fix black and recover relecov project name for testing

.gitignore

@@ -9,9 +9,9 @@ migrations/
 virtualenv/
 manage.py
 install_*.txt
+initial_*.txt
 relecov_platform/
 documents/
-initial_*.txt
 
 # VS code
 .vscode/

conf/template_settings.py

@@ -76,7 +76,7 @@
         "USER": "djangouser",
         "PASSWORD": "djangopass",
         "PORT": "djangoport",
-        "NAME": "pathoweb",
+        "NAME": "relecov",
         "HOST": "djangohost",
     },
 }

core/api/utils/metadata_values.py

@@ -29,7 +29,7 @@ def store_metadata_values(s_data, schema_obj, analysis_date):
     ).last()
     for field, value in s_data.items():
         # This condition avoids error when assessing bioinformatics fields
-        if 'schema_' in field :
+        if "schema_" in field:
             continue
         property_name = core.models.SchemaProperties.objects.filter(
             schemaID=schema_obj, property__iexact=field
@@ -43,7 +43,7 @@ def store_metadata_values(s_data, schema_obj, analysis_date):
             }
         except AttributeError:
             return {
-                "ERROR": f'{core.config.ERROR_FIELD_NOT_DEFINED, field}',
+                "ERROR": f"{core.config.ERROR_FIELD_NOT_DEFINED, field}",
             }
         meta_value_serializer = core.api.serializers.CreateMetadataValueSerializer(
             data=data

core/models.py

@@ -694,7 +694,9 @@ def get_ena_info(self):
         return self.ena_obj.get_ena_data()
 
     def get_state(self):
-        latest_state = SampleStateHistory.objects.filter(sample=self, is_current=True).last()
+        latest_state = SampleStateHistory.objects.filter(
+            sample=self, is_current=True
+        ).last()
         if latest_state and latest_state.state:
             return "%s" % (latest_state.state.get_state())
         return None

core/utils/bioinfo_analysis.py

@@ -48,11 +48,13 @@ def get_bioinfo_analysis_data_from_sample(sample_id):
     # Get all MetadataValues related to the schema and sample
     bioan_fields_qs = core.models.MetadataValues.objects.filter(
         schema_property__schemaID=schema_obj,
-        sample=sample_obj  # Ensure we only fetch for this specific sample
+        sample=sample_obj,  # Ensure we only fetch for this specific sample
     )
 
     # Get the latest analysis_date for this sample
-    latest_analysis_date = bioan_fields_qs.aggregate(Max("analysis_date"))["analysis_date__max"]
+    latest_analysis_date = bioan_fields_qs.aggregate(Max("analysis_date"))[
+        "analysis_date__max"
+    ]
 
     # If no data exists, return None
     if not latest_analysis_date:
@@ -65,9 +67,11 @@ def get_bioinfo_analysis_data_from_sample(sample_id):
             bioan_fields_qs.filter(
                 analysis_date=latest_analysis_date,
                 schema_property=OuterRef("schema_property"),
-                value=OuterRef("value")
-            ).order_by("-generated_at").values("generated_at")[:1]
-        )
+                value=OuterRef("value"),
+            )
+            .order_by("-generated_at")
+            .values("generated_at")[:1]
+        ),
     )
 
     # If still empty, return None
@@ -78,10 +82,7 @@ def get_bioinfo_analysis_data_from_sample(sample_id):
     for bio_field in latest_bioan_fields:
         value = bio_field.get_value() if bio_field else ""
 
-        bio_anlys_data.append([
-            bio_field.schema_property.get_label(),
-            value
-        ])
+        bio_anlys_data.append([bio_field.schema_property.get_label(), value])
     return bio_anlys_data
 
 

core/utils/samples.py

@@ -333,11 +333,12 @@ def get_lab_last_actions(lab_name=None):
             ).last()
             lab_data = [lab[0]]
             for action in action_list:
-                if core.models.SampleStateHistory.objects.filter(sample=sam_obj, state__state__exact=action).exist():
+                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,
-                            state__state__exact=action
+                            sample=sam_obj, state__state__exact=action
                         )
                         .last()
                         .get_date()
@@ -426,9 +427,7 @@ def get_sample_display_data(sample_id, user):
             sample=sample_obj
         ).order_by("-changed_at")
         for action_date_obj in actions_date_objs:
-            actions.append(
-                [action_date_obj.get_state(), action_date_obj.get_date()]
-            )
+            actions.append([action_date_obj.get_state(), action_date_obj.get_date()])
         s_data["actions"] = actions
 
     lab_sample = sample_obj.get_collecting_lab_sample_id()
@@ -527,11 +526,12 @@ def get_sample_per_date_per_lab(lab_name):
     """
     samples_per_date = OrderedDict()
     sample_qs = get_sample_objs_per_lab(lab_name)
-    sequence_date_obj = core.models.SchemaProperties.objects.get(property='sequencing_date')
+    sequence_date_obj = core.models.SchemaProperties.objects.get(
+        property="sequencing_date"
+    )
     s_dates = (
         core.models.MetadataValues.objects.filter(
-            sample__in=sample_qs,
-            schema_property__id=sequence_date_obj.pk
+            sample__in=sample_qs, schema_property__id=sequence_date_obj.pk
         )
         .values_list("value", flat=True)
         .distinct()

core/views.py

@@ -363,9 +363,7 @@ def metadata_form(request):
         m_batch_form = core.utils.samples.create_form_for_batch(
             schema_obj, request.user
         )
-        sample_saved = core.utils.samples.get_sample_pre_recorded(
-            request.user
-        )
+        sample_saved = core.utils.samples.get_sample_pre_recorded(request.user)
         return render(
             request,
             "core/metadataForm.html",