feat: mark queries as started from the UI (#1939) (#1941)

backend/Pipfile

@@ -10,7 +10,7 @@ attrs = "~=24.2"
 beautifulsoup4 = "~=4.9"
 cattrs = "*"
 django = "*"  # whatever django-sodar-core enforces
-django-clone = "~=5.3"
+django-clone = "*"
 django-cryptographic-fields-bihealth = "~=0.6.0"
 django-debug-toolbar = "*"
 django-extensions = "~=3.2"

backend/seqvars/models.py

@@ -24,6 +24,7 @@
 from django.contrib.auth import get_user_model
 from django.db import models, transaction
 from django_pydantic_field.v2.fields import PydanticSchemaField as SchemaField
+import model_clone
 from modelcluster.fields import ParentalKey
 from modelcluster.models import ClusterableModel
 import pydantic
@@ -471,6 +472,9 @@ class Meta:
 class BaseModel(models.Model):
     """Base model with sodar_uuid and creation/update time."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: UUID used in URLs.
     sodar_uuid = models.UUIDField(default=uuid_object.uuid4, unique=True)
     #: DateTime of creation
@@ -881,9 +885,23 @@ def from_predefinedquery(
         return querysettings
 
 
-class SeqvarsQuerySettings(BaseModel):
+class SeqvarsQuerySettings(model_clone.CloneMixin, BaseModel):
     """The query settings for a case."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+    #: Explicitely set the "owned" one-to-one relations to clone.
+    _clone_o2o_fields = [
+        "genotype",
+        "variantprio",
+        "frequency",
+        "consequence",
+        "locus",
+        "phenotypeprio",
+        "quality",
+        "clinvar",
+    ]
+
     #: Custom manager with ``from_predefinedquery()``.
     objects = SeqvarsQuerySettingsManager()
 
@@ -1241,9 +1259,12 @@ def from_presets(
         )
 
 
-class SeqvarsQuerySettingsGenotype(SeqvarsQuerySettingsCategoryBase):
+class SeqvarsQuerySettingsGenotype(model_clone.CloneMixin, SeqvarsQuerySettingsCategoryBase):
     """Query settings for per-sample genotype filtration."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: Custom manager with ``from_presets()``.
     objects = SeqvarsQuerySettingsGenotypeManager()
 
@@ -1332,9 +1353,12 @@ def from_presets(
         )
 
 
-class SeqvarsQuerySettingsQuality(SeqvarsQuerySettingsCategoryBase):
+class SeqvarsQuerySettingsQuality(model_clone.CloneMixin, SeqvarsQuerySettingsCategoryBase):
     """Query settings for per-sample quality filtration."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: Custom manager with ``from_presets()``.
     objects = SeqvarsQuerySettingsQualityManager()
 
@@ -1371,10 +1395,13 @@ def from_presets(
 
 
 class SeqvarsQuerySettingsConsequence(
-    SeqvarsConsequenceSettingsBase, SeqvarsQuerySettingsCategoryBase
+    model_clone.CloneMixin, SeqvarsConsequenceSettingsBase, SeqvarsQuerySettingsCategoryBase
 ):
     """Presets for consequence-related settings within a ``QuerySettingsSet``."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: Custom manager with ``from_presets()``.
     objects = SeqvarsQuerySettingsConsequenceManager()
 
@@ -1404,9 +1431,14 @@ def from_presets(
         )
 
 
-class SeqvarsQuerySettingsLocus(SeqvarsLocusSettingsBase, SeqvarsQuerySettingsCategoryBase):
+class SeqvarsQuerySettingsLocus(
+    model_clone.CloneMixin, SeqvarsLocusSettingsBase, SeqvarsQuerySettingsCategoryBase
+):
     """Presets for locus-related settings within a ``QuerySettingsSet``."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: Custom manager with ``from_presets()``.
     objects = SeqvarsQuerySettingsLocusManager()
 
@@ -1435,9 +1467,14 @@ def from_presets(
         )
 
 
-class SeqvarsQuerySettingsFrequency(SeqvarsFrequencySettingsBase, SeqvarsQuerySettingsCategoryBase):
+class SeqvarsQuerySettingsFrequency(
+    model_clone.CloneMixin, SeqvarsFrequencySettingsBase, SeqvarsQuerySettingsCategoryBase
+):
     """Query settings in the frequency category."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: Custom manager with ``from_presets()``.
     objects = SeqvarsQuerySettingsFrequencyManager()
 
@@ -1468,10 +1505,13 @@ def from_presets(
 
 
 class SeqvarsQuerySettingsPhenotypePrio(
-    SeqvarsPhenotypePrioSettingsBase, SeqvarsQuerySettingsCategoryBase
+    model_clone.CloneMixin, SeqvarsPhenotypePrioSettingsBase, SeqvarsQuerySettingsCategoryBase
 ):
     """Presets for phenotype priorization--related settings within a ``QueryPresetsSetVersion``."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: Custom manager with ``from_presets()``.
     objects = SeqvarsQuerySettingsPhenotypePrioManager()
 
@@ -1500,10 +1540,13 @@ def from_presets(
 
 
 class SeqvarsQuerySettingsVariantPrio(
-    SeqvarsVariantPrioSettingsBase, SeqvarsQuerySettingsCategoryBase
+    model_clone.CloneMixin, SeqvarsVariantPrioSettingsBase, SeqvarsQuerySettingsCategoryBase
 ):
     """Query settings in the variant priorization category."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: Custom manager with ``from_presets()``.
     objects = SeqvarsQuerySettingsVariantPrioManager()
 
@@ -1535,9 +1578,14 @@ def from_presets(
         )
 
 
-class SeqvarsQuerySettingsClinvar(SeqvarsClinvarSettingsBase, SeqvarsQuerySettingsCategoryBase):
+class SeqvarsQuerySettingsClinvar(
+    model_clone.CloneMixin, SeqvarsClinvarSettingsBase, SeqvarsQuerySettingsCategoryBase
+):
     """Query settings in the variant priorization category."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: Custom manager with ``from_presets()``.
     objects = SeqvarsQuerySettingsClinvarManager()
 
@@ -1566,14 +1614,17 @@ def from_predefinedquery(
             return super().create(column_settings=[])
 
 
-class SeqvarsQueryColumnsConfig(SeqvarsColumnsSettingsBase, BaseModel):
+class SeqvarsQueryColumnsConfig(model_clone.CloneMixin, SeqvarsColumnsSettingsBase, BaseModel):
     """Per-query (not execution) configuration of columns.
 
     This will be copied over from the presets to the query and not the query
     settings.  Thus, it will not be persisted by query execution but is
     editable after query execution.
     """
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: Custom manager with ``from_predefinedquery()``.
     objects = SeqvarsQueryColumnsConfigManager()
 
@@ -1619,9 +1670,12 @@ def _pick_query_rank(self, session: CaseAnalysisSession) -> int:
         return rank
 
 
-class SeqvarsQuery(BaseModel):
+class SeqvarsQuery(model_clone.CloneMixin, BaseModel):
     """Allows users to prepare seqvar queries for execution and execute them."""
 
+    #: Let the ``sodar_uuid`` value be re-created when cloning.
+    _clone_excluded_fields = ["sodar_uuid"]
+
     #: Override the manager so we can easily create from predefined queries.
     objects = SeqvarsQueryManager()
 

backend/seqvars/tests/test_models.py

@@ -308,6 +308,35 @@ def test_from_predefinedquery(self):
         self.assertEqual(SeqvarsQuerySettingsQuality.objects.count(), 1)
         self.assertEqual(SeqvarsQuerySettingsClinvar.objects.count(), 1)
 
+    def test_make_clone(self):
+        predefinedquery = SeqvarsPredefinedQueryFactory()
+        session = CaseAnalysisSessionFactory()
+        querysettings = SeqvarsQuerySettings.objects.from_predefinedquery(
+            session=session,
+            predefinedquery=predefinedquery,
+        )
+        self.assertEqual(SeqvarsQuerySettings.objects.count(), 1)
+        self.assertEqual(SeqvarsQuerySettingsGenotype.objects.count(), 1)
+        self.assertEqual(SeqvarsQuerySettingsVariantPrio.objects.count(), 1)
+        self.assertEqual(SeqvarsQuerySettingsFrequency.objects.count(), 1)
+        self.assertEqual(SeqvarsQuerySettingsConsequence.objects.count(), 1)
+        self.assertEqual(SeqvarsQuerySettingsLocus.objects.count(), 1)
+        self.assertEqual(SeqvarsQuerySettingsPhenotypePrio.objects.count(), 1)
+        self.assertEqual(SeqvarsQuerySettingsQuality.objects.count(), 1)
+        self.assertEqual(SeqvarsQuerySettingsClinvar.objects.count(), 1)
+
+        cloned_querysettings = querysettings.make_clone()
+        _ = cloned_querysettings
+        self.assertEqual(SeqvarsQuerySettings.objects.count(), 2)
+        self.assertEqual(SeqvarsQuerySettingsGenotype.objects.count(), 2)
+        self.assertEqual(SeqvarsQuerySettingsVariantPrio.objects.count(), 2)
+        self.assertEqual(SeqvarsQuerySettingsFrequency.objects.count(), 2)
+        self.assertEqual(SeqvarsQuerySettingsConsequence.objects.count(), 2)
+        self.assertEqual(SeqvarsQuerySettingsLocus.objects.count(), 2)
+        self.assertEqual(SeqvarsQuerySettingsPhenotypePrio.objects.count(), 2)
+        self.assertEqual(SeqvarsQuerySettingsQuality.objects.count(), 2)
+        self.assertEqual(SeqvarsQuerySettingsClinvar.objects.count(), 2)
+
 
 class TestSeqvarsQuerySettingsGenotype(TestCaseSnapshot, TestCase):
 

backend/seqvars/tests/test_views_api.py

@@ -13,6 +13,7 @@
 from seqvars.models import (
     SeqvarsPredefinedQuery,
     SeqvarsQuery,
+    SeqvarsQueryExecution,
     SeqvarsQueryPresetsClinvar,
     SeqvarsQueryPresetsColumns,
     SeqvarsQueryPresetsConsequence,
@@ -2136,6 +2137,35 @@ def test_retrieve_nonexisting(self, kwargs_override: dict[str, Any]):
             )
         self.assertEqual(response.status_code, 404)
 
+    def test_start(self):
+        self.assertEqual(SeqvarsQueryExecution.objects.count(), 1)
+        self.assertEqual(SeqvarsQuery.objects.count(), 1)
+
+        with self.login(self.superuser):
+            response = self.client.post(
+                reverse(
+                    "seqvars:api-queryexecution-start",
+                    kwargs={
+                        "query": self.query.sodar_uuid,
+                    },
+                ),
+            )
+        self.assertEqual(response.status_code, 200)
+
+        self.assertEqual(SeqvarsQuery.objects.count(), 1)
+        self.assertEqual(SeqvarsQueryExecution.objects.count(), 2)
+        self.assertEqual(
+            self.query.seqvarsqueryexecution_set.count(),
+            2,
+        )
+        new_seqvarqueryexecution = SeqvarsQueryExecution.objects.exclude(
+            pk=self.queryexecution.pk
+        ).first()
+        self.assertEqual(
+            new_seqvarqueryexecution.state,
+            SeqvarsQueryExecution.STATE_QUEUED,
+        )
+
 
 @freeze_time("2012-01-14 12:00:01")
 class TestResultSetViewSet(ApiViewTestBase):

backend/seqvars/views_api.py

@@ -9,7 +9,7 @@
 from modelcluster.queryset import FakeQuerySet
 from projectroles.models import Project
 from projectroles.views_api import SODARAPIProjectPermission
-from rest_framework import viewsets
+from rest_framework import serializers, viewsets
 from rest_framework.decorators import action
 from rest_framework.pagination import CursorPagination
 from rest_framework.response import Response
@@ -447,13 +447,11 @@ def get_serializer_context(self):
 class SeqvarsQueryViewSet(BaseViewSet):
     """Allow CRUD of the user's queries."""
 
-    # TODO XXX XXX ADD LAUNCH ACTION XXX XXX TODO
-
     #: Define lookup URL kwarg.
     lookup_url_kwarg = "query"
     #: The default serializer class to use.
     serializer_class = SeqvarsQuerySerializer
-    #: Override ``create`` and ``*-detail`` serializer to render all presets.
+    #: Override non-list serializers to serialize all preses.
     action_serializers = {
         "create": SeqvarsQueryDetailsSerializer,
         "retrieve": SeqvarsQueryDetailsSerializer,
@@ -463,10 +461,6 @@ class SeqvarsQueryViewSet(BaseViewSet):
         "create_from": SeqvarsQueryDetailsSerializer,
     }
 
-    # def partial_update(self, *args, **kwargs):
-    #     import pdb; pdb.set_trace()
-    #     return super().partial_update(*args, **kwargs)
-
     @extend_schema(request=SeqvarsQueryCreateFromSerializer)
     @action(methods=["post"], detail=False)
     @transaction.atomic()
@@ -536,8 +530,26 @@ class SeqvarsQueryExecutionViewSet(BaseReadOnlyViewSet):
     #: Override ``retrieve`` serializer to render all presets.
     action_serializers = {
         "retrieve": SeqvarsQueryExecutionDetailsSerializer,
+        "start": SeqvarsQueryExecutionDetailsSerializer,
     }
 
+    @extend_schema(request=serializers.Serializer)
+    @action(methods=["post"], detail=False)
+    @transaction.atomic()
+    def start(self, *args, **kwargs):
+        """Create a new query execution for the given query."""
+        query = None
+        # TODO: check permissions on the source's project
+        query = SeqvarsQuery.objects.get(sodar_uuid=self.kwargs["query"])
+
+        instance = SeqvarsQueryExecution.objects.create(
+            state=SeqvarsQueryExecution.STATE_QUEUED,
+            query=query,
+            querysettings=query.settings.make_clone(),
+        )
+        serializer = self.get_serializer(instance)
+        return Response(serializer.data)
+
     def get_queryset(self):
         """Return queryset with all ``QueryExecution`` records for the given query."""
         result = SeqvarsQueryExecution.objects.all()

backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml

@@ -2764,6 +2764,30 @@ paths:
               schema:
                 $ref: '#/components/schemas/SeqvarsQueryExecutionDetails'
           description: ''
+  /seqvars/api/queryexecution/{query}/start/:
+    post:
+      operationId: seqvars_api_queryexecution_start_create
+      description: Create a new query execution for the given query.
+      parameters:
+      - in: path
+        name: query
+        schema:
+          type: string
+          pattern: ^[0-9a-f-]+$
+        required: true
+      tags:
+      - seqvars
+      security:
+      - basicAuth: []
+      - cookieAuth: []
+      - knoxApiToken: []
+      responses:
+        '200':
+          content:
+            application/vnd.bihealth.varfish+json:
+              schema:
+                $ref: '#/components/schemas/SeqvarsQueryExecutionDetails'
+          description: ''
   /seqvars/api/querypresetsclinvar/{querypresetssetversion}/:
     get:
       operationId: seqvars_api_querypresetsclinvar_list

frontend/ext/varfish-api/src/lib/types.gen.ts

@@ -4160,6 +4160,16 @@ export type SeqvarsApiQueryexecutionRetrieveResponse = (SeqvarsQueryExecutionDet
 
 export type SeqvarsApiQueryexecutionRetrieveError = unknown;
 
+export type SeqvarsApiQueryexecutionStartCreateData = {
+    path: {
+        query: string;
+    };
+};
+
+export type SeqvarsApiQueryexecutionStartCreateResponse = (SeqvarsQueryExecutionDetails);
+
+export type SeqvarsApiQueryexecutionStartCreateError = unknown;
+
 export type SeqvarsApiQuerypresetsclinvarListData = {
     path: {
         querypresetssetversion: string;