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def deco_inside_ctx_method_self(target): """decorator: wrap a class method inside a `with self: ...` context""" def tgt(self, *args, **kwargs): with self: return target(self, *args, **kwargs) return tgt
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def get_added_after( fetch_full_feed, initial_interval, last_fetch_time=None, filter_args=None ): """ Creates the added_after param, or extracts it from the filter_args :param fetch_full_feed: when set to true, will limit added_after :param initial_interval: initial_interval if no :param last_fe...
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def _a_in_b(first, second): """Check if interval a is inside interval b.""" return first.start >= second.start and first.stop <= second.stop
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async def ping_server(): """ Ping Server =========== Returns the message "The Optuna-server is alive!" if the server is running. Parameters ---------- None Returns ------- msg : str A message witnessing that the server is running. """ msg = 'The Optuna-server is alive!' return msg
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def test_from_rsid(rsids, start_rsid): """Continue collecting publications for rsids in list, beginning with start_rsid Args: rsids (list): list of rsids to collect publications on start_rsid (str): rsid identifier to resume collecting publications on Returns: runtime_rsids (list):...
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def get_base_url(host_name, customer_id): """ :arg host_name: the host name of the IDNow gateway server :arg customer_id: your customer id :returns the base url of the IDNow API and the selected customer """ return 'https://{0}/api/v1/{1}'.format(host_name, customer_id)
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import re def cigar_segment_bounds(cigar, start): """ Determine the start and end positions on a chromosome of a non-no-matching part of an RNA-seq read based on a read's cigar string. cigar string meaning: http://bioinformatics.cvr.ac.uk/blog/tag/cigar-string/ Example: '50M25N50M' with ...
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import functools import asyncio def no_block(func): """Turns a blocking function into a non-blocking coroutine function.""" @functools.wraps(func) async def no_blocking_handler(*args, **kwargs): partial = functools.partial(func, *args, **kwargs) return await asyncio.get_event_loop().run_i...
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from typing import List def load_numbers_sorted(txt: str) -> List[int]: """ファイルから番号を読み込みソートしてリストを返す Args: txt (str): ファイルのパス Returns: List[int]: 番号のリスト """ numbers = [] with open(txt) as f: numbers = sorted(map(lambda e: int(e), f)) return numbers
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def translate_pt(p, offset): """Translates point p=(x,y) by offset=(x,y)""" return (p[0] + offset[0], p[1] + offset[1])
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import torch def hsic(k_x: torch.Tensor, k_y: torch.Tensor, centered: bool = False, unbiased: bool = True) -> torch.Tensor: """Compute Hilbert-Schmidt Independence Criteron (HSIC) :param k_x: n by n values of kernel applied to all pairs of x data :param k_y: n by n values of kernel on y data :param c...
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def ratingRange(app): """ Get the rating range of an app. """ rating = 'Unknown' r = app['rating'] if r >= 0 and r <= 1: rating = '0-1' elif r > 1 and r <= 2: rating = '1-2' elif r > 2 and r <= 3: rating = '2-3' elif r > 3 and r <= 4: rating = '3-4' elif r > 4 and r <= 5: rating = '4-5' return rating
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import io def generate_table_definition(schema_and_table, column_info, primary_key=None, foreign_keys=None, diststyle=None, distkey=None, sortkey=None): """Return a CREATE TABLE statement as a string.""" if not column_info: raise Exception('N...
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def gradient_descent_update(x, gradx, learning_rate): """ Performs a gradient descent update. """ # Return the new value for x return x - learning_rate * gradx
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def next_line(grd_file): """ next_line Function returns the next line in the file that is not a blank line, unless the line is '', which is a typical EOF marker. """ done = False while not done: line = grd_file.readline() if line == '': return line, False elif line.strip(): return line, True
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from pathlib import Path import hashlib def file_md5_is_valid(fasta_file: Path, checksum: str) -> bool: """ Checks if the FASTA file matches the MD5 checksum argument. Returns True if it matches and False otherwise. :param fasta_file: Path object for the FASTA file. :param checksum: MD5 checksum...
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def combine_to_int(values): """Combine several byte values to an integer""" multibyte_value = 0 for byte_id, byte in enumerate(values): multibyte_value += 2**(4 * byte_id) * byte return multibyte_value
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import requests from bs4 import BeautifulSoup def get_soup(page_url): """ Returns BeautifulSoup object of the url provided """ try: req = requests.get(page_url) except Exception: print('Failed to establish a connection with the website') return if req.status_code == 404: ...
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def foreign_key_constraint_sql(table): """Return the SQL to add foreign key constraints to a given table""" sql = '' fk_names = list(table.foreign_keys.keys()) for fk_name in sorted(fk_names): foreign_key = table.foreign_keys[fk_name] sql += "FOREIGN KEY({fn}) REFERENCES {tn}({kc}), ".fo...
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from pathlib import Path def get_world_paths() -> list: """ Returns a list of paths to the worlds on the server. """ server_dir = Path(__file__).resolve().parents[1] world_paths = [] for p in server_dir.iterdir(): if p.is_dir and (p / "level.dat").is_file(): world_paths.app...
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import hmac import hashlib def is_valid_webhook_request(webhook_token: str, request_body: str, webhook_signature_header: str) -> bool: """This method verifies that requests to your Webhook URL are genuine and from Buycoins. Args: webhook_token: your webhook token request_body: the body of the...
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def _preprocess_stored_query(query_text, config): """Inject some default code into each stored query.""" ws_id_text = " LET ws_ids = @ws_ids " if 'ws_ids' in query_text else "" return '\n'.join([ config.get('query_prefix', ''), ws_id_text, query_text ])
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def print_scale(skill, points): """Return TeX lines for a skill scale.""" lines = ['\\cvskill{'] lines[0] += skill lines[0] += '}{' lines[0] += str(points) lines[0] += '}\n' return lines
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def _ontology_value(curie): """Get the id component of the curie, 0000001 from CL:0000001 for example.""" return curie.split(":")[1]
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def alias(*alias): """Select a (list of) alias(es).""" valias = [t for t in alias] return {"alias": valias}
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import json def read_json_info(fname): """ Parse info from the video information file. Returns: Dictionary containing information on podcast episode. """ with open(fname) as fin: return json.load(fin)
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def add_ending_slash(directory: str) -> str: """add_ending_slash function Args: directory (str): directory that you want to add ending slash Returns: str: directory name with slash at the end Examples: >>> add_ending_slash("./data") "./data/" """ if directory[-...
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import re def extractCompositeFigureStrings(latexString): """ Returns a list of latex figures as strings stripping out captions. """ # extract figures figureStrings = re.findall(r"\\begin{figure}.*?\\end{figure}", latexString, re.S) # filter composite figures only and remove captions (preserv...
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import re def BCA_formula_from_str(BCA_str): """ Get chemical formula string from BCA string Args: BCA_str: BCA ratio string (e.g. 'B3C1A1') """ if len(BCA_str)==6 and BCA_str[:3]=='BCA': # format: BCAxyz. suitable for single-digit integer x,y,z funits = BCA_str[-3:] e...
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def first_item(iterable, default=None): """ Returns the first item of given iterable. Parameters ---------- iterable : iterable Iterable default : object Default value if the iterable is empty. Returns ------- object First iterable item. """ if not ...
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def rank(value_to_be_ranked, value_providing_rank): """ Returns the rank of ``value_to_be_ranked`` in set of values, ``values``. Works even if ``values`` is a non-orderable collection (e.g., a set). A binary search would be an optimized way of doing this if we can constrain ``values`` to be an order...
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def get_specific_pos_value(img, pos): """ Parameters ---------- img : ndarray image data. pos : list pos[0] is horizontal coordinate, pos[1] is verical coordinate. """ return img[pos[1], pos[0]]
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import re def mrefresh_to_relurl(content): """Get a relative url from the contents of a metarefresh tag""" urlstart = re.compile('.*URL=') _, url = content.split(';') url = urlstart.sub('', url) return url
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import logging def get_previous_version(versions: dict, app: str) -> str: """Looks in the app's .version_history to retrieve the prior version""" try: with open(f"{app}/.version_history", "r") as fh: lines = [line.strip() for line in fh] except FileNotFoundError: logging.warnin...
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import requests def getSBMLFromBiomodelsURN(urn): """ Get SBML string from given BioModels URN. Searches for a BioModels identifier in the given urn and retrieves the SBML from biomodels. For example: urn:miriam:biomodels.db:BIOMD0000000003.xml Handles redirects of the download page. :p...
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import string def list_zero_alphabet() -> list: """Build a list: 0, a, b, c etc.""" score_dirs = ['0'] for char in string.ascii_lowercase: score_dirs.append(char) return score_dirs
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def dim_axis_label(dimensions, separator=', '): """ Returns an axis label for one or more dimensions. """ if not isinstance(dimensions, list): dimensions = [dimensions] return separator.join([d.pprint_label for d in dimensions])
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def _is_camel_case_ab(s, index): """Determine if the index is at 'aB', which is the start of a camel token. For example, with 'workAt', this function detects 'kA'.""" return index >= 1 and s[index - 1].islower() and s[index].isupper()
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def rgb2hex(rgb: tuple) -> str: """ Converts RGB tuple format to HEX string :param rgb: :return: hex string """ return '#%02x%02x%02x' % rgb
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def unix_to_windows_path(path_to_convert, drive_letter='C'): """ For a string representing a POSIX compatible path (usually starting with either '~' or '/'), returns a string representing an equivalent Windows compatible path together with a drive letter. Parameters ---------- path_to_conve...
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def flatten(iterable): """ Unpacks nested iterables into the root `iterable`. Examples: ```python from flashback.iterating import flatten for item in flatten(["a", ["b", ["c", "d"]], "e"]): print(item) #=> "a" #=> "b" #=> "c" #=> "d" ...
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from pathlib import Path def _path_to_str(var): """Make sure var is a string or Path, return string representation.""" if not isinstance(var, (Path, str)): raise ValueError("All path parameters must be either strings or " "pathlib.Path objects. Found type %s." % type(var)) ...
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def has_1080p(manifest): """Return True if any of the video tracks in manifest have a 1080p profile available, else False""" return any(video['width'] >= 1920 for video in manifest['videoTracks'][0]['downloadables'])
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def ms(val): """ Turn a float value into milliseconds as an integer. """ return int(val * 1000)
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import torch def compute_rays_length(rays_d): """Compute ray length. Args: rays_d: [R, 3] float tensor. Ray directions. Returns: rays_length: [R, 1] float tensor. Ray lengths. """ rays_length = torch.norm(rays_d, dim=-1, keepdim=True) # [N_rays, 1] return rays_length
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import itertools def _repeat_elements(arr, n): """ Repeats the elements int the input array, e.g. [1, 2, 3] -> [1, 1, 1, 2, 2, 2, 3, 3, 3] """ ret = list(itertools.chain(*[list(itertools.repeat(elem, n)) for elem in arr])) return ret
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def atlas_slice(atlas, slice_number): """ A function that pulls the data for a specific atlas slice. Parameters ---------- atlas: nrrd Atlas segmentation file that has a stack of slices. slice_number: int The number in the slice that corresponds to the fixed image for r...
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from typing import Dict import aiohttp async def head(url: str) -> Dict: """Fetch headers returned http GET request. :param str url: The URL to perform the GET request for. :rtype: dict :returns: dictionary of lowercase headers """ async with aiohttp.request("HEAD", url) as re...
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def determine_if_pb_should_be_filtered(row, min_junc_after_stop_codon): """PB should be filtered if NMD, a truncation, or protein classification is not likely protein coding (intergenic, antisense, fusion,...) Args: row (pandas Series): protein classification row min_junc_after_stop_codon (...
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def project_to_2D(xyz): """Projection to (0, X, Z) plane.""" return xyz[0], xyz[2]
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def transform_to_dict(closest_list: list) -> dict: """ Returns dict {(latitude, longitude): {film1, film2, ...}, ...} from closest_list [[film1, (latitude, longitude)], ...], where film1, film2 are titles of films, (latitude, longitude) is a coordinates of a place where those films were shoot. ...
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import signal def _signal_exit_code(signum: signal.Signals) -> int: """ Return the exit code corresponding to a received signal. Conventionally, when a program exits due to a signal its exit code is 128 plus the signal number. """ return 128 + int(signum)
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def is_contained(target, keys): """Check is the target json object contained specified keys :param target: target json object :param keys: keys :return: True if all of keys contained or False if anyone is not contained Invalid parameters is always return False. """ if not target or not key...
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def map(x, in_min, in_max, out_min, out_max): """ Map a value from one range to another :param in_min: minimum of input range :param in_max: maximum of input range :param out_min: minimum of output range :param out_max: maximum of output range :return: The value scaled ...
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import itertools def node_extractor(dataframe, *columns): """ Extracts the set of nodes from a given dataframe. :param dataframe: dataframe from which to extract the node list :param columns: list of column names that contain nodes :return: list of all unique nodes that appear in the provided data...
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def _prepare_memoization_key(args, kwargs): """ Make a tuple of arguments which can be used as a key for a memoized function's lookup_table. If some object can't be hashed then used its __repr__ instead. """ key_list = [] for arg in args: try: hash(arg) key_li...
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def by_tag(articles_by_tag, tag): """ Filter a list of (tag, articles) to list of articles by tag""" for a in articles_by_tag: if a[0].slug == tag: return a[1]
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def dp_port_id(switch: str, port: str) -> str: """ Return a unique id of a DP switch port based on switch name and port name :param switch: :param port: :return: """ return 'port+' + switch + ':' + port
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def tuple_list_to_lua(tuple_list): """Given a list of tuples, return a lua table of tables""" def table(it): return "{" + ",".join(map(str, it)) + "}" return table(table(t) for t in tuple_list)
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def fancy_vector(v): """ Returns a given 3-vector or array in a cute way on the shell, if you use 'print' on the return value. """ return "\n / %5.2F \\\n" % (v[0]) + \ " | %5.2F |\n" % (v[1]) + \ " \\ %5.2F /\n" % (v[2])
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def any_of(elements): """ Check to see if the argument is contained in a list of possible elements. :param elements: The elements to check the argument against in the predicate. :return: A predicate to check if the argument is a constituent element. """ def predicate(argument): return a...
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def find_year(films_lst: list, year: int): """ Filter list of films by given year """ filtered_films_lst = [line for line in films_lst if line[1] == str(year)] return filtered_films_lst
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def cal_occurence(correspoding_text_number_list): """ calcualte each occurence of a number in a list """ di = dict() for i in correspoding_text_number_list: i = str(i) s = di.get(i, 0) if s == 0: di[i] = 1 else: di[i] = di[i] + 1 return di
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def ConvertVolumeSizeString(volume_size_gb): """Converts the volume size defined in the schema to an int.""" volume_sizes = { "500 GB (128 GB PD SSD x 4)": 500, "1000 GB (256 GB PD SSD x 4)": 1000, } return volume_sizes[volume_size_gb]
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def get_snps(x: str) -> tuple: """Parse a SNP line and return name, chromsome, position.""" snp, loc = x.split(' ') chrom, position = loc.strip('()').split(':') return snp, chrom, int(position)
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def get_upper_parentwidget(widget, parent_position: int): """This function replaces this: self.parentWidget().parentWidget().parentWidget() with this: get_upper_parentwidget(self, 3) :param widget: QWidget :param parent_position: Which parent :return: Wanted parent widget ...
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def add(n): """Add 1.""" return n + 1
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def sortkey(d): """Split d on "_", reverse and return as a tuple.""" parts=d.split("_") parts.reverse() return tuple(parts)
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def first_n(m: dict, n: int): """Return first n items of dict""" return {k: m[k] for k in list(m.keys())[:n]}
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import pickle def save_calib(filename, calib_params): """ Saves calibration parameters as '.pkl' file. Parameters ---------- filename : str Path to save file, must be '.pkl' extension calib_params : dict Calibration parameters to save Returns ------- saved : bool Saved successfully. """ i...
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def create_P(P_δ, P_ζ, P_ι): """ Combine `P_δ`, `P_ζ` and `P_ι` into a single matrix. Parameters ---------- P_δ : ndarray(float, ndim=1) Probability distribution over the values of δ. P_ζ : ndarray(float, ndim=2) Markov transition matrix for ζ. P_ι : ndarray(float, ndim=1)...
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import typing def median(vals: typing.List[float]) -> float: """Calculate median value of `vals` Arguments: vals {typing.List[float]} -- list of values Returns: float -- median value """ index = int(len(vals) / 2) - 1 return sorted(vals)[index]
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import networkx def nx_find_connected_limited(graph, start_set, end_set, max_depth=3): """Return the neurons in end_set reachable from start_set with limited depth.""" reverse_graph = graph.reverse() reachable = [] for e in end_set: preorder_nodes = list( ( network...
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def hexbyte_2integer_normalizer(first_int_byte, second_int_btye): """Function to normalize integer bytes to a single byte Transform two integer bytes to their hex byte values and normalize their values to a single integer Parameters __________ first_int_byte, second_int_byte : int inte...
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def get_correct_line(df_decisions): """ The passed df has repeated lines for the same file (same chemin_source). We take the most recent one. :param df_decisions: Dataframe of decisions :return: Dataframe without repeated lines (according to the chemin_source column) """ return df_decisions....
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def get_service(vm, port): """Return the service for a given port.""" for service in vm.get('suppliedServices', []): if service['portRange'] == port: return service
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def _project(doc, projection): """Return new doc with items filtered according to projection.""" def _include_key(key, projection): for k, v in projection.items(): if key == k: if v == 0: return False elif v == 1: return...
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import requests import json def folder0_content(folder0_id, host, token): """ Modules ------- request, json ---------- Parameters ---------- folder0_id : Onedata folder level 0 id containing the data to publish. host : OneData provider (e.g., ceta-ciemat-02.datahub.egi.eu). tok...
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import requests import logging def odata_getone(url, headers): """ Get a single object from Odata """ r = requests.get(url, headers=headers) if not r.ok: logging.warning(f"Fetch url {url} hit {r.status_code}") return None rjson = r.json() if 'error' in rjson: loggin...
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from datetime import datetime import pytz def isotime(timestamp): """ISO 8601 formatted date in UTC from unix timestamp""" return datetime.fromtimestamp(timestamp, pytz.utc).isoformat()
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def _get_index_sort_str(env, name): """ Returns a string by which an object with the given name shall be sorted in indices. """ ignored_prefixes = env.config.cmake_index_common_prefix for prefix in ignored_prefixes: if name.startswith(prefix) and name != prefix: return n...
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import requests def tmdb_find_movie(movie: str, tmdb_api_token: str): """ Search the tmdb api for movies by title Args: movie (str): the title of a movie tmdb_api_token (str): your tmdb v3 api token Returns: dict """ url = 'https://api.themoviedb.org/3/search/movie?' ...
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def errorString(node, error): """ Format error messages for node errors returned by checkLinkoStructure. inputs: node - the node for the error. error - a (backset, foreset) tuple, where backset is the set of missing backlinks and foreset is the set of missing forelinks. returns: string ...
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def _Backward3a_T_Ps(P, s): """Backward equation for region 3a, T=f(P,s) Parameters ---------- P : float Pressure [MPa] s : float Specific entropy [kJ/kgK] Returns ------- T : float Temperature [K] References ---------- IAPWS, Revised Supplementary ...
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def format_dB(num): """ Returns a human readable string of dB. The value is divided by 10 to get first decimal digit """ num /= 10 return f'{num:3.1f} {"dB"}'
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def get_fourier_col_name(k, col_name, function_name="sin", seas_name=None): """Returns column name corresponding to a particular fourier term, as returned by fourier_series_fcn :param k: int fourier term :param col_name: str column in the dataframe used to generate fourier series :param...
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def build_binary_value(char_str, bits, alphabet) -> str: """ This method converts a string char_str into binary, using n bits per character and decoding from the supplied alphabet or from ASCII when bits=7 This is almost the inverse method to build_string in the decompress module. :param char_str:...
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def irange(start, end): """Inclusive range from start to end (vs. Python insanity.) irange(1,5) -> 1, 2, 3, 4, 5""" return range( start, end + 1 )
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import unicodedata def sanitize_str(value: str) -> str: """Removes Unicode control (Cc) characters EXCEPT for tabs (\t), newlines (\n only), line separators (U+2028) and paragraph separators (U+2029).""" return "".join(ch for ch in value if unicodedata.category(ch) != 'Cc' and ch not in {'\t', '\n', '\u2028', '\u20...
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from typing import Optional def clean_pin_cite(pin_cite: Optional[str]) -> Optional[str]: """Strip spaces and commas from pin_cite, if it is not None.""" if pin_cite is None: return pin_cite return pin_cite.strip(", ")
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import json def get_json_dump(json_object, indent=4, sort_keys=False): """ Short handle to get a pretty printed str from a JSON object. """ return json.dumps(json_object, indent=indent, sort_keys=sort_keys)
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def heap_sort(arr: list): """ Heap sorting a list. Big-O: O(n log n). @see https://www.geeksforgeeks.org/heap-sort/ """ def heapify(sub: list, rdx: int, siz: int): """ Heapifying range between rdx and size ([rdx:siz]). @param sub: a slice of list. @param rdx: root/p...
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def prompt_for_password(prompt=None): """Fake prompt function that just returns a constant string""" return 'promptpass'
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def get_frame_list(video, jump_size = 6, **kwargs): """ Returns list of frame numbers including first and last frame. """ frame_numbers =\ [frame_number for frame_number in range(0, video.frame_count, jump_size)] last_frame_number = video.frame_count - 1; if frame_numbers[-1] != last_...
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def obter_forca (unidade): """Esta funcao devolve a forca de ataque da unidade dada como argumento""" return unidade[2]
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import itertools def strip_translations_header(translations: str) -> str: """ Strip header from translations generated by ``xgettext``. Header consists of multiple lines separated from the body by an empty line. """ return "\n".join(itertools.dropwhile(len, translations.splitlines()))
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def find_attachments(pattern, cursor): """Return a list of attachments that match the specified pattern. Args: pattern: The path to the attachment, as a SQLite pattern (to be passed to a LIKE clause). cursor: The Cursor object through which the SQLite queries are sent to...
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def should_parse(config, file): """Check if file extension is in list of supported file types (can be configured from cli)""" return file.suffix and file.suffix.lower() in config.filetypes
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def flatten(x): """Flattens nested list""" if isinstance(x, list): return [a for i in x for a in flatten(i)] else: return [x]
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def identity(obj): """Returns the ``obj`` parameter itself :param obj: The parameter to be returned :return: ``obj`` itself >>> identity(5) 5 >>> foo = 2 >>> identity(foo) is foo True """ return obj
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