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Sourcecode: python-biopython version File versions

msre_parse.py

#
# Secret Labs' Regular Expression Engine
#
# convert re-style regular expression to sre pattern
#
# Copyright (c) 1998-2001 by Secret Labs AB.  All rights reserved.
#
# See the sre.py file in Python 2.1 for information on usage and
# redistribution.
#
# Changes for Martel Copyright 2000-2001 by Dalke Scientific Software, LLC
# Distributed under the Biopython License Agreement (see the LICENSE file).

# XXX: show string offset and offending character for all errors

# this module works under 1.5.2 and later.  don't use string methods
import string, sys

from msre_constants import *  # Modified version of Secret Labs' sre_constants
import re  # needed to verify the attr format

SPECIAL_CHARS = ".\\[{()*+?^$|"
REPEAT_CHARS = "*+?{"

DIGITS = tuple("0123456789")

OCTDIGITS = tuple("01234567")
HEXDIGITS = tuple("0123456789abcdefABCDEF")

WHITESPACE = tuple(" \t\n\r\v\f")

ESCAPES = {
    r"\a": (LITERAL, ord("\a")),
    r"\b": (LITERAL, ord("\b")),
    r"\f": (LITERAL, ord("\f")),
    r"\n": (LITERAL, ord("\n")),
    r"\r": (LITERAL, ord("\r")),
    r"\R": (IN, [(CATEGORY, CATEGORY_NEWLINE)]),  # Martel extension
    r"\t": (LITERAL, ord("\t")),
    r"\v": (LITERAL, ord("\v")),
    r"\\": (LITERAL, ord("\\"))
}

CATEGORIES = {
    r"\A": (AT, AT_BEGINNING_STRING), # start of string
    r"\b": (AT, AT_BOUNDARY),
    r"\B": (AT, AT_NON_BOUNDARY),
    r"\d": (IN, [(CATEGORY, CATEGORY_DIGIT)]),
    r"\D": (IN, [(CATEGORY, CATEGORY_NOT_DIGIT)]),
    r"\R": (NEWLINE, None),  # Martel extension
    r"\s": (IN, [(CATEGORY, CATEGORY_SPACE)]),
    r"\S": (IN, [(CATEGORY, CATEGORY_NOT_SPACE)]),
    r"\w": (IN, [(CATEGORY, CATEGORY_WORD)]),
    r"\W": (IN, [(CATEGORY, CATEGORY_NOT_WORD)]),
    r"\Z": (AT, AT_END_STRING), # end of string
}

FLAGS = {
    # standard flags
    "i": SRE_FLAG_IGNORECASE,
    "L": SRE_FLAG_LOCALE,
    "m": SRE_FLAG_MULTILINE,
    "s": SRE_FLAG_DOTALL,
    "x": SRE_FLAG_VERBOSE,
    # extensions
    "t": SRE_FLAG_TEMPLATE,
    "u": SRE_FLAG_UNICODE,
}

# figure out best way to convert hex/octal numbers to integers
try:
    int("10", 8)
    atoi = int # 2.0 and later
except TypeError:
    atoi = string.atoi # 1.5.2

class Pattern:
    # master pattern object.  keeps track of global attributes
    def __init__(self):
        self.flags = 0
        self.open = []
        self.groups = 1
        self.groupdict = {}
    def opengroup(self, name=None):
        gid = self.groups
        self.groups = gid + 1
        if name:
            self.groupdict[name] = gid
        self.open.append(gid)
        return gid
    def closegroup(self, gid):
        self.open.remove(gid)
    def checkgroup(self, gid):
        return gid < self.groups and gid not in self.open

class SubPattern:
    # a subpattern, in intermediate form
    def __init__(self, pattern, data=None):
        self.pattern = pattern
        if not data:
            data = []
        self.data = data
        self.width = None
    def dump(self, level=0):
        nl = 1
        for op, av in self.data:
            print level*"  " + op,; nl = 0
            if op == "in":
                # member sublanguage
                print; nl = 1
                for op, a in av:
                    print (level+1)*"  " + op, a
            elif op == "branch":
                print; nl = 1
                i = 0
                for a in av[1]:
                    if i > 0:
                        print level*"  " + "or"
                    a.dump(level+1); nl = 1
                    i = i + 1
            elif type(av) in (type(()), type([])):
                for a in av:
                    if isinstance(a, SubPattern):
                        if not nl: print
                        a.dump(level+1); nl = 1
                    else:
                        print a, ; nl = 0
            else:
                print av, ; nl = 0
            if not nl: print
    def __repr__(self):
        return repr(self.data)
    def __len__(self):
        return len(self.data)
    def __delitem__(self, index):
        del self.data[index]
    def __getitem__(self, index):
        return self.data[index]
    def __setitem__(self, index, code):
        self.data[index] = code
    def __getslice__(self, start, stop):
        return SubPattern(self.pattern, self.data[start:stop])
    def insert(self, index, code):
        self.data.insert(index, code)
    def append(self, code):
        self.data.append(code)
    def getwidth(self):
        # determine the width (min, max) for this subpattern
        if self.width:
            return self.width
        lo = hi = 0L
        for op, av in self.data:
            if op is BRANCH:
                i = sys.maxint
                j = 0
                for av in av[1]:
                    l, h = av.getwidth()
                    i = min(i, l)
                    j = max(j, h)
                lo = lo + i
                hi = hi + j
            elif op is CALL:
                i, j = av.getwidth()
                lo = lo + i
                hi = hi + j
            elif op is SUBPATTERN:
                i, j = av[1].getwidth()
                lo = lo + i
                hi = hi + j
            elif op in (MIN_REPEAT, MAX_REPEAT):
                i, j = av[2].getwidth()
                lo = lo + long(i) * av[0]
                hi = hi + long(j) * av[1]
            elif op in (ANY, RANGE, IN, LITERAL, NOT_LITERAL, CATEGORY):
                lo = lo + 1
                hi = hi + 1
            elif op == SUCCESS:
                break
        self.width = int(min(lo, sys.maxint)), int(min(hi, sys.maxint))
        return self.width

class Tokenizer:
    def __init__(self, string):
        self.string = string
        self.index = 0
        self.__next()
    def __next(self):
        if self.index >= len(self.string):
            self.next = None
            return
        char = self.string[self.index]
        if char[0] == "\\":
            try:
                c = self.string[self.index + 1]
            except IndexError:
                raise error, "bogus escape"
            char = char + c
        self.index = self.index + len(char)
        self.next = char
    def match(self, char, skip=1):
        if char == self.next:
            if skip:
                self.__next()
            return 1
        return 0
    def get(self):
        this = self.next
        self.__next()
        return this
    def tell(self):
        return self.index, self.next
    def seek(self, index):
        self.index, self.next = index

### Martel changes to allow all XML identifiers
#  '[a-zA-Z_:][-a-zA-Z0-9._:]*'

# Any (optional) attrs are stored after a '?'
# key/values are done in URL-style
#  key1=value1&key2=value2;
# only [-a-zA-Z0-9._] are allowed to be unescaped
# escaping is done with URL-style hex escapes, so '=' becomes '%3D'
# For example:
#   seqdb format="swissprot" version="38"
# can be represented as
#   seqdb?format=swissprot&version=38


# Martel specific changes
def is_firstchar(char):
    return "a" <= char <= "z" or "A" <= char <= "Z" or  char in "_:"

# Martel specific changes
def is_char(char):
    return "a" <= char <= "z" or "A" <= char <= "Z" or \
           "0" <= char <= "9" or char in "._:-"

# Martel specific changes
def isname(name):
    # check that group name is a valid string
    if not name:
        return 0
    if not is_firstchar(name[0]):
        return 0
    for char in name:
        if not is_char(char):
            return 0
    return 1

# More Martel specific changes
# Checks if the serialized form of attrs is correct
_name_with_attr_pattern = re.compile(r"""
[a-zA-Z_:]        # first character of the tag
[-a-zA-Z0-9._:]*  # rest of the tag
(\?                                      # optional attrs flagged with '?'
 (
  ([-a-zA-Z0-9._]|(%[0-9A-Fa-f]{2}))+    # name can contain % escapes
  =                                      # '=' flags value
  ([-a-zA-Z0-9._]|(%[0-9A-Fa-f]{2}))*    # value can contain % escapes
  (&                                     # flag for additional args
    ([-a-zA-Z0-9._]|(%[0-9A-Fa-f]{2}))+  # name
    =                                    # '='
    ([-a-zA-Z0-9._]|(%[0-9A-Fa-f]{2}))*  # value
  )*                                     # 0 or more add'l args
 )?                                      # can have nothing after the '?'
)?                                       # attrs are optional
$                                        # must get full string
""", re.X)

def isname_with_attrs(name):
    # check that group name is a valid string
    if not name:
        return 0
    m = _name_with_attr_pattern.match(name)
    return m is not None
    

### End of Martel changes

def _group(escape, groups):
    # check if the escape string represents a valid group
    try:
        gid = atoi(escape[1:])
        if gid and gid < groups:
            return gid
    except ValueError:
        pass
    return None # not a valid group

def _class_escape(source, escape):
    # handle escape code inside character class
    code = ESCAPES.get(escape)
    if code:
        return code
    code = CATEGORIES.get(escape)
    if code:
        return code
    try:
        if escape[1:2] == "x":
            # hexadecimal escape (exactly two digits)
            while source.next in HEXDIGITS and len(escape) < 4:
                escape = escape + source.get()
            escape = escape[2:]
            if len(escape) != 2:
                raise error, "bogus escape: %s" % repr("\\" + escape)
            return LITERAL, atoi(escape, 16) & 0xff
        elif str(escape[1:2]) in OCTDIGITS:
            # octal escape (up to three digits)
            while source.next in OCTDIGITS and len(escape) < 5:
                escape = escape + source.get()
            escape = escape[1:]
            return LITERAL, atoi(escape, 8) & 0xff
        if len(escape) == 2:
            return LITERAL, ord(escape[1])
    except ValueError:
        pass
    raise error, "bogus escape: %s" % repr(escape)

def _escape(source, escape, state):
    # handle escape code in expression
    code = CATEGORIES.get(escape)
    if code:
        return code
    code = ESCAPES.get(escape)
    if code:
        return code
    try:
        if escape[1:2] == "x":
            # hexadecimal escape
            while source.next in HEXDIGITS and len(escape) < 4:
                escape = escape + source.get()
            if len(escape) != 4:
                raise ValueError
            return LITERAL, atoi(escape[2:], 16) & 0xff
        elif escape[1:2] == "0":
            # octal escape
            while source.next in OCTDIGITS and len(escape) < 4:
                escape = escape + source.get()
            return LITERAL, atoi(escape[1:], 8) & 0xff
        elif escape[1:2] in DIGITS:
            # octal escape *or* decimal group reference (sigh)
            here = source.tell()
            if source.next in DIGITS:
                escape = escape + source.get()
                if (escape[1] in OCTDIGITS and escape[2] in OCTDIGITS and
                    source.next in OCTDIGITS):
                    # got three octal digits; this is an octal escape
                    escape = escape + source.get()
                    return LITERAL, atoi(escape[1:], 8) & 0xff
            # got at least one decimal digit; this is a group reference
            group = _group(escape, state.groups)
            if group:
                if not state.checkgroup(group):
                    raise error, "cannot refer to open group"
                return GROUPREF, group
            raise ValueError
        if len(escape) == 2:
            return LITERAL, ord(escape[1])
    except ValueError:
        pass
    raise error, "bogus escape: %s" % repr(escape)

def _parse_sub(source, state, nested=1):
    # parse an alternation: a|b|c

    items = []
    while 1:
        items.append(_parse(source, state))
        if source.match("|"):
            continue
        if not nested:
            break
        if not source.next or source.match(")", 0):
            break
        else:
            raise error, "pattern not properly closed"

    if len(items) == 1:
        return items[0]

    subpattern = SubPattern(state)

    # check if all items share a common prefix
    while 1:
        prefix = None
        for item in items:
            if not item:
                break
            if prefix is None:
                prefix = item[0]
            elif item[0] != prefix:
                break
        else:
            # all subitems start with a common "prefix".
            # move it out of the branch
            for item in items:
                del item[0]
            subpattern.append(prefix)
            continue # check next one
        break

    # check if the branch can be replaced by a character set
    for item in items:
        if len(item) != 1 or item[0][0] != LITERAL:
            break
    else:
        # we can store this as a character set instead of a
        # branch (the compiler may optimize this even more)
        set = []
        for item in items:
            set.append(item[0])
        subpattern.append((IN, set))
        return subpattern

    subpattern.append((BRANCH, (None, items)))
    return subpattern

def _parse(source, state):
    # parse a simple pattern

    subpattern = SubPattern(state)

    while 1:

        if source.next in ("|", ")"):
            break # end of subpattern
        this = source.get()
        if this is None:
            break # end of pattern

        if state.flags & SRE_FLAG_VERBOSE:
            # skip whitespace and comments
            if this in WHITESPACE:
                continue
            if this == "#":
                while 1:
                    this = source.get()
                    if this in (None, "\n"):
                        break
                continue

        if this and this[0] not in SPECIAL_CHARS:
            subpattern.append((LITERAL, ord(this)))

        elif this == "[":
            # character set
            set = []
##          if source.match(":"):
##              pass # handle character classes
            if source.match("^"):
                set.append((NEGATE, None))
            # check remaining characters
            start = set[:]
            while 1:
                this = source.get()
                if this == "]" and set != start:
                    break
                elif this and this[0] == "\\":
                    code1 = _class_escape(source, this)
                elif this:
                    code1 = LITERAL, ord(this)
                else:
                    raise error, "unexpected end of regular expression"
                if source.match("-"):
                    # potential range
                    this = source.get()
                    if this == "]":
                        if code1[0] is IN:
                            code1 = code1[1][0]
                        set.append(code1)
                        set.append((LITERAL, ord("-")))
                        break
                    else:
                        if this[0] == "\\":
                            code2 = _class_escape(source, this)
                        else:
                            code2 = LITERAL, ord(this)
                        if code1[0] != LITERAL or code2[0] != LITERAL:
                            raise error, "bad character range"
                        lo = code1[1]
                        hi = code2[1]
                        if hi < lo:
                            raise error, "bad character range"
                        set.append((RANGE, (lo, hi)))
                else:
                    if code1[0] is IN:
                        code1 = code1[1][0]
                    set.append(code1)

            # XXX: <fl> should move set optimization to compiler!
            if len(set)==1 and set[0][0] is LITERAL:
                subpattern.append(set[0]) # optimization
            elif len(set)==2 and set[0][0] is NEGATE and set[1][0] is LITERAL:
                subpattern.append((NOT_LITERAL, set[1][1])) # optimization
            else:
                # XXX: <fl> should add charmap optimization here
                subpattern.append((IN, set))

        elif this and this[0] in REPEAT_CHARS:
            # repeat previous item
            if this == "?":
                min, max = 0, 1
            elif this == "*":
                min, max = 0, MAXREPEAT

            elif this == "+":
                min, max = 1, MAXREPEAT
            elif this == "{":
                here = source.tell()
                min, max = 0, MAXREPEAT
### Martel changes to allow a named reference for the repeat count
# APD -- 21 Aug 2000
##                lo = hi = ""
##                while source.next in DIGITS:
##                    lo = lo + source.get()
##                if source.match(","):
##                    while source.next in DIGITS:
##                        hi = hi + source.get()
##                else:
##                    hi = lo
##                if not source.match("}"):
##                    subpattern.append((LITERAL, ord(this)))
##                    source.seek(here)
##                    continue
##                if lo:
##                    min = atoi(lo)
##                if hi:
##                    max = atoi(hi)
                lo = hi = ""
                while source.next in DIGITS or \
                      isname(lo + source.next):
                    lo = lo + source.get()
                if source.match(","):
                    while source.next in DIGITS or \
                          isname(hi + source.next):
                        hi = hi + source.get()
                else:
                    hi = lo
                if not source.match("}"):
                    subpattern.append((LITERAL, ord(this)))
                    source.seek(here)
                    continue
                if lo:
                    if is_firstchar(lo[:1]):
                        min = lo
                    else:
                        min = atoi(lo)
                if hi:
                    if is_firstchar(hi[:1]):
                        max = hi
                    else:
                        max = atoi(hi)

                if type(lo) == type(hi) == type(0):
                    if max < min:
                        raise error, "bad repeat interval"
### End of Martel named group repeat changes
            else:
                raise error, "not supported"
            # figure out which item to repeat
            if subpattern:
                item = subpattern[-1:]
            else:
                item = None
            if not item or (len(item) == 1 and item[0][0] == AT):
                raise error, "nothing to repeat"
            if item[0][0] in (MIN_REPEAT, MAX_REPEAT):
                raise error, "multiple repeat"
            if source.match("?"):
                subpattern[-1] = (MIN_REPEAT, (min, max, item))
            else:
                subpattern[-1] = (MAX_REPEAT, (min, max, item))

        elif this == ".":
            subpattern.append((ANY, None))

        elif this == "(":
            group = 1
            name = None
            if source.match("?"):
                group = 0
                # options
                if source.match("P"):
                    # python extensions
                    if source.match("<"):
                        # named group: skip forward to end of name
                        name = ""
                        while 1:
                            char = source.get()
                            if char is None:
                                raise error, "unterminated name"
                            if char == ">":
                                break
                            name = name + char
                        group = 1
                        if not isname_with_attrs(name):
                            raise error, "bad character in group name"
                    elif source.match("="):
                        # named backreference
                        name = ""
                        while 1:
                            char = source.get()
                            if char is None:
                                raise error, "unterminated name"
                            if char == ")":
                                break
                            name = name + char
                        if not isname(name):
                            raise error, "bad character in group name"
                        gid = state.groupdict.get(name)
                        if gid is None:
                            raise error, "unknown group name"
                        subpattern.append((GROUPREF, gid))
                        continue
                    else:
                        char = source.get()
                        if char is None:
                            raise error, "unexpected end of pattern"
                        raise error, "unknown specifier: ?P%s" % char
                elif source.match(":"):
                    # non-capturing group
                    group = 2
                elif source.match("#"):
                    # comment
                    while 1:
                        if source.next is None or source.next == ")":
                            break
                        source.get()
                    if not source.match(")"):
                        raise error, "unbalanced parenthesis"
                    continue
                elif source.next in ("=", "!", "<"):
                    # lookahead assertions
                    char = source.get()
                    dir = 1
                    if char == "<":
                        if source.next not in ("=", "!"):
                            raise error, "syntax error"
                        dir = -1 # lookbehind
                        char = source.get()
                    p = _parse_sub(source, state)
                    if not source.match(")"):
                        raise error, "unbalanced parenthesis"
                    if char == "=":
                        subpattern.append((ASSERT, (dir, p)))
                    else:
                        subpattern.append((ASSERT_NOT, (dir, p)))
                    continue
                else:
                    # flags
                    if not FLAGS.has_key(source.next):
                        raise error, "unexpected end of pattern"
                    while FLAGS.has_key(source.next):
                        state.flags = state.flags | FLAGS[source.get()]
            if group:
                # parse group contents
                if group == 2:
                    # anonymous group
                    group = None
                else:
                    group = state.opengroup(name)
                p = _parse_sub(source, state)
                if not source.match(")"):
                    raise error, "unbalanced parenthesis"
                if group is not None:
                    state.closegroup(group)
                subpattern.append((SUBPATTERN, (group, p)))
            else:
                while 1:
                    char = source.get()
                    if char is None:
                        raise error, "unexpected end of pattern"
                    if char == ")":
                        break
                    raise error, "unknown extension"

        elif this == "^":
            subpattern.append((AT, AT_BEGINNING))

        elif this == "$":
            subpattern.append((AT, AT_END))

        elif this and this[0] == "\\":
            code = _escape(source, this, state)
            subpattern.append(code)

        else:
            raise error, "parser error"

    return subpattern

def parse(str, flags=0, pattern=None):
    # parse 're' pattern into list of (opcode, argument) tuples

    source = Tokenizer(str)

    if pattern is None:
        pattern = Pattern()
    pattern.flags = flags
    pattern.str = str

    p = _parse_sub(source, pattern, 0)

    tail = source.get()
    if tail == ")":
        raise error, "unbalanced parenthesis"
    elif tail:
        raise error, "bogus characters at end of regular expression"

    if flags & SRE_FLAG_DEBUG:
        p.dump()

    if not (flags & SRE_FLAG_VERBOSE) and p.pattern.flags & SRE_FLAG_VERBOSE:
        # the VERBOSE flag was switched on inside the pattern.  to be
        # on the safe side, we'll parse the whole thing again...
        return parse(str, p.pattern.flags)

    return p

def parse_template(source, pattern):
    # parse 're' replacement string into list of literals and
    # group references
    s = Tokenizer(source)
    p = []
    a = p.append
    def literal(literal, p=p):
        if p and p[-1][0] is LITERAL:
            p[-1] = LITERAL, p[-1][1] + literal
        else:
            p.append((LITERAL, literal))
    sep = source[:0]
    if type(sep) is type(""):
        char = chr
    else:
        char = unichr
    while 1:
        this = s.get()
        if this is None:
            break # end of replacement string
        if this and this[0] == "\\":
            # group
            if this == "\\g":
                name = ""
                if s.match("<"):
                    while 1:
                        char = s.get()
                        if char is None:
                            raise error, "unterminated group name"
                        if char == ">":
                            break
                        name = name + char
                if not name:
                    raise error, "bad group name"
                try:
                    index = atoi(name)
                except ValueError:
                    if not isname(name):
                        raise error, "bad character in group name"
                    try:
                        index = pattern.groupindex[name]
                    except KeyError:
                        raise IndexError, "unknown group name"
                a((MARK, index))
            elif len(this) > 1 and this[1] in DIGITS:
                code = None
                while 1:
                    group = _group(this, pattern.groups+1)
                    if group:
                        if (s.next not in DIGITS or
                            not _group(this + s.next, pattern.groups+1)):
                            code = MARK, group
                            break
                    elif s.next in OCTDIGITS:
                        this = this + s.get()
                    else:
                        break
                if not code:
                    this = this[1:]
                    code = LITERAL, char(atoi(this[-6:], 8) & 0xff)
                if code[0] is LITERAL:
                    literal(code[1])
                else:
                    a(code)
            else:
                try:
                    this = char(ESCAPES[this][1])
                except KeyError:
                    pass
                literal(this)
        else:
            literal(this)
    # convert template to groups and literals lists
    i = 0
    groups = []
    literals = []
    for c, s in p:
        if c is MARK:
            groups.append((i, s))
            literals.append(None)
        else:
            literals.append(s)
        i = i + 1
    return groups, literals

def expand_template(template, match):
    g = match.group
    sep = match.string[:0]
    groups, literals = template
    literals = literals[:]
    try:
        for index, group in groups:
            literals[index] = s = g(group)
            if s is None:
                raise IndexError
    except IndexError:
        raise error, "empty group"
    return string.join(literals, sep)

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