Release 0.9.2

promort/VERSION

@@ -1 +1 @@
-0.9.1
+0.9.2

promort/predictions_manager/migrations/0003_prediction_review_required.py

@@ -0,0 +1,18 @@
+# Generated by Django 3.1.13 on 2022-02-18 14:17
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('predictions_manager', '0002_auto_20210915_1608'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='prediction',
+            name='review_required',
+            field=models.BooleanField(default=False),
+        ),
+    ]

promort/predictions_manager/models.py

@@ -37,6 +37,11 @@ class Prediction(models.Model):
     type = models.CharField(max_length=7, choices=PREDICTION_TYPES, blank=False, null=False)
     omero_id = models.IntegerField(blank=True, null=True, default=None)
     provenance = models.TextField(blank=True, null=True)
+    review_required = models.BooleanField(blank=False, null=False, default=False)
+
+    def require_review(self):
+        self.review_required = True
+        self.save()
 
 
 class TissueFragmentsCollection(models.Model):

promort/predictions_manager/serializers.py

@@ -32,7 +32,8 @@ class PredictionSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = Prediction
-        fields = ('id', 'label', 'creation_date', 'slide', 'type', 'omero_id', 'provenance')
+        fields = ('id', 'label', 'creation_date', 'slide', 'type', 'omero_id', 'provenance',
+                  'review_required')
         read_only_fields = ('id', 'creation_date')
 
     def validate_provenance(self, value):
@@ -48,8 +49,9 @@ class PredictionDetailsSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = Prediction
-        fields = ('id', 'label', 'creation_date', 'slide', 'type', 'omero_id', 'provenance')
-        read_only_fields = ('id', 'label', 'creation_date', 'slide', 'type', 'omero_id', 'provenance')
+        fields = ('id', 'label', 'creation_date', 'slide', 'type', 'omero_id', 'provenance', 'review_required')
+        read_only_fields = ('id', 'label', 'creation_date', 'slide', 'type', 'omero_id', 'provenance',
+                            'review_required')
 
 
 class TissueFragmentsCollectionSerializer(serializers.ModelSerializer):

promort/predictions_manager/views.py

@@ -46,6 +46,22 @@ class PredictionDetail(GenericDetailView):
     permission_classes = (permissions.IsAuthenticated, )
 
 
+class PredictionRequireReview(APIView):
+    permission_classes = (permissions.IsAuthenticated, )
+
+    def _find_prediction(self, label):
+        try:
+            prediction = Prediction.objects.get(label=label)
+            return prediction
+        except Prediction.DoesNotExist:
+            raise NotFound(f'No prediction review item with label \'{label}\'')
+
+    def put(self, request, label, format=None):
+        prediction = self._find_prediction(label)
+        prediction.require_review()
+        return Response(status=status.HTTP_204_NO_CONTENT)
+
+
 class TissueFragmentsCollectionList(GenericListView):
     model = TissueFragmentsCollection
     model_serializer = TissueFragmentsCollectionSerializer

promort/promort/urls.py

@@ -43,7 +43,7 @@
 
 
 class NumericString:
-    regex = '[0-9]+'
+    regex = r'[0-9]+'
 
     def to_python(self, value):
         return value
@@ -52,11 +52,18 @@ def to_url(self, value):
         return value
 
 
-class SemiSlug:
-    """
-    A slug comprising letters from A to F
-    """
-    regex = r'[A-Fa-f0-9\-.]+'
+class RandomCaseLabel:
+    regex = r'[A-Fa-f0-9]+'
+
+    def to_python(self, value):
+        return value
+
+    def to_url(self, value):
+        return value
+
+
+class RandomSlideLabel:
+    regex = r'[A-Fa-f0-9]+\-[A-Za-z0-9]+'
 
     def to_python(self, value):
         return value
@@ -66,7 +73,8 @@ def to_url(self, value):
 
 
 register_converter(NumericString, 'num')
-register_converter(SemiSlug, 'semislug')
+register_converter(RandomCaseLabel, 'rclabel')
+register_converter(RandomSlideLabel, 'rslabel')
 
 urlpatterns = [
     # authentication
@@ -118,14 +126,13 @@ def to_url(self, value):
         qmv.QuestionnairePanelAnswersDetail.as_view()),
 
     # ROIs annotation steps details
-    path(
-        'api/rois_annotation_steps/<semislug:label>/clinical_annotation_steps/',
-        rmv.ClinicalAnnotationStepsList.as_view()),
+    path('api/rois_annotation_steps/<rslabel:label>/clinical_annotation_steps/',
+         rmv.ClinicalAnnotationStepsList.as_view()),
 
     # ROIs
-    path('api/rois_annotation_steps/<semislug:label>/rois_list/',
+    path('api/rois_annotation_steps/<rslabel:label>/rois_list/',
          ROIsTreeList.as_view()),
-    path('api/rois_annotation_steps/<semislug:label>/slices/',
+    path('api/rois_annotation_steps/<rslabel:label>/slices/',
          SliceList.as_view()),
     path('api/slices/<num:pk>/cores/', CoreList.as_view()),
     path('api/slices/<num:pk>/', SliceDetail.as_view()),
@@ -135,38 +142,38 @@ def to_url(self, value):
 
     # clinical annotations data
     path(
-        'api/rois_annotation_steps/<semislug:rois_annotation_step>/rois_list/<semislug:clinical_annotation_step>/',
+        'api/rois_annotation_steps/<rslabel:rois_annotation_step>/rois_list/<rslabel:clinical_annotation_step>/',
         AnnotatedROIsTreeList.as_view()),
     path(
-        'api/clinical_annotation_steps/<semislug:clinical_annotation_step>/annotations_list/',
+        'api/clinical_annotation_steps/<rslabel:clinical_annotation_step>/annotations_list/',
         ClinicalAnnotationStepAnnotationsList.as_view()),
     path('api/slices/<num:slice_id>/clinical_annotations/',
          SliceAnnotationList.as_view()),
-    path('api/slices/<num:slice_id>/clinical_annotations/<semislug:label>/',
+    path('api/slices/<num:slice_id>/clinical_annotations/<rslabel:label>/',
          SliceAnnotationDetail.as_view()),
     path('api/cores/<num:core_id>/clinical_annotations/',
          CoreAnnotationList.as_view()),
-    path('api/cores/<num:core_id>/clinical_annotations/<semislug:label>/',
+    path('api/cores/<num:core_id>/clinical_annotations/<rslabel:label>/',
          CoreAnnotationDetail.as_view()),
     path('api/focus_regions/<num:focus_region_id>/clinical_annotations/',
          FocusRegionAnnotationList.as_view()),
     path(
-        'api/focus_regions/<num:focus_region_id>/clinical_annotations/<semislug:label>/',
+        'api/focus_regions/<num:focus_region_id>/clinical_annotations/<rslabel:label>/',
         FocusRegionAnnotationDetail.as_view()),
 
     # ROIs annotations
     path('api/rois_annotations/', rmv.ROIsAnnotationsList.as_view()),
-    path('api/rois_annotations/annotations/<semislug:label>/',
+    path('api/rois_annotations/annotations/<rclabel:label>/',
          rmv.ROIsAnnotationDetail.as_view()),
-    path('api/rois_annotations/steps/<semislug:label>/reset/',
+    path('api/rois_annotations/steps/<rslabel:label>/reset/',
          rmv.ROIsAnnotationStepReopen.as_view()),
-    path('api/rois_annotations/steps/<semislug:label>/',
+    path('api/rois_annotations/steps/<rslabel:label>/',
          rmv.ROIsAnnotationStepDetail.as_view()),
     path('api/rois_annotations/<slug:case>/',
          rmv.ROIsAnnotationsDetail.as_view()),
 
     # quality control
-    path('api/rois_annotations/steps/<semislug:label>/slide_evaluation/',
+    path('api/rois_annotations/steps/<rslabel:label>/slide_evaluation/',
          SlideEvaluationDetail.as_view()),
     path('api/rois_annotations/<slug:case>/<slug:reviewer>/',
          rmv.ROIsAnnotationCreation.as_view()),
@@ -177,9 +184,9 @@ def to_url(self, value):
     path('api/clinical_annotations/', rmv.ClinicalAnnotationsList.as_view()),
     path('api/clinical_annotations/<slug:case>/',
          rmv.ClinicalAnnotationsDetail.as_view()),
-    path('api/clinical_annotations/annotations/<semislug:label>/',
+    path('api/clinical_annotations/annotations/<rclabel:label>/',
          rmv.ClinicalAnnotationDetail.as_view()),
-    path('api/clinical_annotations/steps/<semislug:label>/',
+    path('api/clinical_annotations/steps/<rslabel:label>/',
          rmv.ClinicalAnnotationStepDetail.as_view()),
     path(
         'api/clinical_annotations/<slug:case>/<slug:reviewer>/<num:rois_review>/',
@@ -191,12 +198,13 @@ def to_url(self, value):
     # predictions reviews
     path('api/prediction_reviews/', rmv.PredictionReviewsList.as_view()),
     path('api/prediction_reviews/<slug:slide>/', rmv.PredictionReviewsDetail.as_view()),
-    path('api/prediction_review/<semislug:label>/', rmv.PredictionReviewDetail.as_view()),
-    path('api/prediction_review/<semislug:label>/prediction/', rmv.PredictionByReviewDetail.as_view()),
+    path('api/prediction_review/<rclabel:label>/', rmv.PredictionReviewDetail.as_view()),
+    path('api/prediction_review/<rclabel:label>/prediction/', rmv.PredictionByReviewDetail.as_view()),
 
     # predictions
     path('api/predictions/', pmv.PredictionList.as_view()),
     path('api/predictions/<slug:pk>/', pmv.PredictionDetail.as_view()),
+    path('api/predictions/<slug:pk>/require_review/', pmv.PredictionRequireReview.as_view()),
 
     #  tissue fragments
     path('api/tissue_fragments_collections/',
@@ -206,15 +214,14 @@ def to_url(self, value):
          ),  # GET, DELETE, PUT (se usi GenericDetailView)
     path('api/tissue_fragments_collections/<slug:coll_id>/fragments/',
          pmv.TissueFragmentList.as_view()),  # POST
-    path(
-        'api/tissue_fragments_collections/<slug:coll_id>/fragments/<slug:pk>/',
-        pmv.TissueFragmentsDetail.as_view()),  # DELETE
+    path('api/tissue_fragments_collections/<slug:coll_id>/fragments/<slug:pk>/',
+         pmv.TissueFragmentsDetail.as_view()),  # DELETE
 
     # worklists
     path('api/worklist/', UserWorkList.as_view()),
-    path('api/worklist/rois_annotations/<semislug:label>/',
+    path('api/worklist/rois_annotations/<rclabel:label>/',
          UserWorklistROIsAnnotation.as_view()),
-    path('api/worklist/clinical_annotations/<semislug:label>/',
+    path('api/worklist/clinical_annotations/<rclabel:label>/',
          UserWorklistClinicalAnnotation.as_view()),
     path('api/worklist/admin/<slug:username>/', WorkListAdmin.as_view()),
 

promort/reviews_manager/management/commands/build_prediction_reviews_worklist.py

@@ -48,7 +48,7 @@ def _get_prediction_reviews_manager_users(self):
         return prev_manager_group.user_set.all()
 
     def _get_predictions_list(self, prediction_type):
-        return Prediction.objects.filter(type=prediction_type).all()
+        return Prediction.objects.filter(type=prediction_type, review_required=True).all()
 
     def _check_duplicated(self, prediction, reviewer):
         annotation_objs = PredictionReview.objects.filter(prediction=prediction, reviewer=reviewer)