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
|
import pytest
from gn3.db.sample_data import insert_sample_data
from gn3.db.sample_data import delete_sample_data
@pytest.mark.unit_test
def test_insert_sample_data(mocker):
mock_conn = mocker.MagicMock()
strain_id, data_id, inbredset_id = 1, 17373, 20
with mock_conn.cursor() as cursor:
cursor.fetchone.side_effect = (0, [19, ], 0)
mocker.patch('gn3.db.sample_data.get_sample_data_ids',
return_value=(strain_id, data_id, inbredset_id))
insert_sample_data(conn=mock_conn,
trait_name=35,
data="BXD1,18,3,0,M",
csv_header="Strain Name,Value,SE,Count,Sex",
phenotype_id=10007)
calls = [mocker.call("SELECT Id FROM PublishData where Id = %s "
"AND StrainId = %s",
(data_id, strain_id)),
mocker.call("INSERT INTO PublishData "
"(StrainId, Id, value) VALUES (%s, %s, %s)",
(strain_id, data_id, '18')),
mocker.call("INSERT INTO PublishSE "
"(StrainId, DataId, error) VALUES (%s, %s, %s)",
(strain_id, data_id, '3')),
mocker.call("INSERT INTO NStrain "
"(StrainId, DataId, count) VALUES (%s, %s, %s)",
(strain_id, data_id, '0')),
mocker.call("SELECT Id FROM CaseAttribute WHERE Name = %s",
("Sex",)),
mocker.call("SELECT StrainId FROM CaseAttributeXRefNew "
"WHERE StrainId = %s AND "
"CaseAttributeId = %s AND InbredSetId = %s",
(strain_id, 19, inbredset_id)),
mocker.call("INSERT INTO CaseAttributeXRefNew "
"(StrainId, CaseAttributeId, Value, "
"InbredSetId) VALUES (%s, %s, %s, %s)",
(strain_id, 19, 'M', inbredset_id))
]
cursor.execute.assert_has_calls(calls, any_order=False)
@pytest.mark.unit_test
def test_delete_sample_data(mocker):
mock_conn = mocker.MagicMock()
strain_id, data_id, inbredset_id = 1, 17373, 20
with mock_conn.cursor() as cursor:
cursor.fetchone.side_effect = (0, [19, ], 0)
mocker.patch('gn3.db.sample_data.get_sample_data_ids',
return_value=(strain_id, data_id, inbredset_id))
delete_sample_data(conn=mock_conn,
trait_name=35,
data="BXD1,18,3,0,M",
csv_header="Strain Name,Value,SE,Count,Sex",
phenotype_id=10007)
calls = [mocker.call("DELETE FROM PublishData WHERE "
"StrainId = %s AND Id = %s",
(strain_id, data_id)),
mocker.call("DELETE FROM PublishSE WHERE "
"StrainId = %s AND DataId = %s",
(strain_id, data_id)),
mocker.call("DELETE FROM NStrain WHERE "
"StrainId = %s AND DataId = %s",
(strain_id, data_id)),
mocker.call("DELETE FROM CaseAttributeXRefNew WHERE "
"StrainId = %s AND CaseAttributeId = "
"(SELECT CaseAttributeId FROM "
"CaseAttribute WHERE Name = %s) "
"AND InbredSetId = %s",
(strain_id, "Sex", inbredset_id)),
]
cursor.execute.assert_has_calls(calls, any_order=False)
|
