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-rw-r--r--gn3/computations/correlations.py5
-rw-r--r--mypy.ini3
-rw-r--r--tests/integration/test_correlation.py2
-rw-r--r--tests/unit/computations/test_correlation.py11
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(
diff --git a/mypy.ini b/mypy.ini
index 8266756..4465656 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -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'),