diff options
| -rw-r--r-- | gn3/db/species.py | 7 | ||||
| -rw-r--r-- | tests/unit/db/test_species.py | 6 |
2 files changed, 7 insertions, 6 deletions
diff --git a/gn3/db/species.py b/gn3/db/species.py index 743e797..e43ec14 100644 --- a/gn3/db/species.py +++ b/gn3/db/species.py @@ -3,7 +3,6 @@ groups. Particularly useful when generating the menu """ from typing import Any, Optional, Tuple -from MySQLdb import escape_string def get_all_species(conn: Any) -> Optional[Tuple]: @@ -23,15 +22,15 @@ def get_chromosome(name: str, is_species: bool, conn: Any) -> Optional[Tuple]: "Length FROM Chr_Length, Species WHERE " "Chr_Length.SpeciesId = Species.SpeciesId AND " "Species.Name = " - f"'{escape_string(name).decode('UTF-8')}' ORDER BY OrderId") + "%(name)s ORDER BY OrderId") if not is_species: _sql = ("SELECT Chr_Length.Name, Chr_Length.OrderId, " "Length FROM Chr_Length, InbredSet WHERE " "Chr_Length.SpeciesId = InbredSet.SpeciesId AND " "InbredSet.Name = " - f"'{escape_string(name).decode('UTF-8')}' ORDER BY OrderId") + "%(name)s ORDER BY OrderId") with conn.cursor() as cursor: - cursor.execute(_sql) + cursor.execute(_sql, {'name': name}) return cursor.fetchall() def translate_to_mouse_gene_id(species: str, geneid: int, conn: Any) -> int: diff --git a/tests/unit/db/test_species.py b/tests/unit/db/test_species.py index 073931e..ee9658f 100644 --- a/tests/unit/db/test_species.py +++ b/tests/unit/db/test_species.py @@ -24,7 +24,8 @@ class TestChromosomes(TestCase): "SELECT Chr_Length.Name, Chr_Length.OrderId, " "Length FROM Chr_Length, Species WHERE " "Chr_Length.SpeciesId = Species.SpeciesId AND " - "Species.Name = 'TestCase' ORDER BY OrderId" + "Species.Name = %(name)s ORDER BY OrderId", + {'name': 'TestCase'} ) @pytest.mark.unit_test @@ -40,7 +41,8 @@ class TestChromosomes(TestCase): "SELECT Chr_Length.Name, Chr_Length.OrderId, " "Length FROM Chr_Length, InbredSet WHERE " "Chr_Length.SpeciesId = InbredSet.SpeciesId AND " - "InbredSet.Name = 'TestCase' ORDER BY OrderId" + "InbredSet.Name = %(name)s ORDER BY OrderId", + {'name': 'TestCase'} ) @pytest.mark.unit_test |