diff --git a/backend/metagenedb/api/catalog/views/gene.py b/backend/metagenedb/api/catalog/views/gene.py
index c36bdbaa771d5e58cb9598b0898775047d11e3fd..f60033e5c1926356cfc49cf93fa0394c1b019599 100644
--- a/backend/metagenedb/api/catalog/views/gene.py
+++ b/backend/metagenedb/api/catalog/views/gene.py
@@ -1,7 +1,8 @@
import pandas as pd
+import django_filters.rest_framework
from drf_yasg import openapi
from drf_yasg.utils import swagger_auto_schema
-from rest_framework.viewsets import GenericViewSet
+from rest_framework.viewsets import GenericViewSet, ModelViewSet
from rest_framework import mixins
from rest_framework import status
from rest_framework.decorators import action
@@ -15,16 +16,14 @@ from metagenedb.apps.catalog.serializers import GeneSerializer
# Define global variable for API documentation
window_size_param = openapi.Parameter('window_size', in_=openapi.IN_QUERY, description='Size of the window.',
type=openapi.TYPE_INTEGER, default=10000)
-gene_length_schema = openapi.Schema("pouet", {}, type={'hihi': 'haha'})
-gene_length_response = openapi.Response('Get the distribution of gene length for a given window size', schema=gene_length_schema)
+# gene_length_schema = openapi.Schema("pouet", {}, type={'hihi': 'haha'})
+# gene_length_response = openapi.Response('Get the distribution of gene length for a given window size', schema=gene_length_schema)
-class GeneViewSet(mixins.ListModelMixin,
- mixins.RetrieveModelMixin,
- GenericViewSet):
+class GeneViewSet(ModelViewSet):
queryset = Gene.objects.all()
serializer_class = GeneSerializer
- GENE_LENGTH_COL = 'gene_length'
+ GENE_LENGTH_COL = 'length'
def _count_windows(self, df, window_size=10000, window_col=GENE_LENGTH_COL):
"""
@@ -48,10 +47,9 @@ class GeneViewSet(mixins.ListModelMixin,
@swagger_auto_schema(
manual_parameters=[window_size_param],
responses={
- '200': gene_length_response,
+ # '200': gene_length_response,
'204': 'no content'
},
- security=[],
operation_id='List of categories',
)
@action(methods=['get'], detail=False)
diff --git a/backend/metagenedb/apps/catalog/admin/gene.py b/backend/metagenedb/apps/catalog/admin/gene.py
index c9104b6042547f873ccff75621910e1615c93cdf..694e7b2088e7819781840fcbc30c3a65fc795080 100644
--- a/backend/metagenedb/apps/catalog/admin/gene.py
+++ b/backend/metagenedb/apps/catalog/admin/gene.py
@@ -6,7 +6,7 @@ from metagenedb.apps.catalog.models import Gene
@admin.register(Gene)
class GeneAdmin(admin.ModelAdmin):
- list_display = ('gene_id', 'gene_length', 'get_functions', 'get_taxonomy')
+ list_display = ('gene_id', 'length', 'get_functions', 'get_taxonomy')
search_fields = ('gene_id',)
def get_functions(self, obj):
diff --git a/backend/metagenedb/apps/catalog/migrations/0007_gene_length_positive.py b/backend/metagenedb/apps/catalog/migrations/0007_length_name_and_positive_int.py
similarity index 63%
rename from backend/metagenedb/apps/catalog/migrations/0007_gene_length_positive.py
rename to backend/metagenedb/apps/catalog/migrations/0007_length_name_and_positive_int.py
index 7e90fa6d9a1f9d19a3baa6ec071d68f465da1c8b..1fa58595519485a705ada5a5e214cfb3ce097e83 100644
--- a/backend/metagenedb/apps/catalog/migrations/0007_gene_length_positive.py
+++ b/backend/metagenedb/apps/catalog/migrations/0007_length_name_and_positive_int.py
@@ -1,4 +1,4 @@
-# Generated by Django 2.2.1 on 2019-08-07 13:20
+# Generated by Django 2.2.1 on 2019-08-07 14:10
from django.db import migrations, models
@@ -15,4 +15,9 @@ class Migration(migrations.Migration):
name='gene_length',
field=models.PositiveIntegerField(),
),
+ migrations.RenameField(
+ model_name='gene',
+ old_name='gene_length',
+ new_name='length',
+ ),
]
diff --git a/backend/metagenedb/apps/catalog/models/gene.py b/backend/metagenedb/apps/catalog/models/gene.py
index 755ea4bf054460739ea0f85f789c44ad244eb435..06c14ddfe4048267769f3dc3903ee3b42fe2d1b5 100644
--- a/backend/metagenedb/apps/catalog/models/gene.py
+++ b/backend/metagenedb/apps/catalog/models/gene.py
@@ -5,7 +5,7 @@ from .function import Function
class Gene(models.Model):
gene_id = models.CharField(max_length=100, unique=True, db_index=True)
- gene_length = models.PositiveIntegerField()
+ length = models.PositiveIntegerField()
functions = models.ManyToManyField(Function)
taxonomy = models.ForeignKey(
'Taxonomy', related_name='genes',
diff --git a/backend/metagenedb/apps/catalog/serializers/gene.py b/backend/metagenedb/apps/catalog/serializers/gene.py
index 1928f2e9dcfa116b619f4fd5eb47de90890f041a..fe869af6ff5c223980768deb672f079c16893d4b 100644
--- a/backend/metagenedb/apps/catalog/serializers/gene.py
+++ b/backend/metagenedb/apps/catalog/serializers/gene.py
@@ -4,7 +4,7 @@ from metagenedb.apps.catalog.serializers import FunctionSerializer
class GeneSerializer(serializers.ModelSerializer):
- functions = FunctionSerializer(many=True, read_only=True)
+ functions = FunctionSerializer(many=True, required=False)
taxonomy = serializers.SlugRelatedField(
queryset=Taxonomy.objects.all(),
slug_field='tax_id',
@@ -13,4 +13,4 @@ class GeneSerializer(serializers.ModelSerializer):
class Meta:
model = Gene
- fields = ('gene_id', 'gene_length', 'functions', 'taxonomy')
+ fields = ('gene_id', 'length', 'functions', 'taxonomy')
diff --git a/backend/metagenedb/settings/django.py b/backend/metagenedb/settings/django.py
index 4d0e7982a88cfbbde063c7ce69d528de6efe986e..9973a7ece95efcfc0fdcde09d9edeace4f7fcf67 100644
--- a/backend/metagenedb/settings/django.py
+++ b/backend/metagenedb/settings/django.py
@@ -106,7 +106,7 @@ REST_FRAMEWORK = {
# 'rest_framework.authentication.BasicAuthentication',
),
'DEFAULT_PAGINATION_CLASS': 'rest_framework.pagination.PageNumberPagination',
- 'PAGE_SIZE': 100
+ 'PAGE_SIZE': 100,
}
diff --git a/backend/metagenedb/urls.py b/backend/metagenedb/urls.py
index 7d8394ea367992c9542a44f164645384d1eb6ad9..cc83bb9a5264e37636eaffc19cd2fd6436721c08 100644
--- a/backend/metagenedb/urls.py
+++ b/backend/metagenedb/urls.py
@@ -39,4 +39,5 @@ urlpatterns = [
path('admin/', admin.site.urls),
url(r'^swagger(?P<format>\.json|\.yaml)$', schema_view.without_ui(cache_timeout=0), name='schema-json'),
url(r'^swagger/$', schema_view.with_ui('swagger', cache_timeout=0), name='schema-swagger-ui'),
+ url(r'^redoc/$', schema_view.with_ui('redoc', cache_timeout=0), name='schema-redoc'),
]
diff --git a/nginx/dev/dev.conf b/nginx/dev/dev.conf
index 4b2b44eaf93ead7d244e153d7c97bc7f359dfdd8..112daecc6e15679ee671585e6f97d44cee93cab5 100644
--- a/nginx/dev/dev.conf
+++ b/nginx/dev/dev.conf
@@ -41,7 +41,7 @@ http {
}
# backend urls
- location ~ ^/(admin|api|swagger|static) {
+ location ~ ^/(admin|api|swagger|redoc|static) {
proxy_redirect off;
proxy_pass http://backend;
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;