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authorBonfaceKilz2021-05-17 09:15:04 +0300
committerGitHub2021-05-17 09:15:04 +0300
commit7884948a77ca352a16879e3c9d0bb6e6ffb7408e (patch)
treed5dd5bf9233c326166177981f458b2e33bb5b17f /tests/unit
parent46a96ec0b89620eed4874ada565a9643ac19a042 (diff)
parent72dbf91c9f053aa1eb5fa7fc52103b4b8ac71a58 (diff)
downloadgenenetwork3-7884948a77ca352a16879e3c9d0bb6e6ffb7408e.tar.gz
Merge pull request #11 from genenetwork/feature/minor-fixes
Feature/minor fixes
Diffstat (limited to 'tests/unit')
-rw-r--r--tests/unit/computations/test_correlation.py45
1 files changed, 17 insertions, 28 deletions
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index 6414c3b..d264738 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -10,9 +10,8 @@ from gn3.computations.correlations import do_bicor
from gn3.computations.correlations import compute_sample_r_correlation
from gn3.computations.correlations import compute_all_sample_correlation
from gn3.computations.correlations import filter_shared_sample_keys
-from gn3.computations.correlations import tissue_lit_corr_for_probe_type
-from gn3.computations.correlations import tissue_correlation_for_trait_list
-from gn3.computations.correlations import lit_correlation_for_trait_list
+from gn3.computations.correlations import tissue_correlation_for_trait
+from gn3.computations.correlations import lit_correlation_for_trait
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
@@ -214,20 +213,8 @@ class TestCorrelation(TestCase):
filter_shared_samples.assert_called_once_with(
this_trait_data.get("trait_sample_data"), traits_dataset[0].get("trait_sample_data"))
- @unittest.skip("not implemented")
- def test_tissue_lit_corr_for_probe_type(self):
- """Tests for doing tissue and lit correlation for trait list\
- if both the dataset and target dataset are probeset runs\
- on after initial correlation has been done
- """
-
- results = tissue_lit_corr_for_probe_type(
- corr_type="tissue", top_corr_results={})
-
- self.assertEqual(results, (None, None))
-
@mock.patch("gn3.computations.correlations.compute_corr_coeff_p_value")
- def test_tissue_correlation_for_trait_list(self, mock_compute_corr_coeff):
+ def test_tissue_correlation_for_trait(self, mock_compute_corr_coeff):
"""Test given a primary tissue values for a trait and and a list of\
target tissues for traits do the tissue correlation for them
"""
@@ -236,8 +223,8 @@ class TestCorrelation(TestCase):
target_tissues_values = [1, 2, 3]
mock_compute_corr_coeff.side_effect = [(0.4, 0.9), (-0.2, 0.91)]
expected_tissue_results = {"1456_at": {"tissue_corr": 0.4,
- "p_value": 0.9, "tissue_number": 3}}
- tissue_results = tissue_correlation_for_trait_list(
+ "tissue_p_val": 0.9, "tissue_number": 3}}
+ tissue_results = tissue_correlation_for_trait(
primary_tissue_values, target_tissues_values,
corr_method="pearson", trait_id="1456_at",
compute_corr_p_value=mock_compute_corr_coeff)
@@ -246,7 +233,7 @@ class TestCorrelation(TestCase):
@mock.patch("gn3.computations.correlations.fetch_lit_correlation_data")
@mock.patch("gn3.computations.correlations.map_to_mouse_gene_id")
- def test_lit_correlation_for_trait_list(self, mock_mouse_gene_id, fetch_lit_data):
+ def test_lit_correlation_for_trait(self, mock_mouse_gene_id, fetch_lit_data):
"""Fetch results from db call for lit correlation given a trait list\
after doing correlation
"""
@@ -260,7 +247,7 @@ class TestCorrelation(TestCase):
fetch_lit_data.side_effect = [(15, 9), (17, 8), (11, 12)]
- lit_results = lit_correlation_for_trait_list(
+ lit_results = lit_correlation_for_trait(
conn=conn, target_trait_lists=target_trait_lists,
species="rat", trait_gene_id="12")
@@ -289,7 +276,7 @@ class TestCorrelation(TestCase):
input trait mouse gene id and mouse gene id
"""
- expected_db_results = [namedtuple("lit_coeff", "val")(x*0.1)
+ expected_db_results = [("val", x*0.1)
for x in range(1, 4)]
conn = DataBase(expected_results=expected_db_results)
expected_results = ("1", 0.1)
@@ -375,10 +362,10 @@ class TestCorrelation(TestCase):
self.assertEqual(results, expected_results)
- @mock.patch("gn3.computations.correlations.lit_correlation_for_trait_list")
+ @mock.patch("gn3.computations.correlations.lit_correlation_for_trait")
def test_compute_all_lit_correlation(self, mock_lit_corr):
"""Test for compute all lit correlation which acts\
- as an abstraction for lit_correlation_for_trait_list
+ as an abstraction for lit_correlation_for_trait
and is used in the api/correlation/lit
"""
@@ -395,7 +382,7 @@ class TestCorrelation(TestCase):
self.assertEqual(lit_correlation_results, expected_mocked_lit_results)
- @mock.patch("gn3.computations.correlations.tissue_correlation_for_trait_list")
+ @mock.patch("gn3.computations.correlations.tissue_correlation_for_trait")
@mock.patch("gn3.computations.correlations.process_trait_symbol_dict")
def test_compute_all_tissue_correlation(self, process_trait_symbol, mock_tissue_corr):
"""Test for compute all tissue corelation which abstracts
@@ -417,13 +404,15 @@ class TestCorrelation(TestCase):
target_tissue_data = {"trait_symbol_dict": target_trait_symbol,
"symbol_tissue_vals_dict": target_symbol_tissue_vals}
- mock_tissue_corr.side_effect = [{"tissue_corr": -0.5, "p_value": 0.9, "tissue_number": 3},
- {"tissue_corr": 1.11, "p_value": 0.2, "tissue_number": 3}]
+ mock_tissue_corr.side_effect = [{"tissue_corr": -0.5, "tissue_p_val": 0.9,
+ "tissue_number": 3},
+ {"tissue_corr": 1.11, "tissue_p_val": 0.2,
+ "tissue_number": 3}]
expected_results = [{"1412_at":
- {"tissue_corr": 1.11, "p_value": 0.2, "tissue_number": 3}},
+ {"tissue_corr": 1.11, "tissue_p_val": 0.2, "tissue_number": 3}},
{"1418702_a_at":
- {"tissue_corr": -0.5, "p_value": 0.9, "tissue_number": 3}}]
+ {"tissue_corr": -0.5, "tissue_p_val": 0.9, "tissue_number": 3}}]
results = compute_all_tissue_correlation(
primary_tissue_dict=primary_tissue_dict,