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-rw-r--r--tests/unit/db/test_sample_data.py236
1 files changed, 142 insertions, 94 deletions
diff --git a/tests/unit/db/test_sample_data.py b/tests/unit/db/test_sample_data.py
index 0fa2604..2524e07 100644
--- a/tests/unit/db/test_sample_data.py
+++ b/tests/unit/db/test_sample_data.py
@@ -1,3 +1,4 @@
+"""Tests for gn3.db.sample_data"""
import pytest
import gn3
@@ -9,132 +10,179 @@ from gn3.db.sample_data import update_sample_data
@pytest.mark.unit_test
def test_insert_sample_data(mocker):
+ """Test that inserts work properly"""
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.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):
+ """Test that deletes work properly"""
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.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": "BXD1,18",
- "csv_header": "Strain Name,Value"},
- "insert": {"data": "BXD1,2,F",
- "csv_header": "Strain Name,SE,Sex"},
- "update": {"data": "BXD1,1",
- "csv_header": "Strain Name,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": "BXD1,2,F",
- "csv_header": "Strain Name,SE,Sex"},
- "update": {"data": "BXD1,19,1",
- "csv_header": "Strain Name,Value,Count"},
- })
+ """Test that extracting the correct dict of 'actions' work properly"""
+ 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": "BXD1,18", "csv_header": "Strain Name,Value"},
+ "insert": {"data": "BXD1,2,F", "csv_header": "Strain Name,SE,Sex"},
+ "update": {"data": "BXD1,1", "csv_header": "Strain Name,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": "BXD1,2,F", "csv_header": "Strain Name,SE,Sex"},
+ "update": {"data": "BXD1,19,1", "csv_header": "Strain Name,Value,Count"},
+ }
@pytest.mark.unit_test
def test_update_sample_data(mocker):
+ """Test that updates work properly"""
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)
+ 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,
+ )
+ # pylint: disable=[E1101]
gn3.db.sample_data.insert_sample_data.assert_called_once_with(
conn=mock_conn,
trait_name=35,
data="BXD1,2,F",
csv_header="Strain Name,SE,Sex",
- phenotype_id=10007)
+ phenotype_id=10007,
+ )
+ # pylint: disable=[E1101]
gn3.db.sample_data.delete_sample_data.assert_called_once_with(
conn=mock_conn,
trait_name=35,
data="BXD1,18",
csv_header="Strain Name,Value",
- phenotype_id=10007)
+ 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)
+ [
+ mocker.call(
+ "UPDATE NStrain SET count = %s "
+ "WHERE StrainId = %s AND DataId = %s",
+ ("1", strain_id, data_id),
+ )
+ ],
+ any_order=False,
+ )
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 18:43:05 +0000