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def repeat(s: str, n: int) -> str: """ Return s repeated n times; if n is negative, return the empty string. >>> repeat('yes', 4) 'yesyesyesyes' >>> repeat('no', 0) '' >>> repeat('no', -2) '' >>> repeat('yesnomaybe', 3) 'yesnomaybeyesnomaybeyesnomaybe' """ return s * n
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def set_or_callable(value): """Convert single str or None to a set. Pass through callables and sets.""" if value is None: return frozenset() if callable(value): return value if isinstance(value, (frozenset, set, list)): return frozenset(value) return frozenset([str(value)])
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def add_id(pos_list, image_id=0): """ Add id for gather feature, for inference. """ new_list = [] for item in pos_list: new_list.append((image_id, item[0], item[1])) return new_list
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def is_empty_tensor(t): """Returns whether t is an empty tensor.""" return len(t.size()) == 0
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import numpy def sinusoid( frequency, sampling_frequency=16000, duration=0.025 ): """Generate a sinusoid signal. Args: frequency (int): the frequency of the sinusoidal signal. sampling_frequency (int, optional): sampling frequency in Hz. Defaults to 16000. duration (float, optional): duration of the output sinusoid in seconds. Defaults to 0.025. Returns: numpy.array: a sinusoid. """ times = numpy.arange(int(sampling_frequency * duration)) return numpy.sin(2 * numpy.pi * frequency * times / sampling_frequency)
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def isNotTrue (b) : """return True if b is not equal to True, return False otherwise >>> isNotTrue(True) False >>> isNotTrue(False) True >>> isNotTrue("hello world") True """ # take care: not(X or Y) is (not X) and (not Y) if b is not True and b != True : # base case: b not equals to True => return True return True else : # otherwise: solve the problem recursively return isNotTrue(not b) == (False or ...)
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def search(variable: str, target: str) -> str: """Search serice using mwapi on wikidata Args: variable (str): variable name (?film, ?director...) target (str): value to search for Returns: str: service query """ if variable is None or target is None: return "" return f""" SERVICE wikibase:mwapi {{ bd:serviceParam wikibase:api "EntitySearch" . bd:serviceParam wikibase:endpoint "www.wikidata.org" . bd:serviceParam mwapi:search "{target}" . bd:serviceParam mwapi:language "en" . {variable} wikibase:apiOutputItem mwapi:item . }} """
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def postprocess_question(text): """postprocess the output of question generation model for fair readable. output. Args: text (text): generated question to be processed. Returns: str: clean readable text. """ output = text.replace("question: ", "") output = output.strip() return output
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def get_job_data(job, average, qubit_idx, scale_factor): """ Retrieve data from a job that has already run. """ job_results = job.result(timeout=120) # Timeout after 120 s result_data = [] for i in range(len(job_results.results)): if average: # Get avg data result_data.append(job_results.get_memory(i)[qubit_idx] * scale_factor) else: # Get single data result_data.append(job_results.get_memory(i)[:, qubit_idx] * scale_factor) return result_data
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def expand_url(url, protocol): """ Expands the given URL to a full URL by adding the magento soap/wsdl parts :param url: URL to be expanded :param service: 'xmlrpc' or 'soap' """ if protocol == 'soap': ws_part = 'api/?wsdl' elif protocol == 'xmlrpc': ws_part = 'index.php/api/xmlrpc' else: ws_part = 'index.php/rest/V1' return url.endswith('/') and url + ws_part or url + '/' + ws_part
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def inner_product(x, y): """Inner product.""" return x.dot(y)
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def to_millis(seconds): """ Converts the time parameter in seconds to milliseconds. If the given time is negative, returns the original value. :param seconds: (Number), the given time in seconds. :return: (int), result of the conversation in milliseconds. """ if seconds >= 0: return int(seconds * 1000) return seconds
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from pathlib import Path import re def find_version(): """Retrieve the version.""" constpy = Path("dataplaybook/const.py").read_text() version_match = re.search(r"^VERSION = ['\"]([^'\"]+)['\"]", constpy, re.M) if version_match: return version_match.group(1) raise RuntimeError("Unable to find version string.")
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def escape_nl(msg): """ It's nice to know if we actually sent a complete line ending in \n, so escape it for display. """ if msg != '' and msg[-1] == "\n": return msg[:-1] + "\\n" return msg
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def noun(name: str, num: int) -> str: """ This function returns a noun in it's right for a specific quantity :param name: :param num: :return: """ if num == 0 or num > 1: return name + "s" return name
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def get_assessor_dict(assessor_label, assessor_path): """ Generate the dictionary for an assessor from the folder in the queue :param assessor_label: assessor label :param assessor_path: assessor path on the station :return: None """ assessor_dict = dict() keys = ['project_id', 'subject_label', 'session_label', 'label', 'proctype', 'path'] labels = assessor_label.split('-x-') if len(labels) > 3: values = [labels[0], labels[1], labels[2], assessor_label, labels[-1], assessor_path] assessor_dict = dict(list(zip(keys, values))) return assessor_dict
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import torch def _rmse(y, y_hat): """RMSE""" y_hat = y_hat.unsqueeze(1) if y_hat.dim() == 1 else y_hat y = y.unsqueeze(1) if y.dim() == 1 else y assert y.shape == y_hat.shape assert y.dim() == 2 assert y.shape[-1] == 1 return torch.nn.functional.mse_loss(y, y_hat).pow(0.5)
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import re def build_tx_cigar(exons, strand): """builds a single CIGAR string representing an alignment of the transcript sequence to a reference sequence, including introns. The input exons are expected to be in transcript order, and the resulting CIGAR is also in transcript order. >>> build_tx_cigar([], 1) is None True """ cigarelem_re = re.compile(r"\d+[=DIMNX]") def _reverse_cigar(c): return ''.join(reversed(cigarelem_re.findall(c))) if len(exons) == 0: return None # flip orientation of all CIGARs if on - strand if strand == -1: cigars = [_reverse_cigar(e["cigar"]) for e in exons] else: cigars = [e["cigar"] for e in exons] tx_cigar = [cigars[0]] # exon 1 for i in range(1, len(cigars)): # and intron + exon pairs thereafter intron = str(exons[i]["alt_start_i"] - exons[i - 1]["alt_end_i"]) + "N" tx_cigar += [intron, cigars[i]] tx_cigar_str = "".join(tx_cigar) return tx_cigar_str
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def DictionaryofDate_valuetoArrays(Date_value): """Returns (array): date, value """ date = Date_value.keys() date.sort() value = [] for d in date: value.append(Date_value[d]) return date, value
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import os def _in_load_test_mode(): """Returns True if the default values should be used instead of the server provided bot_config.py. This also disables server telling the bot to restart. """ return os.environ.get('SWARMING_LOAD_TEST') == '1'
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import re def cassini_time(time): """Parse Cassini time. Parameters ---------- time: str, int or float Cassini time. Returns ------- float Parsed Cassini time as float. Raises ------ ValueError If the input time pattern is invalid. Examples -------- >>> cassini_time('v1487096932_1') 1487096932.0 >>> cassini_time(1483230358.172) 1483230358.172 """ cassini_time = re.findall(r'(\d{10})(\.\d+)?', str(time)) if not cassini_time: raise ValueError(f'Cassini time invalid: `{time}`') return float(''.join(cassini_time[0]))
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def pods_by_uid(pods): """Construct a dict of pods, keyed by pod uid""" return {pod["metadata"]["uid"]: pod for pod in pods}
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def _tags_conform_to_filter(tags, filter): """Mirrors Bazel tag filtering for test_suites. This makes sure that the target has all of the required tags and none of the excluded tags before we include them within a test_suite. For more information on filtering inside Bazel, see com.google.devtools.build.lib.packages.TestTargetUtils.java. Args: tags: all of the tags for the test target filter: a struct containing excluded_tags and required_tags Returns: True if this target passes the filter and False otherwise. """ # None of the excluded tags can be present. for exclude in filter.excluded_tags: if exclude in tags: return False # All of the required tags must be present. for required in filter.required_tags: if required not in tags: return False # All filters have been satisfied. return True
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import optparse def get_options(): """define options for this script and interpret the command line""" optParser = optparse.OptionParser() optParser.add_option("--nogui", action="store_true", default=False, help="run the commandline version of sumo") options, args = optParser.parse_args() return options
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def set_max_results(uri, max): """Set max-results parameter if it is not set already.""" max_str = str(max) if uri.find('?') == -1: return uri + '?max-results=' + max_str else: if uri.find('max-results') == -1: return uri + '&max-results=' + max_str else: return uri
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import torch def kronecker(mat1, mat2): """ kronecker product between 2 2D tensors :param mat1: 2d torch.Tensor :param mat2: 2d torch.Tensor :return: kronecker product of mat1 and mat2 """ s1 = mat1.size() s2 = mat2.size() return torch.ger(mat1.view(-1), mat2.view(-1)).reshape(*(s1 + s2)).permute([0, 2, 1, 3]).reshape(s1[0] * s2[0], s1[1] * s2[1])
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def StringCompression(s: str) -> str: """Compresses the specified string using counts of repeated characters. >>> StringCompression("") '' >>> StringCompression("a") 'a' >>> StringCompression("ab") 'ab' >>> StringCompression("abc") 'abc' >>> StringCompression("aba") 'aba' >>> StringCompression("aa") 'a2' >>> StringCompression("aab") 'a2b1' >>> StringCompression("aabaa") 'a2b1a2' >>> StringCompression("aabaabbcddeeef") 'a2b1a2b2c1d2e3f1' >>> StringCompression("aabcccccaaa") 'a2b1c5a3' """ compressed_segments = [] i = 0 while i < len(s): current_character = s[i] count = 1 while i + 1 < len(s) and current_character == s[i + 1]: i += 1 count += 1 compressed_segments.append((current_character, count)) i += 1 if all(map(lambda x: x[1] == 1, compressed_segments)): return s compressed_s = "".join( [f"{character}{count}" for character, count in compressed_segments] ) return compressed_s
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import re def possibly_fix_width(text): """Heuristic to possibly mark-up text as monospaced if it looks like a URL, or an environment variable name, etc.""" if text in ['', '--']: return text # stringify the arguments if type(text) not in [type('string'), type(u'Unicode')]: text = "%r" % text if text[0] in "$/" or "}" == text[-1] or re.match(r'^[A-Z_\${}:-]+$', text): return '`%s`' % text return text
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def weighted_score(raw_earned, raw_possible, weight): """ Returns a tuple that represents the weighted (earned, possible) score. If weight is None or raw_possible is 0, returns the original values. When weight is used, it defines the weighted_possible. This allows course authors to specify the exact maximum value for a problem when they provide a weight. """ assert raw_possible is not None cannot_compute_with_weight = weight is None or raw_possible == 0 if cannot_compute_with_weight: return raw_earned, raw_possible else: return float(raw_earned) * weight / raw_possible, float(weight)
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def addr_entry(key): """querries the user for address data, cleans it""" # getting the input rawline = input( 'please enter ' + key + ': ' ) # get rid of trailing whitespace line = rawline.strip() # replace tabs line = line.replace('\t', ' ') # remove forbidden strings trans_tab = dict.fromkeys( map(ord, '\:.\"\'!@#$\\\/'), None ) line = line.translate(trans_tab) if rawline != line: print( 'Warning: string has been changed: \'' + rawline + '\' to \'' + line + '\'.' ) return line
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import argparse def parse_arguments(): """ Read in the config file specifying all of the parameters """ parser = argparse.ArgumentParser(description="Learn subgraph embeddings") parser.add_argument("-config_path", type=str, default=None, help="Load config file") args = parser.parse_args() return args
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def harmonic_epmi_score(pdict, wlist1, wlist2): """ Calculate harmonic mean of exponentiated PMI over all word pairs in two word lists, given pre-computed PMI dictionary - If harmonic ePMI is undefined, return -inf """ total_recip_epmi = None # Number of pairs for which PMI exists N = 0 for word1 in wlist1: for word2 in wlist2: # Enforce alphabetical order in pair pair = tuple(sorted([word1, word2])) wi, wj = pair if wi in pdict and wj in pdict[wi]: if total_recip_epmi is None: total_recip_epmi = 0 total_recip_epmi += 1/(2**pdict[wi][wj]) N += 1 if total_recip_epmi is not None: return N/total_recip_epmi else: return float("-inf")
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def optional_apply(f, value): """ If `value` is not None, return `f(value)`, otherwise return None. >>> optional_apply(int, None) is None True >>> optional_apply(int, '123') 123 Args: f: The function to apply on `value`. value: The value, maybe None. """ if value is not None: return f(value)
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def repl_func(m): """process regular expression match groups for word upper-casing problem""" return m.group(1) + m.group(2).upper()
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def prod(F, E): """Check that the factorization of P-1 is correct. F is the list of factors of P-1, E lists the number of occurrences of each factor.""" x = 1 for y, z in zip(F, E): x *= y**z return x
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def sort_data(data, cols): """Sort `data` rows and order columns""" return data.sort_values(cols)[cols + ['value']].reset_index(drop=True)
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import torch def argval_subsample_idx(values, n, polarity="MAX"): """values is a list, n an int, polarity is MAX or MIN""" assert n > 0 descending = {"MAX": True, "MIN": False}[polarity] _, idxs = torch.sort(torch.Tensor(values), descending=descending) return idxs.tolist()[:n]
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import logging def sanitise_graphite_url(current_skyline_app, graphite_url): """ Transform any targets in the URL that need modifications like double encoded forward slash and return whether the URL was sanitised and the url. :param current_skyline_app: the Skyline app calling the function :param graphite_url: the URL :type current_skyline_app: str :type graphite_url: str :return: sanitised, url :rtype: tuple """ sanitised_url = graphite_url sanitised = False current_logger = None if '.%2F' in sanitised_url: try: sanitised_url = graphite_url.replace('.%2F', '.%252F') sanitised = True try: current_skyline_app_logger = str(current_skyline_app) + 'Log' current_logger = logging.getLogger(current_skyline_app_logger) except: pass if current_logger: current_logger.info('sanitise_graphite_url - transformed %s to %s' % ( graphite_url, str(graphite_url))) except: pass if '+' in graphite_url: try: new_sanitised_url = sanitised_url.replace('+', '%2B') sanitised_url = new_sanitised_url sanitised = True try: current_skyline_app_logger = str(current_skyline_app) + 'Log' current_logger = logging.getLogger(current_skyline_app_logger) except: pass if current_logger: current_logger.info('sanitise_graphite_url - transformed %s to %s' % ( graphite_url, str(sanitised_url))) except: pass return sanitised, sanitised_url
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def _union_all(iterables): """Return a set representing the union of all the contents of an iterable of iterables. """ out = set() for iterable in iterables: out.update(iterable) return out
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from typing import List def construct_relative_positions(pos: int, max_length: int) -> List[int]: """Construct relative positions to a specified pos Args: pos: the pos that will be `0` max_length: max sequence length Returns: a list of relative positions Raises: ValueError: if pos is less than 0 or greater equal than max_length """ if pos < 0 or pos >= max_length: raise ValueError(f"pos: {pos} is not in [0, {max_length})") positions = list(range(0, max_length, 1)) positions = list(map(lambda x: abs(x - pos), positions)) return positions
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import subprocess import os def score(molfile1, molfile2, path_to_lsalign='/data/rsg/chemistry/yangk/LSalign/src'): """ LSalign similarity score for two molecules, each in a separate molfile whose path is given as input. """ with open('tmp.txt', 'w') as f: subprocess.call([os.path.join(path_to_lsalign, 'LSalign'), molfile1, molfile2, '-rf 1'], stdout=f) with open('tmp.txt', 'r') as f: lines = f.readlines() score_row = lines[3].strip().split() pc_score_avg = (float(score_row[2]) + float(score_row[3])) * 0.5 return pc_score_avg
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import pathlib def _match_path(p1, p2): """Compare two paths from right to left and return True if they could refer to the same file. As a special case, if the second argument is None, or empty, it is always considered a match. This simplifies query logic when the target does not have a path component. If p2 starts with "./" then the paths must math entirely. This to allow addressing in the case where a path is a prefix of another. """ if not p2: return True part1 = pathlib.Path(p1).parts part2 = pathlib.Path(p2).parts if p2.startswith(".") and part2 and not part2[0].startswith("."): minlen = 0 else: minlen = min(len(part1), len(part2)) return part1[-minlen:] == part2[-minlen:]
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import argparse def create_parent_parser(prog_name): """ Create parent parser Args: prog_name (str): program name Returns: parser: parent argument parser Raises: DistributionNotFound: version of family not found """ parent_parser = argparse.ArgumentParser(prog=prog_name, add_help=False) parent_parser.add_argument( '-v', '--verbose', action='count', help='enable more verbose output') return parent_parser
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import re def has_text_an_image(text): """ :param text: String with base64 data :return: true if text has base64 data otherwise false """ regex_to_extract = r'data:image.+\"' return re.search(regex_to_extract, text)
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def _extract_asm_mnemonic(asm): """ :param asm: :type asm: """ return asm.split()[0].strip().upper()
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def get_spaces(depth): """returns the required number of spaces for indentation purpose""" return ' ' * (depth * 4 - 2)
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import re def _clean(arr): """Convert ratio values for missing pieces of the tax into "unclassified" and remove empty entries. Rules: - if all the cols are unclassified then remove row. - if there is no classification for either genus, subfamily or family then remove row. - collapse unclassified values from low to high - example: Caudovirales unclassified unclassified unclassified should be: Caudovirales """ converted_tax = [] for tax_value in arr[::-1]: if tax_value == "" or \ tax_value == "\n" or \ re.match(r"^[+-]?\d(>?\.\d+)?$", tax_value): converted_tax.append("unclassified") else: converted_tax.append(tax_value.strip()) # rule 1 if len(converted_tax) == converted_tax.count("unclassified"): return tuple(("unclassified",)) # rule 2 and 3 result = [] for i in range(0, len(converted_tax) - 1): if not (converted_tax[i] == "unclassified" and converted_tax[i + 1] == "unclassified"): result.append(converted_tax[i]) if converted_tax[-1] != "unclassified": result.append(converted_tax[-1]) return tuple(result)
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from os import popen def unixgetaddr(program): """Get the hardware address on a Unix machine.""" for line in popen(program): words = line.lower().split() if 'hwaddr' in words: addr = words[words.index('hwaddr') + 1] return int(addr.replace(':', ''), 16) if 'ether' in words: addr = words[words.index('ether') + 1] return int(addr.replace(':', ''), 16)
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def sequence_id(sqlite_connection): """ Функция возвращает список из id всех остановок """ try: cur = sqlite_connection.cursor() cur.execute("SELECT _id FROM stopsker") seq = list() for elem in cur.fetchall(): seq.append(int(elem[0])) except Exception as exp: print({exp}) exit() else: return seq
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def add_matches(flight_matches, flight_ids): """ Add new matches to the flight_ids dict. Returns the number of newly matched flights. """ matches = 0 for i in flight_matches.index: prev_id = flight_matches.loc[i, 'FLIGHT_ID_x'] next_id = flight_matches.loc[i, 'FLIGHT_ID_y'] if next_id not in flight_ids: flight_ids[next_id] = prev_id matches += 1 return matches
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def get_requirements_from_file(requirements_file): """ Get requirements from file. :param str req_file: Name of file to parse for requirements. :return: List of requirements :rtype: list(str) """ requirements = [] with open(requirements_file) as f: for line in f: line = line.strip() if line and not line.startswith(("#", "-e")): requirements.append(line) return requirements
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from typing import Tuple from typing import List def extract_encoded_headers(payload: bytes) -> Tuple[str, bytes]: """This function's purpose is to extract lines that can be decoded using the UTF-8 decoder. >>> extract_encoded_headers("Host: developer.mozilla.org\\r\\nX-Hello-World: 死の漢字\\r\\n\\r\\n".encode("utf-8")) ('Host: developer.mozilla.org\\r\\nX-Hello-World: 死の漢字\\r\\n', b'') >>> extract_encoded_headers("Host: developer.mozilla.org\\r\\nX-Hello-World: 死の漢字\\r\\n\\r\\nThat IS totally random.".encode("utf-8")) ('Host: developer.mozilla.org\\r\\nX-Hello-World: 死の漢字\\r\\n', b'That IS totally random.') """ result: str = "" lines: List[bytes] = payload.splitlines() index: int = 0 for line, index in zip(lines, range(0, len(lines))): if line == b"": return result, b"\r\n".join(lines[index + 1 :]) try: result += line.decode("utf-8") + "\r\n" except UnicodeDecodeError: break return result, b"\r\n".join(lines[index + 1 :])
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def formatted_loss_components_string(components: dict) -> str: """ Formats the components returned by calc_LV_Lbeta """ total_loss = components['L_V']+components['L_beta'] fractions = { k : v/total_loss for k, v in components.items() } fkey = lambda key: f'{components[key]:+.4f} ({100.*fractions[key]:.1f}%)' s = ( 'L_V+L_beta = {L:.4f}' '\n L_V = {L_V}' '\n L_V_attractive = {L_V_attractive}' '\n L_V_repulsive = {L_V_repulsive}' '\n L_beta = {L_beta}' '\n L_beta_noise = {L_beta_noise}' '\n L_beta_sig = {L_beta_sig}' .format(L=total_loss,**{k : fkey(k) for k in components}) ) if 'L_beta_norms_term' in components: s += ( '\n L_beta_norms_term = {L_beta_norms_term}' '\n L_beta_logbeta_term = {L_beta_logbeta_term}' .format(**{k : fkey(k) for k in components}) ) if 'L_p' in components: s += f'\n L_p = {fkey("L_p")}' for key in sorted(k for k in components.keys() if k.startswith('L_p_')): s += f'\n {key:<20}= {fkey(key)}' s += f'\nTOTAL: L_V + L_beta + L_p = {total_loss+components["L_p"]}' return s
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def filter_ignore(annotations, filter_fns): """ Set the ``ignore`` attribute of the annotations to **True** when they do not pass the provided filter functions. Args: annotations (dict or list): Dictionary containing box objects per image ``{"image_id": [box, box, ...], ...}`` or list of annotations filter_fns (list or fn): List of filter functions that get applied or single filter function Returns: (dict or list): boxes after filtering """ if callable(filter_fns): filter_fns = [filter_fns] if isinstance(annotations, dict): for _, values in annotations.items(): for anno in values: if not anno.ignore: for fn in filter_fns: if not fn(anno): anno.ignore = True break else: for anno in annotations: if not anno.ignore: for fn in filter_fns: if not fn(anno): anno.ignore = True break return annotations
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def update_dict_params_for_calibration(params): """ Update some specific parameters that are stored in a dictionary but are updated during calibration. For example, we may want to update params['default']['compartment_periods']['incubation'] using the parameter ['default']['compartment_periods_incubation'] :param params: dict contains the model parameters :return: the updated dictionary """ if "n_imported_cases_final" in params: params["data"]["n_imported_cases"][-1] = params["n_imported_cases_final"] for location in ["school", "work", "home", "other_locations"]: if "npi_effectiveness_" + location in params: params["npi_effectiveness"][location] = params["npi_effectiveness_" + location] for comp_type in [ "incubation", "infectious", "late", "hospital_early", "hospital_late", "icu_early", "icu_late", ]: if "compartment_periods_" + comp_type in params: params["compartment_periods"][comp_type] = params["compartment_periods_" + comp_type] return params
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def counting_sort(numbers): """Sort given numbers (integers) by counting occurrences of each number, then looping over counts and copying that many numbers into output list. Running time: O(n + k) where k is the range of numbers, because if k is really high then affects the run time significantly. Memory usage: O(k) because the number of total arrays is equal to the value of k""" # creating a temp array with 0, times however many based on the max value of numbers + 1 b/c indexing starts at 1 temp_array = [0] * (max(numbers) + 1) # loop through numbers for num in numbers: # if the temp array's index of that number is 0 - meaning it's empty then set it to be 1 if temp_array[num] == 0: temp_array[num] = 1 # else there's already something in there so just add one to it else: temp_array[num] += 1 numbers = [] # loop through the temp_array for y in range(len(temp_array)): # if it's index is not equal to 0 then we add the count; and looping until it's index value is 0 while temp_array[y] != 0: numbers.append(y) temp_array[y] -= 1 return numbers
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def _unit_fun(x): """unit function""" return x
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import math import statistics def _get_average_da(streams_da: dict) -> dict: """Calculate average data availability among all data streams""" total_results = {} for k, v in streams_da.items(): for i, j in v.items(): if i not in total_results: total_results[i] = [] total_results[i].append(j) return {k: math.ceil(statistics.mean(v)) for k, v in total_results.items()}
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import os def basename(fullname): """os.path.basename""" return os.path.basename(fullname)
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def fixture_extended(): """Return a /forecast/extended/pollen/<ZIP> response.""" return { "Type": "pollen", "ForecastDate": "2018-06-12T00:00:00-04:00", "Location": { "ZIP": "80238", "City": "DENVER", "State": "CO", "periods": [ {"Period": "2018-06-12T13:47:12.897", "Index": 6.60}, {"Period": "2018-06-13T13:47:12.897", "Index": 6.30}, {"Period": "2018-06-14T13:47:12.897", "Index": 7.60}, {"Period": "2018-06-15T13:47:12.897", "Index": 7.60}, {"Period": "2018-06-16T13:47:12.897", "Index": 7.30}, ], "DisplayLocation": "Denver, CO", }, }
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def is_sequencing(lane_info): """ Determine if we are just sequencing and not doing any follow-up analysis """ if lane_info['experiment_type'] in ('De Novo','Whole Genome'): return True else: return False
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import string def _split_punc(source): """Split leading or trailing punctuation.""" tokens = source.split(" ") new_tokens = [] for token in tokens: if all(char in string.punctuation for char in token): new_tokens.append(token) continue leading_punc = None for punc in string.punctuation: if token.startswith(punc): leading_punc = punc token = token.lstrip(punc) break trailing_punc = None for punc in string.punctuation: if token.endswith(punc): trailing_punc = punc token = token.rstrip(punc) break if leading_punc: new_tokens.append(leading_punc) if token: new_tokens.append(token) if trailing_punc: new_tokens.append(trailing_punc) return " ".join(new_tokens)
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def get_cluster_name(tags): """ Get the cluster name from the list of specified tags :param tags: tags :type tags: [str] :returns: cluster name :rtype: str """ for tag in tags: if tag.startswith("storm.cluster.name:"): return tag.replace("storm.cluster.name:", "") return None
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from typing import BinaryIO import io import wave import struct def fixture_two_chunk_plain_wav() -> BinaryIO: """Creates a fixture WAVE file with two distinct sections. The audio is 100Hz mono. Each section 10 samples long. Samples in the first alternate between +/-(1 << 5) and in the second between +/-(1 << 10). Returns: File-like object with the bytes of the fixture WAVE file, positioned at the beginning. """ sample_rate = 100 chunk_duration_samples = 10 plain_wav_io = io.BytesIO() with wave.open(plain_wav_io, 'wb') as writer: writer.setnchannels(1) writer.setsampwidth(2) writer.setframerate(sample_rate) signs = [pow(-1, i) for i in range(chunk_duration_samples)] for magnitude in [(1 << 5), (1 << 10)]: writer.writeframes( struct.pack('<%dh' % len(signs), *[magnitude * s for s in signs])) plain_wav_io.seek(0) return plain_wav_io
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def _detailed_parse_choice(choice): """Return Selected Choice's Full Name string as per its codename. Choices are based as per our server. :param choice: str The code name of the choice :return: str Return Selected Choice's Full Name string as per its codename """ # Return Choice Full Name string if choice == "gensim-sum": return "Text Rank Algorithm Based (Gensim)" elif choice == "spacy-sum": return "Frequency Based (Spacy)" elif choice == "nltk-sum": return "Frequency Based (NLTK)" elif choice == "sumy-lsa-sum": return "Latent Semantic Analysis Based (Sumy)" elif choice == "sumy-luhn-sum": return "Luhn Algorithm Based (Sumy)" elif choice == "sumy-text-rank-sum": return "Text Rank Algorithm Based (Sumy)"
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def compute_mass_list(dialog_idx, sen_idx): """ Most confusing step... dialog_idx = [41, 81, 134, ...] means the first dialogue of the subtitle is plain_text[0:41] the second dialogue of the subtitle is plain_text[41:81] the third dialogue of the subtitle is plain_text[81:134] sen_idx = [81, 204, ...] means the first sentence of the subtitle is plain_text[0:81] the second sentence of the subtitle is plain_text[81:204] Usually the len(dialog_idx) is larger than the len(sen_idx), because one sentence may so long that the video maker have to split it into multiple dialogues. What this function want to do is try to figure out each sentence belongs to which dialogues. For example: Sentence: Coding has been the bread and butter for developers since the dawn of computing. [(5, 41), (6, 81)] means the "Coding has been the bread and butter for"(length equals to 41) is the 5th dialogue of the subtitle, "developers since the dawn of computing"(from position 41 to 81) is the 6th dialogue of the subtitle. mass_list = [[(1, a), (2, b)], [(3, c)], [(4, d), (5, e), (6, f)]] means a subtitle include 3 sentence (the length of the list record_each_sentence, len(record_each_sentence)) In the first sentence: there are 2 dialogues, the first dialogue is first_sentence[0:a] the second dialogue is first_sentence[a:b] In the second sentence: there are 1 dialogues, the third dialogue of the whole subtitle is second_sentence[0:c] :param dialog_idx: :param sen_idx: :return: record_each_sentence """ i = 0 j = 1 mass_list = [] one_sentence = [] while i < len(dialog_idx): if dialog_idx[i] > sen_idx[j]: mass_list.append(one_sentence) one_sentence = [] j += 1 else: one_sentence.append((i + 1, dialog_idx[i] - sen_idx[j - 1])) i += 1 mass_list.append(one_sentence) return mass_list
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import re def do_parse_pod_name(text): """Find the pod name from the failure and return the pod name.""" p = re.search(r' pod (\S+)', text) if p: return re.sub(r'[\'"\\:]', '', p.group(1)) else: return ""
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def _testProduct_to_dict(product_obj, ctx): """ Returns testProduct instance in dict format. Args: product_obj (_TestProduct): testProduct instance. ctx (SerializationContext): Metadata pertaining to the serialization operation. Returns: dict: product_obj as a dictionary. """ return {"productId": product_obj.product_id, "productName": product_obj.name, "price": product_obj.price, "tags": product_obj.tags, "dimensions": product_obj.dimensions, "warehouseLocation": product_obj.location}
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def hxltm_hastag_de_csvhxlated(csv_caput: list) -> list: """hxltm_hastag_de_csvhxlated [summary] Make this type of conversion: - 'item__conceptum__codicem' => '#item+conceptum+codicem' - 'item__rem__i_ara__is_arab' => '#item+rem+i_ara+is_arab' - '' => '' Args: csv_caput (list): Array of input items Returns: [list]: """ resultatum = [] for item in csv_caput: if len(item): resultatum.append('#' + item.replace('__', '+').replace('?', '')) else: resultatum.append('') return resultatum
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def preprocessing(df, attribute): """ This is the base preprocessing for french. It scapes \ char and replace all ocurrence of - :df: pandas data frame. :attribute: atribute of df. """ return getattr(df, attribute).map(lambda sent: sent.lower().replace('\'', '\\\' ').replace('-', ' '))
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import pickle def load_pickle(file, decompress=True): """ Load a .pickle file. :param file: file .pickle to load. :param decompress: the compress or not the file :return: loaded data. """ with open(file, "rb") as f: if decompress: data = pickle.load(f) else: data = f.read() return data
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def latex(df): """Converte o DF fornecido para tabela LaTeX""" return print(df.to_latex())
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def get_accountinfo(msg: dict) -> str: """ Returns a dictionary containing the account id and an array of prowler group checks. """ if msg == "": raise IndexError else: try: account_id = msg['Id'] return account_id except KeyError as err: raise err
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import os def add_suffix(img_file,suffix): """ add suffix for a given file name, and not change the file type :param img_file: img file, e.g. "xxx.jpg" :param suffix: "——abcde" :return: "xxx——abcde.jpg" """ name = os.path.splitext(img_file)[0] type_ = os.path.splitext(img_file)[1] file_name = name + suffix + type_ return file_name
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def shp2geojsonOgr(layer): """Shapefile to Geojson conversion using ogr.""" cmd = 'ogr2ogr -f GeoJSON -t_srs'\ + ' crs:84'\ + ' {layer}.geojson'\ + ' {layer}.shp' cmd = cmd.format(layer=layer) return cmd
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def lut_canonical_potential_edge(potential_edge): """Returns a canonical name of a potential edge, with respect to LUT height. Parameters ---------- potential_edge : str Instantiated name of the potential edge to be canonicized. Returns ------- str A canonical potential edge. """ prefix, u, v = potential_edge.split("__") lut_span = int(v.split('_')[1]) - int(u.split('_')[1]) if lut_span < 0: offset_str = "lutm%d_" % abs(lut_span) else: offset_str = "lutp%d_" % abs(lut_span) canonical = "__".join([prefix, '_'.join(u.split('_')[2:]),\ offset_str + '_'.join(v.split('_')[2:])]) return canonical
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def encode_boolean(value): """ Returns 1 or 0 if the value is True or False. None gets interpreted as False. Otherwise, the original value is returned. """ if value is True: return 1 if value is False or value is None: return 0 return value
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def validate_sami_id(candidate_sami_id): """Dummy validation function for SAMI IDs, always returns true.""" return True
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def get_workloads(month): """Calls the same method on the Month model.""" return month.get_workloads()
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def associate_node_id(tr, node=""): """ Returns a dictionary with key 'id' and value as the ID associated with the node string. """ return {"id": tr.get_uml_id(name=node)}
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import argparse def parse_arguments(args): """ Parse the arguments from the user """ parser = argparse.ArgumentParser( description= "Filter UniRef EC list\n", formatter_class=argparse.RawTextHelpFormatter) parser.add_argument( "-i","--input", help="the UniRef EC triplet file [map_EC_to_triplet_AC_U50_U90_Swissprot_and_Trembl.txt]\n", required=True) parser.add_argument( "-o","--output", help="the filtered UniRef file to write\n", required=True) parser.add_argument( "-u","--uniref", help="the UniRef type\n", choices=["50","90"], required=True) parser.add_argument( "-m","--min-ec-level", help="the minimum EC level for filtering\n", choices=["1","2","3","4"], required=True) return parser.parse_args()
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import os def extract_games(world_folder): """ Locate the games in a world folder. """ envs = [] for filename in os.listdir(world_folder): if filename.endswith(".ulx"): envs.append(world_folder + "/" + filename) return envs
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def clause_words(clause_tree): """ Returns the constants in a clause. These will be everything that is not a keyword. """ if clause_tree == []: return [] elif clause_tree[0] == 'func': assert(len(clause_tree) == 3) if clause_tree[2] == []: return [clause_tree[1]] else: return [clause_tree[1]] + [clause_words(c) for c in clause_tree[2]] elif clause_tree[0] == 'var': return [] else: return [clause_words(c) for c in clause_tree[1:]]
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import re def find_nonAscii(text): """ Return the first appearance of a non-ASCII character (in a `Match` object), or `None`. """ regex = re.compile(r'([^\x00-\x7F])+') return re.search(regex, text)
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def linear_search(arr, x): """ Performs a linear search :param arr: Iterable of elements :param x: Element to search for :return: Index if element found else None """ l = len(arr) for i in range(l): if arr[i] == x: return i return None
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import argparse def arg_parser() -> dict: """Parse CLI arguments. Returns: dict: parsed arguments in dictionary """ parser = argparse.ArgumentParser(description=__doc__) parser.add_argument("words", nargs="+", type=str, help="Sentence that will be translated") return parser.parse_args().__dict__
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def out_labels(G, q): """Returns a list of each of the labels appearing on the edges starting at `q` in `G`. Parameters ---------- G : labeled graph q : vertex in `G` Examples -------- >>> G = nx.MultiDiGraph() >>> G.add_edge(1, 2, label="a") >>> G.add_edge(1, 3, label="a") >>> G.add_edge(1, 1, label="b") >>> sd.out_labels(G, 1) ['a', 'a', 'b'] """ return [label for (_, _, label) in G.out_edges(q, data="label")]
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def convert_tf_config_to_jax_bert(config): """Convert TF BERT model config to be compatible with JAX BERT model. Args: config: dictionary of TF model configurations Returns: dictionary of param names and values compatible with JAX BERT model """ unnecessary_keys = ['initializer_range', 'backward_compatible', 'embedding_size'] for key in unnecessary_keys: if key in config: config.pop(key) # change TF parameter names to match JAX parameter names mapping = { 'attention_dropout_rate': 'attention_probs_dropout_prob', 'hidden_activation': 'hidden_act', 'dropout_rate': 'hidden_dropout_prob', 'emb_dim': 'hidden_size', 'mlp_dim': 'intermediate_size', 'max_len': 'max_position_embeddings', 'num_heads': 'num_attention_heads', 'num_layers': 'num_hidden_layers' } for jax_key, tf_key in mapping.items(): config[jax_key] = config.pop(tf_key) return config
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def find_sequences_before(context, strip): """ Returns a list of sequences that are before the strip in the current context """ return [s for s in context.sequences if s.frame_final_end <= strip.frame_final_start]
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import math def update_one_contribute_score(user_total_click_num): """ item cf update sim contribution score by user """ return 1/math.log10(1+user_total_click_num)
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def get_percent_alloc(values): """ Determines a portfolio's allocations. Parameters ---------- values : pd.DataFrame Contains position values or amounts. Returns ------- allocations : pd.DataFrame Positions and their allocations. """ return values.divide( values.sum(axis='columns'), axis='rows' )
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import argparse def parse_args(): """Argument parser.""" parser = argparse.ArgumentParser(description='Argument parser for AUPR-in/AUPR-out evaluations.') parser.add_argument('--algo_name', type=str, default='e3outlier-0.1') parser.add_argument('--positive', type=str, default='inliers', choices=['inliers', 'outliers'], help='Whether the positive class is inliers or outliers') parser.add_argument('--results_dir', type=str, default='./results') parser.add_argument('--dataset', type=str, default='cifar10') return parser.parse_args()
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def format_latex(ss): """ Formats a string so that it is compatible with Latex. :param ss: The string to format :type ss: string :return: The formatted string :rtype: string """ tt = (str(ss).replace('_', ' ') .replace('%', '\%') ) return tt
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def MatchingFileType(file_name, extensions): """Returns true if the file name ends with one of the given extensions.""" return bool([ext for ext in extensions if file_name.lower().endswith(ext)])
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def escape_path(value: bytes) -> str: """ Take a binary path value, and return a printable string, with special characters escaped. """ def human_readable_byte(b: int) -> str: if b < 0x20 or b >= 0x7F: return "\\x{:02x}".format(b) elif b == ord(b"\\"): return "\\\\" return chr(b) return "".join(human_readable_byte(b) for b in value)
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def raw_reward_threshold(threshold): """Return a reward processor that cut off at a threshold.""" def fn(metadata): if metadata['raw_reward'] > threshold: return 1. elif metadata['raw_reward'] > 0: return -1 return metadata['raw_reward'] return fn
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import socket def get_hostname() -> str: """ Get the current hostname, or fall back to localhost. """ try: return socket.getfqdn() except: return 'localhost'
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def SerializeEntries(entries): """Serializes given triplets of python and wire values and a descriptor.""" output = [] for python_format, wire_format, type_descriptor in entries: if wire_format is None or (python_format and type_descriptor.IsDirty(python_format)): wire_format = type_descriptor.ConvertToWireFormat(python_format) output.extend(wire_format) return "".join(output)
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import socket import subprocess import json def get_instance_identification(): """ Gets an identifier for an instance. Gets EC2 instanceId if possible, else local hostname """ instance_id = socket.gethostname() try: # "special tactics" for getting instance data inside EC2 instance_data = subprocess.check_output( ["curl", "--silent", "http://169.254.169.254/latest/dynamic/instance-identity/document"]) # convert from json to dict if "bytes" in str(type(instance_data)): instance_data = instance_data.decode() instance_data = json.loads(instance_data) # get the instanceId if 'instanceId' in instance_data: instance_id = instance_data['instanceId'] except Exception as e: raise Exception("{}\nFailed to get instance identification. " "Check if you are actually on an aws EC2 server.".format(e)) return instance_id
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from datetime import datetime def get_submission_data_from_pushshift(raw_submission): """Creates a submission object from a Pushshift Submission JSON Parameters: raw_submission (dict): Pushshift Submission instance Returns: dict: object with information about a submission, like body, author or URL """ if (not 'selftext' in raw_submission) or ('selftext' in raw_submission and raw_submission["selftext"] == "") or \ ('selftext' in raw_submission and raw_submission["selftext"] is not None and raw_submission["selftext"].strip() == "") or \ raw_submission["selftext"] == "[deleted]" or raw_submission["selftext"] == "[removed]": return None date = datetime.fromtimestamp(raw_submission["created_utc"]) if 'created_utc' in raw_submission else None return { "author": raw_submission["author"] if 'author' in raw_submission else None, "created_utc": raw_submission["created_utc"] if 'created_utc' in raw_submission else None, "date": date.strftime('%Y-%m-%d %H:%M:%S') if date is not None else None, "id": raw_submission["id"] if 'id' in raw_submission else None, "is_original_content": raw_submission["is_original_content"] if 'is_original_content' in raw_submission else None, "is_text_only": raw_submission["is_self"] if 'is_self' in raw_submission else None, "locked": raw_submission["locked"] if 'locked' in raw_submission else None, "num_comments": raw_submission["num_comments"] if 'num_comments' in raw_submission else None, "over_18": raw_submission["over_18"] if 'over_18' in raw_submission else None, "permalink": raw_submission["permalink"] if 'permalink' in raw_submission else None, "score": raw_submission["score"] if 'score' in raw_submission else None, "body": raw_submission["selftext"] if 'selftext' in raw_submission else None, "spoiler": raw_submission["spoiler"] if 'spoiler' in raw_submission else None, "stickied": raw_submission["stickied"] if 'stickied' in raw_submission else None, "subreddit_id": raw_submission["subreddit_id"] if 'subreddit_id' in raw_submission else None, "subreddit_name": raw_submission["subreddit"] if 'subreddit' in raw_submission else None, "title": raw_submission["title"] if 'title' in raw_submission else None, "upvote_ratio": raw_submission["upvote_ratio"] if 'upvote_ratio' in raw_submission else None, "url": raw_submission["url"] if 'url' in raw_submission else None }
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