diff --git a/lnschema_core/models.py b/lnschema_core/models.py index 3c7d2291..833766d5 100644 --- a/lnschema_core/models.py +++ b/lnschema_core/models.py @@ -121,7 +121,7 @@ def inspect( field: str | StrField | None = None, *, mute: bool = False, - **kwargs, + organism: str | Registry | None = None, ) -> InspectResult: """Inspect if values are mappable to a field. @@ -134,6 +134,7 @@ def inspect( against the source ID or `'name'` to map against the ontologies field names. mute: Mute logging. + organism: An Organism name or record. See Also: :meth:`~lamindb.core.CanValidate.validate` @@ -162,7 +163,7 @@ def validate( field: str | StrField | None = None, *, mute: bool = False, - **kwargs, + organism: str | Registry | None = None, ) -> np.ndarray: """Validate values against existing values of a string field. @@ -206,7 +207,7 @@ def standardize( public_aware: bool = True, keep: Literal["first", "last", False] = "first", synonyms_field: str = "synonyms", - **kwargs, + organism: str | Registry | None = None, ) -> list[str] | dict[str, str]: """Maps input synonyms to standardized names. @@ -227,6 +228,7 @@ def standardize( When a field is converted into return_field, keep marks which matches to keep when multiple return_field values map to the same field value. synonyms_field: A field containing the concatenated synonyms. + organism: An Organism name or record. Returns: If `return_mapper` is `False`: a list of standardized names. Otherwise, @@ -400,7 +402,11 @@ class Registry(models.Model): @classmethod def from_values( - cls, values: ListLike, field: StrField | None = None, **kwargs + cls, + values: ListLike, + field: StrField | None = None, + organism: Registry | str | None = None, + public_source: Registry | None = None, ) -> list[Registry]: """Bulk create validated records by parsing values for an identifier (a name, an id, etc.). @@ -408,7 +414,8 @@ def from_values( values: A list of values for an identifier, e.g. `["name1", "name2"]`. field: A `Registry` field to look up, e.g., `bt.CellMarker.name`. - **kwargs: Additional conditions for creation of records, e.g., `organism="human"`. + organism: An Organism name or record. + public_source: A PublicSource record. Returns: A list of validated records. For bionty registries, also returns knowledge-coupled records. @@ -1400,7 +1407,9 @@ def from_values( # type: ignore field: FieldAttr = Feature.name, type: str | None = None, name: str | None = None, - **kwargs, + mute: bool = False, + organism: Registry | str | None = None, + public_source: Registry | None = None, ) -> FeatureSet | None: """Create feature set for validated features. @@ -1430,7 +1439,9 @@ def from_df( df: pd.DataFrame, field: FieldAttr = Feature.name, name: str | None = None, - **kwargs, + mute: bool = False, + organism: Registry | str | None = None, + public_source: Registry | None = None, ) -> FeatureSet | None: """Create feature set for validated features.""" pass