diff options
Diffstat (limited to 'tests/unit/computations')
| -rw-r--r-- | tests/unit/computations/test_correlation.py | 14 |
1 files changed, 7 insertions, 7 deletions
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py index 9450094..f2d65bd 100644 --- a/tests/unit/computations/test_correlation.py +++ b/tests/unit/computations/test_correlation.py @@ -1,5 +1,4 @@ """Module contains the tests for correlation""" -import unittest from unittest import TestCase from unittest import mock @@ -16,7 +15,7 @@ from gn3.computations.correlations import fetch_lit_correlation_data from gn3.computations.correlations import query_formatter from gn3.computations.correlations import map_to_mouse_gene_id from gn3.computations.correlations import compute_all_lit_correlation -from gn3.computations.correlations import compute_all_tissue_correlation +from gn3.computations.correlations import compute_tissue_correlation from gn3.computations.correlations import map_shared_keys_to_values from gn3.computations.correlations import process_trait_symbol_dict from gn3.computations.correlations2 import compute_correlation @@ -173,7 +172,6 @@ class TestCorrelation(TestCase): self.assertEqual(results, (filtered_this_samplelist, filtered_target_samplelist)) - @unittest.skip("Test needs to be refactored ") @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): @@ -181,7 +179,7 @@ class TestCorrelation(TestCase): filter_shared_samples.return_value = (["1.23", "6.565", "6.456"], [ "6.266", "6.565", "6.456"]) - sample_r_corr.return_value = ([-1.0, 0.9, 6]) + sample_r_corr.return_value = (["1419792_at", -1.0, 0.9, 6]) this_trait_data = { "trait_id": "1455376_at", @@ -204,13 +202,14 @@ class TestCorrelation(TestCase): } ] - sample_all_results = [{"1419792_at": {"corr_coeffient": -1.0, + sample_all_results = [{"1419792_at": {"corr_coefficient": -1.0, "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) sample_r_corr.assert_called_once_with( + trait_name='1419792_at', corr_method="pearson", trait_vals=['1.23', '6.565', '6.456'], target_samples_vals=['6.266', '6.565', '6.456']) filter_shared_samples.assert_called_once_with( @@ -417,7 +416,7 @@ class TestCorrelation(TestCase): {"1418702_a_at": {"tissue_corr": -0.5, "tissue_p_val": 0.9, "tissue_number": 3}}] - results = compute_all_tissue_correlation( + results = compute_tissue_correlation( primary_tissue_dict=primary_tissue_dict, target_tissues_data=target_tissue_data, corr_method="pearson") @@ -491,4 +490,5 @@ class TestCorrelation(TestCase): [None, None, None, None, 2, None, None, 3, None, None], (0.0, 2)]]: with self.subTest(dbdata=dbdata, userdata=userdata): - self.assertEqual(compute_correlation(dbdata, userdata), expected) + self.assertEqual(compute_correlation( + dbdata, userdata), expected) |