From db3f33e9d632672bedf13090d18b6ba7ee5c2871 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Fri, 15 Nov 2019 13:28:12 +0100
Subject: [PATCH] add detailed option for function API
---
.../metagenedb/api/catalog/views/function.py | 17 ++++++++++++++++-
.../api/catalog/views/test_function.py | 0
.../common/utils/external_api/test_togows.py | 0
.../common/utils/external_api/togows.py | 10 +++++++++-
backend/metagenedb/settings/django.py | 3 +++
5 files changed, 28 insertions(+), 2 deletions(-)
create mode 100644 backend/metagenedb/api/catalog/views/test_function.py
create mode 100644 backend/metagenedb/common/utils/external_api/test_togows.py
diff --git a/backend/metagenedb/api/catalog/views/function.py b/backend/metagenedb/api/catalog/views/function.py
index 949909d..45f7ec7 100644
--- a/backend/metagenedb/api/catalog/views/function.py
+++ b/backend/metagenedb/api/catalog/views/function.py
@@ -1,19 +1,34 @@
+
+import logging
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 GetFunctionExternalInfo
from .bulk_viewset import BulkViewSet
+logger = logging.getLogger(__name__)
+
+
class FunctionViewSet(BulkViewSet):
queryset = Function.objects.all()
serializer_class = FunctionSerializer
lookup_field = 'function_id'
filterset_class = FunctionFilter
+ def _get_external_info(self, db_data):
+ detailed_info_retriever = GetFunctionExternalInfo(db_data['function_id'],
+ db_data['source'])
+ detailed_data = detailed_info_retriever.get_details() # @TODO check consistency?
+ return detailed_data
+
def retrieve(self, request, *args, **kwargs):
instance = self.get_object()
serializer = self.get_serializer(instance)
- return Response(serializer.data)
+ returned_data = serializer.data
+ if request.query_params.get('detailed', None):
+ returned_data = self._get_external_info(returned_data)
+ return Response(returned_data)
diff --git a/backend/metagenedb/api/catalog/views/test_function.py b/backend/metagenedb/api/catalog/views/test_function.py
new file mode 100644
index 0000000..e69de29
diff --git a/backend/metagenedb/common/utils/external_api/test_togows.py b/backend/metagenedb/common/utils/external_api/test_togows.py
new file mode 100644
index 0000000..e69de29
diff --git a/backend/metagenedb/common/utils/external_api/togows.py b/backend/metagenedb/common/utils/external_api/togows.py
index d319e0f..28cd6f7 100644
--- a/backend/metagenedb/common/utils/external_api/togows.py
+++ b/backend/metagenedb/common/utils/external_api/togows.py
@@ -1,5 +1,7 @@
import logging
+from django.conf import settings
+
from bioapi.togows import TogoWSEntryAPI
@@ -21,7 +23,13 @@ class GetFunctionExternalInfo:
Get detailed information from KEGG orthology through Togows.
"""
kegg_api = TogoWSEntryAPI("kegg-orthology")
- return kegg_api.get(self.function_id)[0]
+ response = kegg_api.get(self.function_id)[0]
+ response[settings.API_KEY_ADDITIONAL_INFO] = {
+ 'comment': f"Information retrieved from external source: {kegg_api.url}",
+ 'url': f"{kegg_api.url}{self.function_id}"
+ }
+ return response
def get_details(self):
+ logger.info("Retrieving information from KEGG through togows")
return getattr(self, f"_get_{self.source}", self._get_unknown_source)()
diff --git a/backend/metagenedb/settings/django.py b/backend/metagenedb/settings/django.py
index 53496e4..99b3700 100644
--- a/backend/metagenedb/settings/django.py
+++ b/backend/metagenedb/settings/django.py
@@ -146,3 +146,6 @@ STATIC_ROOT = public_root('static')
STATIC_URL = env.str('STATIC_URL', default='/static/')
SECRET_KEY = env.str('SECRET_KEY', default='')
+
+# -- key for API when additional information is added to the payload
+API_KEY_ADDITIONAL_INFO = env.str('API_KEY_ADDITIONAL_INFO', default='metagenedb_additional_info')
--
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