def __init__(self, parse_method=None, precedence=9):
gt_lt_e = Literal("<") ^ Literal("<=") ^ Literal(">") ^ Literal(">=")
And.__init__(self, gt_lt_e + Integer())
BaseType.__init__(self, precedence)
if parse_method:
self.addParseAction(parse_method)
def __init__(self, parse_method=None, precedence=9):
gt_lt_e = Literal('<') ^ Literal("<=") ^ Literal('>') ^ Literal(">=")
And.__init__(self, [gt_lt_e + Integer()])
BaseType.__init__(self, precedence)
if parse_method:
self.addParseAction(parse_method)
def load_symbols_file(self, file):
file = self.xkb_basedir / file
try:
return self.loaded[file]
except KeyError:
pass
sections = []
def quoted(name):
return QuotedString(quoteChar='"', unquoteResults=True)
# Callback, toks[0] is "foo" for xkb_symbols "foo"
def new_symbols_section(name, loc, toks):
assert len(toks) == 1
sections.append(XkbSymbols(file, toks[0]))
# Callback, toks[0] is "foo(bar)" for include "foo(bar)"
def append_includes(name, loc, toks):
assert len(toks) == 1
sections[-1].includes.append(toks[0])
EOL = LineEnd().suppress()
SECTIONTYPE = (
"default",
"partial",
"hidden",
"alphanumeric_keys",
"modifier_keys",
"keypad_keys",
"function_keys",
"alternate_group",
)
NAME = quoted("name").setParseAction(new_symbols_section)
INCLUDE = (lit("include") +
quoted("include").setParseAction(append_includes) + EOL)
# We only care about includes
OTHERLINE = And([~lit("};"), ~lit("include") + Regex(".*")]) + EOL
with open(file) as fd:
types = OneOrMore(oneOf(SECTIONTYPE)).suppress()
include_or_other = Or([INCLUDE, OTHERLINE.suppress()])
section = (types + lit("xkb_symbols") + NAME + lit("{") +
OneOrMore(include_or_other) + lit("};"))
grammar = OneOrMore(section)
grammar.ignore(cppStyleComment)
try:
result = grammar.parseFile(fd)
except ParseException as e:
raise XkbLoader.XkbParserException(str(e))
self.loaded[file] = sections
return sections
def __init__(self,
range_parse_method=None,
item_parse_method=None,
range_symbol='..',
precedence=10):
And.__init__(
self,
Integer(item_parse_method) + Literal(range_symbol) +
Integer(item_parse_method))
BaseType.__init__(self, precedence)
if range_parse_method:
self.addParseAction(range_parse_method)
def __antlrAlternativeConverter(pyparsingRules, antlrAlternative):
elementList = []
for element in antlrAlternative.elements:
rule = None
if hasattr(element.atom, "c1") and element.atom.c1 != "":
regex = r"[" + str(element.atom.c1[0]) + "-" + str(element.atom.c2[0] + "]")
rule = Regex(regex)("anonymous_regex")
elif hasattr(element, "block") and element.block != "":
rule = __antlrAlternativesConverter(pyparsingRules, element.block)
else:
ruleRef = element.atom[0]
assert ruleRef in pyparsingRules
rule = pyparsingRules[ruleRef](ruleRef)
if hasattr(element, "op") and element.op != "":
if element.op == "+":
rule = Group(OneOrMore(rule))("anonymous_one_or_more")
elif element.op == "*":
rule = Group(ZeroOrMore(rule))("anonymous_zero_or_more")
elif element.op == "?":
rule = Optional(rule)
else:
raise Exception("rule operator not yet implemented : " + element.op)
rule = rule
elementList.append(rule)
if len(elementList) > 1:
rule = Group(And(elementList))("anonymous_and")
else:
rule = elementList[0]
assert rule is not None
return rule
def __antlrAlternativeConverter(pyparsingRules, antlrAlternative):
elementList = []
for element in antlrAlternative.elements:
rule = None
if hasattr(element.atom, 'c1') and element.atom.c1 != '':
regex = r'[' + str(
element.atom.c1[0]) + '-' + str(element.atom.c2[0] + ']')
rule = Regex(regex)("anonymous_regex")
elif hasattr(element, 'block') and element.block != '':
rule = __antlrAlternativesConverter(pyparsingRules, element.block)
else:
ruleRef = element.atom
assert ruleRef in pyparsingRules
rule = pyparsingRules[element.atom](element.atom)
if hasattr(element, 'op') and element.op != '':
if element.op == '+':
rule = Group(OneOrMore(rule))("anonymous_one_or_more")
elif element.op == '*':
rule = Group(ZeroOrMore(rule))("anonymous_zero_or_more")
elif element.op == '?':
rule = Optional(rule)
else:
raise Exception('rule operator not yet implemented : ' +
element.op)
rule = rule
elementList.append(rule)
if len(elementList) > 1:
rule = Group(And(elementList))("anonymous_and")
else:
rule = elementList[0]
assert rule != None
return rule
def __init__(self):
self.continued = False
ds9_attr_parser = get_ds9_attr_parser()
ds9_shape_in_comment_defs = dict(text=wcs_shape(CoordOdd, CoordEven),
vector=wcs_shape(CoordOdd, CoordEven,
Distance, Angle),
composite=wcs_shape(CoordOdd, CoordEven, Angle),
projection=wcs_shape(CoordOdd, CoordEven, CoordOdd, CoordEven, Distance),
segment=wcs_shape(CoordOdd, CoordEven,
repeat=(0,2)),
)
regionShape = define_shape_helper(ds9_shape_in_comment_defs)
regionShape = regionShape.setParseAction(lambda s, l, tok: Shape(tok[0], tok[1:]))
self.parser_default = ds9_attr_parser
cont = CaselessKeyword("||").setParseAction(self.set_continued).suppress()
line = Optional(And([regionShape,
Optional(cont)])) \
+ ds9_attr_parser
self.parser_with_shape = line
def nest(*content):
"""Define a delimited list by enumerating each element of the list."""
if len(content) == 0:
raise ValueError('no arguments supplied')
return And([LPF, content[0]] +
list(itt.chain.from_iterable(zip(itt.repeat(C), content[1:]))) +
[RPF])
def build(parsers: dict):
comma = Literal(",")
rb = Literal(")")
lb = Literal("(")
srb = Literal("]")
slb = Literal("[")
number = Regex(r"0|[1-9][0-9]*")
string = quotedString()
name = Word(alphanums)
label = Keyword(STRONG) | Keyword(WEAK) | Literal(SHORT_WEAK)
param = Combine(Keyword(PARAM) + slb + number + srb)
marker = Keyword(RESULT) | Keyword(TRUE) | Keyword(FALSE) | Keyword(
THIS) | Keyword(_THIS) | param
function = Keyword(GET)
get = Literal(GETATTR)
operator1 = Literal(MUL) | Literal(DIV) | Literal(MOD)
operator2 = Literal(ADD) | Literal(SUB)
operator3 = Literal(EQUAL) | Literal(NOT_EQUAL)
operator3 |= And(Keyword(word) for word in IS_NOT.split(" ")) | Keyword(IS)
operator4 = Literal(GREATER_OR_EQUAL) | Literal(GREATER) | Literal(
LOWER_OR_EQUAL) | Literal(LOWER)
operator5 = Keyword(AND)
operator6 = Keyword(OR)
operator7 = Keyword(FOLLOW)
expression = Forward()
string_st = string.setParseAction(parsers[STRING])
name_st = name.setParseAction(parsers[STRING])
marker_st = marker.setParseAction(parsers[MARKER])
tuple_st = expression + ZeroOrMore(comma + expression)
round_invocation_st = (lb + Optional(tuple_st) + rb).setParseAction(
parsers[INVOCATION])
function_st = (function + Suppress(round_invocation_st)).setParseAction(
parsers[FUNCTION])
getattr_st = (marker_st | name_st) + OneOrMore(
(get + Suppress(name_st)).setParseAction(parsers[OPERATOR]))
atom_st = (lb + expression +
rb) | function_st | string_st | getattr_st | marker_st
operator_st = atom_st + ZeroOrMore(
(operator1 + Suppress(atom_st)).setParseAction(parsers[OPERATOR]))
operator_st = operator_st + ZeroOrMore(
(operator2 + Suppress(operator_st)).setParseAction(parsers[OPERATOR]))
operator_st = operator_st + ZeroOrMore(
(operator3 + Suppress(operator_st)).setParseAction(parsers[OPERATOR]))
operator_st = operator_st + ZeroOrMore(
(operator4 + Suppress(operator_st)).setParseAction(parsers[OPERATOR]))
operator_st = operator_st + ZeroOrMore(
(operator5 + Suppress(operator_st)).setParseAction(parsers[OPERATOR]))
operator_st = operator_st + ZeroOrMore(
(operator6 + Suppress(operator_st)).setParseAction(parsers[OPERATOR]))
operator_st = operator_st + ZeroOrMore(
(operator7 + Suppress(operator_st)).setParseAction(parsers[OPERATOR]))
expression << operator_st
getattr_st.enablePackrat()
statement = (Optional(label, STRONG) +
Suppress(expression)).setParseAction(parsers[LABEL])
return ZeroOrMore(statement) + StringEnd()
def get_fragment_language() -> ParserElement:
"""Build a protein fragment parser."""
_fragment_value_inner = fragment_range | missing_fragment(FRAGMENT_MISSING)
_fragment_value = _fragment_value_inner | And(
[Suppress('"'), _fragment_value_inner,
Suppress('"')])
parser_element = fragment_tag + nest(
_fragment_value + Optional(WCW + quote(FRAGMENT_DESCRIPTION)))
return parser_element
def define_shape(name, shape_args, args_repeat=None):
lparen = Literal("(").suppress()
rparen = Literal(")").suppress()
comma = Literal(",").suppress()
shape_name = CaselessKeyword(name)
if args_repeat is None:
shape_with_parens = And(
[shape_name, lparen,
as_comma_separated_list(shape_args), rparen])
shape_with_spaces = shape_name + And(shape_args)
else:
n1, n2 = args_repeat
sl = []
ss = shape_args[:n1]
if ss:
sl.append(as_comma_separated_list(ss))
ss = shape_args[n1:n2]
if ss:
ar = as_comma_separated_list(ss)
if sl:
sl.extend([comma + ar, ZeroOrMore(comma + ar)])
else:
sl.extend([ar, ZeroOrMore(comma + ar)])
ss = shape_args[n2:]
if ss:
if sl:
sl.extend([comma, as_comma_separated_list(ss)])
else:
sl.extend([as_comma_separated_list(ss)])
sl = [shape_name, lparen] + sl + [rparen]
shape_with_parens = And(sl)
shape_with_spaces = shape_name + OneOrMore(And(shape_args))
return (shape_with_parens | shape_with_spaces)
def as_comma_separated_list(al):
l = [al[0]]
comma = Literal(",").suppress()
for a1 in al[1:]:
l.append(comma)
l.append(a1)
return And(l)
def get_fragment_language():
_fragment_value_inner = fragment_range | missing_fragment(FRAGMENT_MISSING)
_fragment_value = (_fragment_value_inner | And(
[Suppress('"'), _fragment_value_inner,
Suppress('"')]))
language = fragment_tag + nest(_fragment_value +
Optional(WCW + quote(FRAGMENT_DESCRIPTION)))
return language
def _parse_ascii_data(self, header_tokens, file_mmap, buffer_offset,
aggregate_data_types):
"""
Parse the data portion of a PLY file assuming it uses ASCII format.
:param header_tokens:
:param file_mmap:
:param buffer_offset:
:param aggregate_data_types:
:return:
"""
# Define the grammar of the body
number = pyparsing_common.number()
body_expr = list()
for element in header_tokens.elements:
sequences = list()
for prop in element.properties:
for variable in prop:
if "index_type" in variable:
sequences.append(countedArray(number))
else:
sequences.append(number(variable.name))
element_data = Group(And(sequences))
body_expr.append(Group(element_data * element.count)(element.name))
ascii_grammar = And(body_expr)
# Tokenize the body data
body_tokens = ascii_grammar.parseString(
file_mmap[buffer_offset:].decode("ascii"), parseAll=True)
# Convert the data to arrays.
element_data = dict()
for name, dtype in aggregate_data_types.items():
element_data[name] = array.array(dtype,
self._flatten(body_tokens[name]))
return element_data
def make_date_parser():
date_expr = ppc.iso8601_date.copy()
date_expr.setParseAction(ppc.convertToDate())
expr_last = And(
CaselessKeyword('LAST') & ppc.integer.setResultsName('n')
& StringEnd()).setResultsName('interval').setParseAction(handle_last)
expr_prev = And(
CaselessKeyword('PREVIOUS') & Or(
CaselessKeyword('DAY').setResultsName('day')
| CaselessKeyword('WEEK').setResultsName('week')
| CaselessKeyword('MONTH').setResultsName('month')) +
StringEnd()).setResultsName('interval').setParseAction(handle_previous)
expr_fromto_date = And(
CaselessKeyword('FROM') + date_expr.setResultsName('start') +
CaselessKeyword('TO') + date_expr.setResultsName('end') +
StringEnd()).setResultsName('interval').setParseAction(handle_fromto)
parser = expr_fromto_date | expr_last | expr_prev
return parser
def __init__(self):
RegionPusher.__init__(self)
self.shape_definition = ds9_shape_defs
regionShape = define_shape_helper(self.shape_definition)
regionShape = regionShape.setParseAction(
lambda s, l, tok: Shape(tok[0], tok[1:]))
regionExpr = define_expr(
regionShape,
negate_func=lambda s, l, tok: tok[-1].set_exclude(),
)
coord_command_keys = [
'PHYSICAL', 'IMAGE', 'FK4', 'B1950', 'FK5', 'J2000', 'GALACTIC',
'ECLIPTIC', 'ICRS', 'LINEAR', 'AMPLIFIER', 'DETECTOR'
]
coordCommandLiterals = define_simple_literals(coord_command_keys)
coordCommandWCS = Combine(
CaselessLiteral("WCS") + Optional(Word(alphas)))
coordCommand = (coordCommandLiterals | coordCommandWCS)
coordCommand.setParseAction(lambda s, l, tok: CoordCommand(tok[-1]))
regionGlobal = comment_shell_like(CaselessKeyword("global"),
lambda s, l, tok: Global(tok[-1]))
regionAtom = (regionExpr | coordCommand | regionGlobal)
regionAtom = regionAtom.setParseAction(self.pushAtom)
regionComment = comment_shell_like(Literal("#"),
parseAction=self.pushComment)
line_simple = define_line(atom=regionAtom,
separator=Literal(";"),
comment=regionComment)
line_w_composite = And([regionAtom,
CaselessKeyword("||").setParseAction(self.set_continued)
]) \
+ Optional(regionComment)
line = Or([line_simple, line_w_composite])
self.parser = Optional(line) + StringEnd()
def __init__(self):
self.fragment_range = (ppc.integer | '?')(FRAGMENT_START) + '_' + (
ppc.integer | '?' | '*')(FRAGMENT_STOP)
self.missing_fragment = Keyword('?')(FRAGMENT_MISSING)
self._fragment_value_inner = self.fragment_range | self.missing_fragment(
FRAGMENT_MISSING)
self._fragment_value = (self._fragment_value_inner | And(
[Suppress('"'), self._fragment_value_inner,
Suppress('"')]))
self.language = fragment_tag + nest(
self._fragment_value + Optional(WCW + quote(FRAGMENT_DESCRIPTION)))
super(FragmentParser, self).__init__(self.language)
def __init__(self):
self.continued = False
ds9_attr_parser = get_ds9_attr_parser()
regionShape = define_shape_helper(ds9_shape_in_comment_defs)
regionShape = regionShape.setParseAction(
lambda s, l, tok: Shape(tok[0], tok[1:]))
self.parser_default = ds9_attr_parser
cont = CaselessKeyword("||").setParseAction(
self.set_continued).suppress()
line = Optional(And([regionShape, Optional(cont)])) + ds9_attr_parser
self.parser_with_shape = line
def parse_value_comparison(op_string):
""" Ex:
10
<=10
<10
>=10
>10
"""
num = Word(nums + ".") # matches 1 or 1.1
ltgt = oneOf("< <= > >=")
parser = num | And([ltgt, num])
try:
return parser.parseString(op_string).asList()
except ParseException:
#:TODO what should really happen here?
raise ValueError("'%s' is not a Valid operation" % op_string)
def _aggregate_property(cls, name, prefix, *keywords):
"""
Create a property group from the specified name,
the pattern prefix (a ParseElement instance), and an iterable of keywords.
Example:
aggregate_property('position', CaselessKeyword('property'), *[CaselessKeyword('x'), ...])
:param name:
:param prefix:
:param keywords:
:return:
"""
aggregates = list()
for keyword in keywords:
aggregates.append(Group(prefix + keyword("name")))
return Group(And(aggregates))(name)
def __init__(self):
RegionPusher.__init__(self)
self.shape_definition = ds9_shape_defs
regionShape = define_shape_helper(self.shape_definition)
regionShape = regionShape.setParseAction(
lambda s, l, tok: Shape(tok[0], tok[1:]))
regionExpr = define_expr(
regionShape,
negate_func=lambda s, l, tok: tok[-1].set_exclude(),
)
coord_command_keys = "PHYSICAL IMAGE FK4 B1950 FK5 J2000 GALACTIC ECLIPTIC ICRS LINEAR AMPLIFIER DETECTOR".split(
)
coordCommand = define_simple_literals(
coord_command_keys,
parseAction=lambda s, l, tok: CoordCommand(tok[-1]))
regionGlobal = comment_shell_like(CaselessKeyword("global"),
lambda s, l, tok: Global(tok[-1]))
regionAtom = (regionExpr | coordCommand | regionGlobal)
regionAtom = regionAtom.setParseAction(self.pushAtom)
regionComment = comment_shell_like(Literal("#"),
parseAction=self.pushComment)
line_simple = define_line(atom=regionAtom,
separator=Literal(";"),
comment=regionComment)
line_w_composite = And([regionAtom,
CaselessKeyword("||").setParseAction(self.set_continued)
]) \
+ Optional(regionComment)
line = Or([line_simple, line_w_composite])
self.parser = Optional(line) + StringEnd()
def __init__(
self,
annotation_to_term: Optional[Mapping[str, Set[str]]] = None,
annotation_to_pattern: Optional[Mapping[str, Pattern]] = None,
annotation_to_local: Optional[Mapping[str, Set[str]]] = None,
citation_clearing: bool = True,
required_annotations: Optional[List[str]] = None,
) -> None:
"""Initialize the control statement parser.
:param annotation_to_term: A dictionary of {annotation: set of valid values} defined with URL for parsing
:param annotation_to_pattern: A dictionary of {annotation: regular expression string}
:param annotation_to_local: A dictionary of {annotation: set of valid values} for parsing defined with LIST
:param citation_clearing: Should :code:`SET Citation` statements clear evidence and all annotations?
:param required_annotations: Annotations that are required
"""
self.citation_clearing = citation_clearing
self.annotation_to_term = annotation_to_term or {}
self.annotation_to_pattern = annotation_to_pattern or {}
self.annotation_to_local = annotation_to_local or {}
self.statement_group = None
self.citation_db = None
self.citation_db_id = None
self.evidence = None
self.annotations = {}
self.required_annotations = required_annotations or []
annotation_key = ppc.identifier('key').setParseAction(
self.handle_annotation_key)
self.set_statement_group = set_statement_group_stub().setParseAction(
self.handle_set_statement_group)
self.set_citation = set_citation_stub.setParseAction(
self.handle_set_citation)
self.set_evidence = set_evidence_stub.setParseAction(
self.handle_set_evidence)
set_command_prefix = And([annotation_key('key'), Suppress('=')])
self.set_command = set_command_prefix + qid('value')
self.set_command.setParseAction(self.handle_set_command)
self.set_command_list = set_command_prefix + delimited_quoted_list(
'values')
self.set_command_list.setParseAction(self.handle_set_command_list)
self.unset_command = annotation_key('key')
self.unset_command.addParseAction(self.handle_unset_command)
self.unset_evidence = supporting_text_tags(EVIDENCE)
self.unset_evidence.setParseAction(self.handle_unset_evidence)
self.unset_citation = Suppress(BEL_KEYWORD_CITATION)
self.unset_citation.setParseAction(self.handle_unset_citation)
self.unset_statement_group = Suppress(BEL_KEYWORD_STATEMENT_GROUP)
self.unset_statement_group.setParseAction(
self.handle_unset_statement_group)
self.unset_list = delimited_unquoted_list('values')
self.unset_list.setParseAction(self.handle_unset_list)
self.unset_all = unset_all.setParseAction(self.handle_unset_all)
self.set_statements = set_tag + MatchFirst([
self.set_statement_group,
self.set_citation,
self.set_evidence,
self.set_command,
self.set_command_list,
])
self.unset_statements = unset_tag + MatchFirst([
self.unset_all,
self.unset_citation,
self.unset_evidence,
self.unset_statement_group,
self.unset_command,
self.unset_list,
])
self.language = self.set_statements | self.unset_statements
super(ControlParser, self).__init__(self.language)
def __init__(
self,
manager,
namespace_to_term_to_encoding: Optional[
NamespaceTermEncodingMapping] = None,
namespace_to_pattern: Optional[Mapping[str, Pattern]] = None,
annotation_to_term: Optional[Mapping[str, Set[str]]] = None,
annotation_to_pattern: Optional[Mapping[str, Pattern]] = None,
annotation_to_local: Optional[Mapping[str, Set[str]]] = None,
default_namespace: Optional[Set[str]] = None,
allow_redefinition: bool = False,
skip_validation: bool = False,
upgrade_urls: bool = False,
) -> None:
"""Build a metadata parser.
:param manager: A cache manager
:param namespace_to_term_to_encoding:
An enumerated namespace mapping from {namespace keyword: {(identifier, name): encoding}}
:param namespace_to_pattern:
A regular expression namespace mapping from {namespace keyword: regex string}
:param annotation_to_term: Enumerated annotation mapping from {annotation keyword: set of valid values}
:param annotation_to_pattern: Regular expression annotation mapping from {annotation keyword: regex string}
:param default_namespace: A set of strings that can be used without a namespace
:param skip_validation: If true, don't download and cache namespaces/annotations
"""
#: This metadata parser's internal definition cache manager
self.manager = manager
self.disallow_redefinition = not allow_redefinition
self.skip_validation = skip_validation
self.upgrade_urls = upgrade_urls
#: A dictionary of cached {namespace keyword: {(identifier, name): encoding}}
self.namespace_to_term_to_encoding = namespace_to_term_to_encoding or {}
#: A set of namespaces's URLs that can't be cached
self.uncachable_namespaces = set()
#: A dictionary of {namespace keyword: regular expression string}
self.namespace_to_pattern = namespace_to_pattern or {}
#: A set of names that can be used without a namespace
self.default_namespace = set(
default_namespace) if default_namespace is not None else None
#: A dictionary of cached {annotation keyword: set of values}
self.annotation_to_term = annotation_to_term or {}
#: A dictionary of {annotation keyword: regular expression string}
self.annotation_to_pattern = annotation_to_pattern or {}
#: A dictionary of cached {annotation keyword: set of values}
self.annotation_to_local = annotation_to_local or {}
#: A dictionary containing the document metadata
self.document_metadata = {}
#: A dictionary from {namespace keyword: BEL namespace URL}
self.namespace_url_dict = {}
#: A dictionary from {annotation keyword: BEL annotation URL}
self.annotation_url_dict = {}
self.document = And([
set_tag,
Suppress(BEL_KEYWORD_DOCUMENT),
word('key'),
Suppress('='),
qid('value'),
])
namespace_tag = And([
define_tag,
Suppress(BEL_KEYWORD_NAMESPACE),
ppc.identifier('name'), as_tag
])
self.namespace_url = And([namespace_tag, url_tag, quote('url')])
self.namespace_pattern = And(
[namespace_tag,
Suppress(BEL_KEYWORD_PATTERN),
quote('value')])
annotation_tag = And([
define_tag,
Suppress(BEL_KEYWORD_ANNOTATION),
ppc.identifier('name'), as_tag
])
self.annotation_url = And([annotation_tag, url_tag, quote('url')])
self.annotation_list = And(
[annotation_tag, list_tag,
delimited_quoted_list('values')])
self.annotation_pattern = And(
[annotation_tag,
Suppress(BEL_KEYWORD_PATTERN),
quote('value')])
self.document.setParseAction(self.handle_document)
self.namespace_url.setParseAction(self.handle_namespace_url)
self.namespace_pattern.setParseAction(self.handle_namespace_pattern)
self.annotation_url.setParseAction(self.handle_annotations_url)
self.annotation_list.setParseAction(self.handle_annotation_list)
self.annotation_pattern.setParseAction(self.handle_annotation_pattern)
self.language = MatchFirst([
self.document,
self.namespace_url,
self.annotation_url,
self.annotation_list,
self.annotation_pattern,
self.namespace_pattern,
]).setName('BEL Metadata')
super(MetadataParser, self).__init__(self.language)
def __init__(
self,
graph,
namespace_to_term: Optional[Mapping[str, Mapping[str, str]]] = None,
namespace_to_pattern: Optional[Mapping[str, Pattern]] = None,
annotation_to_term: Optional[Mapping[str, Set[str]]] = None,
annotation_to_pattern: Optional[Mapping[str, Pattern]] = None,
annotation_to_local: Optional[Mapping[str, Set[str]]] = None,
allow_naked_names: bool = False,
allow_nested: bool = False,
disallow_unqualified_translocations: bool = False,
citation_clearing: bool = True,
skip_validation: bool = False,
autostreamline: bool = True,
required_annotations: Optional[List[str]] = None,
) -> None:
"""Build a BEL parser.
:param pybel.BELGraph graph: The BEL Graph to use to store the network
:param namespace_to_term: A dictionary of {namespace: {name: encoding}}. Delegated to
:class:`pybel.parser.parse_identifier.IdentifierParser`
:param namespace_to_pattern: A dictionary of {namespace: regular expression strings}. Delegated to
:class:`pybel.parser.parse_identifier.IdentifierParser`
:param annotation_to_term: A dictionary of {annotation: set of values}. Delegated to
:class:`pybel.parser.ControlParser`
:param annotation_to_pattern: A dictionary of {annotation: regular expression strings}. Delegated to
:class:`pybel.parser.ControlParser`
:param annotation_to_local: A dictionary of {annotation: set of values}. Delegated to
:class:`pybel.parser.ControlParser`
:param allow_naked_names: If true, turn off naked namespace failures. Delegated to
:class:`pybel.parser.parse_identifier.IdentifierParser`
:param allow_nested: If true, turn off nested statement failures. Delegated to
:class:`pybel.parser.parse_identifier.IdentifierParser`
:param disallow_unqualified_translocations: If true, allow translocations without TO and FROM clauses.
:param citation_clearing: Should :code:`SET Citation` statements clear evidence and all annotations?
Delegated to :class:`pybel.parser.ControlParser`
:param autostreamline: Should the parser be streamlined on instantiation?
:param required_annotations: Optional list of required annotations
"""
self.graph = graph
self.allow_nested = allow_nested
self.disallow_unqualified_translocations = disallow_unqualified_translocations
if skip_validation:
self.control_parser = ControlParser(
citation_clearing=citation_clearing,
required_annotations=required_annotations,
)
self.identifier_parser = IdentifierParser(
allow_naked_names=allow_naked_names, )
else:
self.control_parser = ControlParser(
annotation_to_term=annotation_to_term,
annotation_to_pattern=annotation_to_pattern,
annotation_to_local=annotation_to_local,
citation_clearing=citation_clearing,
required_annotations=required_annotations,
)
self.identifier_parser = IdentifierParser(
allow_naked_names=allow_naked_names,
namespace_to_term=namespace_to_term,
namespace_to_pattern=namespace_to_pattern,
)
self.control_parser.get_line_number = self.get_line_number
self.identifier_parser.get_line_number = self.get_line_number
identifier = Group(self.identifier_parser.language)(IDENTIFIER)
ungrouped_identifier = self.identifier_parser.language
# 2.2 Abundance Modifier Functions
#: `2.2.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_protein_modifications>`_
self.pmod = get_protein_modification_language(
self.identifier_parser.identifier_qualified)
#: `2.2.4 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_cellular_location>`_
self.location = get_location_language(self.identifier_parser.language)
opt_location = pyparsing.Optional(WCW + self.location)
#: PyBEL BEL Specification variant
self.gmod = get_gene_modification_language(
self.identifier_parser.identifier_qualified)
# 2.6 Other Functions
#: `2.6.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_fusion_fus>`_
self.fusion = get_fusion_language(self.identifier_parser.language)
# 2.1 Abundance Functions
#: `2.1.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XcomplexA>`_
self.general_abundance = general_abundance_tags + nest(
ungrouped_identifier + opt_location)
self.gene_modified = ungrouped_identifier + pyparsing.Optional(
WCW + delimitedList(Group(variant | gsub | self.gmod))(VARIANTS))
self.gene_fusion = Group(self.fusion)(FUSION)
self.gene_fusion_legacy = Group(
get_legacy_fusion_langauge(identifier, 'c'))(FUSION)
#: `2.1.4 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XgeneA>`_
self.gene = gene_tag + nest(
MatchFirst([
self.gene_fusion, self.gene_fusion_legacy, self.gene_modified
]) + opt_location)
self.mirna_modified = ungrouped_identifier + pyparsing.Optional(
WCW + delimitedList(Group(variant))(VARIANTS)) + opt_location
#: `2.1.5 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XmicroRNAA>`_
self.mirna = mirna_tag + nest(self.mirna_modified)
self.protein_modified = ungrouped_identifier + pyparsing.Optional(
WCW + delimitedList(
Group(MatchFirst([self.pmod, variant, fragment, psub, trunc])))
(VARIANTS))
self.protein_fusion = Group(self.fusion)(FUSION)
self.protein_fusion_legacy = Group(
get_legacy_fusion_langauge(identifier, 'p'))(FUSION)
#: `2.1.6 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XproteinA>`_
self.protein = protein_tag + nest(
MatchFirst([
self.protein_fusion,
self.protein_fusion_legacy,
self.protein_modified,
]) + opt_location)
self.rna_modified = ungrouped_identifier + pyparsing.Optional(
WCW + delimitedList(Group(variant))(VARIANTS))
self.rna_fusion = Group(self.fusion)(FUSION)
self.rna_fusion_legacy = Group(
get_legacy_fusion_langauge(identifier, 'r'))(FUSION)
#: `2.1.7 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XrnaA>`_
self.rna = rna_tag + nest(
MatchFirst([
self.rna_fusion,
self.rna_fusion_legacy,
self.rna_modified,
]) + opt_location)
self.single_abundance = MatchFirst([
self.general_abundance, self.gene, self.mirna, self.protein,
self.rna
])
#: `2.1.2 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XcomplexA>`_
self.complex_singleton = complex_tag + nest(ungrouped_identifier +
opt_location)
self.complex_list = complex_tag + nest(
delimitedList(Group(self.single_abundance
| self.complex_singleton))(MEMBERS) +
opt_location)
self.complex_abundances = self.complex_list | self.complex_singleton
# Definition of all simple abundances that can be used in a composite abundance
self.simple_abundance = self.complex_abundances | self.single_abundance
self.simple_abundance.setParseAction(self.check_function_semantics)
#: `2.1.3 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XcompositeA>`_
self.composite_abundance = composite_abundance_tag + nest(
delimitedList(Group(self.simple_abundance))(MEMBERS) +
opt_location)
self.abundance = self.simple_abundance | self.composite_abundance
# 2.4 Process Modifier Function
# backwards compatibility with BEL v1.0
molecular_activity_default = oneOf(list(
language.activity_labels)).setParseAction(
handle_molecular_activity_default)
#: `2.4.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XmolecularA>`_
self.molecular_activity = molecular_activity_tags + nest(
molecular_activity_default | self.identifier_parser.language)
# 2.3 Process Functions
#: `2.3.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_biologicalprocess_bp>`_
self.biological_process = biological_process_tag + nest(
ungrouped_identifier)
#: `2.3.2 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_pathology_path>`_
self.pathology = pathology_tag + nest(ungrouped_identifier)
self.bp_path = self.biological_process | self.pathology
self.bp_path.setParseAction(self.check_function_semantics)
self.activity_standard = activity_tag + nest(
Group(self.simple_abundance)(TARGET) +
pyparsing.Optional(WCW + Group(self.molecular_activity)(EFFECT)))
activity_legacy_tags = oneOf(language.activities)(MODIFIER)
self.activity_legacy = activity_legacy_tags + nest(
Group(self.simple_abundance)(TARGET))
self.activity_legacy.setParseAction(handle_activity_legacy)
#: `2.3.3 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#Xactivity>`_
self.activity = self.activity_standard | self.activity_legacy
self.process = self.bp_path | self.activity
# 2.5 Transformation Functions
from_loc = Suppress(FROM_LOC) + nest(identifier(FROM_LOC))
to_loc = Suppress(TO_LOC) + nest(identifier(TO_LOC))
self.cell_secretion = cell_secretion_tag + nest(
Group(self.simple_abundance)(TARGET))
self.cell_surface_expression = cell_surface_expression_tag + nest(
Group(self.simple_abundance)(TARGET))
self.translocation_standard = nest(
Group(self.simple_abundance)(TARGET) + WCW +
Group(from_loc + WCW + to_loc)(EFFECT))
self.translocation_legacy = nest(
Group(self.simple_abundance)(TARGET) + WCW +
Group(identifier(FROM_LOC) + WCW + identifier(TO_LOC))(EFFECT))
self.translocation_legacy.addParseAction(handle_legacy_tloc)
self.translocation_unqualified = nest(
Group(self.simple_abundance)(TARGET))
if self.disallow_unqualified_translocations:
self.translocation_unqualified.setParseAction(
self.handle_translocation_illegal)
#: `2.5.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_translocations>`_
self.translocation = translocation_tag + MatchFirst([
self.translocation_unqualified, self.translocation_standard,
self.translocation_legacy
])
#: `2.5.2 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_degradation_deg>`_
self.degradation = degradation_tags + nest(
Group(self.simple_abundance)(TARGET))
#: `2.5.3 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_reaction_rxn>`_
self.reactants = Suppress(REACTANTS) + nest(
delimitedList(Group(self.simple_abundance)))
self.products = Suppress(PRODUCTS) + nest(
delimitedList(Group(self.simple_abundance)))
self.reaction = reaction_tags + nest(
Group(self.reactants)(REACTANTS),
Group(self.products)(PRODUCTS))
self.transformation = MatchFirst([
self.cell_secretion, self.cell_surface_expression,
self.translocation, self.degradation, self.reaction
])
# 3 BEL Relationships
self.bel_term = MatchFirst(
[self.transformation, self.process, self.abundance]).streamline()
self.bel_to_bel_relations = [
association_tag,
increases_tag,
decreases_tag,
positive_correlation_tag,
negative_correlation_tag,
causes_no_change_tag,
orthologous_tag,
is_a_tag,
equivalent_tag,
partof_tag,
directly_increases_tag,
directly_decreases_tag,
analogous_tag,
regulates_tag,
]
self.bel_to_bel = triple(self.bel_term,
MatchFirst(self.bel_to_bel_relations),
self.bel_term)
# Mixed Relationships
#: `3.1.5 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_ratelimitingstepof>`_
self.rate_limit = triple(
MatchFirst(
[self.biological_process, self.activity, self.transformation]),
rate_limit_tag, self.biological_process)
#: `3.4.6 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_subprocessof>`_
self.subprocess_of = triple(
MatchFirst([self.process, self.activity, self.transformation]),
subprocess_of_tag, self.process)
#: `3.3.2 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_transcribedto>`_
self.transcribed = triple(self.gene, transcribed_tag, self.rna)
#: `3.3.3 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_translatedto>`_
self.translated = triple(self.rna, translated_tag, self.protein)
#: `3.4.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_hasmember>`_
self.has_member = triple(self.abundance, has_member_tag,
self.abundance)
#: `3.4.2 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_hasmembers>`_
self.abundance_list = Suppress('list') + nest(
delimitedList(Group(self.abundance)))
self.has_members = triple(self.abundance, has_members_tag,
self.abundance_list)
self.has_members.setParseAction(self.handle_has_members)
self.has_components = triple(self.abundance, has_components_tag,
self.abundance_list)
self.has_components.setParseAction(self.handle_has_components)
self.has_list = self.has_members | self.has_components
# `3.4.3 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_hascomponent>`_
self.has_component = triple(
self.complex_abundances | self.composite_abundance,
has_component_tag, self.abundance)
self.biomarker = triple(self.bel_term, biomarker_tags, self.process)
self.has_variant_relation = triple(self.abundance, has_variant_tags,
self.abundance)
self.part_of_reaction = triple(self.reaction, part_of_reaction_tags,
self.abundance)
self.relation = MatchFirst([
self.bel_to_bel,
# self.has_member,
# self.has_component,
self.subprocess_of,
self.rate_limit,
self.biomarker,
self.transcribed,
self.translated,
# self.has_variant_relation,
# self.part_of_reaction,
])
self.relation.setParseAction(self._handle_relation_harness)
self.unqualified_relation = MatchFirst([
self.has_member, self.has_component, self.has_variant_relation,
self.part_of_reaction
])
self.unqualified_relation.setParseAction(
self.handle_unqualified_relation)
#: 3.1 Causal Relationships - nested. Not enabled by default.
causal_relation_tags = MatchFirst([
increases_tag, decreases_tag, directly_decreases_tag,
directly_increases_tag
])
self.nested_causal_relationship = triple(
self.bel_term, causal_relation_tags,
nest(triple(self.bel_term, causal_relation_tags, self.bel_term)))
self.nested_causal_relationship.setParseAction(
self.handle_nested_relation)
self.label_relationship = And([
Group(self.bel_term)(SUBJECT),
Suppress('labeled'),
quote(OBJECT)
])
self.label_relationship.setParseAction(self.handle_label_relation)
# has_members is handled differently from all other relations becuase it gets distrinbuted
self.relation = MatchFirst([
self.has_list,
self.nested_causal_relationship,
self.relation,
self.unqualified_relation,
self.label_relationship,
])
self.singleton_term = (self.bel_term + StringEnd()).setParseAction(
self.handle_term)
self.statement = self.relation | self.singleton_term
self.language = self.control_parser.language | self.statement
self.language.setName('BEL')
super(BELParser, self).__init__(self.language,
streamline=autostreamline)
EVIDENCE,
)
from ..utils import citation_dict
__all__ = ['ControlParser']
logger = logging.getLogger(__name__)
set_tag = Suppress(BEL_KEYWORD_SET)
unset_tag = Suppress(BEL_KEYWORD_UNSET)
unset_all = Suppress(BEL_KEYWORD_ALL)
supporting_text_tags = oneOf([BEL_KEYWORD_EVIDENCE, BEL_KEYWORD_SUPPORT])
set_statement_group_stub = And(
[Suppress(BEL_KEYWORD_STATEMENT_GROUP),
Suppress('='),
qid('group')])
set_citation_stub = And([
Suppress(BEL_KEYWORD_CITATION),
Suppress('='),
delimited_quoted_list('values')
])
set_evidence_stub = And(
[Suppress(supporting_text_tags),
Suppress('='),
quote('value')])
class ControlParser(BaseParser):
"""A parser for BEL control statements.
def create_grammar(container_ids, secret_ids):
""" Create the grammar for the editfile """
from pyparsing import (nums, alphas, lineEnd, stringEnd,
OneOrMore, ZeroOrMore, SkipTo, Optional, And,
Word, CharsNotIn, Empty, QuotedString, Literal,
Suppress, Group, Combine, originalTextFor, Forward,
ParserElement)
# Read from bottom to top
whiteSpaceChars = ' \t'
ParserElement.setDefaultWhitespaceChars(whiteSpaceChars)
word = Empty() + CharsNotIn(whiteSpaceChars + '\n')
quotedString = QuotedString(quoteChar='"', escChar='\\').setParseAction(
# NOTE the second replace is a work-around for
# pyparsing bug #68.
# https://sourceforge.net/p/pyparsing/bugs/68/
lambda s,l,t: t[0].replace("\\n", "\n").replace(
"\\\\", "\\"))
def secretIdNumberParseAction(s, loc, tokens):
v = int(tokens[0])
if not v in secret_ids:
raise ParseException(s, loc, "Not a valid secret id")
return v
secretIdNumber = Word(nums).setParseAction(secretIdNumberParseAction)
def containerIdParseAction(s, loc, tokens):
v = int(tokens[0])
if not v in container_ids:
raise ParseException(s, loc, "Not a valid container id")
return v
containerId = Word(nums).setParseAction(containerIdParseAction)
key = quotedString | word
secretString = ~Literal('#') + (quotedString | word)
secretId = Suppress('#') + secretIdNumber
secret = secretString | secretId
note = quotedString | originalTextFor(OneOrMore(word))
containerKeyword = Suppress('CONTAINER')
entry = (~containerKeyword + Group(key - secret - Optional(note))
- Suppress(lineEnd))
comment = Suppress(lineEnd | '#' + SkipTo(lineEnd))
line = comment | entry
containerLine = containerKeyword + containerId + comment
# Instead of the following recursive grammar, we could have simply used
#
# containerBlock = ZeroOrMore(comment) + Group(containerLine
# + Group(OneOrMore(line)))
# multipleContainers = OneOrMore(containerBlock)
#
# but then any parsing error in line will result in a "expected stringEnd"
# or "expected CONTAINER".
_multipleContainers_head = Forward()
_multipleContainers_body = Forward()
_multipleContainers_head << (stringEnd | comment + _multipleContainers_head
| containerLine + _multipleContainers_body)
_multipleContainers_body << (stringEnd
| (containerLine | line) + _multipleContainers_body)
_multipleContainers_entry = And([entry])
multipleContainers = And([_multipleContainers_head]) # TODO ibidem below
containerLine.setParseAction(lambda s,l,t: [[None, t[0]]])
def multipleContainersParseAction(s, loc, tokens):
curEntries = []
curId = None
ret = []
for t in tuple(tokens) + ((None, None),):
if t[0] is not None:
assert curId is not None
curEntries.append(t)
continue
if curId is not None:
ret.append([curId, curEntries])
curId = t[1]
curEntries = []
return ret
multipleContainers.setParseAction(multipleContainersParseAction)
oneContainer = ZeroOrMore(line) + stringEnd
oneContainer.setParseAction(lambda s,l,t: [[None, t]])
grammar = multipleContainers | oneContainer
return grammar
class BELParser(BaseParser):
"""Build a parser backed by a given dictionary of namespaces."""
def __init__(
self,
graph,
namespace_to_term: Optional[Mapping[str, Mapping[str, str]]] = None,
namespace_to_pattern: Optional[Mapping[str, Pattern]] = None,
annotation_to_term: Optional[Mapping[str, Set[str]]] = None,
annotation_to_pattern: Optional[Mapping[str, Pattern]] = None,
annotation_to_local: Optional[Mapping[str, Set[str]]] = None,
allow_naked_names: bool = False,
allow_nested: bool = False,
disallow_unqualified_translocations: bool = False,
citation_clearing: bool = True,
skip_validation: bool = False,
autostreamline: bool = True,
required_annotations: Optional[List[str]] = None,
) -> None:
"""Build a BEL parser.
:param pybel.BELGraph graph: The BEL Graph to use to store the network
:param namespace_to_term: A dictionary of {namespace: {name: encoding}}. Delegated to
:class:`pybel.parser.parse_identifier.IdentifierParser`
:param namespace_to_pattern: A dictionary of {namespace: regular expression strings}. Delegated to
:class:`pybel.parser.parse_identifier.IdentifierParser`
:param annotation_to_term: A dictionary of {annotation: set of values}. Delegated to
:class:`pybel.parser.ControlParser`
:param annotation_to_pattern: A dictionary of {annotation: regular expression strings}. Delegated to
:class:`pybel.parser.ControlParser`
:param annotation_to_local: A dictionary of {annotation: set of values}. Delegated to
:class:`pybel.parser.ControlParser`
:param allow_naked_names: If true, turn off naked namespace failures. Delegated to
:class:`pybel.parser.parse_identifier.IdentifierParser`
:param allow_nested: If true, turn off nested statement failures. Delegated to
:class:`pybel.parser.parse_identifier.IdentifierParser`
:param disallow_unqualified_translocations: If true, allow translocations without TO and FROM clauses.
:param citation_clearing: Should :code:`SET Citation` statements clear evidence and all annotations?
Delegated to :class:`pybel.parser.ControlParser`
:param autostreamline: Should the parser be streamlined on instantiation?
:param required_annotations: Optional list of required annotations
"""
self.graph = graph
self.allow_nested = allow_nested
self.disallow_unqualified_translocations = disallow_unqualified_translocations
if skip_validation:
self.control_parser = ControlParser(
citation_clearing=citation_clearing,
required_annotations=required_annotations,
)
self.identifier_parser = IdentifierParser(
allow_naked_names=allow_naked_names, )
else:
self.control_parser = ControlParser(
annotation_to_term=annotation_to_term,
annotation_to_pattern=annotation_to_pattern,
annotation_to_local=annotation_to_local,
citation_clearing=citation_clearing,
required_annotations=required_annotations,
)
self.identifier_parser = IdentifierParser(
allow_naked_names=allow_naked_names,
namespace_to_term=namespace_to_term,
namespace_to_pattern=namespace_to_pattern,
)
self.control_parser.get_line_number = self.get_line_number
self.identifier_parser.get_line_number = self.get_line_number
identifier = Group(self.identifier_parser.language)(IDENTIFIER)
ungrouped_identifier = self.identifier_parser.language
# 2.2 Abundance Modifier Functions
#: `2.2.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_protein_modifications>`_
self.pmod = get_protein_modification_language(
self.identifier_parser.identifier_qualified)
#: `2.2.4 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_cellular_location>`_
self.location = get_location_language(self.identifier_parser.language)
opt_location = pyparsing.Optional(WCW + self.location)
#: PyBEL BEL Specification variant
self.gmod = get_gene_modification_language(
self.identifier_parser.identifier_qualified)
# 2.6 Other Functions
#: `2.6.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_fusion_fus>`_
self.fusion = get_fusion_language(self.identifier_parser.language)
# 2.1 Abundance Functions
#: `2.1.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XcomplexA>`_
self.general_abundance = general_abundance_tags + nest(
ungrouped_identifier + opt_location)
self.gene_modified = ungrouped_identifier + pyparsing.Optional(
WCW + delimitedList(Group(variant | gsub | self.gmod))(VARIANTS))
self.gene_fusion = Group(self.fusion)(FUSION)
self.gene_fusion_legacy = Group(
get_legacy_fusion_langauge(identifier, 'c'))(FUSION)
#: `2.1.4 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XgeneA>`_
self.gene = gene_tag + nest(
MatchFirst([
self.gene_fusion, self.gene_fusion_legacy, self.gene_modified
]) + opt_location)
self.mirna_modified = ungrouped_identifier + pyparsing.Optional(
WCW + delimitedList(Group(variant))(VARIANTS)) + opt_location
#: `2.1.5 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XmicroRNAA>`_
self.mirna = mirna_tag + nest(self.mirna_modified)
self.protein_modified = ungrouped_identifier + pyparsing.Optional(
WCW + delimitedList(
Group(MatchFirst([self.pmod, variant, fragment, psub, trunc])))
(VARIANTS))
self.protein_fusion = Group(self.fusion)(FUSION)
self.protein_fusion_legacy = Group(
get_legacy_fusion_langauge(identifier, 'p'))(FUSION)
#: `2.1.6 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XproteinA>`_
self.protein = protein_tag + nest(
MatchFirst([
self.protein_fusion,
self.protein_fusion_legacy,
self.protein_modified,
]) + opt_location)
self.rna_modified = ungrouped_identifier + pyparsing.Optional(
WCW + delimitedList(Group(variant))(VARIANTS))
self.rna_fusion = Group(self.fusion)(FUSION)
self.rna_fusion_legacy = Group(
get_legacy_fusion_langauge(identifier, 'r'))(FUSION)
#: `2.1.7 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XrnaA>`_
self.rna = rna_tag + nest(
MatchFirst([
self.rna_fusion,
self.rna_fusion_legacy,
self.rna_modified,
]) + opt_location)
self.single_abundance = MatchFirst([
self.general_abundance, self.gene, self.mirna, self.protein,
self.rna
])
#: `2.1.2 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XcomplexA>`_
self.complex_singleton = complex_tag + nest(ungrouped_identifier +
opt_location)
self.complex_list = complex_tag + nest(
delimitedList(Group(self.single_abundance
| self.complex_singleton))(MEMBERS) +
opt_location)
self.complex_abundances = self.complex_list | self.complex_singleton
# Definition of all simple abundances that can be used in a composite abundance
self.simple_abundance = self.complex_abundances | self.single_abundance
self.simple_abundance.setParseAction(self.check_function_semantics)
#: `2.1.3 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XcompositeA>`_
self.composite_abundance = composite_abundance_tag + nest(
delimitedList(Group(self.simple_abundance))(MEMBERS) +
opt_location)
self.abundance = self.simple_abundance | self.composite_abundance
# 2.4 Process Modifier Function
# backwards compatibility with BEL v1.0
molecular_activity_default = oneOf(list(
language.activity_labels)).setParseAction(
handle_molecular_activity_default)
#: `2.4.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#XmolecularA>`_
self.molecular_activity = molecular_activity_tags + nest(
molecular_activity_default | self.identifier_parser.language)
# 2.3 Process Functions
#: `2.3.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_biologicalprocess_bp>`_
self.biological_process = biological_process_tag + nest(
ungrouped_identifier)
#: `2.3.2 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_pathology_path>`_
self.pathology = pathology_tag + nest(ungrouped_identifier)
self.bp_path = self.biological_process | self.pathology
self.bp_path.setParseAction(self.check_function_semantics)
self.activity_standard = activity_tag + nest(
Group(self.simple_abundance)(TARGET) +
pyparsing.Optional(WCW + Group(self.molecular_activity)(EFFECT)))
activity_legacy_tags = oneOf(language.activities)(MODIFIER)
self.activity_legacy = activity_legacy_tags + nest(
Group(self.simple_abundance)(TARGET))
self.activity_legacy.setParseAction(handle_activity_legacy)
#: `2.3.3 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#Xactivity>`_
self.activity = self.activity_standard | self.activity_legacy
self.process = self.bp_path | self.activity
# 2.5 Transformation Functions
from_loc = Suppress(FROM_LOC) + nest(identifier(FROM_LOC))
to_loc = Suppress(TO_LOC) + nest(identifier(TO_LOC))
self.cell_secretion = cell_secretion_tag + nest(
Group(self.simple_abundance)(TARGET))
self.cell_surface_expression = cell_surface_expression_tag + nest(
Group(self.simple_abundance)(TARGET))
self.translocation_standard = nest(
Group(self.simple_abundance)(TARGET) + WCW +
Group(from_loc + WCW + to_loc)(EFFECT))
self.translocation_legacy = nest(
Group(self.simple_abundance)(TARGET) + WCW +
Group(identifier(FROM_LOC) + WCW + identifier(TO_LOC))(EFFECT))
self.translocation_legacy.addParseAction(handle_legacy_tloc)
self.translocation_unqualified = nest(
Group(self.simple_abundance)(TARGET))
if self.disallow_unqualified_translocations:
self.translocation_unqualified.setParseAction(
self.handle_translocation_illegal)
#: `2.5.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_translocations>`_
self.translocation = translocation_tag + MatchFirst([
self.translocation_unqualified, self.translocation_standard,
self.translocation_legacy
])
#: `2.5.2 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_degradation_deg>`_
self.degradation = degradation_tags + nest(
Group(self.simple_abundance)(TARGET))
#: `2.5.3 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_reaction_rxn>`_
self.reactants = Suppress(REACTANTS) + nest(
delimitedList(Group(self.simple_abundance)))
self.products = Suppress(PRODUCTS) + nest(
delimitedList(Group(self.simple_abundance)))
self.reaction = reaction_tags + nest(
Group(self.reactants)(REACTANTS),
Group(self.products)(PRODUCTS))
self.transformation = MatchFirst([
self.cell_secretion, self.cell_surface_expression,
self.translocation, self.degradation, self.reaction
])
# 3 BEL Relationships
self.bel_term = MatchFirst(
[self.transformation, self.process, self.abundance]).streamline()
self.bel_to_bel_relations = [
association_tag,
increases_tag,
decreases_tag,
positive_correlation_tag,
negative_correlation_tag,
causes_no_change_tag,
orthologous_tag,
is_a_tag,
equivalent_tag,
partof_tag,
directly_increases_tag,
directly_decreases_tag,
analogous_tag,
regulates_tag,
]
self.bel_to_bel = triple(self.bel_term,
MatchFirst(self.bel_to_bel_relations),
self.bel_term)
# Mixed Relationships
#: `3.1.5 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_ratelimitingstepof>`_
self.rate_limit = triple(
MatchFirst(
[self.biological_process, self.activity, self.transformation]),
rate_limit_tag, self.biological_process)
#: `3.4.6 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_subprocessof>`_
self.subprocess_of = triple(
MatchFirst([self.process, self.activity, self.transformation]),
subprocess_of_tag, self.process)
#: `3.3.2 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_transcribedto>`_
self.transcribed = triple(self.gene, transcribed_tag, self.rna)
#: `3.3.3 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_translatedto>`_
self.translated = triple(self.rna, translated_tag, self.protein)
#: `3.4.1 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_hasmember>`_
self.has_member = triple(self.abundance, has_member_tag,
self.abundance)
#: `3.4.2 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_hasmembers>`_
self.abundance_list = Suppress('list') + nest(
delimitedList(Group(self.abundance)))
self.has_members = triple(self.abundance, has_members_tag,
self.abundance_list)
self.has_members.setParseAction(self.handle_has_members)
self.has_components = triple(self.abundance, has_components_tag,
self.abundance_list)
self.has_components.setParseAction(self.handle_has_components)
self.has_list = self.has_members | self.has_components
# `3.4.3 <http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_hascomponent>`_
self.has_component = triple(
self.complex_abundances | self.composite_abundance,
has_component_tag, self.abundance)
self.biomarker = triple(self.bel_term, biomarker_tags, self.process)
self.has_variant_relation = triple(self.abundance, has_variant_tags,
self.abundance)
self.part_of_reaction = triple(self.reaction, part_of_reaction_tags,
self.abundance)
self.relation = MatchFirst([
self.bel_to_bel,
# self.has_member,
# self.has_component,
self.subprocess_of,
self.rate_limit,
self.biomarker,
self.transcribed,
self.translated,
# self.has_variant_relation,
# self.part_of_reaction,
])
self.relation.setParseAction(self._handle_relation_harness)
self.unqualified_relation = MatchFirst([
self.has_member, self.has_component, self.has_variant_relation,
self.part_of_reaction
])
self.unqualified_relation.setParseAction(
self.handle_unqualified_relation)
#: 3.1 Causal Relationships - nested. Not enabled by default.
causal_relation_tags = MatchFirst([
increases_tag, decreases_tag, directly_decreases_tag,
directly_increases_tag
])
self.nested_causal_relationship = triple(
self.bel_term, causal_relation_tags,
nest(triple(self.bel_term, causal_relation_tags, self.bel_term)))
self.nested_causal_relationship.setParseAction(
self.handle_nested_relation)
self.label_relationship = And([
Group(self.bel_term)(SUBJECT),
Suppress('labeled'),
quote(OBJECT)
])
self.label_relationship.setParseAction(self.handle_label_relation)
# has_members is handled differently from all other relations becuase it gets distrinbuted
self.relation = MatchFirst([
self.has_list,
self.nested_causal_relationship,
self.relation,
self.unqualified_relation,
self.label_relationship,
])
self.singleton_term = (self.bel_term + StringEnd()).setParseAction(
self.handle_term)
self.statement = self.relation | self.singleton_term
self.language = self.control_parser.language | self.statement
self.language.setName('BEL')
super(BELParser, self).__init__(self.language,
streamline=autostreamline)
@property
def _namespace_dict(self) -> Mapping[str, Mapping[str, str]]:
"""Get the dictionary of {namespace: {name: encoding}} stored in the internal identifier parser."""
return self.identifier_parser.namespace_to_terms
@property
def _allow_naked_names(self) -> bool:
"""Return if naked names should be parsed (``True``), or if errors should be thrown (``False``)."""
return self.identifier_parser.allow_naked_names
def get_annotations(self) -> Dict:
"""Get the current annotations in this parser."""
return self.control_parser.get_annotations()
def clear(self):
"""Clear the graph and all control parser data (current citation, annotations, and statement group)."""
self.graph.clear()
self.control_parser.clear()
def handle_nested_relation(self, line: str, position: int,
tokens: ParseResults):
"""Handle nested statements.
If :code:`allow_nested` is False, raises a ``NestedRelationWarning``.
:raises: NestedRelationWarning
"""
if not self.allow_nested:
raise NestedRelationWarning(self.get_line_number(), line, position)
self._handle_relation_harness(
line, position, {
SUBJECT: tokens[SUBJECT],
RELATION: tokens[RELATION],
OBJECT: tokens[OBJECT][SUBJECT],
})
self._handle_relation_harness(
line, position, {
SUBJECT: tokens[OBJECT][SUBJECT],
RELATION: tokens[OBJECT][RELATION],
OBJECT: tokens[OBJECT][OBJECT],
})
return tokens
def check_function_semantics(self, line: str, position: int,
tokens: ParseResults) -> ParseResults:
"""Raise an exception if the function used on the tokens is wrong.
:raises: InvalidFunctionSemantic
"""
if not self._namespace_dict or NAMESPACE not in tokens:
return tokens
namespace, name = tokens[NAMESPACE], tokens[NAME]
if namespace in self.identifier_parser.namespace_to_pattern:
return tokens
if self._allow_naked_names and tokens[
NAMESPACE] == DIRTY: # Don't check dirty names in lenient mode
return tokens
valid_functions = set(
itt.chain.from_iterable(
belns_encodings.get(k, set())
for k in self._namespace_dict[namespace][name]))
if not valid_functions:
raise InvalidEntity(self.get_line_number(), line, position,
namespace, name)
if tokens[FUNCTION] not in valid_functions:
raise InvalidFunctionSemantic(self.get_line_number(), line,
position, tokens[FUNCTION],
namespace, name, valid_functions)
return tokens
def handle_term(self, _, __, tokens: ParseResults) -> ParseResults:
"""Handle BEL terms (the subject and object of BEL relations)."""
self.ensure_node(tokens)
return tokens
def _handle_list_helper(self, tokens: ParseResults,
relation: str) -> ParseResults:
"""Provide the functionality for :meth:`handle_has_members` and :meth:`handle_has_components`."""
parent_node_dsl = self.ensure_node(tokens[0])
for child_tokens in tokens[2]:
child_node_dsl = self.ensure_node(child_tokens)
self.graph.add_unqualified_edge(parent_node_dsl, child_node_dsl,
relation)
return tokens
def handle_has_members(self, _, __, tokens: ParseResults) -> ParseResults:
"""Handle list relations like ``p(X) hasMembers list(p(Y), p(Z), ...)``."""
return self._handle_list_helper(tokens, HAS_MEMBER)
def handle_has_components(self, _, __,
tokens: ParseResults) -> ParseResults:
"""Handle list relations like ``p(X) hasComponents list(p(Y), p(Z), ...)``."""
return self._handle_list_helper(tokens, HAS_COMPONENT)
def _add_qualified_edge_helper(self, u, v, relation, annotations,
subject_modifier, object_modifier) -> str:
"""Add a qualified edge from the internal aspects of the parser."""
return self.graph.add_qualified_edge(
u,
v,
relation=relation,
evidence=self.control_parser.evidence,
citation=self.control_parser.citation.copy(),
annotations=annotations,
subject_modifier=subject_modifier,
object_modifier=object_modifier,
**{LINE: self.get_line_number()})
def _add_qualified_edge(self, u, v, relation, annotations,
subject_modifier, object_modifier) -> str:
"""Add an edge, then adds the opposite direction edge if it should."""
sha512 = self._add_qualified_edge_helper(
u,
v,
relation=relation,
annotations=annotations,
subject_modifier=subject_modifier,
object_modifier=object_modifier,
)
if relation in TWO_WAY_RELATIONS:
self._add_qualified_edge_helper(
v,
u,
relation=relation,
annotations=annotations,
object_modifier=subject_modifier,
subject_modifier=object_modifier,
)
return sha512
def _handle_relation(self, tokens: ParseResults) -> str:
"""Handle a relation."""
subject_node_dsl = self.ensure_node(tokens[SUBJECT])
object_node_dsl = self.ensure_node(tokens[OBJECT])
subject_modifier = modifier_po_to_dict(tokens[SUBJECT])
object_modifier = modifier_po_to_dict(tokens[OBJECT])
annotations = {
annotation_name: ({ae: True
for ae in annotation_entry} if isinstance(
annotation_entry, set) else {
annotation_entry: True
})
for annotation_name, annotation_entry in
self.control_parser.annotations.items()
}
return self._add_qualified_edge(
subject_node_dsl,
object_node_dsl,
relation=tokens[RELATION],
annotations=annotations,
subject_modifier=subject_modifier,
object_modifier=object_modifier,
)
def _handle_relation_harness(
self, line: str, position: int,
tokens: Union[ParseResults, Dict]) -> ParseResults:
"""Handle BEL relations based on the policy specified on instantiation.
Note: this can't be changed after instantiation!
"""
if not self.control_parser.citation:
raise MissingCitationException(self.get_line_number(), line,
position)
if not self.control_parser.evidence:
raise MissingSupportWarning(self.get_line_number(), line, position)
missing_required_annotations = self.control_parser.get_missing_required_annotations(
)
if missing_required_annotations:
raise MissingAnnotationWarning(self.get_line_number(), line,
position,
missing_required_annotations)
self._handle_relation(tokens)
return tokens
def handle_unqualified_relation(self, _, __,
tokens: ParseResults) -> ParseResults:
"""Handle unqualified relations."""
subject_node_dsl = self.ensure_node(tokens[SUBJECT])
object_node_dsl = self.ensure_node(tokens[OBJECT])
relation = tokens[RELATION]
self.graph.add_unqualified_edge(subject_node_dsl, object_node_dsl,
relation)
return tokens
def handle_label_relation(self, line: str, position: int,
tokens: ParseResults) -> ParseResults:
"""Handle statements like ``p(X) label "Label for X"``.
:raises: RelabelWarning
"""
subject_node_dsl = self.ensure_node(tokens[SUBJECT])
description = tokens[OBJECT]
if self.graph.has_node_description(subject_node_dsl):
raise RelabelWarning(
line_number=self.get_line_number(),
line=line,
position=position,
node=self.graph.node,
old_label=self.graph.get_node_description(subject_node_dsl),
new_label=description)
self.graph.set_node_description(subject_node_dsl, description)
return tokens
def ensure_node(self, tokens: ParseResults) -> BaseEntity:
"""Turn parsed tokens into canonical node name and makes sure its in the graph."""
if MODIFIER in tokens:
return self.ensure_node(tokens[TARGET])
node = parse_result_to_dsl(tokens)
self.graph.add_node_from_data(node)
return node
def handle_translocation_illegal(self, line: str, position: int,
tokens: ParseResults) -> None:
"""Handle a malformed translocation."""
raise MalformedTranslocationWarning(self.get_line_number(), line,
position, tokens)
def __init__(self, parse_method=None, field_separator=":", precedence=11):
And.__init__(self, FieldName() + Literal(field_separator))
BaseType.__init__(self, precedence)
if parse_method:
self.addParseAction(parse_method)
def __init__(self, range_parse_method=None, item_parse_method=None, range_symbol="..", precedence=10):
And.__init__(self, Integer(item_parse_method) + Literal(range_symbol) + Integer(item_parse_method))
BaseType.__init__(self, precedence)
if range_parse_method:
self.addParseAction(range_parse_method)
def __init__(self, parse_method=None, precedence=11):
And.__init__(self, [QuotedString() + Literal('~') + Integer()])
BaseType.__init__(self, precedence)
if parse_method:
self.addParseAction(parse_method)
def __init__(self, parse_method=None, field_separator=':', precedence=11):
And.__init__(self, [FieldName() + Literal(field_separator)])
BaseType.__init__(self, precedence)
if parse_method:
self.addParseAction(parse_method)
else:
message += crlf
message.leaveWhitespace()
build_message()
dispatcher.connect(build_message, 'parser.trailing_spaces', 'config')
dispatcher.connect(build_message, 'parser.soft_eol', 'config')
chanstring = charclass((0x01, 0x06), (0x08, 0x09), (0x0B, 0x0C), (0x0E, 0x1F),
(0x21, 0x2B), (0x2D, 0x39), (0x3B, 0xFF))
channelid = 5 * (charclass((0x41, 0x5A)) ^ digit)
channel = And([
Or([oneOf('# + &'), Literal('!') + Group(channelid)]),
Group(OneOrMore(chanstring)),
Optional(Suppress(Literal(':')) + Group(OneOrMore(chanstring)))
])
###
# Wildcard expressions
###
wildone = Literal('?')
wildmany = Literal('*')
nowild = charclass((0x01, 0x29), (0x2B, 0x3E), (0x40, 0xFF))
noesc = charclass((0x01, 0x5B), (0x5D, 0xFF))
mask = Optional(wildone ^ wildmany) + \
ZeroOrMore(nowild ^ (noesc + wildone) ^ (noesc + wildmany))
# Fall back to regex for parsing wildcards
matchone = '[%s-%s]' % (chr(0x01), chr(0xFF))
def __init__(self,
manager,
namespace_dict=None,
annotation_dict=None,
namespace_regex=None,
annotation_regex=None,
default_namespace=None,
allow_redefinition=False):
"""
:param pybel.manager.Manager manager: A cache manager
:param dict[str,dict[str,str]] namespace_dict: A dictionary of pre-loaded, enumerated namespaces from
{namespace keyword: {name: encoding}}
:param dict[str,set[str] annotation_dict: A dictionary of pre-loaded, enumerated annotations from
{annotation keyword: set of valid values}
:param dict[str,str] namespace_regex: A dictionary of pre-loaded, regular expression namespaces from
{namespace keyword: regex string}
:param dict[str,str] annotation_regex: A dictionary of pre-loaded, regular expression annotations from
{annotation keyword: regex string}
:param set[str] default_namespace: A set of strings that can be used without a namespace
"""
#: This metadata parser's internal definition cache manager
self.manager = manager
self.disallow_redefinition = not allow_redefinition
#: A dictionary of cached {namespace keyword: {name: encoding}}
self.namespace_dict = {} if namespace_dict is None else namespace_dict
#: A dictionary of cached {annotation keyword: set of values}
self.annotation_dict = {} if annotation_dict is None else annotation_dict
#: A dictionary of {namespace keyword: regular expression string}
self.namespace_regex = {} if namespace_regex is None else namespace_regex
#: A set of names that can be used without a namespace
self.default_namespace = set(
default_namespace) if default_namespace is not None else None
#: A dictionary of {annotation keyword: regular expression string}
self.annotation_regex = {} if annotation_regex is None else annotation_regex
#: A set of namespaces's URLs that can't be cached
self.uncachable_namespaces = set()
#: A dictionary containing the document metadata
self.document_metadata = {}
#: A dictionary from {namespace keyword: BEL namespace URL}
self.namespace_url_dict = {}
#: A dictionary from {namespace keyword: OWL namespace URL}
self.namespace_owl_dict = {}
#: A dictionary from {annotation keyword: BEL annotation URL}
self.annotation_url_dict = {}
#: A dictionary from {annotation keyword: OWL annotation URL}
self.annotation_owl_dict = {}
#: A set of annotation keywords that are defined ad-hoc in the BEL script
self.annotation_lists = set()
self.document = And([
set_tag,
Suppress(BEL_KEYWORD_DOCUMENT),
word('key'),
Suppress('='),
qid('value')
])
namespace_tag = And([
define_tag,
Suppress(BEL_KEYWORD_NAMESPACE),
ppc.identifier('name'), as_tag
])
self.namespace_url = And([namespace_tag, url_tag, quote('url')])
self.namespace_owl = And([
namespace_tag, owl_tag,
Optional(function_tags('functions')),
quote('url')
])
self.namespace_pattern = And(
[namespace_tag,
Suppress(BEL_KEYWORD_PATTERN),
quote('value')])
annotation_tag = And([
define_tag,
Suppress(BEL_KEYWORD_ANNOTATION),
ppc.identifier('name'), as_tag
])
self.annotation_url = And([annotation_tag, url_tag, quote('url')])
self.annotation_owl = And([annotation_tag, owl_tag, quote('url')])
self.annotation_list = And(
[annotation_tag, list_tag,
delimited_quoted_list('values')])
self.annotation_pattern = And(
[annotation_tag,
Suppress(BEL_KEYWORD_PATTERN),
quote('value')])
self.document.setParseAction(self.handle_document)
self.namespace_url.setParseAction(self.handle_namespace_url)
self.namespace_owl.setParseAction(self.handle_namespace_owl)
self.namespace_pattern.setParseAction(self.handle_namespace_pattern)
self.annotation_url.setParseAction(self.handle_annotations_url)
self.annotation_owl.setParseAction(self.handle_annotation_owl)
self.annotation_list.setParseAction(self.handle_annotation_list)
self.annotation_pattern.setParseAction(self.handle_annotation_pattern)
self.language = MatchFirst([
self.document, self.namespace_url, self.namespace_owl,
self.annotation_url, self.annotation_list, self.annotation_owl,
self.annotation_pattern, self.namespace_pattern
]).setName('BEL Metadata')
super(MetadataParser, self).__init__(self.language)
class MetadataParser(BaseParser):
"""A parser for the document and definitions section of a BEL document.
.. seealso::
BEL 1.0 Specification for the `DEFINE <http://openbel.org/language/web/version_1.0/bel_specification_version_1.0.html#_define>`_ keyword
"""
def __init__(self,
manager,
namespace_dict=None,
annotation_dict=None,
namespace_regex=None,
annotation_regex=None,
default_namespace=None,
allow_redefinition=False):
"""
:param pybel.manager.Manager manager: A cache manager
:param dict[str,dict[str,str]] namespace_dict: A dictionary of pre-loaded, enumerated namespaces from
{namespace keyword: {name: encoding}}
:param dict[str,set[str] annotation_dict: A dictionary of pre-loaded, enumerated annotations from
{annotation keyword: set of valid values}
:param dict[str,str] namespace_regex: A dictionary of pre-loaded, regular expression namespaces from
{namespace keyword: regex string}
:param dict[str,str] annotation_regex: A dictionary of pre-loaded, regular expression annotations from
{annotation keyword: regex string}
:param set[str] default_namespace: A set of strings that can be used without a namespace
"""
#: This metadata parser's internal definition cache manager
self.manager = manager
self.disallow_redefinition = not allow_redefinition
#: A dictionary of cached {namespace keyword: {name: encoding}}
self.namespace_dict = {} if namespace_dict is None else namespace_dict
#: A dictionary of cached {annotation keyword: set of values}
self.annotation_dict = {} if annotation_dict is None else annotation_dict
#: A dictionary of {namespace keyword: regular expression string}
self.namespace_regex = {} if namespace_regex is None else namespace_regex
#: A set of names that can be used without a namespace
self.default_namespace = set(
default_namespace) if default_namespace is not None else None
#: A dictionary of {annotation keyword: regular expression string}
self.annotation_regex = {} if annotation_regex is None else annotation_regex
#: A set of namespaces's URLs that can't be cached
self.uncachable_namespaces = set()
#: A dictionary containing the document metadata
self.document_metadata = {}
#: A dictionary from {namespace keyword: BEL namespace URL}
self.namespace_url_dict = {}
#: A dictionary from {namespace keyword: OWL namespace URL}
self.namespace_owl_dict = {}
#: A dictionary from {annotation keyword: BEL annotation URL}
self.annotation_url_dict = {}
#: A dictionary from {annotation keyword: OWL annotation URL}
self.annotation_owl_dict = {}
#: A set of annotation keywords that are defined ad-hoc in the BEL script
self.annotation_lists = set()
self.document = And([
set_tag,
Suppress(BEL_KEYWORD_DOCUMENT),
word('key'),
Suppress('='),
qid('value')
])
namespace_tag = And([
define_tag,
Suppress(BEL_KEYWORD_NAMESPACE),
ppc.identifier('name'), as_tag
])
self.namespace_url = And([namespace_tag, url_tag, quote('url')])
self.namespace_owl = And([
namespace_tag, owl_tag,
Optional(function_tags('functions')),
quote('url')
])
self.namespace_pattern = And(
[namespace_tag,
Suppress(BEL_KEYWORD_PATTERN),
quote('value')])
annotation_tag = And([
define_tag,
Suppress(BEL_KEYWORD_ANNOTATION),
ppc.identifier('name'), as_tag
])
self.annotation_url = And([annotation_tag, url_tag, quote('url')])
self.annotation_owl = And([annotation_tag, owl_tag, quote('url')])
self.annotation_list = And(
[annotation_tag, list_tag,
delimited_quoted_list('values')])
self.annotation_pattern = And(
[annotation_tag,
Suppress(BEL_KEYWORD_PATTERN),
quote('value')])
self.document.setParseAction(self.handle_document)
self.namespace_url.setParseAction(self.handle_namespace_url)
self.namespace_owl.setParseAction(self.handle_namespace_owl)
self.namespace_pattern.setParseAction(self.handle_namespace_pattern)
self.annotation_url.setParseAction(self.handle_annotations_url)
self.annotation_owl.setParseAction(self.handle_annotation_owl)
self.annotation_list.setParseAction(self.handle_annotation_list)
self.annotation_pattern.setParseAction(self.handle_annotation_pattern)
self.language = MatchFirst([
self.document, self.namespace_url, self.namespace_owl,
self.annotation_url, self.annotation_list, self.annotation_owl,
self.annotation_pattern, self.namespace_pattern
]).setName('BEL Metadata')
super(MetadataParser, self).__init__(self.language)
def handle_document(self, line, position, tokens):
"""Handles statements like ``SET DOCUMENT X = "Y"``
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param pyparsing.ParseResult tokens: The tokens from PyParsing
"""
key = tokens['key']
value = tokens['value']
if key not in DOCUMENT_KEYS:
raise InvalidMetadataException(self.line_number, line, position,
key, value)
norm_key = DOCUMENT_KEYS[key]
if norm_key in self.document_metadata:
log.warning('Tried to overwrite metadata: %s', key)
return tokens
self.document_metadata[norm_key] = value
if norm_key == METADATA_VERSION:
self.raise_for_version(line, position, value)
return tokens
def raise_for_redefined_namespace(self, line, position, namespace):
"""Raises an exception if a namespace is already defined
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param str namespace: The namespace being parsed
:raises: RedefinedNamespaceError
"""
if self.disallow_redefinition and self.has_namespace(namespace):
raise RedefinedNamespaceError(self.line_number, line, position,
namespace)
def handle_namespace_url(self, line, position, tokens):
"""Handles statements like ``DEFINE NAMESPACE X AS URL "Y"``
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param pyparsing.ParseResult tokens: The tokens from PyParsing
:raises: RedefinedNamespaceError
:raises: pybel.resources.exc.ResourceError
"""
namespace = tokens['name']
self.raise_for_redefined_namespace(line, position, namespace)
url = tokens['url']
namespace_result = self.manager.ensure_namespace(url)
if isinstance(namespace_result, dict):
self.namespace_dict[namespace] = namespace_result
self.uncachable_namespaces.add(url)
else:
self.namespace_dict[namespace] = namespace_result.to_values()
self.namespace_url_dict[namespace] = url
return tokens
def handle_namespace_owl(self, line, position, tokens):
"""Handles statements like ``DEFINE NAMESPACE X AS OWL "Y"``
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param pyparsing.ParseResult tokens: The tokens from PyParsing
:raises: RedefinedNamespaceError
"""
namespace = tokens['name']
self.raise_for_redefined_namespace(line, position, namespace)
functions = str(tokens['functions']
) if 'functions' in tokens else BELNS_ENCODING_STR
url = tokens['url']
terms = self.manager.get_namespace_owl_terms(url, namespace)
self.namespace_dict[namespace] = {term: functions for term in terms}
self.namespace_owl_dict[namespace] = url
return tokens
def handle_namespace_pattern(self, line, position, tokens):
"""Handles statements like ``DEFINE NAMESPACE X AS PATTERN "Y"``
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param pyparsing.ParseResult tokens: The tokens from PyParsing
:raises: RedefinedNamespaceError
"""
namespace = tokens['name']
self.raise_for_redefined_namespace(line, position, namespace)
self.namespace_regex[namespace] = tokens['value']
return tokens
def raise_for_redefined_annotation(self, line, position, annotation):
"""Raises an exception if the given annotation is already defined
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param str annotation: The annotation being parsed
:raises: RedefinedAnnotationError
"""
if self.disallow_redefinition and self.has_annotation(annotation):
raise RedefinedAnnotationError(self.line_number, line, position,
annotation)
def handle_annotation_owl(self, line, position, tokens):
"""Handles statements like ``DEFINE ANNOTATION X AS OWL "Y"``
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param pyparsing.ParseResult tokens: The tokens from PyParsing
:raises: RedefinedAnnotationError
"""
annotation = tokens['name']
self.raise_for_redefined_annotation(line, position, annotation)
url = tokens['url']
self.annotation_dict[
annotation] = self.manager.get_annotation_owl_terms(
url, annotation)
self.annotation_owl_dict[annotation] = url
return tokens
def handle_annotations_url(self, line, position, tokens):
"""Handles statements like ``DEFINE ANNOTATION X AS URL "Y"``
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param pyparsing.ParseResult tokens: The tokens from PyParsing
:raises: RedefinedAnnotationError
"""
keyword = tokens['name']
self.raise_for_redefined_annotation(line, position, keyword)
url = tokens['url']
self.annotation_dict[keyword] = self.manager.get_annotation_entries(
url)
self.annotation_url_dict[keyword] = url
return tokens
def handle_annotation_list(self, line, position, tokens):
"""Handles statements like ``DEFINE ANNOTATION X AS LIST {"Y","Z", ...}``
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param pyparsing.ParseResult tokens: The tokens from PyParsing
:raises: RedefinedAnnotationError
"""
annotation = tokens['name']
self.raise_for_redefined_annotation(line, position, annotation)
values = set(tokens['values'])
self.annotation_dict[annotation] = values
self.annotation_lists.add(annotation)
return tokens
def handle_annotation_pattern(self, line, position, tokens):
"""Handles statements like ``DEFINE ANNOTATION X AS PATTERN "Y"``
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param pyparsing.ParseResult tokens: The tokens from PyParsing
:raises: RedefinedAnnotationError
"""
annotation = tokens['name']
self.raise_for_redefined_annotation(line, position, annotation)
self.annotation_regex[annotation] = tokens['value']
return tokens
def has_enumerated_annotation(self, annotation):
"""Checks if this annotation is defined by an enumeration
:param str annotation: The keyword of a annotation
:rtype: bool
"""
return annotation in self.annotation_dict
def has_regex_annotation(self, annotation):
"""Checks if this annotation is defined by a regular expression
:param str annotation: The keyword of a annotation
:rtype: bool
"""
return annotation in self.annotation_regex
def has_annotation(self, annotation):
"""Checks if this annotation is defined
:param str annotation: The keyword of a annotation
:rtype: bool
"""
return self.has_enumerated_annotation(
annotation) or self.has_regex_annotation(annotation)
def has_enumerated_namespace(self, namespace):
"""Checks if this namespace is defined by an enumeration
:param str namespace: The keyword of a namespace
:rtype: bool
"""
return namespace in self.namespace_dict
def has_regex_namespace(self, namespace):
"""Checks if this namespace is defined by a regular expression
:param str namespace: The keyword of a namespace
:rtype: bool
"""
return namespace in self.namespace_regex
def has_namespace(self, namespace):
"""Checks if this namespace is defined
:param str namespace: The keyword of a namespace
:rtype: bool
"""
return self.has_enumerated_namespace(
namespace) or self.has_regex_namespace(namespace)
def raise_for_version(self, line, position, version):
"""Checks that a version string is valid for BEL documents, meaning it's either in the YYYYMMDD or semantic version
format
:param str line: The line being parsed
:param int position: The position in the line being parsed
:param str version: A version string
:raises: VersionFormatWarning
"""
if valid_date_version(version):
return
if not SEMANTIC_VERSION_STRING_RE.match(version):
raise VersionFormatWarning(self.line_number, line, position,
version)