add basis for swagger documentation of API

backend/Pipfile

@@ -4,50 +4,52 @@ url = "https://pypi.org/simple"
 verify_ssl = true
 
 [dev-packages]
-atomicwrites = "==1.3.0"
-attrs = "==19.1.0"
-coverage = "==4.5.3"
-entrypoints = "==0.3"
-flake8 = "==3.7.7"
-importlib-metadata = "==0.18"
-kiwisolver = "==1.1.0"
-mccabe = "==0.6.1"
-more-itertools = "==7.0.0"
-pluggy = "==0.12.0"
-py = "==1.8.0"
-pycodestyle = "==2.5.0"
-pyflakes = "==2.1.1"
-pyparsing = "==2.4.0"
-pytest = "==4.6.3"
-pytest-cov = "==2.7.1"
-pytest-django = "==3.5.0"
-wcwidth = "==0.1.7"
-zipp = "==0.5.1"
-Cycler = "==0.10.0"
+atomicwrites = "*"
+attrs = "*"
+coverage = "*"
+entrypoints = "*"
+flake8 = "*"
+importlib-metadata = "*"
+kiwisolver = "*"
+mccabe = "*"
+more-itertools = "*"
+pluggy = "*"
+py = "*"
+pycodestyle = "*"
+pyflakes = "*"
+pyparsing = "*"
+pytest = "*"
+pytest-cov = "*"
+pytest-django = "*"
+wcwidth = "*"
+zipp = "*"
+Cycler = "*"
 jupyter = "*"
 
 [packages]
-certifi = "==2019.6.16"
-chardet = "==3.0.4"
-django-cors-headers = "==3.0.2"
-django-environ = "==0.4.5"
-django-extensions = "==2.1.7"
-django-filter = "==2.1.0"
-djangorestframework = "==3.9.4"
-djangorestframework-jwt = "==1.11.0"
-idna = "==2.8"
-numpy = "==1.16.4"
-pandas = "==0.24.2"
-psycopg2 = "==2.8.2"
-python-dateutil = "==2.8.0"
-pytz = "==2019.1"
-requests = "==2.22.0"
-six = "==1.12.0"
-sqlparse = "==0.3.0"
-urllib3 = "==1.25.3"
-Django = "==2.2.1"
-PyJWT = "==1.7.1"
+certifi = "*"
+chardet = "*"
+django-cors-headers = "*"
+django-environ = "*"
+django-extensions = "*"
+django-filter = "*"
+djangorestframework = "*"
+djangorestframework-jwt = "*"
+idna = "*"
+numpy = "*"
+pandas = "*"
+psycopg2 = "*"
+python-dateutil = "*"
+pytz = "*"
+requests = "*"
+six = "*"
+sqlparse = "*"
+urllib3 = "*"
+Django = "*"
+PyJWT = "*"
 metagenedb = {editable = true,path = "."}
+drf-yasg = "*"
+packaging = "*"
 
 [requires]
 python_version = "3.7"

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

 import pandas as pd
+from drf_yasg import openapi
+from drf_yasg.utils import swagger_auto_schema
 from rest_framework.viewsets import GenericViewSet
 from rest_framework import mixins
 from rest_framework import status
@@ -10,6 +12,13 @@ from metagenedb.apps.catalog.models import Gene
 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('return JSON content', schema=gene_length_schema)
+
+
 class GeneViewSet(mixins.ListModelMixin,
                   mixins.RetrieveModelMixin,
                   GenericViewSet):
@@ -36,6 +45,16 @@ class GeneViewSet(mixins.ListModelMixin,
             'labels': labels
         }
 
+    @swagger_auto_schema(
+        manual_parameters=[window_size_param],
+        responses = {
+            '200': gene_length_response,
+            '204': 'no content'
+        },        
+        security=[],
+        operation_id='List of categories',
+        operation_description='Get the distribution of gene length for a given window size.',
+    )
     @action(methods=['get'], detail=False)
     def gene_length(self, request, window_size=10000):
         if 'window_size' in request.query_params:

backend/metagenedb/settings/django.py

@@ -19,6 +19,7 @@ INSTALLED_APPS = [
     'rest_framework',
     'django_extensions',
     'corsheaders',
+    'drf_yasg',
 ]
 
 MIDDLEWARE = [

backend/metagenedb/urls.py

@@ -15,9 +15,28 @@ Including another URLconf
 """
 from django.contrib import admin
 from django.urls import include, path
+from django.conf.urls import url
+from rest_framework import permissions
+from drf_yasg.views import get_schema_view
+from drf_yasg import openapi
+
+
+schema_view = get_schema_view(
+   openapi.Info(
+      title="Metagenedb API",
+      default_version='v1',
+      description="API documentation for metagenedb",
+      contact=openapi.Contact(email="kehillio@pasteur.fr"),
+      license=openapi.License(name="License not defined"),
+   ),
+   public=True,
+   permission_classes=(permissions.AllowAny,),
+)
 
 
 urlpatterns = [
     path('api/', include(('metagenedb.api.urls', 'api'))),
     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'),
 ]

ci/kubernetes/ingress.yaml

@@ -24,6 +24,14 @@ spec:
           serviceName: backend
           servicePort: 8000
       - path: /api
+        backend:
+          serviceName: backend
+          servicePort: 8000
+      - path: /swagger
+        backend:
+          serviceName: backend
+          servicePort: 8000
+      - path: /redoc
         backend:
           serviceName: backend
           servicePort: 8000
\ No newline at end of file

docker-compose.yaml

@@ -48,9 +48,7 @@ services:
       - NODE_ENV=development
 
   nginx:
-    build:
-      context: .
-      dockerfile: nginx/dev/Dockerfile
+    image: nginx:1.13.12-alpine
     ports:
       - "80:80"
     depends_on:

nginx/dev/dev.conf

@@ -41,18 +41,12 @@ http {
     }
 
     # backend urls
-    location ~ ^/(admin|api|catalog|auth) {
+    location ~ ^/(admin|api|swagger|static) {
       proxy_redirect off;
       proxy_pass http://backend;
       proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
       proxy_set_header Host $http_host;
     }
 
-    # static files
-    location /static {
-      autoindex on;
-      alias /usr/src/app/static;
-    }
-
   }
 }