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authorBonfaceKilz2022-04-06 15:53:18 +0300
committerBonfaceKilz2022-04-07 11:54:28 +0300
commita7b7cdd1a5f1a9d071c5fd11c6f1fefa5302a838 (patch)
tree9bbbc43c05d55afcd8961a666ec4b7b936bf5de9 /tests
parent9e905e596f2b1b17ad78a86fff01aafe1cc8b108 (diff)
downloadgenenetwork3-a7b7cdd1a5f1a9d071c5fd11c6f1fefa5302a838.tar.gz
Use case attribute id inside brackets if present during updates
* gn3/db/sample_data.py: Import "parse_csv_column". (update_sample_data): If an id is present in the column header, use it. * tests/unit/db/test_sample_data.py (test_update_sample_data): Update tests to capture the above.
Diffstat (limited to 'tests')
-rw-r--r--tests/unit/db/test_sample_data.py27
1 files changed, 21 insertions, 6 deletions
diff --git a/tests/unit/db/test_sample_data.py b/tests/unit/db/test_sample_data.py
index dad7169..af00393 100644
--- a/tests/unit/db/test_sample_data.py
+++ b/tests/unit/db/test_sample_data.py
@@ -154,7 +154,6 @@ 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),
@@ -164,19 +163,20 @@ def test_update_sample_data(mocker):
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",
+ original_data="BXD1,18,x,0,x,M,x,Red",
+ updated_data="BXD1,x,2,1,2,F,2,Green",
+ csv_header="Strain Name,Value,SE,Count,pH,Sex (13),Age,Color",
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",
+ data="BXD1,2,2,2",
+ csv_header="Strain Name,SE,pH,Age",
phenotype_id=10007,
)
+
# pylint: disable=[E1101]
gn3.db.sample_data.delete_sample_data.assert_called_once_with(
conn=mock_conn,
@@ -185,12 +185,27 @@ def test_update_sample_data(mocker):
csv_header="Strain Name,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),
+ ),
+ mocker.call(
+ "UPDATE CaseAttributeXRefNew SET Value = %s "
+ "WHERE StrainId = %s AND CaseAttributeId = %s AND "
+ "InbredSetId = %s",
+ ("F", strain_id, "13", inbredset_id),
+ ),
+ mocker.call(
+ "UPDATE CaseAttributeXRefNew SET Value = %s "
+ "WHERE StrainId = %s AND CaseAttributeId = "
+ "(SELECT CaseAttributeId FROM "
+ "CaseAttribute WHERE Name = %s) "
+ "AND InbredSetId = %s",
+ ("Green", strain_id, "Color", inbredset_id),
)
],
any_order=False,