lamindb 1.5.2__py3-none-any.whl → 1.6a2__py3-none-any.whl

lamindb/curators/_legacy.py

@@ -11,11 +11,7 @@ from lamindb_setup.core import deprecated
 from lamindb_setup.core.upath import UPath
 
 from lamindb.core._compat import is_package_installed
-from lamindb.models.artifact import (
-    data_is_anndata,
-    data_is_mudata,
-    data_is_spatialdata,
-)
+from lamindb.models.artifact import data_is_scversedatastructure
 
 from ..errors import InvalidArgument
 
@@ -24,12 +20,12 @@ if TYPE_CHECKING:
     from mudata import MuData
     from spatialdata import SpatialData
 
-    from lamindb.models import Record
+    from lamindb.models import SQLRecord
 from lamindb.base.types import FieldAttr  # noqa
 from lamindb.models import (
     Artifact,
     Feature,
-    Record,
+    SQLRecord,
     Run,
     Schema,
 )
@@ -153,7 +149,7 @@ class CatManager:
                     revises=revises,
                     run=run,
                 )
-            elif data_is_mudata(self._dataset):
+            elif data_is_scversedatastructure(self._dataset, "MuData"):
                 artifact = Artifact.from_mudata(
                     self._dataset,
                     key=key,
@@ -161,7 +157,7 @@ class CatManager:
                     revises=revises,
                     run=run,
                 )
-            elif data_is_spatialdata(self._dataset):
+            elif data_is_scversedatastructure(self._dataset, "SpatialData"):
                 artifact = Artifact.from_spatialdata(
                     self._dataset,
                     key=key,
@@ -192,7 +188,7 @@ class DataFrameCatManager(CatManager):
         columns_field: FieldAttr = Feature.name,
         columns_names: Iterable[str] | None = None,
         categoricals: dict[str, FieldAttr] | None = None,
-        sources: dict[str, Record] | None = None,
+        sources: dict[str, SQLRecord] | None = None,
         index: Feature | None = None,
     ) -> None:
         self._non_validated = None
@@ -331,14 +327,14 @@ class AnnDataCatManager(CatManager):
         var_index: FieldAttr | None = None,
         categoricals: dict[str, FieldAttr] | None = None,
         obs_columns: FieldAttr = Feature.name,
-        sources: dict[str, Record] | None = None,
+        sources: dict[str, SQLRecord] | None = None,
     ) -> None:
         if isinstance(var_index, str):
             raise TypeError(
                 "var_index parameter has to be a field, e.g. Gene.ensembl_gene_id"
             )
 
-        if not data_is_anndata(data):
+        if not data_is_scversedatastructure(data, "AnnData"):
             raise TypeError("data has to be an AnnData object")
 
         if "symbol" in str(var_index):
@@ -473,7 +469,7 @@ class MuDataCatManager(CatManager):
         mdata: MuData | Artifact,
         var_index: dict[str, FieldAttr] | None = None,
         categoricals: dict[str, FieldAttr] | None = None,
-        sources: dict[str, Record] | None = None,
+        sources: dict[str, SQLRecord] | None = None,
     ) -> None:
         super().__init__(
             dataset=mdata,
@@ -665,7 +661,7 @@ class SpatialDataCatManager(CatManager):
         sdata: Any,
         var_index: dict[str, FieldAttr],
         categoricals: dict[str, dict[str, FieldAttr]] | None = None,
-        sources: dict[str, dict[str, Record]] | None = None,
+        sources: dict[str, dict[str, SQLRecord]] | None = None,
         *,
         sample_metadata_key: str | None = "sample",
     ) -> None:
@@ -937,7 +933,7 @@ class TiledbsomaCatManager(CatManager):
         var_index: dict[str, tuple[str, FieldAttr]],
         categoricals: dict[str, FieldAttr] | None = None,
         obs_columns: FieldAttr = Feature.name,
-        sources: dict[str, Record] | None = None,
+        sources: dict[str, SQLRecord] | None = None,
     ):
         self._obs_fields = categoricals or {}
         self._var_fields = var_index
@@ -1342,7 +1338,7 @@ class CellxGeneAnnDataCatManager(AnnDataCatManager):
         *,
         schema_version: Literal["4.0.0", "5.0.0", "5.1.0", "5.2.0"] = "5.2.0",
         defaults: dict[str, str] = None,
-        extra_sources: dict[str, Record] = None,
+        extra_sources: dict[str, SQLRecord] = None,
     ) -> None:
         """CELLxGENE schema curator.
 
@@ -1972,7 +1968,7 @@ def from_anndata(
     categoricals: dict[str, FieldAttr] | None = None,
     obs_columns: FieldAttr = Feature.name,
     organism: str | None = None,
-    sources: dict[str, Record] | None = None,
+    sources: dict[str, SQLRecord] | None = None,
 ) -> AnnDataCatManager:
     if organism is not None:
         logger.warning("organism is ignored, define it on the dtype level")
@@ -2012,7 +2008,7 @@ def from_tiledbsoma(
     categoricals: dict[str, FieldAttr] | None = None,
     obs_columns: FieldAttr = Feature.name,
     organism: str | None = None,
-    sources: dict[str, Record] | None = None,
+    sources: dict[str, SQLRecord] | None = None,
 ) -> TiledbsomaCatManager:
     if organism is not None:
         logger.warning("organism is ignored, define it on the dtype level")
@@ -2032,7 +2028,7 @@ def from_spatialdata(
     var_index: dict[str, FieldAttr],
     categoricals: dict[str, dict[str, FieldAttr]] | None = None,
     organism: str | None = None,
-    sources: dict[str, dict[str, Record]] | None = None,
+    sources: dict[str, dict[str, SQLRecord]] | None = None,
     *,
     sample_metadata_key: str = "sample",
 ):