Source code for pronto.metadata

import datetime
import functools
import typing
from typing import Dict, List, Optional, Set, Tuple

from .synonym import SynonymType
from .pv import PropertyValue
from .utils.impl import set
from .utils.meta import roundrepr, typechecked

[docs]@roundrepr @functools.total_ordering class Subset(object): """A definition of a subset in an ontology. Attributes: name (`str`): The name of the subset, as an OBO short identifier. description (`str`): A description of the subset, as defined in the metadata part of the ontology file. """ name: str description: str __slots__ = ("__weakref__", "name", "description") if typing.TYPE_CHECKING: __annotations__: Dict[str, str] @typechecked() def __init__(self, name: str, description: str): str = name self.description: str = description
[docs] def __eq__(self, other: object) -> bool: if isinstance(other, Subset): return == return False
[docs] def __lt__(self, other: object) -> bool: if not isinstance(other, Subset): return typing.cast(bool, NotImplemented) return <
[docs] def __hash__(self) -> int: return hash((Subset,
[docs]class Metadata(object): """A mapping containing metadata about the current ontology. Attributes: format_version (`str`): The OBO format version of the referenced ontology. **1.4** is the default since ``pronto`` can only parse and write OBO documents of that format version. data_version (`str` or `None`): The OBO data version of the ontology, which is then expanded to the ``versionIRI`` if translated to OWL. ontology (`str` or `None`): The identifier of the ontology, either as a short OBO identifier or as a full IRI. date (`~datetime.datetime` or `None`): The date the ontology was last modified, if any. default_namespace (`str` or `None`): The default namespace to use for entity frames lacking a ``namespace`` clause. namespace_id_rule (`str` or `None`): The production rule for identifiers in the current ontology document. *soft-deprecated, used mostly by OBO-Edit or other outdated tools*. owl_axioms (`list` of `str`): A list of OWL axioms that cannot be expressed in OBO language, serialized in OWL2 Functional syntax. saved_by (`str` or `None`): The name of the person that last saved the ontology file. auto_generated_by (`str` or `None`): The name of the software that was used to generate the file. subsetdefs (`set` of `str`): A set of ontology subsets declared in the ontology files. imports (`set` of `str`): A set of references to other ontologies that are imported by the current ontology. OBO requires all entities referenced in the file to be reachable through imports (excluding databases cross-references). synonymtypedefs (`set` of `~pronto.SynonymType`): A set of user-defined synonym types including a description and an optional scope. idspaces (`dict` of `str` to couple of `str`): A mapping between a local ID space and a global ID space, with an optional description of the mapping. remarks (`set` of `str`): A set of general comments for this file, which will be preserved by a parser/serializer as opposed to inline comments using ``!``. annotations (`set` of `PropertyValue`): A set of annotations relevant to the whole file. OBO property-values are semantically equivalent to ``owl:AnnotationProperty`` in OWL2. unreserved (`dict` of `str` to `set` of `str`): A mapping of unreserved tags to values found in the ontology header. """ format_version: Optional[str] data_version: Optional[str] ontology: Optional[str] date: Optional[datetime.datetime] default_namespace: Optional[str] namespace_id_rule: Optional[str] owl_axioms: List[str] saved_by: Optional[str] auto_generated_by: Optional[str] subsetdefs: Set[Subset] imports: Set[str] synonymtypedefs: Set[SynonymType] idspaces: Dict[str, Tuple[str, Optional[str]]] # FIXME: better typing? remarks: Set[str] annotations: Set[PropertyValue] unreserved: Dict[str, Set[str]] if typing.TYPE_CHECKING: __annotations__: Dict[str, str] def __init__( self, format_version: Optional[str] = "1.4", data_version: Optional[str] = None, ontology: Optional[str] = None, date: Optional[datetime.datetime] = None, default_namespace: Optional[str] = None, namespace_id_rule: Optional[str] = None, owl_axioms: Optional[List[str]] = None, saved_by: Optional[str] = None, auto_generated_by: Optional[str] = None, subsetdefs: Set[Subset] = None, imports: Optional[Dict[str, str]] = None, synonymtypedefs: Set[SynonymType] = None, idspaces: Dict[str, Tuple[str, Optional[str]]] = None, remarks: Set[str] = None, annotations: Set[PropertyValue] = None, **unreserved: Set[str], ): self.format_version = format_version self.data_version = data_version self.ontology = ontology = date self.default_namespace = default_namespace self.namespace_id_rule = namespace_id_rule self.owl_axioms = owl_axioms or list() self.saved_by = saved_by self.auto_generated_by = auto_generated_by self.subsetdefs = set(subsetdefs) if subsetdefs is not None else set() self.imports = set(imports) if imports is not None else set() self.synonymtypedefs = ( set(synonymtypedefs) if synonymtypedefs is not None else set() ) self.idspaces = idspaces or dict() self.remarks = remarks or set() self.annotations = annotations or set() self.unreserved = unreserved
[docs] def __bool__(self) -> bool: """Return `False` if the instance does not contain any metadata. """ return any(bool(getattr(self, x)) for x in self.__annotations__)