Remove any use of our ORM in the migrations and tests

Many of the migrations and their respective unit tests used the ORM of
`aiida-core` or the database model classes directly. However, as the
database models evolve and change, during migrations one cannot rely on
the current implementation of the database models or the ORM as it may
not be commensurate of their state at the time of the migration. This
means that the migrations absolutely have to be written relying only on
raw SQL or on the model classes that are provided through the migration
mechanism of the various backends, as they will make sure that those
fake classes reflect the state of the models at the time of the migration.

.pre-commit-config.yaml

@@ -100,7 +100,6 @@
         aiida/backends/tests/cmdline/commands/test_node.py|
         aiida/backends/tests/cmdline/commands/test_user.py|
         aiida/backends/tests/cmdline/commands/test_work.py|
-        aiida/backends/tests/test_computer.py|
         aiida/backends/tests/test_dataclasses.py|
         aiida/backends/tests/test_dbimporters.py|
         aiida/backends/tests/test_export_and_import.py|

aiida/backends/djsite/db/migrations/0026_trajectory_symbols_to_attribute.py

@@ -22,6 +22,7 @@
 from django.db import migrations
 
 from aiida.backends.djsite.db.migrations import upgrade_schema_version
+from aiida.backends.general.migrations.utils import load_numpy_array_from_repository
 from . import ModelModifierV0025
 
 REVISION = '1.0.26'
@@ -30,35 +31,27 @@
 
 def create_trajectory_symbols_attribute(apps, _):
     """Create the symbols attribute from the repository array for all `TrajectoryData` nodes."""
-    from aiida.orm import load_node
-
+    DbNode = apps.get_model('db', 'DbNode')
     DbAttribute = apps.get_model('db', 'DbAttribute')
 
-    modifier = ModelModifierV0025(DbAttribute)
+    modifier = ModelModifierV0025(apps, DbAttribute)
 
-    DbNode = apps.get_model('db', 'DbNode')
-    trajectories_pk = DbNode.objects.filter(type='node.data.array.trajectory.TrajectoryData.').values_list(
-        'id', flat=True)
-    for t_pk in trajectories_pk:
-        trajectory = load_node(t_pk)
-        symbols = trajectory.get_array('symbols').tolist()
-        modifier.set_value_for_node(DbNode.objects.get(pk=trajectory.pk), 'symbols', symbols)
+    nodes = DbNode.objects.filter(type='node.data.array.trajectory.TrajectoryData.').values_list('id', 'uuid')
+    for pk, uuid in nodes:
+        symbols = load_numpy_array_from_repository(uuid, 'symbols').tolist()
+        modifier.set_value_for_node(DbNode.objects.get(pk=pk), 'symbols', symbols)
 
 
 def delete_trajectory_symbols_attribute(apps, _):
     """Delete the symbols attribute for all `TrajectoryData` nodes."""
-    from aiida.orm import load_node
-
+    DbNode = apps.get_model('db', 'DbNode')
     DbAttribute = apps.get_model('db', 'DbAttribute')
 
-    modifier = ModelModifierV0025(DbAttribute)
+    modifier = ModelModifierV0025(apps, DbAttribute)
 
-    DbNode = apps.get_model('db', 'DbNode')
-    trajectories_pk = DbNode.objects.filter(type='node.data.array.trajectory.TrajectoryData.').values_list(
-        'id', flat=True)
-    for t_pk in trajectories_pk:
-        trajectory = load_node(t_pk)
-        modifier.del_value_for_node(DbNode.objects.get(pk=trajectory.pk), 'symbols')
+    nodes = DbNode.objects.filter(type='node.data.array.trajectory.TrajectoryData.').values_list('id', flat=True)
+    for pk in nodes:
+        modifier.del_value_for_node(DbNode.objects.get(pk=pk), 'symbols')
 
 
 class Migration(migrations.Migration):

aiida/backends/djsite/db/migrations/0027_delete_trajectory_symbols_array.py

@@ -22,6 +22,7 @@
 from django.db import migrations
 
 from aiida.backends.djsite.db.migrations import upgrade_schema_version
+from aiida.backends.general.migrations import utils
 from . import ModelModifierV0025
 
 REVISION = '1.0.27'
@@ -30,44 +31,31 @@
 
 def delete_trajectory_symbols_array(apps, _):
     """Delete the symbols array from all `TrajectoryData` nodes."""
-    from aiida.orm import load_node
-
+    DbNode = apps.get_model('db', 'DbNode')
     DbAttribute = apps.get_model('db', 'DbAttribute')
 
-    modifier = ModelModifierV0025(DbAttribute)
+    modifier = ModelModifierV0025(apps, DbAttribute)
 
-    DbNode = apps.get_model('db', 'DbNode')
-    trajectories_pk = DbNode.objects.filter(type='node.data.array.trajectory.TrajectoryData.').values_list(
-        'id', flat=True)
-    for t_pk in trajectories_pk:
-        trajectory = load_node(t_pk)
-        modifier.del_value_for_node(DbNode.objects.get(pk=trajectory.pk), 'array|symbols')
-        trajectory.delete_object('symbols.npy', force=True)
+    nodes = DbNode.objects.filter(type='node.data.array.trajectory.TrajectoryData.').values_list('id', 'uuid')
+    for pk, uuid in nodes:
+        modifier.del_value_for_node(DbNode.objects.get(pk=pk), 'array|symbols')
+        utils.delete_numpy_array_from_repository(uuid, 'symbols')
 
 
 def create_trajectory_symbols_array(apps, _):
     """Create the symbols array for all `TrajectoryData` nodes."""
     import numpy
-    import tempfile
-    from aiida.orm import load_node
 
+    DbNode = apps.get_model('db', 'DbNode')
     DbAttribute = apps.get_model('db', 'DbAttribute')
 
-    modifier = ModelModifierV0025(DbAttribute)
+    modifier = ModelModifierV0025(apps, DbAttribute)
 
-    DbNode = apps.get_model('db', 'DbNode')
-    trajectories_pk = DbNode.objects.filter(type='node.data.array.trajectory.TrajectoryData.').values_list(
-        'id', flat=True)
-    for t_pk in trajectories_pk:
-        trajectory = load_node(t_pk)
-        symbols = numpy.array(trajectory.get_attribute('symbols'))
-        # Save the .npy file (using set_array raises ModificationNotAllowed error)
-        with tempfile.NamedTemporaryFile() as handle:
-            numpy.save(handle, symbols)
-            handle.flush()
-            handle.seek(0)
-            trajectory.put_object_from_filelike(handle, 'symbols.npy')
-        modifier.set_value_for_node(DbNode.objects.get(pk=trajectory.pk), 'array|symbols', list(symbols.shape))
+    nodes = DbNode.objects.filter(type='node.data.array.trajectory.TrajectoryData.').values_list('id', 'uuid')
+    for pk, uuid in nodes:
+        symbols = numpy.array(modifier.get_value_for_node(pk, 'symbols'))
+        utils.store_numpy_array_in_repository(uuid, 'symbols', symbols)
+        modifier.set_value_for_node(DbNode.objects.get(pk=pk), 'array|symbols', list(symbols.shape))
 
 
 class Migration(migrations.Migration):