1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
|
"""module contains integration tests for correlation"""
from unittest import TestCase
from unittest import mock
import pytest
from gn3.app import create_app
class CorrelationIntegrationTest(TestCase):
"""class for correlation integration tests"""
def setUp(self):
self.app = create_app().test_client()
@pytest.mark.integration_test
@mock.patch("gn3.api.correlation.compute_all_sample_correlation")
def test_sample_r_correlation(self, mock_compute_samples):
"""Test /api/correlation/sample_r/{method}"""
this_trait_data = {
"trait_id": "1455376_at",
"trait_sample_data": {
"C57BL/6J": "6.138",
"DBA/2J": "6.266",
"B6D2F1": "6.434",
"D2B6F1": "6.55",
"BXS2": "6.7"
}}
traits_dataset = [
{
"trait_id": "14192_at",
"trait_sample_data": {
"DBA/2J": "7.13",
"D2B6F1": "5.65",
"BXD2": "1.46"
}
}
]
correlation_input_data = {"corr_method": "pearson",
"this_trait": this_trait_data,
"target_dataset": traits_dataset}
expected_results = [
{
"sample_r": "-0.407",
"p_value": "6.234e-04"
},
{
"sample_r": "0.398",
"sample_p": "8.614e-04"
}
]
mock_compute_samples.return_value = expected_results
api_response = {
"corr_results": expected_results
}
response = self.app.post("/api/correlation/sample_r/pearson",
json=correlation_input_data, follow_redirects=True)
self.assertEqual(response.status_code, 200)
self.assertEqual(response.get_json(), api_response)
@pytest.mark.integration_test
@mock.patch("gn3.api.correlation.compute_all_lit_correlation")
@mock.patch("gn3.api.correlation.database_connector")
def test_lit_correlation(self, database_connector, mock_compute_corr):
"""Test api/correlation/lit_corr/{species}/{gene_id}"""
mock_compute_corr.return_value = []
database_connector.return_value = (mock.Mock(), mock.Mock())
post_data = {"1426678_at": "68031",
"1426679_at": "68036",
"1426680_at": "74777"}
response = self.app.post(
"/api/correlation/lit_corr/mouse/16", json=post_data, follow_redirects=True)
self.assertEqual(mock_compute_corr.call_count, 1)
self.assertEqual(response.status_code, 200)
@pytest.mark.integration_test
@mock.patch("gn3.api.correlation.compute_tissue_correlation")
def test_tissue_correlation(self, mock_tissue_corr):
"""Test api/correlation/tissue_corr/{corr_method}"""
mock_tissue_corr.return_value = {}
target_trait_symbol_dict = {
"1418702_a_at": "Bxdc1", "1412_at": "Bxdc2"}
symbol_tissue_dict = {
"bxdc1": [12, 21.1, 11.4, 16.7], "bxdc2": [12, 20.1, 12.4, 1.1]}
primary_dict = {"trait_id": "1449593_at", "tissue_values": [1, 2, 3]}
target_tissue_data = {
"trait_symbol_dict": target_trait_symbol_dict,
"symbol_tissue_vals_dict": symbol_tissue_dict
}
tissue_corr_input_data = {"primary_tissue": primary_dict,
"target_tissues_dict": target_tissue_data}
response = self.app.post("/api/correlation/tissue_corr/spearman",
json=tissue_corr_input_data, follow_redirects=True)
self.assertEqual(response.status_code, 200)
|
