From 8924454a4c94eb829f39de2da050eaa446d2d2b6 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Mon, 9 Sep 2019 15:19:36 +0200
Subject: [PATCH] Clean code
---
backend/metagenedb/api/catalog/views/bulk_viewset.py | 7 ++-----
backend/metagenedb/apps/catalog/serializers/gene.py | 1 -
backend/metagenedb/common/utils/parsers/igc.py | 1 -
backend/metagenedb/common/utils/parsers/kegg.py | 1 -
backend/metagenedb/common/utils/parsers/ncbi_taxonomy.py | 1 -
backend/scripts/populate_db/import_igc_data.py | 1 -
backend/scripts/populate_db/import_ncbi_taxonomy.py | 1 -
backend/scripts/populate_db/load_kegg_ko.py | 1 -
8 files changed, 2 insertions(+), 12 deletions(-)
diff --git a/backend/metagenedb/api/catalog/views/bulk_viewset.py b/backend/metagenedb/api/catalog/views/bulk_viewset.py
index 2641290..1ed6165 100644
--- a/backend/metagenedb/api/catalog/views/bulk_viewset.py
+++ b/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)
diff --git a/backend/metagenedb/apps/catalog/serializers/gene.py b/backend/metagenedb/apps/catalog/serializers/gene.py
index 9c4f72b..1c684a3 100644
--- a/backend/metagenedb/apps/catalog/serializers/gene.py
+++ b/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__)
diff --git a/backend/metagenedb/common/utils/parsers/igc.py b/backend/metagenedb/common/utils/parsers/igc.py
index 296ed9b..5790c5d 100644
--- a/backend/metagenedb/common/utils/parsers/igc.py
+++ b/backend/metagenedb/common/utils/parsers/igc.py
@@ -1,6 +1,5 @@
import logging
-logging.basicConfig(level=logging.INFO)
_LOGGER = logging.getLogger(__name__)
diff --git a/backend/metagenedb/common/utils/parsers/kegg.py b/backend/metagenedb/common/utils/parsers/kegg.py
index 2ed3f87..68701c4 100644
--- a/backend/metagenedb/common/utils/parsers/kegg.py
+++ b/backend/metagenedb/common/utils/parsers/kegg.py
@@ -1,6 +1,5 @@
import logging
-logging.basicConfig(level=logging.INFO)
_LOGGER = logging.getLogger(__name__)
diff --git a/backend/metagenedb/common/utils/parsers/ncbi_taxonomy.py b/backend/metagenedb/common/utils/parsers/ncbi_taxonomy.py
index d67d3d1..e3b298e 100644
--- a/backend/metagenedb/common/utils/parsers/ncbi_taxonomy.py
+++ b/backend/metagenedb/common/utils/parsers/ncbi_taxonomy.py
@@ -1,6 +1,5 @@
import logging
-logging.basicConfig(level=logging.INFO)
_LOGGER = logging.getLogger(__name__)
diff --git a/backend/scripts/populate_db/import_igc_data.py b/backend/scripts/populate_db/import_igc_data.py
index 4d629c7..5933764 100755
--- a/backend/scripts/populate_db/import_igc_data.py
+++ b/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__)
diff --git a/backend/scripts/populate_db/import_ncbi_taxonomy.py b/backend/scripts/populate_db/import_ncbi_taxonomy.py
index 510cd32..339bdcb 100755
--- a/backend/scripts/populate_db/import_ncbi_taxonomy.py
+++ b/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)
diff --git a/backend/scripts/populate_db/load_kegg_ko.py b/backend/scripts/populate_db/load_kegg_ko.py
index 55d0960..ada7880 100755
--- a/backend/scripts/populate_db/load_kegg_ko.py
+++ b/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"
--
GitLab