fix when table but no shapes_key provided

Author: quentinblampey

spatialdata_xenium_explorer/cli/app.py

@@ -12,12 +12,24 @@ def write(
         None,
         help="Path to a directory where Xenium Explorer's outputs will be saved. By default, writes to the same path as `sdata_path` but with the `.explorer` suffix",
     ),
+    image_key: str = typer.Option(
+        None,
+        help="Name of the image of interest (key of `sdata.images`). This argument doesn't need to be provided if there is only one image.",
+    ),
+    shapes_key: str = typer.Option(
+        None,
+        help="Name of the cell shapes (key of `sdata.shapes`). This argument doesn't need to be provided if there is only one shapes key or a table with only one region.",
+    ),
+    points_key: str = typer.Option(
+        None,
+        help="Name of the transcripts (key of `sdata.points`). This argument doesn't need to be provided if there is only one points key.",
+    ),
     gene_column: str = typer.Option(
         None, help="Column name of the points dataframe containing the gene names"
     ),
-    shapes_key: str = typer.Option(
+    layer: str = typer.Option(
         None,
-        help="Key for the boundaries. By default, uses the baysor boundaires, else the cellpose boundaries",
+        help="Layer of `sdata.table` where the gene counts are saved. If `None`, uses `sdata.table.X`.",
     ),
     lazy: bool = typer.Option(
         True,
@@ -31,10 +43,6 @@ def write(
         None,
         help="string that indicated which files should be created. `'-ib'` means everything except images and boundaries, while `'+tocm'` means only transcripts/observations/counts/metadata (each letter corresponds to one explorer file). By default, keeps everything",
     ),
-    save_h5ad: bool = typer.Option(
-        True,
-        help="Whether to save the adata as h5ad in the explorer directory (for convenience only, since h5ad is faster to open than the original .zarr table)",
-    ),
 ):
     """Convert a spatialdata object to Xenium Explorer's inputs"""
     from pathlib import Path
@@ -51,12 +59,14 @@ def write(
     write(
         output_path,
         sdata,
+        image_key=image_key,
         shapes_key=shapes_key,
+        points_key=points_key,
         gene_column=gene_column,
+        layer=layer,
         lazy=lazy,
         ram_threshold_gb=ram_threshold_gb,
         mode=mode,
-        save_h5ad=save_h5ad,
     )
 
 

spatialdata_xenium_explorer/converter.py

@@ -74,11 +74,11 @@ def write(
     image_key, image = get_spatial_image(sdata, image_key, return_key=True)
 
     ### Saving cell categories and gene counts
-    if sdata.table is not None and shapes_key is not None:
+    if sdata.table is not None:
         adata = sdata.table
 
         region = adata.uns["spatialdata_attrs"]["region"]
-        region = region if isinstance(region, list) else region
+        region = region if isinstance(region, list) else [region]
 
         if len(region) == 1:
             assert (

spatialdata_xenium_explorer/utils.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import logging
 from pathlib import Path
 
 import dask.array as da
@@ -12,6 +13,8 @@
 from spatialdata.models import SpatialElement
 from spatialdata.transformations import Identity, get_transformation, set_transformation
 
+log = logging.getLogger(__name__)
+
 
 def explorer_file_path(path: str, filename: str, is_dir: bool):
     path: Path = Path(path)
@@ -94,13 +97,12 @@ def get_key(sdata: SpatialData, attr: str, key: str | None = None):
 
     elements = getattr(sdata, attr)
 
-    if not len(elements):
+    if len(elements) != 1:
+        log.warn(
+            f"Trying to get an element key of `sdata.{attr}`, but it contains multiple values and no key was provided. It will not be saved to the xenium explorer."
+        )
         return None
 
-    assert (
-        len(elements) == 1
-    ), f"Trying to get an element key of `sdata.{attr}`, but it contains multiple values and no dict key was provided"
-
     return next(iter(elements.keys()))