def parse_element(cls, indent_stack):
"""Sets ``connect`` attribute to the rule"""
return (
Keyword("@connect").suppress() + Literal('(').suppress() +
quotedString.setResultsName('field').setParseAction(removeQuotes) +
Optional(Literal(',').suppress() +
SkipTo(')')).setResultsName('func') +
Literal(')').suppress()).setResultsName("connect").setParseAction(
lambda toks: {
'connected_field': toks.field,
'update_function': toks.func[0] if toks.func else None
})
def parse_element(cls, indent_stack):
"""Sets ``connect`` attribute to the rule"""
return (Keyword("@connect").suppress() +
Literal('(').suppress() +
quotedString.setResultsName('field')
.setParseAction(removeQuotes) +
Optional(Literal(',').suppress() +
SkipTo(')')).setResultsName('func') +
Literal(')').suppress()
).setResultsName("connect").setParseAction(
lambda toks: {
'connected_field': toks.field,
'update_function': toks.func[0]
if toks.func else None
})
def _create_parser() -> ParserElement:
"""
Creates the parser to use for parsing filter expressions.
:return: The created parser.
"""
# Defining what a variable is.
main_variable = '${' + Word(alphanums + '-._ ') + '}'
main_variable = main_variable.setResultsName('variable')
main_variable.setParseAction(lambda toks: toks[1])
second_variable = main_variable.copy().setResultsName('second_variable')
# Defining what an operator is.
operator = oneOf(' '.join(Operator.symbols()))
operator = operator.setResultsName('operator')
# Defining what the different possible values are.
real = pyparsing_common.real.setResultsName('real')
integer = pyparsing_common.integer.setResultsName('integer')
boolean = oneOf('true false', caseless=True)
boolean = boolean.setResultsName('boolean')
boolean.setParseAction(lambda toks: list(map(lambda b: b.lower() == 'true', toks)))
string = quotedString.setResultsName('string')
string.setParseAction(lambda toks: list(map(lambda s: s[1:-1], toks)))
# Defining what a single value is.
single_value = real | integer | boolean | string
single_value = single_value.setResultsName('value')
# Defining what a list of values is.
list_value = '[' + delimitedList(single_value) + ']'
list_value = list_value.setResultsName('list')
# Defining what a general value is.
value = single_value | list_value
# Defining what a complete expression is.
variable_right = value + operator + main_variable
variable_right = variable_right.setResultsName('right')
variable_left = main_variable + operator + value
variable_left = variable_left.setResultsName('left')
both_variable = main_variable + operator + second_variable
both_variable = both_variable.setResultsName('both')
return variable_right | variable_left | both_variable | main_variable
_sign = Word("+-", exact=1)
number = (
Combine(Optional(_sign) + Word(nums) + Optional("." + Optional(Word(nums))))
.setName("number")
.setResultsName("number")
)
integer = (
Combine(Optional(_sign) + Word(nums)).setName("number").setResultsName("number")
)
boolean = (upkey("true") | upkey("false")).setName("bool")
binary = Combine("b" + quotedString)
value = Forward()
json_value = Forward()
string = quotedString.setResultsName("str")
json_primitive = (
null.setResultsName("null") | number | string | boolean.setResultsName("bool")
)
set_primitive = (
number.setResultsName("number")
| quotedString.setResultsName("str")
| binary.setResultsName("binary")
)
primitive = json_primitive | binary.setResultsName("binary")
_emptyset = Keyword("()").setResultsName("set")
set_ = (
Suppress("(") + delimitedList(Group(set_primitive)) + Suppress(")")
).setResultsName("set")
list_ = (
Suppress("[") + Optional(delimitedList(json_value)) + Suppress("]")
diffusion_entry_ = Group((diffusion_constant_2d_.setResultsName('2D') | diffusion_constant_3d_.setResultsName('3D')) + Suppress(equal) + (function_entry_.setResultsName('function') | (identifier | numarg).setResultsName('variable')))
molecule_entry = Group(molecule_definition + Optional(Group(lbrace + Optional(diffusion_entry_.setResultsName('diffusionFunction')) + (ZeroOrMore(statement)).setResultsName('moleculeParameters') + rbrace)))
hashed_molecule_section = Group(hashsymbol + Suppress(define_molecules_) + lbrace + OneOrMore(molecule_entry) + rbrace)
# hash function entry
function_name = Group(identifier + '()')
math_function_entry = Group(function_name.setResultsName('functionName') + Suppress(equal) + Group(restOfLine).setResultsName('functionBody'))
hashed_function_section = Group(hashsymbol + Suppress(define_functions_) + lbrace + ZeroOrMore(math_function_entry) + rbrace)
# hash reaction entry
hashed_reaction_section = Group(hashsymbol + Suppress(define_reactions_) + lbrace + OneOrMore(reaction_definition) + rbrace)
# hash observable entry
count_definition = Group(count_ + lbracket + species_definition.setResultsName('speciesPattern') + Suppress(',') + identifier + rbracket)
observable_entry = Group(lbrace + Group(delimitedList(count_definition, delim='+')).setResultsName('patterns') + rbrace + Suppress('=>') + quotedString.setResultsName('outputfile'))
bngobservable_entry = Group((species_ | molecules_).setResultsName('obskey') + identifier.setResultsName('obsname') + Group(delimitedList(species_definition, delim=',')).setResultsName('obspatterns'))
hashed_observable_section = Group(hashsymbol + Suppress(reaction_data_output_) + lbrace + OneOrMore(statement).setResultsName('statements') + ZeroOrMore(observable_entry).setResultsName('mdlobs') + ZeroOrMore(bngobservable_entry).setResultsName('bngobs') + rbrace)
# hash initialization entry
key = identifier + Suppress('=')
value = restOfLine
release_site_definition = Group(identifier.setResultsName('name') + release_site_ + lbrace + dictOf(key, value).setResultsName('entries') + rbrace)
object_definition = Group(identifier.setResultsName('compartmentName') + Suppress(object_) + (bracketidentifier | identifier) + (nestedExpr('{', '}', content=statement)).setResultsName('compartmentOptions'))
hashed_initialization_section = Group(hashsymbol + Suppress(instantiate_) + identifier.setResultsName('name') +
identifier.setResultsName('type') + lbrace + Group(ZeroOrMore(release_site_definition | object_definition)).setResultsName('entries') + rbrace)
other_sections = section_enclosure_
# statement = Group(identifier + equal + (quotedString | OneOrMore(mathElements))) + Suppress(LineEnd() | StringEnd())
grammar = ZeroOrMore(Suppress(other_sections) | Suppress(statement) | hashed_system_constants.setResultsName('systemConstants') |
_TABLE_NAME = _SQL_ID.setResultsName("table")
_PROCEDURE_NAME = _sql_identifier(Word(alphanums + "_.:").setResultsName("name")).setResultsName('name')
_SELECT_COLUMN_LIST = delimitedList(Group(_SELECT_COLUMN), combine=False).setResultsName("columns")
_SQL_ARG = Optional(_SQL_DIRECTION, default='IN') + _SQL_ID + _SQL_TYPE
_SQL_ARGS = delimitedList(Group(_SQL_ARG), combine=False)
_RETURN_TYPE = oneOf("object array", caseless=True).setResultsName("type")
# expressions
_DEFINE_FUNCTION = _DEFINE + _ID + nestedExpr(content=_ID_LIST, ignoreExpr=None).setResultsName("args") + \
Suppress(White()) + Regex(".*$").setResultsName("body")
_DEFINE_VAR = _DEFINE + _ID + _VALUE
_UNDEFINE = _UNDEF + _ID
_INCLUDE_FILE = _INCLUDE + quotedString.setResultsName("filename")
_EXPAND_VAR = Suppress('$') + _ID
_EXPAND_FUNC = Suppress('$') + _ID + nestedExpr(content=_VALUE_LIST, ignoreExpr=None).setResultsName("args")
_IF_EXPR = _IF + SkipTo(lineEnd, include=True).setResultsName("condition")
_ELSE_EXPR = _ELSE + lineEnd
_ENDIF_EXPR = _ENDIF + lineEnd
_RETURN_HINT_EXPR = _select_hint(Optional(_ID + Suppress(Literal(":"))) + _RETURN_TYPE).setResultsName("hint")
_TEMP_TABLE_EXPR = _SQL_ID.setResultsName('table') + \
nestedExpr(content=delimitedList(Group(_SQL_ID + _SQL_TYPE)), ignoreExpr=None).setResultsName('columns') +\
Suppress(Literal(';'))
_PROCEDURE_COMMENT_FORMAT = Optional(_TEMP_TABLE_EXPR) + Optional(_RETURNS + oneOf("union", caseless=True).setResultsName("mode")) + lineEnd
_CREATE_PROCEDURE = _CREATE + Optional(_DEFINER + '=' + _SQL_ID) + _PROCEDURE + _PROCEDURE_NAME + \
lbrace + ZeroOrMore(math_function_entry) +
rbrace)
# hash reaction entry
hashed_reaction_section = Group(hashsymbol + Suppress(define_reactions_) +
lbrace + OneOrMore(reaction_definition) +
rbrace)
# hash observable entry
count_definition = Group(count_ + lbracket +
species_definition.setResultsName('speciesPattern') +
Suppress(',') + identifier + rbracket)
observable_entry = Group(lbrace + Group(
delimitedList(count_definition, delim='+')).setResultsName('patterns') +
rbrace + Suppress('=>') +
quotedString.setResultsName('outputfile'))
bngobservable_entry = Group((species_ | molecules_).setResultsName('obskey') +
identifier.setResultsName('obsname') +
Group(delimitedList(species_definition, delim=',')
).setResultsName('obspatterns'))
hashed_observable_section = Group(
hashsymbol + Suppress(reaction_data_output_) + lbrace +
OneOrMore(statement).setResultsName('statements') +
ZeroOrMore(observable_entry).setResultsName('mdlobs') +
ZeroOrMore(bngobservable_entry).setResultsName('bngobs') + rbrace)
# hash initialization entry
key = identifier + Suppress('=')
value = restOfLine
release_site_definition = Group(
upkey('number') |
upkey('binary'))\
.setName('type').setResultsName('type')
_sign = Word('+-', exact=1)
number = Combine(Optional(_sign) + Word(nums) +
Optional('.' + Optional(Word(nums)))) \
.setName('number').setResultsName('number')
integer = Combine(Optional(_sign) + Word(nums)) \
.setName('number').setResultsName('number')
boolean = (upkey('true') | upkey('false')).setName('bool')
binary = Combine('b' + quotedString)
value = Forward()
json_value = Forward()
string = quotedString.setResultsName('str')
json_primitive = (null.setResultsName('null') |
number | string |
boolean.setResultsName('bool'))
set_primitive = (number.setResultsName('number') |
quotedString.setResultsName('str') |
binary.setResultsName('binary'))
primitive = (json_primitive | binary.setResultsName('binary'))
_emptyset = Keyword('()').setResultsName('set')
set_ = (Suppress('(') + delimitedList(Group(set_primitive)) +
Suppress(')')).setResultsName('set')
list_ = (Suppress('[') + Optional(delimitedList(json_value)) +
Suppress(']')).setResultsName('list')
key_val = (Group(quotedString.setResultsName('str')) + Suppress(':') +
json_value)
dict_ = (Suppress('{') + Optional(delimitedList(Group(key_val))) +
_SELECT_COLUMN_LIST = delimitedList(Group(_SELECT_COLUMN),
combine=False).setResultsName("columns")
_SQL_ARG = Optional(_SQL_DIRECTION, default='IN') + _SQL_ID + _SQL_TYPE
_SQL_ARGS = delimitedList(Group(_SQL_ARG), combine=False)
_RETURN_TYPE = oneOf("object array", caseless=True).setResultsName("type")
# expressions
_DEFINE_FUNCTION = _DEFINE + _ID + nestedExpr(content=_ID_LIST, ignoreExpr=None).setResultsName("args") + \
Suppress(White()) + Regex(".*$").setResultsName("body")
_DEFINE_VAR = _DEFINE + _ID + SkipTo(lineEnd,
include=True).setResultsName("value")
_UNDEFINE = _UNDEF + _ID
_INCLUDE_FILE = _INCLUDE + quotedString.setResultsName("filename")
_EXPAND_VAR = Suppress('$') + _ID
_EXPAND_FUNC = Suppress('$') + _ID + nestedExpr(
content=_VALUE_LIST, ignoreExpr=None).setResultsName("args")
_IF_EXPR = _IF + SkipTo(lineEnd, include=True).setResultsName("condition")
_ELSE_EXPR = _ELSE + lineEnd
_ENDIF_EXPR = _ENDIF + lineEnd
_RETURN_HINT_EXPR = _select_hint(
Optional(_ID + Suppress(Literal(":"))) +
_RETURN_TYPE).setResultsName("hint")
_TEMP_TABLE_EXPR = _SQL_ID.setResultsName('table') + \
nestedExpr(content=delimitedList(Group(_SQL_ID + _SQL_TYPE)), ignoreExpr=None).setResultsName('columns') +\
Suppress(Literal(';'))
# pylint: disable=C0103
backtickString = Regex(r'`[^`]*`').setName("string enclosed in backticks")
and_, from_, into, in_, table_key, null, where_ = \
map(upkey, ['and', 'from', 'into', 'in', 'table', 'null', 'where'])
var = Word(alphas, alphanums + '_-').setName('variable').setResultsName('var')
expr = Combine(Optional('m') + backtickString).setName('python expression').setResultsName('python')
table = var.setResultsName('table')
type_ = (upkey('string') |
upkey('number') |
upkey('binary'))\
.setName('type').setResultsName('type')
_sign = Word('+-', exact=1)
num = Combine(Optional(_sign) + Word(nums) +
Optional('.' + Optional(Word(nums)))).setName('number')
primitive = (null.setResultsName('null') |
num.setResultsName('number') |
quotedString.setResultsName('str') |
Combine('b' + quotedString).setResultsName('binary'))
_emptyset = Keyword('()').setResultsName('set')
set_ = (Suppress('(') + delimitedList(Group(primitive)) +
Suppress(')')).setResultsName('set')
value = Group(primitive | expr | set_ | _emptyset).setName('value')
# Wrap these in a group so they can be used independently
primitive = Group(primitive | expr).setName('primitive')
set_ = Group(set_ | _emptyset | expr).setName('set')
diffusion_entry_ = Group((diffusion_constant_2d_.setResultsName('2D') | diffusion_constant_3d_.setResultsName('3D')) + Suppress(equal) + (function_entry_.setResultsName('function') | (identifier | numarg).setResultsName('variable')))
molecule_entry = Group(molecule_definition + Optional(Group(lbrace + Optional(diffusion_entry_.setResultsName('diffusionFunction')) + (ZeroOrMore(statement)).setResultsName('moleculeParameters') + rbrace)))
hashed_molecule_section = Group(hashsymbol + Suppress(define_molecules_) + lbrace + OneOrMore(molecule_entry) + rbrace)
#hash function entry
function_name = Group(identifier + '()')
math_function_entry = Group(function_name.setResultsName('functionName') + Suppress(equal) + Group(restOfLine).setResultsName('functionBody'))
hashed_function_section = Group(hashsymbol + Suppress(define_functions_) + lbrace + ZeroOrMore(math_function_entry) +rbrace)
# hash reaction entry
hashed_reaction_section = Group(hashsymbol + Suppress(define_reactions_) + lbrace + OneOrMore(reaction_definition) + rbrace)
# hash observable entry
count_definition = Group(count_ + lbracket + species_definition.setResultsName('speciesPattern') + Suppress(',') + identifier + rbracket)
observable_entry = Group(lbrace + Group(delimitedList(count_definition, delim='+')).setResultsName('patterns') + rbrace + Suppress('=>') + quotedString.setResultsName('outputfile'))
bngobservable_entry = Group((species_ | molecules_).setResultsName('obskey') + identifier.setResultsName('obsname') + Group(delimitedList(species_definition, delim=',')).setResultsName('obspatterns'))
hashed_observable_section = Group(hashsymbol + Suppress(reaction_data_output_) + lbrace + OneOrMore(statement).setResultsName('statements') + ZeroOrMore(observable_entry).setResultsName('mdlobs') + ZeroOrMore(bngobservable_entry).setResultsName('bngobs') + rbrace)
# hash initialization entry
key = identifier + Suppress('=')
value = restOfLine
release_site_definition = Group(identifier.setResultsName('name') + release_site_ + lbrace + dictOf(key,value).setResultsName('entries') + rbrace)
object_definition = Group(identifier.setResultsName('compartmentName') + Suppress(object_) + (bracketidentifier | identifier) + (nestedExpr('{', '}',content=statement)).setResultsName('compartmentOptions'))
hashed_initialization_section = Group(hashsymbol + Suppress(instantiate_) + identifier.setResultsName('name') +
identifier.setResultsName('type') + lbrace + Group(ZeroOrMore(release_site_definition | object_definition)).setResultsName('entries') + rbrace )
other_sections = section_enclosure_
#statement = Group(identifier + equal + (quotedString | OneOrMore(mathElements))) + Suppress(LineEnd() | StringEnd())
grammar = ZeroOrMore(Suppress(other_sections) | Suppress(statement) | hashed_system_constants.setResultsName('systemConstants')
