def make_fileitem_from_path(
self, filename, subpath, is_annotation=False, is_shallow=False
) -> FileItem:
if is_annotation and filename.endswith(self.annotation_file_suffix):
name = filename[: -len(self.annotation_file_suffix)]
ext = self.annotation_file_suffix
else:
name = filename
ext = ""
item = FileItem(
subpath=subpath,
name=name,
ext=ext,
type=ItemType.annotation if is_annotation else ItemType.h5ad,
)
if not is_annotation and not is_shallow:
annotations = self.make_annotations_for_fileitem(item)
item.annotations = annotations
return item
def create_annotation(self, item: FileItem, name: str) -> FileItem:
annotation = self.make_fileitem_from_path(
name, self.get_annotations_subpath(item), is_annotation=True)
item.annotations = (item.annotations or []).append(annotation)
return annotation