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import pytest
import gn3
from gn3.db.sample_data import __extract_actions
from gn3.db.sample_data import delete_sample_data
from gn3.db.sample_data import insert_sample_data
from gn3.db.sample_data import update_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)
@pytest.mark.unit_test
def test_extract_actions():
assert (__extract_actions(original_data="BXD1,18,x,0,x",
updated_data="BXD1,x,2,1,F",
csv_header="Strain Name,Value,SE,Count,Sex") ==
{
"delete": {"data": "18", "csv_header": "Value"},
"insert": {"data": "2,F", "csv_header": "SE,Sex"},
"update": {"data": "1", "csv_header": "Count"},
})
assert(__extract_actions(original_data="BXD1,18,x,0,x",
updated_data="BXD1,19,2,1,F",
csv_header="Strain Name,Value,SE,Count,Sex") ==
{
"delete": None,
"insert": {"data": "2,F", "csv_header": "SE,Sex"},
"update": {"data": "19,1", "csv_header": "Value,Count"},
})
@pytest.mark.unit_test
def test_update_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))
mocker.patch('gn3.db.sample_data.insert_sample_data',
return_value=1)
mocker.patch('gn3.db.sample_data.delete_sample_data',
return_value=1)
update_sample_data(conn=mock_conn,
trait_name=35,
original_data="BXD1,18,x,0,x",
updated_data="BXD1,x,2,1,F",
csv_header="Strain Name,Value,SE,Count,Sex",
phenotype_id=10007)
gn3.db.sample_data.insert_sample_data.assert_called_once_with(
conn=mock_conn,
trait_name=35,
data="2,F",
csv_header="SE,Sex",
phenotype_id=10007)
gn3.db.sample_data.delete_sample_data.assert_called_once_with(
conn=mock_conn,
trait_name=35,
data="18",
csv_header="Value",
phenotype_id=10007)
cursor.execute.assert_has_calls(
[mocker.call("UPDATE NStrain SET count = %s "
"WHERE StrainId = %s AND DataId = %s",
('1', strain_id, data_id))],
any_order=False)
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