fix flake linting

core/api/utils/metadata_values.py

@@ -39,7 +39,7 @@ def store_metadata_values(s_data, schema_obj, analysis_date):
                 "value": value,
                 "sample": sample_obj.id,
                 "schema_property": property_name.id,
-                "analysis_date": analysis_date, # FIXME: allowed format is: YYYY-MM-DD. Add "Not provided" value too
+                "analysis_date": analysis_date,  # FIXME: allowed format is: YYYY-MM-DD. Add "Not provided" value too
             }
         except AttributeError:
             return {

core/api/views.py

@@ -98,7 +98,7 @@
 @api_view(["POST"])
 @permission_classes([IsAuthenticated])
 # FIXME: When input data has not ENA value, it returns 404, but samples were successfully added to database.
-#          - Proposal: emit a warning message instead  
+#          - Proposal: emit a warning message instead
 def create_sample_data(request):
     if request.method == "POST":
         data = request.data
@@ -441,7 +441,7 @@ def create_metadata_value(request):
                 {"ERROR": core.config.ERROR_ANALYSIS_ALREADY_DEFINED},
                 status=status.HTTP_400_BAD_REQUEST,
             )
-    # FIXME: 'analysis_date' create errors when it is none. A custom serializer that allows both specific date format and "not-provided" value should be added. 
+    # FIXME: 'analysis_date' create errors when it is none. A custom serializer that allows both specific date format and "not-provided" value should be added.
     stored_data = core.api.utils.metadata_values.store_metadata_values(
         data, schema_obj, analysis_date
     )

core/models.py

@@ -365,6 +365,7 @@ def get_lineage_name(self):
     def get_lineage_id(self):
         return "%s" % (self.pk)
 
+
 # FIXME: Lineage tables should be removed in #181
 class LineageFieldsManager(models.Manager):
     def create_new_field(self, data):

core/utils/bioinfo_analysis.py

@@ -2,7 +2,8 @@
 import core.models
 import core.utils.samples
 import core.utils.schema
-from django.db.models import Max, F, Subquery, OuterRef
+from django.db.models import Max, Subquery, OuterRef
+
 
 def get_bio_analysis_stats_from_lab(lab_name=None):
     """Get the number of samples that are analized and compare with the number
@@ -27,6 +28,7 @@ def get_bio_analysis_stats_from_lab(lab_name=None):
         bio_stats["received"] = len(sample_objs)
     return bio_stats
 
+
 def get_bioinfo_analysis_data_from_sample(sample_id):
     """Get the latest bioinfo analysis data for the sample, ensuring unique values"""
 
@@ -80,11 +82,9 @@ def get_bioinfo_analysis_data_from_sample(sample_id):
             bio_field.schema_property.get_label(),
             value
         ])
-
     return bio_anlys_data
 
 
-
 # FIXME: Replace BioinfoAnalysisField wit MetadataValue
 # TODO: I think this function belongs to dashboard app
 def get_bioinfo_analyis_fields_utilization(schema_obj=None):

core/utils/samples.py

@@ -336,7 +336,7 @@ def get_lab_last_actions(lab_name=None):
                 if core.models.SampleStateHistory.objects.filter(sample=sam_obj, state__state__exact=action).exist():
                     lab_data.append(
                         core.models.SampleStateHistory.objects.filter(
-                            sample=sam_obj, 
+                            sample=sam_obj,
                             state__state__exact=action
                         )
                         .last()

core/utils/schema.py

@@ -227,7 +227,7 @@ def store_schema_properties(schema_obj, s_properties, required):
             )
         except (KeyError, DataError) as e:
             print(prop_key, " error ", e)
-            return {"ERROR": e }
+            return {"ERROR": e}
             # schema_obj.delete()
         if "options" in data:
             for item in s_properties[prop_key]["enum"]:

core/views.py

@@ -171,6 +171,7 @@ def search_sample(request):
         )
     return render(request, "core/searchSample.html", {"search_data": search_data})
 
+
 # FIXME: This needs a template or error message when user != admin tryies to access.
 @login_required
 def metadata_visualization(request):