From a2daa682c712ac57e5977b4396842bdec8ba15d0 Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <hillion.kenzo@posteo.net>
Date: Fri, 16 Apr 2021 11:23:16 +0200
Subject: [PATCH] detailed source from doi.org
---
.../api/catalog/qparams_validators/source.py | 7 ++++
.../metagenedb/api/catalog/views/source.py | 33 +++++++++++++++++--
.../common/utils/external_api/doi_api.py | 27 +++++++++++++++
frontend/src/views/genedetail/genedetail.html | 2 +-
4 files changed, 66 insertions(+), 3 deletions(-)
create mode 100644 backend/metagenedb/api/catalog/qparams_validators/source.py
create mode 100644 backend/metagenedb/common/utils/external_api/doi_api.py
diff --git a/backend/metagenedb/api/catalog/qparams_validators/source.py b/backend/metagenedb/api/catalog/qparams_validators/source.py
new file mode 100644
index 0000000..7bdd0a2
--- /dev/null
+++ b/backend/metagenedb/api/catalog/qparams_validators/source.py
@@ -0,0 +1,7 @@
+from marshmallow import fields
+
+from metagenedb.common.django_default.qparams_validators import PaginatedQueryParams
+
+
+class SourceQueryParams(PaginatedQueryParams):
+ detailed = fields.Boolean()
diff --git a/backend/metagenedb/api/catalog/views/source.py b/backend/metagenedb/api/catalog/views/source.py
index fe888f8..6781dbb 100644
--- a/backend/metagenedb/api/catalog/views/source.py
+++ b/backend/metagenedb/api/catalog/views/source.py
@@ -1,7 +1,12 @@
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
@swagger_auto_schema(
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'])
+ try:
+ 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" %
+ not_implemented_error)
+ detailed_data = db_data
+ return detailed_data
+
@swagger_auto_schema(
operation_description="Retrieve gene source from a name",
operation_summary="API to retrieve gene source.",
tags=['Source'],
)
- def retrieve(self, *args, **kwargs):
- return super().retrieve(*args, **kwargs)
+ def retrieve(self, request, *args, **kwargs):
+ try:
+ query_params = self.query_params_parser().load(request.query_params)
+ except ValidationError as validation_error:
+ error_message = validation_error.normalized_messages()
+ error_message.update({
+ '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 = serializer.data
+ if query_params.get('detailed', False) is True:
+ returned_data = self._get_external_info(returned_data)
+ return Response(returned_data)
@swagger_auto_schema(
tags=['Source'],
diff --git a/backend/metagenedb/common/utils/external_api/doi_api.py b/backend/metagenedb/common/utils/external_api/doi_api.py
new file mode 100644
index 0000000..98de500
--- /dev/null
+++ b/backend/metagenedb/common/utils/external_api/doi_api.py
@@ -0,0 +1,27 @@
+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.
+ """
+ logger.info("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
diff --git a/frontend/src/views/genedetail/genedetail.html b/frontend/src/views/genedetail/genedetail.html
index e2b9a97..a37e07c 100644
--- a/frontend/src/views/genedetail/genedetail.html
+++ b/frontend/src/views/genedetail/genedetail.html
@@ -69,7 +69,7 @@
<v-toolbar class="tertiary white--text" dense>
<v-icon class="white--text">format_list_bulleted</v-icon>
<v-toolbar-title>
- Gene source
+ Gene catalog
</v-toolbar-title>
</v-toolbar>
<!-- Simple information -->
--
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