JorgeVB/code_unlearning_dataset · Data Studio

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Download file def download_file(url): """Download file""" response = requests.get(url, stream=True) fp = tempfile.NamedTemporaryFile() for chunk in response.iter_content(chunk_size=1024): if chunk: # filter out keep-alive new chunks fp.write(chunk) # log.info(f'Download file ...
Returns the first true value in the iterable. If no true value is found, returns default If pred is not None, returns the first item for which pred(item) is true. def first_true(iterable, default=False, pred=None): """Returns the first true value in the iterable. If no true value is found, r...
Create hash Id from edge record Args: edge (Mapping[str, Any]): edge record to create hash from Returns: str: Murmur3 128 bit hash def _create_hash_from_doc(doc: Mapping[str, Any]) -> str: """Create hash Id from edge record Args: edge (Mapping[str, Any]): edge record to creat...
Return the current elapsed time since start If the `elapsed` property is called in the context manager scope, the elapsed time bewteen start and property access is returned. However, if it is accessed outside of the context manager scope, it returns the elapsed time bewteen entering and ...
Load edges into Edgestore def load_edges_into_db( nanopub_id: str, nanopub_url: str, edges: list = [], edges_coll_name: str = edges_coll_name, nodes_coll_name: str = nodes_coll_name, ): """Load edges into Edgestore""" start_time = datetime.datetime.now() # Clean out edges for nanopub ...
Yield documents from edge for loading into ArangoDB def edge_iterator(edges=[], edges_fn=None): """Yield documents from edge for loading into ArangoDB""" for edge in itertools.chain(edges, files.read_edges(edges_fn)): subj = copy.deepcopy(edge["edge"]["subject"]) subj_id = str(utils._create_h...
Add nanopubstore start_dt to belapi.state_mgmt collection Args: url: url of nanopubstore start_dt: datetime of last query against nanopubstore for new ID's def update_nanopubstore_start_dt(url: str, start_dt: str): """Add nanopubstore start_dt to belapi.state_mgmt collection Args: ...
Get last start_dt recorded for getting new nanopub ID's def get_nanopubstore_start_dt(url: str): """Get last start_dt recorded for getting new nanopub ID's""" hostname = urllib.parse.urlsplit(url)[1] start_dates_doc = state_mgmt.get(start_dates_doc_key) if start_dates_doc and start_dates_doc.get("sta...
Get modified and deleted nanopub urls Limited by last datetime retrieved (start_dt). Modified includes new and updated nanopubs Returns: dict: {'modified': [], 'deleted': []} def get_nanopub_urls(ns_root_url: str = None, start_dt: str = None) -> dict: """Get modified and deleted nanopub urls ...
Get Nanopub from nanopubstore given url def get_nanopub(url): """Get Nanopub from nanopubstore given url""" r = bel.utils.get_url(url, cache=False) if r and r.json(): return r.json() else: return {}
BEL Pipeline - BEL Nanopubs into BEL Edges This will process BEL Nanopubs into BEL Edges by validating, orthologizing (if requested), canonicalizing, and then computing the BEL Edges based on the given rule_set. \b input_fn: If input fn has *.gz, will read as a gzip file If input fn ha...
Validate nanopubs def nanopub_validate(ctx, input_fn, output_fn, api, config_fn): """Validate nanopubs""" if config_fn: config = bel.db.Config.merge_config(ctx.config, override_config_fn=config_fn) else: config = ctx.config api = utils.first_true( [api, config["bel_api"]["serv...
Convert belscript to nanopubs_bel format This will convert the OpenBEL BELScript file format to nanopub_bel-1.0.0 format. \b input_fn: If input fn has .gz, will read as a gzip file \b output_fn: If output fn has .gz, will written as a gzip file If output fn has *.jso...
Reformat between JSON, YAML, JSONLines formats \b input_fn: If input fn has .gz, will read as a gzip file \b output_fn: If output fn has .gz, will written as a gzip file If output fn has .jsonl, will written as a JSONLines file IF output fn has .json, will be writ...
Collect statistics on nanopub file input_fn can be json, jsonl or yaml and additionally gzipped def nanopub_stats(ctx, input_fn): """Collect statistics on nanopub file input_fn can be json, jsonl or yaml and additionally gzipped """ counts = { "nanopubs": 0, "assertions": {"total...
Canonicalize statement Target namespaces can be provided in the following manner: bel stmt canonicalize "<BELStmt>" --namespace_targets '{"HGNC": ["EG", "SP"], "CHEMBL": ["CHEBI"]}' the value of target_namespaces must be JSON and embedded in single quotes reserving double quotes fo...
Create BEL Edges from BEL Statement def edges(ctx, statement, rules, species, namespace_targets, version, api, config_fn): """Create BEL Edges from BEL Statement""" if config_fn: config = bel.db.Config.merge_config(ctx.config, override_config_fn=config_fn) else: config = ctx.config # ...
Setup Elasticsearch namespace indexes This will by default only create the indexes and run the namespace index mapping if the indexes don't exist. The --delete option will force removal of the index if it exists. The index_name should be aliased to the index 'terms' when it's ready def elasticsearch...
Setup ArangoDB database db_name: Either 'belns' or 'edgestore' - must be one or the other This will create the database, collections and indexes on the collection if it doesn't exist. The --delete option will force removal of the database if it exists. def arangodb(delete, db_name): """Setup ArangoD...
Validate nanopub against jsonschema for nanopub Args: nanopub (Mapping[str, Any]): nanopub dict schema (Mapping[str, Any]): nanopub schema Returns: Tuple[bool, List[str]]: bool: Is valid? Yes = True, No = False List[Tuple[str, str]]: Validation issues, empty if...
Create CityHash64 from nanopub for duplicate check TODO - check that this hash value is consistent between C# and Python running on laptop and server Build string to hash Collect flat array of (all values.strip()): nanopub.type.name nanopub.type.version One of: na...
Validates using the nanopub schema Args: nanopub (Mapping[str, Any]): nanopub dict Returns: Tuple[bool, List[Tuple[str, str]]]: bool: Is valid? Yes = True, No = False List[Tuple[str, str]]: Validation issues, empty if valid, tuple is ('ERROR\|WAR...
Validate context Args: context (Mapping[str, Any]): context dictionary of type, id and label Returns: Tuple[bool, List[Tuple[str, str]]]: bool: Is valid? Yes = True, No = False List[Tuple[str, str]]: Validation issues, empty if valid, tuple is (...
Create BEL Edges from BEL nanopub Args: nanopub (Mapping[str, Any]): bel nanopub namespace_targets (Mapping[str, List[str]]): what namespaces to canonicalize rules (List[str]): which computed edge rules to process, default is all, look at BEL Specification yam...
parse command line options and run commands. def main_hrun(): """ parse command line options and run commands.""" parser = argparse.ArgumentParser(description="Tools for http(s) test. Base on rtsf.") parser.add_argument( '--log-level', default='INFO', help="Specify ...
Return path to .pyd after successful build command. :return: Path to .pyd file or None. def find_pyd_file(): """ Return path to .pyd after successful build command. :return: Path to .pyd file or None. """ if not os.path.isdir("./build"): raise NotADirectoryError for path, dirs, fi...
Dereference the FFI result to a list of coordinates def _void_array_to_nested_list(res, _func, _args): """ Dereference the FFI result to a list of coordinates """ try: shape = res.coords.len, 2 ptr = cast(res.coords.data, POINTER(c_double)) array = np.ctypeslib.as_array(ptr, shape) ...
Parse file extension. - .json: uncompressed, utf-8 encode json file - .gz: compressed, utf-8 encode json file def is_json_file(abspath): """Parse file extension. - .json: uncompressed, utf-8 encode json file - .gz: compressed, utf-8 encode json file """ abspath = abspath.lower() f...
Convert file extension to lowercase. def lower_ext(abspath): """Convert file extension to lowercase. """ fname, ext = os.path.splitext(abspath) return fname + ext.lower()
Load Json from file. If file are not exists, returns ``default``. :param abspath: file path. use absolute path as much as you can. extension has to be ``.json`` or ``.gz`` (for compressed Json). :type abspath: string :param default: default ``dict()``, if ``abspath`` not exists, return the ...
Dump Json serializable object to file. Provides multiple choice to customize the behavior. :param data: Serializable python object. :type data: dict or list :param abspath: ``save as`` path, file extension has to be ``.json`` or ``.gz`` (for compressed Json) :type abspath: string :par...
A stable version of :func:`dump`, this method will silently overwrite existing file. There's a issue with :func:`dump`: If your program is interrupted while writing, you got an incomplete file, and you also lose the original file. So this method write json to a temporary file first, then rename to wh...
Return json string in pretty format. 中文文档将字典转化成格式化后的字符串。 def pretty_dumps(data): """Return json string in pretty format. 中文文档将字典转化成格式化后的字符串。 """ try: return json.dumps(data, sort_keys=True, indent=4, ensure_ascii=False) except: return json.dumps(data, sort_...
Compute left and right padding values. Here we use the convention that if the padding size is odd, we pad the odd part to the right and the even part to the left. Parameters ---------- small : int Old size of original 1D array large : int New size off padded 1D array R...
Perform linear padding for complex array The input array `av` is padded with a linear ramp starting at the edges and going outwards to an average value computed from a band of thickness `stlen` at the outer boundary of the array. Pads will only be appended, not prepended to the array. If the inpu...
2D component of `pad_add` def _pad_add_1d(av, size, stlen): """ 2D component of `pad_add` """ assert len(size) == 1 padx = _get_pad_left_right(av.shape[0], size[0]) mask = np.zeros(av.shape, dtype=bool) mask[stlen:-stlen] = True border = av[~mask] if av.dtype.name.count("complex"): ...
Removes linear padding from array This is a convenience function that does the opposite of `pad_add`. Parameters ---------- pv : 1D or 2D ndarray The array from which the padding will be removed. size : tuple of length 1 (1D) or 2 (2D), optional The final size of the un-padded ...
Simple rate limit function using redis def rate_limit(self): """ Simple rate limit function using redis """ rate_limited_msg = False while True: is_rate_limited = self.limit.is_rate_limited(uuid) if is_rate_limited: time.sleep(0.3) # sav...
Sends a file to virus total for assessment def scan_file(self, filename, apikey): """ Sends a file to virus total for assessment """ url = self.base_url + "file/scan" params = {'apikey': apikey} scanfile = {"file": open(filename, 'rb')} response = requests.post(u...
just send the hash, check the date def rescan_file(self, filename, sha256hash, apikey): """ just send the hash, check the date """ url = self.base_url + "file/rescan" params = { 'apikey': apikey, 'resource': sha256hash } rate_limit_clear ...
retrieve report from file scan def binary_report(self, sha256sum, apikey): """ retrieve report from file scan """ url = self.base_url + "file/report" params = {"apikey": apikey, "resource": sha256sum} rate_limit_clear = self.rate_limit() if rate_limit_clear: ...
Send IP address for list of past malicous domain associations def send_ip(self, ipaddr, apikey): """ Send IP address for list of past malicous domain associations """ url = self.base_url + "ip-address/report" parameters = {"ip": ipaddr, "apikey": apikey} rate_limit_clear...
Send URLS for list of past malicous associations def url_report(self, scan_url, apikey): """ Send URLS for list of past malicous associations """ url = self.base_url + "url/report" params = {"apikey": apikey, 'resource': scan_url} rate_limit_clear = self.rate_limit() ...
Returns a list of package requirements read from the file. def _read_requirements(filename, extra_packages): """Returns a list of package requirements read from the file.""" requirements_file = open(filename).read() hard_requirements = [] for line in requirements_file.splitlines(): if _is_requ...
Reference a field in string separated by a delimiter def field(ctx, text, index, delimiter=' '): """ Reference a field in string separated by a delimiter """ splits = text.split(delimiter) # remove our delimiters and whitespace splits = [f for f in splits if f != delimiter and len(f.strip()) >...
Converts the given date to the number of seconds since January 1st, 1970 UTC def epoch(ctx, datetime): """ Converts the given date to the number of seconds since January 1st, 1970 UTC """ return conversions.to_decimal(str(conversions.to_datetime(datetime, ctx).timestamp()), ctx)
Formats digits in text for reading in TTS def read_digits(ctx, text): """ Formats digits in text for reading in TTS """ def chunk(value, chunk_size): return [value[i: i + chunk_size] for i in range(0, len(value), chunk_size)] text = conversions.to_string(text, ctx).strip() if not text:...
Removes the first word from the given text string def remove_first_word(ctx, text): """ Removes the first word from the given text string """ text = conversions.to_string(text, ctx).lstrip() first = first_word(ctx, text) return text[len(first):].lstrip() if first else ''
Extracts the nth word from the given text string def word(ctx, text, number, by_spaces=False): """ Extracts the nth word from the given text string """ return word_slice(ctx, text, number, conversions.to_integer(number, ctx) + 1, by_spaces)
Returns the number of words in the given text string def word_count(ctx, text, by_spaces=False): """ Returns the number of words in the given text string """ text = conversions.to_string(text, ctx) by_spaces = conversions.to_boolean(by_spaces, ctx) return len(__get_words(text, by_spaces))
Extracts a substring spanning from start up to but not-including stop def word_slice(ctx, text, start, stop=0, by_spaces=False): """ Extracts a substring spanning from start up to but not-including stop """ text = conversions.to_string(text, ctx) start = conversions.to_integer(start, ctx) stop ...
Takes a single parameter (date as string) and returns it in the format defined by the org def format_date(ctx, text): """ Takes a single parameter (date as string) and returns it in the format defined by the org """ dt = conversions.to_datetime(text, ctx) return dt.astimezone(ctx.timezone).strftime...
Takes a single parameter (administrative boundary as a string) and returns the name of the leaf boundary def format_location(ctx, text): """ Takes a single parameter (administrative boundary as a string) and returns the name of the leaf boundary """ text = conversions.to_string(text, ctx) return te...
Tries to match the text with the given pattern and returns the value of matching group def regex_group(ctx, text, pattern, group_num): """ Tries to match the text with the given pattern and returns the value of matching group """ text = conversions.to_string(text, ctx) pattern = conversions.to_stri...
Helper function which splits the given text string into words. If by_spaces is false, then text like '01-02-2014' will be split into 3 separate words. For backwards compatibility, this is the default for all expression functions. :param text: the text to split :param by_spaces: whether words should be s...
Rounding for decimals with support for negative digits def decimal_round(number, num_digits, rounding=ROUND_HALF_UP): """ Rounding for decimals with support for negative digits """ exp = Decimal(10) ** -num_digits if num_digits >= 0: return number.quantize(exp, rounding) else: ...
Parses an ISO8601 formatted datetime from a string value def parse_json_date(value): """ Parses an ISO8601 formatted datetime from a string value """ if not value: return None return datetime.datetime.strptime(value, JSON_DATETIME_FORMAT).replace(tzinfo=pytz.UTC)
Formats a datetime as ISO8601 in UTC with millisecond precision, e.g. "2014-10-03T09:41:12.790Z" def format_json_date(value): """ Formats a datetime as ISO8601 in UTC with millisecond precision, e.g. "2014-10-03T09:41:12.790Z" """ if not value: return None # %f will include 6 microsecond d...
Removes all non-printable characters from a text string def clean(ctx, text): """ Removes all non-printable characters from a text string """ text = conversions.to_string(text, ctx) return ''.join([c for c in text if ord(c) >= 32])
Joins text strings into one text string def concatenate(ctx, *text): """ Joins text strings into one text string """ result = '' for arg in text: result += conversions.to_string(arg, ctx) return result
Formats the given number in decimal format using a period and commas def fixed(ctx, number, decimals=2, no_commas=False): """ Formats the given number in decimal format using a period and commas """ value = _round(ctx, number, decimals) format_str = '{:f}' if no_commas else '{:,f}' return forma...
Returns the first characters in a text string def left(ctx, text, num_chars): """ Returns the first characters in a text string """ num_chars = conversions.to_integer(num_chars, ctx) if num_chars < 0: raise ValueError("Number of chars can't be negative") return conversions.to_string(tex...
Repeats text a given number of times def rept(ctx, text, number_times): """ Repeats text a given number of times """ if number_times < 0: raise ValueError("Number of times can't be negative") return conversions.to_string(text, ctx) * conversions.to_integer(number_times, ctx)
Returns the last characters in a text string def right(ctx, text, num_chars): """ Returns the last characters in a text string """ num_chars = conversions.to_integer(num_chars, ctx) if num_chars < 0: raise ValueError("Number of chars can't be negative") elif num_chars == 0: retu...
Substitutes new_text for old_text in a text string def substitute(ctx, text, old_text, new_text, instance_num=-1): """ Substitutes new_text for old_text in a text string """ text = conversions.to_string(text, ctx) old_text = conversions.to_string(old_text, ctx) new_text = conversions.to_string(...
Returns a numeric code for the first character in a text string def _unicode(ctx, text): """ Returns a numeric code for the first character in a text string """ text = conversions.to_string(text, ctx) if len(text) == 0: raise ValueError("Text can't be empty") return ord(text[0])
Defines a date value def date(ctx, year, month, day): """ Defines a date value """ return _date(conversions.to_integer(year, ctx), conversions.to_integer(month, ctx), conversions.to_integer(day, ctx))
Calculates the number of days, months, or years between two dates. def datedif(ctx, start_date, end_date, unit): """ Calculates the number of days, months, or years between two dates. """ start_date = conversions.to_date(start_date, ctx) end_date = conversions.to_date(end_date, ctx) unit = conv...
Moves a date by the given number of months def edate(ctx, date, months): """ Moves a date by the given number of months """ return conversions.to_date_or_datetime(date, ctx) + relativedelta(months=conversions.to_integer(months, ctx))
Defines a time value def time(ctx, hours, minutes, seconds): """ Defines a time value """ return _time(conversions.to_integer(hours, ctx), conversions.to_integer(minutes, ctx), conversions.to_integer(seconds, ctx))
Returns the absolute value of a number def _abs(ctx, number): """ Returns the absolute value of a number """ return conversions.to_decimal(abs(conversions.to_decimal(number, ctx)), ctx)
Rounds a number down to the nearest integer def _int(ctx, number): """ Rounds a number down to the nearest integer """ return conversions.to_integer(conversions.to_decimal(number, ctx).to_integral_value(ROUND_FLOOR), ctx)
Returns the maximum value of all arguments def _max(ctx, *number): """ Returns the maximum value of all arguments """ if len(number) == 0: raise ValueError("Wrong number of arguments") result = conversions.to_decimal(number[0], ctx) for arg in number[1:]: arg = conversions.to_d...
Returns the remainder after number is divided by divisor def mod(ctx, number, divisor): """ Returns the remainder after number is divided by divisor """ number = conversions.to_decimal(number, ctx) divisor = conversions.to_decimal(divisor, ctx) return number - divisor * _int(ctx, number / divis...
Returns the result of a number raised to a power def _power(ctx, number, power): """ Returns the result of a number raised to a power """ return decimal_pow(conversions.to_decimal(number, ctx), conversions.to_decimal(power, ctx))
Returns a random integer number between the numbers you specify def randbetween(ctx, bottom, top): """ Returns a random integer number between the numbers you specify """ bottom = conversions.to_integer(bottom, ctx) top = conversions.to_integer(top, ctx) return random.randint(bottom, top)
Rounds a number to a specified number of digits def _round(ctx, number, num_digits): """ Rounds a number to a specified number of digits """ number = conversions.to_decimal(number, ctx) num_digits = conversions.to_integer(num_digits, ctx) return decimal_round(number, num_digits, ROUND_HALF_UP)
Rounds a number down, toward zero def rounddown(ctx, number, num_digits): """ Rounds a number down, toward zero """ number = conversions.to_decimal(number, ctx) num_digits = conversions.to_integer(num_digits, ctx) return decimal_round(number, num_digits, ROUND_DOWN)
Rounds a number up, away from zero def roundup(ctx, number, num_digits): """ Rounds a number up, away from zero """ number = conversions.to_decimal(number, ctx) num_digits = conversions.to_integer(num_digits, ctx) return decimal_round(number, num_digits, ROUND_UP)
Returns the sum of all arguments def _sum(ctx, *number): """ Returns the sum of all arguments """ if len(number) == 0: raise ValueError("Wrong number of arguments") result = Decimal(0) for arg in number: result += conversions.to_decimal(arg, ctx) return result
Truncates a number to an integer by removing the fractional part of the number def trunc(ctx, number): """ Truncates a number to an integer by removing the fractional part of the number """ return conversions.to_integer(conversions.to_decimal(number, ctx).to_integral_value(ROUND_DOWN), ctx)
Returns TRUE if and only if all its arguments evaluate to TRUE def _and(ctx, *logical): """ Returns TRUE if and only if all its arguments evaluate to TRUE """ for arg in logical: if not conversions.to_boolean(arg, ctx): return False return True
Returns one value if the condition evaluates to TRUE, and another value if it evaluates to FALSE def _if(ctx, logical_test, value_if_true=0, value_if_false=False): """ Returns one value if the condition evaluates to TRUE, and another value if it evaluates to FALSE """ return value_if_true if conversion...
Returns TRUE if any argument is TRUE def _or(ctx, *logical): """ Returns TRUE if any argument is TRUE """ for arg in logical: if conversions.to_boolean(arg, ctx): return True return False
Return the sum1_ij and sum2_ij values given the input indices and data instances. Notes ----- This is called in `Binning.update_sums` to compute the `sum1` and `sum2` contributions for indices `(i,j)` Parameters ---------- i,j : array_like the bin indices for these pairs da...
Set the binning info we need from the `edges` def _setup(self): """ Set the binning info we need from the `edges` """ dtype = [('inv', 'f8'), ('min', 'f8'), ('max', 'f8'),('N', 'i4'), ('spacing','object')] dtype = numpy.dtype(dtype) self._info = numpy.empty(self...
Linearize bin indices. This function is called by subclasses. Refer to the source code of :py:class:`RBinning` for an example. Parameters ---------- args : list a list of bin index, (xi, yi, zi, ..) Returns ------- linearlized bin index ...
The main function that digitizes the pair counts, calls bincount for the appropriate `sum1` and `sum2` values, and adds them to the input arrays, will modify sum1, sum2, N, and centers_sum inplace. def update_sums(self, r, i, j, data1, data2, sum1, sum2, N=None, centers_sum=None): """ ...
Return the shapes of the summation arrays, given the input data and shape of the bins def sum_shapes(self, data1, data2): """ Return the shapes of the summation arrays, given the input data and shape of the bins """ # the linear shape (put extra dimensions first) ...
Update the mean coordinate sums def _update_mean_coords(self, dig, N, centers_sum, **paircoords): """ Update the mean coordinate sums """ if N is None or centers_sum is None: return N.flat[:] += utils.bincount(dig, 1., minlength=N.size) for i, dim in enumerate(self.dims...
Internal function that performs the pair-counting def work(self, i): """ Internal function that performs the pair-counting """ n1, n2 = self.p[i] # initialize the total arrays for this process sum1 = numpy.zeros_like(self.sum1g) sum2 = 1. if not self.pts...
The internal reduce function that sums the results from various processors def reduce(self, sum1, sum2, *args): """ The internal reduce function that sums the results from various processors """ self.sum1g[...] += sum1 if not self.pts_only: self.sum2g[...] += sum...
r"""PSIS leave-one-out log predictive densities. Computes the log predictive densities given posterior samples of the log likelihood terms :math:`p(y_i\|\theta^s)` in input parameter `log_lik`. Returns a sum of the leave-one-out log predictive densities `loo`, individual leave-one-out log predictive den...
Pareto smoothed importance sampling (PSIS). Parameters ---------- lw : ndarray Array of size n x m containing m sets of n log weights. It is also possible to provide one dimensional array of length n. Reff : scalar, optional relative MCMC efficiency ``N_eff / N`` overwrite...
Estimate the paramaters for the Generalized Pareto Distribution (GPD) Returns empirical Bayes estimate for the parameters of the two-parameter generalized Parato distribution given the data. Parameters ---------- x : ndarray One dimensional data array sort : bool or ndarray, optional ...
Inverse Generalised Pareto distribution function. def gpinv(p, k, sigma): """Inverse Generalised Pareto distribution function.""" x = np.empty(p.shape) x.fill(np.nan) if sigma <= 0: return x ok = (p > 0) & (p < 1) if np.all(ok): if np.abs(k) < np.finfo(float).eps: np...
Sum of vector where numbers are represented by their logarithms. Calculates ``np.log(np.sum(np.exp(x), axis=axis))`` in such a fashion that it works even when elements have large magnitude. def sumlogs(x, axis=None, out=None): """Sum of vector where numbers are represented by their logarithms. Calcul...
Adds functions from a library module :param library: the library module :return: def add_library(self, library): """ Adds functions from a library module :param library: the library module :return: """ for fn in library.__dict__.copy().values(): ...
Invokes the given function :param ctx: the evaluation context :param name: the function name (case insensitive) :param arguments: the arguments to be passed to the function :return: the function return value def invoke_function(self, ctx, name, arguments): """ Invokes th...
Builds a listing of all functions sorted A-Z, with their names and descriptions def build_listing(self): """ Builds a listing of all functions sorted A-Z, with their names and descriptions """ def func_entry(name, func): args, varargs, defaults = self._get_arg_spec(func) ...

Download file def download_file(url): """Download file""" response = requests.get(url, stream=True) fp = tempfile.NamedTemporaryFile() for chunk in response.iter_content(chunk_size=1024): if chunk: # filter out keep-alive new chunks fp.write(chunk) # log.info(f'Download file ...

Returns the first true value in the iterable. If no true value is found, returns *default* If *pred* is not None, returns the first item for which pred(item) is true. def first_true(iterable, default=False, pred=None): """Returns the first true value in the iterable. If no true value is found, r...

Create hash Id from edge record Args: edge (Mapping[str, Any]): edge record to create hash from Returns: str: Murmur3 128 bit hash def _create_hash_from_doc(doc: Mapping[str, Any]) -> str: """Create hash Id from edge record Args: edge (Mapping[str, Any]): edge record to creat...

Return the current elapsed time since start If the `elapsed` property is called in the context manager scope, the elapsed time bewteen start and property access is returned. However, if it is accessed outside of the context manager scope, it returns the elapsed time bewteen entering and ...

Load edges into Edgestore def load_edges_into_db( nanopub_id: str, nanopub_url: str, edges: list = [], edges_coll_name: str = edges_coll_name, nodes_coll_name: str = nodes_coll_name, ): """Load edges into Edgestore""" start_time = datetime.datetime.now() # Clean out edges for nanopub ...

Yield documents from edge for loading into ArangoDB def edge_iterator(edges=[], edges_fn=None): """Yield documents from edge for loading into ArangoDB""" for edge in itertools.chain(edges, files.read_edges(edges_fn)): subj = copy.deepcopy(edge["edge"]["subject"]) subj_id = str(utils._create_h...

Add nanopubstore start_dt to belapi.state_mgmt collection Args: url: url of nanopubstore start_dt: datetime of last query against nanopubstore for new ID's def update_nanopubstore_start_dt(url: str, start_dt: str): """Add nanopubstore start_dt to belapi.state_mgmt collection Args: ...

Get last start_dt recorded for getting new nanopub ID's def get_nanopubstore_start_dt(url: str): """Get last start_dt recorded for getting new nanopub ID's""" hostname = urllib.parse.urlsplit(url)[1] start_dates_doc = state_mgmt.get(start_dates_doc_key) if start_dates_doc and start_dates_doc.get("sta...

Get modified and deleted nanopub urls Limited by last datetime retrieved (start_dt). Modified includes new and updated nanopubs Returns: dict: {'modified': [], 'deleted': []} def get_nanopub_urls(ns_root_url: str = None, start_dt: str = None) -> dict: """Get modified and deleted nanopub urls ...

Get Nanopub from nanopubstore given url def get_nanopub(url): """Get Nanopub from nanopubstore given url""" r = bel.utils.get_url(url, cache=False) if r and r.json(): return r.json() else: return {}

BEL Pipeline - BEL Nanopubs into BEL Edges This will process BEL Nanopubs into BEL Edges by validating, orthologizing (if requested), canonicalizing, and then computing the BEL Edges based on the given rule_set. \b input_fn: If input fn has *.gz, will read as a gzip file If input fn ha...

Validate nanopubs def nanopub_validate(ctx, input_fn, output_fn, api, config_fn): """Validate nanopubs""" if config_fn: config = bel.db.Config.merge_config(ctx.config, override_config_fn=config_fn) else: config = ctx.config api = utils.first_true( [api, config["bel_api"]["serv...

Convert belscript to nanopubs_bel format This will convert the OpenBEL BELScript file format to nanopub_bel-1.0.0 format. \b input_fn: If input fn has *.gz, will read as a gzip file \b output_fn: If output fn has *.gz, will written as a gzip file If output fn has *.jso...

Reformat between JSON, YAML, JSONLines formats \b input_fn: If input fn has *.gz, will read as a gzip file \b output_fn: If output fn has *.gz, will written as a gzip file If output fn has *.jsonl*, will written as a JSONLines file IF output fn has *.json*, will be writ...

Collect statistics on nanopub file input_fn can be json, jsonl or yaml and additionally gzipped def nanopub_stats(ctx, input_fn): """Collect statistics on nanopub file input_fn can be json, jsonl or yaml and additionally gzipped """ counts = { "nanopubs": 0, "assertions": {"total...

Canonicalize statement Target namespaces can be provided in the following manner: bel stmt canonicalize "<BELStmt>" --namespace_targets '{"HGNC": ["EG", "SP"], "CHEMBL": ["CHEBI"]}' the value of target_namespaces must be JSON and embedded in single quotes reserving double quotes fo...

Create BEL Edges from BEL Statement def edges(ctx, statement, rules, species, namespace_targets, version, api, config_fn): """Create BEL Edges from BEL Statement""" if config_fn: config = bel.db.Config.merge_config(ctx.config, override_config_fn=config_fn) else: config = ctx.config # ...

Setup Elasticsearch namespace indexes This will by default only create the indexes and run the namespace index mapping if the indexes don't exist. The --delete option will force removal of the index if it exists. The index_name should be aliased to the index 'terms' when it's ready def elasticsearch...

Setup ArangoDB database db_name: Either 'belns' or 'edgestore' - must be one or the other This will create the database, collections and indexes on the collection if it doesn't exist. The --delete option will force removal of the database if it exists. def arangodb(delete, db_name): """Setup ArangoD...

Validate nanopub against jsonschema for nanopub Args: nanopub (Mapping[str, Any]): nanopub dict schema (Mapping[str, Any]): nanopub schema Returns: Tuple[bool, List[str]]: bool: Is valid? Yes = True, No = False List[Tuple[str, str]]: Validation issues, empty if...

Create CityHash64 from nanopub for duplicate check TODO - check that this hash value is consistent between C# and Python running on laptop and server Build string to hash Collect flat array of (all values.strip()): nanopub.type.name nanopub.type.version One of: na...

Validates using the nanopub schema Args: nanopub (Mapping[str, Any]): nanopub dict Returns: Tuple[bool, List[Tuple[str, str]]]: bool: Is valid? Yes = True, No = False List[Tuple[str, str]]: Validation issues, empty if valid, tuple is ('ERROR|WAR...

Validate context Args: context (Mapping[str, Any]): context dictionary of type, id and label Returns: Tuple[bool, List[Tuple[str, str]]]: bool: Is valid? Yes = True, No = False List[Tuple[str, str]]: Validation issues, empty if valid, tuple is (...

Create BEL Edges from BEL nanopub Args: nanopub (Mapping[str, Any]): bel nanopub namespace_targets (Mapping[str, List[str]]): what namespaces to canonicalize rules (List[str]): which computed edge rules to process, default is all, look at BEL Specification yam...

parse command line options and run commands. def main_hrun(): """ parse command line options and run commands.""" parser = argparse.ArgumentParser(description="Tools for http(s) test. Base on rtsf.") parser.add_argument( '--log-level', default='INFO', help="Specify ...

Return path to .pyd after successful build command. :return: Path to .pyd file or None. def find_pyd_file(): """ Return path to .pyd after successful build command. :return: Path to .pyd file or None. """ if not os.path.isdir("./build"): raise NotADirectoryError for path, dirs, fi...

Dereference the FFI result to a list of coordinates def _void_array_to_nested_list(res, _func, _args): """ Dereference the FFI result to a list of coordinates """ try: shape = res.coords.len, 2 ptr = cast(res.coords.data, POINTER(c_double)) array = np.ctypeslib.as_array(ptr, shape) ...

Parse file extension. - *.json: uncompressed, utf-8 encode json file - *.gz: compressed, utf-8 encode json file def is_json_file(abspath): """Parse file extension. - *.json: uncompressed, utf-8 encode json file - *.gz: compressed, utf-8 encode json file """ abspath = abspath.lower() f...

Convert file extension to lowercase. def lower_ext(abspath): """Convert file extension to lowercase. """ fname, ext = os.path.splitext(abspath) return fname + ext.lower()

Load Json from file. If file are not exists, returns ``default``. :param abspath: file path. use absolute path as much as you can. extension has to be ``.json`` or ``.gz`` (for compressed Json). :type abspath: string :param default: default ``dict()``, if ``abspath`` not exists, return the ...

Dump Json serializable object to file. Provides multiple choice to customize the behavior. :param data: Serializable python object. :type data: dict or list :param abspath: ``save as`` path, file extension has to be ``.json`` or ``.gz`` (for compressed Json) :type abspath: string :par...

A stable version of :func:`dump`, this method will silently overwrite existing file. There's a issue with :func:`dump`: If your program is interrupted while writing, you got an incomplete file, and you also lose the original file. So this method write json to a temporary file first, then rename to wh...

Return json string in pretty format. **中文文档** 将字典转化成格式化后的字符串。 def pretty_dumps(data): """Return json string in pretty format. **中文文档** 将字典转化成格式化后的字符串。 """ try: return json.dumps(data, sort_keys=True, indent=4, ensure_ascii=False) except: return json.dumps(data, sort_...

Compute left and right padding values. Here we use the convention that if the padding size is odd, we pad the odd part to the right and the even part to the left. Parameters ---------- small : int Old size of original 1D array large : int New size off padded 1D array R...

Perform linear padding for complex array The input array `av` is padded with a linear ramp starting at the edges and going outwards to an average value computed from a band of thickness `stlen` at the outer boundary of the array. Pads will only be appended, not prepended to the array. If the inpu...

2D component of `pad_add` def _pad_add_1d(av, size, stlen): """ 2D component of `pad_add` """ assert len(size) == 1 padx = _get_pad_left_right(av.shape[0], size[0]) mask = np.zeros(av.shape, dtype=bool) mask[stlen:-stlen] = True border = av[~mask] if av.dtype.name.count("complex"): ...

Removes linear padding from array This is a convenience function that does the opposite of `pad_add`. Parameters ---------- pv : 1D or 2D ndarray The array from which the padding will be removed. size : tuple of length 1 (1D) or 2 (2D), optional The final size of the un-padded ...

Simple rate limit function using redis def rate_limit(self): """ Simple rate limit function using redis """ rate_limited_msg = False while True: is_rate_limited = self.limit.is_rate_limited(uuid) if is_rate_limited: time.sleep(0.3) # sav...

Sends a file to virus total for assessment def scan_file(self, filename, apikey): """ Sends a file to virus total for assessment """ url = self.base_url + "file/scan" params = {'apikey': apikey} scanfile = {"file": open(filename, 'rb')} response = requests.post(u...

just send the hash, check the date def rescan_file(self, filename, sha256hash, apikey): """ just send the hash, check the date """ url = self.base_url + "file/rescan" params = { 'apikey': apikey, 'resource': sha256hash } rate_limit_clear ...

retrieve report from file scan def binary_report(self, sha256sum, apikey): """ retrieve report from file scan """ url = self.base_url + "file/report" params = {"apikey": apikey, "resource": sha256sum} rate_limit_clear = self.rate_limit() if rate_limit_clear: ...

Send IP address for list of past malicous domain associations def send_ip(self, ipaddr, apikey): """ Send IP address for list of past malicous domain associations """ url = self.base_url + "ip-address/report" parameters = {"ip": ipaddr, "apikey": apikey} rate_limit_clear...

Send URLS for list of past malicous associations def url_report(self, scan_url, apikey): """ Send URLS for list of past malicous associations """ url = self.base_url + "url/report" params = {"apikey": apikey, 'resource': scan_url} rate_limit_clear = self.rate_limit() ...

Returns a list of package requirements read from the file. def _read_requirements(filename, extra_packages): """Returns a list of package requirements read from the file.""" requirements_file = open(filename).read() hard_requirements = [] for line in requirements_file.splitlines(): if _is_requ...

Reference a field in string separated by a delimiter def field(ctx, text, index, delimiter=' '): """ Reference a field in string separated by a delimiter """ splits = text.split(delimiter) # remove our delimiters and whitespace splits = [f for f in splits if f != delimiter and len(f.strip()) >...

Converts the given date to the number of seconds since January 1st, 1970 UTC def epoch(ctx, datetime): """ Converts the given date to the number of seconds since January 1st, 1970 UTC """ return conversions.to_decimal(str(conversions.to_datetime(datetime, ctx).timestamp()), ctx)

Formats digits in text for reading in TTS def read_digits(ctx, text): """ Formats digits in text for reading in TTS """ def chunk(value, chunk_size): return [value[i: i + chunk_size] for i in range(0, len(value), chunk_size)] text = conversions.to_string(text, ctx).strip() if not text:...

Removes the first word from the given text string def remove_first_word(ctx, text): """ Removes the first word from the given text string """ text = conversions.to_string(text, ctx).lstrip() first = first_word(ctx, text) return text[len(first):].lstrip() if first else ''

Extracts the nth word from the given text string def word(ctx, text, number, by_spaces=False): """ Extracts the nth word from the given text string """ return word_slice(ctx, text, number, conversions.to_integer(number, ctx) + 1, by_spaces)

Returns the number of words in the given text string def word_count(ctx, text, by_spaces=False): """ Returns the number of words in the given text string """ text = conversions.to_string(text, ctx) by_spaces = conversions.to_boolean(by_spaces, ctx) return len(__get_words(text, by_spaces))

Extracts a substring spanning from start up to but not-including stop def word_slice(ctx, text, start, stop=0, by_spaces=False): """ Extracts a substring spanning from start up to but not-including stop """ text = conversions.to_string(text, ctx) start = conversions.to_integer(start, ctx) stop ...

Takes a single parameter (date as string) and returns it in the format defined by the org def format_date(ctx, text): """ Takes a single parameter (date as string) and returns it in the format defined by the org """ dt = conversions.to_datetime(text, ctx) return dt.astimezone(ctx.timezone).strftime...

Takes a single parameter (administrative boundary as a string) and returns the name of the leaf boundary def format_location(ctx, text): """ Takes a single parameter (administrative boundary as a string) and returns the name of the leaf boundary """ text = conversions.to_string(text, ctx) return te...

Tries to match the text with the given pattern and returns the value of matching group def regex_group(ctx, text, pattern, group_num): """ Tries to match the text with the given pattern and returns the value of matching group """ text = conversions.to_string(text, ctx) pattern = conversions.to_stri...

Helper function which splits the given text string into words. If by_spaces is false, then text like '01-02-2014' will be split into 3 separate words. For backwards compatibility, this is the default for all expression functions. :param text: the text to split :param by_spaces: whether words should be s...

Rounding for decimals with support for negative digits def decimal_round(number, num_digits, rounding=ROUND_HALF_UP): """ Rounding for decimals with support for negative digits """ exp = Decimal(10) ** -num_digits if num_digits >= 0: return number.quantize(exp, rounding) else: ...

Parses an ISO8601 formatted datetime from a string value def parse_json_date(value): """ Parses an ISO8601 formatted datetime from a string value """ if not value: return None return datetime.datetime.strptime(value, JSON_DATETIME_FORMAT).replace(tzinfo=pytz.UTC)

Formats a datetime as ISO8601 in UTC with millisecond precision, e.g. "2014-10-03T09:41:12.790Z" def format_json_date(value): """ Formats a datetime as ISO8601 in UTC with millisecond precision, e.g. "2014-10-03T09:41:12.790Z" """ if not value: return None # %f will include 6 microsecond d...

Removes all non-printable characters from a text string def clean(ctx, text): """ Removes all non-printable characters from a text string """ text = conversions.to_string(text, ctx) return ''.join([c for c in text if ord(c) >= 32])

Joins text strings into one text string def concatenate(ctx, *text): """ Joins text strings into one text string """ result = '' for arg in text: result += conversions.to_string(arg, ctx) return result

Formats the given number in decimal format using a period and commas def fixed(ctx, number, decimals=2, no_commas=False): """ Formats the given number in decimal format using a period and commas """ value = _round(ctx, number, decimals) format_str = '{:f}' if no_commas else '{:,f}' return forma...

Returns the first characters in a text string def left(ctx, text, num_chars): """ Returns the first characters in a text string """ num_chars = conversions.to_integer(num_chars, ctx) if num_chars < 0: raise ValueError("Number of chars can't be negative") return conversions.to_string(tex...

Repeats text a given number of times def rept(ctx, text, number_times): """ Repeats text a given number of times """ if number_times < 0: raise ValueError("Number of times can't be negative") return conversions.to_string(text, ctx) * conversions.to_integer(number_times, ctx)

Returns the last characters in a text string def right(ctx, text, num_chars): """ Returns the last characters in a text string """ num_chars = conversions.to_integer(num_chars, ctx) if num_chars < 0: raise ValueError("Number of chars can't be negative") elif num_chars == 0: retu...

Substitutes new_text for old_text in a text string def substitute(ctx, text, old_text, new_text, instance_num=-1): """ Substitutes new_text for old_text in a text string """ text = conversions.to_string(text, ctx) old_text = conversions.to_string(old_text, ctx) new_text = conversions.to_string(...

Returns a numeric code for the first character in a text string def _unicode(ctx, text): """ Returns a numeric code for the first character in a text string """ text = conversions.to_string(text, ctx) if len(text) == 0: raise ValueError("Text can't be empty") return ord(text[0])

Defines a date value def date(ctx, year, month, day): """ Defines a date value """ return _date(conversions.to_integer(year, ctx), conversions.to_integer(month, ctx), conversions.to_integer(day, ctx))

Calculates the number of days, months, or years between two dates. def datedif(ctx, start_date, end_date, unit): """ Calculates the number of days, months, or years between two dates. """ start_date = conversions.to_date(start_date, ctx) end_date = conversions.to_date(end_date, ctx) unit = conv...

Moves a date by the given number of months def edate(ctx, date, months): """ Moves a date by the given number of months """ return conversions.to_date_or_datetime(date, ctx) + relativedelta(months=conversions.to_integer(months, ctx))

Defines a time value def time(ctx, hours, minutes, seconds): """ Defines a time value """ return _time(conversions.to_integer(hours, ctx), conversions.to_integer(minutes, ctx), conversions.to_integer(seconds, ctx))

Returns the absolute value of a number def _abs(ctx, number): """ Returns the absolute value of a number """ return conversions.to_decimal(abs(conversions.to_decimal(number, ctx)), ctx)

Rounds a number down to the nearest integer def _int(ctx, number): """ Rounds a number down to the nearest integer """ return conversions.to_integer(conversions.to_decimal(number, ctx).to_integral_value(ROUND_FLOOR), ctx)

Returns the maximum value of all arguments def _max(ctx, *number): """ Returns the maximum value of all arguments """ if len(number) == 0: raise ValueError("Wrong number of arguments") result = conversions.to_decimal(number[0], ctx) for arg in number[1:]: arg = conversions.to_d...

Returns the remainder after number is divided by divisor def mod(ctx, number, divisor): """ Returns the remainder after number is divided by divisor """ number = conversions.to_decimal(number, ctx) divisor = conversions.to_decimal(divisor, ctx) return number - divisor * _int(ctx, number / divis...

Returns the result of a number raised to a power def _power(ctx, number, power): """ Returns the result of a number raised to a power """ return decimal_pow(conversions.to_decimal(number, ctx), conversions.to_decimal(power, ctx))

Returns a random integer number between the numbers you specify def randbetween(ctx, bottom, top): """ Returns a random integer number between the numbers you specify """ bottom = conversions.to_integer(bottom, ctx) top = conversions.to_integer(top, ctx) return random.randint(bottom, top)

Rounds a number to a specified number of digits def _round(ctx, number, num_digits): """ Rounds a number to a specified number of digits """ number = conversions.to_decimal(number, ctx) num_digits = conversions.to_integer(num_digits, ctx) return decimal_round(number, num_digits, ROUND_HALF_UP)

Rounds a number down, toward zero def rounddown(ctx, number, num_digits): """ Rounds a number down, toward zero """ number = conversions.to_decimal(number, ctx) num_digits = conversions.to_integer(num_digits, ctx) return decimal_round(number, num_digits, ROUND_DOWN)

Rounds a number up, away from zero def roundup(ctx, number, num_digits): """ Rounds a number up, away from zero """ number = conversions.to_decimal(number, ctx) num_digits = conversions.to_integer(num_digits, ctx) return decimal_round(number, num_digits, ROUND_UP)

Returns the sum of all arguments def _sum(ctx, *number): """ Returns the sum of all arguments """ if len(number) == 0: raise ValueError("Wrong number of arguments") result = Decimal(0) for arg in number: result += conversions.to_decimal(arg, ctx) return result

Truncates a number to an integer by removing the fractional part of the number def trunc(ctx, number): """ Truncates a number to an integer by removing the fractional part of the number """ return conversions.to_integer(conversions.to_decimal(number, ctx).to_integral_value(ROUND_DOWN), ctx)

Returns TRUE if and only if all its arguments evaluate to TRUE def _and(ctx, *logical): """ Returns TRUE if and only if all its arguments evaluate to TRUE """ for arg in logical: if not conversions.to_boolean(arg, ctx): return False return True

Returns one value if the condition evaluates to TRUE, and another value if it evaluates to FALSE def _if(ctx, logical_test, value_if_true=0, value_if_false=False): """ Returns one value if the condition evaluates to TRUE, and another value if it evaluates to FALSE """ return value_if_true if conversion...

Returns TRUE if any argument is TRUE def _or(ctx, *logical): """ Returns TRUE if any argument is TRUE """ for arg in logical: if conversions.to_boolean(arg, ctx): return True return False

Return the sum1_ij and sum2_ij values given the input indices and data instances. Notes ----- This is called in `Binning.update_sums` to compute the `sum1` and `sum2` contributions for indices `(i,j)` Parameters ---------- i,j : array_like the bin indices for these pairs da...

Set the binning info we need from the `edges` def _setup(self): """ Set the binning info we need from the `edges` """ dtype = [('inv', 'f8'), ('min', 'f8'), ('max', 'f8'),('N', 'i4'), ('spacing','object')] dtype = numpy.dtype(dtype) self._info = numpy.empty(self...

Linearize bin indices. This function is called by subclasses. Refer to the source code of :py:class:`RBinning` for an example. Parameters ---------- args : list a list of bin index, (xi, yi, zi, ..) Returns ------- linearlized bin index ...

The main function that digitizes the pair counts, calls bincount for the appropriate `sum1` and `sum2` values, and adds them to the input arrays, will modify sum1, sum2, N, and centers_sum inplace. def update_sums(self, r, i, j, data1, data2, sum1, sum2, N=None, centers_sum=None): """ ...

Return the shapes of the summation arrays, given the input data and shape of the bins def sum_shapes(self, data1, data2): """ Return the shapes of the summation arrays, given the input data and shape of the bins """ # the linear shape (put extra dimensions first) ...

Update the mean coordinate sums def _update_mean_coords(self, dig, N, centers_sum, **paircoords): """ Update the mean coordinate sums """ if N is None or centers_sum is None: return N.flat[:] += utils.bincount(dig, 1., minlength=N.size) for i, dim in enumerate(self.dims...

Internal function that performs the pair-counting def work(self, i): """ Internal function that performs the pair-counting """ n1, n2 = self.p[i] # initialize the total arrays for this process sum1 = numpy.zeros_like(self.sum1g) sum2 = 1. if not self.pts...

The internal reduce function that sums the results from various processors def reduce(self, sum1, sum2, *args): """ The internal reduce function that sums the results from various processors """ self.sum1g[...] += sum1 if not self.pts_only: self.sum2g[...] += sum...

r"""PSIS leave-one-out log predictive densities. Computes the log predictive densities given posterior samples of the log likelihood terms :math:`p(y_i|\theta^s)` in input parameter `log_lik`. Returns a sum of the leave-one-out log predictive densities `loo`, individual leave-one-out log predictive den...

Pareto smoothed importance sampling (PSIS). Parameters ---------- lw : ndarray Array of size n x m containing m sets of n log weights. It is also possible to provide one dimensional array of length n. Reff : scalar, optional relative MCMC efficiency ``N_eff / N`` overwrite...

Estimate the paramaters for the Generalized Pareto Distribution (GPD) Returns empirical Bayes estimate for the parameters of the two-parameter generalized Parato distribution given the data. Parameters ---------- x : ndarray One dimensional data array sort : bool or ndarray, optional ...

Inverse Generalised Pareto distribution function. def gpinv(p, k, sigma): """Inverse Generalised Pareto distribution function.""" x = np.empty(p.shape) x.fill(np.nan) if sigma <= 0: return x ok = (p > 0) & (p < 1) if np.all(ok): if np.abs(k) < np.finfo(float).eps: np...

Sum of vector where numbers are represented by their logarithms. Calculates ``np.log(np.sum(np.exp(x), axis=axis))`` in such a fashion that it works even when elements have large magnitude. def sumlogs(x, axis=None, out=None): """Sum of vector where numbers are represented by their logarithms. Calcul...

Adds functions from a library module :param library: the library module :return: def add_library(self, library): """ Adds functions from a library module :param library: the library module :return: """ for fn in library.__dict__.copy().values(): ...

Invokes the given function :param ctx: the evaluation context :param name: the function name (case insensitive) :param arguments: the arguments to be passed to the function :return: the function return value def invoke_function(self, ctx, name, arguments): """ Invokes th...

Builds a listing of all functions sorted A-Z, with their names and descriptions def build_listing(self): """ Builds a listing of all functions sorted A-Z, with their names and descriptions """ def func_entry(name, func): args, varargs, defaults = self._get_arg_spec(func) ...