Relecov core linting after file and import updates

relecov_core/api/utils/samples.py

@@ -3,12 +3,17 @@
 import relecov_core.models
 import relecov_core.utils.samples
 
+
 def prepare_fields_in_sample(s_data):
     """Add sample state and set to None GISAID and ENA if not set"""
-    if not relecov_core.models.SampleState.objects.filter(state__exact="Defined").exists():
+    if not relecov_core.models.SampleState.objects.filter(
+        state__exact="Defined"
+    ).exists():
         return {"ERROR": ERROR_INTIAL_SETTINGS_NOT_DEFINED}
     s_data["state"] = (
-        relecov_core.models.SampleState.objects.filter(state__exact="Defined").last().get_state_id()
+        relecov_core.models.SampleState.objects.filter(state__exact="Defined")
+        .last()
+        .get_state_id()
     )
     if "biosample_accession_ENA" not in s_data:
         s_data["biosample_accession_ENA"] = None
@@ -49,15 +54,21 @@ def split_sample_data(data):
 
     # add user and state to sample data
     split_data["sample"]["state"] = (
-        relecov_core.models.SampleState.objects.filter(state__exact="Defined").last().get_state_id()
+        relecov_core.models.SampleState.objects.filter(state__exact="Defined")
+        .last()
+        .get_state_id()
     )
-    split_data["sample"]["user"] = relecov_core.utils.samples.get_user_id_from_collecting_institution(
-        split_data["sample"]["collecting_institution"]
+    split_data["sample"]["user"] = (
+        relecov_core.utils.samples.get_user_id_from_collecting_institution(
+            split_data["sample"]["collecting_institution"]
+        )
     )
     if relecov_core.models.Sample.objects.all().exists():
-        last_unique_value = relecov_core.models.Sample.objects.all().last().get_unique_id()
-        split_data["sample"]["sample_unique_id"] = relecov_core.utils.samples.increase_unique_value(
-            last_unique_value
+        last_unique_value = (
+            relecov_core.models.Sample.objects.all().last().get_unique_id()
+        )
+        split_data["sample"]["sample_unique_id"] = (
+            relecov_core.utils.samples.increase_unique_value(last_unique_value)
         )
     else:
         split_data["sample"]["sample_unique_id"] = "AAA-0001"

relecov_core/api/utils/variants.py

@@ -14,10 +14,13 @@
     ERROR_UNABLE_TO_STORE_IN_DATABASE,
 )
 
+
 def create_or_get_filter_obj(filter_value):
     """Return the filter instance or create if not exists"""
     if relecov_core.models.Filter.objects.filter(filter__iexact=filter_value).exists():
-        return relecov_core.models.Filter.objects.filter(filter__iexact=filter_value).last()
+        return relecov_core.models.Filter.objects.filter(
+            filter__iexact=filter_value
+        ).last()
     filter_serializer = CreateFilterSerializer(data={"filter": filter_value})
     if filter_serializer.is_valid():
         filter_obj = filter_serializer.save()
@@ -28,7 +31,9 @@ def create_or_get_filter_obj(filter_value):
 def create_or_get_effect_obj(effect_value):
     """Return the effect instance or create if not exists"""
     if relecov_core.models.Effect.objects.filter(effect__iexact=effect_value).exists():
-        return relecov_core.models.Effect.objects.filter(effect__iexact=effect_value).last()
+        return relecov_core.models.Effect.objects.filter(
+            effect__iexact=effect_value
+        ).last()
     effect_serializer = CreateEffectSerializer(data={"effect": effect_value})
     if effect_serializer.is_valid():
         effect_obj = effect_serializer.save()
@@ -90,9 +95,9 @@ def get_variant_id(data):
 
 
 def get_variant_analysis_defined(s_obj):
-    return relecov_core.models.VariantInSample.objects.filter(sampleID_id=s_obj).values_list(
-        "analysis_date", flat=True
-    )
+    return relecov_core.models.VariantInSample.objects.filter(
+        sampleID_id=s_obj
+    ).values_list("analysis_date", flat=True)
 
 
 def get_required_variant_ann_id(data):

relecov_core/utils/plotly_graphics.py

@@ -109,6 +109,7 @@ def gauge_graphic(data):
     plot_div = plot(graph, output_type="div", config={"displaylogo": False})
     return plot_div
 
+
 # FIXME: This function es never called within the platform
 def bullet_graphic(value, title):
     point = str(value)