use sqlalchemy2 syntax everywhere

compendium_v2/publishers/survey_publisher_2022.py

@@ -13,7 +13,7 @@ import math
 import json
 import html
 
-from sqlalchemy import text
+from sqlalchemy import text, delete
 from collections import defaultdict
 
 import compendium_v2
@@ -228,10 +228,10 @@ def transfer_staff_data(nren_dict):
     for nren_name, nren_info in data.items():
         if sum([nren_info[question] for question in StaffQuestion]) == 0:
             logger.info(f'{nren_name} has no staff data. Deleting if exists.')
-            db.session.query(model.NrenStaff).filter(
+            db.session.execute(delete(model.NrenStaff).where(
                 model.NrenStaff.nren_id == nren_dict[nren_name].id,
-                model.NrenStaff.year == 2022,
-            ).delete()
+                model.NrenStaff.year == 2022
+            ))
             continue
 
         employed = nren_info[StaffQuestion.PERMANENT_FTE] + nren_info[StaffQuestion.SUBCONTRACTED_FTE]
@@ -364,9 +364,9 @@ def transfer_charging_structure(nren_dict):
 
 def transfer_ec_projects(nren_dict):
     # delete all existing EC projects, in case something changed
-    db.session.query(model.ECProject).filter(
-        model.ECProject.year == 2022,
-    ).delete()
+    db.session.execute(
+        delete(model.ECProject).where(model.ECProject.year == 2022)
+    )
 
     rows = query_question(ECQuestion.EC_PROJECT)
     for row in rows:

compendium_v2/publishers/survey_publisher_v1.py

@@ -11,6 +11,8 @@ import logging
 import math
 import click
 
+from sqlalchemy import select
+
 import compendium_v2
 from compendium_v2.environment import setup_logging
 from compendium_v2 import survey_db
@@ -29,7 +31,7 @@ def db_budget_migration(nren_dict):
     with survey_db.session_scope() as survey_session:
 
         # move data from Survey DB budget table
-        data = survey_session.query(survey_model.Nrens)
+        data = survey_session.scalars(select(survey_model.Nrens))
         for nren in data:
             for budget in nren.budgets:
                 abbrev = nren.abbreviation.upper()

test/test_survey_publisher_2022.py

+from sqlalchemy import select
+
 from compendium_v2.db import db, model
 from compendium_v2.publishers.survey_publisher_2022 import _cli, FundingSource, \
     StaffQuestion, OrgQuestion, ChargingStructure, ECQuestion
@@ -193,12 +195,16 @@ def test_publisher(app, mocker, dummy_config):
     _cli(dummy_config, app)
 
     with app.app_context():
-        budgets = db.session.query(model.BudgetEntry).order_by(model.BudgetEntry.nren_id.asc()).all()
+        budgets = db.session.scalars(
+            select(model.BudgetEntry).order_by(model.BudgetEntry.nren_id.asc())
+        ).all()
         assert len(budgets) == 3
         assert budgets[0].nren.name.lower() == 'nren1'
         assert budgets[0].budget == 100
 
-        funding_sources = db.session.query(model.FundingSource).order_by(model.FundingSource.nren_id.asc()).all()
+        funding_sources = db.session.scalars(
+            select(model.FundingSource).order_by(model.FundingSource.nren_id.asc())
+        ).all()
         assert len(funding_sources) == 3
         assert funding_sources[0].nren.name.lower() == 'nren1'
         assert funding_sources[0].client_institutions == 10
@@ -215,7 +221,9 @@ def test_publisher(app, mocker, dummy_config):
         assert funding_sources[2].european_funding == 30
         assert funding_sources[2].other == 30
 
-        staff_data = db.session.query(model.NrenStaff).order_by(model.NrenStaff.nren_id.asc()).all()
+        staff_data = db.session.scalars(
+            select(model.NrenStaff).order_by(model.NrenStaff.nren_id.asc())
+        ).all()
 
         assert len(staff_data) == 3
         assert staff_data[0].nren.name.lower() == 'nren1'
@@ -236,7 +244,9 @@ def test_publisher(app, mocker, dummy_config):
         assert staff_data[2].permanent_fte == 30
         assert staff_data[2].subcontracted_fte == 0
 
-        _org_data = db.session.query(model.ParentOrganization).order_by(model.ParentOrganization.nren_id.asc()).all()
+        _org_data = db.session.scalars(
+            select(model.ParentOrganization).order_by(model.ParentOrganization.nren_id.asc())
+        ).all()
 
         assert len(_org_data) == 2
         assert _org_data[0].nren.name.lower() == 'nren1'
@@ -245,8 +255,9 @@ def test_publisher(app, mocker, dummy_config):
         assert _org_data[1].nren.name.lower() == 'nren3'
         assert _org_data[1].organization == 'Org3'
 
-        charging_structures = db.session.query(model.ChargingStructure).order_by(
-            model.ChargingStructure.nren_id.asc()).all()
+        charging_structures = db.session.scalars(
+            select(model.ChargingStructure).order_by(model.ChargingStructure.nren_id.asc())
+        ).all()
         assert len(charging_structures) == 3
         assert charging_structures[0].nren.name.lower() == 'nren1'
         assert charging_structures[0].fee_type == model.FeeType.no_charge
@@ -255,7 +266,9 @@ def test_publisher(app, mocker, dummy_config):
         assert charging_structures[2].nren.name.lower() == 'nren3'
         assert charging_structures[2].fee_type == model.FeeType.other
 
-        _ec_data = db.session.query(model.ECProject).order_by(model.ECProject.nren_id.asc()).all()
+        _ec_data = db.session.scalars(
+            select(model.ECProject).order_by(model.ECProject.nren_id.asc())
+        ).all()
 
         assert len(_ec_data) == 3
         assert _ec_data[0].nren.name.lower() == 'nren2'

test/test_survey_publisher_v1.py

 import os
 
+from sqlalchemy import select, func
+
 from compendium_v2 import db
 from compendium_v2.db import model
 from compendium_v2.publishers.survey_publisher_v1 import _cli
@@ -18,13 +20,13 @@ def test_publisher(mocked_survey_db, app, mocker, dummy_config):
     _cli(dummy_config, app)
 
     with app.app_context():
-        budget_count = db.session.query(model.BudgetEntry.year).count()
+        budget_count = db.session.scalar(select(func.count(model.BudgetEntry.year)))
         assert budget_count
-        funding_source_count = db.session.query(model.FundingSource.year).count()
+        funding_source_count = db.session.scalar(select(func.count(model.FundingSource.year)))
         assert funding_source_count
-        charging_structure_count = db.session.query(model.ChargingStructure.year).count()
+        charging_structure_count = db.session.scalar(select(func.count(model.ChargingStructure.year)))
         assert charging_structure_count
-        staff_data = db.session.query(model.NrenStaff).order_by(model.NrenStaff.year.asc()).all()
+        staff_data = db.session.scalars(select(model.NrenStaff).order_by(model.NrenStaff.year.asc())).all()
 
         # data should only be saved for the NRENs we have saved in the database
         staff_data_nrens = set([staff.nren.name for staff in staff_data])
@@ -70,7 +72,7 @@ def test_publisher(mocked_survey_db, app, mocker, dummy_config):
         assert kifu_data[5].technical_fte == 133
         assert kifu_data[5].non_technical_fte == 45
 
-        ecproject_data = db.session.query(model.ECProject).all()
+        ecproject_data = db.session.scalars(select(model.ECProject)).all()
         # test a couple of random entries
         surf2017 = [x for x in ecproject_data if x.nren.name == 'SURF' and x.year == 2017]
         assert len(surf2017) == 1
@@ -84,7 +86,7 @@ def test_publisher(mocked_survey_db, app, mocker, dummy_config):
         assert len(kifu2019) == 4
         assert kifu2019[3].project == 'SuperHeroes for Science'
 
-        parent_data = db.session.query(model.ParentOrganization).all()
+        parent_data = db.session.scalars(select(model.ParentOrganization)).all()
         # test a random entry
         asnet2021 = [x for x in parent_data if x.nren.name == 'ASNET-AM' and x.year == 2021]
         assert len(asnet2021) == 1