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view CodonSwitchTool/sre_yield.py @ 2:aad5e435e4dc draft default tip
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author | gianmarco_piccinno |
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date | Tue, 21 May 2019 05:24:56 -0400 |
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#!/usr/bin/env python2 # # Copyright 2011-2016 Google Inc. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # # vim: sw=2 sts=2 et """This module can generate all strings that match a regular expression. The regex is parsed using the SRE module that is standard in python, then the data structure is executed to form a bunch of iterators. """ __author__ = 'alexperry@google.com (Alex Perry)' __all__ = ['Values', 'AllStrings', 'AllMatches', 'ParseError'] import bisect import math import re import sre_constants import sre_parse import string import sys import types import cachingseq import fastdivmod try: xrange = xrange except NameError: xrange = range _RE_METACHARS = r'$^{}*+\\' _ESCAPED_METACHAR = r'\\[' + _RE_METACHARS + r']' ESCAPED_METACHAR_RE = re.compile(_ESCAPED_METACHAR) # ASCII by default, see https://github.com/google/sre_yield/issues/3 CHARSET = [chr(c) for c in range(256)] WORD = string.ascii_letters + string.digits + '_' try: DEFAULT_RE_FLAGS = re.ASCII except AttributeError: DEFAULT_RE_FLAGS = 0 STATE_START, STATE_MIDDLE, STATE_END = list(range(3)) def Not(chars): return ''.join(sorted(set(CHARSET) - set(chars))) CATEGORIES = { sre_constants.CATEGORY_WORD: WORD, sre_constants.CATEGORY_NOT_WORD: Not(WORD), sre_constants.CATEGORY_DIGIT: string.digits, sre_constants.CATEGORY_NOT_DIGIT: Not(string.digits), sre_constants.CATEGORY_SPACE: string.whitespace, sre_constants.CATEGORY_NOT_SPACE: Not(string.whitespace), } # This constant varies between builds of Python; this is the lower value. MAX_REPEAT_COUNT = 65535 class ParseError(Exception): pass def slice_indices(slice_obj, size): """slice_obj.indices() except this one supports longs.""" # start stop step start = slice_obj.start stop = slice_obj.stop step = slice_obj.step # We don't always update a value for negative indices (if we wrote it here # due to None). if step is None: step = 1 if start is None: if step > 0: start = 0 else: start = size - 1 else: start = _adjust_index(start, size) if stop is None: if step > 0: stop = size else: stop = -1 else: stop = _adjust_index(stop, size) return (start, stop, step) def _adjust_index(n, size): if n < 0: n += size if n < 0: raise IndexError("Out of range") if n > size: n = size return n def _xrange(*args): """Because xrange doesn't support longs :(""" # prefer real xrange if it works try: return xrange(*args) except OverflowError: return _bigrange(*args) def _bigrange(*args): if len(args) == 1: start = 0; stop = args[0]; step = 1 elif len(args) == 2: start, stop = args step = 1 elif len(args) == 3: start, stop, step = args else: raise ValueError("Too many args for _bigrange") i = start while True: yield i i += step if step < 0 and i <= stop: break if step > 0 and i >= stop: break class WrappedSequence(object): """This wraps a sequence, purely as a base clase for the other uses.""" def __init__(self, raw): # Derived classes will likely override this constructor self.raw = raw # Note that we can't use the function len() because it insists on trying # to convert the returned number from a long-int to an ordinary int. self.length = raw.__len__() def get_item(self, i, d=None): i = _adjust_index(i, self.length) if hasattr(self.raw, 'get_item'): return self.raw.get_item(i, d) return self.raw[i] def __len__(self): return self.length def __getitem__(self, i): # If the user wanted a slice, we provide a wrapper if isinstance(i, slice): result = SlicedSequence(self, slicer=i) if result.__len__() < 16: # Short lists are unpacked result = [item for item in result] return result i = _adjust_index(i, self.length) # Usually we just call the user-provided function return self.get_item(i) def __iter__(self): for i in _xrange(int(self.length)): yield self.get_item(i) def _sign(x): if x > 0: return 1 else: return -1 class SlicedSequence(WrappedSequence): """This is part of an immutable and potentially arbitrarily long list.""" def __init__(self, raw, slicer=None): # Derived classes will likely override this constructor self.raw = raw if slicer is None: self.start, self.stop, self.step = 0, raw.__len__(), 1 else: self.start, self.stop, self.step = slice_indices(slicer, raw.__len__()) # Integer round up, depending on step direction self.length = ((self.stop - self.start + self.step - _sign(self.step)) / self.step) def get_item(self, i, d=None): j = i * self.step + self.start return self.raw[j] class ConcatenatedSequence(WrappedSequence): """This is equivalent to using extend() but without unpacking the lists.""" def __init__(self, *alternatives): self.list_lengths = [(a, a.__len__()) for a in alternatives] self.length = sum(a_len for _, a_len in self.list_lengths) def get_item(self, i, d=None): for a, a_len in self.list_lengths: if i < a_len: return a[i] i -= a_len raise IndexError('Too Big') def __contains__(self, item): for a, _ in self.list_lengths: if item in a: return True return False def __repr__(self): return '{concat ' + repr(self.list_lengths) + '}' class CombinatoricsSequence(WrappedSequence): """This uses all combinations of one item from each passed list.""" def __init__(self, *components): self.list_lengths = [(a, a.__len__()) for a in components] self.length = 1 for _, c_len in self.list_lengths: self.length *= c_len def get_item(self, i, d=None): result = [] if i < 0: i += self.length if i < 0 or i >= self.length: raise IndexError("Index %d out of bounds" % (i,)) if len(self.list_lengths) == 1: # skip unnecessary ''.join -- big speedup return self.list_lengths[0][0][i] for c, c_len in self.list_lengths: i, mod = divmod(i, c_len) if hasattr(c, 'get_item'): result.append(c.get_item(mod, d)) else: result.append(c[mod]) return ''.join(result) def __repr__(self): return '{combin ' + repr(self.list_lengths) + '}' class RepetitiveSequence(WrappedSequence): """This chooses an entry from a list, many times, and concatenates.""" def __init__(self, content, lowest=1, highest=1): self.content = content self.content_length = content.__len__() self.length = fastdivmod.powersum(self.content_length, lowest, highest) self.lowest = lowest self.highest = highest def arbitrary_entry(i): return (fastdivmod.powersum(self.content_length, lowest, i+lowest-1), i+lowest) def entry_from_prev(i, prev): return (prev[0] + (self.content_length ** prev[1]), prev[1] + 1) self.offsets = cachingseq.CachingFuncSequence( arbitrary_entry, highest - lowest+1, entry_from_prev) # This needs to be a constant in order to reuse caclulations in future # calls to bisect (a moving target will produce more misses). if self.offsets[-1][0] > sys.maxsize: i = 0 while i + 2 < len(self.offsets): if self.offsets[i+1][0] > sys.maxsize: self.index_of_offset = i self.offset_break = self.offsets[i][0] break i += 1 else: self.index_of_offset = len(self.offsets) self.offset_break = sys.maxsize def get_item(self, i, d=None): """Finds out how many repeats this index implies, then picks strings.""" if i < self.offset_break: by_bisect = bisect.bisect_left(self.offsets, (i, -1), hi=self.index_of_offset) else: by_bisect = bisect.bisect_left(self.offsets, (i, -1), lo=self.index_of_offset) if by_bisect == len(self.offsets) or self.offsets[by_bisect][0] > i: by_bisect -= 1 num = i - self.offsets[by_bisect][0] count = self.offsets[by_bisect][1] if count > 100 and self.content_length < 1000: content = list(self.content) else: content = self.content result = [] if count == 0: return '' for modulus in fastdivmod.divmod_iter(num, self.content_length): result.append(content[modulus]) leftover = count - len(result) if leftover: assert leftover > 0 result.extend([content[0]] * leftover) # smallest place value ends up on the right return ''.join(result[::-1]) def __repr__(self): return '{repeat base=%d low=%d high=%d}' % (self.content_length, self.lowest, self.highest) class SaveCaptureGroup(WrappedSequence): def __init__(self, parsed, key): self.key = key super(SaveCaptureGroup, self).__init__(parsed) def get_item(self, n, d=None): rv = super(SaveCaptureGroup, self).get_item(n, d) if d is not None: d[self.key] = rv return rv class ReadCaptureGroup(WrappedSequence): def __init__(self, n): self.num = n self.length = 1 def get_item(self, i, d=None): if i != 0: raise IndexError(i) if d is None: raise ValueError('ReadCaptureGroup with no dict') return d.get(self.num, "fail") class RegexMembershipSequence(WrappedSequence): """Creates a sequence from the regex, knows how to test membership.""" def empty_list(self, *_): return [] def nothing_added(self, *_): return [''] def branch_values(self, _, items): """Converts SRE parser data into literals and merges those lists.""" return ConcatenatedSequence( *[self.sub_values(parsed) for parsed in items]) def max_repeat_values(self, min_count, max_count, items): """Sequential expansion of the count to be combinatorics.""" max_count = min(max_count, self.max_count) return RepetitiveSequence( self.sub_values(items), min_count, max_count) def in_values(self, items): # Special case which distinguishes branch from charset operator if items and items[0][0] == sre_constants.NEGATE: items = self.branch_values(None, items[1:]) return [item for item in self.charset if item not in items] return self.branch_values(None, items) def not_literal(self, y): return self.in_values(((sre_constants.NEGATE,), (sre_constants.LITERAL, y),)) def category(self, y): return CATEGORIES[y] def groupref(self, n): self.has_groupref = True return ReadCaptureGroup(n) def get_item(self, i, d=None): """Typically only pass i. d is an internal detail, for consistency with other classes. If you care about the capture groups, you should use RegexMembershipSequenceMatches instead, which returns a Match object instead of a string.""" if self.has_groupref or d is not None: if d is None: d = {} return super(RegexMembershipSequence, self).get_item(i, d) else: return super(RegexMembershipSequence, self).get_item(i) def sub_values(self, parsed): """This knows how to convert one piece of parsed pattern.""" # If this is a subpattern object, we just want its data if isinstance(parsed, sre_parse.SubPattern): parsed = parsed.data # A list indicates sequential elements of a string if isinstance(parsed, list): elements = [self.sub_values(p) for p in parsed] return CombinatoricsSequence(*elements) # If not a list, a tuple represents a specific match type if isinstance(parsed, tuple) and parsed: matcher, arguments = parsed if not isinstance(arguments, tuple): arguments = (arguments,) if matcher in self.backends: self.check_anchor_state(matcher, arguments) return self.backends[matcher](*arguments) # No idea what to do here raise ParseError(repr(parsed)) def maybe_save(self, *args): # Python 3.6 has group, add_flags, del_flags, parsed # while earlier versions just have group, parsed group = args[0] parsed = args[-1] rv = self.sub_values(parsed) if group is not None: rv = SaveCaptureGroup(rv, group) return rv def check_anchor_state(self, matcher, arguments): # A bit of a hack to support zero-width leading anchors. The goal is # that /^(a|b)$/ will match properly, and that /a^b/ or /a\bb/ throws # an error. (It's unfortunate that I couldn't easily handle /$^/ which # matches the empty string; I went for the common case.) # # There are three states, for example: # / STATE_START # | / STATE_START (^ causes no transition here, but is illegal at STATE_MIDDLE or STATE_END) # | | / STATE_START (\b causes no transition here, but advances MIDDLE to END) # | | | / (same as above for ^) # | | | | / STATE_MIDDLE (anything besides ^ and \b advances START to MIDDLE) # | | | | | / still STATE_MIDDLE # . . . . . . / advances MIDDLE to END # ^ \b ^ X Y \b $ old_state = self.state if self.state == STATE_START: if matcher == sre_constants.AT: if arguments[0] in (sre_constants.AT_END, sre_constants.AT_END_STRING): self.state = STATE_END elif arguments[0] == sre_constants.AT_NON_BOUNDARY: # This is nonsensical at beginning of string raise ParseError('Anchor %r found at START state' % (arguments[0],)) # All others (AT_BEGINNING, AT_BEGINNING_STRING, and AT_BOUNDARY) remain in START. elif matcher != sre_constants.SUBPATTERN: self.state = STATE_MIDDLE # subpattern remains in START elif self.state == STATE_END: if matcher == sre_constants.AT: if arguments[0] not in ( sre_constants.AT_END, sre_constants.AT_END_STRING, sre_constants.AT_BOUNDARY): raise ParseError('Anchor %r found at END state' % (arguments[0],)) # those three remain in END elif matcher != sre_constants.SUBPATTERN: raise ParseError('Non-end-anchor %r found at END state' % (arguments[0],)) # subpattern remains in END else: # self.state == STATE_MIDDLE if matcher == sre_constants.AT: if arguments[0] not in ( sre_constants.AT_END, sre_constants.AT_END_STRING, sre_constants.AT_BOUNDARY): raise ParseError('Anchor %r found at MIDDLE state' % (arguments[0],)) # All others (AT_END, AT_END_STRING, AT_BOUNDARY) advance to END. self.state = STATE_END def __init__(self, pattern, flags=0, charset=CHARSET, max_count=None): # If the RE module cannot compile it, we give up quickly self.matcher = re.compile(r'(?:%s)\Z' % pattern, flags) if not flags & re.DOTALL: charset = ''.join(c for c in charset if c != '\n') self.charset = charset self.named_group_lookup = self.matcher.groupindex flags |= DEFAULT_RE_FLAGS # https://github.com/google/sre_yield/issues/3 if flags & re.IGNORECASE: raise ParseError('Flag "i" not supported. https://github.com/google/sre_yield/issues/4') elif flags & re.UNICODE: raise ParseError('Flag "u" not supported. https://github.com/google/sre_yield/issues/3') elif flags & re.LOCALE: raise ParseError('Flag "l" not supported. https://github.com/google/sre_yield/issues/5') if max_count is None: self.max_count = MAX_REPEAT_COUNT else: self.max_count = max_count self.has_groupref = False # Configure the parser backends self.backends = { sre_constants.LITERAL: lambda y: [chr(y)], sre_constants.RANGE: lambda l, h: [chr(c) for c in range(l, h+1)], sre_constants.SUBPATTERN: self.maybe_save, sre_constants.BRANCH: self.branch_values, sre_constants.MIN_REPEAT: self.max_repeat_values, sre_constants.MAX_REPEAT: self.max_repeat_values, sre_constants.AT: self.nothing_added, sre_constants.ASSERT: self.empty_list, sre_constants.ASSERT_NOT: self.empty_list, sre_constants.ANY: lambda _: self.in_values(((sre_constants.NEGATE,),)), sre_constants.IN: self.in_values, sre_constants.NOT_LITERAL: self.not_literal, sre_constants.CATEGORY: self.category, sre_constants.GROUPREF: self.groupref, } self.state = STATE_START # Now build a generator that knows all possible patterns self.raw = self.sub_values(sre_parse.parse(pattern, flags)) # Configure this class instance to know about that result self.length = self.raw.__len__() def __contains__(self, item): # Since we have a regex, we can search the list really cheaply return self.matcher.match(item) is not None class RegexMembershipSequenceMatches(RegexMembershipSequence): def __getitem__(self, i): if isinstance(i, slice): result = SlicedSequence(self, slicer=i) if result.__len__() < 16: # Short lists are unpacked result = [item for item in result] return result d = {} s = super(RegexMembershipSequenceMatches, self).get_item(i, d) return Match(s, d, self.named_group_lookup) def AllStrings(regex, flags=0, charset=CHARSET, max_count=None): """Constructs an object that will generate all matching strings.""" return RegexMembershipSequence(regex, flags, charset, max_count=max_count) Values = AllStrings class Match(object): def __init__(self, string, groups, named_groups): # TODO keep group(0) only, and spans for the rest. self._string = string self._groups = groups self._named_groups = named_groups self.lastindex = len(groups) + 1 def group(self, n=0): if n == 0: return self._string if not isinstance(n, int): n = self._named_groups[n] return self._groups[n] def groups(self): return tuple(self._groups[i] for i in range(1, self.lastindex)) def groupdict(self): d = {} for k, v in self._named_groups.items(): d[k] = self._groups[v] return d def span(self, n=0): raise NotImplementedError() def AllMatches(regex, flags=0, charset=CHARSET, max_count=None): """Constructs an object that will generate all matching strings.""" return RegexMembershipSequenceMatches(regex, flags, charset, max_count=max_count) def main(argv=None): """This module can be executed on the command line for testing.""" if argv is None: argv = sys.argv for arg in argv[1:]: for i in AllStrings(arg): print(i) if __name__ == '__main__': main()