diff --git a/backend/metagenedb/apps/catalog/admin/__init__.py b/backend/metagenedb/apps/catalog/admin/__init__.py
index 567ddd843314df2c5b013ac498b52b1978a051d1..d5ce815f298d298bce8e620d51ec901b3a229c78 100644
--- a/backend/metagenedb/apps/catalog/admin/__init__.py
+++ b/backend/metagenedb/apps/catalog/admin/__init__.py
@@ -1,2 +1,5 @@
from .gene import GeneAdmin
from .function import FunctionAdmin, KeggOrthologyAdmin
+
+
+__all__ = ['GeneAdmin', 'FunctionAdmin', 'KeggOrthologyAdmin']
diff --git a/backend/metagenedb/apps/catalog/admin/admin.py b/backend/metagenedb/apps/catalog/admin/admin.py
index 4e43b5e374617026418c78677ab04beb40f512f4..a92351921adefef1cd572383ad2ac9589e5ac366 100644
--- a/backend/metagenedb/apps/catalog/admin/admin.py
+++ b/backend/metagenedb/apps/catalog/admin/admin.py
@@ -26,4 +26,3 @@ class FunctionAdmin(admin.ModelAdmin):
list_display = ('function_id', 'name', 'source')
search_fields = ('function_id',)
-
diff --git a/backend/metagenedb/apps/catalog/migrations/0001_initial.py b/backend/metagenedb/apps/catalog/migrations/0001_initial.py
index bb17ec5277c9623867a3da2e71689fbeb3c45fec..37343b3c254618c9d3a2a8da9168617b0fb35868 100644
--- a/backend/metagenedb/apps/catalog/migrations/0001_initial.py
+++ b/backend/metagenedb/apps/catalog/migrations/0001_initial.py
@@ -18,13 +18,13 @@ class Migration(migrations.Migration):
('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
('function_id', models.CharField(db_index=True, max_length=100)),
('name', models.CharField(max_length=100)),
- ('source', models.CharField(choices=[('undef', 'Undefined'), ('kegg', 'KEGG'), ('eggnog', 'EggNOG')], default='undef', max_length=10)),
+ ('source', models.CharField(choices=[('undef', 'Undefined'), ('kegg', 'KEGG'), ('eggnog', 'EggNOG')], default='undef', max_length=10)), # noqa
],
),
migrations.CreateModel(
name='KeggOrthology',
fields=[
- ('function_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='catalog.Function')),
+ ('function_ptr', models.OneToOneField(auto_created=True, on_delete=django.db.models.deletion.CASCADE, parent_link=True, primary_key=True, serialize=False, to='catalog.Function')), # noqa
('ec_number', models.CharField(blank=True, default='', max_length=200)),
('long_name', models.CharField(max_length=500)),
],
diff --git a/backend/metagenedb/apps/catalog/models/__init__.py b/backend/metagenedb/apps/catalog/models/__init__.py
index 2369fe8f0cd547bf0aa6493e52a9a1738addb2c1..c1a956affe6d0c48173dc355d08efe57a8ac2833 100644
--- a/backend/metagenedb/apps/catalog/models/__init__.py
+++ b/backend/metagenedb/apps/catalog/models/__init__.py
@@ -1,2 +1,5 @@
from .function import Function, KeggOrthology
from .gene import Gene
+
+
+__all__ = ['Function', 'KeggOrthology', 'Gene']
diff --git a/backend/metagenedb/apps/catalog/models/gene.py b/backend/metagenedb/apps/catalog/models/gene.py
index 15dbdf5d05555ce5a9633c790a7de20c9ececcdd..c5f46eacd316fc57e91ce12375a8a9ba92a9ad27 100644
--- a/backend/metagenedb/apps/catalog/models/gene.py
+++ b/backend/metagenedb/apps/catalog/models/gene.py
@@ -10,4 +10,3 @@ class Gene(models.Model):
def __str__(self):
return self.gene_id
-
diff --git a/backend/metagenedb/apps/catalog/serializers.py b/backend/metagenedb/apps/catalog/serializers.py
index df3dea846d7f78c6fb2cad449ee73629d8c7eeaf..38f09757fd7ebf4a5019e6b2dfb0435d25d25040 100644
--- a/backend/metagenedb/apps/catalog/serializers.py
+++ b/backend/metagenedb/apps/catalog/serializers.py
@@ -14,4 +14,3 @@ class GeneSerializer(serializers.ModelSerializer):
class Meta:
model = Gene
fields = ('gene_id', 'gene_length', 'functions')
-
diff --git a/backend/metagenedb/apps/catalog/tests.py b/backend/metagenedb/apps/catalog/tests.py
deleted file mode 100644
index 7ce503c2dd97ba78597f6ff6e4393132753573f6..0000000000000000000000000000000000000000
--- a/backend/metagenedb/apps/catalog/tests.py
+++ /dev/null
@@ -1,3 +0,0 @@
-from django.test import TestCase
-
-# Create your tests here.
diff --git a/backend/metagenedb/apps/catalog/views.py b/backend/metagenedb/apps/catalog/views.py
index 2122635b2f9004632b6395885e2a8d97f2c3b30b..0868f0b7db0b4c19b846273b9dc6c3be3d3b91b5 100644
--- a/backend/metagenedb/apps/catalog/views.py
+++ b/backend/metagenedb/apps/catalog/views.py
@@ -11,6 +11,7 @@ from .serializers import GeneSerializer
def index(request):
return HttpResponse(f"Welcome to the catalog page.")
+
@api_view(['GET'])
def gene_list(request):
"""
@@ -37,7 +38,7 @@ def gene_list(request):
return Response({'data': serializer.data, 'count': paginator.count, 'numpages': paginator.num_pages,
'nextlink': '/api/genes/?page=' + str(nextPage),
'prevlink': '/api/genes/?page=' + str(previousPage)})
-
+
@api_view(['GET'])
def gene_detail(request, gene_id):
diff --git a/backend/metagenedb/tests/test_user.py b/backend/metagenedb/tests/test_user.py
new file mode 100644
index 0000000000000000000000000000000000000000..272cf7d3916fe24c9e5271263acfadc1953b4a9e
--- /dev/null
+++ b/backend/metagenedb/tests/test_user.py
@@ -0,0 +1,14 @@
+from django.contrib.auth.models import User
+from django.test import TestCase
+
+
+class TestDatabase(TestCase):
+ def test_create_user(self):
+ user = User.objects.create_user(
+ username='user',
+ email='user@foo.com',
+ password='pass'
+ )
+ user.save()
+ user_count = User.objects.all().count()
+ self.assertEqual(user_count, 1)
diff --git a/backend/metagenedb/urls.py b/backend/metagenedb/urls.py
index a2d54e9bb2fb0ba4c4ab5b63b7abe1858cc610c3..be868ef3b1183bdc9ea4ed12de35d51e58b79ae8 100644
--- a/backend/metagenedb/urls.py
+++ b/backend/metagenedb/urls.py
@@ -16,7 +16,6 @@ Including another URLconf
from django.contrib import admin
from django.urls import include, path
-from rest_framework import routers
urlpatterns = [
path('admin/', admin.site.urls),
diff --git a/backend/requirements_dev.txt b/backend/requirements_dev.txt
index 48137105e41605ec2066cce99fd59538471f8fa0..ee46230ab129e2674f1665e132c28b03d3a8b82a 100644
--- a/backend/requirements_dev.txt
+++ b/backend/requirements_dev.txt
@@ -49,3 +49,4 @@ traitlets==4.3.2
wcwidth==0.1.7
webencodings==0.5.1
widgetsnbextension==3.4.2
+flake8
diff --git a/backend/scripts/import_igc_data.py b/backend/scripts/import_igc_data.py
index ea87b304c00bec5f4c6d617764418d4c39e85007..9ddf43e61546915b23d7581be29e2db662b0e068 100755
--- a/backend/scripts/import_igc_data.py
+++ b/backend/scripts/import_igc_data.py
@@ -12,7 +12,7 @@ from django.core.exceptions import ValidationError
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "metagenedb.settings")
django.setup()
-from metagenedb.apps.catalog.models import Gene, Function
+from metagenedb.apps.catalog.models import Gene, Function # noqa
logging.basicConfig(level=logging.INFO)
_LOGGER = logging.getLogger(__name__)
diff --git a/backend/scripts/load_kegg_ko.py b/backend/scripts/load_kegg_ko.py
index 10cd10406b029fcde8e282aaf4177f471a6063ca..c0b6952f1187eb98e1d11e01a740fe3d12509e4b 100755
--- a/backend/scripts/load_kegg_ko.py
+++ b/backend/scripts/load_kegg_ko.py
@@ -12,7 +12,7 @@ from django.core.exceptions import ValidationError
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "metagenedb.settings")
django.setup()
-from metagenedb.apps.catalog.models import KeggOrthology
+from metagenedb.apps.catalog.models import KeggOrthology # noqa
logging.basicConfig(level=logging.INFO)
_LOGGER = logging.getLogger(__name__)
@@ -62,7 +62,7 @@ def create_kegg_ko(kegg_ko):
def run():
- args = parse_arguments()
+ args = parse_arguments() # noqa
all_ko = requests.get("http://rest.kegg.jp/list/ko")
all_ko.raise_for_status()
inserted_kegg = 0
@@ -84,6 +84,5 @@ def run():
# Create unknown entry
-
if __name__ == "__main__":
run()
diff --git a/backend/setup.py b/backend/setup.py
index ee295906cf08d9a8ec55fc3848599103cd790745..ad1f80066b3b53daf70e71a3c8b94fc2db5de8db 100644
--- a/backend/setup.py
+++ b/backend/setup.py
@@ -11,5 +11,4 @@ setup(name="metagenedb",
'djangorestframework'
],
packages=find_packages(),
- scripts=['scripts/manage.py'],
-)
+ scripts=['scripts/manage.py'])