Mercurial > repos > jpayne > bioproject_to_srr_2
diff charset_normalizer/api.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/api.py Sun May 05 23:32:17 2024 -0400 @@ -0,0 +1,626 @@ +import logging +from os import PathLike +from typing import BinaryIO, List, Optional, Set, Union + +from .cd import ( + coherence_ratio, + encoding_languages, + mb_encoding_languages, + merge_coherence_ratios, +) +from .constant import IANA_SUPPORTED, TOO_BIG_SEQUENCE, TOO_SMALL_SEQUENCE, TRACE +from .md import mess_ratio +from .models import CharsetMatch, CharsetMatches +from .utils import ( + any_specified_encoding, + cut_sequence_chunks, + iana_name, + identify_sig_or_bom, + is_cp_similar, + is_multi_byte_encoding, + should_strip_sig_or_bom, +) + +# Will most likely be controversial +# logging.addLevelName(TRACE, "TRACE") +logger = logging.getLogger("charset_normalizer") +explain_handler = logging.StreamHandler() +explain_handler.setFormatter( + logging.Formatter("%(asctime)s | %(levelname)s | %(message)s") +) + + +def from_bytes( + sequences: Union[bytes, bytearray], + steps: int = 5, + chunk_size: int = 512, + threshold: float = 0.2, + cp_isolation: Optional[List[str]] = None, + cp_exclusion: Optional[List[str]] = None, + preemptive_behaviour: bool = True, + explain: bool = False, + language_threshold: float = 0.1, + enable_fallback: bool = True, +) -> CharsetMatches: + """ + Given a raw bytes sequence, return the best possibles charset usable to render str objects. + If there is no results, it is a strong indicator that the source is binary/not text. + By default, the process will extract 5 blocks of 512o each to assess the mess and coherence of a given sequence. + And will give up a particular code page after 20% of measured mess. Those criteria are customizable at will. + + The preemptive behavior DOES NOT replace the traditional detection workflow, it prioritize a particular code page + but never take it for granted. Can improve the performance. + + You may want to focus your attention to some code page or/and not others, use cp_isolation and cp_exclusion for that + purpose. + + This function will strip the SIG in the payload/sequence every time except on UTF-16, UTF-32. + By default the library does not setup any handler other than the NullHandler, if you choose to set the 'explain' + toggle to True it will alter the logger configuration to add a StreamHandler that is suitable for debugging. + Custom logging format and handler can be set manually. + """ + + if not isinstance(sequences, (bytearray, bytes)): + raise TypeError( + "Expected object of type bytes or bytearray, got: {0}".format( + type(sequences) + ) + ) + + if explain: + previous_logger_level: int = logger.level + logger.addHandler(explain_handler) + logger.setLevel(TRACE) + + length: int = len(sequences) + + if length == 0: + logger.debug("Encoding detection on empty bytes, assuming utf_8 intention.") + if explain: + logger.removeHandler(explain_handler) + logger.setLevel(previous_logger_level or logging.WARNING) + return CharsetMatches([CharsetMatch(sequences, "utf_8", 0.0, False, [], "")]) + + if cp_isolation is not None: + logger.log( + TRACE, + "cp_isolation is set. use this flag for debugging purpose. " + "limited list of encoding allowed : %s.", + ", ".join(cp_isolation), + ) + cp_isolation = [iana_name(cp, False) for cp in cp_isolation] + else: + cp_isolation = [] + + if cp_exclusion is not None: + logger.log( + TRACE, + "cp_exclusion is set. use this flag for debugging purpose. " + "limited list of encoding excluded : %s.", + ", ".join(cp_exclusion), + ) + cp_exclusion = [iana_name(cp, False) for cp in cp_exclusion] + else: + cp_exclusion = [] + + if length <= (chunk_size * steps): + logger.log( + TRACE, + "override steps (%i) and chunk_size (%i) as content does not fit (%i byte(s) given) parameters.", + steps, + chunk_size, + length, + ) + steps = 1 + chunk_size = length + + if steps > 1 and length / steps < chunk_size: + chunk_size = int(length / steps) + + is_too_small_sequence: bool = len(sequences) < TOO_SMALL_SEQUENCE + is_too_large_sequence: bool = len(sequences) >= TOO_BIG_SEQUENCE + + if is_too_small_sequence: + logger.log( + TRACE, + "Trying to detect encoding from a tiny portion of ({}) byte(s).".format( + length + ), + ) + elif is_too_large_sequence: + logger.log( + TRACE, + "Using lazy str decoding because the payload is quite large, ({}) byte(s).".format( + length + ), + ) + + prioritized_encodings: List[str] = [] + + specified_encoding: Optional[str] = ( + any_specified_encoding(sequences) if preemptive_behaviour else None + ) + + if specified_encoding is not None: + prioritized_encodings.append(specified_encoding) + logger.log( + TRACE, + "Detected declarative mark in sequence. Priority +1 given for %s.", + specified_encoding, + ) + + tested: Set[str] = set() + tested_but_hard_failure: List[str] = [] + tested_but_soft_failure: List[str] = [] + + fallback_ascii: Optional[CharsetMatch] = None + fallback_u8: Optional[CharsetMatch] = None + fallback_specified: Optional[CharsetMatch] = None + + results: CharsetMatches = CharsetMatches() + + sig_encoding, sig_payload = identify_sig_or_bom(sequences) + + if sig_encoding is not None: + prioritized_encodings.append(sig_encoding) + logger.log( + TRACE, + "Detected a SIG or BOM mark on first %i byte(s). Priority +1 given for %s.", + len(sig_payload), + sig_encoding, + ) + + prioritized_encodings.append("ascii") + + if "utf_8" not in prioritized_encodings: + prioritized_encodings.append("utf_8") + + for encoding_iana in prioritized_encodings + IANA_SUPPORTED: + if cp_isolation and encoding_iana not in cp_isolation: + continue + + if cp_exclusion and encoding_iana in cp_exclusion: + continue + + if encoding_iana in tested: + continue + + tested.add(encoding_iana) + + decoded_payload: Optional[str] = None + bom_or_sig_available: bool = sig_encoding == encoding_iana + strip_sig_or_bom: bool = bom_or_sig_available and should_strip_sig_or_bom( + encoding_iana + ) + + if encoding_iana in {"utf_16", "utf_32"} and not bom_or_sig_available: + logger.log( + TRACE, + "Encoding %s won't be tested as-is because it require a BOM. Will try some sub-encoder LE/BE.", + encoding_iana, + ) + continue + if encoding_iana in {"utf_7"} and not bom_or_sig_available: + logger.log( + TRACE, + "Encoding %s won't be tested as-is because detection is unreliable without BOM/SIG.", + encoding_iana, + ) + continue + + try: + is_multi_byte_decoder: bool = is_multi_byte_encoding(encoding_iana) + except (ModuleNotFoundError, ImportError): + logger.log( + TRACE, + "Encoding %s does not provide an IncrementalDecoder", + encoding_iana, + ) + continue + + try: + if is_too_large_sequence and is_multi_byte_decoder is False: + str( + sequences[: int(50e4)] + if strip_sig_or_bom is False + else sequences[len(sig_payload) : int(50e4)], + encoding=encoding_iana, + ) + else: + decoded_payload = str( + sequences + if strip_sig_or_bom is False + else sequences[len(sig_payload) :], + encoding=encoding_iana, + ) + except (UnicodeDecodeError, LookupError) as e: + if not isinstance(e, LookupError): + logger.log( + TRACE, + "Code page %s does not fit given bytes sequence at ALL. %s", + encoding_iana, + str(e), + ) + tested_but_hard_failure.append(encoding_iana) + continue + + similar_soft_failure_test: bool = False + + for encoding_soft_failed in tested_but_soft_failure: + if is_cp_similar(encoding_iana, encoding_soft_failed): + similar_soft_failure_test = True + break + + if similar_soft_failure_test: + logger.log( + TRACE, + "%s is deemed too similar to code page %s and was consider unsuited already. Continuing!", + encoding_iana, + encoding_soft_failed, + ) + continue + + r_ = range( + 0 if not bom_or_sig_available else len(sig_payload), + length, + int(length / steps), + ) + + multi_byte_bonus: bool = ( + is_multi_byte_decoder + and decoded_payload is not None + and len(decoded_payload) < length + ) + + if multi_byte_bonus: + logger.log( + TRACE, + "Code page %s is a multi byte encoding table and it appear that at least one character " + "was encoded using n-bytes.", + encoding_iana, + ) + + max_chunk_gave_up: int = int(len(r_) / 4) + + max_chunk_gave_up = max(max_chunk_gave_up, 2) + early_stop_count: int = 0 + lazy_str_hard_failure = False + + md_chunks: List[str] = [] + md_ratios = [] + + try: + for chunk in cut_sequence_chunks( + sequences, + encoding_iana, + r_, + chunk_size, + bom_or_sig_available, + strip_sig_or_bom, + sig_payload, + is_multi_byte_decoder, + decoded_payload, + ): + md_chunks.append(chunk) + + md_ratios.append( + mess_ratio( + chunk, + threshold, + explain is True and 1 <= len(cp_isolation) <= 2, + ) + ) + + if md_ratios[-1] >= threshold: + early_stop_count += 1 + + if (early_stop_count >= max_chunk_gave_up) or ( + bom_or_sig_available and strip_sig_or_bom is False + ): + break + except ( + UnicodeDecodeError + ) as e: # Lazy str loading may have missed something there + logger.log( + TRACE, + "LazyStr Loading: After MD chunk decode, code page %s does not fit given bytes sequence at ALL. %s", + encoding_iana, + str(e), + ) + early_stop_count = max_chunk_gave_up + lazy_str_hard_failure = True + + # We might want to check the sequence again with the whole content + # Only if initial MD tests passes + if ( + not lazy_str_hard_failure + and is_too_large_sequence + and not is_multi_byte_decoder + ): + try: + sequences[int(50e3) :].decode(encoding_iana, errors="strict") + except UnicodeDecodeError as e: + logger.log( + TRACE, + "LazyStr Loading: After final lookup, code page %s does not fit given bytes sequence at ALL. %s", + encoding_iana, + str(e), + ) + tested_but_hard_failure.append(encoding_iana) + continue + + mean_mess_ratio: float = sum(md_ratios) / len(md_ratios) if md_ratios else 0.0 + if mean_mess_ratio >= threshold or early_stop_count >= max_chunk_gave_up: + tested_but_soft_failure.append(encoding_iana) + logger.log( + TRACE, + "%s was excluded because of initial chaos probing. Gave up %i time(s). " + "Computed mean chaos is %f %%.", + encoding_iana, + early_stop_count, + round(mean_mess_ratio * 100, ndigits=3), + ) + # Preparing those fallbacks in case we got nothing. + if ( + enable_fallback + and encoding_iana in ["ascii", "utf_8", specified_encoding] + and not lazy_str_hard_failure + ): + fallback_entry = CharsetMatch( + sequences, encoding_iana, threshold, False, [], decoded_payload + ) + if encoding_iana == specified_encoding: + fallback_specified = fallback_entry + elif encoding_iana == "ascii": + fallback_ascii = fallback_entry + else: + fallback_u8 = fallback_entry + continue + + logger.log( + TRACE, + "%s passed initial chaos probing. Mean measured chaos is %f %%", + encoding_iana, + round(mean_mess_ratio * 100, ndigits=3), + ) + + if not is_multi_byte_decoder: + target_languages: List[str] = encoding_languages(encoding_iana) + else: + target_languages = mb_encoding_languages(encoding_iana) + + if target_languages: + logger.log( + TRACE, + "{} should target any language(s) of {}".format( + encoding_iana, str(target_languages) + ), + ) + + cd_ratios = [] + + # We shall skip the CD when its about ASCII + # Most of the time its not relevant to run "language-detection" on it. + if encoding_iana != "ascii": + for chunk in md_chunks: + chunk_languages = coherence_ratio( + chunk, + language_threshold, + ",".join(target_languages) if target_languages else None, + ) + + cd_ratios.append(chunk_languages) + + cd_ratios_merged = merge_coherence_ratios(cd_ratios) + + if cd_ratios_merged: + logger.log( + TRACE, + "We detected language {} using {}".format( + cd_ratios_merged, encoding_iana + ), + ) + + results.append( + CharsetMatch( + sequences, + encoding_iana, + mean_mess_ratio, + bom_or_sig_available, + cd_ratios_merged, + decoded_payload, + ) + ) + + if ( + encoding_iana in [specified_encoding, "ascii", "utf_8"] + and mean_mess_ratio < 0.1 + ): + logger.debug( + "Encoding detection: %s is most likely the one.", encoding_iana + ) + if explain: + logger.removeHandler(explain_handler) + logger.setLevel(previous_logger_level) + return CharsetMatches([results[encoding_iana]]) + + if encoding_iana == sig_encoding: + logger.debug( + "Encoding detection: %s is most likely the one as we detected a BOM or SIG within " + "the beginning of the sequence.", + encoding_iana, + ) + if explain: + logger.removeHandler(explain_handler) + logger.setLevel(previous_logger_level) + return CharsetMatches([results[encoding_iana]]) + + if len(results) == 0: + if fallback_u8 or fallback_ascii or fallback_specified: + logger.log( + TRACE, + "Nothing got out of the detection process. Using ASCII/UTF-8/Specified fallback.", + ) + + if fallback_specified: + logger.debug( + "Encoding detection: %s will be used as a fallback match", + fallback_specified.encoding, + ) + results.append(fallback_specified) + elif ( + (fallback_u8 and fallback_ascii is None) + or ( + fallback_u8 + and fallback_ascii + and fallback_u8.fingerprint != fallback_ascii.fingerprint + ) + or (fallback_u8 is not None) + ): + logger.debug("Encoding detection: utf_8 will be used as a fallback match") + results.append(fallback_u8) + elif fallback_ascii: + logger.debug("Encoding detection: ascii will be used as a fallback match") + results.append(fallback_ascii) + + if results: + logger.debug( + "Encoding detection: Found %s as plausible (best-candidate) for content. With %i alternatives.", + results.best().encoding, # type: ignore + len(results) - 1, + ) + else: + logger.debug("Encoding detection: Unable to determine any suitable charset.") + + if explain: + logger.removeHandler(explain_handler) + logger.setLevel(previous_logger_level) + + return results + + +def from_fp( + fp: BinaryIO, + steps: int = 5, + chunk_size: int = 512, + threshold: float = 0.20, + cp_isolation: Optional[List[str]] = None, + cp_exclusion: Optional[List[str]] = None, + preemptive_behaviour: bool = True, + explain: bool = False, + language_threshold: float = 0.1, + enable_fallback: bool = True, +) -> CharsetMatches: + """ + Same thing than the function from_bytes but using a file pointer that is already ready. + Will not close the file pointer. + """ + return from_bytes( + fp.read(), + steps, + chunk_size, + threshold, + cp_isolation, + cp_exclusion, + preemptive_behaviour, + explain, + language_threshold, + enable_fallback, + ) + + +def from_path( + path: Union[str, bytes, PathLike], # type: ignore[type-arg] + steps: int = 5, + chunk_size: int = 512, + threshold: float = 0.20, + cp_isolation: Optional[List[str]] = None, + cp_exclusion: Optional[List[str]] = None, + preemptive_behaviour: bool = True, + explain: bool = False, + language_threshold: float = 0.1, + enable_fallback: bool = True, +) -> CharsetMatches: + """ + Same thing than the function from_bytes but with one extra step. Opening and reading given file path in binary mode. + Can raise IOError. + """ + with open(path, "rb") as fp: + return from_fp( + fp, + steps, + chunk_size, + threshold, + cp_isolation, + cp_exclusion, + preemptive_behaviour, + explain, + language_threshold, + enable_fallback, + ) + + +def is_binary( + fp_or_path_or_payload: Union[PathLike, str, BinaryIO, bytes], # type: ignore[type-arg] + steps: int = 5, + chunk_size: int = 512, + threshold: float = 0.20, + cp_isolation: Optional[List[str]] = None, + cp_exclusion: Optional[List[str]] = None, + preemptive_behaviour: bool = True, + explain: bool = False, + language_threshold: float = 0.1, + enable_fallback: bool = False, +) -> bool: + """ + Detect if the given input (file, bytes, or path) points to a binary file. aka. not a string. + Based on the same main heuristic algorithms and default kwargs at the sole exception that fallbacks match + are disabled to be stricter around ASCII-compatible but unlikely to be a string. + """ + if isinstance(fp_or_path_or_payload, (str, PathLike)): + guesses = from_path( + fp_or_path_or_payload, + steps=steps, + chunk_size=chunk_size, + threshold=threshold, + cp_isolation=cp_isolation, + cp_exclusion=cp_exclusion, + preemptive_behaviour=preemptive_behaviour, + explain=explain, + language_threshold=language_threshold, + enable_fallback=enable_fallback, + ) + elif isinstance( + fp_or_path_or_payload, + ( + bytes, + bytearray, + ), + ): + guesses = from_bytes( + fp_or_path_or_payload, + steps=steps, + chunk_size=chunk_size, + threshold=threshold, + cp_isolation=cp_isolation, + cp_exclusion=cp_exclusion, + preemptive_behaviour=preemptive_behaviour, + explain=explain, + language_threshold=language_threshold, + enable_fallback=enable_fallback, + ) + else: + guesses = from_fp( + fp_or_path_or_payload, + steps=steps, + chunk_size=chunk_size, + threshold=threshold, + cp_isolation=cp_isolation, + cp_exclusion=cp_exclusion, + preemptive_behaviour=preemptive_behaviour, + explain=explain, + language_threshold=language_threshold, + enable_fallback=enable_fallback, + ) + + return not guesses