Make sure to save the general metadata from an SE.

ArtifactDB · Oct 26, 2023 · dea7297 · dea7297
1 parent c086934
commit dea7297
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Showing 3 changed files with 37 additions and 4 deletions.
diff --git a/src/dolomite_se/load_summarized_experiment.py b/src/dolomite_se/load_summarized_experiment.py
@@ -52,8 +52,17 @@ def load_summarized_experiment(meta: dict[str, Any], project, **kwargs) -> Summa
         except Exception as ex:
             raise ValueError("failed to load assay '" + curname + "' from '" + meta["$schema"] + "'; " + str(ex))
 
+    other_meta = None 
+    if "other_data" in se_meta:
+        try:
+            child_meta = acquire_metadata(project, se_meta["other_data"]["resource"]["path"])
+            other_meta = load_object(child_meta, project)
+        except Exception as ex:
+            raise ValueError("failed to load other metadata from '" + meta["$schema"] + "'; " + str(ex))
+
     return SummarizedExperiment(
         assays=assays,
         row_data=row_data,
-        col_data=col_data
+        col_data=col_data,
+        metadata=other_meta,
     )
diff --git a/src/dolomite_se/stage_summarized_experiment.py b/src/dolomite_se/stage_summarized_experiment.py
@@ -61,20 +61,28 @@ def stage_summarized_experiment(
 
     if x.row_data.row_names is not None or x.row_data.shape[1] > 0:
         try:
-            rd_meta = stage_object(x.row_data, dir, path + "/row_data", **data_frame_args)
+            rd_meta = stage_object(x.row_data, dir, path + "/row_data", is_child=True, **data_frame_args)
             rd_stub = write_metadata(rd_meta, dir)
         except Exception as ex:
             raise ValueError("failed to stage row data for a " + str(type(x)) + "; " + str(ex))
         se_meta["row_data"] = { "resource": rd_stub }
 
     if x.col_data.row_names is not None or x.col_data.shape[1] > 0:
         try:
-            cd_meta = stage_object(x.col_data, dir, path + "/column_data", **data_frame_args)
+            cd_meta = stage_object(x.col_data, dir, path + "/column_data", is_child=True, **data_frame_args)
             cd_stub = write_metadata(cd_meta, dir)
         except Exception as ex:
-            raise ValueError("failed to stage row data for a " + str(type(x)) + "; " + str(ex))
+            raise ValueError("failed to stage column data for a " + str(type(x)) + "; " + str(ex))
         se_meta["column_data"] = { "resource": cd_stub }
 
+    if x.metadata is not None and len(x.metadata):
+        try:
+            o_meta = stage_object(x.metadata, dir, path + "/other_data", is_child=True)
+            o_stub = write_metadata(o_meta, dir)
+        except Exception as ex:
+            raise ValueError("failed to stage other metadata for a " + str(type(x)) + "; " + str(ex))
+        se_meta["other_data"] = { "resource": o_stub }
+
     return {
         "$schema": "summarized_experiment/v1.json",
         "path": path + "/experiment.json",

diff --git a/tests/test_stage_summarized_experiment.py b/tests/test_stage_summarized_experiment.py
@@ -71,3 +71,19 @@ def test_stage_summarized_experiment_with_dimdata():
     assert isinstance(roundtrip, summarizedexperiment.SummarizedExperiment)
     assert se.row_data.row_names == roundtrip.row_data.row_names
     assert se.col_data.row_names == roundtrip.col_data.row_names
+
+
+def test_stage_summarized_experiment_with_other_meta():
+    x = numpy.random.rand(1000, 200)
+    se = summarizedexperiment.SummarizedExperiment(
+        assays={ "counts": x },
+        metadata={"YAY":2, "FOO":'a'}
+    )
+
+    dir = mkdtemp()
+    info = stage_object(se, dir, "se")
+    assert "other_data" in info["summarized_experiment"]
+    write_metadata(info, dir)
+
+    roundtrip = load_object(info, dir)
+    assert roundtrip.metadata == se.metadata