ".", "_dll", ".", "JLINKARM_SetBPEx", "(", "int", "(", "addr", ")", ",", "flags", ")", "if", "handle", "<=", "0", ":", "raise", "errors", ".", "JLinkException", "(", "'Breakpoint could not be set.'", ")", "return", "handle" ]
Restart workflow from beginning with given engine UUID and any data .
def restart_worker ( uuid , * * kwargs ) : if 'stop_on_halt' not in kwargs : kwargs [ 'stop_on_halt' ] = False engine = WorkflowEngine . from_uuid ( uuid = uuid , * * kwargs ) if "data" not in kwargs : objects = workflow_object_class . query ( id_workflow = uuid ) else : data = kwargs . pop ( "data" ) if not isinstance ( data , ( list , tuple ) ) : data = [ data ] objects = get_workflow_object_instances ( data , engine ) db . session . commit ( ) engine . process ( objects , * * kwargs ) return engine
10,207
https://github.com/inveniosoftware-contrib/invenio-workflows/blob/9c09fd29509a3db975ac2aba337e6760d8cfd3c2/invenio_workflows/worker_engine.py#L65-L95
[ "def", "_max_weight_operator", "(", "ops", ":", "Iterable", "[", "PauliTerm", "]", ")", "->", "Union", "[", "None", ",", "PauliTerm", "]", ":", "mapping", "=", "dict", "(", ")", "# type: Dict[int, str]", "for", "op", "in", "ops", ":", "for", "idx", ",", "op_str", "in", "op", ":", "if", "idx", "in", "mapping", ":", "if", "mapping", "[", "idx", "]", "!=", "op_str", ":", "return", "None", "else", ":", "mapping", "[", "idx", "]", "=", "op_str", "op", "=", "functools", ".", "reduce", "(", "mul", ",", "(", "PauliTerm", "(", "op", ",", "q", ")", "for", "q", ",", "op", "in", "mapping", ".", "items", "(", ")", ")", ",", "sI", "(", ")", ")", "return", "op" ]
Analyze data and create corresponding WorkflowObjects .
def get_workflow_object_instances ( data , engine ) : workflow_objects = [ ] data_type = engine . get_default_data_type ( ) for data_object in data : if isinstance ( data_object , workflow_object_class . _get_current_object ( ) ) : if not data_object . data_type : data_object . data_type = data_type if data_object . id : data_object . log . debug ( "Existing workflow object found for " "this object." ) if data_object . status == data_object . known_statuses . COMPLETED : data_object . status = data_object . known_statuses . INITIAL workflow_objects . append ( data_object ) else : # Data is not already a WorkflowObject, we then # add the running object to run through the workflow. current_obj = create_data_object_from_data ( data_object , engine , data_type ) workflow_objects . append ( current_obj ) return workflow_objects
10,208
https://github.com/inveniosoftware-contrib/invenio-workflows/blob/9c09fd29509a3db975ac2aba337e6760d8cfd3c2/invenio_workflows/worker_engine.py#L136-L184
[ "def", "status", "(", "self", ",", "remote", "=", "False", ")", ":", "if", "remote", ":", "components", "=", "urlparse", ".", "urlparse", "(", "self", ".", "endpoint", ")", "try", ":", "result", "=", "self", ".", "session", ".", "get", "(", "components", "[", "0", "]", "+", "\"://\"", "+", "components", "[", "1", "]", "+", "\"/status\"", ",", "timeout", "=", "self", ".", "timeout", ")", "except", "Exception", "as", "e", ":", "if", "self", ".", "logger", ":", "self", ".", "logger", ".", "debug", "(", "\"Failed to connect to server for status: %s\"", ",", "e", ")", "result", "=", "None", "if", "result", "and", "result", ".", "status_code", "==", "200", ":", "self", ".", "server_status", "=", "result", ".", "json", "(", ")", "self", ".", "server_status", "[", "\"endpoint\"", "]", "=", "self", ".", "endpoint", "elif", "result", ":", "if", "self", ".", "logger", ":", "self", ".", "logger", ".", "debug", "(", "\"Server status response not understandable: Status: %d, Body: %s\"", ",", "result", ".", "status_code", ",", "result", ".", "text", ")", "self", ".", "server_status", "=", "{", "\"endpoint\"", ":", "self", ".", "endpoint", ",", "\"status\"", ":", "(", "\"Unexpected HTTP status \"", "+", "str", "(", "result", ".", "status_code", ")", "+", "\" at: \"", "+", "strftime", "(", "\"%d %b %Y %H:%M:%S +0000\"", ",", "gmtime", "(", ")", ")", ")", "}", "else", ":", "self", ".", "server_status", "=", "{", "\"endpoint\"", ":", "self", ".", "endpoint", ",", "\"status\"", ":", "\"Unreachable at: \"", "+", "strftime", "(", "\"%d %b %Y %H:%M:%S +0000\"", ",", "gmtime", "(", ")", ")", "}", "return", "self", ".", "local_status", ",", "self", ".", "server_status" ]
Create a new WorkflowObject from given data and return it .
def create_data_object_from_data ( data_object , engine , data_type ) : # Data is not already a WorkflowObject, we first # create an initial object for each data object. return workflow_object_class . create ( data = data_object , id_workflow = engine . uuid , status = workflow_object_class . known_statuses . INITIAL , data_type = data_type , )
10,209
https://github.com/inveniosoftware-contrib/invenio-workflows/blob/9c09fd29509a3db975ac2aba337e6760d8cfd3c2/invenio_workflows/worker_engine.py#L187-L210
[ "def", "max_texture_limit", "(", "self", ")", ":", "max_unit_array", "=", "(", "gl", ".", "GLint", "*", "1", ")", "(", ")", "gl", ".", "glGetIntegerv", "(", "gl", ".", "GL_MAX_TEXTURE_IMAGE_UNITS", ",", "max_unit_array", ")", "return", "max_unit_array", "[", "0", "]" ]
prints the rst page of the command what
def _print_rst ( self , what ) : print print "Command - %s::" % what exec ( "h = self.do_%s.__doc__" % what ) # noinspection PyUnboundLocalVariable h = textwrap . dedent ( h ) . replace ( "::\n\n" , "" ) h = textwrap . dedent ( h ) . replace ( "\n" , "\n " ) print h
10,210
https://github.com/cloudmesh-cmd3/cmd3/blob/92e33c96032fd3921f159198a0e57917c4dc34ed/cmd3/plugins/rst.py#L11-L27
[ "def", "_mmUpdateDutyCycles", "(", "self", ")", ":", "period", "=", "self", ".", "getDutyCyclePeriod", "(", ")", "unionSDRArray", "=", "numpy", ".", "zeros", "(", "self", ".", "getNumColumns", "(", ")", ")", "unionSDRArray", "[", "list", "(", "self", ".", "_mmTraces", "[", "\"unionSDR\"", "]", ".", "data", "[", "-", "1", "]", ")", "]", "=", "1", "self", ".", "_mmData", "[", "\"unionSDRDutyCycle\"", "]", "=", "UnionTemporalPoolerMonitorMixin", ".", "_mmUpdateDutyCyclesHelper", "(", "self", ".", "_mmData", "[", "\"unionSDRDutyCycle\"", "]", ",", "unionSDRArray", ",", "period", ")", "self", ".", "_mmData", "[", "\"persistenceDutyCycle\"", "]", "=", "UnionTemporalPoolerMonitorMixin", ".", "_mmUpdateDutyCyclesHelper", "(", "self", ".", "_mmData", "[", "\"persistenceDutyCycle\"", "]", ",", "self", ".", "_poolingActivation", ",", "period", ")" ]
Allow loading of JSON rule data .
def load_json ( cls , data , default_rule = None , raise_error = False ) : rules = { k : _parser . parse_rule ( v , raise_error ) for k , v in json . loads ( data ) . items ( ) } return cls ( rules , default_rule )
10,211
https://github.com/garenchan/policy/blob/7709ae5f371146f8c90380d0877a5e59d731f644/policy/enforcer.py#L30-L36
[ "def", "delete_entity", "(", "self", ",", "entity_id", ",", "mount_point", "=", "DEFAULT_MOUNT_POINT", ")", ":", "api_path", "=", "'/v1/{mount_point}/entity/id/{id}'", ".", "format", "(", "mount_point", "=", "mount_point", ",", "id", "=", "entity_id", ",", ")", "return", "self", ".", "_adapter", ".", "delete", "(", "url", "=", "api_path", ",", ")" ]
Allow loading of rule data from a dictionary .
def from_dict ( cls , rules_dict : dict , default_rule = None , raise_error = False ) : # Parse the rules stored in the dictionary rules = { k : _parser . parse_rule ( v , raise_error ) for k , v in rules_dict . items ( ) } return cls ( rules , default_rule )
10,212
https://github.com/garenchan/policy/blob/7709ae5f371146f8c90380d0877a5e59d731f644/policy/enforcer.py#L39-L46
[ "def", "_make_chunk_size", "(", "self", ",", "req_size", ")", ":", "size", "=", "req_size", "size", "+=", "2", "*", "self", ".", "_chunk_size_t_size", "# Two size fields", "size", "=", "self", ".", "_chunk_min_size", "if", "size", "<", "self", ".", "_chunk_min_size", "else", "size", "if", "size", "&", "self", ".", "_chunk_align_mask", ":", "# If the chunk would not be aligned", "size", "=", "(", "size", "&", "~", "self", ".", "_chunk_align_mask", ")", "+", "self", ".", "_chunk_align_mask", "+", "1", "# Fix it", "return", "size" ]
Created a new Rules object based on the provided dict of rules .
def _set_rules ( self , rules : dict , overwrite = True ) : if not isinstance ( rules , dict ) : raise TypeError ( 'rules must be an instance of dict or Rules,' 'got %r instead' % type ( rules ) ) if overwrite : self . rules = Rules ( rules , self . default_rule ) else : self . rules . update ( rules )
10,213
https://github.com/garenchan/policy/blob/7709ae5f371146f8c90380d0877a5e59d731f644/policy/enforcer.py#L103-L113
[ "def", "run_experiment", "(", "self", ")", ":", "try", ":", "self", ".", "sign_up", "(", ")", "self", ".", "participate", "(", ")", "if", "self", ".", "sign_off", "(", ")", ":", "self", ".", "complete_experiment", "(", "\"worker_complete\"", ")", "else", ":", "self", ".", "complete_experiment", "(", "\"worker_failed\"", ")", "finally", ":", "self", ".", "driver", ".", "quit", "(", ")" ]
Load rules from policy file or cache .
def load_rules ( self , force_reload = False , overwrite = True ) : # double-checked locking if self . load_once and self . _policy_loaded : return with self . _load_lock : if self . load_once and self . _policy_loaded : return reloaded , data = _cache . read_file ( self . policy_file , force_reload = force_reload ) self . _policy_loaded = True if reloaded or not self . rules : rules = Rules . load_json ( data , self . default_rule , self . raise_error ) self . _set_rules ( rules , overwrite = overwrite ) LOG . debug ( 'Reload policy file: %s' , self . policy_file )
10,214
https://github.com/garenchan/policy/blob/7709ae5f371146f8c90380d0877a5e59d731f644/policy/enforcer.py#L115-L131
[ "def", "is_valid_assignment", "(", "self", ",", "mtf_dimension_name", ",", "mesh_dimension_name", ")", ":", "return", "(", "(", "mtf_dimension_name", "in", "self", ".", "_splittable_mtf_dimension_names", ")", "and", "(", "self", ".", "_mtf_dimension_name_to_size_gcd", "[", "mtf_dimension_name", "]", "%", "self", ".", "_mesh_dimension_name_to_size", "[", "mesh_dimension_name", "]", "==", "0", ")", ")" ]
Checks authorization of a rule against the target and credentials .
def enforce ( self , rule , target , creds , exc = None , * args , * * kwargs ) : self . load_rules ( ) if isinstance ( rule , checks . BaseCheck ) : result = rule ( target , creds , self , rule ) elif not self . rules : # No rules means we're going to fail closed. result = False else : try : # Evaluate the rule result = self . rules [ rule ] ( target , creds , self , rule ) except KeyError : LOG . debug ( 'Rule [%s] does not exist' , rule ) # If the rule doesn't exist, fail closed result = False if self . raise_error and not result : if exc : raise exc ( * args , * * kwargs ) else : raise PolicyNotAuthorized ( rule , target , creds ) return result
10,215
https://github.com/garenchan/policy/blob/7709ae5f371146f8c90380d0877a5e59d731f644/policy/enforcer.py#L133-L158
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Returns the flattened keys of BoundSpatialPoints in a schema
def get_flattened_bsp_keys_from_schema ( schema ) : keys = [ ] for key in schema . declared_fields . keys ( ) : field = schema . declared_fields [ key ] if isinstance ( field , mm . fields . Nested ) and isinstance ( field . schema , BoundSpatialPoint ) : keys . append ( "{}.{}" . format ( key , "position" ) ) return keys
10,216
https://github.com/seung-lab/EMAnnotationSchemas/blob/ca81eff0f449bd7eb0392e0982db8f3636446a9e/emannotationschemas/utils.py#L14-L29
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Return and generate if required the lock for this request .
def lock ( self ) -> asyncio . Lock : if self . lock_key not in self . request . custom_content : self . request . custom_content [ self . lock_key ] = asyncio . Lock ( ) return self . request . custom_content [ self . lock_key ]
10,217
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/triggers.py#L94-L102
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Get the value from the API . Make sure to use a lock in order not to fetch the value twice at the same time .
async def get_value ( self ) : cc = self . request . custom_content async with self . lock : if self . content_key not in cc : cc [ self . content_key ] = await self . call_api ( ) return cc [ self . content_key ]
10,218
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/triggers.py#L119-L131
[ "def", "music_search", "(", "self", ",", "entitiy_type", ",", "query", ",", "*", "*", "kwargs", ")", ":", "return", "self", ".", "make_request", "(", "'music'", ",", "entitiy_type", ",", "query", ",", "kwargs", ")" ]
If there is a text layer inside the request try to find a matching text in the specified intent .
async def rank ( self ) -> Optional [ float ] : if not self . request . has_layer ( l . RawText ) : return tl = self . request . get_layer ( l . RawText ) matcher = Matcher ( [ tuple ( Trigram ( y ) for y in x ) for x in await self . intent . strings ( self . request ) ] ) return matcher % Trigram ( tl . text )
10,219
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/triggers.py#L163-L178
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Look for the QuickReply layer s slug into available choices .
def _rank_qr ( self , choices ) : from bernard . platforms . facebook import layers as fbl try : qr = self . request . get_layer ( fbl . QuickReply ) self . chosen = choices [ qr . slug ] self . slug = qr . slug if self . when is None or self . when == qr . slug : return 1.0 except KeyError : pass
10,220
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/triggers.py#L200-L214
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Try to match the TextLayer with choice s intents .
async def _rank_text ( self , choices ) : tl = self . request . get_layer ( l . RawText ) best = 0.0 for slug , params in choices . items ( ) : strings = [ ] if params [ 'intent' ] : intent = getattr ( intents , params [ 'intent' ] ) strings += await intent . strings ( self . request ) if params [ 'text' ] : strings . append ( ( params [ 'text' ] , ) ) matcher = Matcher ( [ tuple ( Trigram ( y ) for y in x ) for x in strings ] ) score = matcher % Trigram ( await render ( tl . text , self . request ) ) if score > best : self . chosen = params self . slug = slug best = score if self . when is None or self . slug == self . when : return best
10,221
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/triggers.py#L216-L243
[ "def", "close", "(", "self", ")", ":", "if", "self", ".", "_access", "is", "not", "None", ":", "_logger", ".", "debug", "(", "\"Cleaning up\"", ")", "pci_cleanup", "(", "self", ".", "_access", ")", "self", ".", "_access", "=", "None" ]
Feature type specific check of global recommended attributes .
def check_recommended_attributes ( self , dataset ) : results = [ ] recommended_ctx = TestCtx ( BaseCheck . MEDIUM , 'Recommended global attributes' ) # Check time_coverage_duration and resolution for attr in [ 'time_coverage_duration' , 'time_coverage_resolution' ] : attr_value = getattr ( dataset , attr , '' ) try : parse_duration ( attr_value ) recommended_ctx . assert_true ( True , '' ) # Score it True! except Exception : recommended_ctx . assert_true ( False , '{} should exist and be ISO-8601 format (example: PT1M30S), currently: {}' . format ( attr , attr_value ) ) results . append ( recommended_ctx . to_result ( ) ) return results
10,222
https://github.com/ioos/cc-plugin-ncei/blob/963fefd7fa43afd32657ac4c36aad4ddb4c25acf/cc_plugin_ncei/ncei_timeseries.py#L154-L171
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Checks that the feature types of this dataset are consitent with a time series incomplete dataset
def check_dimensions ( self , dataset ) : required_ctx = TestCtx ( BaseCheck . HIGH , 'All geophysical variables are time-series incomplete feature types' ) message = '{} must be a valid timeseries feature type. It must have dimensions of (timeSeries, time).' message += ' And all coordinates must have dimensions of (timeSeries)' for variable in util . get_geophysical_variables ( dataset ) : is_valid = util . is_multi_timeseries_incomplete ( dataset , variable ) required_ctx . assert_true ( is_valid , message . format ( variable ) ) return required_ctx . to_result ( )
10,223
https://github.com/ioos/cc-plugin-ncei/blob/963fefd7fa43afd32657ac4c36aad4ddb4c25acf/cc_plugin_ncei/ncei_timeseries.py#L181-L196
[ "def", "txn_removeAssociation", "(", "self", ",", "server_url", ",", "handle", ")", ":", "self", ".", "db_remove_assoc", "(", "server_url", ",", "handle", ")", "return", "self", ".", "cur", ".", "rowcount", ">", "0" ]
Read a file if it has been modified .
def read_file ( filename : str , force_reload = False ) : if force_reload : _delete_cached_file ( filename ) reloaded = False mtime = os . path . getmtime ( filename ) cache_info = CACHE . setdefault ( filename , { } ) if not cache_info or mtime > cache_info . get ( 'mtime' , 0 ) : LOG . debug ( 'Reloading cached file %s' , filename ) with open ( filename ) as fp : cache_info [ 'data' ] = fp . read ( ) cache_info [ 'mtime' ] = mtime reloaded = True return reloaded , cache_info [ 'data' ]
10,224
https://github.com/garenchan/policy/blob/7709ae5f371146f8c90380d0877a5e59d731f644/policy/_cache.py#L19-L41
[ "def", "get_stores_secrets_volumes", "(", "cls", ",", "stores_secrets", ")", ":", "volumes", "=", "[", "]", "volume_mounts", "=", "[", "]", "for", "store_secret", "in", "stores_secrets", ":", "store", "=", "store_secret", "[", "'store'", "]", "if", "store", "in", "{", "GCS", ",", "S3", "}", ":", "secrets_volumes", ",", "secrets_volume_mounts", "=", "get_volume_from_secret", "(", "volume_name", "=", "cls", ".", "STORE_SECRET_VOLUME_NAME", ".", "format", "(", "store", ")", ",", "mount_path", "=", "cls", ".", "STORE_SECRET_KEY_MOUNT_PATH", ".", "format", "(", "store", ")", ",", "secret_name", "=", "store_secret", "[", "'persistence_secret'", "]", ",", ")", "volumes", "+=", "secrets_volumes", "volume_mounts", "+=", "secrets_volume_mounts", "return", "volumes", ",", "volume_mounts" ]
Use the validator set on a separate attribute on the class .
def use_model_attr ( attr ) : def use_model_validator ( instance , attribute , value ) : getattr ( instance , attr ) ( instance , attribute , value ) return use_model_validator
10,225
https://github.com/COALAIP/pycoalaip/blob/cecc8f6ff4733f0525fafcee63647753e832f0be/coalaip/model_validators.py#L13-L18
[ "def", "_openResources", "(", "self", ")", ":", "try", ":", "rate", ",", "data", "=", "scipy", ".", "io", ".", "wavfile", ".", "read", "(", "self", ".", "_fileName", ",", "mmap", "=", "True", ")", "except", "Exception", "as", "ex", ":", "logger", ".", "warning", "(", "ex", ")", "logger", ".", "warning", "(", "\"Unable to read wav with memmory mapping. Trying without now.\"", ")", "rate", ",", "data", "=", "scipy", ".", "io", ".", "wavfile", ".", "read", "(", "self", ".", "_fileName", ",", "mmap", "=", "False", ")", "self", ".", "_array", "=", "data", "self", ".", "attributes", "[", "'rate'", "]", "=", "rate" ]
Must include at least a name key .
def is_creation_model ( instance , attribute , value ) : creation_name = value . get ( 'name' ) if not isinstance ( creation_name , str ) : instance_name = instance . __class__ . __name__ err_str = ( "'name' must be given as a string in the '{attr}' " "parameter of a '{cls}'. Given " "'{value}'" ) . format ( attr = attribute . name , cls = instance_name , value = creation_name ) raise ModelDataError ( err_str )
10,226
https://github.com/COALAIP/pycoalaip/blob/cecc8f6ff4733f0525fafcee63647753e832f0be/coalaip/model_validators.py#L45-L56
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Must include a manifestationOfWork key .
def is_manifestation_model ( instance , attribute , value ) : instance_name = instance . __class__ . __name__ is_creation_model ( instance , attribute , value ) manifestation_of = value . get ( 'manifestationOfWork' ) if not isinstance ( manifestation_of , str ) : err_str = ( "'manifestationOfWork' must be given as a string in the " "'{attr}' parameter of a '{cls}'. Given " "'{value}'" ) . format ( attr = attribute . name , cls = instance_name , value = manifestation_of ) print ( err_str )
10,227
https://github.com/COALAIP/pycoalaip/blob/cecc8f6ff4733f0525fafcee63647753e832f0be/coalaip/model_validators.py#L68-L81
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Define a preprocessor to run after the arguments are parsed and before the function is executed when running in console script mode .
def add_preprocessor ( preproc ) : def decorator ( func ) : func = ScriptAdaptor . _wrap ( func ) func . _add_preprocessor ( preproc ) return func return decorator
10,228
https://github.com/klmitch/turnstile/blob/8fe9a359b45e505d3192ab193ecf9be177ab1a17/turnstile/tools.py#L255-L269
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Define a postprocessor to run after the function is executed when running in console script mode .
def add_postprocessor ( postproc ) : def decorator ( func ) : func = ScriptAdaptor . _wrap ( func ) func . _add_postprocessor ( postproc ) return func return decorator
10,229
https://github.com/klmitch/turnstile/blob/8fe9a359b45e505d3192ab193ecf9be177ab1a17/turnstile/tools.py#L272-L289
[ "def", "associate_devices", "(", "self", ",", "thing_names", ",", "config_file", ",", "region", "=", "None", ",", "profile_name", "=", "None", ")", ":", "# TODO remove this function when Group discovery is enriched", "logging", ".", "info", "(", "\"associate_devices thing_names:{0}\"", ".", "format", "(", "thing_names", ")", ")", "config", "=", "GroupConfigFile", "(", "config_file", "=", "config_file", ")", "if", "region", "is", "None", ":", "region", "=", "self", ".", "_region", "devices", "=", "config", "[", "'devices'", "]", "if", "type", "(", "thing_names", ")", "is", "str", ":", "thing_names", "=", "[", "thing_names", "]", "iot_client", "=", "_get_iot_session", "(", "region", "=", "region", ",", "profile_name", "=", "profile_name", ")", "for", "thing_name", "in", "thing_names", ":", "thing", "=", "iot_client", ".", "describe_thing", "(", "thingName", "=", "thing_name", ")", "logging", ".", "info", "(", "\"Found existing Thing:{0}\"", ".", "format", "(", "thing", ")", ")", "p", "=", "iot_client", ".", "list_thing_principals", "(", "thingName", "=", "thing_name", ")", "logging", ".", "info", "(", "\"Existing Thing has principals:{0}\"", ".", "format", "(", "p", ")", ")", "devices", "[", "thing_name", "]", "=", "{", "'thing_arn'", ":", "thing", "[", "'attributes'", "]", "[", "'thingArn'", "]", ",", "'cert_arn'", ":", "p", "[", "'principals'", "]", "[", "0", "]", ",", "'cert_id'", ":", "thing", "[", "'attributes'", "]", "[", "'certificateId'", "]", ",", "'thing_name'", ":", "thing_name", "}", "logging", ".", "info", "(", "\"Thing:'{0}' associated with config:'{1}'\"", ".", "format", "(", "thing_name", ",", "config_file", ")", ")", "config", "[", "'devices'", "]", "=", "devices" ]
Set up logging for the script based on the configuration specified by the logging attribute of the command line arguments .
def _setup_logging ( args ) : log_conf = getattr ( args , 'logging' , None ) if log_conf : logging . config . fileConfig ( log_conf ) else : logging . basicConfig ( )
10,230
https://github.com/klmitch/turnstile/blob/8fe9a359b45e505d3192ab193ecf9be177ab1a17/turnstile/tools.py#L292-L308
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Set up or update limits in the Redis database .
def setup_limits ( conf_file , limits_file , do_reload = True , dry_run = False , debug = False ) : # If dry_run is set, default debug to True if dry_run : debug = True # Connect to the database... conf = config . Config ( conf_file = conf_file ) db = conf . get_database ( ) limits_key = conf [ 'control' ] . get ( 'limits_key' , 'limits' ) control_channel = conf [ 'control' ] . get ( 'channel' , 'control' ) # Parse the limits file limits_tree = etree . parse ( limits_file ) # Now, we parse the limits XML file lims = [ ] for idx , lim in enumerate ( limits_tree . getroot ( ) ) : # Skip tags we don't recognize if lim . tag != 'limit' : warnings . warn ( "Unrecognized tag %r in limits file at index %d" % ( lim . tag , idx ) ) continue # Construct the limit and add it to the list of limits try : lims . append ( parse_limit_node ( db , idx , lim ) ) except Exception as exc : warnings . warn ( "Couldn't understand limit at index %d: %s" % ( idx , exc ) ) continue # Now that we have the limits, let's install them if debug : print >> sys . stderr , "Installing the following limits:" for lim in lims : print >> sys . stderr , " %r" % lim if not dry_run : database . limit_update ( db , limits_key , lims ) # Were we requested to reload the limits? if do_reload is False : return # OK, figure out what kind of reload to do params = [ ] if do_reload is True : # Nothing to do; use default semantics pass elif ( isinstance ( do_reload , ( int , long , float ) ) or ( isinstance ( do_reload , basestring ) and do_reload . isdigit ( ) ) ) : params = [ 'spread' , do_reload ] else : params = [ str ( do_reload ) ] # Issue the reload command if debug : cmd = [ 'reload' ] cmd . extend ( params ) print >> sys . stderr , ( "Issuing command: %s" % ' ' . join ( str ( c ) for c in cmd ) ) if not dry_run : database . command ( db , control_channel , 'reload' , * params )
10,231
https://github.com/klmitch/turnstile/blob/8fe9a359b45e505d3192ab193ecf9be177ab1a17/turnstile/tools.py#L473-L555
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Given a Limit object generate an XML node .
def make_limit_node ( root , limit ) : # Build the base limit node limit_node = etree . SubElement ( root , 'limit' , { 'class' : limit . _limit_full_name } ) # Walk through all the recognized attributes for attr in sorted ( limit . attrs ) : desc = limit . attrs [ attr ] attr_type = desc . get ( 'type' , str ) value = getattr ( limit , attr ) # Determine the default value, if we have one... if 'default' in desc : default = ( desc [ 'default' ] ( ) if callable ( desc [ 'default' ] ) else desc [ 'default' ] ) # Skip attributes that have their default settings if value == default : continue # Set up the attr node attr_node = etree . SubElement ( limit_node , 'attr' , name = attr ) # Treat lists and dicts specially if attr_type == list : for val in value : val_node = etree . SubElement ( attr_node , 'value' ) val_node . text = str ( val ) elif attr_type == dict : for key , val in sorted ( value . items ( ) , key = lambda x : x [ 0 ] ) : val_node = etree . SubElement ( attr_node , 'value' , key = key ) val_node . text = str ( val ) else : attr_node . text = str ( value )
10,232
https://github.com/klmitch/turnstile/blob/8fe9a359b45e505d3192ab193ecf9be177ab1a17/turnstile/tools.py#L562-L602
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Dump the current limits from the Redis database .
def dump_limits ( conf_file , limits_file , debug = False ) : # Connect to the database... conf = config . Config ( conf_file = conf_file ) db = conf . get_database ( ) limits_key = conf [ 'control' ] . get ( 'limits_key' , 'limits' ) # Now, grab all the limits lims = [ limits . Limit . hydrate ( db , msgpack . loads ( lim ) ) for lim in db . zrange ( limits_key , 0 , - 1 ) ] # Build up the limits tree root = etree . Element ( 'limits' ) limit_tree = etree . ElementTree ( root ) for idx , lim in enumerate ( lims ) : if debug : print >> sys . stderr , "Dumping limit index %d: %r" % ( idx , lim ) make_limit_node ( root , lim ) # Write out the limits file if limits_file == '-' : limits_file = sys . stdout if debug : print >> sys . stderr , "Dumping limits to file %r" % limits_file limit_tree . write ( limits_file , xml_declaration = True , encoding = 'UTF-8' , pretty_print = True )
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Run the external control daemon .
def remote_daemon ( conf_file ) : eventlet . monkey_patch ( ) conf = config . Config ( conf_file = conf_file ) daemon = remote . RemoteControlDaemon ( None , conf ) daemon . serve ( )
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Issue a command to all running control daemons .
def turnstile_command ( conf_file , command , arguments = [ ] , channel = None , debug = False ) : # Connect to the database... conf = config . Config ( conf_file = conf_file ) db = conf . get_database ( ) control_channel = conf [ 'control' ] . get ( 'channel' , 'control' ) # Now, set up the command command = command . lower ( ) ts_conv = False if command == 'ping' : # We handle 'ping' specially; first, figure out the channel if arguments : channel = arguments [ 0 ] else : channel = str ( uuid . uuid4 ( ) ) arguments = [ channel ] # Next, add on a timestamp if len ( arguments ) < 2 : arguments . append ( time . time ( ) ) ts_conv = True # Limit the argument list length arguments = arguments [ : 2 ] # OK, the command is all set up. Let us now send the command... if debug : cmd = [ command ] + arguments print >> sys . stderr , ( "Issuing command: %s" % ' ' . join ( cmd ) ) database . command ( db , control_channel , command , * arguments ) # Were we asked to listen on a channel? if not channel : return # OK, let's subscribe to the channel... pubsub = db . pubsub ( ) pubsub . subscribe ( channel ) # Now we listen... try : count = 0 for msg in pubsub . listen ( ) : # Make sure the message is one we're interested in if debug : formatted = pprint . pformat ( msg ) print >> sys . stderr , "Received message: %s" % formatted if ( msg [ 'type' ] not in ( 'pmessage' , 'message' ) or msg [ 'channel' ] != channel ) : continue count += 1 # Figure out the response response = msg [ 'data' ] . split ( ':' ) # If this is a 'pong' and ts_conv is true, add an RTT to # the response if ts_conv and response [ 0 ] == 'pong' : try : rtt = ( time . time ( ) - float ( response [ 2 ] ) ) * 100 response . append ( '(RTT %.2fms)' % rtt ) except Exception : # IndexError or ValueError, probably; ignore it pass # Print out the response print "Response % 5d: %s" % ( count , ' ' . join ( response ) ) except KeyboardInterrupt : # We want to break out of the loop, but not return any error # to the caller... pass
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Run the compactor daemon .
def compactor_daemon ( conf_file ) : eventlet . monkey_patch ( ) conf = config . Config ( conf_file = conf_file ) compactor . compactor ( conf )
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https://github.com/klmitch/turnstile/blob/8fe9a359b45e505d3192ab193ecf9be177ab1a17/turnstile/tools.py#L820-L829
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Ensures that the function is wrapped in a ScriptAdaptor object . If it is not a new ScriptAdaptor will be returned . If it is the ScriptAdaptor is returned .
def _wrap ( cls , func ) : if isinstance ( func , cls ) : return func return functools . update_wrapper ( cls ( func ) , func )
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[ "def", "delete_repository_config", "(", "namespace", ",", "name", ",", "snapshot_id", ")", ":", "uri", "=", "\"configurations/{0}/{1}/{2}\"", ".", "format", "(", "namespace", ",", "name", ",", "snapshot_id", ")", "return", "__delete", "(", "uri", ")" ]
Set up an argparse . ArgumentParser object by adding all the arguments taken by the function .
def setup_args ( self , parser ) : # Add all the arguments to the argument parser for args , kwargs in self . _arguments : parser . add_argument ( * args , * * kwargs )
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[ "def", "mass_properties", "(", "self", ")", ":", "mass", "=", "triangles", ".", "mass_properties", "(", "triangles", "=", "self", ".", "triangles", ",", "crosses", "=", "self", ".", "triangles_cross", ",", "density", "=", "self", ".", "_density", ",", "center_mass", "=", "self", ".", "_center_mass", ",", "skip_inertia", "=", "False", ")", "# if magical clean- up mode is enabled", "# and mesh is watertight/wound correctly but with negative", "# volume it means that every triangle is probably facing", "# inwards, so we invert it in- place without dumping cache", "if", "(", "self", ".", "_validate", "and", "self", ".", "is_watertight", "and", "self", ".", "is_winding_consistent", "and", "np", ".", "linalg", ".", "det", "(", "mass", "[", "'inertia'", "]", ")", "<", "0.0", "and", "mass", "[", "'mass'", "]", "<", "0.0", "and", "mass", "[", "'volume'", "]", "<", "0.0", ")", ":", "# negate mass properties so we don't need to recalculate", "mass", "[", "'inertia'", "]", "=", "-", "mass", "[", "'inertia'", "]", "mass", "[", "'mass'", "]", "=", "-", "mass", "[", "'mass'", "]", "mass", "[", "'volume'", "]", "=", "-", "mass", "[", "'volume'", "]", "# invert the faces and normals of the mesh", "self", ".", "invert", "(", ")", "return", "mass" ]
Given a Namespace object drawn from argparse determines the keyword arguments to pass to the underlying function . Note that if the underlying function accepts all keyword arguments the dictionary returned will contain the entire contents of the Namespace object . Also note that an AttributeError will be raised if any argument required by the function is not set in the Namespace object .
def get_kwargs ( self , args ) : # Now we need to figure out which arguments the final function # actually needs kwargs = { } argspec = inspect . getargspec ( self . _func ) required = set ( argspec . args [ : - len ( argspec . defaults ) ] if argspec . defaults else argspec . args ) for arg_name in argspec . args : try : kwargs [ arg_name ] = getattr ( args , arg_name ) except AttributeError : if arg_name in required : # If this happens, that's a programming failure raise # If the function accepts any keyword argument, add whatever # remains if argspec . keywords : for key , value in args . __dict__ . items ( ) : if key in kwargs : # Already handled continue kwargs [ key ] = value return kwargs
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Call the function as a console script . Command line arguments are parsed preprocessors are called then the function is called . If a debug attribute is set by the command line arguments and it is True any exception raised by the underlying function will be reraised ; otherwise the return value will be either the return value of the function or the text contents of the exception .
def console ( self ) : # First, let's parse the arguments parser = argparse . ArgumentParser ( description = self . description ) self . setup_args ( parser ) args = parser . parse_args ( ) # Next, let's run the preprocessors in order for proc in self . _preprocess : try : proc ( args ) except Exception as exc : if getattr ( args , 'debug' , False ) : raise return str ( exc ) # Finally, safely call the underlying function result = self . safe_call ( self . get_kwargs ( args ) , args ) # Now, run the postprocessors in order for proc in self . _postprocess : result = proc ( args , result ) return result
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Import a class based on its full name .
def import_class ( name : Text ) -> Type : parts = name . split ( '.' ) module_name = parts [ : - 1 ] class_name = parts [ - 1 ] module_ = importlib . import_module ( '.' . join ( module_name ) ) return getattr ( module_ , class_name )
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[ "def", "render", "(", "self", ",", "data", ",", "accepted_media_type", "=", "None", ",", "renderer_context", "=", "None", ")", ":", "if", "'SWAGGER_JSON_PATH'", "in", "os", ".", "environ", ":", "with", "io", ".", "open", "(", "os", ".", "environ", "[", "'SWAGGER_JSON_PATH'", "]", ",", "'rb'", ")", "as", "f", ":", "return", "f", ".", "read", "(", ")", "else", ":", "return", "super", "(", "ConditionalOpenAPIRenderer", ",", "self", ")", ".", "render", "(", "data", ",", "accepted_media_type", ",", "renderer_context", ")" ]
Make a json - serializable type recursively read - only
def make_ro ( obj : Any , forgive_type = False ) : if isinstance ( obj , ( str , bytes , int , float , bool , RoDict , RoList ) ) or obj is None : return obj elif isinstance ( obj , Mapping ) : return RoDict ( obj , forgive_type ) elif isinstance ( obj , Sequence ) : return RoList ( obj , forgive_type ) elif forgive_type : return obj else : raise ValueError ( 'Trying to make read-only an object of type "{}"' . format ( obj . __class__ . __name__ ) )
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Copy a RO object into a RW structure made with standard Python classes .
def make_rw ( obj : Any ) : if isinstance ( obj , RoDict ) : return { k : make_rw ( v ) for k , v in obj . items ( ) } elif isinstance ( obj , RoList ) : return [ make_rw ( x ) for x in obj ] else : return obj
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Given an URL change the query string to include the values specified in the dictionary .
def patch_qs ( url : Text , data : Dict [ Text , Text ] ) -> Text : qs_id = 4 p = list ( urlparse ( url ) ) qs = parse_qsl ( p [ qs_id ] ) # type: List[Tuple[Text, Text]] patched_qs = list ( chain ( filter ( lambda x : x [ 0 ] not in data , qs ) , data . items ( ) , ) ) p [ qs_id ] = urlencode ( patched_qs ) return urlunparse ( p )
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Checks that all keys present in subset are present and have the same value in full_set . If a key is in full_set but not in subset then True will be returned anyways .
def dict_is_subset ( subset : Any , full_set : Any ) -> bool : if not isinstance ( subset , full_set . __class__ ) : return False elif isinstance ( subset , dict ) : for k , v in subset . items ( ) : if k not in full_set or not dict_is_subset ( v , full_set [ k ] ) : return False return True elif isinstance ( subset , list ) : if len ( subset ) != len ( full_set ) : return False for a , b in zip ( subset , full_set ) : if not dict_is_subset ( a , b ) : return False return True else : return subset == full_set
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Transform a class exp into an actual regex
def _compile ( self , expression ) : x = self . RE_PYTHON_VAR . sub ( '(?:\\1,)' , expression ) x = self . RE_SPACES . sub ( '' , x ) return re . compile ( x )
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Transforms a list of objects into a matchable string
def _make_string ( self , objects : List [ Any ] ) -> Text : return '' . join ( x . __class__ . __name__ + ',' for x in objects )
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Return True if the list of objects matches the expression .
def match ( self , objects : List [ Any ] ) -> bool : s = self . _make_string ( objects ) m = self . _compiled_expression . match ( s ) return m is not None
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Gets a config opt from conf file under section sect .
def get_conf ( conf , sect , opt ) : argu = getattr ( args , "mambupy_" + opt . lower ( ) ) if not argu : envir = os . environ . get ( "MAMBUPY_" + opt . upper ( ) ) if not envir : try : return conf . get ( sect , opt ) except NoSectionError : return default_configs [ opt ] return envir return argu
10,249
https://github.com/jstitch/MambuPy/blob/2af98cc12e7ed5ec183b3e97644e880e70b79ee8/MambuPy/mambuconfig.py#L119-L152
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Get ISO8601 - formatted timestamp string .
def iso8601timestamp ( T = None , nanos = True , utc = False ) : T = time . time ( ) if T is None else T Ti = math . floor ( T ) Tn = round ( ( T - Ti ) * 1e9 ) if Tn >= 1e9 : Ti += 1 Tn = 0 s = time . gmtime ( Ti ) if utc else time . localtime ( Ti ) f = time . strftime ( "%Y%m%dT%H%M%S" , s ) n = ".{:09d}" . format ( Tn ) if nanos else "" tz = "Z" if utc else time . strftime ( "%z" , s ) return f + n + tz
10,250
https://github.com/obilaniu/Nauka/blob/1492a4f9d204a868c1a8a1d327bd108490b856b4/src/nauka/fhs.py#L5-L18
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Create working directory for experiment if not existing already .
def createWorkDir ( baseDir , projName , expUUID , expNames = [ ] , nanos = True , utc = False ) : # # First, ensure the project's top-level hierarchy, especially by-uuid/, # exists, so that the only possible failure is due to the creation of # one additional directory. # projDir = os . path . join ( baseDir , projName ) byuuidDir = os . path . join ( projDir , "by-uuid" ) bytimeDir = os . path . join ( projDir , "by-time" ) bynameDir = os . path . join ( projDir , "by-name" , * expNames ) byuuidPath = os . path . join ( byuuidDir , expUUID ) os . makedirs ( byuuidDir , mode = 0o755 , exist_ok = True ) os . makedirs ( bytimeDir , mode = 0o755 , exist_ok = True ) os . makedirs ( bynameDir , mode = 0o755 , exist_ok = True ) # # Attempt the creation of the experiment workDir by its UUID. Record # whether we were the original creators. # try : preexisting = False os . makedirs ( byuuidPath , mode = 0o755 , exist_ok = False ) except FileExistsError : preexisting = True # # If we were the first to create this working directory, additionally # make symlinks pointing to it from the auxiliary directories. # if not preexisting : expTime = iso8601timestamp ( nanos = nanos , utc = utc ) expTimeUUID = expTime + "-" + expUUID bytimePath = os . path . join ( bytimeDir , expTimeUUID ) bynamePath = os . path . join ( bynameDir , expUUID ) os . symlink ( os . path . relpath ( byuuidPath , bytimeDir ) , bytimePath , True ) os . symlink ( os . path . relpath ( byuuidPath , bynameDir ) , bynamePath , True ) # # Create handy .rsync-filter files. # with contextlib . suppress ( OSError ) : with open ( os . path . join ( baseDir , ".rsync-filter" ) , "x" ) as f : f . write ( "#\n" "# rsync filter rules.\n" "#\n" "# When the argument -F is given to rsync, the rules within will be obeyed.\n" "#\n" ) with contextlib . suppress ( OSError ) : with open ( os . path . join ( projDir , ".rsync-filter" ) , "x" ) as f : f . write ( "#\n" "# rsync filter rules.\n" "#\n" "# When the argument -F is given to rsync, the rules within will be obeyed.\n" "#\n" ) # # Return the constructed workDir. # return byuuidPath
10,251
https://github.com/obilaniu/Nauka/blob/1492a4f9d204a868c1a8a1d327bd108490b856b4/src/nauka/fhs.py#L21-L89
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Creates a string representation of time since the given start_time .
def humanize_timesince ( start_time ) : # pylint:disable=too-many-return-statements if not start_time : return start_time delta = local_now ( ) - start_time # assumption: negative delta values originate from clock # differences on different app server machines if delta . total_seconds ( ) < 0 : return 'a few seconds ago' num_years = delta . days // 365 if num_years > 0 : return '{} year{} ago' . format ( * ( ( num_years , 's' ) if num_years > 1 else ( num_years , '' ) ) ) num_weeks = delta . days // 7 if num_weeks > 0 : return '{} week{} ago' . format ( * ( ( num_weeks , 's' ) if num_weeks > 1 else ( num_weeks , '' ) ) ) num_days = delta . days if num_days > 0 : return '{} day{} ago' . format ( * ( ( num_days , 's' ) if num_days > 1 else ( num_days , '' ) ) ) num_hours = delta . seconds // 3600 if num_hours > 0 : return '{} hour{} ago' . format ( * ( ( num_hours , 's' ) if num_hours > 1 else ( num_hours , '' ) ) ) num_minutes = delta . seconds // 60 if num_minutes > 0 : return '{} minute{} ago' . format ( * ( ( num_minutes , 's' ) if num_minutes > 1 else ( num_minutes , '' ) ) ) return 'a few seconds ago'
10,252
https://github.com/polyaxon/hestia/blob/382ed139cff8bf35c987cfc30a31b72c0d6b808e/hestia/humanize.py#L7-L43
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Creates a string representation of timedelta .
def humanize_timedelta ( seconds ) : hours , remainder = divmod ( seconds , 3600 ) days , hours = divmod ( hours , 24 ) minutes , seconds = divmod ( remainder , 60 ) if days : result = '{}d' . format ( days ) if hours : result += ' {}h' . format ( hours ) if minutes : result += ' {}m' . format ( minutes ) return result if hours : result = '{}h' . format ( hours ) if minutes : result += ' {}m' . format ( minutes ) return result if minutes : result = '{}m' . format ( minutes ) if seconds : result += ' {}s' . format ( seconds ) return result return '{}s' . format ( seconds )
10,253
https://github.com/polyaxon/hestia/blob/382ed139cff8bf35c987cfc30a31b72c0d6b808e/hestia/humanize.py#L46-L72
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Overrides default start behaviour by raising ConnectionError instead of custom requests_mock . exceptions . NoMockAddress .
def start ( self ) : if self . _http_last_send is not None : raise RuntimeError ( 'HttpMock has already been started' ) # 1) save request.Session.send in self._last_send # 2) replace request.Session.send with MockerCore send function super ( HttpMock , self ) . start ( ) # 3) save MockerCore send function in self._http_last_send # 4) replace request.Session.send with HttpMock send function self . _patch_last_send ( )
10,254
https://github.com/peopledoc/mock-services/blob/fd3838280df8869725b538768357435eedf299c1/mock_services/http_mock.py#L63-L76
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Unregisters a handler
def unhandle ( self , handler ) : h , _ , _ = self . _extract ( handler ) key = hash ( h ) with self . _hlock : if key not in self . handlers : raise ValueError ( 'Handler "%s" was not found' % str ( h ) ) handlers = self . handlers . copy ( ) del handlers [ key ] self . handlers = handlers return self
10,255
https://github.com/axel-events/axel/blob/08a663347ef21614b96f92f60f4de57a502db73c/axel/axel.py#L163-L173
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Stores all registered handlers in a queue for processing
def fire ( self , * args , * * kw ) : result = [ ] with self . _hlock : handlers = self . handlers if self . threads == 0 : # same-thread execution - synchronized for k in handlers : # handler, memoize, timeout h , m , t = handlers [ k ] try : r = self . _memoize ( h , m , t , * args , * * kw ) result . append ( tuple ( r ) ) except : result . append ( ( False , self . _error ( sys . exc_info ( ) ) , h ) ) elif self . threads > 0 : # multi-thread execution - desynchronized if self.threads > 1 queue = Queue ( ) # result lock just in case [].append() is not # thread-safe in other Python implementations rlock = RLock ( ) def _execute ( * args , * * kw ) : """ Executes all handlers stored in the queue """ while True : try : item = queue . get ( ) if item is None : queue . task_done ( ) break # handler, memoize, timeout h , m , t = handlers [ item ] # call under active lock try : r = self . _memoize ( h , m , t , * args , * * kw ) if not self . asynch : with rlock : result . append ( tuple ( r ) ) except : if not self . asynch : with rlock : result . append ( ( False , self . _error ( sys . exc_info ( ) ) , h ) ) queue . task_done ( ) except Empty : # never triggered, just to be safe break if handlers : threads = self . _threads ( handlers = handlers ) for _ in range ( threads ) : t = Thread ( target = _execute , args = args , kwargs = kw ) t . daemon = True t . start ( ) for k in handlers : queue . put ( k ) if self . asynch : # main thread, no locking required h , _ , _ = handlers [ k ] result . append ( ( None , None , h ) ) for _ in range ( threads ) : queue . put ( None ) # stop each worker if not self . asynch : queue . join ( ) return tuple ( result ) or None
10,256
https://github.com/axel-events/axel/blob/08a663347ef21614b96f92f60f4de57a502db73c/axel/axel.py#L175-L247
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Discards all registered handlers and cached results
def clear ( self ) : with self . _hlock : self . handlers . clear ( ) with self . _mlock : self . memoize . clear ( )
10,257
https://github.com/axel-events/axel/blob/08a663347ef21614b96f92f60f4de57a502db73c/axel/axel.py#L254-L259
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Controls the time allocated for the execution of a method
def _timeout ( self , timeout , handler , * args , * * kw ) : t = spawn_thread ( target = handler , args = args , kw = kw ) t . daemon = True t . start ( ) t . join ( timeout ) if not t . is_alive ( ) : if t . exc_info : return t . exc_info return t . result else : try : msg = '[%s] Execution was forcefully terminated' raise RuntimeError ( msg % t . name ) except : return sys . exc_info ( )
10,258
https://github.com/axel-events/axel/blob/08a663347ef21614b96f92f60f4de57a502db73c/axel/axel.py#L336-L352
[ "def", "find_package_indexes_in_dir", "(", "self", ",", "simple_dir", ")", ":", "packages", "=", "sorted", "(", "{", "# Filter out all of the \"non\" normalized names here", "canonicalize_name", "(", "x", ")", "for", "x", "in", "os", ".", "listdir", "(", "simple_dir", ")", "}", ")", "# Package indexes must be in directories, so ignore anything else.", "packages", "=", "[", "x", "for", "x", "in", "packages", "if", "os", ".", "path", ".", "isdir", "(", "os", ".", "path", ".", "join", "(", "simple_dir", ",", "x", ")", ")", "]", "return", "packages" ]
Calculates maximum number of threads that will be started
def _threads ( self , handlers ) : if self . threads < len ( handlers ) : return self . threads return len ( handlers )
10,259
https://github.com/axel-events/axel/blob/08a663347ef21614b96f92f60f4de57a502db73c/axel/axel.py#L354-L358
[ "def", "GetAttachmentIdFromMediaId", "(", "media_id", ")", ":", "altchars", "=", "'+-'", "if", "not", "six", ".", "PY2", ":", "altchars", "=", "altchars", ".", "encode", "(", "'utf-8'", ")", "# altchars for '+' and '/'. We keep '+' but replace '/' with '-'", "buffer", "=", "base64", ".", "b64decode", "(", "str", "(", "media_id", ")", ",", "altchars", ")", "resoure_id_length", "=", "20", "attachment_id", "=", "''", "if", "len", "(", "buffer", ")", ">", "resoure_id_length", ":", "# We are cutting off the storage index.", "attachment_id", "=", "base64", ".", "b64encode", "(", "buffer", "[", "0", ":", "resoure_id_length", "]", ",", "altchars", ")", "if", "not", "six", ".", "PY2", ":", "attachment_id", "=", "attachment_id", ".", "decode", "(", "'utf-8'", ")", "else", ":", "attachment_id", "=", "media_id", "return", "attachment_id" ]
Read raw data and calculate temperature and humidity .
def update ( self ) : if not self . _ok : self . log_error ( "Trying to restore OK mode w/ soft reset" ) self . _ok = self . _soft_reset ( ) try : self . _bus . write_byte ( self . _i2c_add , CMD_READ_TEMP_NOHOLD ) sleep ( MEASUREMENT_WAIT_TIME ) buf_t = self . _bus . read_i2c_block_data ( self . _i2c_add , CMD_READ_TEMP_HOLD , 3 ) self . _bus . write_byte ( self . _i2c_add , CMD_READ_HUM_NOHOLD ) sleep ( MEASUREMENT_WAIT_TIME ) buf_h = self . _bus . read_i2c_block_data ( self . _i2c_add , CMD_READ_HUM_HOLD , 3 ) except OSError as exc : self . _ok = False self . log_error ( "Bad reading: %s" , exc ) return if self . _crc8check ( buf_t ) : temp = ( buf_t [ 0 ] << 8 | buf_t [ 1 ] ) & 0xFFFC self . _temperature = self . _calc_temp ( temp ) if self . _crc8check ( buf_h ) : humid = ( buf_h [ 0 ] << 8 | buf_h [ 1 ] ) & 0xFFFC rh_actual = self . _calc_humid ( humid ) # For temperature coefficient compensation rh_final = self . _temp_coefficient ( rh_actual , self . _temperature ) rh_final = 100.0 if rh_final > 100 else rh_final # Clamp > 100 rh_final = 0.0 if rh_final < 0 else rh_final # Clamp < 0 self . _humidity = rh_final else : self . _humidity = - 255 self . _ok = False self . log_error ( "Bad CRC error with humidity" ) else : self . _temperature = - 255 self . _ok = False self . log_error ( "Bad CRC error with temperature" )
10,260
https://github.com/azogue/i2csense/blob/ecc6806dcee9de827a5414a9e836d271fedca9b9/i2csense/htu21d.py#L87-L126
[ "def", "update_notebook_actions", "(", "self", ")", ":", "if", "self", ".", "recent_notebooks", ":", "self", ".", "clear_recent_notebooks_action", ".", "setEnabled", "(", "True", ")", "else", ":", "self", ".", "clear_recent_notebooks_action", ".", "setEnabled", "(", "False", ")", "client", "=", "self", ".", "get_current_client", "(", ")", "if", "client", ":", "if", "client", ".", "get_filename", "(", ")", "!=", "WELCOME", ":", "self", ".", "save_as_action", ".", "setEnabled", "(", "True", ")", "self", ".", "open_console_action", ".", "setEnabled", "(", "True", ")", "self", ".", "options_menu", ".", "clear", "(", ")", "add_actions", "(", "self", ".", "options_menu", ",", "self", ".", "menu_actions", ")", "return", "self", ".", "save_as_action", ".", "setEnabled", "(", "False", ")", "self", ".", "open_console_action", ".", "setEnabled", "(", "False", ")", "self", ".", "options_menu", ".", "clear", "(", ")", "add_actions", "(", "self", ".", "options_menu", ",", "self", ".", "menu_actions", ")" ]
Return workflow owner access token .
def get_owner_access_token ( self ) : from . database import Session db_session = Session . object_session ( self ) owner = db_session . query ( User ) . filter_by ( id_ = self . owner_id ) . first ( ) return owner . access_token
10,261
https://github.com/reanahub/reana-db/blob/4efcb46d23af035689964d8c25a804c5a8f1dfc3/reana_db/models.py#L167-L173
[ "def", "_mmUpdateDutyCycles", "(", "self", ")", ":", "period", "=", "self", ".", "getDutyCyclePeriod", "(", ")", "unionSDRArray", "=", "numpy", ".", "zeros", "(", "self", ".", "getNumColumns", "(", ")", ")", "unionSDRArray", "[", "list", "(", "self", ".", "_mmTraces", "[", "\"unionSDR\"", "]", ".", "data", "[", "-", "1", "]", ")", "]", "=", "1", "self", ".", "_mmData", "[", "\"unionSDRDutyCycle\"", "]", "=", "UnionTemporalPoolerMonitorMixin", ".", "_mmUpdateDutyCyclesHelper", "(", "self", ".", "_mmData", "[", "\"unionSDRDutyCycle\"", "]", ",", "unionSDRArray", ",", "period", ")", "self", ".", "_mmData", "[", "\"persistenceDutyCycle\"", "]", "=", "UnionTemporalPoolerMonitorMixin", ".", "_mmUpdateDutyCyclesHelper", "(", "self", ".", "_mmData", "[", "\"persistenceDutyCycle\"", "]", ",", "self", ".", "_poolingActivation", ",", "period", ")" ]
Update database workflow status .
def update_workflow_status ( db_session , workflow_uuid , status , new_logs = '' , message = None ) : try : workflow = db_session . query ( Workflow ) . filter_by ( id_ = workflow_uuid ) . first ( ) if not workflow : raise Exception ( 'Workflow {0} doesn\'t exist in database.' . format ( workflow_uuid ) ) if status : workflow . status = status if new_logs : workflow . logs = ( workflow . logs or '' ) + new_logs + '\n' db_session . commit ( ) except Exception as e : raise e
10,262
https://github.com/reanahub/reana-db/blob/4efcb46d23af035689964d8c25a804c5a8f1dfc3/reana_db/models.py#L176-L198
[ "def", "removefromreadergroup", "(", "self", ",", "groupname", ")", ":", "hresult", ",", "hcontext", "=", "SCardEstablishContext", "(", "SCARD_SCOPE_USER", ")", "if", "0", "!=", "hresult", ":", "raise", "EstablishContextException", "(", "hresult", ")", "try", ":", "hresult", "=", "SCardRemoveReaderFromGroup", "(", "hcontext", ",", "self", ".", "name", ",", "groupname", ")", "if", "0", "!=", "hresult", ":", "raise", "RemoveReaderFromGroupException", "(", "hresult", ",", "self", ".", "name", ",", "groupname", ")", "finally", ":", "hresult", "=", "SCardReleaseContext", "(", "hcontext", ")", "if", "0", "!=", "hresult", ":", "raise", "ReleaseContextException", "(", "hresult", ")" ]
Parse address and returns host and port
def parse_server_addr ( str_addr , default_port = 26000 ) : m = ADDR_STR_RE . match ( str_addr ) if m is None : raise ValueError ( 'Bad address string "{0}"' . format ( str_addr ) ) dct = m . groupdict ( ) port = dct . get ( 'port' ) if port is None : port = default_port else : port = int ( port ) # Caution: could raise ValueEror or TypeError if port == 0 : raise ValueError ( "Port can't be zero" ) host = dct [ 'host' ] if dct [ 'host' ] else dct [ 'host6' ] return host , port
10,263
https://github.com/bacher09/xrcon/blob/6a883f780265cbca31af7a379dc7cb28fdd8b73f/xrcon/utils.py#L103-L142
[ "def", "deploy_template", "(", "access_token", ",", "subscription_id", ",", "resource_group", ",", "deployment_name", ",", "template", ",", "parameters", ")", ":", "endpoint", "=", "''", ".", "join", "(", "[", "get_rm_endpoint", "(", ")", ",", "'/subscriptions/'", ",", "subscription_id", ",", "'/resourcegroups/'", ",", "resource_group", ",", "'/providers/Microsoft.Resources/deployments/'", ",", "deployment_name", ",", "'?api-version='", ",", "DEPLOYMENTS_API", "]", ")", "properties", "=", "{", "'template'", ":", "template", "}", "properties", "[", "'mode'", "]", "=", "'Incremental'", "properties", "[", "'parameters'", "]", "=", "parameters", "template_body", "=", "{", "'properties'", ":", "properties", "}", "body", "=", "json", ".", "dumps", "(", "template_body", ")", "return", "do_put", "(", "endpoint", ",", "body", ",", "access_token", ")" ]
Request a go to assignment .
def request_goto ( self , tc = None ) : if not tc : tc = TextHelper ( self . editor ) . word_under_cursor ( select_whole_word = True ) if not self . _definition or isinstance ( self . sender ( ) , QAction ) : self . select_word ( tc ) if self . _definition is not None : QTimer . singleShot ( 100 , self . _goto_def )
10,264
https://github.com/pyQode/pyqode.cobol/blob/eedae4e320a4b2d0c44abb2c3061091321648fb7/pyqode/cobol/modes/goto.py#L122-L137
[ "def", "get_directory_properties", "(", "self", ",", "share_name", ",", "directory_name", ",", "timeout", "=", "None", ",", "snapshot", "=", "None", ")", ":", "_validate_not_none", "(", "'share_name'", ",", "share_name", ")", "_validate_not_none", "(", "'directory_name'", ",", "directory_name", ")", "request", "=", "HTTPRequest", "(", ")", "request", ".", "method", "=", "'GET'", "request", ".", "host_locations", "=", "self", ".", "_get_host_locations", "(", ")", "request", ".", "path", "=", "_get_path", "(", "share_name", ",", "directory_name", ")", "request", ".", "query", "=", "{", "'restype'", ":", "'directory'", ",", "'timeout'", ":", "_int_to_str", "(", "timeout", ")", ",", "'sharesnapshot'", ":", "_to_str", "(", "snapshot", ")", "}", "return", "self", ".", "_perform_request", "(", "request", ",", "_parse_directory", ",", "[", "directory_name", "]", ")" ]
Return a copy of the template with the specified name . If not found or an error occurs during the load return None .
def get_template ( name ) : path = os . path . join ( base_dir , name ) if path not in templates : try : templates [ path ] = Template ( path ) except IOError : return None return copy . deepcopy ( templates [ path ] )
10,265
https://github.com/jasonrbriggs/proton/blob/e734734750797ef0caaa1680379e07b86d7a53e3/python/proton/template.py#L366-L379
[ "def", "__normalize", "(", "self", ")", ":", "# Don't normalize if we're already normalizing or intializing", "if", "self", ".", "__normalizing", "is", "True", "or", "self", ".", "__initialized", "is", "False", ":", "return", "self", ".", "__normalizing", "=", "True", "self", ".", "__normalize_grades", "(", ")", "self", ".", "__normalize_progress", "(", ")", "self", ".", "__normalizing", "=", "False" ]
Set the content of an xml element marked with the matching eid attribute .
def set_value ( self , eid , val , idx = '*' ) : if eid in self . __element_ids : elems = self . __element_ids [ eid ] if type ( val ) in SEQ_TYPES : idx = 0 if idx == '*' : for elem in elems : self . __set_value ( eid , elem , val , idx ) elif idx < len ( elems ) : self . __set_value ( eid , elems [ idx ] , val , idx )
10,266
https://github.com/jasonrbriggs/proton/blob/e734734750797ef0caaa1680379e07b86d7a53e3/python/proton/template.py#L220-L232
[ "def", "get_dummy_request", "(", "language", "=", "None", ")", ":", "if", "settings", ".", "ALLOWED_HOSTS", "and", "settings", ".", "ALLOWED_HOSTS", "!=", "\"*\"", ":", "host", "=", "settings", ".", "ALLOWED_HOSTS", "[", "0", "]", "else", ":", "host", "=", "Site", ".", "objects", ".", "get_current", "(", ")", ".", "domain", "request", "=", "RequestFactory", "(", ")", ".", "get", "(", "\"/\"", ",", "HTTP_HOST", "=", "host", ")", "request", ".", "session", "=", "{", "}", "request", ".", "LANGUAGE_CODE", "=", "language", "or", "settings", ".", "LANGUAGE_CODE", "# Needed for plugin rendering.", "request", ".", "current_page", "=", "None", "if", "'django.contrib.auth'", "in", "settings", ".", "INSTALLED_APPS", ":", "from", "django", ".", "contrib", ".", "auth", ".", "models", "import", "AnonymousUser", "request", ".", "user", "=", "AnonymousUser", "(", ")", "return", "request" ]
Set the value of an xml attribute marked with the matching aid attribute .
def set_attribute ( self , aid , attrib , val , idx = '*' ) : if aid in self . __attrib_ids : elems = self . __attrib_ids [ aid ] if idx == '*' : for elem in elems : self . __set_attribute ( elem , attrib , val ) elif idx < len ( elems ) : elem = elems [ idx ] self . __set_attribute ( elem , attrib , val )
10,267
https://github.com/jasonrbriggs/proton/blob/e734734750797ef0caaa1680379e07b86d7a53e3/python/proton/template.py#L244-L255
[ "def", "_copy_database_data_clientside", "(", "self", ",", "tables", ",", "source", ",", "destination", ")", ":", "# Retrieve database rows", "rows", "=", "self", ".", "get_database_rows", "(", "tables", ",", "source", ")", "# Retrieve database columns", "cols", "=", "self", ".", "get_database_columns", "(", "tables", ",", "source", ")", "# Validate rows and columns", "for", "r", "in", "list", "(", "rows", ".", "keys", "(", ")", ")", ":", "assert", "r", "in", "tables", "for", "c", "in", "list", "(", "cols", ".", "keys", "(", ")", ")", ":", "assert", "c", "in", "tables", "# Change database to destination", "self", ".", "change_db", "(", "destination", ")", "# Get insert queries", "insert_queries", "=", "self", ".", "_get_insert_commands", "(", "rows", ",", "cols", ")", "# Execute insert queries", "self", ".", "_execute_insert_commands", "(", "insert_queries", ")" ]
Hide the element with the matching eid . If no match look for an element with a matching rid .
def hide ( self , eid , index = 0 ) : elems = None if eid in self . __element_ids : elems = self . __element_ids [ eid ] elif eid in self . __repeat_ids : elems = self . __repeat_ids [ eid ] if elems and index < len ( elems ) : elem = elems [ index ] elem . parent . children . remove ( elem )
10,268
https://github.com/jasonrbriggs/proton/blob/e734734750797ef0caaa1680379e07b86d7a53e3/python/proton/template.py#L279-L291
[ "def", "create_api_client", "(", "api", "=", "'BatchV1'", ")", ":", "k8s_config", ".", "load_incluster_config", "(", ")", "api_configuration", "=", "client", ".", "Configuration", "(", ")", "api_configuration", ".", "verify_ssl", "=", "False", "if", "api", "==", "'extensions/v1beta1'", ":", "api_client", "=", "client", ".", "ExtensionsV1beta1Api", "(", ")", "elif", "api", "==", "'CoreV1'", ":", "api_client", "=", "client", ".", "CoreV1Api", "(", ")", "elif", "api", "==", "'StorageV1'", ":", "api_client", "=", "client", ".", "StorageV1Api", "(", ")", "else", ":", "api_client", "=", "client", ".", "BatchV1Api", "(", ")", "return", "api_client" ]
Repeat an xml element marked with the matching rid .
def repeat ( self , rid , count , index = 0 ) : elems = None if rid in self . __repeat_ids : elems = self . __repeat_ids [ rid ] elif rid in self . __element_ids : elems = self . __element_ids if elems and index < len ( elems ) : elem = elems [ index ] self . __repeat ( elem , count )
10,269
https://github.com/jasonrbriggs/proton/blob/e734734750797ef0caaa1680379e07b86d7a53e3/python/proton/template.py#L293-L305
[ "def", "_setup_conn_old", "(", "*", "*", "kwargs", ")", ":", "host", "=", "__salt__", "[", "'config.option'", "]", "(", "'kubernetes.api_url'", ",", "'http://localhost:8080'", ")", "username", "=", "__salt__", "[", "'config.option'", "]", "(", "'kubernetes.user'", ")", "password", "=", "__salt__", "[", "'config.option'", "]", "(", "'kubernetes.password'", ")", "ca_cert", "=", "__salt__", "[", "'config.option'", "]", "(", "'kubernetes.certificate-authority-data'", ")", "client_cert", "=", "__salt__", "[", "'config.option'", "]", "(", "'kubernetes.client-certificate-data'", ")", "client_key", "=", "__salt__", "[", "'config.option'", "]", "(", "'kubernetes.client-key-data'", ")", "ca_cert_file", "=", "__salt__", "[", "'config.option'", "]", "(", "'kubernetes.certificate-authority-file'", ")", "client_cert_file", "=", "__salt__", "[", "'config.option'", "]", "(", "'kubernetes.client-certificate-file'", ")", "client_key_file", "=", "__salt__", "[", "'config.option'", "]", "(", "'kubernetes.client-key-file'", ")", "# Override default API settings when settings are provided", "if", "'api_url'", "in", "kwargs", ":", "host", "=", "kwargs", ".", "get", "(", "'api_url'", ")", "if", "'api_user'", "in", "kwargs", ":", "username", "=", "kwargs", ".", "get", "(", "'api_user'", ")", "if", "'api_password'", "in", "kwargs", ":", "password", "=", "kwargs", ".", "get", "(", "'api_password'", ")", "if", "'api_certificate_authority_file'", "in", "kwargs", ":", "ca_cert_file", "=", "kwargs", ".", "get", "(", "'api_certificate_authority_file'", ")", "if", "'api_client_certificate_file'", "in", "kwargs", ":", "client_cert_file", "=", "kwargs", ".", "get", "(", "'api_client_certificate_file'", ")", "if", "'api_client_key_file'", "in", "kwargs", ":", "client_key_file", "=", "kwargs", ".", "get", "(", "'api_client_key_file'", ")", "if", "(", "kubernetes", ".", "client", ".", "configuration", ".", "host", "!=", "host", "or", "kubernetes", ".", "client", ".", "configuration", ".", "user", "!=", "username", "or", "kubernetes", ".", "client", ".", "configuration", ".", "password", "!=", "password", ")", ":", "# Recreates API connection if settings are changed", "kubernetes", ".", "client", ".", "configuration", ".", "__init__", "(", ")", "kubernetes", ".", "client", ".", "configuration", ".", "host", "=", "host", "kubernetes", ".", "client", ".", "configuration", ".", "user", "=", "username", "kubernetes", ".", "client", ".", "configuration", ".", "passwd", "=", "password", "if", "ca_cert_file", ":", "kubernetes", ".", "client", ".", "configuration", ".", "ssl_ca_cert", "=", "ca_cert_file", "elif", "ca_cert", ":", "with", "tempfile", ".", "NamedTemporaryFile", "(", "prefix", "=", "'salt-kube-'", ",", "delete", "=", "False", ")", "as", "ca", ":", "ca", ".", "write", "(", "base64", ".", "b64decode", "(", "ca_cert", ")", ")", "kubernetes", ".", "client", ".", "configuration", ".", "ssl_ca_cert", "=", "ca", ".", "name", "else", ":", "kubernetes", ".", "client", ".", "configuration", ".", "ssl_ca_cert", "=", "None", "if", "client_cert_file", ":", "kubernetes", ".", "client", ".", "configuration", ".", "cert_file", "=", "client_cert_file", "elif", "client_cert", ":", "with", "tempfile", ".", "NamedTemporaryFile", "(", "prefix", "=", "'salt-kube-'", ",", "delete", "=", "False", ")", "as", "c", ":", "c", ".", "write", "(", "base64", ".", "b64decode", "(", "client_cert", ")", ")", "kubernetes", ".", "client", ".", "configuration", ".", "cert_file", "=", "c", ".", "name", "else", ":", "kubernetes", ".", "client", ".", "configuration", ".", "cert_file", "=", "None", "if", "client_key_file", ":", "kubernetes", ".", "client", ".", "configuration", ".", "key_file", "=", "client_key_file", "elif", "client_key", ":", "with", "tempfile", ".", "NamedTemporaryFile", "(", "prefix", "=", "'salt-kube-'", ",", "delete", "=", "False", ")", "as", "k", ":", "k", ".", "write", "(", "base64", ".", "b64decode", "(", "client_key", ")", ")", "kubernetes", ".", "client", ".", "configuration", ".", "key_file", "=", "k", ".", "name", "else", ":", "kubernetes", ".", "client", ".", "configuration", ".", "key_file", "=", "None", "return", "{", "}" ]
Replace an xml element marked with the matching eid . If the replacement value is an Element or TextElement it s swapped in untouched . If it s a Template the children of the root element in the template are used . Otherwise the replacement value is wrapped with a TextElement .
def replace ( self , eid , replacement , index = 0 ) : if eid in self . __element_ids : elems = self . __element_ids [ eid ] elif eid in self . __repeat_ids : elems = self . __repeat_ids [ eid ] else : return if index < len ( elems ) : elem = elems [ index ] current_pos = elem . parent . children . index ( elem ) elem . parent . children . remove ( elem ) replacement_type = type ( replacement ) if replacement_type in ( Element , TextElement ) : self . check_element ( replacement , True ) elem . parent . children . insert ( current_pos , replacement ) replacement . parent = elem . parent elif replacement_type == Template : for child in replacement . root . children : elem . parent . children . insert ( current_pos , child ) child . parent = elem . parent current_pos += 1 self . __merge_ids ( self . __element_ids , replacement . __element_ids ) self . __merge_ids ( self . __attrib_ids , replacement . __attrib_ids ) self . __merge_ids ( self . __repeat_ids , replacement . __repeat_ids ) else : elem . parent . children . insert ( current_pos , TextElement ( replacement ) )
10,270
https://github.com/jasonrbriggs/proton/blob/e734734750797ef0caaa1680379e07b86d7a53e3/python/proton/template.py#L316-L347
[ "def", "from_file", "(", "cls", ",", "h5_file", ")", ":", "return", "cls", "(", "{", "country", ":", "HDF5DailyBarReader", ".", "from_file", "(", "h5_file", ",", "country", ")", "for", "country", "in", "h5_file", ".", "keys", "(", ")", "}", ")" ]
Updates the has algorithm and optionally the number of rounds to use .
def set_hasher ( self , hash , rounds = None ) : hash = hash . replace ( '-' , '_' ) if hash not in VALID_HASHERS : raise WrongHashAlgorithm ( WRONG_HASH_MESSAGE ) hasher = getattr ( ph , hash ) utils . test_hasher ( hasher ) default_rounds = getattr ( hasher , 'default_rounds' , 1 ) min_rounds = getattr ( hasher , 'min_rounds' , 1 ) max_rounds = getattr ( hasher , 'max_rounds' , float ( "inf" ) ) rounds = min ( max ( rounds or default_rounds , min_rounds ) , max_rounds ) op = { 'schemes' : VALID_HASHERS + DEPRECATED_HASHERS , 'deprecated' : DEPRECATED_HASHERS , 'default' : hash , hash + '__default_rounds' : rounds } self . hasher = CryptContext ( * * op ) self . hash = hash . replace ( '_' , '-' ) # For testing self . rounds = rounds
10,271
https://github.com/jpscaletti/authcode/blob/91529b6d0caec07d1452758d937e1e0745826139/authcode/auth.py#L140-L167
[ "def", "build_agency", "(", "pfeed", ")", ":", "return", "pd", ".", "DataFrame", "(", "{", "'agency_name'", ":", "pfeed", ".", "meta", "[", "'agency_name'", "]", ".", "iat", "[", "0", "]", ",", "'agency_url'", ":", "pfeed", ".", "meta", "[", "'agency_url'", "]", ".", "iat", "[", "0", "]", ",", "'agency_timezone'", ":", "pfeed", ".", "meta", "[", "'agency_timezone'", "]", ".", "iat", "[", "0", "]", ",", "}", ",", "index", "=", "[", "0", "]", ")" ]
Convert a string to a boolean value .
def to_bool ( value , do_raise = True ) : value = value . lower ( ) # Try it as an integer if value . isdigit ( ) : return bool ( int ( value ) ) # OK, check it against the true/false values... if value in _str_true : return True elif value in _str_false : return False # Not recognized if do_raise : raise ValueError ( "invalid literal for to_bool(): %r" % value ) return False
10,272
https://github.com/klmitch/turnstile/blob/8fe9a359b45e505d3192ab193ecf9be177ab1a17/turnstile/config.py#L228-L254
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Transform this layer into another layer type
async def become ( self , layer_type : Type [ L ] , request : 'Request' ) -> L : raise ValueError ( 'Cannot become "{}"' . format ( layer_type . __name__ ) )
10,273
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/layers/definitions.py#L75-L80
[ "def", "get_file_descriptor", "(", "self", ")", ":", "return", "self", ".", "_subscription", ".", "connection", "and", "self", ".", "_subscription", ".", "connection", ".", "_sock", ".", "fileno", "(", ")" ]
Transforms the translatable string into an actual string and put it inside a RawText .
async def become ( self , layer_type : Type [ L ] , request : 'Request' ) : if layer_type != RawText : super ( Text , self ) . become ( layer_type , request ) return RawText ( await render ( self . text , request ) )
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https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/layers/definitions.py#L110-L118
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Make the register storage .
def _make_register ( self ) -> BaseRegisterStore : s = settings . REGISTER_STORE store_class = import_class ( s [ 'class' ] ) return store_class ( * * s [ 'params' ] )
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[ "def", "get_attachment_content", "(", "self", ",", "ticket_id", ",", "attachment_id", ")", ":", "msg", "=", "self", ".", "__request", "(", "'ticket/{}/attachments/{}/content'", ".", "format", "(", "str", "(", "ticket_id", ")", ",", "str", "(", "attachment_id", ")", ")", ",", "text_response", "=", "False", ")", "lines", "=", "msg", ".", "split", "(", "b'\\n'", ",", "3", ")", "if", "(", "len", "(", "lines", ")", "==", "4", ")", "and", "(", "self", ".", "RE_PATTERNS", "[", "'invalid_attachment_pattern_bytes'", "]", ".", "match", "(", "lines", "[", "2", "]", ")", "or", "self", ".", "RE_PATTERNS", "[", "'does_not_exist_pattern_bytes'", "]", ".", "match", "(", "lines", "[", "2", "]", ")", ")", ":", "return", "None", "return", "msg", "[", "msg", ".", "find", "(", "b'\\n'", ")", "+", "2", ":", "-", "3", "]" ]
Load the transitions file .
def _make_transitions ( self ) -> List [ Transition ] : module_name = settings . TRANSITIONS_MODULE module_ = importlib . import_module ( module_name ) return module_ . transitions
10,276
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/fsm.py#L150-L157
[ "def", "user_deleted_from_site_event", "(", "event", ")", ":", "userid", "=", "event", ".", "principal", "catalog", "=", "api", ".", "portal", ".", "get_tool", "(", "'portal_catalog'", ")", "query", "=", "{", "'object_provides'", ":", "WORKSPACE_INTERFACE", "}", "query", "[", "'workspace_members'", "]", "=", "userid", "workspaces", "=", "[", "IWorkspace", "(", "b", ".", "_unrestrictedGetObject", "(", ")", ")", "for", "b", "in", "catalog", ".", "unrestrictedSearchResults", "(", "query", ")", "]", "for", "workspace", "in", "workspaces", ":", "workspace", ".", "remove_from_team", "(", "userid", ")" ]
Sometimes we load states from the database . In order to avoid loading an arbitrary class we list here the state classes that are allowed .
def _make_allowed_states ( self ) -> Iterator [ Text ] : for trans in self . transitions : yield trans . dest . name ( ) if trans . origin : yield trans . origin . name ( )
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https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/fsm.py#L159-L169
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Find the best trigger for this request or go away .
async def _find_trigger ( self , request : Request , origin : Optional [ Text ] = None , internal : bool = False ) -> Tuple [ Optional [ BaseTrigger ] , Optional [ Type [ BaseState ] ] , Optional [ bool ] , ] : reg = request . register if not origin : origin = reg . get ( Register . STATE ) logger . debug ( 'From state: %s' , origin ) results = await asyncio . gather ( * ( x . rank ( request , origin ) for x in self . transitions if x . internal == internal ) ) if len ( results ) : score , trigger , state , dnr = max ( results , key = lambda x : x [ 0 ] ) if score >= settings . MINIMAL_TRIGGER_SCORE : return trigger , state , dnr return None , None , None
10,278
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/fsm.py#L171-L203
[ "def", "_read_data", "(", "fname", ")", ":", "energy", "=", "[", "]", "with", "open", "(", "fname", ",", "'r'", ")", "as", "f", ":", "for", "line", "in", "f", ":", "CE", "=", "abs", "(", "float", "(", "line", ".", "strip", "(", ")", ".", "split", "(", ")", "[", "0", "]", ")", ")", "VASP", "=", "abs", "(", "float", "(", "line", ".", "strip", "(", ")", ".", "split", "(", ")", "[", "1", "]", ")", ")", "conc", "=", "[", "i", "for", "i", "in", "line", ".", "strip", "(", ")", ".", "split", "(", ")", "[", "2", ":", "]", "]", "conc_f", "=", "[", "]", "for", "c", "in", "conc", ":", "if", "'['", "in", "c", "and", "']'", "in", "c", ":", "conc_f", ".", "append", "(", "int", "(", "c", "[", "1", ":", "-", "1", "]", ")", ")", "elif", "'['", "in", "c", ":", "conc_f", ".", "append", "(", "int", "(", "c", "[", "1", ":", "-", "1", "]", ")", ")", "elif", "']'", "in", "c", "or", "','", "in", "c", ":", "conc_f", ".", "append", "(", "int", "(", "c", "[", ":", "-", "1", "]", ")", ")", "else", ":", "conc_f", ".", "append", "(", "int", "(", "c", ")", ")", "energy", ".", "append", "(", "[", "CE", ",", "VASP", ",", "conc_f", "]", ")", "return", "energy" ]
If we re confused find which state to call .
def _confused_state ( self , request : Request ) -> Type [ BaseState ] : origin = request . register . get ( Register . STATE ) if origin in self . _allowed_states : try : return import_class ( origin ) except ( AttributeError , ImportError ) : pass return import_class ( settings . DEFAULT_STATE )
10,279
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/fsm.py#L206-L219
[ "def", "_read_body_by_chunk", "(", "self", ",", "response", ",", "file", ",", "raw", "=", "False", ")", ":", "reader", "=", "ChunkedTransferReader", "(", "self", ".", "_connection", ")", "file_is_async", "=", "hasattr", "(", "file", ",", "'drain'", ")", "while", "True", ":", "chunk_size", ",", "data", "=", "yield", "from", "reader", ".", "read_chunk_header", "(", ")", "self", ".", "_data_event_dispatcher", ".", "notify_read", "(", "data", ")", "if", "raw", ":", "file", ".", "write", "(", "data", ")", "if", "not", "chunk_size", ":", "break", "while", "True", ":", "content", ",", "data", "=", "yield", "from", "reader", ".", "read_chunk_body", "(", ")", "self", ".", "_data_event_dispatcher", ".", "notify_read", "(", "data", ")", "if", "not", "content", ":", "if", "raw", ":", "file", ".", "write", "(", "data", ")", "break", "content", "=", "self", ".", "_decompress_data", "(", "content", ")", "if", "file", ":", "file", ".", "write", "(", "content", ")", "if", "file_is_async", ":", "yield", "from", "file", ".", "drain", "(", ")", "content", "=", "self", ".", "_flush_decompressor", "(", ")", "if", "file", ":", "file", ".", "write", "(", "content", ")", "if", "file_is_async", ":", "yield", "from", "file", ".", "drain", "(", ")", "trailer_data", "=", "yield", "from", "reader", ".", "read_trailer", "(", ")", "self", ".", "_data_event_dispatcher", ".", "notify_read", "(", "trailer_data", ")", "if", "file", "and", "raw", ":", "file", ".", "write", "(", "trailer_data", ")", "if", "file_is_async", ":", "yield", "from", "file", ".", "drain", "(", ")", "response", ".", "fields", ".", "parse", "(", "trailer_data", ")" ]
Build the state for this request .
async def _build_state ( self , request : Request , message : BaseMessage , responder : Responder ) -> Tuple [ Optional [ BaseState ] , Optional [ BaseTrigger ] , Optional [ bool ] , ] : trigger , state_class , dnr = await self . _find_trigger ( request ) if trigger is None : if not message . should_confuse ( ) : return None , None , None state_class = self . _confused_state ( request ) logger . debug ( 'Next state: %s (confused)' , state_class . name ( ) ) else : logger . debug ( 'Next state: %s' , state_class . name ( ) ) state = state_class ( request , responder , trigger , trigger ) return state , trigger , dnr
10,280
https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/fsm.py#L221-L245
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Execute the state or if execution fails handle it .
async def _run_state ( self , responder , state , trigger , request ) -> BaseState : user_trigger = trigger # noinspection PyBroadException try : if trigger : await state . handle ( ) else : await state . confused ( ) for i in range ( 0 , settings . MAX_INTERNAL_JUMPS + 1 ) : if i == settings . MAX_INTERNAL_JUMPS : raise MaxInternalJump ( ) trigger , state_class , dnr = await self . _find_trigger ( request , state . name ( ) , True ) if not trigger : break logger . debug ( 'Jumping to state: %s' , state_class . name ( ) ) state = state_class ( request , responder , trigger , user_trigger ) await state . handle ( ) except Exception : logger . exception ( 'Error while handling state "%s"' , state . name ( ) ) responder . clear ( ) reporter . report ( request , state . name ( ) ) await state . error ( ) return state
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https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/fsm.py#L247-L281
[ "def", "set_descriptor", "(", "dev", ",", "desc", ",", "desc_type", ",", "desc_index", ",", "wIndex", "=", "None", ")", ":", "wValue", "=", "desc_index", "|", "(", "desc_type", "<<", "8", ")", "bmRequestType", "=", "util", ".", "build_request_type", "(", "util", ".", "CTRL_OUT", ",", "util", ".", "CTRL_TYPE_STANDARD", ",", "util", ".", "CTRL_RECIPIENT_DEVICE", ")", "dev", ".", "ctrl_transfer", "(", "bmRequestType", "=", "bmRequestType", ",", "bRequest", "=", "0x07", ",", "wValue", "=", "wValue", ",", "wIndex", "=", "wIndex", ",", "data_or_wLength", "=", "desc", ")" ]
Build the next register to store .
async def _build_state_register ( self , state : BaseState , request : Request , responder : Responder ) -> Dict : return { Register . STATE : state . name ( ) , Register . TRANSITION : await responder . make_transition_register ( request ) , }
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https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/engine/fsm.py#L283-L299
[ "def", "files_comments_delete", "(", "self", ",", "*", ",", "file", ":", "str", ",", "id", ":", "str", ",", "*", "*", "kwargs", ")", "->", "SlackResponse", ":", "kwargs", ".", "update", "(", "{", "\"file\"", ":", "file", ",", "\"id\"", ":", "id", "}", ")", "return", "self", ".", "api_call", "(", "\"files.comments.delete\"", ",", "json", "=", "kwargs", ")" ]
runGetResults - Simple method to run a command and return the results of the execution as a dict .
def runGetResults ( cmd , stdout = True , stderr = True , encoding = sys . getdefaultencoding ( ) ) : if stderr in ( 'stdout' , subprocess . STDOUT ) : stderr = subprocess . STDOUT elif stderr == True or stderr == subprocess . PIPE : stderr = subprocess . PIPE else : stderr = None if stdout == True or stdout == subprocess . STDOUT : stdout = subprocess . PIPE else : stdout = None if stderr == subprocess . PIPE : raise ValueError ( 'Cannot redirect stderr to stdout if stdout is not captured.' ) if issubclass ( cmd . __class__ , ( list , tuple ) ) : shell = False else : shell = True try : pipe = subprocess . Popen ( cmd , stdout = stdout , stderr = stderr , shell = shell ) except Exception as e : try : if shell is True : cmdStr = ' ' . join ( cmd ) else : cmdStr = cmd except : cmdStr = repr ( cmd ) raise SimpleCommandFailure ( 'Failed to execute "%s": %s' % ( cmdStr , str ( e ) ) , returnCode = 255 ) streams = [ ] fileNoToKey = { } ret = { } if stdout == subprocess . PIPE : streams . append ( pipe . stdout ) fileNoToKey [ pipe . stdout . fileno ( ) ] = 'stdout' ret [ 'stdout' ] = [ ] if stderr == subprocess . PIPE : streams . append ( pipe . stderr ) fileNoToKey [ pipe . stderr . fileno ( ) ] = 'stderr' ret [ 'stderr' ] = [ ] returnCode = None time . sleep ( .02 ) while returnCode is None or streams : returnCode = pipe . poll ( ) while True : ( readyToRead , junk1 , junk2 ) = select . select ( streams , [ ] , [ ] , .005 ) if not readyToRead : # Don't strangle CPU time . sleep ( .01 ) break for readyStream in readyToRead : retKey = fileNoToKey [ readyStream . fileno ( ) ] curRead = readyStream . read ( ) if curRead in ( b'' , '' ) : streams . remove ( readyStream ) continue ret [ retKey ] . append ( curRead ) for key in list ( ret . keys ( ) ) : ret [ key ] = b'' . join ( ret [ key ] ) if encoding : ret [ key ] = ret [ key ] . decode ( encoding ) ret [ 'returnCode' ] = returnCode return ret
10,283
https://github.com/kata198/python-subprocess2/blob/8544b0b651d8e14de9fdd597baa704182e248b01/subprocess2/simple.py#L31-L144
[ "def", "build_synchronize_decorator", "(", ")", ":", "lock", "=", "threading", ".", "Lock", "(", ")", "def", "lock_decorator", "(", "fn", ")", ":", "@", "functools", ".", "wraps", "(", "fn", ")", "def", "lock_decorated", "(", "*", "args", ",", "*", "*", "kwargs", ")", ":", "with", "lock", ":", "return", "fn", "(", "*", "args", ",", "*", "*", "kwargs", ")", "return", "lock_decorated", "return", "lock_decorator" ]
Create a context store . By default using the default configured context store but you can use a custom class if you want to using the store setting .
def create_context_store ( name = 'default' , ttl = settings . CONTEXT_DEFAULT_TTL , store = settings . CONTEXT_STORE ) -> 'BaseContextStore' : store_class = import_class ( store [ 'class' ] ) return store_class ( name = name , ttl = ttl , * * store [ 'params' ] )
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https://github.com/BernardFW/bernard/blob/9c55703e5ffe5717c9fa39793df59dbfa5b4c5ab/src/bernard/storage/context/base.py#L34-L68
[ "def", "handle_input", "(", "self", ")", ":", "difference", "=", "self", ".", "check_state", "(", ")", "if", "not", "difference", ":", "return", "self", ".", "events", "=", "[", "]", "self", ".", "handle_new_events", "(", "difference", ")", "self", ".", "update_timeval", "(", ")", "self", ".", "events", ".", "append", "(", "self", ".", "sync_marker", "(", "self", ".", "timeval", ")", ")", "self", ".", "write_to_pipe", "(", "self", ".", "events", ")" ]
Return text in camelCase style .
def camelcase ( text , acronyms = None ) : words , _case , _sep = case_parse . parse_case ( text , acronyms ) if words : words [ 0 ] = words [ 0 ] . lower ( ) return '' . join ( words )
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https://github.com/AlejandroFrias/case-conversion/blob/79ebce1403fbdac949b2da21b8f6fbe3234ddb31/case_conversion/case_conversion.py#L13-L29
[ "def", "point_lm", "(", "self", ",", "context", ")", ":", "lm", "=", "np", ".", "empty", "(", "context", ".", "shape", ",", "context", ".", "dtype", ")", "# Print the array schema", "montblanc", ".", "log", ".", "info", "(", "context", ".", "array_schema", ".", "shape", ")", "# Print the space of iteration", "montblanc", ".", "log", ".", "info", "(", "context", ".", "iter_args", ")", "(", "ls", ",", "us", ")", "=", "context", ".", "dim_extents", "(", "'npsrc'", ")", "lm", "[", ":", ",", "0", "]", "=", "0.0008", "lm", "[", ":", ",", "1", "]", "=", "0.0036", "lm", "[", ":", ",", ":", "]", "=", "0", "return", "lm" ]
Return text in dot . case style .
def dotcase ( text , acronyms = None ) : words , _case , _sep = case_parse . parse_case ( text , acronyms ) return '.' . join ( [ w . lower ( ) for w in words ] )
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https://github.com/AlejandroFrias/case-conversion/blob/79ebce1403fbdac949b2da21b8f6fbe3234ddb31/case_conversion/case_conversion.py#L148-L162
[ "def", "detach_storage", "(", "self", ",", "server", ",", "address", ")", ":", "body", "=", "{", "'storage_device'", ":", "{", "'address'", ":", "address", "}", "}", "url", "=", "'/server/{0}/storage/detach'", ".", "format", "(", "server", ")", "res", "=", "self", ".", "post_request", "(", "url", ",", "body", ")", "return", "Storage", ".", "_create_storage_objs", "(", "res", "[", "'server'", "]", "[", "'storage_devices'", "]", ",", "cloud_manager", "=", "self", ")" ]
Return text in seperate words style .
def separate_words ( text , acronyms = None ) : words , _case , _sep = case_parse . parse_case ( text , acronyms , preserve_case = True ) return ' ' . join ( words )
10,287
https://github.com/AlejandroFrias/case-conversion/blob/79ebce1403fbdac949b2da21b8f6fbe3234ddb31/case_conversion/case_conversion.py#L165-L179
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Initialize the DB .
def init_db ( ) : import reana_db . models if not database_exists ( engine . url ) : create_database ( engine . url ) Base . metadata . create_all ( bind = engine )
10,288
https://github.com/reanahub/reana-db/blob/4efcb46d23af035689964d8c25a804c5a8f1dfc3/reana_db/database.py#L28-L33
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Read in the significant pathways file as a pandas . DataFrame .
def _load_significant_pathways_file ( path_to_file ) : feature_pathway_df = pd . read_table ( path_to_file , header = 0 , usecols = [ "feature" , "side" , "pathway" ] ) feature_pathway_df = feature_pathway_df . sort_values ( by = [ "feature" , "side" ] ) return feature_pathway_df
10,289
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L552-L561
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Permute the pathways across features for one side in the network . Used in permute_pathways_across_features
def _pathway_feature_permutation ( pathway_feature_tuples , permutation_max_iters ) : pathways , features = [ list ( elements_at_position ) for elements_at_position in zip ( * pathway_feature_tuples ) ] original_pathways = pathways [ : ] random . shuffle ( pathways ) feature_block_locations = { } i = 0 while i < len ( pathways ) : starting_index = i current_feature = features [ i ] pathway_set = set ( ) # input is grouped by feature, so we want to keep track of the start # and end of a given "block" of the same feature--this corresponds # to all the pathways overrepresented in that feature. while i < len ( pathways ) and features [ i ] == current_feature : # check the results of the permutation. if `pathway_set` does # not contain the current pathway, we are maintaining the # necessary invariants in our permutation thus far. if pathways [ i ] not in pathway_set : pathway_set . add ( pathways [ i ] ) else : k = 0 random_pathway = None while True : # select another random pathway from the list # and get the feature to which it belongs j = random . choice ( range ( 0 , len ( pathways ) ) ) random_pathway = pathways [ j ] random_feature = features [ j ] if ( random_pathway != pathways [ i ] and random_pathway not in pathway_set ) : # if this is a feature we have not already seen, # we are done. if random_feature not in feature_block_locations : break # otherwise, look at the indices that correspond # to that feature's block of pathways feature_block_start , feature_block_end = feature_block_locations [ random_feature ] pathway_block = pathways [ feature_block_start : feature_block_end ] # make sure that the current pathway is not in # that block--ensures that we maintain the invariant # after the swap if pathways [ i ] not in pathway_block : break k += 1 if k > permutation_max_iters : print ( "Permutation step: reached the maximum " "number of iterations {0}." . format ( permutation_max_iters ) ) return None pathway_set . add ( random_pathway ) pathways [ j ] = pathways [ i ] pathways [ i ] = random_pathway i += 1 ending_index = i feature_block_locations [ current_feature ] = ( starting_index , ending_index ) if original_pathways == pathways : return None return list ( zip ( pathways , features ) )
10,290
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L568-L652
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Applied during the permutation test . Update the edges in the network to be weighted by their odds ratios . The odds ratio measures how unexpected the observed edge weight is based on the expected weight .
def weight_by_edge_odds_ratios ( self , edges_expected_weight , flag_as_significant ) : for edge_id , expected_weight in edges_expected_weight : edge_obj = self . edges [ edge_id ] edge_obj . weight /= expected_weight if edge_id in flag_as_significant : edge_obj . significant = True else : edge_obj . significant = False
10,291
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L223-L247
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Combine this network with another network . The aggregation step takes the union of the edges in the two networks where we take the sum of weights for edges common to both networks .
def aggregate ( self , merge ) : self . features = set ( ) self . n_features += merge . n_features vertex_id_conversion = self . convert_pathway_mapping ( merge . pathways ) for edge_id , edge in merge . edges . items ( ) : edge_key = self . remapped_edge ( vertex_id_conversion , edge_id ) if edge_key in self . edges : if self . edges [ edge_key ] . which_features : self . edges [ edge_key ] . which_features = [ ] self . edges [ edge_key ] . weight += edge . weight else : vertex0_id , vertex1_id = edge_key new_edge_obj = Edge ( vertex0_id , vertex1_id , [ ] ) new_edge_obj . weight = edge . weight self . edges [ edge_key ] = new_edge_obj self . _add_edge_to_vertex ( vertex0_id , new_edge_obj ) self . _add_edge_to_vertex ( vertex1_id , new_edge_obj )
10,292
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L249-L276
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To avoid duplicate edges where the vertex ids are reversed we maintain that the vertex ids are ordered so that the corresponding pathway names are alphabetical .
def edge_tuple ( self , vertex0_id , vertex1_id ) : pw0 = self . __getitem__ ( vertex0_id ) pw1 = self . __getitem__ ( vertex1_id ) if not pw0 or not pw1 : return None if pw0 < pw1 : return ( vertex0_id , vertex1_id ) elif pw0 > pw1 : return ( vertex1_id , vertex0_id ) else : return None
10,293
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L332-L360
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Updates self . pathways and self . n_pathways .
def add_pathway ( self , pathway ) : if pathway not in self . pathways : self . pathways [ pathway ] = self . n_pathways self . n_pathways += 1 return self . pathways [ pathway ]
10,294
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L362-L373
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Get the pathways associated with an edge .
def get_edge_pathways ( self , edge_id ) : vertex0_id , vertex1_id = edge_id pw0 = self . get_pathway_from_vertex_id ( vertex0_id ) pw1 = self . get_pathway_from_vertex_id ( vertex1_id ) if not pw0 or not pw1 : return None return ( pw0 , pw1 )
10,295
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L388-L405
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Get the vertex object that corresponds to a pathway name
def get_vertex_obj_from_pathway ( self , pathway ) : if pathway in self . pathways : vertex_id = self . pathways [ pathway ] return self . vertices [ vertex_id ] else : return None
10,296
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L422-L437
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Get the pathways adjacent to this pathway in the network
def get_adjacent_pathways ( self , pathway ) : vertex_id = self . pathways [ pathway ] adjacent = self . vertices [ vertex_id ] . get_adjacent_vertex_ids ( ) adjacent_pathways = [ ] for adjacent_id in adjacent : adjacent_pathways . append ( self . get_pathway_from_vertex_id ( adjacent_id ) ) return adjacent_pathways
10,297
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L439-L456
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Conversion of the network to a pandas . DataFrame .
def to_dataframe ( self , drop_weights_below = 0 , whitelist = None ) : network_df_cols = [ "pw0" , "pw1" , "weight" ] if self . features : network_df_cols . append ( "features" ) network_df = pd . DataFrame ( columns = network_df_cols ) idx = 0 edge_pathways = set ( ) for ( v0 , v1 ) , edge_obj in self . edges . items ( ) : if ( edge_obj . weight > drop_weights_below and ( whitelist is None or ( v0 , v1 ) in whitelist ) ) : row = [ self . __getitem__ ( v0 ) , self . __getitem__ ( v1 ) , edge_obj . weight ] edge_pathways . add ( v0 ) edge_pathways . add ( v1 ) if self . features : features = edge_obj . features_to_string ( ) row . append ( features ) network_df . loc [ idx ] = row idx += 1 # faster to append by index. network_df = network_df . sort_values ( by = [ "weight" ] , ascending = False ) print ( "The pathway co-occurrence network " "contains {0} pathways." . format ( len ( edge_pathways ) ) ) return network_df
10,298
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L458-L501
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Adds the edge to the Vertex object s edges dictionary
def _add_edge_to_vertex ( self , vertex_id , edge ) : connected_to = edge . connected_to ( vertex_id ) if vertex_id not in self . vertices : vertex_obj = Vertex ( vertex_id ) self . vertices [ vertex_id ] = vertex_obj self . vertices [ vertex_id ] . edges [ connected_to ] = edge . weight
10,299
https://github.com/greenelab/PathCORE-T/blob/9d079d5ebffea2fe9fb9ab557588d51ad67d2c9c/pathcore/network.py#L503-L510
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