Bump sqlalchemy from 1.4.46 to 2.0.1

Pipfile

@@ -29,7 +29,7 @@ pyodbc = "~=4.0"
 python-dotenv = "~=1.0"
 requests = "~=2.28"
 slackclient = "~=2.9"
-sqlalchemy = "~=1.4"
+sqlalchemy = "~=2.0"
 pymongo = "~=4.3.3"
 
 [requires]

lighthouse/helpers/mysql.py

@@ -34,8 +34,8 @@ def get_table(sql_engine: Engine, table_name: str) -> Table:
     Returns:
         Table: a SQLAlchemy Table object.
     """
-    metadata = MetaData(sql_engine)
+    metadata = MetaData()
 
-    metadata.reflect()
+    metadata.reflect(sql_engine)
 
     return metadata.tables[table_name]

setup_test_db.py

@@ -1,4 +1,6 @@
 # flake8: noqa
+from sqlalchemy import text
+
 import lighthouse.config.test as config
 from lighthouse.helpers.mysql import create_mysql_connection_engine
 
@@ -11,6 +13,7 @@
 create_db = """
 CREATE DATABASE IF NOT EXISTS `unified_warehouse_test` /*!40100 DEFAULT CHARACTER SET latin1 */;
 """
+
 drop_table_lh_sample = """
 DROP TABLE IF EXISTS `unified_warehouse_test`.`lighthouse_sample`;
 """
@@ -186,25 +189,25 @@
 """
 
 with sql_engine.connect() as connection:
-    connection.execute(create_db)
+    connection.execute(text(create_db))
 
     print("*** Dropping table LIGHTHOUSE SAMPLE ***")
-    connection.execute(drop_table_lh_sample)
+    connection.execute(text(drop_table_lh_sample))
     print("*** Dropping table STOCK RESOURCE ***")
-    connection.execute(drop_table_stock_resource)
+    connection.execute(text(drop_table_stock_resource))
     print("*** Dropping table STUDY ***")
-    connection.execute(drop_table_study)
+    connection.execute(text(drop_table_study))
     print("*** Dropping table SAMPLE ***")
-    connection.execute(drop_table_sample)
+    connection.execute(text(drop_table_sample))
 
     print("*** Creating table SAMPLE ***")
-    connection.execute(create_table_sample)
+    connection.execute(text(create_table_sample))
     print("*** Creating table STUDY ***")
-    connection.execute(create_table_study)
+    connection.execute(text(create_table_study))
     print("*** Creating table STOCK RESOURCE ***")
-    connection.execute(create_table_stock_resource)
+    connection.execute(text(create_table_stock_resource))
     print("*** Creating table LIGHTHOUSE SAMPLE ***")
-    connection.execute(create_table_lh_sample)
+    connection.execute(text(create_table_lh_sample))
 
 print("Initialising the test MySQL events warehouse database")
 
@@ -350,36 +353,36 @@
 
 
 with sql_engine.connect() as connection:
-    connection.execute(create_db)
+    connection.execute(text(create_db))
 
     print("*** Dropping table ROLES ***")
-    connection.execute(drop_table_roles)
+    connection.execute(text(drop_table_roles))
     print("*** Dropping table ROLE TYPES ***")
-    connection.execute(drop_table_role_types)
+    connection.execute(text(drop_table_role_types))
     print("*** Dropping table EVENTS ***")
-    connection.execute(drop_table_events)
+    connection.execute(text(drop_table_events))
     print("*** Dropping table EVENT TYPES ***")
-    connection.execute(drop_table_event_types)
+    connection.execute(text(drop_table_event_types))
     print("*** Dropping table SUBJECT ***")
-    connection.execute(drop_table_subjects)
+    connection.execute(text(drop_table_subjects))
     print("*** Dropping table SUBJECT TYPES ***")
-    connection.execute(drop_table_subject_types)
+    connection.execute(text(drop_table_subject_types))
     print("*** Dropping view CHERRYPICKED SAMPLES ***")
-    connection.execute(drop_view_cherrypicked_samples)
+    connection.execute(text(drop_view_cherrypicked_samples))
 
     print("*** Creating table SUBJECT TYPES ***")
-    connection.execute(create_table_subject_types)
+    connection.execute(text(create_table_subject_types))
     print("*** Creating table SUBJECTS ***")
-    connection.execute(create_table_subjects)
+    connection.execute(text(create_table_subjects))
     print("*** Creating table EVENT TYPES ***")
-    connection.execute(create_table_event_types)
+    connection.execute(text(create_table_event_types))
     print("*** Creating table EVENTS ***")
-    connection.execute(create_table_events)
+    connection.execute(text(create_table_events))
     print("*** Creating table ROLE TYPES ***")
-    connection.execute(create_table_role_types)
+    connection.execute(text(create_table_role_types))
     print("*** Creating table ROLES ***")
-    connection.execute(create_table_roles)
+    connection.execute(text(create_table_roles))
     print("*** Creating view CHERRYPICKED SAMPLES ***")
-    connection.execute(create_cherrypicked_samples_view)
+    connection.execute(text(create_cherrypicked_samples_view))
 
 print("Done")