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def build_list_type_validator(item_validator): """Return a function which validates that the value is a list of items which are validated using item_validator. """ def validate_list_of_type(value): return [item_validator(item) for item in validate_list(value)] return validate_list_of_type
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def prepare_untran(feat_type, tgt_dir, untran_dir): """ Preprocesses untranscribed audio.""" org_dir = str(untran_dir) wav_dir = os.path.join(str(tgt_dir), "wav", "untranscribed") feat_dir = os.path.join(str(tgt_dir), "feat", "untranscribed") if not os.path.isdir(wav_dir): os.makedirs(wav_di...
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def randomString(size: int = 20, chars: str = string.ascii_letters + string.digits) -> str: """ Generate a random string of the specified size. Ensure that the size is less than the length of chars as this function uses random.choice which uses random sampling without replacement. ...
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def remove(self, id_option_vip): """Remove Option VIP from by the identifier. :param id_option_vip: Identifier of the Option VIP. Integer value and greater than zero. :return: None :raise InvalidParameterError: Option VIP identifier is null and invalid. :raise OptionVipNotFoun...
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def get_stats(self): """Return a string describing the stats""" ostr = '' errtotal = self.deletions['total']+self.insertions['total']+self.mismatches ostr += "ALIGNMENT_COUNT\t"+str(self.alignment_count)+"\n" ostr += "ALIGNMENT_BASES\t"+str(self.alignment_length)+"\n" ostr += "ANY_ERROR\t"+str(e...
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def _process_current(self, handle, op, dest_path=None, dest_name=None): """Process current member with 'op' operation.""" unrarlib.RARProcessFileW(handle, op, dest_path, dest_name)
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def attach(self, lun_or_snap, skip_hlu_0=False): """ Attaches lun, snap or member snap of cg snap to host. Don't pass cg snapshot in as `lun_or_snap`. :param lun_or_snap: the lun, snap, or a member snap of cg snap :param skip_hlu_0: whether to skip hlu 0 :return: the hlu number...
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def document(schema): """Print a documented teleport version of the schema.""" teleport_schema = from_val(schema) return json.dumps(teleport_schema, sort_keys=True, indent=2)
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def symbolic_run_get_cons(trace): ''' Execute a symbolic run that follows a concrete run; return constraints generated and the stdin data produced ''' m2 = Manticore.linux(prog, workspace_url='mem:') f = Follower(trace) m2.verbosity(VERBOSITY) m2.register_plugin(f) def on_term_test...
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def add_experiences(self, curr_all_info: AllBrainInfo, next_all_info: AllBrainInfo, take_action_outputs): """ Adds experiences to each agent's experience history. :param curr_all_info: Dictionary of all current brains and corresponding BrainInfo. :param next_all_info: Dictionary of all c...
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def get_map_values(self, lons, lats, ibin=None): """Return the map values corresponding to a set of coordinates. Parameters ---------- lons : array-like 'Longitudes' (RA or GLON) lats : array-like 'Latitidues' (DEC or GLAT) ibin : int or array-l...
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def free(host, port, timeout=float('Inf')): """ Wait for the specified port to become free (dropping or rejecting requests). Return when the port is free or raise a Timeout if timeout has elapsed. Timeout may be specified in seconds or as a timedelta. If timeout is None or ∞, the routine will run indefinitely. ...
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def status(self, vm_name=None): ''' Return the results of a `vagrant status` call as a list of one or more Status objects. A Status contains the following attributes: - name: The VM name in a multi-vm environment. 'default' otherwise. - state: The state of the underlying guest...
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def prepare_blacklist(src, dst, duration=3600, src_port1=None, src_port2=None, src_proto='predefined_tcp', dst_port1=None, dst_port2=None, dst_proto='predefined_tcp'): """ Create a blacklist entry. A blacklist can be added directly from...
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async def set( self, key, value, ttl=SENTINEL, dumps_fn=None, namespace=None, _cas_token=None, _conn=None ): """ Stores the value in the given key with ttl if specified :param key: str :param value: obj :param ttl: int the expiration time in seconds. Due to memcached...
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def get_assignment_group(self, course_id, assignment_group_id, grading_period_id=None, include=None, override_assignment_dates=None): """ Get an Assignment Group. Returns the assignment group with the given id. """ path = {} data = {} params = {} ...
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def flp_nonlinear_mselect(I,J,d,M,f,c,K): """flp_nonlinear_mselect -- use multiple selection model Parameters: - I: set of customers - J: set of facilities - d[i]: demand for customer i - M[j]: capacity of facility j - f[j]: fixed cost for using a facility in point j ...
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def parse(self, instrs): """Parse an IR instruction. """ instrs_reil = [] try: for instr in instrs: instr_lower = instr.lower() # If the instruction to parsed is not in the cache, # parse it and add it to the cache. ...
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def name_insert_prefix(records, prefix): """ Given a set of sequences, insert a prefix for each sequence's name. """ logging.info('Applying _name_insert_prefix generator: ' 'Inserting prefix ' + prefix + ' for all ' 'sequence IDs.') for record in records: ne...
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def createSQL(self, sql, args=()): """ For use with auto-committing statements such as CREATE TABLE or CREATE INDEX. """ before = time.time() self._execSQL(sql, args) after = time.time() if after - before > 2.0: log.msg('Extremely long CREATE: ...
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def _CreateTaskStorageWriter(self, path, task): """Creates a task storage writer. Args: path (str): path to the storage file. task (Task): task. Returns: SQLiteStorageFileWriter: storage writer. """ return SQLiteStorageFileWriter( self._session, path, storage_type...
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def unpack(s): """Unpack a MXImageRecord to string. Parameters ---------- s : str String buffer from ``MXRecordIO.read``. Returns ------- header : IRHeader Header of the image record. s : str Unpacked string. Examples -------- >>> record = mx.record...
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def start_centroid_distance(item_a, item_b, max_value): """ Distance between the centroids of the first step in each object. Args: item_a: STObject from the first set in TrackMatcher item_b: STObject from the second set in TrackMatcher max_value: Maximum distance value used as scali...
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def asnumpy(self): """Returns a ``numpy.ndarray`` object with value copied from this array. Examples -------- >>> x = mx.nd.ones((2,3)) >>> y = x.asnumpy() >>> type(y) <type 'numpy.ndarray'> >>> y array([[ 1., 1., 1.], [ 1., 1., ...
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def stage_signature(vcs, signature): """Add `signature` to the list of staged signatures Args: vcs (easyci.vcs.base.Vcs) signature (basestring) Raises: AlreadyStagedError """ evidence_path = _get_staged_history_path(vcs) staged = get_staged_signatures(vcs) if signat...
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def stop(self): """ Stop ZMQ tools. :return: self """ LOGGER.debug("zeromq.Driver.stop") for publisher in self.publishers_registry: publisher.stop() self.publishers_registry.clear() for subscriber in self.subscribers_registry: if su...
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def get_smtp_mail(self): """ Returns the SMTP formatted email, as it may be passed to sendmail. :rtype: string :return: The SMTP formatted mail. """ header = self.get_smtp_header() body = self.get_body().replace('\n', '\r\n') return header + '\r\n' + bod...
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def from_string(cls, s): """Instantiate Relations from a relations string.""" tables = [] seen = set() current_table = None lines = list(reversed(s.splitlines())) # to pop() in right order while lines: line = lines.pop().strip() table_m = re.match...
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def parse_netmhcpan28_stdout( stdout, prediction_method_name="netmhcpan", sequence_key_mapping=None): """ # Affinity Threshold for Strong binding peptides 50.000', # Affinity Threshold for Weak binding peptides 500.000', # Rank Threshold for Strong binding peptides 0.500', ...
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def get_transactions_filtered(self, asset_id, operation=None): """Get a list of transactions filtered on some criteria """ txids = backend.query.get_txids_filtered(self.connection, asset_id, operation) for txid in txids: yield ...
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def list_available_devices(): """ List all available devices for the respective backend returns: devices: a list of dictionaries with the keys 'identifier' and 'instance': \ [ {'identifier': 'usb://0x04f9:0x2015/C5Z315686', 'instance': pyusb.core.Device()}, ] The 'identifier' is of the form...
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def default_instruction_to_svg_dict(self, instruction): """Returns an xml-dictionary with the same content as :meth:`default_instruction_to_svg` If no file ``default.svg`` was loaded, an empty svg-dict is returned. """ instruction_type = instruction.type default_type = "...
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def make_flow_labels(graph, flow, capac): """Generate arc labels for a flow in a graph with capacities. :param graph: adjacency list or adjacency dictionary :param flow: flow matrix or adjacency dictionary :param capac: capacity matrix or adjacency dictionary :returns: listdic graph representation...
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def _handle_double_click(self, event): """ Double click with left mouse button focuses the state and toggles the collapse status""" if event.get_button()[1] == 1: # Left mouse button path_info = self.tree_view.get_path_at_pos(int(event.x), int(event.y)) if path_info: # Valid en...
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def quote_identifier(identifier: str, mixed: Union[SQLCompiler, Engine, Dialect]) -> str: """ Converts an SQL identifier to a quoted version, via the SQL dialect in use. Args: identifier: the identifier to be quoted mixed: an SQLAlchemy :class:`SQLCompiler`, :class:...
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def write(self, content): """Save content on disk""" with io.open(self.target, 'w', encoding='utf-8') as fp: fp.write(content) if not content.endswith(u'\n'): fp.write(u'\n')
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def run(cmd, background=False): """ Executes the given command If background flag is True the command will run in background and this method will return a :class:`Popen` object If background is False (default) the command will run in this thread and this method will return stdout. A Comma...
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def rm_corr(data=None, x=None, y=None, subject=None, tail='two-sided'): """Repeated measures correlation. Parameters ---------- data : pd.DataFrame Dataframe. x, y : string Name of columns in ``data`` containing the two dependent variables. subject : string Name of colum...
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def confirm(pid, record, template, **kwargs): """Confirm email address.""" recid = int(pid.pid_value) token = request.view_args['token'] # Validate token data = EmailConfirmationSerializer.compat_validate_token(token) if data is None: flash(_("Invalid confirmation link."), category='da...
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def get_col_rgba(color, transparency=None, opacity=None): """This class converts a Gdk.Color into its r, g, b parts and adds an alpha according to needs If both transparency and opacity is None, alpha is set to 1 => opaque :param Gdk.Color color: Color to extract r, g and b from :param float | None t...
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def ui_clear_clicked_image(self, value): """ Setter for **self.__ui_clear_clicked_image** attribute. :param value: Attribute value. :type value: unicode """ if value is not None: assert type(value) is unicode, "'{0}' attribute: '{1}' type is not 'unicode'!"....
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def transformer(self): """ Creates the internal transformer that maps the cluster center's high dimensional space to its two dimensional space. """ ttype = self.embedding.lower() # transformer method type if ttype == 'mds': return MDS(n_components=2, random_s...
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def get_uri_obj(uri, storage_args={}): """ Retrieve the underlying storage object based on the URI (i.e., scheme). :param str uri: URI to get storage object for :param dict storage_args: Keyword arguments to pass to the underlying storage object """ if isinstance(uri, BaseURI): return uri ...
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def weights_to_cpu(state_dict): """Copy a model state_dict to cpu. Args: state_dict (OrderedDict): Model weights on GPU. Returns: OrderedDict: Model weights on GPU. """ state_dict_cpu = OrderedDict() for key, val in state_dict.items(): state_dict_cpu[key] = val.cpu() ...
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def magic_session(db_session=None, url=None): """Either does nothing with the session you already have or makes one that commits and closes no matter what happens """ if db_session is not None: yield db_session else: session = get_session(url, expire_on_commit=False) try: ...
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def calc_pvalues(query, gene_sets, background=20000, **kwargs): """ calculate pvalues for all categories in the graph :param set query: set of identifiers for which the p value is calculated :param dict gene_sets: gmt file dict after background was set :param set background: total number of genes in yo...
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def handle_button(self, event, event_type): """Convert the button information from quartz into evdev format.""" # 0 for left # 1 for right # 2 for middle/center # 3 for side mouse_button_number = self._get_mouse_button_number(event) # Identify buttons 3,4,5 ...
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def list_lbaas_pools(self, retrieve_all=True, **_params): """Fetches a list of all lbaas_pools for a project.""" return self.list('pools', self.lbaas_pools_path, retrieve_all, **_params)
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def appendSpacePadding(str, blocksize=AES_blocksize): 'Pad with spaces' pad_len = paddingLength(len(str), blocksize) padding = '\0'*pad_len return str + padding
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def submitted_projects(raw_df): """ Return all submitted projects. """ df = raw_df.astype({'PRONAC': str, 'CgcCpf': str}) submitted_projects = df.groupby('CgcCpf')[ 'PRONAC' ].agg(['unique', 'nunique']) submitted_projects.columns = ['pronac_list', 'num_pronacs'] return submitte...
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def example_delete_topics(a, topics): """ delete topics """ # Call delete_topics to asynchronously delete topics, a future is returned. # By default this operation on the broker returns immediately while # topics are deleted in the background. But here we give it some time (30s) # to propagate in t...
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def exists_uda(self, name, database=None): """ Checks if a given UDAF exists within a specified database Parameters ---------- name : string, UDAF name database : string, database name Returns ------- if_exists : boolean """ retur...
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def get_global_config_dir(): """Returns global config location. E.g. ~/.config/dvc/config. Returns: str: path to the global config directory. """ from appdirs import user_config_dir return user_config_dir( appname=Config.APPNAME, appauthor=Config.APPAUTH...
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def _or_join(self, close_group=False): """Combine terms with OR. There must be a term added before using this method. Arguments: close_group (bool): If ``True``, will end the current group and start a new one. If ``False``, will continue current group. ...
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def _authorization_header(cls, credentials): """ Creates authorization headers if the provider supports it. See: http://en.wikipedia.org/wiki/Basic_access_authentication. :param credentials: :class:`.Credentials` :returns: Headers as :class:`dict`. ...
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def add_directory(self, relativePath, description=None, clean=False, raiseError=True, ntrials=3): """ Add a directory in the repository and creates its attribute in the Repository with utc timestamp. It insures adding all the missing directories in the path. ...
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def run_task(self, task_name, **options): """ Runs a named CumulusCI task for the current project with optional support for overriding task options via kwargs. Examples: | =Keyword= | =task_name= | =task_options= | =comment= | |...
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def _onCompletionListItemSelected(self, index): """Item selected. Insert completion to editor """ model = self._widget.model() selectedWord = model.words[index] textToInsert = selectedWord[len(model.typedText()):] self._qpart.textCursor().insertText(textToInsert) ...
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def conf_as_dict(conf_filename, encoding=None, case_sensitive=False): """ 读入 ini 配置文件,返回根据配置文件内容生成的字典类型变量; :param: * conf_filename: (string) 需要读入的 ini 配置文件长文件名 * encoding: (string) 文件编码 * case_sensitive: (bool) 是否大小写敏感,默认为 False :return: * flag: (bool) 读取配置文件是否正确,正确返回 Tr...
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def getAtomic(rates, ver, lamb, br, reactfn): """ prompt atomic emissions (nm) 844.6 777.4 """ with h5py.File(reactfn, 'r') as f: lambnew = f['/atomic/lambda'].value.ravel(order='F') # some are not 1-D! vnew = np.concatenate((rates.loc[..., 'po3p3p'].values[..., None], ...
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def extract(self, msg): """Yield an ordered dictionary if msg['type'] is in keys_by_type.""" def normal(key): v = msg.get(key) if v is None: return v normalizer = self.normalizers.get(key, lambda x: x) return normalizer(v) def odic...
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def dvds_new_releases(self, **kwargs): """Gets the upcoming movies from the API. Args: page_limit (optional): number of movies to show per page, default=16 page (optional): results page number, default=1 country (optional): localized data for selected country, default="us"...
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def run_epoch(self, epoch_info: EpochInfo, source: 'vel.api.Source'): """ Run full epoch of learning """ epoch_info.on_epoch_begin() lr = epoch_info.optimizer.param_groups[-1]['lr'] print("|-------- Epoch {:06} Lr={:.6f} ----------|".format(epoch_info.global_epoch_idx, lr)) sel...
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def quote_header_value(value, extra_chars='', allow_token=True): """Quote a header value if necessary. :param value: the value to quote. :param extra_chars: a list of extra characters to skip quoting. :param allow_token: if this is enabled token values are returned unchanged. """ value ...
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def _get_flat_db_sources(self, model): """ Return a flattened representation of the individual ``sources`` lists. """ sources = [] for source in self.sources: for sub_source in self.expand_source(source): target_field = self.resolve_source(model, sub_source) ...
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def create_stash(self, payload, path=None): """ Create a stash. (JSON document) """ if path: self._request('POST', '/stashes/{}'.format(path), json=payload) else: self._request('POST', '/stashes', json=payload) return True
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def all_agents(stmts): """Return a list of all of the agents from a list of statements. Only agents that are not None and have a TEXT entry are returned. Parameters ---------- stmts : list of :py:class:`indra.statements.Statement` Returns ------- agents : list of :py:class:`indra.stat...
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def save(self, info): """ Handles saving the current model to the last file. """ save_file = self.save_file if not isfile(save_file): self.save_as(info) else: fd = None try: fd = open(save_file, "wb") dot_code =...
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def resolve_include(self, t): """Resolve a tuple-ized #include line. This handles recursive expansion of values without "" or <> surrounding the name until an initial " or < is found, to handle #include FILE where FILE is a #define somewhere else.""" s = t[1] ...
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def attach_volume(self, xml_bytes): """Parse the XML returned by the C{AttachVolume} function. @param xml_bytes: XML bytes with a C{AttachVolumeResponse} root element. @return: a C{dict} with status and attach_time keys. TODO: volumeId, instanceId, device """ ...
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def _AsList(arg): """Encapsulates an argument in a list, if it's not already iterable.""" if (isinstance(arg, string_types) or not isinstance(arg, collections.Iterable)): return [arg] else: return list(arg)
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def iter_parsed_values(self, field: Field) -> Iterable[Tuple[str, Any]]: """ Walk the dictionary of parsers and emit all non-null values. """ for key, func in self.parsers.items(): value = func(field) if not value: continue yield key, ...
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def query_tissue_specificity(): """ Returns list of tissue specificity by query parameters --- tags: - Query functions parameters: - name: comment in: query type: string required: false description: Comment to tissue specificity default: '%APP6...
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def _parse_resource(resource): """ Parses and completes resource information """ resource = resource.strip() if resource else resource if resource in {ME_RESOURCE, USERS_RESOURCE}: return resource elif '@' in resource and not resource.startswith(USERS_RESOURCE): #...
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def load_json(json_file, **kwargs): """ Open and load data from a JSON file .. code:: python reusables.load_json("example.json") # {u'key_1': u'val_1', u'key_for_dict': {u'sub_dict_key': 8}} :param json_file: Path to JSON file as string :param kwargs: Additional arguments for the ...
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def GetSummary(self): """Gets a client summary object. Returns: rdf_client.ClientSummary Raises: ValueError: on bad cloud type """ summary = rdf_client.ClientSummary() summary.client_id = self.client_id summary.timestamp = self.timestamp summary.system_info.release = self.o...
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def create_framework( bundles, properties=None, auto_start=False, wait_for_stop=False, auto_delete=False, ): # type: (Union[list, tuple], dict, bool, bool, bool) -> Framework """ Creates a Pelix framework, installs the given bundles and returns its instance reference. If *auto_st...
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def exponential(x, y, xscale, yscale): """ Two-dimensional oriented exponential decay pattern. """ if xscale==0.0 or yscale==0.0: return x*0.0 with float_error_ignore(): x_w = np.divide(x,xscale) y_h = np.divide(y,yscale) return np.exp(-np.sqrt(x_w*x_w+y_h*y_h))
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def do_photometry(self): """ Does photometry and estimates uncertainties by calculating the scatter around a linear fit to the data in each orientation. This function is called by other functions and generally the user will not need to interact with it directly. """ ...
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def get_subgraphs_by_annotation(graph, annotation, sentinel=None): """Stratify the given graph into sub-graphs based on the values for edges' annotations. :param pybel.BELGraph graph: A BEL graph :param str annotation: The annotation to group by :param Optional[str] sentinel: The value to stick unannot...
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def add_factors(self, *factors): """ Associate a factor to the graph. See factors class for the order of potential values Parameters ---------- *factor: pgmpy.factors.factors object A factor object on any subset of the variables of the model which ...
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def write_path(target, path, value, separator='/'): """Write a value deep into a dict building any intermediate keys. :param target: a dict to write data to :param path: a key or path to a key (path is delimited by `separator`) :param value: the value to write to the key :keyword separator: the sep...
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def update_user(self, user_is_artist="", artist_level="", artist_specialty="", real_name="", tagline="", countryid="", website="", bio=""): """Update the users profile information :param user_is_artist: Is the user an artist? :param artist_level: If the user is an artist, what level are they ...
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def evaluate_model(self, accuracy, num_steps, feed_vars=(), feed_data=None, summary_tag=None, print_every=0): """Evaluates the given model. Args: accuracy: The metric that is bein...
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def descendents(self, method=None, state=None): """ Find descendant tasks, optionally filtered by method and/or state. :param method: (optional) filter for tasks, eg. "buildArch". :param state: (optional) filter for tasks, eg. task_states.OPEN. :returns: deferred that when fired...
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def write_word(self, offset, word): """ .. _write_word: Writes one word from a device, see read_word_. """ self._lock = True if(offset > self.current_max_offset): raise BUSError("Offset({}) exceeds address space of BUS({})".format(offset, self.current_max_offset)) self.writes += 1 self.truncat...
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def find_message_handler(self, handler_name, handler_type='primary'): """Returns the MessageHandler given its name and type for this class.""" ret = lib.EnvFindDefmessageHandler( self._env, self._cls, handler_name.encode(), handler_type.encode()) if ret == 0: raise CLIPSE...
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def evaluated_variants(self, case_id): """Returns variants that has been evaluated Return all variants, snvs/indels and svs from case case_id which have a entry for 'acmg_classification', 'manual_rank', 'dismiss_variant' or if they are commented. Args: case_id(str) ...
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def join(self, _id): """ Join a room """ if not SockJSRoomHandler._room.has_key(self._gcls() + _id): SockJSRoomHandler._room[self._gcls() + _id] = set() SockJSRoomHandler._room[self._gcls() + _id].add(self)
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def simulate(): '''instantiate and execute network simulation''' #separate model execution from parameters for safe import from other files nest.ResetKernel() ''' Configuration of the simulation kernel by the previously defined time resolution used in the simulation. Setting "print_time" to Tru...
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def add_subsegment(self, subsegment): """ Add input subsegment as a child subsegment. """ self._check_ended() subsegment.parent_id = self.id self.subsegments.append(subsegment)
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def license(): ''' Print the Bokeh license to the console. Returns: None ''' from os.path import join with open(join(__path__[0], 'LICENSE.txt')) as lic: print(lic.read())
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def datasets_create_new(self, dataset_new_request, **kwargs): # noqa: E501 """Create a new dataset # noqa: E501 This method makes a synchronous HTTP request by default. To make an asynchronous HTTP request, please pass async_req=True >>> thread = api.datasets_create_new(dataset_new_re...
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def apply_to(self, A): """Apply the coordinate transformation to points in A. """ if A.ndim == 1: A = np.expand_dims(A, axis=0) rows, cols = A.shape A_new = np.hstack([A, np.ones((rows, 1))]) A_new = np.transpose(self.T.dot(np.transpose(A_new))) return A_new[...
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def update_from_stats(self, stats): """Update columns based on partition statistics""" sd = dict(stats) for c in self.columns: if c not in sd: continue stat = sd[c] if stat.size and stat.size > c.size: c.size = stat.size ...
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def save_cursor(self): """Push the current cursor position onto the stack.""" self.savepoints.append(Savepoint(copy.copy(self.cursor), self.g0_charset, self.g1_charset, self.charset...
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def get_channel_access_token(self, channel): """Return the token and sig for the given channel :param channel: the channel or channel name to get the access token for :type channel: :class:`channel` | :class:`str` :returns: The token and sig for the given channel :rtype: (:class...
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def authenticated(f): """Decorator that authenticates to Keystone automatically.""" @wraps(f) def new_f(self, *args, **kwargs): if not self.nova_client.client.auth_token: self.authenticate() return f(self, *args, **kwargs) return new_f
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def convert_errno(e): """ Convert an errno value (as from an ``OSError`` or ``IOError``) into a standard SFTP result code. This is a convenience function for trapping exceptions in server code and returning an appropriate result. :param int e: an errno code, as from ``OSError.e...
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def create_router(self, name, ext_network=None, admin_state_up=True): ''' Creates a new router ''' body = {'name': name, 'admin_state_up': admin_state_up} if ext_network: net_id = self._find_network_id(ext_network) body['external_gateway_in...
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