🧪 TESTS: SQLA Migrations -> pytest (#5192)

This PR primarily converts the SQLA Migrations tests,
from using `AiidaTestCase` to using pytest fixtures,
and splits them out into multiple files
(to improve readability).

The tests are functionally equivalent,
just restructured and with a reduction in duplication when using `sqlalchemy.Session` contexts
(hence the reduction in lines).

One more test has been added (`tests/backends/aiida_sqlalchemy/migrations/test_all_basic.py`),
to cycle though all migration versions and try migrating them down&up from&to the latest revision
(against an empty database).
The list of versions is dynamically generated,
to ensure none are missed.

To ensure a fully empty database,
an option has been added to the test manager `aiida_profile.reset_db(with_user=False)` (defaults to `True`),
whereby the default User will not be auto-generated.
This was required for some migrations to succeed when migrating `down` then `up`,
and was how the current unittest implementation worked.

aiida/manage/tests/main.py

@@ -117,8 +117,8 @@ def use_profile(self, profile_name):
     def has_profile_open(self):
         return self._manager and self._manager.has_profile_open()
 
-    def reset_db(self):
-        return self._manager.reset_db()
+    def reset_db(self, with_user=True):
+        return self._manager.reset_db(with_user=with_user)
 
     def destroy_all(self):
         if self._manager:
@@ -166,20 +166,20 @@ def _select_db_test_case(self, backend):
             self._test_case = SqlAlchemyTests()
             self._test_case.test_session = get_scoped_session()
 
-    def reset_db(self):
+    def reset_db(self, with_user=True):
         self._test_case.clean_db()  # will drop all users
         manager.reset_manager()
-        self.init_db()
+        self.init_db(with_user=with_user)
 
-    def init_db(self):
+    def init_db(self, with_user=True):
         """Initialise the database state for running of tests.
 
         Adds default user if necessary.
         """
         from aiida.cmdline.commands.cmd_user import set_default_user
         from aiida.orm import User
 
-        if not User.objects.get_default():
+        if with_user and not User.objects.get_default():
             user_dict = get_user_dict(_DEFAULT_PROFILE_INFO)
             try:
                 user = User(**user_dict)

tests/backends/aiida_sqlalchemy/migrations/conftest.py

@@ -0,0 +1,93 @@
+# -*- coding: utf-8 -*-
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved.                     #
+# This file is part of the AiiDA code.                                    #
+#                                                                         #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file        #
+# For further information please visit http://www.aiida.net               #
+###########################################################################
+"""Tests for the migration engine (Alembic) as well as for the AiiDA migrations for SQLAlchemy."""
+from contextlib import contextmanager
+from typing import Iterator
+
+import pytest
+from sqlalchemy.orm import Session
+
+from aiida.backends.sqlalchemy.manager import SqlaBackendManager
+
+
+class Migrator:
+    """A class to yield from the ``perform_migrations`` fixture."""
+
+    def __init__(self, backend, manager: SqlaBackendManager) -> None:
+        self.backend = backend
+        self._manager = manager
+
+    def migrate_up(self, revision: str) -> None:
+        """Migrate up to a given revision."""
+        self._manager.migrate_up(revision)
+        if revision != 'head':
+            assert self._manager.get_schema_version_backend() == revision
+
+    def migrate_down(self, revision: str) -> None:
+        """Migrate down to a given revision."""
+        self._manager.migrate_down(revision)
+        assert self._manager.get_schema_version_backend() == revision
+
+    def get_current_table(self, table_name):
+        """
+        Return a Model instantiated at the correct migration.
+        Note that this is obtained by inspecting the database and not
+        by looking into the models file.
+        So, special methods possibly defined in the models files/classes are not present.
+
+        For instance, you can do::
+
+          DbGroup = self.get_current_table('db_dbgroup')
+
+        :param table_name: the name of the table.
+        """
+        from alembic.migration import MigrationContext  # pylint: disable=import-error
+        from sqlalchemy.ext.automap import automap_base  # pylint: disable=import-error,no-name-in-module
+
+        with self.backend.get_session().bind.begin() as connection:
+            context = MigrationContext.configure(connection)
+            bind = context.bind
+
+            base = automap_base()
+            # reflect the tables
+            base.prepare(autoload_with=bind.engine)
+
+            return getattr(base.classes, table_name)
+
+    @contextmanager
+    def session(self) -> Iterator[Session]:
+        """A context manager for a new session."""
+        with self.backend.get_session().bind.begin() as connection:
+            session = Session(connection.engine, future=True)
+            try:
+                yield session
+            except Exception:
+                session.rollback()
+                raise
+            finally:
+                session.close()
+
+
+@pytest.fixture()
+def perform_migrations(aiida_profile, backend, request):
+    """A fixture to setup the database for migration tests"""
+    # note downgrading to 1830c8430131 requires adding columns to `DbUser` and hangs if a user is present
+    aiida_profile.reset_db(with_user=False)
+    migrator = Migrator(backend, SqlaBackendManager())
+    marker = request.node.get_closest_marker('migrate_down')
+    if marker is not None:
+        assert marker.args, 'No version given'
+        migrator.migrate_down(marker.args[0])
+    yield migrator
+    # clear the database
+    # note this assumes the current schema contains the tables specified in `clean_db`
+    aiida_profile.reset_db(with_user=False)
+    # ensure that the database is migrated back up to the latest version, once finished
+    migrator.migrate_up('head')

tests/backends/aiida_sqlalchemy/migrations/test_10_group_update.py

@@ -0,0 +1,102 @@
+# -*- coding: utf-8 -*-
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved.                     #
+# This file is part of the AiiDA code.                                    #
+#                                                                         #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file        #
+# For further information please visit http://www.aiida.net               #
+###########################################################################
+"""Tests for group migrations: 118349c10896 -> 0edcdd5a30f0"""
+from .conftest import Migrator
+
+
+def test_group_typestring(perform_migrations: Migrator):
+    """Test the migration that renames the DbGroup type strings.
+
+    Verify that the type strings are properly migrated.
+    """
+    # starting revision
+    perform_migrations.migrate_down('118349c10896')  # 118349c10896_default_link_label.py
+
+    # setup the database
+    DbGroup = perform_migrations.get_current_table('db_dbgroup')  # pylint: disable=invalid-name
+    DbUser = perform_migrations.get_current_table('db_dbuser')  # pylint: disable=invalid-name
+    with perform_migrations.session() as session:
+        default_user = DbUser(email='[email protected]')
+        session.add(default_user)
+        session.commit()
+
+        # test user group type_string: 'user' -> 'core'
+        group_user = DbGroup(label='01', user_id=default_user.id, type_string='user')
+        session.add(group_user)
+        # test upf group type_string: 'data.upf' -> 'core.upf'
+        group_data_upf = DbGroup(label='02', user_id=default_user.id, type_string='data.upf')
+        session.add(group_data_upf)
+        # test auto.import group type_string: 'auto.import' -> 'core.import'
+        group_autoimport = DbGroup(label='03', user_id=default_user.id, type_string='auto.import')
+        session.add(group_autoimport)
+        # test auto.run group type_string: 'auto.run' -> 'core.auto'
+        group_autorun = DbGroup(label='04', user_id=default_user.id, type_string='auto.run')
+        session.add(group_autorun)
+
+        session.commit()
+
+        # Store values for later tests
+        group_user_pk = group_user.id
+        group_data_upf_pk = group_data_upf.id
+        group_autoimport_pk = group_autoimport.id
+        group_autorun_pk = group_autorun.id
+
+    # migrate up
+    perform_migrations.migrate_up('bf591f31dd12')  # bf591f31dd12_dbgroup_type_string.py
+
+    # perform some checks
+    DbGroup = perform_migrations.get_current_table('db_dbgroup')  # pylint: disable=invalid-name
+    with perform_migrations.session() as session:
+        group_user = session.query(DbGroup).filter(DbGroup.id == group_user_pk).one()
+        assert group_user.type_string == 'core'
+
+        # test upf group type_string: 'data.upf' -> 'core.upf'
+        group_data_upf = session.query(DbGroup).filter(DbGroup.id == group_data_upf_pk).one()
+        assert group_data_upf.type_string == 'core.upf'
+
+        # test auto.import group type_string: 'auto.import' -> 'core.import'
+        group_autoimport = session.query(DbGroup).filter(DbGroup.id == group_autoimport_pk).one()
+        assert group_autoimport.type_string == 'core.import'
+
+        # test auto.run group type_string: 'auto.run' -> 'core.auto'
+        group_autorun = session.query(DbGroup).filter(DbGroup.id == group_autorun_pk).one()
+        assert group_autorun.type_string == 'core.auto'
+
+
+def test_group_extras(perform_migrations: Migrator):
+    """Test migration to add the `extras` JSONB column to the `DbGroup` model.
+
+    Verify that the model now has an extras column with empty dictionary as default.
+    """
+    # starting revision
+    perform_migrations.migrate_down('bf591f31dd12')  # bf591f31dd12_dbgroup_type_string.py
+
+    # setup the database
+    DbGroup = perform_migrations.get_current_table('db_dbgroup')  # pylint: disable=invalid-name
+    DbUser = perform_migrations.get_current_table('db_dbuser')  # pylint: disable=invalid-name
+    with perform_migrations.session() as session:
+        default_user = DbUser(email='[email protected]')
+        session.add(default_user)
+        session.commit()
+
+        group = DbGroup(label='01', user_id=default_user.id, type_string='user')
+        session.add(group)
+        session.commit()
+
+        group_pk = group.id
+
+    # migrate up
+    perform_migrations.migrate_up('0edcdd5a30f0')  # 0edcdd5a30f0_dbgroup_extras.py
+
+    # perform some checks
+    DbGroup = perform_migrations.get_current_table('db_dbgroup')  # pylint: disable=invalid-name
+    with perform_migrations.session() as session:
+        group = session.query(DbGroup).filter(DbGroup.id == group_pk).one()
+        assert group.extras == {}