change name gene length to length

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

 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)

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):

backend/metagenedb/apps/catalog/migrations/0007_gene_length_positive.py → backend/metagenedb/apps/catalog/migrations/0007_length_name_and_positive_int.py

-# 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',
+        ),
     ]

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',

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')

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,
 }
 
 

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'),
 ]

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;