Source code for qiime2.core.type.semantic

# ----------------------------------------------------------------------------
# Copyright (c) 2016-2023, 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 types
import itertools

from qiime2.core.type.grammar import IncompleteExp, UnionExp, IntersectionExp
from qiime2.core.type.template import TypeTemplate, PredicateTemplate
from qiime2.core.type.util import is_semantic_type, is_qiime_type

    # Predicates:
    'range', 'choice', 'properties', 'arguments',
    # Primitives:
    'integer', 'int', 'string', 'str', 'metadata', 'metadatacolumn',
    'categoricalmetadatacolumn', 'numericmetadatacolumn', 'column',
    'categoricalcolumn', 'numericcolumn', 'metacol', 'categoricalmetacol',
    'numericmetacol', 'metadatacategory', 'float', 'double', 'number', 'set',
    'list', 'bag', 'multiset', 'map', 'dict', 'nominal', 'ordinal',
    'categorical', 'numeric', 'interval', 'ratio', 'continuous', 'discrete',
    'tuple', 'row', 'record',
    # Type System:
    'semantictype', 'propertymap', 'propertiesmap', 'typemap', 'typevariable',

def _validate_name(name):
    if type(name) is not str:
        raise TypeError("Names of semantic types must be strings, not %r."
                        % name)
    if name.lower() in _RESERVED_NAMES:
        raise ValueError("%r is a reserved name." % name)

[docs] def SemanticType(name, field_names=None, field_members=None, variant_of=None): """Create a new semantic type. Parameters ---------- name : str The name of the semantic type: this should match the variable to which the semantic type is assigned. field_names : str, iterable of str, optional Name(s) of the fields where member types can be placed. This makes the type a composite type, meaning that fields must be provided to produce realized semantic types. These names will define ad-hoc variant types accessible as `name`.field[`field_names` member]. field_members : mapping, optional A mapping of strings in `field_names` to one or more semantic types which are known to be members of the field (the variant type). variant_of : VariantField, iterable of VariantField, optional Define the semantic type to be a member of one or more variant types allowing it to be placed in the respective fields defined by those variant types. Returns ------- A Semantic Type There are several (private) types which may be returned, but anything returned by this factory will cause `is_semantic_type` to return True. """ _validate_name(name) variant_of = _munge_variant_of(variant_of) field_names = _munge_field_names(field_names) field_members = _munge_field_members(field_names, field_members) return SemanticTemplate(name, field_names, field_members, variant_of)
def _munge_variant_of(variant_of): if variant_of is None: variant_of = () elif isinstance(variant_of, VariantField): variant_of = (variant_of,) else: variant_of = tuple(variant_of) for variant in variant_of: if not isinstance(variant, VariantField): raise ValueError("Element %r of %r is not a variant field" " (ExampleType.field['name'])." % (variant, variant_of)) return variant_of def _munge_field_names(field_names): if field_names is None: return () if type(field_names) is str: return (field_names,) field_names = tuple(field_names) for field_name in field_names: if type(field_name) is not str: raise ValueError("Field name %r from %r is not a string." % (field_name, field_names)) if len(set(field_names)) != len(field_names): raise ValueError("Duplicate field names in %r." % field_names) return field_names def _munge_field_members(field_names, field_members): if field_names is None: return {} fixed = {k: () for k in field_names} if field_members is None: return fixed if not isinstance(field_members, raise ValueError("") fixed.update(field_members) for key, value in field_members.items(): if key not in field_names: raise ValueError("Field member key: %r is not in `field_names`" " (%r)." % (key, field_names)) if is_qiime_type(value) and is_semantic_type(value): fixed[key] = (value,) else: value = tuple(value) for v in value: if not is_semantic_type(v): raise ValueError("Field member: %r (of field %r) is not a" " semantic type." % (v, key)) fixed[key] = value return fixed class VariantField: def __init__(self, type_name, field_name, field_members): self.type_name = type_name self.field_name = field_name self.field_members = field_members def is_member(self, semantic_type): for field_member in self.field_members: if isinstance(field_member, IncompleteExp): # Pseudo-subtyping like Foo[X] <= Foo[Any]. # (IncompleteExp will never have __le__ because you # are probably doing something wrong with it (this totally # doesn't count!)) if == return True # ... it doesn't count because this is a way of restricting our # ontology and isn't really crucial. Where it matters would be # in function application where the semantics must be defined # precisely and Foo[Any] is anything but precise. else: if semantic_type <= field_member: return True return False def __repr__(self): return "%s.field[%r]" % (self.type_name, self.field_name) class SemanticTemplate(TypeTemplate): public_proxy = 'field', def __init__(self, name, field_names, field_members, variant_of): = name self.field_names = field_names self.__field = {f: VariantField(name, f, field_members[f]) for f in self.field_names} self.variant_of = variant_of @property def field(self): return types.MappingProxyType(self.__field) def __eq__(self, other): return (type(self) is type(other) and == and self.fields == other.fields and self.variant_of == other.variant_of) def __hash__(self): return (hash(type(self)) ^ hash( ^ hash(self.fields) ^ hash(self.variant_of)) def get_kind(self): return 'semantic-type' def get_name(self): return def get_field_names(self): return self.field_names def is_element_expr(self, self_expr, value): import qiime2.sdk if not isinstance(value, qiime2.sdk.Artifact): return False return value.type <= self_expr def is_element(self, value): raise NotImplementedError def validate_field(self, name, field): raise NotImplementedError def validate_fields_expr(self, self_expr, fields_expr): self.validate_field_count(len(fields_expr)) for expr, varf in zip(fields_expr, [self.field[n] for n in self.field_names]): if (expr.template is not None and hasattr(expr.template, 'is_variant')): check = expr.template.is_variant else: check = self.is_variant if not check(expr, varf): raise TypeError("%r is not a variant of %r" % (expr, varf)) @classmethod def is_variant(cls, expr, varf): if isinstance(expr, UnionExp): return all(cls.is_variant(e, varf) for e in expr.members) if isinstance(expr, IntersectionExp): return any(cls.is_variant(e, varf) for e in expr.members) return varf.is_member(expr) or varf in expr.template.variant_of def validate_predicate(self, predicate): if not isinstance(predicate, Properties): raise TypeError() def update_ast(self, ast): ast['builtin'] = False
[docs] class Properties(PredicateTemplate): def __init__(self, *include, exclude=()): if len(include) == 1 and isinstance(include[0], (list, tuple, set, frozenset)): include = tuple(include[0]) if type(exclude) is str: exclude = (exclude,) self.include = tuple(include) self.exclude = tuple(exclude) for prop in itertools.chain(self.include, self.exclude): if type(prop) is not str: raise TypeError("%r in %r is not a string." % (prop, self)) def __hash__(self): return hash(frozenset(self.include)) ^ hash(frozenset(self.exclude)) def __eq__(self, other): return (type(self) is type(other) and set(self.include) == set(other.include) and set(self.exclude) == set(other.exclude)) def __repr__(self): args = [] if self.include: args.append(', '.join(repr(s) for s in self.include)) if self.exclude: args.append("exclude=%r" % list(self.exclude)) return "%s(%s)" % (self.__class__.__name__, ', '.join(args)) def is_symbol_subtype(self, other): if type(self) is not type(other): return False return (set(other.include) <= set(self.include) and set(other.exclude) <= set(self.exclude)) def is_symbol_supertype(self, other): if type(self) is not type(other): return False return (set(other.include) >= set(self.include) and set(other.exclude) >= set(self.exclude)) def collapse_intersection(self, other): if type(self) is not type(other): return None new_include_set = set(self.include) | set(other.include) new_exclude_set = set(self.exclude) | set(other.exclude) new_include = [] new_exclude = [] for inc in itertools.chain(self.include, other.include): if inc in new_include_set: new_include.append(inc) new_include_set.remove(inc) for exc in itertools.chain(self.exclude, other.exclude): if exc in new_exclude_set: new_exclude.append(exc) new_exclude_set.remove(exc) return self.__class__(*new_include, exclude=new_exclude).template def get_kind(self): return 'semantic-type' def get_name(self): return self.__class__.__name__ def is_element(self, expr): return True # attached TypeExp checks this def get_union_membership_expr(self, self_expr): return 'predicate-' + self.get_name() def update_ast(self, ast): ast['include'] = list(self.include) ast['exclude'] = list(self.exclude)