def parse_mapping(data):
'''
Takes a list of strings and returns the (character,configuration) mapping in it
The 'data' passed is actually the metadata at ths tartting of the file, which specifies
characters which have to be replaced with configurations.
For example, 'u sp 5d' indicates that u is to be replaced with 'sp 5d'
The function uses the fact that different mappings are separated by a gap of at least two spaces.
So, data is parsed to separate out individual mappings. Then, the part after the character is joined
to create a mapping.
'''
mapping = {}
# Defined two grammars, as Optional() wasn't working as expected:
map_parse1 = CharsNotIn(' ') + White() + Word(alphanums) + White(exact=1) + Word(alphanums) + White(min=2) + restOfLine
map_parse2 = CharsNotIn(' ') + White() + Word(alphanums) + White(min=2) + restOfLine
for row in data:
row_copy = row
while len(row_copy) > 0:
# If it's a two-level confiugration:
try:
temp = map_parse1.parseString(row_copy)
mapping[temp[0]] = ' '.join([temp[2],temp[4]])
row_copy = temp[-1]
except:
# If it's a single-level configuration:
try:
temp = map_parse2.parseString(row_copy)
mapping[temp[0]] = temp[2]
row_copy = temp[-1]
except:
# Parsing error, so mappings must be complete
return mapping
def param_substitude(lines, param_dict):
mask_par = (CharsNotIn('{{}}')[0, ] + '{{' + WRD_p + '}}' +
CharsNotIn('{{}}')[0, ])[1, ] + Char('\n')[0, 1]
# mask_par.setParseAction(param_set)
mask_par.setParseAction(lambda tokens: param_set(tokens, param_dict))
for line_to, line in enumerate(lines):
line = line.rstrip()
if not line:
continue
lines[line_to] = mask_par.transformString(line)
return lines
def init_latex_parser(self):
# these variables will be used to define valid lists of characters
lowers = 'qwertyuiopasdfghjklzxcvbnm'
uppers = lowers.upper()
alphas = lowers + uppers
digits = '1234567890'
other_word_symbols = '-_'
word_chars = alphas + other_word_symbols + digits
punctuation_symbols = '.!?:;…'
command_symbol = '\\'
white_characters = CharsNotIn(word_chars + punctuation_symbols +
command_symbol)
# define grammar
word = Word(word_chars)
command = command_symbol + OneOrMore(
alphas
) # as far as i can tell, only alphas are allowed in a latex command (bar the special commands such as \&).
punc = Word(punctuation_symbols)
white_and_word = Group(Suppress(Optional(white_characters)) + word)
white_and_command = Group(
Suppress(Optional(white_characters)) + command)
white_and_punc = Group(Suppress(Optional(white_characters)) + punc)
sentence = ZeroOrMore(white_and_word) + white_and_punc
pure_piece = ZeroOrMore(sentence)
bracketed_piece = '{' + pure_piece + Suppress(
ZeroOrMore(white_characters)) + '}'
self.parser = content.parseString
class NLPyParser(NLBaseParser):
"""pyparsing--based implementation of the NLBaseParser
"""
notSpace = CharsNotIn(" \n")
eq = Literal('=').suppress()
value = (QuotedString('"', escChar=chr(92), unquoteResults=False) \
^ OneOrMore(notSpace))
ts = Group(Literal('ts') + eq + value)
event = Group(Literal('event') + eq + value)
name = ~oneOf("ts event") + Word(alphanums + '-_.')
nv = ZeroOrMore(Group(name + eq + value))
nvp = Each([ts, event, nv]) + White('\n').suppress() + StringEnd()
def parseLine(self, line):
try:
rlist = self.nvp.parseString(line).asList()
except ParseException as E:
raise ValueError(E)
result = {}
for a in rlist:
if self.parse_date and a[0] == 'ts':
result[a[0]] = parse_ts(a[1])
else:
result[a[0]] = a[1]
return result
def PIs():
"""Parses Processing Instructions
PI ::= '<?' PITarget (S (Char* - (Char* '?>' Char*)))? '?>'
>>> tests=(
... '''<?foo?>''',
... '''<?foo ?>''',
... '''<?foo abc def ghi ?>''',
... '''<?xml-stylesheet foo="bla" bar="x" ?>''',
... '''<?xml-stylesheet
... foo="bla"
... foo="x"
... ?>''',
... )
>>> p=PIs()
>>> for t in tests:
... result=p.parseString(t)
... print result
['foo']
['foo', ' ']
['foo', ' abc def ghi ']
['xml-stylesheet', ' foo="bla" bar="x" ']
['xml-stylesheet', '\\n foo="bla"\\n foo="x"\\n ']
"""
pi=Suppress('<?') + \
Word(alphas, alphanums+'-_')('pitarget') + \
ZeroOrMore(CharsNotIn('?>'))('picontents') + \
Suppress('?>')
return pi
def _parser_piece_text():
"""
Return PyParsing element to the text of a markdown link.
"""
# No double line breaks in markdown links
double_line_break = (Word("\n\r", exact=1) + Optional(Word(" \t")) +
Word("\n\r", exact=1))
# We will ignore escaped square brackets when match finding balanced
# square brackets.
ignore = Literal("\\[") | Literal("\\]")
# The text parser will match text inside balanced brackets using the
# nestedExpr helper function from PyParsing.
#
# Next we define the content that is allowed inside the brackets.
content_character = ~FollowedBy(double_line_break) + CharsNotIn(
"[]", exact=1)
# Normally with nestedExpr, the content parser would be separately applied
# to each whitespace-separated string within the nested expression.
# However, since we set whitespaceChars to '', the content parser is
# applied to characters one-at-a-time.
#
# If this ever changes, we would need to change content to something
# like Combine(OneOrMore(~ignore + content_character))
content = content_character
text = originalTextFor(
nestedExpr(
opener="[",
closer="]",
content=content,
ignoreExpr=ignore,
)).setResultsName("text")
text.addParseAction(lambda s, l, toks: toks[0][1:-1])
return text
def pyparse_blk(text):
def create_add_block(tokens):
return Block.Block(tokens.title,
tokens.color if tokens.color else 'white')
left_bracket, right_bracket, equal_sign = map(Suppress, '[]=')
color = (Word('#', hexnums, exact=7) | Word(alphanums, alphas))('color')
empty_block = (
left_bracket +
right_bracket)('empty_block').setParseAction(lambda: EmptyBlock)
new_lines = Word('/')('new_lines').setParseAction(
lambda tokens: len(tokens.new_lines))
title = CharsNotIn('[]/\n')('title').setParseAction(
lambda tokens: tokens.title.strip())
block_data = Optional(color + Suppress(':')) + Optional(title)
block_data.addParseAction(create_add_block)
blocks = Forward()
block = left_bracket + block_data + blocks + right_bracket
blocks << Group(
ZeroOrMore(Optional(new_lines) + OneOrMore(empty_block | block)))
stack = [Block.create_root_block()]
try:
result = blocks.parseString(text, parseAll=True)
assert len(result) == 1
blocks_list = result.asList()[0]
populate_children(blocks_list, stack)
except (ParseSyntaxException, ParseException) as parse_err:
raise ValueError('Error {{0}}: {0}'.format(parse_err.lineno))
return stack[0]
def func_tokens(dictionary, parse_action):
func_name = Word(alphas + '_', alphanums + '_')
func_ident = Combine('$' + func_name.copy()('funcname'))
func_tok = func_ident + originalTextFor(nestedExpr())('args')
func_tok.leaveWhitespace()
func_tok.setParseAction(parse_action)
func_tok.enablePackrat()
rx_tok = Combine(Literal('$').suppress() + Word(nums)('num'))
def replace_token(tokens):
index = int(tokens.num)
return dictionary.get(index, '')
rx_tok.setParseAction(replace_token)
strip = lambda s, l, tok: tok[0].strip()
text_tok = CharsNotIn(',').setParseAction(strip)
quote_tok = QuotedString('"')
if dictionary:
arglist = Optional(delimitedList(quote_tok | rx_tok | text_tok))
else:
arglist = Optional(delimitedList(quote_tok | text_tok))
return func_tok, arglist, rx_tok
def pyparsing_parse(text):
"""
>>> import os
>>> dirname = os.path.join(os.path.dirname(__file__), "data")
>>> filename = os.path.join(dirname, "error1.blk")
>>> pyparsing_parse(open(filename, encoding="utf8").read())
Traceback (most recent call last):
...
ValueError: Error {0}: syntax error, line 8
>>> filename = os.path.join(dirname, "error2.blk")
>>> pyparsing_parse(open(filename, encoding="utf8").read())
Traceback (most recent call last):
...
ValueError: Error {0}: syntax error, line 1
>>> filename = os.path.join(dirname, "error3.blk")
>>> pyparsing_parse(open(filename, encoding="utf8").read())
Traceback (most recent call last):
...
ValueError: Error {0}: syntax error, line 4
>>> expected = "[white: ]\\n[lightblue: Director]\\n/\\n/\\n[white: ]\\n[lightgreen: Secretary]\\n/\\n/\\n[white: Minion #1]\\n[white: ]\\n[white: Minion #2]"
>>> filename = os.path.join(dirname, "hierarchy.blk")
>>> blocks = pyparsing_parse(open(filename, encoding="utf8").read())
>>> str(blocks).strip() == expected
True
>>> expected = "[#00CCDE: MessageBox Window\\n[lightgray: Frame\\n[white: ]\\n[white: Message text]\\n/\\n/\\n[goldenrod: OK Button]\\n[white: ]\\n[#ff0505: Cancel Button]\\n/\\n[white: ]\\n]\\n]"
>>> filename = os.path.join(dirname, "messagebox.blk")
>>> blocks = pyparsing_parse(open(filename, encoding="utf8").read())
>>> str(blocks).strip() == expected
True
"""
def add_block(tokens):
return Block.Block(tokens.name,
tokens.color if tokens.color else "white")
left_bracket, right_bracket = map(Suppress, "[]")
new_rows = Word("/")("new_rows").setParseAction(
lambda tokens: len(tokens.new_rows))
name = CharsNotIn("[]/\n")("name").setParseAction(
lambda tokens: tokens.name.strip())
color = (Word("#", hexnums, exact=7) | Word(alphas, alphanums))("color")
empty_node = (left_bracket +
right_bracket).setParseAction(lambda: EmptyBlock)
nodes = Forward()
node_data = Optional(color + Suppress(":")) + Optional(name)
node_data.setParseAction(add_block)
node = left_bracket - node_data + nodes + right_bracket
nodes << Group(
ZeroOrMore(Optional(new_rows) + OneOrMore(node | empty_node)))
stack = [Block.get_root_block()]
try:
results = nodes.parseString(text, parseAll=True)
assert len(results) == 1
items = results.asList()[0]
populate_children(items, stack)
except (ParseException, ParseSyntaxException) as err:
raise ValueError("Error {{0}}: syntax error, line "
"{0}".format(err.lineno))
return stack[0]
def fromString(inputText):
text = nestedExpr("/*", "*/").suppress().transformString(inputText)
semicolon = Suppress(Word(";"))
quote = Suppress(Word("\""))
op = Suppress(Word("{"))
cl = Suppress(Word("}"))
opp = Suppress(Word("("))
clp = Suppress(Word(")"))
lt = Suppress(Word("<"))
gt = Suppress(Word(">"))
eq = Suppress(Word("="))
identifier = Word(alphas+"_",alphanums+"_")
typeIdentifier = Word(alphas+"_",alphanums+"_:")
structIdentifer = Group(typeIdentifier.setResultsName('type') + identifier.setResultsName('identifier') + Optional(eq) + Optional(CharsNotIn(";").setResultsName('defaultValue')) + semicolon)
structIdentifers = Group(OneOrMore(structIdentifer))
## Imports
idslImport = Suppress(Word("import")) + quote + CharsNotIn("\";").setResultsName('path') + quote + semicolon
idslImports = ZeroOrMore(idslImport)
structDef = Word("struct").setResultsName('type') + identifier.setResultsName('name') + op + structIdentifers.setResultsName("structIdentifiers") + cl + semicolon
dictionaryDef = Word("dictionary").setResultsName('type') + lt + CharsNotIn("<>").setResultsName('content') + gt + identifier.setResultsName('name') + semicolon
sequenceDef = Word("sequence").setResultsName('type') + lt + typeIdentifier.setResultsName('typeSequence') + gt + identifier.setResultsName('name') + semicolon
enumDef = Word("enum").setResultsName('type') + identifier.setResultsName('name') + op + CharsNotIn("{}").setResultsName('content') + cl + semicolon
exceptionDef = Word("exception").setResultsName('type') + identifier.setResultsName('name') + op + CharsNotIn("{}").setResultsName('content') + cl + semicolon
raiseDef = Suppress(Word("throws")) + typeIdentifier + ZeroOrMore( Literal(',') + typeIdentifier )
decoratorDef = Literal('idempotent') | Literal('out')
retValDef = typeIdentifier.setResultsName('ret')
firstParam = Group( Optional(decoratorDef.setResultsName('decorator')) + typeIdentifier.setResultsName('type') + identifier.setResultsName('name'))
nextParam = Suppress(Word(',')) + firstParam
params = firstParam + ZeroOrMore(nextParam)
remoteMethodDef = Group(Optional(decoratorDef.setResultsName('decorator')) + retValDef.setResultsName('ret') + typeIdentifier.setResultsName('name') + opp + Optional( params).setResultsName('params') + clp + Optional(raiseDef.setResultsName('raise')) + semicolon )
interfaceDef = Word('interface').setResultsName('type') + typeIdentifier.setResultsName('name') + op + Group(ZeroOrMore(remoteMethodDef)).setResultsName('methods') + cl + semicolon
moduleContent = Group(structDef | enumDef | exceptionDef | dictionaryDef | sequenceDef | interfaceDef)
module = Suppress(Word("module")) + identifier.setResultsName("name") + op + ZeroOrMore(moduleContent).setResultsName("contents") + cl + semicolon
IDSL = idslImports.setResultsName("imports") + module.setResultsName("module")
IDSL.ignore( cppStyleComment )
tree = IDSL.parseString(text)
return tree
class Include(object):
rule = (INCLUDE + LOPBRACK + CharsNotIn('>')("header") +
ROPBRACK).setParseAction(lambda t: Include(t.header))
def __init__(self, header, parent=''):
self.header = header
self.parent = parent
def __repr__(self):
return "#include <{}>".format(self.header)
class NginxParser(object):
"""
A class that parses nginx configuration with pyparsing
"""
# constants
left_bracket = Literal("{").suppress()
right_bracket = Literal("}").suppress()
semicolon = Literal(";").suppress()
space = White().suppress()
key = Word(alphanums + "_/")
value = CharsNotIn("{};,")
location = CharsNotIn("{};," + string.whitespace)
# modifier for location uri [ = | ~ | ~* | ^~ ]
modifier = Literal("=") | Literal("~*") | Literal("~") | Literal("^~")
# rules
assignment = (key + Optional(space + value) + semicolon)
block = Forward()
block << Group(
Group(key + Optional(space + modifier) + Optional(space + location))
+ left_bracket
+ Group(ZeroOrMore(Group(assignment) | block))
+ right_bracket)
script = OneOrMore(Group(assignment) | block).ignore(pythonStyleComment)
def __init__(self, source):
self.source = source
def parse(self):
"""
Returns the parsed tree.
"""
return self.script.parseString(self.source)
def as_list(self):
"""
Returns the list of tree.
"""
return self.parse().asList()
class RawNginxParser(object):
# pylint: disable=expression-not-assigned
"""A class that parses nginx configuration with pyparsing."""
# constants
space = Optional(White())
nonspace = Regex(r"\S+")
left_bracket = Literal("{").suppress()
right_bracket = space.leaveWhitespace() + Literal("}").suppress()
semicolon = Literal(";").suppress()
key = Word(alphanums + "_/+-.")
dollar_var = Combine(Literal('$') + nonspace)
condition = Regex(r"\(.+\)")
# Matches anything that is not a special character AND any chars in single
# or double quotes
value = Regex(r"((\".*\")?(\'.*\')?[^\{\};,]?)+")
location = CharsNotIn("{};," + string.whitespace)
# modifier for location uri [ = | ~ | ~* | ^~ ]
modifier = Literal("=") | Literal("~*") | Literal("~") | Literal("^~")
# rules
comment = space + Literal('#') + restOfLine()
assignment = space + key + Optional(space + value,
default=None) + semicolon
location_statement = space + Optional(modifier) + Optional(space +
location +
space)
if_statement = space + Literal("if") + space + condition + space
map_statement = space + Literal(
"map") + space + nonspace + space + dollar_var + space
block = Forward()
block << Group(
# key could for instance be "server" or "http", or "location" (in which case
# location_statement needs to have a non-empty location)
(Group(space + key + location_statement) ^ Group(if_statement)
^ Group(map_statement)).leaveWhitespace() + left_bracket +
Group(ZeroOrMore(Group(comment | assignment) | block) +
space).leaveWhitespace() + right_bracket)
script = OneOrMore(Group(comment | assignment) ^ block) + space + stringEnd
script.parseWithTabs()
def __init__(self, source):
self.source = source
def parse(self):
"""Returns the parsed tree."""
return self.script.parseString(self.source)
def as_list(self):
"""Returns the parsed tree as a list."""
return self.parse().asList()
def grammar(self, value):
seps = list({value.list_sep, value.range_sep, value.step_sep})
quotedstr = pp.quotedString.setParseAction(pp.removeQuotes)
self.tokens = OrderedDict({
'regex': Literal('r').suppress() + quotedstr,
'quoted': quotedstr,
'colnum': Grammar.integer,
'sep': Or(seps),
'name': CharsNotIn(seps),
})
def initGrammar(self):
L_Equals = Word("=")
N_comment = htmlComment()
N_name = CharsNotIn("{}|[]")
N_simpleText = SkipTo(
oneOf(["{{", "|", "[[", "]]", "}}", "'''", "<ref"]))
N_elements = Forward()
N_apostrofs = QuotedString("'''").setParseAction(
lambda s, l, t: {'APOSTROFS': t})
N_link = nestedExpr(
opener="[[",
closer="]]",
content=N_name +
Optional("|" + delimitedList(CharsNotIn("[]"), delim="|"))
).setParseAction(self.genLink)
N_header = Group(L_Equals + SkipTo("=") + L_Equals).setParseAction(
lambda s, l, t: {'HEADER': t})
N_template = Forward()
N_key = CharsNotIn("{}|=")
# N_value = ZeroOrMore(CharsNotIn("{}|")) + ZeroOrMore(N_template + ZeroOrMore(CharsNotIn("{}|"))).setResultsName('VALUE')
N_keyValues = "|" + delimitedList(
Group(Optional(N_key) + Optional("=" + N_elements)), delim="|")
N_label_content = N_template | ("{{" + OneOrMore("!") +
"}}") | CharsNotIn("{}|")
N_label = nestedExpr(opener="{", closer="}", content=N_label_content)
N_template << nestedExpr(
opener="{{", closer="}}", content=N_name +
Optional(N_keyValues)).setParseAction(self.genTemplate)
ref_start, ref_end = makeHTMLTags("ref")
N_named_ref = ref_start + SkipTo(ref_end) + ref_end
N_named_ref.setParseAction(lambda s, l, t: {'REF': t})
N_element = N_comment | N_simpleText | N_named_ref | N_apostrofs | N_link | N_header | N_template | N_label
# N_ref = nestedExpr( opener="<ref>", closer="</ref>", content=N_elements).setParseAction( lambda s,l,t: {'REF' : t} )
N_elements << ZeroOrMore(N_element)
self.N_S = N_elements
def initGrammar(self):
N_comment = htmlComment().setParseAction(self.genComment)
N_name = CharsNotIn("{}|[]")
N_link = nestedExpr(
opener="[[",
closer="]]",
content=N_name +
Optional("|" + delimitedList(CharsNotIn("[]"), delim="|"))
).setParseAction(self.genLink).setDebug(True)
L_Equals = Word("=")
N_header = Group(L_Equals + SkipTo("=") + L_Equals).setParseAction(
self.genHeader)
N_element = Forward()
N_template = Forward().setDebug(True)
N_key = CharsNotIn("{}|=")
N_internalText = CharsNotIn("{}|=<[") + SkipTo(
Literal("{{") | Literal("[[") | Literal("<!--") | Literal("<ref")
| Literal("|") | Literal("}}")) #CharsNotIn("{}|[]<")
N_insideElements = OneOrMore(N_element | N_internalText).setDebug(True)
N_keyValue = Group(
Optional(N_key) +
Optional(Literal("=") + N_insideElements)).setDebug(True)
N_keyValues = "|" + delimitedList(N_keyValue, delim="|")
N_keyValues.setDebug(True)
#N_label_content = N_template | ("{{"+OneOrMore("!")+"}}") | CharsNotIn("{}|")
#N_label = nestedExpr( opener="{", closer="}", content = N_label_content)
N_template << nestedExpr(
opener="{{", closer="}}", content=N_name +
Optional(N_keyValues)).setParseAction(self.genTemplate)
#ref_start, ref_end = makeHTMLTags("ref")
#N_named_ref = ref_start + SkipTo(ref_end) + ref_end
#N_named_ref.setParseAction( lambda s,l,t: {'REF' : t} )
N_element = N_comment | N_link | N_header | N_template
N_element.setDebug(True)
self.N_S = N_element
def pattern():
"""pyparsing pattern
"""
def attachLocation(s, loc, tocs):
"""pyparsing callback. Saves path position in the original string
"""
return [(loc, tocs[0])]
path = CharsNotIn(" \t")("path")
path.setParseAction(attachLocation)
longPath = CharsNotIn(" \t", min=2)("path")
longPath.setParseAction(attachLocation)
slashPath = Combine(Literal('/') + Optional(CharsNotIn(" \t")))("path")
slashPath.setParseAction(attachLocation)
pat = ((Literal('f ') + Optional(White()) + Optional(path)) ^ longPath ^ slashPath) + \
Optional(White() + Word(nums)("line"))
pat.leaveWhitespace()
pat.setParseAction(CommandOpen.create)
return pat
def get_parser():
from pyparsing import CharsNotIn, ParserElement, Suppress, ZeroOrMore
ParserElement.enablePackrat()
word = CharsNotIn(f"{PERIOD}{LBRACK}{RBRACK}")
idx = Suppress(LBRACK) + word + Suppress(RBRACK)
attr = Suppress(PERIOD) + word
parser = word + ZeroOrMore(attr ^ idx)
parser.setParseAction(PERIOD.join)
return parser
def build_parser():
key = Word(alphanums).setResultsName('key')
value = restOfLine.setParseAction(lambda string, location, tokens: tokens[
0].strip()).setResultsName('value')
property_ = Group(key + Suppress(Literal('=')) + value)
properties = Group(OneOrMore(property_)).setResultsName('properties')
section_name = (Suppress('[') + OneOrMore(CharsNotIn(']')) +
Suppress(']')).setResultsName('section')
section = Group(section_name + properties)
ini_file = ZeroOrMore(section).setResultsName('sections')
ini_file.ignore(pythonStyleComment)
return ini_file
def _getControls(self, index=1):
identifier = QuotedString('"') | CharsNotIn(',')
arglist = delimitedList(identifier)
docstr = self.doc[1:]
if index:
return [(arglist.parseString(line)[index]).strip()
for line in docstr]
else:
ret = []
for line in docstr:
ret.append([z.strip() for z in arglist.parseString(line)])
return ret
def query_from_string(cls, filter_string):
"""
TODO:
* handle values with " via: a.b.c.d="hello\"world"
* handle keys with " via: a.\"b.c="yeah"
* handle key with __ in it
"""
filter_string_raw = filter_string
filter_string = str(filter_string)
unicode_spaces = list(set(
str(c) for c in filter_string if c.isspace()))
unicode_spaces_other = unicode_spaces + [u'(', u')', u'=', u'"']
atom = CharsNotIn(unicode_spaces_other)
atom_inside_quotes = CharsNotIn(u'"')
atom_quoted = Literal('"') + Optional(atom_inside_quotes) + Literal(
'"')
EQUAL = Literal('=')
grammar = (atom_quoted | atom) + EQUAL + Optional((atom_quoted | atom))
grammar.setParseAction(cls.BoolOperand)
boolExpr = infixNotation(
grammar,
[
("and", 2, opAssoc.LEFT, cls.BoolAnd),
("or", 2, opAssoc.LEFT, cls.BoolOr),
],
)
try:
res = boolExpr.parseString('(' + filter_string + ')')
except ParseException:
raise RuntimeError(u"Invalid query %s" % filter_string_raw)
if len(res) > 0:
return res[0].result
raise RuntimeError("Parsing the filter_string %s went terribly wrong" %
filter_string)
def __init__(self):
self.ALPHA_LABEL = Regex(r'alpha\[\d+\]:')
self.LNL_LABEL = Literal('Final GAMMA-based Score of best tree')
self.FRQ_LABEL = Regex(r'Base frequencies: (?=\d+)') ^ Regex(
r'ML estimate base freqs\[\d+\]:')
self.NAMES_LABEL = Regex(r'Partition: \d+ with name:\s+')
self.RATES_LABEL = Regex(r'rates\[\d+\].+?:')
self.MODEL_LABEL = Literal('Substitution Matrix:')
self.alpha = OneOrMore(
Suppress(SkipTo(self.ALPHA_LABEL)) + Suppress(self.ALPHA_LABEL) +
FLOAT)
self.lnl = Suppress(SkipTo(self.LNL_LABEL)) + Suppress(
self.LNL_LABEL) + FLOAT
self.frq = OneOrMore(
Group(
Suppress(SkipTo(self.FRQ_LABEL)) + Suppress(self.FRQ_LABEL) +
OneOrMore(FLOAT)))
self.names = OneOrMore(
Suppress(SkipTo(self.NAMES_LABEL)) + Suppress(self.NAMES_LABEL) +
CharsNotIn('\n') + Suppress(LineEnd()))
self.rates = OneOrMore(
Group(
Suppress(SkipTo(self.RATES_LABEL)) +
Suppress(self.RATES_LABEL) + OneOrMore(FLOAT)))
self.model = Suppress(SkipTo(self.MODEL_LABEL)) + Suppress(
self.MODEL_LABEL) + WORD
MODEL_LABEL = Literal('Substitution Matrix:')
SCORE_LABEL = Literal('Final GAMMA likelihood:')
DESC_LABEL = Literal('Model Parameters of Partition')
NAME_LEADIN = Literal(', Name:')
DATATYPE_LEADIN = Literal(', Type of Data:')
ALPHA_LEADIN = Literal('alpha:')
TREELENGTH_LEADIN = Literal('Tree-Length:')
RATES_LABEL = Regex(r'rate \w <-> \w:')
FREQS_LABEL = Regex(r'freq pi\(\w\):')
model = Suppress(SkipTo(MODEL_LABEL)) + Suppress(MODEL_LABEL) + WORD
likelihood = Suppress(
SkipTo(SCORE_LABEL)) + Suppress(SCORE_LABEL) + FLOAT
description = Suppress(
SkipTo(DESC_LABEL)) + Suppress(DESC_LABEL) + INT + Suppress(
NAME_LEADIN) + SPACEDWORD + Suppress(DATATYPE_LEADIN) + WORD
alpha = Suppress(ALPHA_LEADIN) + FLOAT
rates = Suppress(RATES_LABEL) + FLOAT
freqs = Suppress(FREQS_LABEL) + FLOAT
self._dash_f_e_parser = (Group(OneOrMore(model)) + likelihood + Group(
OneOrMore(
Group(description + alpha + Suppress(TREELENGTH_LEADIN) +
Suppress(FLOAT) + Group(OneOrMore(rates)) +
Group(OneOrMore(freqs))))))
def grammar():
parenthesis = Forward()
parenthesis <<= "(" + ZeroOrMore(CharsNotIn("()") | parenthesis) + ")"
field_def = OneOrMore(Word(alphanums + "_\"'`:-") | parenthesis)
field_def.setParseAction(field_act)
tablename_def = (Word(alphas + "`_") | QuotedString("\""))
field_list_def = field_def + ZeroOrMore(Suppress(",") + field_def)
field_list_def.setParseAction(field_list_act)
create_table_def = Literal(
"CREATE") + "TABLE" + tablename_def.setResultsName(
"tableName") + "(" + field_list_def.setResultsName(
"fields") + ")" + ";"
create_table_def.setParseAction(create_table_act)
add_fkey_def = Literal(
"ALTER") + "TABLE" + "ONLY" + tablename_def.setResultsName(
"tableName") + "ADD" + "CONSTRAINT" + Word(
alphanums + "_") + "FOREIGN" + "KEY" + "(" + Word(
alphanums +
"_").setResultsName("keyName") + ")" + "REFERENCES" + Word(
alphanums +
"_").setResultsName("fkTable") + "(" + Word(
alphanums +
"_").setResultsName("fkCol") + ")" + Optional(
Literal("DEFERRABLE")) + ";"
add_fkey_def.setParseAction(add_fkey_act)
other_statement_def = OneOrMore(CharsNotIn(";")) + ";"
other_statement_def.setParseAction(other_statement_act)
comment_def = "--" + ZeroOrMore(CharsNotIn("\n"))
comment_def.setParseAction(other_statement_act)
return OneOrMore(comment_def | create_table_def | add_fkey_def
| other_statement_def)
class Include:
"""
Rule to parse #include directives.
"""
rule = (INCLUDE + LOPBRACK + CharsNotIn('>')("header") +
ROPBRACK).setParseAction(lambda t: Include(t.header))
def __init__(self, header: CharsNotIn, parent: str = ''):
self.header = header
self.parent = parent
def __repr__(self) -> str:
return "#include <{}>".format(self.header)
def getSignatures(signatureFile):
fp = open(signatureFile, "rb")
content = fp.read()
fp.close()
litteral = Word(alphas + nums + "_")
regex_pattern = CharsNotIn("(")
tags = (OneOrMore(Group('#' + litteral))).setResultsName("tags")
hierarchy_modifier = oneOf("<= =")
java_type = Group(
Optional(hierarchy_modifier) +
Word(alphas + nums + "_" + "." + "[" + "]" + "$"))
return_type = (java_type | "*").setResultsName("return_type")
method_name = (litteral | "<init>"
| regex_pattern).setResultsName("method_name")
parameter = Group((java_type + litteral))
parameter_list = (delimitedList(parameter)
| "*").setResultsName("parameters")
body_instruction = (CharsNotIn("{;}"))
signature_body = (delimitedList(body_instruction,
";")).setResultsName("signature_body")
class_name = (java_type
| Group(Optional(hierarchy_modifier) +
CharsNotIn(":"))).setResultsName("class_name")
signature_stmt = Group((Optional(tags) + return_type + class_name+":"+method_name+ \
"(" + Optional(parameter_list) + ")"+"{"+Optional(signature_body)+"}"))
grammar = OneOrMore(signature_stmt)
grammar.ignore(dblSlashComment)
result = grammar.parseString(content)
#IPython.embed()
#debug_db_data(content,result)
signatures = [Signature(sig) for sig in result]
return signatures
def __init__(self, debug=False):
aggregate = Forward().setResultsName("OFC")
aggregate_open_tag, aggregate_close_tag = self._tag()
content_open_tag = self._tag(closed=False)
content = Group(content_open_tag + CharsNotIn("<\r\n"))
aggregate << Group(aggregate_open_tag \
+ Dict(OneOrMore(aggregate | content)) \
+ aggregate_close_tag)
self.parser = Group(aggregate).setResultsName("document")
if (debug):
self.parser.setDebugActions(ofxtools._ofxtoolsStartDebugAction,
ofxtools._ofxtoolsSuccessDebugAction,
ofxtools._ofxtoolsExceptionDebugAction)
def __init__(self, debug=False):
# Parser definition for headers
header = Group(
Word(alphas) + Literal(":").suppress() +
Optional(CharsNotIn("\r\n")))
headers = Dict(OneOrMore(header)).setResultsName("header")
# Parser definition for OFX body
aggregate = Forward().setResultsName("OFX")
aggregate_open_tag, aggregate_close_tag = self._tag()
content_open_tag = self._tag(closed=False)
content = Group(content_open_tag + CharsNotIn("<\r\n"))
aggregate << Group(aggregate_open_tag \
+ Dict(ZeroOrMore(aggregate | content)) \
+ aggregate_close_tag)
body = Group(aggregate).setResultsName("body")
# The parser as a whole
self.parser = headers + body
if (debug):
self.parser.setDebugActions(_ofxStartDebugAction,
_ofxSuccessDebugAction,
_ofxExceptionDebugAction)
def Syntax():
delimitedList = (lambda x: x + ZeroOrMore(Suppress(",") + x) +
Optional(Suppress(",")))
dbl_quoted = Suppress('"') + Optional(CharsNotIn('"')) + Suppress('"')
lelem = Word(alphanums + "-_")
relem = Literal("true") | Literal("false") | Word(nums +
".") | dbl_quoted
dict_ = Forward()
assignment = lelem + Suppress("=") + (relem | (dict_))
dict_ << Suppress("{") + Group(
Dict(delimitedList(Group(assignment)))
| (dbl_quoted + Suppress(",") + Word(nums + "."))
| delimitedList(dict_)) + Suppress("}")
return Dict(delimitedList(Group(assignment)))
def parse_final():
'''
Takes the parsed data( list of lists), and performs substitutions according to the mapping specified
as the start of the file. Applies first mapping for first half of the document, and second mapping
for the second half.
The substitutions are performed by trying to match every field with the grammar below, and making
substitutions whenever the grammar's rule s satisfied.
'''
first_mapping = []
second_mapping = []
parsed_data = []
if not parse_data(first_mapping, second_mapping,parsed_data):
return False
SUBS = CharsNotIn('(') + "(" + Word(alphanums) + ")" + restOfLine
for row in parsed_data:
for i in range(len(row)):
# First half of data ; first mapping will apply:
if len(row)>6:
try:
parsed = SUBS.parseString(row[i])
parsed[0] = first_mapping[parsed[0]]
row[i] = ''.join(parsed)
# print parsed
except:
pass
# Second half of data ; second mapping will apply:
else:
try:
parsed = SUBS.parseString(row[i])
parsed[0] = second_mapping[parsed[0]]
row[i] = ''.join(parsed)
except:
pass
return parsed_data
def makeNewickParser():
# pyparsing
from pyparsing import Combine, Optional, Literal, CaselessLiteral, \
Word, alphanums, \
nums, oneOf, Group, Dict, Forward, \
ParseResults, CharsNotIn, ZeroOrMore
# literals
lparen = Literal("(").suppress()
rparen = Literal(")").suppress()
colon = Literal(":").suppress()
semicolon = Literal(":").suppress()
comma = Literal(",").suppress()
point = Literal(".")
e = CaselessLiteral("E")
# terminal rules
name = Word(alphanums + "_" + "-" + "." + "+")
fnumber = Combine(Word("+-"+nums, nums) +
Optional(point + Optional(Word(nums))) +
Optional(e + Word("+-"+nums, nums)))
dist = fnumber
bootstrap = fnumber
# recursive rules
subtree = Forward()
subtreelist = Forward()
subtree << \
Group(
(
(lparen + subtreelist + rparen).setResultsName("subtree") |
name.setResultsName("name")
) +
Optional(
CharsNotIn(",);").setResultsName("data")
)
)
subtreelist << subtree + Optional(comma + subtreelist)
# top level rule
tree = subtree + Word(";").suppress()
return tree.parseString
def parse_variadic_templates(txt):
template_param_type = Word(alphas)
template_variadic = Literal('...')
template_id = Word(alphas)
template_variadic_param = Group(template_param_type + template_variadic +
template_id)
template_param = Group(template_param_type + template_id)
# template_params = Group ( delimitedList( template_variadic_param | Optional(template_param) ) )
template_params = (Optional(OneOrMore(template_param + ',')) +
template_variadic_param +
Optional(OneOrMore(',' + template_param)))
template_params_no_variadic = (template_param +
Optional(OneOrMore(',' + template_param)))
template_decl = Optional("template" + Literal("<") +
template_params_no_variadic +
Literal(">")) + "template" + Literal(
"<") + template_params + Literal(">")
block_content = Forward()
block = nestedExpr('{', '}', content=block_content) + Literal(';') * (0, 1)
block_content << (CharsNotIn('{}') | block)
decl = originalTextFor(template_decl + CharsNotIn('{') + block)
template_file = Forward()
code_block = decl | White() | Word(printables)
template_file << (Optional(OneOrMore(code_block)) | template_file)
parsed = template_file.parseString(txt)
return parsed
def process_task_lists(content: str) -> str:
item = Group(CharsNotIn('\n') + (StringEnd() | '\n')).leaveWhitespace()
checkbox = oneOf(['[ ]', '[x]'])
marker = Suppress(oneOf(['+', '-', '*']) | Word(nums) + '.')
#
indent = oneOf([' ', '\t']).leaveWhitespace()
indents = Group(ZeroOrMore(indent))
#
list_item = Group(indents + marker + checkbox + item)
#
before = Suppress(StringStart() | Literal('\n\n')).leaveWhitespace()
list_ = before + OneOrMore(list_item)
#
list_.setParseAction(replace_list)
return list_.transformString(content)
def pattern():
"""pyparsing pattern of the command
"""
def attachLocation(s, loc, tocs):
return [(loc, tocs[0])]
from pyparsing import CharsNotIn, Literal, Optional, White # delayed import, performance optimization
path = CharsNotIn(" \t")("path")
path.setParseAction(attachLocation)
pat = (Literal('s ') + Optional(White()) + Optional(path))
pat.leaveWhitespace()
pat.setParseAction(CommandSaveAs.create)
return pat
SUPPORT_MISSING_VALUES = True
# from the RFCs ABNF description
nilvalue = Word("-")
digit = Regex("[0-9]{1}")
nonzero_digit = Regex("[1-9]{1}")
printusascii = printables
sp = White(" ", exact=1)
octet = Regex("[\x00-\xFF]")
utf_8_string = Regex("[\x00-\xFF]*")
BOM = "\xef\xbb\xbf"
bom = Regex(BOM)
msg_utf8 = bom + utf_8_string
msg_any = utf_8_string
msg = Combine(Or([msg_utf8, msg_any])).setResultsName("MSG")
sd_name = CharsNotIn('= ]"', 1, 32)
param_name = sd_name.setResultsName("SD_PARAM_NAME")
param_value = QuotedString(quoteChar='"', escChar="\\", multiline=True)
param_value = param_value.setResultsName("SD_PARAM_VALUE")
sd_id = sd_name.setResultsName("SD_ID")
sd_param = Group(param_name + Regex("=") + param_value)
sd_params = Group(ZeroOrMore(Group(sp + sd_param.setResultsName("SD_PARAM"))))
sd_element = Group("[" + sd_id + sd_params.setResultsName("SD_PARAMS") + "]")
sd_element = sd_element.setResultsName("SD_ELEMENT")
sd_elements = Group(OneOrMore(sd_element))
structured_data = Or([nilvalue, sd_elements.setResultsName("SD_ELEMENTS")])
structured_data = structured_data.setResultsName("STRUCTURED_DATA")
time_hour = Regex("0[0-9]|1[0-9]|2[0-3]")
time_minute = Regex("[0-5][0-9]")
time_second = time_minute
time_secfrac = Regex("\.[0-9]{1,6}")
SUPPORT_MISSING_VALUES = True
# from the RFCs ABNF description
nilvalue = Word("-")
digit = Regex("[0-9]{1}")
nonzero_digit = Regex("[1-9]{1}")
printusascii = printables
sp = White(" ", exact=1)
octet = Regex('[\x00-\xFF]')
utf_8_string = Regex('[\x00-\xFF]*')
BOM = '\xef\xbb\xbf'
bom = Regex(BOM)
msg_utf8 = bom + utf_8_string
msg_any = utf_8_string
msg = Combine(Or([msg_utf8, msg_any])).setResultsName('MSG')
sd_name = CharsNotIn('= ]"', 1, 32)
param_name = sd_name.setResultsName('SD_PARAM_NAME')
param_value = QuotedString(quoteChar='"', escChar='\\', multiline=True)
param_value = param_value.setResultsName('SD_PARAM_VALUE')
sd_id = sd_name.setResultsName('SD_ID')
sd_param = Group(param_name + Regex('=') + param_value)
sd_params = Group(ZeroOrMore(Group(sp+sd_param.setResultsName('SD_PARAM'))))
sd_element = Group('['+sd_id+sd_params.setResultsName('SD_PARAMS')+']')
sd_element = sd_element.setResultsName('SD_ELEMENT')
sd_elements = Group(OneOrMore(sd_element))
structured_data = Or([nilvalue, sd_elements.setResultsName('SD_ELEMENTS')])
structured_data = structured_data.setResultsName('STRUCTURED_DATA')
time_hour = Regex('0[0-9]|1[0-9]|2[0-3]')
time_minute = Regex('[0-5][0-9]')
time_second = time_minute
time_secfrac = Regex('\.[0-9]{1,6}')
