Mercurial > repos > jpayne > bioproject_to_srr_2
diff charset_normalizer/cd.py @ 7:5eb2d5e3bf22
planemo upload for repository https://toolrepo.galaxytrakr.org/view/jpayne/bioproject_to_srr_2/556cac4fb538
author | jpayne |
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date | Sun, 05 May 2024 23:32:17 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/charset_normalizer/cd.py Sun May 05 23:32:17 2024 -0400 @@ -0,0 +1,395 @@ +import importlib +from codecs import IncrementalDecoder +from collections import Counter +from functools import lru_cache +from typing import Counter as TypeCounter, Dict, List, Optional, Tuple + +from .constant import ( + FREQUENCIES, + KO_NAMES, + LANGUAGE_SUPPORTED_COUNT, + TOO_SMALL_SEQUENCE, + ZH_NAMES, +) +from .md import is_suspiciously_successive_range +from .models import CoherenceMatches +from .utils import ( + is_accentuated, + is_latin, + is_multi_byte_encoding, + is_unicode_range_secondary, + unicode_range, +) + + +def encoding_unicode_range(iana_name: str) -> List[str]: + """ + Return associated unicode ranges in a single byte code page. + """ + if is_multi_byte_encoding(iana_name): + raise IOError("Function not supported on multi-byte code page") + + decoder = importlib.import_module( + "encodings.{}".format(iana_name) + ).IncrementalDecoder + + p: IncrementalDecoder = decoder(errors="ignore") + seen_ranges: Dict[str, int] = {} + character_count: int = 0 + + for i in range(0x40, 0xFF): + chunk: str = p.decode(bytes([i])) + + if chunk: + character_range: Optional[str] = unicode_range(chunk) + + if character_range is None: + continue + + if is_unicode_range_secondary(character_range) is False: + if character_range not in seen_ranges: + seen_ranges[character_range] = 0 + seen_ranges[character_range] += 1 + character_count += 1 + + return sorted( + [ + character_range + for character_range in seen_ranges + if seen_ranges[character_range] / character_count >= 0.15 + ] + ) + + +def unicode_range_languages(primary_range: str) -> List[str]: + """ + Return inferred languages used with a unicode range. + """ + languages: List[str] = [] + + for language, characters in FREQUENCIES.items(): + for character in characters: + if unicode_range(character) == primary_range: + languages.append(language) + break + + return languages + + +@lru_cache() +def encoding_languages(iana_name: str) -> List[str]: + """ + Single-byte encoding language association. Some code page are heavily linked to particular language(s). + This function does the correspondence. + """ + unicode_ranges: List[str] = encoding_unicode_range(iana_name) + primary_range: Optional[str] = None + + for specified_range in unicode_ranges: + if "Latin" not in specified_range: + primary_range = specified_range + break + + if primary_range is None: + return ["Latin Based"] + + return unicode_range_languages(primary_range) + + +@lru_cache() +def mb_encoding_languages(iana_name: str) -> List[str]: + """ + Multi-byte encoding language association. Some code page are heavily linked to particular language(s). + This function does the correspondence. + """ + if ( + iana_name.startswith("shift_") + or iana_name.startswith("iso2022_jp") + or iana_name.startswith("euc_j") + or iana_name == "cp932" + ): + return ["Japanese"] + if iana_name.startswith("gb") or iana_name in ZH_NAMES: + return ["Chinese"] + if iana_name.startswith("iso2022_kr") or iana_name in KO_NAMES: + return ["Korean"] + + return [] + + +@lru_cache(maxsize=LANGUAGE_SUPPORTED_COUNT) +def get_target_features(language: str) -> Tuple[bool, bool]: + """ + Determine main aspects from a supported language if it contains accents and if is pure Latin. + """ + target_have_accents: bool = False + target_pure_latin: bool = True + + for character in FREQUENCIES[language]: + if not target_have_accents and is_accentuated(character): + target_have_accents = True + if target_pure_latin and is_latin(character) is False: + target_pure_latin = False + + return target_have_accents, target_pure_latin + + +def alphabet_languages( + characters: List[str], ignore_non_latin: bool = False +) -> List[str]: + """ + Return associated languages associated to given characters. + """ + languages: List[Tuple[str, float]] = [] + + source_have_accents = any(is_accentuated(character) for character in characters) + + for language, language_characters in FREQUENCIES.items(): + target_have_accents, target_pure_latin = get_target_features(language) + + if ignore_non_latin and target_pure_latin is False: + continue + + if target_have_accents is False and source_have_accents: + continue + + character_count: int = len(language_characters) + + character_match_count: int = len( + [c for c in language_characters if c in characters] + ) + + ratio: float = character_match_count / character_count + + if ratio >= 0.2: + languages.append((language, ratio)) + + languages = sorted(languages, key=lambda x: x[1], reverse=True) + + return [compatible_language[0] for compatible_language in languages] + + +def characters_popularity_compare( + language: str, ordered_characters: List[str] +) -> float: + """ + Determine if a ordered characters list (by occurrence from most appearance to rarest) match a particular language. + The result is a ratio between 0. (absolutely no correspondence) and 1. (near perfect fit). + Beware that is function is not strict on the match in order to ease the detection. (Meaning close match is 1.) + """ + if language not in FREQUENCIES: + raise ValueError("{} not available".format(language)) + + character_approved_count: int = 0 + FREQUENCIES_language_set = set(FREQUENCIES[language]) + + ordered_characters_count: int = len(ordered_characters) + target_language_characters_count: int = len(FREQUENCIES[language]) + + large_alphabet: bool = target_language_characters_count > 26 + + for character, character_rank in zip( + ordered_characters, range(0, ordered_characters_count) + ): + if character not in FREQUENCIES_language_set: + continue + + character_rank_in_language: int = FREQUENCIES[language].index(character) + expected_projection_ratio: float = ( + target_language_characters_count / ordered_characters_count + ) + character_rank_projection: int = int(character_rank * expected_projection_ratio) + + if ( + large_alphabet is False + and abs(character_rank_projection - character_rank_in_language) > 4 + ): + continue + + if ( + large_alphabet is True + and abs(character_rank_projection - character_rank_in_language) + < target_language_characters_count / 3 + ): + character_approved_count += 1 + continue + + characters_before_source: List[str] = FREQUENCIES[language][ + 0:character_rank_in_language + ] + characters_after_source: List[str] = FREQUENCIES[language][ + character_rank_in_language: + ] + characters_before: List[str] = ordered_characters[0:character_rank] + characters_after: List[str] = ordered_characters[character_rank:] + + before_match_count: int = len( + set(characters_before) & set(characters_before_source) + ) + + after_match_count: int = len( + set(characters_after) & set(characters_after_source) + ) + + if len(characters_before_source) == 0 and before_match_count <= 4: + character_approved_count += 1 + continue + + if len(characters_after_source) == 0 and after_match_count <= 4: + character_approved_count += 1 + continue + + if ( + before_match_count / len(characters_before_source) >= 0.4 + or after_match_count / len(characters_after_source) >= 0.4 + ): + character_approved_count += 1 + continue + + return character_approved_count / len(ordered_characters) + + +def alpha_unicode_split(decoded_sequence: str) -> List[str]: + """ + Given a decoded text sequence, return a list of str. Unicode range / alphabet separation. + Ex. a text containing English/Latin with a bit a Hebrew will return two items in the resulting list; + One containing the latin letters and the other hebrew. + """ + layers: Dict[str, str] = {} + + for character in decoded_sequence: + if character.isalpha() is False: + continue + + character_range: Optional[str] = unicode_range(character) + + if character_range is None: + continue + + layer_target_range: Optional[str] = None + + for discovered_range in layers: + if ( + is_suspiciously_successive_range(discovered_range, character_range) + is False + ): + layer_target_range = discovered_range + break + + if layer_target_range is None: + layer_target_range = character_range + + if layer_target_range not in layers: + layers[layer_target_range] = character.lower() + continue + + layers[layer_target_range] += character.lower() + + return list(layers.values()) + + +def merge_coherence_ratios(results: List[CoherenceMatches]) -> CoherenceMatches: + """ + This function merge results previously given by the function coherence_ratio. + The return type is the same as coherence_ratio. + """ + per_language_ratios: Dict[str, List[float]] = {} + for result in results: + for sub_result in result: + language, ratio = sub_result + if language not in per_language_ratios: + per_language_ratios[language] = [ratio] + continue + per_language_ratios[language].append(ratio) + + merge = [ + ( + language, + round( + sum(per_language_ratios[language]) / len(per_language_ratios[language]), + 4, + ), + ) + for language in per_language_ratios + ] + + return sorted(merge, key=lambda x: x[1], reverse=True) + + +def filter_alt_coherence_matches(results: CoherenceMatches) -> CoherenceMatches: + """ + We shall NOT return "English—" in CoherenceMatches because it is an alternative + of "English". This function only keeps the best match and remove the em-dash in it. + """ + index_results: Dict[str, List[float]] = dict() + + for result in results: + language, ratio = result + no_em_name: str = language.replace("—", "") + + if no_em_name not in index_results: + index_results[no_em_name] = [] + + index_results[no_em_name].append(ratio) + + if any(len(index_results[e]) > 1 for e in index_results): + filtered_results: CoherenceMatches = [] + + for language in index_results: + filtered_results.append((language, max(index_results[language]))) + + return filtered_results + + return results + + +@lru_cache(maxsize=2048) +def coherence_ratio( + decoded_sequence: str, threshold: float = 0.1, lg_inclusion: Optional[str] = None +) -> CoherenceMatches: + """ + Detect ANY language that can be identified in given sequence. The sequence will be analysed by layers. + A layer = Character extraction by alphabets/ranges. + """ + + results: List[Tuple[str, float]] = [] + ignore_non_latin: bool = False + + sufficient_match_count: int = 0 + + lg_inclusion_list = lg_inclusion.split(",") if lg_inclusion is not None else [] + if "Latin Based" in lg_inclusion_list: + ignore_non_latin = True + lg_inclusion_list.remove("Latin Based") + + for layer in alpha_unicode_split(decoded_sequence): + sequence_frequencies: TypeCounter[str] = Counter(layer) + most_common = sequence_frequencies.most_common() + + character_count: int = sum(o for c, o in most_common) + + if character_count <= TOO_SMALL_SEQUENCE: + continue + + popular_character_ordered: List[str] = [c for c, o in most_common] + + for language in lg_inclusion_list or alphabet_languages( + popular_character_ordered, ignore_non_latin + ): + ratio: float = characters_popularity_compare( + language, popular_character_ordered + ) + + if ratio < threshold: + continue + elif ratio >= 0.8: + sufficient_match_count += 1 + + results.append((language, round(ratio, 4))) + + if sufficient_match_count >= 3: + break + + return sorted( + filter_alt_coherence_matches(results), key=lambda x: x[1], reverse=True + )