aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--gn3/db/sample_data.py21
-rw-r--r--tests/unit/db/test_sample_data.py59
2 files changed, 47 insertions, 33 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py
index 47be5b0..518d2a2 100644
--- a/gn3/db/sample_data.py
+++ b/gn3/db/sample_data.py
@@ -343,25 +343,28 @@ def insert_sample_data(
def __insert_case_attribute(conn, case_attr, value):
if value != "x":
with conn.cursor() as cursor:
- cursor.execute(
- "SELECT Id FROM " "CaseAttribute WHERE Name = %s",
- (case_attr,),
- )
- if case_attr_id := cursor.fetchone():
- case_attr_id = case_attr_id[0]
+ (id_, name) = parse_csv_column(case_attr)
+ if not id_:
+ cursor.execute(
+ "SELECT Id FROM CaseAttribute WHERE Name = %s",
+ (case_attr,),
+ )
+ if case_attr_id := cursor.fetchone():
+ id_ = case_attr_id[0]
+
cursor.execute(
"SELECT StrainId FROM "
"CaseAttributeXRefNew WHERE StrainId = %s "
"AND CaseAttributeId = %s "
"AND InbredSetId = %s",
- (strain_id, case_attr_id, inbredset_id),
+ (strain_id, id_, inbredset_id),
)
- if (not cursor.fetchone()) and case_attr_id:
+ if (not cursor.fetchone()) and id_:
cursor.execute(
"INSERT INTO CaseAttributeXRefNew "
"(StrainId, CaseAttributeId, Value, InbredSetId) "
"VALUES (%s, %s, %s, %s)",
- (strain_id, case_attr_id, value, inbredset_id),
+ (strain_id, id_, value, inbredset_id),
)
row_count = cursor.rowcount
return row_count
diff --git a/tests/unit/db/test_sample_data.py b/tests/unit/db/test_sample_data.py
index af00393..e7d7fb0 100644
--- a/tests/unit/db/test_sample_data.py
+++ b/tests/unit/db/test_sample_data.py
@@ -21,6 +21,7 @@ def test_insert_sample_data(mocker):
19,
],
0,
+ 0,
)
mocker.patch(
"gn3.db.sample_data.get_sample_data_ids",
@@ -29,45 +30,55 @@ def test_insert_sample_data(mocker):
insert_sample_data(
conn=mock_conn,
trait_name=35,
- data="BXD1,18,3,0,M",
- csv_header="Strain Name,Value,SE,Count,Sex",
+ data="BXD1,18,3,0,Red,M",
+ csv_header="Strain Name,Value,SE,Count,Color,Sex (13)",
phenotype_id=10007,
)
calls = [
mocker.call(
- "SELECT Id FROM PublishData where Id = %s "
- "AND StrainId = %s",
- (data_id, strain_id),
+ "SELECT Id FROM PublishData where Id = %s AND StrainId = %s",
+ (17373, 1),
+ ),
+ mocker.call(
+ "INSERT INTO PublishData (StrainId, Id, value) "
+ "VALUES (%s, %s, %s)",
+ (1, 17373, "18"),
+ ),
+ mocker.call(
+ "INSERT INTO PublishSE (StrainId, DataId, error) VALUES "
+ "(%s, %s, %s)",
+ (1, 17373, "3"),
),
mocker.call(
- "INSERT INTO PublishData "
- "(StrainId, Id, value) VALUES (%s, %s, %s)",
- (strain_id, data_id, "18"),
+ "INSERT INTO NStrain (StrainId, DataId, count) VALUES "
+ "(%s, %s, %s)",
+ (1, 17373, "0"),
),
mocker.call(
- "INSERT INTO PublishSE "
- "(StrainId, DataId, error) VALUES (%s, %s, %s)",
- (strain_id, data_id, "3"),
+ "SELECT Id FROM CaseAttribute WHERE Name = %s", ("Color",)
),
mocker.call(
- "INSERT INTO NStrain "
- "(StrainId, DataId, count) VALUES (%s, %s, %s)",
- (strain_id, data_id, "0"),
+ "SELECT StrainId FROM CaseAttributeXRefNew WHERE "
+ "StrainId = %s AND CaseAttributeId = %s AND InbredSetId = %s",
+ (1, 19, 20),
),
mocker.call(
- "SELECT Id FROM CaseAttribute WHERE Name = %s", ("Sex",)
+ "INSERT INTO CaseAttributeXRefNew (StrainId, "
+ "CaseAttributeId, Value, InbredSetId) VALUES "
+ "(%s, %s, %s, %s)",
+ (1, 19, "Red", 20),
),
mocker.call(
- "SELECT StrainId FROM CaseAttributeXRefNew "
- "WHERE StrainId = %s AND "
- "CaseAttributeId = %s AND InbredSetId = %s",
- (strain_id, 19, inbredset_id),
+ "SELECT StrainId FROM CaseAttributeXRefNew WHERE "
+ "StrainId = %s AND CaseAttributeId = %s AND "
+ "InbredSetId = %s",
+ (1, "13", 20),
),
mocker.call(
- "INSERT INTO CaseAttributeXRefNew "
- "(StrainId, CaseAttributeId, Value, "
- "InbredSetId) VALUES (%s, %s, %s, %s)",
- (strain_id, 19, "M", inbredset_id),
+ "INSERT INTO CaseAttributeXRefNew (StrainId, "
+ "CaseAttributeId, Value, InbredSetId) VALUES "
+ "(%s, %s, %s, %s)",
+ (1, "13", "M", 20),
),
]
cursor.execute.assert_has_calls(calls, any_order=False)
@@ -206,7 +217,7 @@ def test_update_sample_data(mocker):
"CaseAttribute WHERE Name = %s) "
"AND InbredSetId = %s",
("Green", strain_id, "Color", inbredset_id),
- )
+ ),
],
any_order=False,
)