From f482559fbc2ec1c8311f85f0ca58566d5a70cd8f Mon Sep 17 00:00:00 2001
From: Kenzo-Hugo Hillion <kenzo-hugo.hillion1@pasteur.fr>
Date: Thu, 12 Dec 2019 12:41:20 +0100
Subject: [PATCH] allow filtering on version through eggnog API
---
.../api/catalog/filters/__init__.py | 2 +-
.../api/catalog/filters/function.py | 9 ++-
.../catalog/qparams_validators/function.py | 13 ++++
.../views/{bulk_viewset.py => base.py} | 75 ++++++++++---------
.../metagenedb/api/catalog/views/function.py | 17 +++--
backend/metagenedb/api/catalog/views/gene.py | 2 +-
.../metagenedb/api/catalog/views/taxonomy.py | 2 +-
.../{test_bulk_viewset.py => test_base.py} | 0
8 files changed, 74 insertions(+), 46 deletions(-)
rename backend/metagenedb/api/catalog/views/{bulk_viewset.py => base.py} (98%)
rename backend/metagenedb/api/catalog/views/{test_bulk_viewset.py => test_base.py} (100%)
diff --git a/backend/metagenedb/api/catalog/filters/__init__.py b/backend/metagenedb/api/catalog/filters/__init__.py
index 7ad133f..b00f602 100644
--- a/backend/metagenedb/api/catalog/filters/__init__.py
+++ b/backend/metagenedb/api/catalog/filters/__init__.py
@@ -1,3 +1,3 @@
-from .function import FunctionFilter # noqa
+from .function import EggNOGFilter, FunctionFilter # noqa
from .gene import GeneFilter # noqa
from .taxonomy import TaxonomyFilter # noqa
diff --git a/backend/metagenedb/api/catalog/filters/function.py b/backend/metagenedb/api/catalog/filters/function.py
index 963f19d..735fdc2 100644
--- a/backend/metagenedb/api/catalog/filters/function.py
+++ b/backend/metagenedb/api/catalog/filters/function.py
@@ -1,5 +1,5 @@
from django_filters import rest_framework as filters
-from metagenedb.apps.catalog.models import Function
+from metagenedb.apps.catalog.models import Function, EggNOG
class FunctionFilter(filters.FilterSet):
@@ -7,3 +7,10 @@ class FunctionFilter(filters.FilterSet):
class Meta:
model = Function
fields = ['source']
+
+
+class EggNOGFilter(filters.FilterSet):
+
+ class Meta:
+ model = EggNOG
+ fields = ['version']
diff --git a/backend/metagenedb/api/catalog/qparams_validators/function.py b/backend/metagenedb/api/catalog/qparams_validators/function.py
index b95b016..80a17dc 100644
--- a/backend/metagenedb/api/catalog/qparams_validators/function.py
+++ b/backend/metagenedb/api/catalog/qparams_validators/function.py
@@ -1,7 +1,20 @@
from marshmallow import fields
+from marshmallow.validate import OneOf
+from metagenedb.apps.catalog import models
from metagenedb.common.django_default.qparams_validators import PaginatedQueryParams
+SELECTED_SOURCE = [i[0] for i in models.Function.SOURCE_CHOICES]
+EGGNOG_VERSIONS = [i[0] for i in models.EggNOG.VERSION_CHOICES]
+
class FunctionQueryParams(PaginatedQueryParams):
+ source = fields.String(validate=OneOf(choices=SELECTED_SOURCE))
+
+
+class KeggQueryParams(PaginatedQueryParams):
detailed = fields.Boolean()
+
+
+class EggNOGQueryParams(PaginatedQueryParams):
+ version = fields.String(validate=OneOf(choices=EGGNOG_VERSIONS))
diff --git a/backend/metagenedb/api/catalog/views/bulk_viewset.py b/backend/metagenedb/api/catalog/views/base.py
similarity index 98%
rename from backend/metagenedb/api/catalog/views/bulk_viewset.py
rename to backend/metagenedb/api/catalog/views/base.py
index ce82fa9..62e2f0e 100644
--- a/backend/metagenedb/api/catalog/views/bulk_viewset.py
+++ b/backend/metagenedb/api/catalog/views/base.py
@@ -7,16 +7,51 @@ from metagenedb.common.django_default.permissions import ListAndRetrieveAll
from metagenedb.common.django_default.qparams_validators import PaginatedQueryParams
-class BulkViewSet(ModelViewSet):
+class QParamsValidationViewSet(ModelViewSet):
query_params_parser = PaginatedQueryParams
+
+ def _get_qparams(self, raw_query_params):
+ return self.query_params_parser().load(raw_query_params)
+
+ def list(self, request, *args, **kwargs):
+ try:
+ query_params = self._get_qparams(request.query_params) # noqa
+ 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=status.HTTP_422_UNPROCESSABLE_ENTITY)
+ queryset = self.filter_queryset(self.get_queryset())
+
+ page = self.paginate_queryset(queryset)
+ if page is not None:
+ serializer = self.get_serializer(page, many=True)
+ return self.get_paginated_response(serializer.data)
+
+ serializer = self.get_serializer(queryset, many=True)
+ return Response(serializer.data)
+
+ def retrieve(self, request, *args, **kwargs):
+ try:
+ query_params = self._get_qparams(request.query_params) # noqa
+ 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=status.HTTP_422_UNPROCESSABLE_ENTITY)
+ instance = self.get_object()
+ serializer = self.get_serializer(instance)
+ return Response(serializer.data)
+
+
+class BulkViewSet(QParamsValidationViewSet):
permission_classes = [ListAndRetrieveAll]
def get_objects(self, instance_ids):
return self.queryset.in_bulk(instance_ids, field_name=self.lookup_field)
- def _get_qparams(self, raw_query_params):
- return self.query_params_parser().load(raw_query_params)
-
def _created_payload(self, serializer, request):
if isinstance(request.data, list):
return {
@@ -83,35 +118,3 @@ class BulkViewSet(ModelViewSet):
self._updated_payload(create_serializer, update_serializer, request),
status=status.HTTP_201_CREATED, headers=headers
)
-
- def list(self, request, *args, **kwargs):
- try:
- query_params = self._get_qparams(request.query_params) # noqa
- 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=status.HTTP_422_UNPROCESSABLE_ENTITY)
- queryset = self.filter_queryset(self.get_queryset())
-
- page = self.paginate_queryset(queryset)
- if page is not None:
- serializer = self.get_serializer(page, many=True)
- return self.get_paginated_response(serializer.data)
-
- serializer = self.get_serializer(queryset, many=True)
- return Response(serializer.data)
-
- def retrieve(self, request, *args, **kwargs):
- try:
- query_params = self._get_qparams(request.query_params) # noqa
- 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=status.HTTP_422_UNPROCESSABLE_ENTITY)
- instance = self.get_object()
- serializer = self.get_serializer(instance)
- return Response(serializer.data)
diff --git a/backend/metagenedb/api/catalog/views/function.py b/backend/metagenedb/api/catalog/views/function.py
index 3dcb685..3a968b1 100644
--- a/backend/metagenedb/api/catalog/views/function.py
+++ b/backend/metagenedb/api/catalog/views/function.py
@@ -5,13 +5,15 @@ from rest_framework.response import Response
from rest_framework.status import HTTP_422_UNPROCESSABLE_ENTITY
from rest_framework.viewsets import ModelViewSet
-from metagenedb.api.catalog.filters import FunctionFilter
-from metagenedb.api.catalog.qparams_validators.function import FunctionQueryParams
+from metagenedb.api.catalog.filters import FunctionFilter, EggNOGFilter
+from metagenedb.api.catalog.qparams_validators.function import (
+ EggNOGQueryParams, FunctionQueryParams, KeggQueryParams
+)
from metagenedb.apps.catalog.models import EggNOG, Function, KeggOrthology
from metagenedb.apps.catalog.serializers import EggNOGSerializer, FunctionSerializer, KeggOrthologySerializer
from metagenedb.common.utils.external_api.togows import GetFunctionExternalInfo
-from .bulk_viewset import BulkViewSet
+from .base import BulkViewSet, QParamsValidationViewSet
logger = logging.getLogger(__name__)
@@ -22,13 +24,14 @@ class FunctionViewSet(BulkViewSet):
serializer_class = FunctionSerializer
lookup_field = 'function_id'
filterset_class = FunctionFilter
+ query_params_parser = FunctionQueryParams
-class KeggOrthologyViewSet(ModelViewSet):
+class KeggOrthologyViewSet(QParamsValidationViewSet):
queryset = KeggOrthology.objects.all()
serializer_class = KeggOrthologySerializer
lookup_field = 'function_id'
- query_params_parser = FunctionQueryParams
+ query_params_parser = KeggQueryParams
def _get_external_info(self, db_data):
detailed_info_retriever = GetFunctionExternalInfo(db_data['function_id'], 'kegg')
@@ -57,7 +60,9 @@ class KeggOrthologyViewSet(ModelViewSet):
return Response(returned_data)
-class EggNOGViewSet(ModelViewSet):
+class EggNOGViewSet(QParamsValidationViewSet):
queryset = EggNOG.objects.all()
serializer_class = EggNOGSerializer
lookup_field = 'function_id'
+ filterset_class = EggNOGFilter
+ query_params_parser = EggNOGQueryParams
diff --git a/backend/metagenedb/api/catalog/views/gene.py b/backend/metagenedb/api/catalog/views/gene.py
index 8a2aadf..6189e74 100644
--- a/backend/metagenedb/api/catalog/views/gene.py
+++ b/backend/metagenedb/api/catalog/views/gene.py
@@ -14,7 +14,7 @@ from metagenedb.api.catalog.filters import GeneFilter
from metagenedb.api.catalog.qparams_validators.gene import GeneLengthQueryParams, GeneQueryParams, TaxCountQueryParams
from metagenedb.apps.catalog.serializers import GeneSerializer
-from .bulk_viewset import BulkViewSet
+from .base import BulkViewSet
class DocGeneLength(object):
diff --git a/backend/metagenedb/api/catalog/views/taxonomy.py b/backend/metagenedb/api/catalog/views/taxonomy.py
index e6dc49c..c32363a 100644
--- a/backend/metagenedb/api/catalog/views/taxonomy.py
+++ b/backend/metagenedb/api/catalog/views/taxonomy.py
@@ -7,7 +7,7 @@ from metagenedb.api.catalog.qparams_validators.taxonomy import TaxonomyQueryPara
from metagenedb.apps.catalog.models import Taxonomy
from metagenedb.apps.catalog.serializers import TaxonomySerializer
-from .bulk_viewset import BulkViewSet
+from .base import BulkViewSet
class TaxonomyViewSet(BulkViewSet):
diff --git a/backend/metagenedb/api/catalog/views/test_bulk_viewset.py b/backend/metagenedb/api/catalog/views/test_base.py
similarity index 100%
rename from backend/metagenedb/api/catalog/views/test_bulk_viewset.py
rename to backend/metagenedb/api/catalog/views/test_base.py
--
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