Exclude directories having no h5ad files

cellxgene_gateway/items/file/fileitem_source.py

@@ -63,7 +63,7 @@ class FileItemSource(ItemSource):
 
         return item_tree
 
-    def scan_directory(self, subpath="") -> dict:
+    def scan_directory(self, subpath: str = "") -> ItemTree:
         base_path = os.path.join(self.base_path, subpath)
 
         if not os.path.exists(base_path):
@@ -100,6 +100,9 @@ class FileItemSource(ItemSource):
             branches = [
                 self.scan_directory(os.path.join(subpath, subdir)) for subdir in subdirs
             ]
+            # Exclude branches without files as leaves. Since traversal is applied pre-order,
+            # branch.branches has already been processed and we don't need to check deeper nesting.
+            branches = [branch for branch in branches if branch.items or branch.branches]
 
         return ItemTree(subpath, items, branches)
 

cellxgene_gateway/items/s3/s3item_source.py

@@ -116,6 +116,7 @@ class S3ItemSource(ItemSource):
         branches = None
         if len(subdir_keys) > 0:
             branches = [self.scan_directory(key) for key in subdir_keys]
+            branches = [branch for branch in branches if branch.items or branch.branches]
 
         return ItemTree(directory_key, items, branches)