more queries

apis/python/remote_tests/test_03_versions.py

@@ -65,64 +65,58 @@ def test_basic_readback(conftest_context, uri_and_info):
         assert adata.X.shape == (2700, 13714)
 
 
-## ----------------------------------------------------------------
-### Slicing and filtering objects
-## exp.obs.read(
-##    coords=[slice(0, 99)],
-##    value_filter="total_counts > 4000",
-##    column_names=["soma_joinid", "obs_id", "total_counts"],
-## ).concat().to_pandas()
-## exp.obs.read(
-##    coords=[slice(0, 99)],
-##    value_filter='parity == "even" and total_counts > 4000',
-##    column_names=["soma_joinid", "obs_id", "total_counts", "parity"],
-## ).concat().to_pandas()
-## exp.ms["RNA"].var.read(
-##    value_filter="var_id in ['ANXA1', 'IFI44', 'IFI44L', 'OAS1']",
-##    column_names=["var_id", "gene_ids", "mean_counts"],
-## ).concat().to_pandas()
-#
-## ----------------------------------------------------------------
-### Slicing and filtering experiments
-## exp.uri
-## query = tiledbsoma.ExperimentAxisQuery(
-##    experiment=exp,
-##    measurement_name="RNA",
-##    obs_query=tiledbsoma.AxisQuery(
-##        value_filter="n_genes_by_counts > 1000",
-##    ),
-##    var_query=tiledbsoma.AxisQuery(
-##        value_filter="n_cells_by_counts > 100",
-##    ),
-## )
-##
-## (query.n_obs, query.n_vars)
-#
-## ----------------------------------------------------------------
-## query.obs().concat().to_pandas()
-## query.X(layer_name="data").tables().concat().to_pandas()
-## query.to_anndata(X_name="data")
-## query.close()
-## with tiledbsoma.ExperimentAxisQuery(
-##    experiment=exp,
-##    measurement_name="RNA",
-##    obs_query=tiledbsoma.AxisQuery(
-##        value_filter="n_genes_by_counts > 1000",
-##    ),
-##    var_query=tiledbsoma.AxisQuery(
-##        value_filter="n_cells_by_counts > 100",
-##    ),
-## ) as query:
-##    print(query.to_anndata(X_name="data"))
-#
-## with tiledbsoma.ExperimentAxisQuery(
-##    experiment=exp,
-##    measurement_name="RNA",
-##    obs_query=tiledbsoma.AxisQuery(
-##        value_filter='n_genes_by_counts > 1000 and parity == "even"',
-##    ),
-##    var_query=tiledbsoma.AxisQuery(
-##        value_filter="n_cells_by_counts > 100",
-##    ),
-## ) as query:
-##    print(query.to_anndata(X_name="data"))
+@pytest.mark.parametrize(
+    "uri_and_info",
+    util_pbmc3k_unprocessed_versions(),
+)
+def test_dataframe_queries(conftest_context, uri_and_info):
+    uri, info = uri_and_info
+    with tiledbsoma.Experiment.open(uri, context=conftest_context) as exp:
+
+        qobs = (
+            exp.obs.read(
+                coords=[slice(0, 99)],
+                value_filter="nFeature_RNA > 1000",
+                column_names=["soma_joinid", "obs_id", "nFeature_RNA"],
+            )
+            .concat()
+            .to_pandas()
+        )
+        assert qobs.shape == (22, 3)
+
+        qvar = (
+            exp.ms["RNA"]
+            .var.read(
+                value_filter="var_id in ['ANXA1', 'IFI44', 'IFI44L', 'OAS1']",
+            )
+            .concat()
+            .to_pandas()
+        )
+        assert qvar.shape == (4, 2)
+
+
+@pytest.mark.parametrize(
+    "uri_and_info",
+    util_pbmc3k_unprocessed_versions(),
+)
+def test_experiment_queries(conftest_context, uri_and_info):
+    uri, info = uri_and_info
+    with tiledbsoma.Experiment.open(uri, context=conftest_context) as exp:
+
+        query = tiledbsoma.ExperimentAxisQuery(
+            experiment=exp,
+            measurement_name="RNA",
+            obs_query=tiledbsoma.AxisQuery(
+                value_filter="nFeature_RNA > 1000",
+            ),
+            var_query=tiledbsoma.AxisQuery(
+                value_filter="var_id in  ['ANXA1', 'IFI44', 'IFI44L', 'OAS1']",
+            ),
+        )
+
+        assert (query.n_obs, query.n_vars) == (530, 4)
+
+
+# tiledbsoma.io.show_experiment_shapes
+# tiledbsoma.io.upgrade_experiment_shapes
+# tiledbsoma.io.resize_experiment