feat: initial set of seqvar stores based on code generated from OpenA…

…PI (#1765) (#1769)

backend/Makefile

@@ -125,4 +125,7 @@ celery:
 
 .PHONY: gen-api-schema
 gen-api-schema:
-	pipenv run $(MANAGE) generateschema | grep -v ^Loading | grep -v '^The ' > ./varfish/tests/drf_openapi_schema/varfish_api_schema.yaml
+	pipenv run $(MANAGE) spectacular \
+	| grep -v ^Loading \
+	| grep -v '^The ' \
+	> ./varfish/tests/drf_openapi_schema/varfish_api_schema.yaml

backend/Pipfile

@@ -59,6 +59,7 @@ rich = "*"
 drf-writable-nested = "*"
 django-modelcluster = "*"
 faker = "*"
+drf-spectacular = {extras = ["sidecar"], version = "*"}
 
 [dev-packages]
 # packages for testing

backend/cases_analysis/views_api.py

@@ -1,7 +1,6 @@
 import sys
 
 from django.db import transaction
-from django_pydantic_field.rest_framework import AutoSchema
 from projectroles.views_api import SODARAPIProjectPermission
 from rest_framework import viewsets
 from rest_framework.generics import get_object_or_404
@@ -41,8 +40,6 @@ class CaseAnalysisViewSet(viewsets.ReadOnlyModelViewSet):
     lookup_field = "sodar_uuid"
     lookup_url_kwarg = "caseanalysis"
 
-    schema = AutoSchema()  # OpenAPI schema generation for pydantic fields
-
     pagination_class = StandardPagination
 
     permission_classes = [CaseProjectPermission]
@@ -57,6 +54,8 @@ def get_queryset(self):
         Currently, this will be at most one.
         """
         result = CaseAnalysis.objects.all()
+        if sys.argv[:2] == ["manage.py", "spectacular"]:
+            return result  # short circuit in schema generation
         result = result.filter(case__sodar_uuid=self.kwargs["case"])
         return result
 
@@ -79,8 +78,6 @@ class CaseAnalysisSessionViewSet(viewsets.ReadOnlyModelViewSet):
     lookup_field = "sodar_uuid"
     lookup_url_kwarg = "caseanalysissession"
 
-    schema = AutoSchema()  # OpenAPI schema generation for pydantic fields
-
     pagination_class = StandardPagination
 
     permission_classes = [CaseProjectPermission]
@@ -96,6 +93,8 @@ def get_queryset(self):
         Currently, this will be at most one.
         """
         result = CaseAnalysisSession.objects.all()
+        if sys.argv[:2] == ["manage.py", "spectacular"]:
+            return result  # short circuit in schema generation
         result = result.filter(
             caseanalysis__case__sodar_uuid=self.kwargs["case"],
             user=self.request.user,

backend/config/settings/base.py

@@ -91,6 +91,7 @@
     "rest_framework_httpsignature",
     "django_saml2_auth",
     "dj_iconify.apps.DjIconifyConfig",
+    "drf_spectacular",
 ]
 
 # Apps specific for this project go here.
@@ -664,6 +665,7 @@
         "rest_framework.authentication.SessionAuthentication",
         "knox.auth.TokenAuthentication",
     ),
+    "DEFAULT_SCHEMA_CLASS": "drf_spectacular.openapi.AutoSchema",
 }
 
 SPECTACULAR_SETTINGS = {
@@ -674,14 +676,16 @@
     "SERVE_INCLUDE_SCHEMA": False,
     # Skip schema generation for some paths.
     "PREPROCESSING_HOOKS": [
-        "varfish.utils.spectacular_preprocess_hook",
+        "varfish.spectacular_utils.spectacular_preprocess_hook",
     ],
     # We add some explicit choices naming to work around warning.
     "ENUM_NAME_OVERRIDES": {
         "VariantRatingEnum": "variants.models.userannos.VARIANT_RATING_CHOICES",
         "GenomeBuildVerbatimEnum": "importer.models.GENOME_BUILD_CHOICES_VERBATIM",
         "GenomeBuildLowerEnum": "cases_files.models.GENOMEBUILD_CHOICES_LOWER",
         "CaseStatusEnum": "variants.models.case.CASE_STATUS_CHOICES",
+        "SeqvarsQueryExecutionStateEnum": "seqvars.models.SeqvarsQueryExecution.STATE_CHOICES",
+        "SeqvarsQueryPresetsSetVersionStatusEnum": "seqvars.models.SeqvarsQueryPresetsSetVersion.STATUS_CHOICES",
     },
     # Sidecar Settings
     "SWAGGER_UI_DIST": "SIDECAR",
@@ -748,6 +752,9 @@ def set_logging(level):
 LOGGING_DEBUG = env.bool("LOGGING_DEBUG", False)
 LOGGING = set_logging("DEBUG" if (DEBUG or LOGGING_DEBUG) else "INFO")
 
+# Propagate exceptions to log.
+DEBUG_PROPAGATE_EXCEPTIONS = DEV
+
 # LDAP configuration
 # ------------------------------------------------------------------------------
 

backend/config/urls.py

@@ -10,6 +10,7 @@
 from django.views.generic import TemplateView
 import django_saml2_auth.views
 from djproxy.views import HttpProxy
+from drf_spectacular.views import SpectacularAPIView, SpectacularRedocView, SpectacularSwaggerView
 from projectroles.views import HomeView as ProjectRolesHomeView
 from sentry_sdk import last_event_id
 
@@ -96,6 +97,21 @@ def handler500(request, *args, **argv):
         url(r"^seqvars/", include("seqvars.urls")),
     ]
 
+# URL Patterns for DRF Spectacular
+# ------------------------------------------------------------------------------
+
+urlpatterns += [
+    # Schema
+    path("api/schema/", SpectacularAPIView.as_view(), name="schema"),
+    # UI
+    path(
+        "api/schema/swagger-ui/",
+        SpectacularSwaggerView.as_view(url_name="schema"),
+        name="swagger-ui",
+    ),
+    path("api/schema/redoc/", SpectacularRedocView.as_view(url_name="schema"), name="redoc"),
+]
+
 
 # URL Patterns for Proxies
 # ------------------------------------------------------------------------------

backend/genepanels/serializers.py

@@ -1,3 +1,4 @@
+from drf_spectacular.utils import extend_schema_field
 from rest_framework import serializers
 
 from genepanels.models import GenePanel, GenePanelCategory
@@ -44,6 +45,7 @@ class Meta:
             "genepanel_set",
         )
 
+    @extend_schema_field(GenePanelSerializer)
     def get_genepanel_set(self, obj):
         """Corresponds to the ``genepanel_set`` field defined above."""
         return GenePanelSerializer(obj.genepanel_set.filter(state="active"), many=True).data

backend/seqvars/admin.py

@@ -1,17 +1,17 @@
 from django.contrib import admin
 
 from seqvars.models import (
-    Query,
-    QueryExecution,
-    QueryPresetsFrequency,
-    QueryPresetsSet,
-    ResultRow,
-    ResultSet,
+    SeqvarsQuery,
+    SeqvarsQueryExecution,
+    SeqvarsQueryPresetsFrequency,
+    SeqvarsQueryPresetsSet,
+    SeqvarsResultRow,
+    SeqvarsResultSet,
 )
 
-admin.site.register(QueryPresetsSet)
-admin.site.register(QueryPresetsFrequency)
-admin.site.register(Query)
-admin.site.register(QueryExecution)
-admin.site.register(ResultSet)
-admin.site.register(ResultRow)
+admin.site.register(SeqvarsQueryPresetsSet)
+admin.site.register(SeqvarsQueryPresetsFrequency)
+admin.site.register(SeqvarsQuery)
+admin.site.register(SeqvarsQueryExecution)
+admin.site.register(SeqvarsResultSet)
+admin.site.register(SeqvarsResultRow)