diff options
| -rw-r--r-- | gn3/db/__init__.py | 16 | ||||
| -rw-r--r-- | tests/unit/db/test_phenotypes.py | 10 |
2 files changed, 13 insertions, 13 deletions
diff --git a/gn3/db/__init__.py b/gn3/db/__init__.py index 8b6bf73..ce92a7d 100644 --- a/gn3/db/__init__.py +++ b/gn3/db/__init__.py @@ -43,18 +43,20 @@ def update(conn: Any, """Run an UPDATE on a table""" if not (any(astuple(data)) and any(astuple(where))): return None + data_ = {k: v for k, v in asdict(data).items() + if v is not None and k in TABLEMAP[table]} + where_ = {k: v for k, v in asdict(where).items() + if v is not None and k in TABLEMAP[table]} sql = f"UPDATE {table} SET " sql += ", ".join(f"{TABLEMAP[table].get(k)} " - f"= '{escape_string(str(v)).decode('utf-8')}'" for - k, v in asdict(data).items() - if v is not None and k in TABLEMAP[table]) + "= %s" for k in data_.keys()) sql += " WHERE " sql += " AND ".join(f"{TABLEMAP[table].get(k)} = " - f"'{escape_string(str(v)).decode('utf-8')}'" for - k, v in asdict(where).items() - if v is not None and k in TABLEMAP[table]) + "%s" for k in where_.keys()) with conn.cursor() as cursor: - cursor.execute(sql) + cursor.execute(sql, + tuple(data_.values()) + tuple(where_.values())) + conn.commit() return cursor.rowcount diff --git a/tests/unit/db/test_phenotypes.py b/tests/unit/db/test_phenotypes.py index fdeca5e..21eb757 100644 --- a/tests/unit/db/test_phenotypes.py +++ b/tests/unit/db/test_phenotypes.py @@ -37,12 +37,10 @@ class TestPhenotypes(TestCase): where=Phenotype(id_=1, owner="Rob")), 1) cursor.execute.assert_called_once_with( "UPDATE Phenotype SET " - "Pre_publication_description = " - "'Test Pre Pub', " - "Post_publication_description = " - "'Test Post Pub', Submitter = 'Rob' " - "WHERE id = '1' AND Owner = 'Rob'" - ) + "Pre_publication_description = %s, " + "Post_publication_description = %s, " + "Submitter = %s WHERE id = %s AND Owner = %s", + ('Test Pre Pub', 'Test Post Pub', 'Rob', 1, 'Rob')) def test_fetch_phenotype(self): """Test that a single phenotype is fetched properly |