Bump sqlalchemy from 1.4.46 to 2.0.1

Pipfile

@@ -32,7 +32,7 @@ pysftp = "~=0.2"
 python-dotenv = "~=1.0"
 requests = "~=2.28"
 slackclient = "~=2.9"
-sqlalchemy = "~=1.4"
+sqlalchemy = "~=2.0"
 lab-share-lib = { git = 'https://github.com/sanger/lab-share-lib.git', ref = 'master', editable = false }
 
 [requires]

setup_test_db.py

@@ -1,4 +1,6 @@
 # flake8: noqa
+from sqlalchemy import text
+
 import crawler.config.test as config
 from crawler.db.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`;
 """
@@ -204,25 +207,25 @@
 """
 
 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")
 
@@ -370,36 +373,36 @@
 """
 
 with sql_engine.connect() as connection:
-    connection.execute(create_db)
+    connection.execute(text(create_db))
 
     print("*** Dropping view CHERRYPICKED SAMPLES ***")
-    connection.execute(drop_view_cherrypicked_samples)
+    connection.execute(text(drop_view_cherrypicked_samples))
     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("*** 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")

tests/conftest.py

@@ -442,8 +442,8 @@ def delete_sql_engine_tables(engine, tables):
 
 
 def get_table(sql_engine, table_name):
-    metadata = MetaData(sql_engine)
-    metadata.reflect()
+    metadata = MetaData()
+    metadata.reflect(sql_engine)
     return metadata.tables[table_name]
 
 

tests/migrations/test_back_populate_source_plate_and_sample_uuids.py

@@ -2,6 +2,7 @@
 
 import pytest
 from pymongo import ASCENDING
+from sqlalchemy import text
 
 from crawler.constants import (
     FIELD_LH_SAMPLE_UUID,
@@ -83,23 +84,23 @@ def test_back_populate_source_plate_uuid_and_sample_uuid_populates_sample_uuid(
         viewed_uuids.append(sample[FIELD_LH_SAMPLE_UUID])
 
     # Now we check in mlwh
-    cursor = query_lighthouse_sample.execute(
-        "SELECT COUNT(*) FROM lighthouse_sample WHERE plate_barcode = '123' AND lh_sample_uuid IS NOT NULL"
+    cursor_result = query_lighthouse_sample.execute(
+        text("SELECT COUNT(*) FROM lighthouse_sample WHERE plate_barcode = '123' AND lh_sample_uuid IS NOT NULL")
     )
 
-    sample_count = cursor.fetchone()[0]
+    sample_count = cursor_result.first()[0]
     assert sample_count == len(samples_after)
 
-    cursor = query_lighthouse_sample.execute(
-        "SELECT * FROM lighthouse_sample WHERE plate_barcode = '123' AND lh_sample_uuid IS NOT NULL"
+    cursor_result = query_lighthouse_sample.execute(
+        text("SELECT * FROM lighthouse_sample WHERE plate_barcode = '123' AND lh_sample_uuid IS NOT NULL")
     )
 
-    obtained_mlwh_samples = list(cursor.fetchall())
+    results = list(cursor_result.mappings())
     mongo_dict = {}
     for sample in samples_after:
         mongo_dict[str(sample[FIELD_MONGODB_ID])] = sample[FIELD_LH_SAMPLE_UUID]
     mlwh_dict = {}
-    for mlsample in obtained_mlwh_samples:
+    for mlsample in results:
         mlwh_dict[mlsample[MLWH_MONGODB_ID]] = mlsample[FIELD_LH_SAMPLE_UUID]
 
     for mongo_id in mongo_dict.keys():
@@ -157,23 +158,23 @@ def test_back_populate_source_plate_uuid_and_sample_uuid_has_source_plate_uuid(
         assert sample[FIELD_LH_SOURCE_PLATE_UUID] == source_plate_uuid
 
     # Now we check in mlwh
-    cursor = query_lighthouse_sample.execute(
-        "SELECT COUNT(*) FROM lighthouse_sample WHERE lh_source_plate_uuid IS NOT NULL"
+    cursor_result = query_lighthouse_sample.execute(
+        text("SELECT COUNT(*) FROM lighthouse_sample WHERE lh_source_plate_uuid IS NOT NULL")
     )
 
-    sample_count = cursor.fetchone()[0]
+    sample_count = cursor_result.first()[0]
     assert sample_count == len(samples_after)
 
-    cursor = query_lighthouse_sample.execute(
-        "SELECT * FROM lighthouse_sample WHERE lh_source_plate_uuid IS NOT NULL ORDER BY mongodb_id ASC"
+    cursor_result = query_lighthouse_sample.execute(
+        text("SELECT * FROM lighthouse_sample WHERE lh_source_plate_uuid IS NOT NULL ORDER BY mongodb_id ASC")
     )
 
-    obtained_mlwh_samples = list(cursor.fetchall())
+    results = list(cursor_result.mappings())
     mongo_dict = {}
     for sample in samples_after:
         mongo_dict[str(sample[FIELD_MONGODB_ID])] = sample[FIELD_LH_SOURCE_PLATE_UUID]
     mlwh_dict = {}
-    for mlsample in obtained_mlwh_samples:
+    for mlsample in results:
         mlwh_dict[mlsample[MLWH_MONGODB_ID]] = mlsample[FIELD_LH_SOURCE_PLATE_UUID]
 
     for mongo_id in mongo_dict.keys():

tests/migrations/test_reconnect_mlwh_with_mongo.py

@@ -1,4 +1,5 @@
 import pytest
+from sqlalchemy import text
 
 from crawler.constants import FIELD_MONGODB_ID, FIELD_PLATE_BARCODE, FIELD_RNA_ID, MLWH_MONGODB_ID, MLWH_RNA_ID
 from migrations import reconnect_mlwh_with_mongo
@@ -35,15 +36,15 @@ def test_reconnect_mlwh_with_mongo_can_connect_with_mlwh(
     reconnect_mlwh_with_mongo.run(config, filepath)
 
     # Now we check in mlwh
-    cursor = query_lighthouse_sample.execute(
-        "SELECT rna_id, mongodb_id FROM lighthouse_sample WHERE plate_barcode = '123'"
+    cursor_result = query_lighthouse_sample.execute(
+        text("SELECT rna_id, mongodb_id FROM lighthouse_sample WHERE plate_barcode = '123'")
     )
+    results = list(cursor_result.mappings())
 
-    obtained_mlwh_samples = list(cursor.fetchall())
-    assert obtained_mlwh_samples[0]["mongodb_id"] == str(samples_in_mongo[0][FIELD_MONGODB_ID])
+    assert results[0]["mongodb_id"] == str(samples_in_mongo[0][FIELD_MONGODB_ID])
 
     mlwh_dict = {}
-    for mlsample in obtained_mlwh_samples:
+    for mlsample in results:
         mlwh_dict[mlsample[MLWH_RNA_ID]] = mlsample[MLWH_MONGODB_ID]
 
     mongo_dict = {}