diff options
| -rw-r--r-- | gn3/computations/correlations.py | 3 | ||||
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 24 |
2 files changed, 14 insertions, 13 deletions
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py index 4432971..3563530 100644 --- a/gn3/computations/correlations.py +++ b/gn3/computations/correlations.py @@ -99,7 +99,8 @@ def do_bicor(x_val, y_val) -> Tuple[float, float]: package :not packaged in guix """ - return (x_val, y_val) + _corr_input = (x_val, y_val) + return (0.0, 0.0) def filter_shared_sample_keys(this_samplelist, diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py index 8bb5cd1..c6fa35e 100644 --- a/tests/unit/computations/test_correlation.py +++ b/tests/unit/computations/test_correlation.py @@ -104,7 +104,7 @@ class TestCorrelation(TestCase): results = do_bicor(x_val=[1, 2, 3], y_val=[4, 5, 6]) - self.assertEqual(results, ([1, 2, 3], [4, 5, 6]) + self.assertEqual(results, (0.0, 0.0) ) @mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value") @@ -291,10 +291,10 @@ class TestCorrelation(TestCase): expected_db_results = [namedtuple("lit_coeff", "val")(x*0.1) for x in range(1, 4)] - database_instance = DataBase(expected_results=expected_db_results) + conn = DataBase(expected_results=expected_db_results) expected_results = ("1", 0.1) - lit_results = fetch_lit_correlation_data(conn=database_instance, + lit_results = fetch_lit_correlation_data(conn=conn, gene_id="1", input_mouse_gene_id="20", mouse_gene_id="15") @@ -305,11 +305,11 @@ class TestCorrelation(TestCase): """Test that corr coeffient returned is 0 given the\ db value if corr coefficient is empty """ - database_instance = mock.Mock() - database_instance.cursor.return_value = DataBase() - database_instance.execute.return_value.fetchone.return_value = None + conn = mock.Mock() + conn.cursor.return_value = DataBase() + conn.execute.return_value.fetchone.return_value = None - lit_results = fetch_lit_correlation_data(conn=database_instance, + lit_results = fetch_lit_correlation_data(conn=conn, input_mouse_gene_id="12", gene_id="16", mouse_gene_id="12") @@ -356,7 +356,7 @@ class TestCorrelation(TestCase): """Test for converting a gene id to mouse geneid\ given a species which is not mouse """ - database_instance = mock.Mock() + conn = mock.Mock() test_data = [("Human", 14), (None, 9), ("Mouse", 15), ("Rat", 14)] database_results = [namedtuple("mouse_id", "mouse")(val) @@ -365,12 +365,12 @@ class TestCorrelation(TestCase): cursor = mock.Mock() cursor.execute.return_value = 1 cursor.fetchone.side_effect = database_results - database_instance.cursor.return_value = cursor + conn.cursor.return_value = cursor expected_results = [12, None, 13, 14] for (species, gene_id) in test_data: mouse_gene_id_results = map_to_mouse_gene_id( - conn=database_instance, species=species, gene_id=gene_id) + conn=conn, species=species, gene_id=gene_id) results.append(mouse_gene_id_results) self.assertEqual(results, expected_results) @@ -382,7 +382,7 @@ class TestCorrelation(TestCase): and is used in the api/correlation/lit """ - database = mock.Mock() + conn = mock.Mock() expected_mocked_lit_results = [{"1412_at": {"gene_id": 11, "lit_corr": 0.9}}, {"1412_a": { "gene_id": 17, "lit_corr": 0.48}}] @@ -390,7 +390,7 @@ class TestCorrelation(TestCase): mock_lit_corr.return_value = expected_mocked_lit_results lit_correlation_results = compute_all_lit_correlation( - conn=database, trait_lists=[("1412_at", 11), ("1412_a", 121)], + conn=conn, trait_lists=[("1412_at", 11), ("1412_a", 121)], species="rat", gene_id=12) self.assertEqual(lit_correlation_results, expected_mocked_lit_results) |