From e7a1e6b6abca77b1dfd2103f34e059c809712dcc Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Sun, 5 May 2024 12:41:59 -0700
Subject: [PATCH] Support non-standard metadata objects when reading from H5AD
 files. (#41)

Fixes an issue where `uns` is not a dictionary. Update tests and documentation.
---
 src/singlecellexperiment/SingleCellExperiment.py | 7 +++++--
 tests/test_sce_io.py                             | 8 ++++++++
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/src/singlecellexperiment/SingleCellExperiment.py b/src/singlecellexperiment/SingleCellExperiment.py
index 0df4ff9..47df2ee 100644
--- a/src/singlecellexperiment/SingleCellExperiment.py
+++ b/src/singlecellexperiment/SingleCellExperiment.py
@@ -1015,7 +1015,9 @@ def from_anndata(cls, input: "anndata.AnnData") -> "SingleCellExperiment":
                 Input data.
 
         Returns:
-            A ``SingleCellExperiment`` object.
+            A ``SingleCellExperiment`` object. If the input contains any data
+            in the ``uns`` attribute, the `metadata` slot of the ``SingleCellExperiment``
+            will contain a key ``uns``.
         """
 
         layers = OrderedDict()
@@ -1028,12 +1030,13 @@ def from_anndata(cls, input: "anndata.AnnData") -> "SingleCellExperiment":
         obsm = _to_normal_dict(input.obsm)
         varp = _to_normal_dict(input.varp)
         obsp = _to_normal_dict(input.obsp)
+        _metadata = {"uns": input.uns} if input.uns is not None else None
 
         return cls(
             assays=layers,
             row_data=biocframe.BiocFrame.from_pandas(input.var),
             column_data=biocframe.BiocFrame.from_pandas(input.obs),
-            metadata=input.uns,
+            metadata=_metadata,
             reduced_dims=obsm,
             row_pairs=varp,
             column_pairs=obsp,
diff --git a/tests/test_sce_io.py b/tests/test_sce_io.py
index 75bd505..a744e55 100644
--- a/tests/test_sce_io.py
+++ b/tests/test_sce_io.py
@@ -129,6 +129,14 @@ def test_SCE_randomAnnData():
     assert tse is not None
     assert isinstance(tse, SingleCellExperiment)
 
+    # to avoid unknown mapping types;
+    # ran into an issue with anndata.compat._overloaded_dict.OverloadedDict when loading a h5ad
+    adata.uns = {".internal": [f"obs_{i+1}" for i in range(n)]}
+    tse = singlecellexperiment.SingleCellExperiment.from_anndata(adata)
+
+    assert tse is not None
+    assert isinstance(tse, SingleCellExperiment)
+
 
 def test_SCE_to_mudata():
     tse = SingleCellExperiment(