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# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import ast
from . import grammar, meta, collection, primitive, semantic, visualization
def string_to_ast(type_expr):
try:
parsed = ast.parse(type_expr)
except SyntaxError:
raise ValueError("%r could not be parsed, it may not be a QIIME 2 type"
" or it may not be an atomic type. Use"
" `ast_to_type` instead." % (type_expr,))
if type(parsed) is not ast.Module:
# I don't think this branch *can* be hit
raise ValueError("%r is not a type expression." % (type_expr,))
try:
expr, = parsed.body
except ValueError:
raise ValueError("Only one type expression may be parse at a time, got"
": %r" % (type_expr,))
return _expr(expr.value)
def _expr(expr):
node = type(expr)
if node is ast.Name:
return _build_atomic(expr.id)
if node is ast.Call:
args = _parse_args(expr.args)
kwargs = _parse_kwargs(expr.keywords)
return _build_predicate(expr.func.id, args, kwargs)
if node is ast.Subscript:
try:
field_expr = expr.slice.value
except AttributeError:
field_expr = expr.slice
if type(field_expr) is ast.Tuple:
field_expr = field_expr.elts
else:
field_expr = (field_expr,)
base = _expr(expr.value)
base['fields'] = [_expr(e) for e in field_expr]
return base
if node is ast.BinOp:
op = type(expr.op)
left = _expr(expr.left)
right = _expr(expr.right)
if op is ast.Mod:
left['predicate'] = right
return left
if op is ast.BitOr:
return _build_union(left, right)
if op is ast.BitAnd:
return _build_intersection(left, right)
raise ValueError("Unknown expression: %r" % node)
def _convert_literals(expr):
node = type(expr)
if node is ast.List:
return [_convert_literals(e) for e in expr.elts]
if node is ast.Set:
return {_convert_literals(e) for e in expr.elts}
if node is ast.Tuple:
return tuple(_convert_literals(e) for e in expr.elts)
if node is ast.Dict:
return {_convert_literals(k): _convert_literals(v)
for k, v in zip(expr.keys, expr.values)}
if node is ast.Constant:
return expr.value
if node is ast.Name and expr.id == 'inf':
return float('inf')
if node is ast.Constant:
return expr.value
raise ValueError("Unknown literal: %r" % node)
def _parse_args(args):
return tuple(_convert_literals(e) for e in args)
def _parse_kwargs(kwargs):
return {e.arg: _convert_literals(e.value) for e in kwargs}
def _build_predicate(name, args, kwargs):
base = {
'type': 'predicate',
'name': name
}
if name == 'Properties':
return _build_properties(base, args, kwargs)
if name == 'Range':
return _build_range(base, args, kwargs)
if name == 'Choices':
return _build_choices(base, args, kwargs)
def _normalize_input_collection(args):
if len(args) == 1 and isinstance(args[0], (list, set, tuple)):
return tuple(args[0])
return args
def _build_choices(base, args, kwargs):
if 'choices' in kwargs:
args = (kwargs['choices'],)
args = _normalize_input_collection(args)
base['choices'] = list(args)
return base
def _build_range(base, args, kwargs):
inclusive_start = kwargs.get('inclusive_start', True)
inclusive_end = kwargs.get('inclusive_end', False)
start = None
end = None
if len(args) == 1:
end = args[0]
elif len(args) != 0:
start, end = args
if start == float('-inf'):
start = None
if end == float('inf'):
end = None
base['range'] = [start, end]
base['inclusive'] = [inclusive_start, inclusive_end]
return base
def _build_properties(base, args, kwargs):
exclude = kwargs.get('exclude', [])
if 'include' in kwargs:
args = (kwargs['include'],)
args = _normalize_input_collection(args)
base['include'] = list(args)
base['exclude'] = list(exclude)
return base
def _build_atomic(name):
return {
'type': 'expression',
'builtin': name in {'Str', 'Int', 'Float', 'Bool',
'List', 'Set', 'Tuple', 'Visualization',
'Metadata', 'MetadataColumn', 'Numeric',
'Categorical'},
'name': name,
'predicate': None,
'fields': []
}
def _build_union(left, right):
return _build_ident(left, right, 'union')
def _build_intersection(left, right):
return _build_ident(left, right, 'intersection')
def _build_ident(left, right, type):
members = []
if left['type'] == type:
members.extend(left['members'])
else:
members.append(left)
if right['type'] == type:
members.extend(right['members'])
else:
members.append(right)
return {
'type': type,
'members': members
}
def ast_to_type(json_ast, scope=None):
if scope is None:
scope = {}
type_ = json_ast['type']
if type_ == 'expression':
predicate = json_ast['predicate']
if predicate is not None:
predicate = ast_to_type(predicate, scope=scope)
fields = json_ast['fields']
if len(fields) > 0:
fields = [ast_to_type(f, scope=scope) for f in fields]
name = json_ast['name']
if not json_ast['builtin']:
base_template = semantic.SemanticType(name).template
elif name == 'Visualization':
return visualization.Visualization
elif name in {'List', 'Set', 'Tuple'}:
base_template = getattr(collection, name).template
else:
base_template = getattr(primitive, name).template
return grammar.TypeExp(base_template,
fields=fields, predicate=predicate)
if type_ == 'predicate':
name = json_ast['name']
if name == 'Choices':
return primitive.Choices(json_ast['choices'])
if name == 'Range':
return primitive.Range(*json_ast['range'],
inclusive_start=json_ast['inclusive'][0],
inclusive_end=json_ast['inclusive'][1])
if name == 'Properties':
return semantic.Properties(json_ast['include'],
exclude=json_ast['exclude'])
if type_ == 'union':
members = [ast_to_type(m, scope=scope) for m in json_ast['members']]
return grammar.UnionExp(members)
if type_ == 'intersection':
members = [ast_to_type(m, scope=scope) for m in json_ast['members']]
return grammar.IntersectionExp(members)
if type_ == 'variable':
var_group = json_ast['group']
if var_group not in scope:
mapping = {}
out_idx = json_ast['outputs']
for entry in json_ast['mapping']:
entry = [ast_to_type(e) for e in entry]
mapping[tuple(entry[:out_idx])] = tuple(entry[out_idx:])
scope[var_group] = list(meta.TypeMap(mapping))
return scope[var_group][json_ast['index']]
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