diff --git a/backend/metagenedb/api/catalog/views/bulk_viewset.py b/backend/metagenedb/api/catalog/views/bulk_viewset.py index 26412907ad1d6cf7f8b6efcfdde1b0e201153e76..1ed61653d194bb86cf8346e78e50acf5b010bb86 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 9c4f72ba377220753c1bc4fec11e2d2dee84bd83..1c684a3e51c1401e0847fa2d4ad62c4081006e82 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 296ed9b2803da02b298233a8b0c1e1e90a9d56d5..5790c5d38ffa188d74ed57ccf12f9736c6b7496b 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 2ed3f8719829505668cba31a409c06e8ecf7dea7..68701c477ca8d11b9e0708cbed2f4308b613c403 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 d67d3d1b670e7cd6199cda735d1e35e15d94dd17..e3b298e85f736c94e814a9afdfdf5e0cf1399ad4 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 4d629c79ff9db37ba86c23cda6effe8b54132e1f..59337649cfbe518a87b45b3481dffaa35baa260c 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 510cd327f83254987114fa0be62f8f6c6dd7e7af..339bdcb9bc6b114f3ac2a54dda78bf2dbfbd7699 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 55d0960aafc6d326a616c879c0d7b8b0bc4e94a1..ada7880148b75be4ed935890c7db92d077f0e900 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"