aboutsummaryrefslogtreecommitdiff
path: root/gn3/db/sample_data.py
diff options
context:
space:
mode:
authorBonfaceKilz2022-03-02 15:45:34 +0300
committerBonfaceKilz2022-03-12 15:33:09 +0300
commitc8fd4f85e735f1654f44f5a0b3d939b34e708208 (patch)
treecc7708e367ce227ca641796bf84d5135e2eef03d /gn3/db/sample_data.py
parentfaf6cb2390940fea013ff0a6db2d5dbf2cc41faf (diff)
downloadgenenetwork3-c8fd4f85e735f1654f44f5a0b3d939b34e708208.tar.gz
Explicitly get CaseAttributeId and fix broken sql query
* gn3/db/sample_data.py (insert_sample_data): Use correct query string. Also, use CaseAttributeId to determine whether case-attributes were inserted. If so, do not attempt an insert.
Diffstat (limited to 'gn3/db/sample_data.py')
-rw-r--r--gn3/db/sample_data.py27
1 files changed, 18 insertions, 9 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py
index dbe968d..3d2faca 100644
--- a/gn3/db/sample_data.py
+++ b/gn3/db/sample_data.py
@@ -270,15 +270,24 @@ def insert_sample_data(conn: Any, # pylint: disable=[R0913]
def __insert_case_attribute(conn, case_attr, value):
if value != "x":
with conn.cursor() as cursor:
- cursor.execute(
- (f"INSERT INTO CaseAttributeXRefNew "
- "StrainId, CaseAttributeId, Value, InbredSetId "
- "VALUES ("
- f"{strain_id}, "
- "(SELECT CaseAttributeId FROM "
- f"CaseAttribute WHERE NAME = %s), "
- "%s)" , (strain_id, case_attr, value, inbredset_id)))
- return cursor.rowcount
+ cursor.execute("SELECT Id FROM "
+ "CaseAttribute WHERE Name = %s",
+ (case_attr,))
+ if case_attr_id := cursor.fetchone():
+ case_attr_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))
+ if (not cursor.fetchone()) and case_attr_id:
+ cursor.execute(
+ "INSERT INTO CaseAttributeXRefNew "
+ "(StrainId, CaseAttributeId, Value, InbredSetId) "
+ "VALUES (%s, %s, %s, %s)",
+ (strain_id, case_attr_id, value, inbredset_id))
+ row_count = cursor.rowcount
+ return row_count
return 0
strain_id, data_id, inbredset_id = get_sample_data_ids(