From 0120036a9086e826443598830344e8e17154067b Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Thu, 14 Nov 2019 17:40:36 +0100
Subject: [PATCH] replace endpoint by class to call different external APIs
---
.../metagenedb/api/catalog/views/function.py | 8 +++++
backend/metagenedb/api/external/urls.py | 7 ----
.../metagenedb/api/external/views/__init__.py | 1 -
.../metagenedb/api/external/views/togows.py | 25 ---------------
backend/metagenedb/api/urls.py | 3 +-
.../utils/external_api}/__init__.py | 0
.../common/utils/external_api/togows.py | 32 +++++++++++++++++++
7 files changed, 41 insertions(+), 35 deletions(-)
delete mode 100644 backend/metagenedb/api/external/urls.py
delete mode 100644 backend/metagenedb/api/external/views/__init__.py
delete mode 100644 backend/metagenedb/api/external/views/togows.py
rename backend/metagenedb/{api/external => common/utils/external_api}/__init__.py (100%)
create mode 100644 backend/metagenedb/common/utils/external_api/togows.py
diff --git a/backend/metagenedb/api/catalog/views/function.py b/backend/metagenedb/api/catalog/views/function.py
index 87d98ac..14906fa 100644
--- a/backend/metagenedb/api/catalog/views/function.py
+++ b/backend/metagenedb/api/catalog/views/function.py
@@ -1,6 +1,9 @@
+from rest_framework.response import Response
+
from metagenedb.api.catalog.filters import FunctionFilter
from metagenedb.apps.catalog.models import Function
from metagenedb.apps.catalog.serializers import FunctionSerializer
+from metagenedb.common.utils.external_api.togows import get_kegg
from .bulk_viewset import BulkViewSet
@@ -10,3 +13,8 @@ class FunctionViewSet(BulkViewSet):
serializer_class = FunctionSerializer
lookup_field = 'function_id'
filterset_class = FunctionFilter
+
+ def retrieve(self, request, *args, **kwargs):
+ instance = self.get_object()
+ serializer = self.get_serializer(instance)
+ return Response(serializer.data)
diff --git a/backend/metagenedb/api/external/urls.py b/backend/metagenedb/api/external/urls.py
deleted file mode 100644
index acc8c56..0000000
--- a/backend/metagenedb/api/external/urls.py
+++ /dev/null
@@ -1,7 +0,0 @@
-from django.urls import path
-
-from metagenedb.api.external.views import KeggInfoTogows
-
-urlpatterns = [
- path(r'togows/<kegg_id>', KeggInfoTogows.as_view(), name='kegg-info'),
-]
diff --git a/backend/metagenedb/api/external/views/__init__.py b/backend/metagenedb/api/external/views/__init__.py
deleted file mode 100644
index fb67f87..0000000
--- a/backend/metagenedb/api/external/views/__init__.py
+++ /dev/null
@@ -1 +0,0 @@
-from .togows import KeggInfoTogows # noqa
diff --git a/backend/metagenedb/api/external/views/togows.py b/backend/metagenedb/api/external/views/togows.py
deleted file mode 100644
index 9fc60b1..0000000
--- a/backend/metagenedb/api/external/views/togows.py
+++ /dev/null
@@ -1,25 +0,0 @@
-from bioapi.togows import TogoWSEntryAPI
-from requests.exceptions import HTTPError
-
-from rest_framework.views import APIView
-from rest_framework.response import Response
-from rest_framework.status import (HTTP_200_OK, HTTP_404_NOT_FOUND)
-
-
-class KeggInfoTogows(APIView):
- """
- Obtain detailed information about KEGG orthology entry.
- """
-
- def get(self, request, kegg_id=None):
- """
- Return a list of all users.
- """
- kegg_api = TogoWSEntryAPI("kegg-orthology")
- try:
- content = kegg_api.get(kegg_id)[0]
- status = HTTP_200_OK
- except HTTPError as http_err:
- content = [{'error': str(http_err)}]
- status = HTTP_404_NOT_FOUND
- return Response(content, status=status)
diff --git a/backend/metagenedb/api/urls.py b/backend/metagenedb/api/urls.py
index 5a521e8..7ab55a6 100644
--- a/backend/metagenedb/api/urls.py
+++ b/backend/metagenedb/api/urls.py
@@ -3,6 +3,5 @@ from django.urls import include, path
urlpatterns = [
path('auth/', include(('metagenedb.api.accounts.urls', 'auth'))),
- path('catalog/', include(('metagenedb.api.catalog.urls', 'catalog'))),
- path('external/', include(('metagenedb.api.external.urls', 'external')))
+ path('catalog/', include(('metagenedb.api.catalog.urls', 'catalog')))
]
diff --git a/backend/metagenedb/api/external/__init__.py b/backend/metagenedb/common/utils/external_api/__init__.py
similarity index 100%
rename from backend/metagenedb/api/external/__init__.py
rename to backend/metagenedb/common/utils/external_api/__init__.py
diff --git a/backend/metagenedb/common/utils/external_api/togows.py b/backend/metagenedb/common/utils/external_api/togows.py
new file mode 100644
index 0000000..3ea4910
--- /dev/null
+++ b/backend/metagenedb/common/utils/external_api/togows.py
@@ -0,0 +1,32 @@
+import logging
+
+from bioapi.togows import TogoWSEntryAPI
+
+
+logger = logging.getLogger(__name__)
+
+
+class GetFunctionExternalInfo:
+
+ def __init__(self, function_id, source):
+ self.function_id = function_id
+ self.source = source
+
+ def _get_unknown_source(self):
+ logger.warning("No source of information for %s from %s" % (self.function_id, self.source))
+ return {}
+
+ def _get_kegg(self):
+ """
+ Get detailed information from KEGG orthology through Togows.
+ """
+ kegg_api = TogoWSEntryAPI("kegg-orthology")
+ return kegg_api.get(self.function_id)[0]
+
+ def get_details(self):
+ return getattr(self, f"_get_{self.source}", self._get_unknown_source)()
+
+
+
+
+
--
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