[r][python] Create an AnnData -> SOMA -> Seurat test (#1263)

apis/system/tests/test_write_anndata_read_seurat.py

@@ -0,0 +1,66 @@
+import anndata as ad
+import pytest
+
+from tiledbsoma import io
+
+from .common import TestWritePythonReadR, embed_python_list_into_R_code
+
+
+class TestAnndataSOMASeurat(TestWritePythonReadR):
+    """
+    This test will perform an AnnData->SOMA->Seurat conversion and verify that the final artifact (Seurat)
+    has the same properties of the initial one (AnnData)
+    """
+
+    @pytest.fixture(scope="class")
+    def h5ad(self):
+        """
+        Fixture that will load an h5ad, convert it to SOMA, deploy it to `self.uri` and return a parsed version of it.
+        """
+        h5ad_path = "apis/python/testdata/pbmc-small.h5ad"
+        io.from_h5ad(self.uri, input_path=h5ad_path, measurement_name="RNA")
+        return ad.read_h5ad(h5ad_path)
+
+    # Prepares an R script with the dependencies and loads the object in seuratObject
+    # Future assertions can be done by appending to this script
+    def base_R_script(self):
+        return f"""
+        library("tiledbsoma")
+        library("SeuratObject")
+        soma <- SOMAOpen("{self.uri}")
+        ms <- soma$ms$get("RNA")
+        query <- SOMAExperimentAxisQuery$new(
+            experiment = soma,
+            measurement_name = "RNA"
+        )
+        seuratObject <- query$to_seurat(c(data = "data"), var_index="var_id", obs_index="obs_id")
+        """
+
+    # tests
+    def test_seurat_dim_matches(self, h5ad):
+        n_var = len(h5ad.var)
+        n_obs = len(h5ad.obs)
+        self.r_assert(
+            f"""
+            stopifnot(ncol(seuratObject) == {n_obs})
+            stopifnot(nrow(seuratObject) == {n_var})
+        """
+        )
+
+    def test_seurat_var_names_match(self, h5ad):
+        var_names = h5ad.var.index.tolist()
+        var_names_list = embed_python_list_into_R_code(var_names)
+        self.r_assert(
+            f"""
+            stopifnot(all.equal(rownames(x = seuratObject), c({var_names_list})))
+        """
+        )
+
+    def test_seurat_obs_names_match(self, h5ad):
+        obs_names = h5ad.obs.index.tolist()
+        obs_names_list = embed_python_list_into_R_code(obs_names)
+        self.r_assert(
+            f"""
+            stopifnot(all.equal(colnames(x = seuratObject), c({obs_names_list})))
+        """
+        )