List tables in metadata (as suggested by @will-moore)

minnerbe · Jun 30, 2023 · 15c9a20 · 15c9a20
1 parent 9b08825
commit 15c9a20
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/latest/generate_anndata_example.py b/latest/generate_anndata_example.py
@@ -33,6 +33,7 @@ def write_anndata(adata, filename, chunks):
     root = zarr.open(filename, mode="w")
     root.array("some_image", np.array([0]), chunks=(1,))
     tables = root.create_group("tables")
+    tables.attrs["tables"] = ["/anndata/obs", "/anndata/var", "/anndata/obsm", "/anndata/varm", "/anndata/obsp", "/anndata/varp"]
     adgroup = tables.create_group("anndata")
     adgroup.attrs["anndata"] = "0.9.1"
     adgroup.attrs["other-metadata"] = "metadata describing how the anndata annotates some_image"
@@ -96,6 +97,7 @@ def write_anndata_suggestion(adata, filename, chunks):
     root = zarr.open(filename, mode="w")
     root.array("some_image", np.array([0]), chunks=(1,))
     tables = root.create_group("tables")
+    tables.attrs["tables"] = ["/anndata/obs", "/anndata/var"]
     adgroup = tables.create_group("anndata")
     adgroup.attrs["anndata"] = "0.9.1"
     adgroup.attrs["other-metadata"] = "metadata describing how the anndata annotates some_image"
@@ -107,7 +109,6 @@ def write_anndata_suggestion(adata, filename, chunks):
     row_names = np.array(["X", "log_transformed", "other_data"])
     layers.create_dataset("row_names", data=row_names, dtype=object, object_codec=numcodecs.VLenUTF8())
     layers.attrs["annotated-data"] = [{"array": "/tables/anndata/X", "dimension": "2"}]
-    obs.attrs["column-order"] = ["row_names"]
 
     # obs (combines obs, obsm, obsp)
     localChunks = (chunks[0],)

diff --git a/latest/index.bs b/latest/index.bs
@@ -237,12 +237,12 @@ The on-disk format of a table group looks like this:
     └── 123.zarr
         |
         ├── .zgroup
-        ├── .zattrs
         |
         └──tables
             |
             ├── .zgroup
-            ├── .zattrs
+            ├── .zattrs          # A table group's `.zattrs` file MUST contain an attribute "tables" that lists all
+            |                    # tables in the group with relative paths, e.g., `{"tables": ["table_1", "some/nested/table_2"]}` 
             |
             └── table_1          # A table group holds arrays (called columns) with one or more dimensions, 
                 |                # where the number of rows n MUST be the same across all arrays.
@@ -253,7 +253,6 @@ The on-disk format of a table group looks like this:
                 ├── column_1     # The table group MAY hold zero, one, or an arbitrary number of column arrays.
                 |   |
                 |   ├── .zarray
-                |   ├── .zattrs
                 |   |
                 |   ├── 0.0
                 |   |   ...
@@ -262,7 +261,6 @@ The on-disk format of a table group looks like this:
                 └── row_names    # The table group SHOULD contain a 1D array of strings of length n called `row_names`.
                     |
                     ├── .zarray
-                    ├── .zattrs
                     |
                     ├── 0
                     |   :