use _write_rfs_to_file()

lindi/LindiH5ZarrStore/LindiH5ZarrStore.py

@@ -12,7 +12,8 @@
     _get_chunk_byte_range,
     _get_byte_range_for_contiguous_dataset,
     _join,
-    _get_chunk_names_for_dataset
+    _get_chunk_names_for_dataset,
+    _write_rfs_to_file,
 )
 from ..conversion.attr_conversion import h5_to_zarr_attr
 from ..conversion.reformat_json import reformat_json
@@ -469,9 +470,8 @@ def write_reference_file_system(self, output_file_name: str):
         if not output_file_name.endswith(".lindi.json"):
             raise Exception("The output file name must end with .lindi.json")
 
-        ret = self.to_reference_file_system()
-        with open(output_file_name, "w") as f:
-            json.dump(ret, f, indent=2)
+        rfs = self.to_reference_file_system()
+        _write_rfs_to_file(rfs=rfs, output_file_name=output_file_name)
 
     def to_reference_file_system(self) -> dict:
         """Create a reference file system corresponding to this store.

lindi/LindiH5ZarrStore/_util.py

@@ -1,4 +1,5 @@
 from typing import IO, List
+import json
 import numpy as np
 import h5py
 
@@ -83,3 +84,10 @@ def _get_chunk_names_for_dataset(chunk_coords_shape: List[int]) -> List[str]:
             for name0 in names0:
                 names.append(f"{i}.{name0}")
         return names
+
+
+def _write_rfs_to_file(*, rfs: dict, output_file_name: str):
+    """Write a reference file system to a file.
+    """
+    with open(output_file_name, "w") as f:
+        json.dump(rfs, f, indent=2, sort_keys=True)

lindi/LindiStagingStore/LindiStagingStore.py

@@ -5,6 +5,7 @@
 from zarr.storage import Store as ZarrStore
 from ..LindiH5pyFile.LindiReferenceFileSystemStore import LindiReferenceFileSystemStore
 from .StagingArea import StagingArea, _random_str
+from ..LindiH5ZarrStore._util import _write_rfs_to_file
 
 
 # Accepts a string path to a file, uploads (or copies) it somewhere, and returns a string URL
@@ -138,9 +139,8 @@ def upload(
                         raise ValueError(f"Could not find url in blob mapping: {url1}")
                     rfs['refs'][k][0] = url2
         with tempfile.TemporaryDirectory() as tmpdir:
-            rfs_fname = f"{tmpdir}/rfs.json"
-            with open(rfs_fname, 'w') as f:
-                json.dump(rfs, f, indent=2, sort_keys=True)
+            rfs_fname = f"{tmpdir}/rfs.lindi.json"
+            _write_rfs_to_file(rfs=rfs, output_file_name=rfs_fname)
             return on_upload_main(rfs_fname)
 
     def consolidate_chunks(self):