lamindb 1.10.1__py3-none-any.whl → 1.11.0__py3-none-any.whl

lamindb/curators/core.py

@@ -5,6 +5,7 @@
 
    Curator
    SlotsCurator
+   ComponentCurator
    CatVector
    CatLookup
    DataFrameCatManager
@@ -15,7 +16,6 @@ from __future__ import annotations
 
 import copy
 import re
-from collections.abc import Iterable
 from typing import TYPE_CHECKING, Any, Callable
 
 import lamindb_setup as ln_setup
@@ -24,7 +24,9 @@ import pandas as pd
 import pandera.pandas as pandera
 from lamin_utils import colors, logger
 from lamindb_setup.core._docs import doc_args
+from lamindb_setup.core.upath import LocalPathClasses
 
+from lamindb.base.dtypes import check_dtype
 from lamindb.base.types import FieldAttr  # noqa
 from lamindb.models import (
     Artifact,
@@ -48,6 +50,7 @@ from lamindb.models.feature import (
 from ..errors import InvalidArgument, ValidationError
 
 if TYPE_CHECKING:
+    from collections.abc import Iterable
     from typing import Any
 
     from anndata import AnnData
@@ -145,6 +148,7 @@ CAT_MANAGER_DOCSTRING = """Manage categoricals by updating registries."""
 
 SLOTS_DOCSTRING = """Access sub curators by slot."""
 
+SLOTS_DETAILS_DOCSTRING = """Uses **slots** to specify which component contains which schema. Slots are keys that identify where features are stored within composite data structures."""
 
 VALIDATE_DOCSTRING = """Validate dataset against Schema.
 
@@ -197,7 +201,21 @@ class Curator:
                 "MuData",
                 "SpatialData",
             }:
-                self._dataset = self._dataset.load(is_run_input=False)
+                # Open remote AnnData Artifacts
+                if not isinstance(self._artifact.path, LocalPathClasses):
+                    if self._artifact.otype in {
+                        "AnnData",
+                    }:
+                        try:
+                            self._dataset = self._dataset.open(mode="r")
+                        # open can raise various errors. Fall back to loading into memory if open fails
+                        except Exception as e:
+                            logger.warning(
+                                f"Unable to open remote AnnData Artifact: {e}. Falling back to loading into memory."
+                            )
+                            self._dataset = self._dataset.load(is_run_input=False)
+                else:
+                    self._dataset = self._dataset.load(is_run_input=False)
         self._schema: Schema | None = schema
         self._is_validated: bool = False
 
@@ -284,9 +302,12 @@ class Curator:
         )
 
 
+@doc_args(SLOTS_DETAILS_DOCSTRING)
 class SlotsCurator(Curator):
     """Curator for a dataset with slots.
 
+    {}
+
     Args:
         dataset: The dataset to validate & annotate.
         schema: A :class:`~lamindb.Schema` object that defines the validation constraints.
@@ -298,7 +319,7 @@ class SlotsCurator(Curator):
         schema: Schema,
     ) -> None:
         super().__init__(dataset=dataset, schema=schema)
-        self._slots: dict[str, DataFrameCurator] = {}
+        self._slots: dict[str, ComponentCurator] = {}
 
         # used for multimodal data structures (not AnnData)
         # in form of {table/modality_key: var_field}
@@ -308,7 +329,7 @@ class SlotsCurator(Curator):
 
     @property
     @doc_args(SLOTS_DOCSTRING)
-    def slots(self) -> dict[str, DataFrameCurator]:
+    def slots(self) -> dict[str, ComponentCurator]:
         """{}"""  # noqa: D415
         return self._slots
 
@@ -336,6 +357,10 @@ class SlotsCurator(Curator):
 
         if self._artifact is None:
             type_mapping = [
+                (
+                    lambda dataset: isinstance(dataset, pd.DataFrame),
+                    Artifact.from_dataframe,
+                ),
                 (
                     lambda dataset: data_is_scversedatastructure(dataset, "AnnData"),
                     Artifact.from_anndata,
@@ -364,12 +389,13 @@ class SlotsCurator(Curator):
                     )
                     break
 
-            self._artifact.schema = self._schema
-            self._artifact.save()
         cat_vectors = {}
         for curator in self._slots.values():
             for key, cat_vector in curator.cat._cat_vectors.items():
                 cat_vectors[key] = cat_vector
+
+        self._artifact.schema = self._schema
+        self._artifact.save()
         return annotate_artifact(  # type: ignore
             self._artifact,
             curator=self,
@@ -377,92 +403,21 @@ class SlotsCurator(Curator):
         )
 
 
-def is_list_of_type(value, expected_type):
-    """Helper function to check if a value is either of expected_type or a list of that type, or a mix of both in a nested structure."""
-    if isinstance(value, Iterable) and not isinstance(value, (str, bytes)):
-        # handle nested lists recursively
-        return all(is_list_of_type(item, expected_type) for item in value)
-    return isinstance(value, expected_type)
-
-
-def check_dtype(expected_type) -> Callable:
-    """Creates a check function for Pandera that validates a column's dtype.
-
-    Supports both standard dtype checking and mixed list/single values for the same type.
-    For example, a column with expected_type 'float' would also accept a mix of float values and lists of floats.
-
-    Args:
-        expected_type: String identifier for the expected type ('int', 'float', 'num', 'str')
-
-    Returns:
-        A function that checks if a series has the expected dtype or contains mixed types
-    """
-
-    def check_function(series):
-        # first check if the series is entirely of the expected dtype (fast path)
-        if expected_type == "int" and pd.api.types.is_integer_dtype(series.dtype):
-            return True
-        elif expected_type == "float" and pd.api.types.is_float_dtype(series.dtype):
-            return True
-        elif expected_type == "num" and pd.api.types.is_numeric_dtype(series.dtype):
-            return True
-        elif expected_type == "str" and pd.api.types.is_string_dtype(series.dtype):
-            return True
-        elif expected_type == "path" and pd.api.types.is_string_dtype(series.dtype):
-            return True
-
-        # if we're here, it might be a mixed column with object dtype
-        # need to check each value individually
-        if series.dtype == "object" and expected_type.startswith("list"):
-            expected_type_member = expected_type.replace("list[", "").removesuffix("]")
-            if expected_type_member == "int":
-                return series.apply(lambda x: is_list_of_type(x, int)).all()
-            elif expected_type_member == "float":
-                return series.apply(lambda x: is_list_of_type(x, float)).all()
-            elif expected_type_member == "num":
-                # for numeric, accept either int or float
-                return series.apply(lambda x: is_list_of_type(x, (int, float))).all()
-            elif (
-                expected_type_member == "str"
-                or expected_type_member == "path"
-                or expected_type_member.startswith("cat[")
-            ):
-                return series.apply(lambda x: is_list_of_type(x, str)).all()
-
-        # if we get here, the validation failed
-        return False
-
-    return check_function
-
-
-# this is also currently used as DictCurator
-class DataFrameCurator(Curator):
-    # the example in the docstring is tested in test_curators_quickstart_example
+# This is also currently used as DictCurator by flattening dictionaries into wide DataFrames.
+# Such an approach was never intended and there is room for a DictCurator in the future.
+# For more context, read https://laminlabs.slack.com/archives/C07DB677JF6/p1753994077716099 and
+# https://www.notion.so/laminlabs/Add-a-DictCurator-2422aeaa55e180b9a513f91d13970836
+class ComponentCurator(Curator):
     """Curator for `DataFrame`.
 
+    Provides all key functionality to validate Pandas DataFrames.
+    This class is not user facing unlike :class:`~lamindb.curators.DataFrameCurator` which extends this
+    class with functionality to validate the `attrs` slot.
+
     Args:
         dataset: The DataFrame-like object to validate & annotate.
         schema: A :class:`~lamindb.Schema` object that defines the validation constraints.
         slot: Indicate the slot in a composite curator for a composite data structure.
-
-    Example:
-
-        For simple example using a flexible schema, see :meth:`~lamindb.Artifact.from_df`.
-
-        Here is an example that enforces a minimal set of columns in the dataframe.
-
-        .. literalinclude:: scripts/curate_dataframe_minimal_errors.py
-            :language: python
-
-        Under-the-hood, this used the following schema.
-
-        .. literalinclude:: scripts/define_mini_immuno_schema_flexible.py
-            :language: python
-
-        Valid features & labels were defined as:
-
-        .. literalinclude:: scripts/define_mini_immuno_features_labels.py
-            :language: python
     """
 
     def __init__(
@@ -478,18 +433,18 @@ class DataFrameCurator(Curator):
         feature_ids: set[int] = set()
 
         if schema.flexible:
-            features += Feature.filter(name__in=self._dataset.keys()).list()
+            features += Feature.filter(name__in=self._dataset.keys()).to_list()
             feature_ids = {feature.id for feature in features}
 
         if schema.n > 0:
             if schema._index_feature_uid is not None:
                 schema_features = [
                     feature
-                    for feature in schema.members.list()
+                    for feature in schema.members.to_list()
                     if feature.uid != schema._index_feature_uid  # type: ignore
                 ]
             else:
-                schema_features = schema.members.list()  # type: ignore
+                schema_features = schema.members.to_list()  # type: ignore
             if feature_ids:
                 features.extend(
                     feature
@@ -580,9 +535,13 @@ class DataFrameCurator(Curator):
         # in the DataFrameCatManager, we use the
         # actual columns of the dataset, not the pandera columns
         # the pandera columns might have additional optional columns
+        if schema.itype == "Composite":
+            columns_field = Feature.name
+        else:
+            columns_field = parse_cat_dtype(schema.itype, is_itype=True)["field"]
         self._cat_manager = DataFrameCatManager(
             self._dataset,
-            columns_field=parse_cat_dtype(schema.itype, is_itype=True)["field"],
+            columns_field=columns_field,
             categoricals=categoricals,
             index=schema.index,
             slot=slot,
@@ -601,6 +560,11 @@ class DataFrameCurator(Curator):
         - Adds missing columns for features
         - Fills missing values for features with default values
         """
+        if self._artifact is not None:
+            raise RuntimeError(
+                "Cannot mutate the dataset when an artifact is passed! Please load the dataset into memory using `dataset.load()` and pass it to a curator."
+            )
+
         for feature in self._schema.members:
             if feature.name not in self._dataset.columns:
                 if feature.default_value is not None or feature.nullable:
@@ -679,35 +643,262 @@ class DataFrameCurator(Curator):
         if not self._is_validated:
             self.validate()  # raises ValidationError if doesn't validate
         if self._artifact is None:
-            self._artifact = Artifact.from_df(
+            self._artifact = Artifact.from_dataframe(
                 self._dataset,
                 key=key,
                 description=description,
                 revises=revises,
                 run=run,
-                format=".csv" if key.endswith(".csv") else None,
+                format=".csv" if key is not None and key.endswith(".csv") else None,
             )
-            self._artifact.schema = self._schema
-            self._artifact.save()
+
+        self._artifact.schema = self._schema
+        self._artifact.save()
         return annotate_artifact(  # type: ignore
             self._artifact,
             cat_vectors=self.cat._cat_vectors,
         )
 
 
+class DataFrameCurator(SlotsCurator):
+    # the example in the docstring is tested in test_curators_quickstart_example
+    """Curator for `DataFrame`.
+
+    Args:
+        dataset: The DataFrame-like object to validate & annotate.
+        schema: A :class:`~lamindb.Schema` object that defines the validation constraints.
+        slot: Indicate the slot in a composite curator for a composite data structure.
+
+    Examples:
+
+        For a simple example using a flexible schema, see :meth:`~lamindb.Artifact.from_dataframe`.
+
+        Here is an example that enforces a minimal set of columns in the dataframe.
+
+        .. literalinclude:: scripts/curate_dataframe_minimal_errors.py
+            :language: python
+
+        Under-the-hood, this used the following schema.
+
+        .. literalinclude:: scripts/define_mini_immuno_schema_flexible.py
+            :language: python
+
+        Valid features & labels were defined as:
+
+        .. literalinclude:: scripts/define_mini_immuno_features_labels.py
+            :language: python
+
+        It is also possible to curate the `attrs` slot.
+
+        .. literalinclude:: scripts/curate_dataframe_attrs.py
+            :language: python
+    """
+
+    def __init__(
+        self,
+        dataset: pd.DataFrame | Artifact,
+        schema: Schema,
+        slot: str | None = None,
+    ) -> None:
+        super().__init__(dataset=dataset, schema=schema)
+
+        # Create atomic curator for features only
+        if len(self._schema.features.all()) > 0:
+            self._atomic_curator = ComponentCurator(
+                dataset=dataset,
+                schema=schema,
+                slot=slot,
+            )
+
+        # Handle (nested) attrs
+        if slot is None and schema.slots:
+            for slot_name, slot_schema in schema.slots.items():
+                if slot_name.startswith("attrs"):
+                    path_parts = slot_name.split(":")
+                    attrs_dict = getattr(self._dataset, "attrs", None)
+                    if attrs_dict is not None:
+                        if len(path_parts) == 1:
+                            data = attrs_dict
+                        else:
+                            deeper_keys = path_parts[1:]
+                            data = _resolve_schema_slot_path(
+                                attrs_dict, deeper_keys, slot_name, "attrs"
+                            )
+                        df = pd.DataFrame([data])
+                        self._slots[slot_name] = ComponentCurator(
+                            df, slot_schema, slot=slot_name
+                        )
+                else:
+                    raise ValueError(
+                        f"Slot '{slot_name}' is not supported for DataFrameCurator. Must be 'attrs'."
+                    )
+
+    @property
+    def cat(self) -> DataFrameCatManager:
+        """Manage categoricals by updating registries."""
+        if hasattr(self, "_atomic_curator"):
+            return self._atomic_curator.cat
+        raise AttributeError("cat is only available for slots DataFrameCurator")
+
+    def standardize(self) -> None:
+        """Standardize the dataset.
+
+        - Adds missing columns for features
+        - Fills missing values for features with default values
+        """
+        if hasattr(self, "_atomic_curator"):
+            self._atomic_curator.standardize()
+        else:
+            for slot_curator in self._slots.values():
+                slot_curator.standardize()
+
+    @doc_args(VALIDATE_DOCSTRING)
+    def validate(self) -> None:
+        """{}."""
+        if hasattr(self, "_atomic_curator"):
+            self._atomic_curator.validate()
+            self._is_validated = self._atomic_curator._is_validated
+        if self._schema.itype == "Composite":
+            super().validate()
+
+    @doc_args(SAVE_ARTIFACT_DOCSTRING)
+    def save_artifact(
+        self, *, key=None, description=None, revises=None, run=None
+    ) -> Artifact:
+        """{}."""
+        if not self._is_validated:
+            self.validate()
+
+        if self._slots:
+            self._slots["columns"] = self._atomic_curator
+            try:
+                return super().save_artifact(
+                    key=key, description=description, revises=revises, run=run
+                )
+            finally:
+                del self._slots["columns"]
+        else:
+            return self._atomic_curator.save_artifact(
+                key=key, description=description, revises=revises, run=run
+            )
+
+
+def _resolve_schema_slot_path(
+    target_dict: dict[str, Any], slot_keys: Iterable[str], slot: str, base_path: str
+) -> Any:
+    """Resolve a schema slot path by traversing nested dictionary keys.
+
+    Args:
+        target_dict: Root dictionary to traverse
+        slot_keys: Sequence of keys defining the paths to traverse
+        slot_name: Schema slot identifier for error context
+        base_path: Base path string for error context
+
+    Returns:
+        The value at the resolved path
+    """
+    current = target_dict
+
+    for key in slot_keys:
+        base_path += f"['{key}']"
+        try:
+            current = current[key]
+        except KeyError:
+            available = (
+                list(current.keys()) if isinstance(current, dict) else "not a dict"
+            )
+            raise InvalidArgument(
+                f"Schema slot '{slot}' requires keys {base_path} but key '{key}' "
+                f"not found. Available keys at this level: {available}"
+            ) from None
+
+    return current
+
+
+def _handle_dict_slots(
+    dataset: ScverseDataStructures, slot: str
+) -> tuple[pd.DataFrame | None, str | None, str | None]:
+    """Handle dict-based slot paths (uns/attrs standalone or of modalities) for all ScverseCurators.
+
+    Supports two patterns:
+        - Direct dict access: "uns", "attrs", "uns:key1:key2", "attrs:key"
+        - Modality dict access: "modality:uns"
+
+    Args:
+        dataset: The scverse datastructure object
+        slot: The slot path string to parse like 'uns:path:to'.
+
+    Returns:
+        tuple: (dataframe, modality_key, remaining_slot_path)
+            - dataframe: Single-row DataFrame containing the resolved data
+            - modality_key: Modality identifier if slot targets modality dict, else None
+            - remaining_slot_path: The dict attribute and nested keys as string
+    """
+    path_parts = slot.split(":")
+
+    # Handle direct dict slots: "uns", "attrs", "uns:key1:key2:..."
+    if len(path_parts) >= 1 and path_parts[0] in ["uns", "attrs"]:
+        dict_attr = getattr(dataset, path_parts[0], None)
+        if dict_attr is not None:
+            if len(path_parts) == 1:
+                return pd.DataFrame([dict_attr]), None, path_parts[0]
+
+            deeper_keys = path_parts[1:]
+            data = _resolve_schema_slot_path(
+                dict_attr, deeper_keys, slot, path_parts[0]
+            )
+            return pd.DataFrame([data]), None, ":".join(path_parts[1:])
+
+    # Handle modality dict slots: "modality:uns", "modality:uns:key1:key2"
+    elif len(path_parts) >= 2 and path_parts[1] in ["uns", "attrs"]:
+        modality, dict_name = path_parts[0], path_parts[1]
+        try:
+            modality_dataset = dataset[modality]
+            dict_attr = getattr(modality_dataset, dict_name, None)
+            if dict_attr is not None:
+                if len(path_parts) == 2:
+                    return pd.DataFrame([dict_attr]), modality, dict_name
+
+                deeper_keys = path_parts[2:]
+                data = _resolve_schema_slot_path(
+                    dict_attr, deeper_keys, slot, f"{modality}.{dict_name}"
+                )
+                return pd.DataFrame([data]), modality, ":".join(path_parts[1:])
+        except (KeyError, AttributeError):
+            pass
+    else:
+        raise InvalidArgument(
+            f"Invalid dict slot pattern '{slot}'. Expected formats: "
+            f"'uns', 'attrs', 'uns:key', 'attrs:key', 'modality:uns'"
+        )
+
+    return None, None, None
+
+
+@doc_args(SLOTS_DETAILS_DOCSTRING)
 class AnnDataCurator(SlotsCurator):
     """Curator for `AnnData`.
 
+    {}
+
     Args:
         dataset: The AnnData-like object to validate & annotate.
         schema: A :class:`~lamindb.Schema` object that defines the validation constraints.
 
-    Example:
+    Examples:
+
+        Curate Ensembl gene IDs and valid features in obs:
 
         .. literalinclude:: scripts/curate_anndata_flexible.py
             :language: python
             :caption: curate_anndata_flexible.py
 
+        Curate `uns` dictionary:
+
+        .. literalinclude:: scripts/curate_anndata_uns.py
+            :language: python
+            :caption: curate_anndata_uns.py
+
     See Also:
         :meth:`~lamindb.Artifact.from_anndata`.
     """
@@ -720,34 +911,37 @@ class AnnDataCurator(SlotsCurator):
         super().__init__(dataset=dataset, schema=schema)
         if not data_is_scversedatastructure(self._dataset, "AnnData"):
             raise InvalidArgument("dataset must be AnnData-like.")
-        if schema.otype != "AnnData":
+        if schema.otype and schema.otype != "AnnData":
             raise InvalidArgument("Schema otype must be 'AnnData'.")
-        self._slots = {
-            slot: DataFrameCurator(
-                (
+
+        for slot, slot_schema in schema.slots.items():
+            if slot not in {"var", "var.T", "obs"} and not slot.startswith("uns"):
+                raise ValueError(
+                    f"AnnDataCurator currently only supports the slots 'var', 'var.T', 'obs', and 'uns', not {slot}"
+                )
+            if slot.startswith("uns"):
+                df, _, _ = _handle_dict_slots(self._dataset, slot)
+            elif slot in {"obs", "var", "var.T"}:
+                df = (
                     getattr(self._dataset, slot.strip(".T")).T
                     if slot == "var.T"
                     or (
-                        # backward compat
                         slot == "var"
                         and schema.slots["var"].itype not in {None, "Feature"}
                     )
                     else getattr(self._dataset, slot)
-                ),
-                slot_schema,
-                slot=slot,
-            )
-            for slot, slot_schema in schema.slots.items()
-            if slot in {"obs", "var", "var.T", "uns"}
-        }
-        if "var" in self._slots and schema.slots["var"].itype not in {None, "Feature"}:
-            logger.warning(
-                "auto-transposed `var` for backward compat, please indicate transposition in the schema definition by calling out `.T`: slots={'var.T': itype=bt.Gene.ensembl_gene_id}"
-            )
-            self._slots["var"].cat._cat_vectors["var_index"] = self._slots[
-                "var"
-            ].cat._cat_vectors.pop("columns")
-            self._slots["var"].cat._cat_vectors["var_index"]._key = "var_index"
+                )
+            self._slots[slot] = ComponentCurator(df, slot_schema, slot=slot)
+
+            # Handle var index naming for backward compat
+            if slot == "var" and schema.slots["var"].itype not in {None, "Feature"}:
+                logger.warning(
+                    "auto-transposed `var` for backward compat, please indicate transposition in the schema definition by calling out `.T`: slots={'var.T': itype=bt.Gene.ensembl_gene_id}"
+                )
+                self._slots["var"].cat._cat_vectors["var_index"] = self._slots[
+                    "var"
+                ].cat._cat_vectors.pop("columns")
+                self._slots["var"].cat._cat_vectors["var_index"]._key = "var_index"
 
 
 def _assign_var_fields_categoricals_multimodal(
@@ -757,11 +951,10 @@ def _assign_var_fields_categoricals_multimodal(
     slot_schema: Schema,
     var_fields: dict[str, FieldAttr],
     cat_vectors: dict[str, dict[str, CatVector]],
-    slots: dict[str, DataFrameCurator],
+    slots: dict[str, ComponentCurator],
 ) -> None:
     """Assigns var_fields and categoricals for multimodal data curators."""
     if modality is not None:
-        # Makes sure that all tables are present
         var_fields[modality] = None
         cat_vectors[modality] = {}
 
@@ -782,15 +975,17 @@ def _assign_var_fields_categoricals_multimodal(
             cat_vectors[modality] = obs_fields
 
 
+@doc_args(SLOTS_DETAILS_DOCSTRING)
 class MuDataCurator(SlotsCurator):
     """Curator for `MuData`.
 
+    {}
+
     Args:
         dataset: The MuData-like object to validate & annotate.
         schema: A :class:`~lamindb.Schema` object that defines the validation constraints.
 
     Example:
-
         .. literalinclude:: scripts/curate_mudata.py
             :language: python
             :caption: curate_mudata.py
@@ -811,12 +1006,32 @@ class MuDataCurator(SlotsCurator):
             raise InvalidArgument("Schema otype must be 'MuData'.")
 
         for slot, slot_schema in schema.slots.items():
-            if ":" in slot:
-                modality, modality_slot = slot.split(":")
-                schema_dataset = self._dataset.__getitem__(modality)
+            # Handle slots: "mdata.uns", "modality:uns"
+            if "uns" in slot:
+                df, modality, modality_slot = _handle_dict_slots(self._dataset, slot)
             else:
-                modality, modality_slot = None, slot
-                schema_dataset = self._dataset
+                # Handle slots: "modality:obs", "modality:var"
+                parts = slot.split(":")
+                if len(parts) == 2:
+                    modality, modality_slot = parts
+                    try:
+                        schema_dataset = self._dataset[modality]
+                        df = getattr(schema_dataset, modality_slot.rstrip(".T"))
+                    except KeyError:
+                        raise InvalidArgument(
+                            f"Modality '{modality}' not found in MuData"
+                        ) from None
+                    except AttributeError:
+                        raise InvalidArgument(
+                            f"Attribute '{modality_slot}' not found on modality '{modality}'"
+                        ) from None
+                else:
+                    # Handle slots: "mdata:obs", "mdata:var" (uns is a dictionary and gets handled above)
+                    modality, modality_slot = None, slot
+                    schema_dataset = self._dataset
+                    df = getattr(schema_dataset, modality_slot.rstrip(".T"))
+
+            # Transpose var if necessary
             if modality_slot == "var" and schema.slots[slot].itype not in {
                 None,
                 "Feature",
@@ -824,19 +1039,12 @@ class MuDataCurator(SlotsCurator):
                 logger.warning(
                     "auto-transposed `var` for backward compat, please indicate transposition in the schema definition by calling out `.T`: slots={'var.T': itype=bt.Gene.ensembl_gene_id}"
                 )
-            self._slots[slot] = DataFrameCurator(
-                (
-                    getattr(schema_dataset, modality_slot.rstrip(".T")).T
-                    if modality_slot == "var.T"
-                    or (
-                        # backward compat
-                        modality_slot == "var"
-                        and schema.slots[slot].itype not in {None, "Feature"}
-                    )
-                    else getattr(schema_dataset, modality_slot)
-                ),
-                slot_schema,
-            )
+                df = df.T
+            elif modality_slot == "var.T":
+                df = df.T
+
+            self._slots[slot] = ComponentCurator(df, slot_schema, slot=slot)
+
             _assign_var_fields_categoricals_multimodal(
                 modality=modality,
                 slot_type=modality_slot,
@@ -846,18 +1054,21 @@ class MuDataCurator(SlotsCurator):
                 cat_vectors=self._cat_vectors,
                 slots=self._slots,
             )
+
         self._columns_field = self._var_fields
 
 
+@doc_args(SLOTS_DETAILS_DOCSTRING)
 class SpatialDataCurator(SlotsCurator):
     """Curator for `SpatialData`.
 
+    {}
+
     Args:
         dataset: The SpatialData-like object to validate & annotate.
         schema: A :class:`~lamindb.Schema` object that defines the validation constraints.
 
     Example:
-
         .. literalinclude:: scripts/curate_spatialdata.py
             :language: python
             :caption: curate_spatialdata.py
@@ -878,69 +1089,75 @@ class SpatialDataCurator(SlotsCurator):
             raise InvalidArgument("Schema otype must be 'SpatialData'.")
 
         for slot, slot_schema in schema.slots.items():
-            split_result = slot.split(":")
-            if (len(split_result) == 2 and split_result[0] == "table") or (
-                len(split_result) == 3 and split_result[0] == "tables"
-            ):
-                if len(split_result) == 2:
-                    table_key, sub_slot = split_result
-                    logger.warning(
-                        f"please prefix slot {slot} with 'tables:' going forward"
-                    )
+            # Handle slots: "sdata:attrs"
+            if slot.startswith("attrs"):
+                df, table_key, table_slot = _handle_dict_slots(self._dataset, slot)
+            else:
+                parts = slot.split(":")
+                # Handle slots: "tables:table_key:obs", "tables:table_key:var"
+                if len(parts) == 3 and parts[0] == "tables":
+                    table_key, table_slot = parts[1], parts[2]
+                    try:
+                        slot_object = self._dataset.tables[table_key]
+                        df = getattr(slot_object, table_slot.rstrip(".T"))
+                    except KeyError:
+                        raise InvalidArgument(
+                            f"Table '{table_key}' not found in sdata.tables"
+                        ) from None
+                    except AttributeError:
+                        raise InvalidArgument(
+                            f"Attribute '{table_slot}' not found on table '{table_key}'"
+                        ) from None
                 else:
-                    table_key, sub_slot = split_result[1], split_result[2]
-                slot_object = self._dataset.tables.__getitem__(table_key)
-                if sub_slot == "var" and schema.slots[slot].itype not in {
-                    None,
-                    "Feature",
-                }:
-                    logger.warning(
-                        "auto-transposed `var` for backward compat, please indicate transposition in the schema definition by calling out `.T`: slots={'var.T': itype=bt.Gene.ensembl_gene_id}"
-                    )
-                data_object = (
-                    getattr(slot_object, sub_slot.rstrip(".T")).T
-                    if sub_slot == "var.T"
-                    or (
-                        # backward compat
-                        sub_slot == "var"
-                        and schema.slots[slot].itype not in {None, "Feature"}
-                    )
-                    else getattr(slot_object, sub_slot)
-                )
-            elif len(split_result) == 1 or (
-                len(split_result) > 1 and split_result[0] == "attrs"
-            ):
-                table_key = None
-                if len(split_result) == 1:
-                    if split_result[0] != "attrs":
+                    # Handle legacy single keys for backward compatibility
+                    if len(parts) == 1 and parts[0] != "attrs":
                         logger.warning(
                             f"please prefix slot {slot} with 'attrs:' going forward"
                         )
-                        sub_slot = slot
-                        data_object = self._dataset.attrs[slot]
+                        try:
+                            df = pd.DataFrame([self._dataset.attrs[slot]])
+                            table_key = None
+                            table_slot = slot
+                        except KeyError:
+                            raise InvalidArgument(
+                                f"Slot '{slot}' not found in sdata.attrs"
+                            ) from None
                     else:
-                        sub_slot = "attrs"
-                        data_object = self._dataset.attrs
-                elif len(split_result) == 2:
-                    sub_slot = split_result[1]
-                    data_object = self._dataset.attrs[split_result[1]]
-                data_object = pd.DataFrame([data_object])
-            self._slots[slot] = DataFrameCurator(data_object, slot_schema, slot)
+                        raise InvalidArgument(f"Unrecognized slot format: {slot}")
+
+            # Handle var transposition logic
+            if table_slot == "var" and schema.slots[slot].itype not in {
+                None,
+                "Feature",
+            }:
+                logger.warning(
+                    "auto-transposed `var` for backward compat, please indicate transposition in the schema definition by calling out `.T`: slots={'var.T': itype=bt.Gene.ensembl_gene_id}"
+                )
+                df = df.T
+            elif table_slot == "var.T":
+                df = df.T
+
+            self._slots[slot] = ComponentCurator(df, slot_schema, slot)
+
             _assign_var_fields_categoricals_multimodal(
                 modality=table_key,
-                slot_type=sub_slot,
+                slot_type=table_slot,
                 slot=slot,
                 slot_schema=slot_schema,
                 var_fields=self._var_fields,
                 cat_vectors=self._cat_vectors,
                 slots=self._slots,
             )
+
         self._columns_field = self._var_fields
 
 
+@doc_args(SLOTS_DETAILS_DOCSTRING)
 class TiledbsomaExperimentCurator(SlotsCurator):
     """Curator for `tiledbsoma.Experiment`.
 
+    {}
+
     Args:
         dataset: The `tiledbsoma.Experiment` object.
         schema: A :class:`~lamindb.Schema` object that defines the validation constraints.
@@ -977,7 +1194,7 @@ class TiledbsomaExperimentCurator(SlotsCurator):
                     .drop("soma_joinid", axis=1, errors="ignore")
                 )
 
-                self._slots[slot] = DataFrameCurator(
+                self._slots[slot] = ComponentCurator(
                     (schema_dataset.T if modality_slot == "var.T" else schema_dataset),
                     slot_schema,
                 )
@@ -990,7 +1207,7 @@ class TiledbsomaExperimentCurator(SlotsCurator):
                     .to_pandas()
                     .drop(["soma_joinid", "obs_id"], axis=1, errors="ignore")
                 )
-                self._slots[slot] = DataFrameCurator(
+                self._slots[slot] = ComponentCurator(
                     schema_dataset,
                     slot_schema,
                 )
@@ -1040,9 +1257,12 @@ class CatVector:
         self._maximal_set = maximal_set
 
         self._all_filters = {"source": self._source, "organism": self._organism}
+
         if self._subtype_str and "=" in self._subtype_str:
             self._all_filters.update(
-                resolve_relation_filters(parse_filter_string(self._subtype_str), self)  # type: ignore
+                resolve_relation_filters(
+                    parse_filter_string(self._subtype_str), self._field.field.model
+                )  # type: ignore
             )
 
         if hasattr(field.field.model, "_name_field"):
@@ -1241,7 +1461,7 @@ class CatVector:
             type_record = registry.get(name=self._subtype_str)
         if df is not None and registry == Feature:
             nonval_columns = Feature.inspect(df.columns, mute=True).non_validated
-            non_validated_records = Feature.from_df(df.loc[:, nonval_columns])
+            non_validated_records = Feature.from_dataframe(df.loc[:, nonval_columns])
         else:
             if (
                 self._organism
@@ -1343,7 +1563,7 @@ class CatVector:
                     warning_message += "\n    for remaining terms:\n"
                 warning_message += f"    → fix typos, remove non-existent values, or save terms via: {colors.cyan(non_validated_hint_print)}"
                 if self._subtype_query_set is not None:
-                    warning_message += f"\n    → a valid label for subtype '{self._subtype_str}' has to be one of {self._subtype_query_set.list('name')}"
+                    warning_message += f"\n    → a valid label for subtype '{self._subtype_str}' has to be one of {self._subtype_query_set.to_list('name')}"
             logger.info(f'mapping "{self._key}" on {colors.italic(model_field)}')
             logger.warning(warning_message)
             if self._cat_manager is not None:
@@ -1493,6 +1713,30 @@ class DataFrameCatManager:
         """The categorical features."""
         return self._categoricals
 
+    def __repr__(self) -> str:
+        cls_name = colors.green(self.__class__.__name__)
+
+        status_str = (
+            f"{colors.green('validated')}"
+            if self._is_validated
+            else f"{colors.yellow('unvalidated')}"
+        )
+
+        info_parts = []
+
+        cat_count = len(self._categoricals)
+        if cat_count > 0:
+            info_parts.append(f"categorical_features={cat_count}")
+
+        if self._slot:
+            info_parts.append(f"slot: {colors.italic(self._slot)}")
+
+        info_str = ", ".join(info_parts)
+        if info_str:
+            return f"{cls_name}({info_str}, {status_str})"
+        else:
+            return f"{cls_name}({status_str})"
+
     def lookup(self, public: bool = False) -> CatLookup:
         """Lookup categories.
 
@@ -1537,7 +1781,9 @@ class DataFrameCatManager:
             key: The key referencing the column in the DataFrame to standardize.
         """
         if self._artifact is not None:
-            raise RuntimeError("can't mutate the dataset when an artifact is passed!")
+            raise RuntimeError(
+                "Cannot mutate the dataset when an artifact is passed! Please load the dataset into memory using `dataset.load()` and pass it to a curator."
+            )
 
         if key == "all":
             logger.warning(
@@ -1610,7 +1856,7 @@ def get_organism_kwargs(
 def annotate_artifact(
     artifact: Artifact,
     *,
-    curator: AnnDataCurator | SlotsCurator | None = None,
+    curator: SlotsCurator | None = None,
     cat_vectors: dict[str, CatVector] | None = None,
 ) -> Artifact:
     from .. import settings
@@ -1643,7 +1889,9 @@ def annotate_artifact(
         )
 
     # annotate with inferred schemas aka feature sets
-    if artifact.otype == "DataFrame":
+    if (
+        artifact.otype == "DataFrame" and getattr(curator, "_schema", None) is None
+    ):  # Prevent overwriting user-defined schemas that contain slots
         features = cat_vectors["columns"].records
         if features is not None:
             index_feature = artifact.schema.index
@@ -1663,7 +1911,11 @@ def annotate_artifact(
                 logger.important(
                     f"not annotating with {len(features)} features as it exceeds {settings.annotation.n_max_records} (ln.settings.annotation.n_max_records)"
                 )
-                itype = parse_cat_dtype(artifact.schema.itype, is_itype=True)["field"]
+                itype = (
+                    Feature.name
+                    if artifact.schema.itype == "Composite"
+                    else parse_cat_dtype(artifact.schema.itype, is_itype=True)["field"]
+                )
                 feature_set = Schema(itype=itype, n=len(features))
             artifact.feature_sets.add(
                 feature_set.save(), through_defaults={"slot": "columns"}
@@ -1698,9 +1950,13 @@ def annotate_artifact(
                 logger.important(
                     f"not annotating with {len(features)} features for slot {slot} as it exceeds {settings.annotation.n_max_records} (ln.settings.annotation.n_max_records)"
                 )
-                itype = parse_cat_dtype(
-                    artifact.schema.slots[slot].itype, is_itype=True
-                )["field"]
+                itype = (
+                    Feature.name
+                    if artifact.schema.slots[slot].itype == "Composite"
+                    else parse_cat_dtype(
+                        artifact.schema.slots[slot].itype, is_itype=True
+                    )["field"]
+                )
                 feature_set = Schema(itype=itype, n=len(features))
             artifact.feature_sets.add(
                 feature_set.save(), through_defaults={"slot": slot}