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authorFrederick Muriuki Muriithi2022-07-29 03:39:32 +0300
committerFrederick Muriuki Muriithi2022-07-29 03:53:49 +0300
commite3622ac213ef6e1be8a38959f7c6ee082c112c95 (patch)
treeb8416a7fbceb8e228c253db6dace099702e4fd4f /tests
parent921b5fe752e4a947595a86572592d5bbdeb16ead (diff)
downloadgenenetwork3-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.py2
-rw-r--r--tests/unit/computations/test_correlation.py11
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'),