linting

wetlab/api/utils/sample.py

@@ -24,7 +24,9 @@ def create_city(data, apps_name):
 
 def create_new_laboratory(lab_data):
     """Create new laboratory instance with the data collected in the request"""
-    if core.models.City.objects.filter(city_name__exact=lab_data["geo_loc_city"]).exists():
+    if core.models.City.objects.filter(
+        city_name__exact=lab_data["geo_loc_city"]
+    ).exists():
         city_id = (
             core.models.City.objects.filter(city_name__exact=lab_data["geo_loc_city"])
             .last()
@@ -79,17 +81,17 @@ def get_sample_fields(apps_name):
         "Only recorded": {"field_name": "only_recorded"},
     }
     if core.models.SampleType.objects.filter(apps_name__exact=apps_name).exists():
-        s_type_objs = core.models.SampleType.objects.filter(apps_name__exact=apps_name).order_by(
-            "sample_type"
-        )
+        s_type_objs = core.models.SampleType.objects.filter(
+            apps_name__exact=apps_name
+        ).order_by("sample_type")
         sample_fields["Type of Sample"]["options"] = []
         for s_type_obj in s_type_objs:
             sample_fields["Type of Sample"]["options"].append(s_type_obj.get_name())
     if core.models.Species.objects.filter(apps_name__exact=apps_name).exists():
         sample_fields["Species"]["options"] = []
-        species_objs = core.models.Species.objects.filter(apps_name__exact=apps_name).order_by(
-            "species_name"
-        )
+        species_objs = core.models.Species.objects.filter(
+            apps_name__exact=apps_name
+        ).order_by("species_name")
         for species_obj in species_objs:
             sample_fields["Species"]["options"].append(species_obj.get_name())
     if core.models.LabRequest.objects.all().exists():
@@ -123,7 +125,9 @@ def get_sample_fields(apps_name):
 
 def get_sample_project_obj(project_name):
     """Check if sampleProyect is defined in database"""
-    if core.models.SampleProjects.objects.filter(sample_project_name__exact=project_name).exists():
+    if core.models.SampleProjects.objects.filter(
+        sample_project_name__exact=project_name
+    ).exists():
         return core.models.SampleProjects.objects.filter(
             sample_project_name__exact=project_name
         ).last()
@@ -134,7 +138,9 @@ def include_instances_in_sample(data, lab_data, apps_name):
     """Collect the instances before creating the sample instance
     If laboratory will be created if it is not defined
     """
-    if core.models.LabRequest.objects.filter(lab_name__exact=data["lab_request"]).exists():
+    if core.models.LabRequest.objects.filter(
+        lab_name__exact=data["lab_request"]
+    ).exists():
         data["lab_request"] = (
             core.models.LabRequest.objects.filter(lab_name__exact=data["lab_request"])
             .last()
@@ -143,9 +149,13 @@ def include_instances_in_sample(data, lab_data, apps_name):
     else:
         lab_data["apps_name"] = apps_name
         data["lab_request"] = create_new_laboratory(lab_data).get_id()
-    if core.models.SampleType.objects.filter(sample_type__exact=data["sample_type"]).exists():
+    if core.models.SampleType.objects.filter(
+        sample_type__exact=data["sample_type"]
+    ).exists():
         data["sample_type"] = (
-            core.models.SampleType.objects.filter(sample_type__exact=data["sample_type"])
+            core.models.SampleType.objects.filter(
+                sample_type__exact=data["sample_type"]
+            )
             .last()
             .get_sample_type_id()
         )
@@ -156,15 +166,19 @@ def include_instances_in_sample(data, lab_data, apps_name):
         # return str("sampleType " + data["sampleType"] + " is not defined in database")
     if core.models.Species.objects.filter(species_name__exact=data["species"]).exists():
         data["species"] = (
-            core.models.Species.objects.filter(species_name__exact=data["species"]).last().get_id()
+            core.models.Species.objects.filter(species_name__exact=data["species"])
+            .last()
+            .get_id()
         )
     else:
         return str("species " + data["species"] + " is not defined in database")
     if data["patient_core"] == "" or data["patient_core"].lower() == "null":
         data["patient_core"] = None
     else:
         try:
-            data["patient_core"] = get_patient_obj(data["patient_core"]).get_patient_id()
+            data["patient_core"] = get_patient_obj(
+                data["patient_core"]
+            ).get_patient_id()
         except AttributeError:
             return str(
                 "patient_core " + data["patient_core"] + " is not defined in database"
@@ -190,7 +204,9 @@ def include_instances_in_sample(data, lab_data, apps_name):
         data["completed_date"] = datetime.now()
     else:
         data["sample_state"] = (
-            core.models.StatesForSample.objects.filter(sample_state_name="Defined").last().get_id()
+            core.models.StatesForSample.objects.filter(sample_state_name="Defined")
+            .last()
+            .get_id()
         )
         data["completed_date"] = None
     return data
@@ -207,16 +223,22 @@ def include_coding(user_name, sample):
             .last()
             .unique_sample_id
         )
-        c_data["unique_sample_id"] = core.utils.samples.increase_unique_value(last_unique_value)
+        c_data["unique_sample_id"] = core.utils.samples.increase_unique_value(
+            last_unique_value
+        )
     c_data["sample_code_id"] = str(user_name + "_" + sample)
     return c_data
 
 
 def get_project_fields_id_and_name(p_obj):
     """Fetch the fields defined for project"""
     fields = []
-    if core.models.SampleProjectsFields.objects.filter(sample_projects_id=p_obj).exists():
-        p_field_objs = core.models.SampleProjectsFields.objects.filter(sample_projects_id=p_obj)
+    if core.models.SampleProjectsFields.objects.filter(
+        sample_projects_id=p_obj
+    ).exists():
+        p_field_objs = core.models.SampleProjectsFields.objects.filter(
+            sample_projects_id=p_obj
+        )
         for p_field_obj in p_field_objs:
             fields.append([p_field_obj.get_field_id(), p_field_obj.get_field_name()])
     return fields
@@ -225,7 +247,9 @@ def get_project_fields_id_and_name(p_obj):
 def get_patient_obj(patient):
     """Get the patient instance"""
     if core.models.PatientCore.objects.filter(patient_code__iexact=patient).exists():
-        return core.models.PatientCore.objects.filter(patient_code__iexact=patient).last()
+        return core.models.PatientCore.objects.filter(
+            patient_code__iexact=patient
+        ).last()
     return False
 
 
@@ -372,7 +396,9 @@ def summarize_samples(data):
                 sample_projects_id=s_project_obj,
                 sample_project_field_description__iexact=data["sample_project_field"],
             ).exists():
-                return {"ERROR": wetlab.config.ERROR_API_NO_SAMPLE_PROJECT_FIELD_DEFINED}
+                return {
+                    "ERROR": wetlab.config.ERROR_API_NO_SAMPLE_PROJECT_FIELD_DEFINED
+                }
 
             s_project_field_objs = core.models.SampleProjectsFields.objects.filter(
                 sample_projects_id=s_project_obj,
@@ -387,7 +413,9 @@ def summarize_samples(data):
         regions = [data["region"]]
     else:
         regions = (
-            core.models.StateInCountry.objects.all().values_list("state_name", flat=True).distinct()
+            core.models.StateInCountry.objects.all()
+            .values_list("state_name", flat=True)
+            .distinct()
         )
     for region in regions:
         summarize["region"][region] = sample_objs.filter(
@@ -400,7 +428,9 @@ def summarize_samples(data):
         summarize.pop("region", None)
     else:
         laboratories = (
-            core.models.LabRequest.objects.all().values_list("lab_name", flat=True).distinct()
+            core.models.LabRequest.objects.all()
+            .values_list("lab_name", flat=True)
+            .distinct()
         )
     for laboratory in laboratories:
         summarize["laboratory"][laboratory] = sample_objs.filter(
@@ -513,7 +543,9 @@ def collect_statistics_information(data):
                             stats_data[par1_val][par2_val] = value
             else:
                 for par1_val in par1_values:
-                    stats_data[par1_val] = core.models.SampleProjectsFieldsValue.objects.filter(
+                    stats_data[
+                        par1_val
+                    ] = core.models.SampleProjectsFieldsValue.objects.filter(
                         sample_project_field_id__sample_projects_id=s_project_obj,
                         sample_project_field_id__sample_project_field_name__iexact=query_params[
                             0
@@ -531,7 +563,9 @@ def collect_statistics_information(data):
                 "fields_value": {},
             }
 
-            num_samples = core.models.Samples.objects.filter(sample_project=s_project_obj).count()
+            num_samples = core.models.Samples.objects.filter(
+                sample_project=s_project_obj
+            ).count()
             s_project_field_objs = core.models.SampleProjectsFields.objects.filter(
                 sample_project_id=s_project_obj
             )

wetlab/api/views.py

@@ -2,10 +2,12 @@
 from drf_yasg import openapi
 from drf_yasg.utils import swagger_auto_schema
 from rest_framework import status
-from rest_framework.authentication import (BasicAuthentication,
-                                           SessionAuthentication)
-from rest_framework.decorators import (api_view, authentication_classes,
-                                       permission_classes)
+from rest_framework.authentication import BasicAuthentication, SessionAuthentication
+from rest_framework.decorators import (
+    api_view,
+    authentication_classes,
+    permission_classes,
+)
 from rest_framework.permissions import IsAuthenticated
 from rest_framework.response import Response
 
@@ -178,7 +180,9 @@ def create_sample_data(request):
             data = data.dict()
         if "sample_name" not in data or "sample_project" not in data:
             return Response(status=status.HTTP_400_BAD_REQUEST)
-        if core.models.Samples.objects.filter(sample_name__iexact=data["sample_name"]).exists():
+        if core.models.Samples.objects.filter(
+            sample_name__iexact=data["sample_name"]
+        ).exists():
             error = {"ERROR": "sample already defined"}
             return Response(error, status=status.HTTP_400_BAD_REQUEST)
         split_data = wetlab.api.utils.sample.split_sample_data(data)
@@ -194,17 +198,23 @@ def create_sample_data(request):
         split_data["s_data"]["sample_user"] = request.user.pk
         # Adding coding for sample
         split_data["s_data"].update(
-            wetlab.api.utils.sample.include_coding(request.user.username, split_data["s_data"]["sample_name"])
+            wetlab.api.utils.sample.include_coding(
+                request.user.username, split_data["s_data"]["sample_name"]
+            )
+        )
+        sample_serializer = wetlab.api.serializers.CreateSampleSerializer(
+            data=split_data["s_data"]
         )
-        sample_serializer = wetlab.api.serializers.CreateSampleSerializer(data=split_data["s_data"])
         if not sample_serializer.is_valid():
             return Response(
                 sample_serializer.errors, status=status.HTTP_400_BAD_REQUEST
             )
         new_sample_id = sample_serializer.save().get_sample_id()
         for d_field in split_data["p_data"]:
             d_field["sample_id"] = new_sample_id
-            s_project_serializer = wetlab.api.serializers.CreateProjectDataSerializer(data=d_field)
+            s_project_serializer = wetlab.api.serializers.CreateProjectDataSerializer(
+                data=d_field
+            )
             if not s_project_serializer.is_valid():
                 return Response(
                     s_project_serializer.errors, status=status.HTTP_400_BAD_REQUEST
@@ -229,13 +239,17 @@ def fetch_run_information(request):
         s_data = []
         for sample in s_list:
             sample = sample.strip()
-            if wetlab.models.SamplesInProject.objects.filter(sample_name__iexact=sample).exists():
+            if wetlab.models.SamplesInProject.objects.filter(
+                sample_name__iexact=sample
+            ).exists():
                 s_found_objs = wetlab.models.SamplesInProject.objects.filter(
                     sample_name__iexact=sample
                 )
                 for s_found_obj in s_found_objs:
                     s_data.append(
-                        wetlab.api.serializers.SampleRunInfoSerializers(s_found_obj, many=False).data
+                        wetlab.api.serializers.SampleRunInfoSerializers(
+                            s_found_obj, many=False
+                        ).data
                     )
             else:
                 s_data.append({"sample_name": sample, "Run data": "Not found"})
@@ -254,8 +268,12 @@ def fetch_sample_information(request):
         sample = request.GET["sample"]
         if not core.modesl.Samples.objects.filter(sample_name__iexact=sample).exists():
             return Response(status=status.HTTP_204_NO_CONTENT)
-        sample_obj = core.models.Samples.objects.filter(sample_name__iexact=sample).last()
-        sample_data = wetlab.api.serializers.SampleSerializer(sample_obj, many=False).data
+        sample_obj = core.models.Samples.objects.filter(
+            sample_name__iexact=sample
+        ).last()
+        sample_data = wetlab.api.serializers.SampleSerializer(
+            sample_obj, many=False
+        ).data
     else:
         if "sample_project_name" in request.GET:
             project_name = request.GET["sample_project_name"]
@@ -300,7 +318,9 @@ def fetch_sample_information(request):
             ).data
         else:
             sample_obj = core.models.Samples.objects.prefetch_related("project_values")
-            sample_data = wetlab.api.serializers.SampleSerializer(sample_obj, many=True).data
+            sample_data = wetlab.api.serializers.SampleSerializer(
+                sample_obj, many=True
+            ).data
     return Response(sample_data, status=status.HTTP_200_OK)
 
 
@@ -329,7 +349,9 @@ def sample_fields(request):
 def sample_project_fields(request):
     if "project" in request.GET:
         project = request.GET["project"].strip()
-        if core.models.SampleProjects.objects.filter(sample_project_name__iexact=project).exists():
+        if core.models.SampleProjects.objects.filter(
+            sample_project_name__iexact=project
+        ).exists():
             s_project_obj = core.models.SampleProjects.objects.filter(
                 sample_project_name__iexact=project
             ).last()
@@ -351,8 +373,12 @@ def get_lab_information_contact(request):
     if "laboratory" in request.GET:
         lab_name = request.GET["laboratory"].strip()
         if core.models.LabRequest.objects.filter(lab_name__iexact=lab_name).exists():
-            lab_req_obj = core.models.LabRequest.objects.filter(lab_name__iexact=lab_name).last()
-            lab_req_serializer = core.models.LabRequestSerializer(lab_req_obj, many=False)
+            lab_req_obj = core.models.LabRequest.objects.filter(
+                lab_name__iexact=lab_name
+            ).last()
+            lab_req_serializer = core.models.LabRequestSerializer(
+                lab_req_obj, many=False
+            )
             return Response(lab_req_serializer.data, status=status.HTTP_200_OK)
         else:
             return Response(status=status.HTTP_204_NO_CONTENT)
@@ -393,7 +419,9 @@ def summarize_data_information(request):
 )
 @api_view(["GET"])
 def statistic_information(request):
-    statistics_data = wetlab.api.utils.sample.collect_statistics_information(request.GET)
+    statistics_data = wetlab.api.utils.sample.collect_statistics_information(
+        request.GET
+    )
     if "ERROR" in statistics_data:
         return Response(status=status.HTTP_400_BAD_REQUEST)
     if len(statistics_data) == 0: