Fix mypy test failure (#634)

* Fix mypy test failure

* Status 400 for unable to create frame

* Lint fixes

* Use literal 0.0

* More informative error message

* Fix APIException code param

Author: annehaley

miqa/core/rest/frame.py

@@ -8,7 +8,7 @@
 from guardian.shortcuts import get_objects_for_user, get_perms
 from rest_framework import mixins, serializers, status
 from rest_framework.decorators import action
-from rest_framework.exceptions import APIException
+from rest_framework.exceptions import APIException, ValidationError
 from rest_framework.permissions import IsAuthenticated
 from rest_framework.response import Response
 from rest_framework.viewsets import GenericViewSet
@@ -125,13 +125,17 @@ def create(self, request, *args, **kwargs):
             scan.save()
         elif 'scan' in serializer.data:
             scan = Scan.objects.get(id=serializer.data['scan'])
+            if not scan:
+                raise ValidationError('Could not create new Frame; Scan not found.')
             if not get_perms(request.user, scan.experiment.project):
                 Response(status=status.HTTP_403_FORBIDDEN)
         else:
             raise APIException(
                 'Provide either a parent scan or grandparent experiment for this frame.'
             )
 
+        if not scan:
+            raise ValidationError('Could not create new Frame; Scan not found.')
         content_serializer = FrameContentSerializer(data=dict(request.data, scan=scan.id))
         content_serializer.is_valid(raise_exception=True)
         new_frame = content_serializer.save()

miqa/core/tasks.py

@@ -214,7 +214,9 @@ def perform_import(import_dict):
                             creator = None
                         note = ''
                         created = (
-                            datetime.now() if settings.REPLACE_NULL_CREATION_DATETIMES else None
+                            datetime.now().strftime('%Y-%m-%d %H:%M')
+                            if settings.REPLACE_NULL_CREATION_DATETIMES
+                            else None
                         )
                         location = {}
                         if last_decision_dict['note']:
@@ -342,7 +344,13 @@ def perform_export(project_id: Optional[str]):
                     frame_object.scan.session_id,
                     frame_object.scan.scan_link,
                 ]
-                last_decision = frame_object.scan.decisions.order_by('created').last()
+                last_decision = (
+                    frame_object.scan.decisions.exclude(created__isnull=True)
+                    .order_by('created')
+                    .last()
+                )
+                if not last_decision:
+                    last_decision = frame_object.scan.decisions.order_by('created').last()
                 if last_decision:
                     location = ''
                     if last_decision.location:

miqa/core/tests/test_import.py

@@ -224,7 +224,7 @@ def test_import_with_relative_path(project_factory):
     import_data(project.id)
 
     frame = Frame.objects.first()
-    assert frame.raw_path == str(Path(__file__).parent / 'data' / 'example.nii.gz')
+    assert frame and frame.raw_path == str(Path(__file__).parent / 'data' / 'example.nii.gz')
 
 
 @pytest.mark.django_db
@@ -234,7 +234,7 @@ def test_import_s3_preserves_path(project_factory):
     import_data(project.id)
 
     frame = Frame.objects.first()
-    assert (
+    assert frame and (
         frame.raw_path
         == 's3://miqa-sample/IXI_small/Guys/IXI002/0828-DTI/IXI002-Guys-0828-DTI-00.nii.gz'
     )

miqa/learning/nn_training.py

@@ -588,7 +588,7 @@ def train_and_save_model(df, count_train, save_path, num_epochs, val_interval, o
         logger.info('-' * 25)
         logger.info(f'epoch {epoch + 1}/{num_epochs}')
         model.train()
-        epoch_loss = 0
+        epoch_loss = 0.0
         step = 0
         epoch_len = len(train_loader.dataset) // train_loader.batch_size
         logger.info(f'epoch_len: {epoch_len}')

miqa/settings.py

@@ -10,9 +10,9 @@
     HerokuProductionBaseConfiguration,
     HttpsMixin,
     ProductionBaseConfiguration,
+    S3StorageMixin,
     SmtpEmailMixin,
     TestingBaseConfiguration,
-    S3StorageMixin,
 )
 from composed_configuration._configuration import _BaseConfiguration
 from configurations import values

mypy.ini

@@ -0,0 +1,3 @@
+[mypy]
+strict = True
+disable_error_code = misc, annotation-unchecked, import, no-untyped-def, no-untyped-call, var-annotated, type-arg, no-any-return, list-item