From e26fc5677bc743df1417c83d2a72d961d13b7a53 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Thu, 9 Apr 2020 16:15:54 +0200
Subject: [PATCH] Add more documentation for metagenedb API
---
backend/metagenedb/api/catalog/urls.py | 2 +-
backend/metagenedb/api/catalog/views/base.py | 13 ++-
.../metagenedb/api/catalog/views/function.py | 88 +++++++++++++++++++
backend/metagenedb/api/catalog/views/gene.py | 32 +++++++
.../api/catalog/views/statistics.py | 14 ++-
.../metagenedb/api/catalog/views/taxonomy.py | 32 +++++++
6 files changed, 175 insertions(+), 6 deletions(-)
diff --git a/backend/metagenedb/api/catalog/urls.py b/backend/metagenedb/api/catalog/urls.py
index 043fbbd..fa35c70 100644
--- a/backend/metagenedb/api/catalog/urls.py
+++ b/backend/metagenedb/api/catalog/urls.py
@@ -4,7 +4,7 @@ from rest_framework.routers import DefaultRouter, DynamicRoute, Route
from metagenedb.api.catalog import views
-from metagenedb.api.catalog.views.celery_test import celery_test_view, test_task_view
+# from metagenedb.api.catalog.views.celery_test import celery_test_view, test_task_view
class CustomRouter(DefaultRouter):
diff --git a/backend/metagenedb/api/catalog/views/base.py b/backend/metagenedb/api/catalog/views/base.py
index 62e2f0e..dbd21b2 100644
--- a/backend/metagenedb/api/catalog/views/base.py
+++ b/backend/metagenedb/api/catalog/views/base.py
@@ -1,13 +1,22 @@
from marshmallow.exceptions import ValidationError
from rest_framework import status
+from rest_framework.mixins import (
+ CreateModelMixin, ListModelMixin, RetrieveModelMixin, UpdateModelMixin
+)
from rest_framework.response import Response
-from rest_framework.viewsets import ModelViewSet
+from rest_framework.viewsets import GenericViewSet
from metagenedb.common.django_default.permissions import ListAndRetrieveAll
from metagenedb.common.django_default.qparams_validators import PaginatedQueryParams
-class QParamsValidationViewSet(ModelViewSet):
+class QParamsValidationViewSet(
+ CreateModelMixin,
+ ListModelMixin,
+ RetrieveModelMixin,
+ UpdateModelMixin,
+ GenericViewSet
+):
query_params_parser = PaginatedQueryParams
def _get_qparams(self, raw_query_params):
diff --git a/backend/metagenedb/api/catalog/views/function.py b/backend/metagenedb/api/catalog/views/function.py
index ce21c8d..207efde 100644
--- a/backend/metagenedb/api/catalog/views/function.py
+++ b/backend/metagenedb/api/catalog/views/function.py
@@ -1,5 +1,6 @@
import logging
+from drf_yasg.utils import swagger_auto_schema
from marshmallow.exceptions import ValidationError
from rest_framework.response import Response
from rest_framework.status import HTTP_422_UNPROCESSABLE_ENTITY
@@ -25,6 +26,36 @@ class FunctionViewSet(BulkViewSet):
filterset_class = FunctionFilter
query_params_parser = FunctionQueryParams
+ @swagger_auto_schema(
+ tags=['Functions'],
+ )
+ def list(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Functions'],
+ )
+ def retrieve(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Functions'],
+ )
+ def create(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Functions'],
+ )
+ def update(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Functions'],
+ )
+ def partial_update(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
class KeggOrthologyViewSet(QParamsValidationViewSet):
queryset = KeggOrthology.objects.all()
@@ -42,6 +73,9 @@ class KeggOrthologyViewSet(QParamsValidationViewSet):
detailed_data = db_data
return detailed_data
+ @swagger_auto_schema(
+ tags=['KEGG'],
+ )
def retrieve(self, request, *args, **kwargs):
try:
query_params = self.query_params_parser().load(request.query_params)
@@ -58,6 +92,30 @@ class KeggOrthologyViewSet(QParamsValidationViewSet):
returned_data = self._get_external_info(returned_data)
return Response(returned_data)
+ @swagger_auto_schema(
+ tags=['KEGG'],
+ )
+ def list(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['KEGG'],
+ )
+ def create(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['KEGG'],
+ )
+ def update(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['KEGG'],
+ )
+ def partial_update(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
class EggNOGViewSet(QParamsValidationViewSet):
queryset = EggNOG.objects.all()
@@ -65,3 +123,33 @@ class EggNOGViewSet(QParamsValidationViewSet):
lookup_field = 'function_id'
filterset_class = EggNOGFilter
query_params_parser = EggNOGQueryParams
+
+ @swagger_auto_schema(
+ tags=['EggNOG'],
+ )
+ def list(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['EggNOG'],
+ )
+ def retrieve(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['EggNOG'],
+ )
+ def create(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['EggNOG'],
+ )
+ def update(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['EggNOG'],
+ )
+ def partial_update(self, *args, **kwargs):
+ super().list(*args, **kwargs)
diff --git a/backend/metagenedb/api/catalog/views/gene.py b/backend/metagenedb/api/catalog/views/gene.py
index 3d73654..04fd2b4 100644
--- a/backend/metagenedb/api/catalog/views/gene.py
+++ b/backend/metagenedb/api/catalog/views/gene.py
@@ -1,3 +1,5 @@
+from drf_yasg.utils import swagger_auto_schema
+
from metagenedb.apps.catalog.models import Gene
from metagenedb.api.catalog.filters import GeneFilter
from metagenedb.api.catalog.qparams_validators.gene import GeneQueryParams
@@ -12,3 +14,33 @@ class GeneViewSet(BulkViewSet):
filterset_class = GeneFilter
query_params_parser = GeneQueryParams
lookup_field = 'gene_id'
+
+ @swagger_auto_schema(
+ tags=['Genes'],
+ )
+ def list(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Genes'],
+ )
+ def retrieve(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Genes'],
+ )
+ def create(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Genes'],
+ )
+ def update(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Genes'],
+ )
+ def partial_update(self, *args, **kwargs):
+ super().list(*args, **kwargs)
diff --git a/backend/metagenedb/api/catalog/views/statistics.py b/backend/metagenedb/api/catalog/views/statistics.py
index f444816..f0e3cfd 100644
--- a/backend/metagenedb/api/catalog/views/statistics.py
+++ b/backend/metagenedb/api/catalog/views/statistics.py
@@ -1,4 +1,5 @@
from django.shortcuts import get_object_or_404
+from drf_yasg.utils import swagger_auto_schema
from rest_framework import viewsets
from rest_framework.response import Response
@@ -7,16 +8,23 @@ from metagenedb.apps.catalog.serializers import StatisticsSerializer
class StatisticsViewSet(viewsets.ViewSet):
- """
- API View that list or retrieve pre-computed statistics from the catalog.
- """
lookup_field = 'stats_id'
+ @swagger_auto_schema(
+ operation_description="List all pre-computed statistics",
+ operation_summary="API to list all pre-computed statistics.",
+ tags=['Statistics'],
+ )
def list(self, request):
queryset = Statistics.objects.all()
serializer = StatisticsSerializer(queryset, many=True)
return Response(serializer.data)
+ @swagger_auto_schema(
+ operation_description="Retrieve pre-computed statistics from an ID",
+ operation_summary="API to retrieve pre-computed statistics.",
+ tags=['Statistics'],
+ )
def retrieve(self, request, stats_id=None):
queryset = Statistics.objects.all()
stats = get_object_or_404(queryset, stats_id=stats_id)
diff --git a/backend/metagenedb/api/catalog/views/taxonomy.py b/backend/metagenedb/api/catalog/views/taxonomy.py
index a05eeb5..86ed8ff 100644
--- a/backend/metagenedb/api/catalog/views/taxonomy.py
+++ b/backend/metagenedb/api/catalog/views/taxonomy.py
@@ -1,3 +1,5 @@
+from drf_yasg.utils import swagger_auto_schema
+
from metagenedb.api.catalog.filters import TaxonomyFilter
from metagenedb.api.catalog.qparams_validators.taxonomy import TaxonomyQueryParams
from metagenedb.apps.catalog.models import Taxonomy
@@ -13,3 +15,33 @@ class TaxonomyViewSet(BulkViewSet):
lookup_field = 'tax_id'
filterset_class = TaxonomyFilter
query_params_parser = TaxonomyQueryParams
+
+ @swagger_auto_schema(
+ tags=['Taxonomy'],
+ )
+ def list(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Taxonomy'],
+ )
+ def retrieve(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Taxonomy'],
+ )
+ def create(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Taxonomy'],
+ )
+ def update(self, *args, **kwargs):
+ super().list(*args, **kwargs)
+
+ @swagger_auto_schema(
+ tags=['Taxonomy'],
+ )
+ def partial_update(self, *args, **kwargs):
+ super().list(*args, **kwargs)
--
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