Auto schema generation

backend/launch_api.sh

@@ -18,6 +18,10 @@ DJANGO_SUPERUSER_PASSWORD="${DJANGO_ADMIN_PASSWORD}" \
 echo "* Collecting static files"
 ./manage.py collectstatic --noinput
 
+# generate OpenAPI schema
+echo "* Generating OpenAPI schema"
+./manage.py spectacular --file /data/schema.yaml
+
 # launch the server
 if [ "$DJANGO_DEBUG" = "1" ] ; then
     echo "* Serving via django runserver (debug mode)"

backend/src/api/apps.py

@@ -4,3 +4,6 @@
 class ApiConfig(AppConfig):
     default_auto_field = "django.db.models.BigAutoField"
     name = "api"
+
+    def ready(self):
+        import api.schema  # noqa

backend/src/api/models.py

@@ -480,6 +480,8 @@ class SearchTerm(models.Model):
     )
     confidence = models.FloatField()
     related_words = models.TextField(null=True, blank=True)
+    log2_prob_prior = models.FloatField(null=True, blank=True)
+    prob = models.FloatField(null=True, blank=True)
 
     class Meta:
         indexes = [

backend/src/api/schema.py

@@ -0,0 +1,19 @@
+"""
+Contains OpenAPI schema definitions in cases where they can't be
+simply inferred from the models/serializers/views.
+"""
+
+from drf_spectacular.extensions import OpenApiAuthenticationExtension
+from api.utils.auth import CsrfExemptSessionAuthentication
+
+
+class CsrfExemptSessionAuthenticationScheme(OpenApiAuthenticationExtension):
+    target_class = CsrfExemptSessionAuthentication
+    name = "csrfExemptCookieAuth"
+
+    def get_security_definition(self, auto_schema):
+        return {
+            "type": "apiKey",
+            "in": "cookie",
+            "name": "sessionid",
+        }

backend/src/api/serializers.py

@@ -39,7 +39,9 @@ class SearchTermSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = SearchTerm
-        fields = ["id", "term", "series_id", "prob", "log2_prob_prior", "related_words"]
+        fields = [
+            "id", "term", "series_id", "prob", "log2_prob_prior", "related_words"
+        ]
 
 
 # ===========================================================================
@@ -133,13 +135,13 @@ class GEOSeriesSerializer(serializers.ModelSerializer):
 
     sample_count = serializers.SerializerMethodField(read_only=True)
 
-    def get_sample_count(self, obj):
+    def get_sample_count(self, obj) -> int:
         """Get the number of samples associated with this series."""
         return obj.samples_ct if obj.samples_ct is not None else 0
 
     confidence = serializers.SerializerMethodField()
 
-    def get_confidence(self, obj):
+    def get_confidence(self, obj) -> dict:
         """Compute confidence level based on prob."""
         if obj.prob is None:
             label = "unknown"
@@ -164,22 +166,22 @@ def get_confidence(self, obj):
 
     platform = serializers.SerializerMethodField()
 
-    def get_platform(self, obj):
-        """Get the platform name associated with this series."""
+    def get_platform(self, obj) -> list[str]:
+        """Get the platform names associated with this series."""
         gse_obj = GEOSeriesToGEOPlatforms.objects.filter(gse=obj.gse).first()
-        return str(gse_obj.platforms) if gse_obj else ""
+        return gse_obj.platforms if gse_obj else []
 
     keywords = serializers.SerializerMethodField()
 
-    def get_keywords(self, obj):
+    def get_keywords(self, obj) -> list[str]:
         """Extract keywords from the series summary."""
         if obj.keywords:
             return [kw.strip() for kw in obj.keywords.split(",")]
         return []
 
     classification = serializers.SerializerMethodField()
 
-    def get_classification(self, obj):
+    def get_classification(self, obj) -> str:
         """Returns values Positive or Negative; supposed to represent 'Classification of study in model training'?"""
         # FIXME: figure out how to actually determine this
         return "Positive"

backend/src/api/views.py

@@ -26,6 +26,10 @@
 from rest_framework.permissions import AllowAny
 from rest_framework.response import Response
 
+from drf_spectacular.utils import extend_schema, OpenApiParameter
+from drf_spectacular.types import OpenApiTypes
+
+
 from .models import (
     Cart,
     CartItem,
@@ -468,7 +472,26 @@ class SearchTermViewSet(viewsets.ReadOnlyModelViewSet):
 # === Ontology search terms from meta-hq
 # ===========================================================================
 
-
+@extend_schema(
+    parameters=[
+        OpenApiParameter(
+            name="query",
+            type=OpenApiTypes.STR,
+            location=OpenApiParameter.QUERY,
+            required=True,
+            description="Search query string",
+        ),
+        OpenApiParameter(
+            name="max_results",
+            type=OpenApiTypes.INT,
+            location=OpenApiParameter.QUERY,
+            required=False,
+            description="Maximum number of results to return",
+            default=50,
+        ),
+    ],
+    responses={200: OntologySearchResultsSerializer(many=True)},
+)
 @api_view(["GET"])
 @permission_classes([AllowAny])
 def ontology_search(request):

backend/src/meta2onto/settings.py

@@ -198,4 +198,5 @@ def is_truthy(value):
         "rest_framework.filters.SearchFilter",
         "rest_framework.filters.OrderingFilter",
     ],
+    "DEFAULT_SCHEMA_CLASS": "drf_spectacular.openapi.AutoSchema",
 }