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| author | BonfaceKilz | 2022-03-02 15:45:34 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2022-03-12 15:33:09 +0300 |
| commit | c8fd4f85e735f1654f44f5a0b3d939b34e708208 (patch) | |
| tree | cc7708e367ce227ca641796bf84d5135e2eef03d /gn3/db | |
| parent | faf6cb2390940fea013ff0a6db2d5dbf2cc41faf (diff) | |
| download | genenetwork3-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')
| -rw-r--r-- | gn3/db/sample_data.py | 27 |
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( |