diff options
| -rw-r--r-- | gn3/computations/correlations.py | 5 | ||||
| -rw-r--r-- | mypy.ini | 3 | ||||
| -rw-r--r-- | tests/integration/test_correlation.py | 2 | ||||
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 11 |
4 files changed, 14 insertions, 7 deletions
diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py index ea1a862..5a9ce62 100644 --- a/gn3/computations/correlations.py +++ b/gn3/computations/correlations.py @@ -162,7 +162,8 @@ def fast_compute_all_sample_correlation(this_trait, corr_results, key=lambda trait_name: -abs(list(trait_name.values())[0]["corr_coefficient"])) -def __corr_compute__(trait_samples, target_trait, corr_method): +def compute_one_sample_correlation(trait_samples, target_trait, corr_method): + """Compute sample correlation against a single trait.""" trait_name = target_trait.get("trait_id") target_trait_data = target_trait["trait_sample_data"] try: @@ -200,7 +201,7 @@ def compute_all_sample_correlation(this_trait, ( corr for corr in pool.starmap( - __corr_compute__, + compute_one_sample_correlation, ((this_trait_samples, trait, corr_method) for trait in target_dataset)) if corr is not None), key=lambda trait_name: -abs( @@ -41,3 +41,6 @@ ignore_missing_imports = True [mypy-sklearn.*] ignore_missing_imports = True + +[mypy-scripts.argparse_actions.*] +ignore_missing_imports = True diff --git a/tests/integration/test_correlation.py b/tests/integration/test_correlation.py index d52ab01..c1d518d 100644 --- a/tests/integration/test_correlation.py +++ b/tests/integration/test_correlation.py @@ -12,7 +12,7 @@ class CorrelationIntegrationTest(TestCase): self.app = create_app().test_client() @pytest.mark.integration_test - @mock.patch("gn3.api.correlation.compute_all_sample_correlation") + @mock.patch("gn3.api.correlation.run_sample_corr_cmd") def test_sample_r_correlation(self, mock_compute_samples): """Test /api/correlation/sample_r/{method}""" this_trait_data = { diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py index 267ced3..e8d4f75 100644 --- a/tests/unit/computations/test_correlation.py +++ b/tests/unit/computations/test_correlation.py @@ -9,7 +9,7 @@ from numpy.testing import assert_almost_equal from gn3.computations.correlations import normalize_values from gn3.computations.correlations import compute_sample_r_correlation -from gn3.computations.correlations import compute_all_sample_correlation +from gn3.computations.correlations import compute_one_sample_correlation from gn3.computations.correlations import filter_shared_sample_keys from gn3.computations.correlations import tissue_correlation_for_trait @@ -164,7 +164,7 @@ class TestCorrelation(TestCase): @pytest.mark.unit_test @mock.patch("gn3.computations.correlations.compute_sample_r_correlation") @mock.patch("gn3.computations.correlations.filter_shared_sample_keys") - def test_compute_all_sample(self, filter_shared_samples, sample_r_corr): + def test_compute_one_sample(self, filter_shared_samples, sample_r_corr): """Given target dataset compute all sample r correlation""" filter_shared_samples.return_value = [iter(val) for val in [( @@ -197,8 +197,11 @@ class TestCorrelation(TestCase): "p_value": 0.9, "num_overlap": 6}}] - self.assertEqual(compute_all_sample_correlation( - this_trait=this_trait_data, target_dataset=traits_dataset), sample_all_results) + self.assertEqual( + compute_one_sample_correlation( + this_trait_data["trait_sample_data"], + traits_dataset[0], "pearson"), + sample_all_results[0]) sample_r_corr.assert_called_once_with( trait_name='1419792_at', corr_method="pearson", trait_vals=('1.23', '6.565', '6.456'), |