fix black linting

core/admin.py

@@ -47,7 +47,13 @@ class ConfigSettingAdmin(admin.ModelAdmin):
 
 
 class SampleStateHistoryAdmin(admin.ModelAdmin):
-    list_display = ["is_current", custom_date_format, "sample_id", "state_id", "error_name_id"]
+    list_display = [
+        "is_current",
+        custom_date_format,
+        "sample_id",
+        "state_id",
+        "error_name_id",
+    ]
 
 
 class EffectAdmin(admin.ModelAdmin):

core/api/utils/common_functions.py

@@ -75,12 +75,13 @@ def add_sample_state_history(sample_obj, state_id, error_name=None):
         # Assign the 'No Error' entry with pk=1 as default
         error_obj = core.models.ErrorName.objects.filter(pk=1).first()
         if not error_obj:
-            raise ValueError("Default error entry with pk=1 does not exist in the database.")
+            raise ValueError(
+                "Default error entry with pk=1 does not exist in the database."
+            )
 
     # Mark previous states as not current
     core.models.SampleStateHistory.objects.filter(
-        sample=sample_obj,
-        is_current=True
+        sample=sample_obj, is_current=True
     ).update(is_current=False)
 
     # Add the new state history

core/api/utils/metadata_values.py

@@ -28,20 +28,17 @@ def store_metadata_values(s_data, schema_obj, analysis_date):
         sequencing_sample_id__iexact=s_data["sequencing_sample_id"]
     ).last()
     for field, value in s_data.items():
-        property_name = (
-            core.models.SchemaProperties.objects.filter(
-                schemaID=schema_obj, property__iexact=field
-            )
-            .last()
-        )
+        property_name = core.models.SchemaProperties.objects.filter(
+            schemaID=schema_obj, property__iexact=field
+        ).last()
         data = {
             "value": value,
             "sample": sample_obj.id,
             "schema_property": property_name.id,
-            "analysis_date": analysis_date
+            "analysis_date": analysis_date,
         }
-        meta_value_serializer = (
-            core.api.serializers.CreateMetadataValueSerializer(data=data)
+        meta_value_serializer = core.api.serializers.CreateMetadataValueSerializer(
+            data=data
         )
         if not meta_value_serializer.is_valid():
             return {

core/api/views.py

@@ -136,14 +136,16 @@ def create_sample_data(request):
         sample_id = sample_obj.get_sample_id()
 
         # Add initial state history (after creating the sample)
-        is_first_entry = not core.models.SampleStateHistory.objects.filter(sample=sample_obj).exists()
+        is_first_entry = not core.models.SampleStateHistory.objects.filter(
+            sample=sample_obj
+        ).exists()
         if is_first_entry:
             error_name_obj = core.models.ErrorName.objects.filter(pk=1).first()
             try:
                 core.api.utils.common_functions.add_sample_state_history(
                     sample_obj,
                     state_id=split_data["sample"]["state"],
-                    error_name=error_name_obj
+                    error_name=error_name_obj,
                 )
             except ValueError as e:
                 return Response({"ERROR": str(e)}, status=status.HTTP_400_BAD_REQUEST)
@@ -171,10 +173,12 @@ def create_sample_data(request):
                     core.api.utils.common_functions.add_sample_state_history(
                         sample_obj,
                         state_id=state_id,
-                        error_name=None  # TODO: do not know what to do with this at this point
+                        error_name=None,  # TODO: do not know what to do with this at this point
                     )
                 except ValueError as e:
-                    return Response({"ERROR": str(e)}, status=status.HTTP_400_BAD_REQUEST)
+                    return Response(
+                        {"ERROR": str(e)}, status=status.HTTP_400_BAD_REQUEST
+                    )
 
         # Save GISAID info if included
         if len(split_data["gisaid"]) > 0:
@@ -195,10 +199,12 @@ def create_sample_data(request):
                     core.api.utils.common_functions.add_sample_state_history(
                         sample_obj,
                         state_id=state_id,
-                        error_name=None  # TODO: do not know what to do with this at this point
+                        error_name=None,  # TODO: do not know what to do with this at this point
                     )
                 except ValueError as e:
-                    return Response({"ERROR": str(e)}, status=status.HTTP_400_BAD_REQUEST)
+                    return Response(
+                        {"ERROR": str(e)}, status=status.HTTP_400_BAD_REQUEST
+                    )
 
         # Save AUTHOR info if included
         if len(split_data["author"]) > 0:
@@ -406,7 +412,7 @@ def create_metadata_value(request):
         core.api.utils.common_functions.add_sample_state_history(
             sample_obj,
             state_id=state_id,
-            error_name=None  # TODO: do not know what to do with this at this point
+            error_name=None,  # TODO: do not know what to do with this at this point
         )
     except ValueError as e:
         return Response({"ERROR": str(e)}, status=status.HTTP_400_BAD_REQUEST)
@@ -657,13 +663,15 @@ def update_state(request):
         # FIXME: it has been tested with error_code == None --> automatically_assigned value "other" (error_code_pk=21). Further testing is required.
         e_data = {
             "error_name": data.get("error_name", None),
-            "error_code": data.get("error_code", None)
+            "error_code": data.get("error_code", None),
         }
-        error_name_obj = core.api.utils.common_functions.handle_sample_errors(dict_error=e_data)
+        error_name_obj = core.api.utils.common_functions.handle_sample_errors(
+            dict_error=e_data
+        )
 
         # Create changed_at field if not provided
         try:
-            current_time = data['changed_at']
+            current_time = data["changed_at"]
         except KeyError:
             current_time = timezone.now()
 
@@ -682,7 +690,9 @@ def update_state(request):
         ).update(is_current=False)
 
         # Serialize and validate the state update
-        sample_state_serializer = core.api.serializers.SampleStateHistorySerializer(data=s_data)
+        sample_state_serializer = core.api.serializers.SampleStateHistorySerializer(
+            data=s_data
+        )
         if not sample_state_serializer.is_valid():
             return Response(
                 sample_state_serializer.errors, status=status.HTTP_400_BAD_REQUEST

core/models.py

@@ -310,7 +310,7 @@ def create_new_value(self, data):
             value=data["value"],
             analysis_date=data["analysis_date"],
             sample=data["sample_id"],
-            schema_property=data["schema_property_id"]
+            schema_property=data["schema_property_id"],
         )
         return new_value
 
@@ -320,14 +320,12 @@ class MetadataValues(models.Model):
     generated_at = models.DateTimeField(auto_now_add=True, null=True, blank=True)
     analysis_date = models.DateField()
     sample = models.ForeignKey(
-        'core.Sample',
-        on_delete=models.CASCADE,
-        related_name="metadata_values"
+        "core.Sample", on_delete=models.CASCADE, related_name="metadata_values"
     )
     schema_property = models.ForeignKey(
-        'core.SchemaProperties',
+        "core.SchemaProperties",
         on_delete=models.CASCADE,
-        related_name="metadata_values"
+        related_name="metadata_values",
     )
 
     class Meta: