Commit a2daa682 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

detailed source from

parent 1c7e6231
from marshmallow import fields
from metagenedb.common.django_default.qparams_validators import PaginatedQueryParams
class SourceQueryParams(PaginatedQueryParams):
detailed = fields.Boolean()
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
from metagenedb.apps.catalog.models import Source
from metagenedb.apps.catalog.serializers import SourceSerializer
from metagenedb.api.catalog.qparams_validators.source import SourceQueryParams
from metagenedb.common.utils.external_api.doi_api import GetDOIExternalInfo
from .base import BulkViewSet
......@@ -10,6 +15,7 @@ class SourceViewSet(BulkViewSet):
queryset = Source.objects.all()
serializer_class = SourceSerializer
lookup_field = 'slug'
query_params_parser = SourceQueryParams
operation_description="List all gene sources",
......@@ -19,13 +25,36 @@ class SourceViewSet(BulkViewSet):
def list(self, *args, **kwargs):
return super().list(*args, **kwargs)
def _get_external_info(self, db_data):
detailed_info_retriever = GetDOIExternalInfo(db_data['doi'])
detailed_data = detailed_info_retriever.get_details()
except NotImplementedError as not_implemented_error:
logger.warning("Could not found API for the source, returning item from the DB. Error: %s" %
detailed_data = db_data
return detailed_data
operation_description="Retrieve gene source from a name",
operation_summary="API to retrieve gene source.",
def retrieve(self, *args, **kwargs):
return super().retrieve(*args, **kwargs)
def retrieve(self, request, *args, **kwargs):
query_params = self.query_params_parser().load(request.query_params)
except ValidationError as validation_error:
error_message = validation_error.normalized_messages()
'allowed_query_params': ', '.join(self.query_params_parser().declared_fields.keys())
return Response(error_message, status=HTTP_422_UNPROCESSABLE_ENTITY)
instance = self.get_object()
serializer = self.get_serializer(instance)
returned_data =
if query_params.get('detailed', False) is True:
returned_data = self._get_external_info(returned_data)
return Response(returned_data)
import logging
from django.conf import settings
from dabeplech import DOIAPI
logger = logging.getLogger(__name__)
class GetDOIExternalInfo:
def __init__(self, doi: str):
self.doi = doi
def get_details(self):
Get detailed information from DOI.
""""Retrieving information from DOI")
api = DOIAPI()
response = api.get(self.doi)
response[settings.API_KEY_ADDITIONAL_INFO] = {
'comment': f"Information retrieved from external source: {api.url}",
'url': f"{api.last_url_requested}"
return response
......@@ -69,7 +69,7 @@
<v-toolbar class="tertiary white--text" dense>
<v-icon class="white--text">format_list_bulleted</v-icon>
Gene source
Gene catalog
<!-- Simple information -->
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