Fix for Dataset.to_zarr with both consolidated and `write_empty_chu…

…nks` (#8326)

* Fixed an issue where Dataset.to_zarr with both `consolidated` and `write_empty_chunks` failed with a ReadOnlyError

doc/whats-new.rst

@@ -142,6 +142,11 @@ Bug fixes
   (:issue:`8290`, :pull:`8297`).
   By `Oliver McCormack <https://github.com/olimcc>`_.
 
+- Fix to_zarr ending in a ReadOnlyError when consolidated metadata was used and the
+  write_empty_chunks was provided.
+  (:issue:`8323`, :pull:`8326`)
+  By `Matthijs Amesz <https://github.com/Metamess>`_.
+
 
 Documentation
 ~~~~~~~~~~~~~

xarray/backends/zarr.py

@@ -675,8 +675,23 @@ def set_variables(self, variables, check_encoding_set, writer, unlimited_dims=No
                 # metadata. This would need some case work properly with region
                 # and append_dim.
                 if self._write_empty is not None:
+                    # Write to zarr_group.chunk_store instead of zarr_group.store
+                    # See https://github.com/pydata/xarray/pull/8326#discussion_r1365311316 for a longer explanation
+                    #    The open_consolidated() enforces a mode of r or r+
+                    #    (and to_zarr with region provided enforces a read mode of r+),
+                    #    and this function makes sure the resulting Group has a store of type ConsolidatedMetadataStore
+                    #    and a 'normal Store subtype for chunk_store.
+                    #    The exact type depends on if a local path was used, or a URL of some sort,
+                    #    but the point is that it's not a read-only ConsolidatedMetadataStore.
+                    #    It is safe to write chunk data to the chunk_store because no metadata would be changed by
+                    #    to_zarr with the region parameter:
+                    #     - Because the write mode is enforced to be r+, no new variables can be added to the store
+                    #       (this is also checked and enforced in xarray.backends.api.py::to_zarr()).
+                    #     - Existing variables already have their attrs included in the consolidated metadata file.
+                    #     - The size of dimensions can not be expanded, that would require a call using `append_dim`
+                    #        which is mutually exclusive with `region`
                     zarr_array = zarr.open(
-                        store=self.zarr_group.store,
+                        store=self.zarr_group.chunk_store,
                         path=f"{self.zarr_group.name}/{name}",
                         write_empty_chunks=self._write_empty,
                     )

xarray/tests/test_backends.py

@@ -2459,7 +2459,8 @@ def test_no_warning_from_open_emptydim_with_chunks(self) -> None:
     @pytest.mark.parametrize("consolidated", [False, True, None])
     @pytest.mark.parametrize("compute", [False, True])
     @pytest.mark.parametrize("use_dask", [False, True])
-    def test_write_region(self, consolidated, compute, use_dask) -> None:
+    @pytest.mark.parametrize("write_empty", [False, True, None])
+    def test_write_region(self, consolidated, compute, use_dask, write_empty) -> None:
         if (use_dask or not compute) and not has_dask:
             pytest.skip("requires dask")
         if consolidated and self.zarr_version > 2:
@@ -2491,6 +2492,7 @@ def test_write_region(self, consolidated, compute, use_dask) -> None:
                     store,
                     region=region,
                     consolidated=consolidated,
+                    write_empty_chunks=write_empty,
                     **self.version_kwargs,
                 )
             with xr.open_zarr(
@@ -2772,9 +2774,12 @@ def roundtrip_dir(
         ) as ds:
             yield ds
 
-    @pytest.mark.parametrize("write_empty", [True, False])
-    def test_write_empty(self, write_empty: bool) -> None:
-        if not write_empty:
+    @pytest.mark.parametrize("consolidated", [True, False, None])
+    @pytest.mark.parametrize("write_empty", [True, False, None])
+    def test_write_empty(
+        self, consolidated: bool | None, write_empty: bool | None
+    ) -> None:
+        if write_empty is False:
             expected = ["0.1.0", "1.1.0"]
         else:
             expected = [