🎨 Do not check embedding in .validate

cellxgene_lamin/curate.py

@@ -270,19 +270,6 @@ def validate(self) -> bool:
                 " reserved from previous schema versions."
             )
 
-        # cellxgene requires an embedding
-        embedding_pattern = r"^[a-zA-Z][a-zA-Z0-9_.-]*$"
-        exclude_key = "spatial"
-        matching_keys = [
-            key
-            for key in self._adata.obsm.keys()
-            if re.match(embedding_pattern, key) and key != exclude_key
-        ]
-        if len(matching_keys) == 0:
-            raise ValueError(
-                "Unable to find an embedding key. Please calculate an embedding."
-            )
-
         return super().validate(organism=self.organism)
 
     def to_cellxgene_anndata(
@@ -305,6 +292,19 @@ def to_cellxgene_anndata(
         # Create a copy since we modify the AnnData object extensively
         adata_cxg = self._adata.copy()
 
+        # cellxgene requires an embedding
+        embedding_pattern = r"^[a-zA-Z][a-zA-Z0-9_.-]*$"
+        exclude_key = "spatial"
+        matching_keys = [
+            key
+            for key in adata_cxg.obsm.keys()
+            if re.match(embedding_pattern, key) and key != exclude_key
+        ]
+        if len(matching_keys) == 0:
+            raise ValueError(
+                "Unable to find an embedding key. Please calculate an embedding."
+            )
+
         # convert name column to ontology_term_id column
         for column in adata_cxg.obs.columns:
             if column in self.categoricals and not column.endswith("_ontology_term_id"):