Clean code

backend/metagenedb/api/catalog/views/bulk_viewset.py

@@ -8,7 +8,6 @@ class BulkViewSet(ModelViewSet):
     def get_objects(self, instance_ids):
         return self.queryset.in_bulk(instance_ids, field_name=self.lookup_field)
 
-
     def _created_payload(self, serializer, request):
         if isinstance(request.data, list):
             return {
@@ -38,12 +37,10 @@ class BulkViewSet(ModelViewSet):
             # perform the classic update
             return super().update(request, *args, **kwargs)
         instance_ids = set([element[self.lookup_field] for element in request.data])
-        instances_set = self.get_objects(instance_ids)
-        instances = [instance for instance in instances_set.values()]
-        serializer = self.get_serializer(instances, data=request.data, many=True)
+        instances = self.get_objects(instance_ids)
+        serializer = self.get_serializer(instances.values(), data=request.data, many=True)
         serializer.is_valid(raise_exception=True)
 
-
         # instance = self.get_object()
         # serializer = self.get_serializer(instance, data=request.data, partial=partial)
         # serializer.is_valid(raise_exception=True)

backend/metagenedb/apps/catalog/serializers/gene.py

@@ -6,7 +6,6 @@ from rest_framework.utils import model_meta
 from metagenedb.apps.catalog.models import Function, Gene, Taxonomy
 from metagenedb.apps.catalog.serializers import FunctionSerializer
 
-logging.basicConfig(level=logging.INFO)
 _LOGGER = logging.getLogger(__name__)
 
 

backend/metagenedb/common/utils/parsers/igc.py

 import logging
 
-logging.basicConfig(level=logging.INFO)
 _LOGGER = logging.getLogger(__name__)
 
 

backend/metagenedb/common/utils/parsers/kegg.py

 import logging
 
-logging.basicConfig(level=logging.INFO)
 _LOGGER = logging.getLogger(__name__)
 
 

backend/metagenedb/common/utils/parsers/ncbi_taxonomy.py

 import logging
 
-logging.basicConfig(level=logging.INFO)
 _LOGGER = logging.getLogger(__name__)
 
 

backend/scripts/populate_db/import_igc_data.py

@@ -10,7 +10,6 @@ from slugify import slugify
 
 from metagenedb.common.utils.parsers import IGCLineParser
 
-logging.basicConfig(level=logging.INFO)
 _LOGGER = logging.getLogger(__name__)
 
 

backend/scripts/populate_db/import_ncbi_taxonomy.py

@@ -15,7 +15,6 @@ django.setup()
 from metagenedb.apps.catalog.models import Taxonomy  # noqa
 from metagenedb.apps.catalog.serializers import TaxonomySerializer  # noqa
 
-logging.basicConfig(level=logging.INFO)
 _LOGGER = logging.getLogger(__name__)
 
 SELECT_RELATED_PARENT = "parent{}".format("__parent" * 40)

backend/scripts/populate_db/load_kegg_ko.py

@@ -18,7 +18,6 @@ django.setup()
 
 from metagenedb.apps.catalog.models import KeggOrthology  # noqa
 
-logging.basicConfig(level=logging.INFO)
 _LOGGER = logging.getLogger(__name__)
 
 KEGG_KO_LIST_API = "http://rest.kegg.jp/list/ko"