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| author | Frederick Muriuki Muriithi | 2022-07-29 03:39:32 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-07-29 03:53:49 +0300 |
| commit | e3622ac213ef6e1be8a38959f7c6ee082c112c95 (patch) | |
| tree | b8416a7fbceb8e228c253db6dace099702e4fd4f /tests | |
| parent | 921b5fe752e4a947595a86572592d5bbdeb16ead (diff) | |
| download | genenetwork3-e3622ac213ef6e1be8a38959f7c6ee082c112c95.tar.gz | |
Fix failing tests
* gn3/computations/correlations.py: rename function
* mypy.ini: deactivate mypy error about missing imports
* tests/integration/test_correlation.py: mock correct function
* tests/unit/computations/test_correlation.py: test correct function
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/integration/test_correlation.py | 2 | ||||
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 11 |
2 files changed, 8 insertions, 5 deletions
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'), |