refactor: move column settings to querysettings (#2042) (#2050)

backend/seqvars/factory_defaults.py

@@ -1195,9 +1195,7 @@ def create_seqvarsquerypresetscolumns(faker: Faker) -> list[SeqvarsQueryPresetsC
     # default column names
     COLUMNS_DEFAULT = (
         "index",
-        "__chrom_pos__",
         "payload.variant_annotation.gene.identity.gene_symbol",
-        "payload.variant_annotation.gene.consequences.hgvs_p",
         "__gene_flags__",
         "__effect__",
         "payload.variant_annotation.gene.consequences.consequences",
@@ -1219,9 +1217,7 @@ def create_seqvarsquerypresetscolumns(faker: Faker) -> list[SeqvarsQueryPresetsC
     # clinvar filter column names
     COLUMNS_CLINVAR = (
         "index",
-        "__chrom_pos__",
         "payload.variant_annotation.gene.identity.gene_symbol",
-        "payload.variant_annotation.gene.consequences.hgvs_p",
         "__gene_flags__",
         "__effect__",
         "payload.variant_annotation.gene.consequences.consequences",

backend/seqvars/migrations/0012_auto_20241024_0823.py

@@ -0,0 +1,66 @@
+# Generated by Django 3.2.25 on 2024-10-24 08:23
+
+import uuid
+
+import django.core.serializers.json
+from django.db import migrations, models
+import django.db.models.deletion
+import django_pydantic_field.compat.django
+import django_pydantic_field.fields
+import model_clone.mixin
+
+import seqvars.models.base
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("seqvars", "0011_alter_seqvarsqueryexecution_options"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="SeqvarsQuerySettingsColumns",
+            fields=[
+                (
+                    "id",
+                    models.AutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("sodar_uuid", models.UUIDField(default=uuid.uuid4, unique=True)),
+                ("date_created", models.DateTimeField(auto_now_add=True)),
+                ("date_modified", models.DateTimeField(auto_now=True)),
+                (
+                    "column_settings",
+                    django_pydantic_field.fields.PydanticSchemaField(
+                        config=None,
+                        default=list,
+                        encoder=django.core.serializers.json.DjangoJSONEncoder,
+                        schema=django_pydantic_field.compat.django.GenericContainer(
+                            list, (seqvars.models.base.SeqvarsColumnConfigPydantic,)
+                        ),
+                    ),
+                ),
+                (
+                    "querysettings",
+                    models.OneToOneField(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="columns",
+                        to="seqvars.seqvarsquerysettings",
+                    ),
+                ),
+            ],
+            options={
+                "abstract": False,
+            },
+            bases=(model_clone.mixin.CloneMixin, models.Model),
+        ),
+        migrations.RemoveField(
+            model_name="seqvarsquery",
+            name="columnsconfig",
+        ),
+        migrations.DeleteModel(
+            name="SeqvarsQueryColumnsConfig",
+        ),
+    ]

backend/seqvars/models/base.py

@@ -885,6 +885,9 @@ def from_predefinedquery(
         SeqvarsQuerySettingsClinvar.objects.from_presets(
             querysettings=querysettings, clinvarpresets=predefinedquery.clinvar
         )
+        SeqvarsQuerySettingsColumns.objects.from_presets(
+            querysettings=querysettings, columnspresets=predefinedquery.columns
+        )
         return querysettings
 
 
@@ -903,6 +906,7 @@ class SeqvarsQuerySettings(model_clone.CloneMixin, BaseModel):
         "phenotypeprio",
         "quality",
         "clinvar",
+        "columns",
     ]
 
     #: Custom manager with ``from_predefinedquery()``.
@@ -1601,38 +1605,37 @@ def __str__(self):
         return f"SeqvarsQuerySettingsClinvar '{self.sodar_uuid}'"
 
 
-class SeqvarsQueryColumnsConfigManager(models.Manager):
-    """Manager for ``SeqvarsQueryColumnsConfig``."""
+class SeqvarsQuerySettingsColumnsManager(models.Manager):
+    """Manager for ``SeqvarsQuerySettingsColumns``."""
 
-    def from_predefinedquery(
+    def from_presets(
         self,
         *,
-        predefinedquery: SeqvarsPredefinedQuery,
-    ) -> "SeqvarsQueryColumnsConfig":
-        if predefinedquery.columns.column_settings:
-            return super().create(
-                column_settings=predefinedquery.columns.column_settings,
-            )
-        else:
-            return super().create(column_settings=[])
+        querysettings: SeqvarsQuerySettings,
+        columnspresets: SeqvarsQueryPresetsColumns,
+    ) -> "SeqvarsQuerySettingsColumns":
+        return super().create(
+            querysettings=querysettings,
+            column_settings=columnspresets.column_settings,
+        )
 
 
-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.
-    """
+class SeqvarsQuerySettingsColumns(model_clone.CloneMixin, SeqvarsColumnsSettingsBase, BaseModel):
+    """Configuration of columns."""
 
     #: Let the ``sodar_uuid`` value be re-created when cloning.
     _clone_excluded_fields = ["sodar_uuid"]
 
     #: Custom manager with ``from_predefinedquery()``.
-    objects = SeqvarsQueryColumnsConfigManager()
+    objects = SeqvarsQuerySettingsColumnsManager()
+
+    #: The owning ``QuerySettings``.
+    querysettings = models.OneToOneField(
+        SeqvarsQuerySettings, on_delete=models.CASCADE, related_name="columns"
+    )
 
     def __str__(self):
-        return f"SeqvarsQueryColumnsConfig '{self.sodar_uuid}'"
+        return f"SeqvarsQuerySettingsColumns '{self.sodar_uuid}'"
 
 
 class SeqvarsQueryManager(models.Manager):
@@ -1658,9 +1661,6 @@ def from_predefinedquery(
             settings=SeqvarsQuerySettings.objects.from_predefinedquery(
                 session=session, predefinedquery=predefinedquery
             ),
-            columnsconfig=SeqvarsQueryColumnsConfig.objects.from_predefinedquery(
-                predefinedquery=predefinedquery
-            ),
         )
         return query
 
@@ -1691,8 +1691,6 @@ class SeqvarsQuery(model_clone.CloneMixin, BaseModel):
     session = models.ForeignKey(CaseAnalysisSession, on_delete=models.CASCADE)
     #: Query settings to be edited in the next query execution.
     settings = models.OneToOneField(SeqvarsQuerySettings, on_delete=models.CASCADE)
-    #: The columns configuration of the query.
-    columnsconfig = models.OneToOneField(SeqvarsQueryColumnsConfig, on_delete=models.PROTECT)
 
     @property
     def case(self) -> typing.Optional[Case]:
@@ -1908,6 +1906,13 @@ class SeqvarsQuerySettingsClinvarPydantic(pydantic.BaseModel):
     allow_conflicting_interpretations: bool = False
 
 
+class SeqvarsQuerySettingsColumnsPydantic(pydantic.BaseModel):
+    """Pydantic representation of ``SeqvarsQuerySettingsColumns``."""
+
+    #: List of columns with their widths.
+    column_settings: typing.List[SeqvarsColumnConfigPydantic] = []
+
+
 class SeqvarsCaseQueryPydantic(pydantic.BaseModel):
     """Pydantic representation of ``SeqvarsCaseQuery``."""
 
@@ -1923,6 +1928,8 @@ class SeqvarsCaseQueryPydantic(pydantic.BaseModel):
     locus: typing.Optional[SeqvarsQuerySettingsLocusPydantic] = None
     #: ClinVar query settings.
     clinvar: typing.Optional[SeqvarsQuerySettingsClinvarPydantic] = None
+    #: Column settings.
+    columns: typing.Optional[SeqvarsQuerySettingsColumnsPydantic] = None
 
 
 class DataSourceInfoPydantic(pydantic.BaseModel):
@@ -1992,13 +1999,13 @@ def values(cls) -> list[str]:
 class SeqvarsVariantScoreColumnPydantic(pydantic.BaseModel):
     """Store information about the variant score columns in the output."""
 
-    #: Name of the scolumn.
+    #: Name of the column.
     name: str
-    #: Label for the scolumn.
+    #: Label for the column.
     label: str
-    #: Description of the scolumn.
+    #: Description of the column.
     description: typing.Optional[str] = None
-    #: Type of the scolumn.
+    #: Type of the column.
     type: SeqvarsVariantScoreColumnTypeChoice
 
 

backend/seqvars/serializers.py

@@ -30,7 +30,6 @@
     SeqvarsPredefinedQuery,
     SeqvarsPrioServicePydantic,
     SeqvarsQuery,
-    SeqvarsQueryColumnsConfig,
     SeqvarsQueryExecution,
     SeqvarsQueryPresetsClinvar,
     SeqvarsQueryPresetsColumns,
@@ -45,6 +44,7 @@
     SeqvarsQuerySettings,
     SeqvarsQuerySettingsCategoryBase,
     SeqvarsQuerySettingsClinvar,
+    SeqvarsQuerySettingsColumns,
     SeqvarsQuerySettingsConsequence,
     SeqvarsQuerySettingsFrequency,
     SeqvarsQuerySettingsGenotype,
@@ -866,6 +866,20 @@ class Meta:
         read_only_fields = fields
 
 
+class SeqvarsQuerySettingsColumnsSerializer(
+    ColumnsSettingsBaseSerializer, SeqvarsQuerySettingsBaseSerializer
+):
+    """Serializer for ``QuerySettingsColumns``."""
+
+    class Meta:
+        model = SeqvarsQuerySettingsColumns
+        fields = (
+            ColumnsSettingsBaseSerializer.Meta.fields
+            + SeqvarsQuerySettingsBaseSerializer.Meta.fields
+        )
+        read_only_fields = fields
+
+
 class SeqvarsQuerySettingsSerializer(BaseModelSerializer):
     """Serializer for ``QuerySettings``."""
 
@@ -933,6 +947,8 @@ class SeqvarsQuerySettingsSerializer(BaseModelSerializer):
     variantprio = serializers.ReadOnlyField(source="variantprio.sodar_uuid")
     #: Serialize ``clinvar`` as its ``sodar_uuid``.
     clinvar = serializers.ReadOnlyField(source="clinvar.sodar_uuid")
+    #: Serialize ``columns`` as its ``sodar_uuid``.
+    columns = serializers.ReadOnlyField(source="columns.sodar_uuid")
 
     def validate(self, attrs):
         """Augment the attributes by the case from context."""
@@ -963,6 +979,7 @@ class Meta:
             "phenotypeprio",
             "variantprio",
             "clinvar",
+            "columns",
         ]
         read_only_fields = fields
 
@@ -1025,6 +1042,8 @@ class SeqvarsQuerySettingsDetailsSerializer(
     variantprio = SeqvarsQuerySettingsVariantPrioSerializer()
     #: Nested serialization of the clinvar settings.
     clinvar = SeqvarsQuerySettingsClinvarSerializer()
+    #: Nested serialization of the columns settings.
+    columns = SeqvarsQuerySettingsColumnsSerializer()
 
     def validate(self, data):
         data = super().validate(data)
@@ -1091,25 +1110,11 @@ class Meta:
             "phenotypeprio",
             "variantprio",
             "clinvar",
+            "columns",
         ]
         read_only_fields = fields
 
 
-class SeqvarsQueryColumnsConfigSerializer(ColumnsSettingsBaseSerializer, BaseModelSerializer):
-    """Serializer for ``QueryColumnsConfig``."""
-
-    def validate(self, attrs):
-        """Augment the attributes by the case from context."""
-        if "query" in self.context:
-            attrs["query"] = self.context["query"]
-        return attrs
-
-    class Meta:
-        model = SeqvarsQueryColumnsConfig
-        fields = BaseModelSerializer.Meta.fields + ColumnsSettingsBaseSerializer.Meta.fields
-        read_only_fields = fields
-
-
 class SeqvarsQueryCreateFromSerializer(serializers.Serializer):
     """Serializer used for drf-spectacular arguments for ``SeqvarsQuerySettingsViewSet.create_from``."""
 
@@ -1159,8 +1164,6 @@ class SeqvarsQueryDetailsSerializer(SeqvarsQuerySerializer, SodarUuidWritableNes
 
     #: For the details serializer, we use a nested details serializer.
     settings = SeqvarsQuerySettingsDetailsSerializer()
-    #: Render the columns configuration here.
-    columnsconfig = SeqvarsQueryColumnsConfigSerializer()
 
     class Meta:
         model = SeqvarsQuery

backend/seqvars/tests/factories.py

@@ -22,7 +22,6 @@
     SeqvarsPredefinedQuery,
     SeqvarsPrioServicePydantic,
     SeqvarsQuery,
-    SeqvarsQueryColumnsConfig,
     SeqvarsQueryExecution,
     SeqvarsQueryPresetsClinvar,
     SeqvarsQueryPresetsColumns,
@@ -36,6 +35,7 @@
     SeqvarsQueryPresetsVariantPrio,
     SeqvarsQuerySettings,
     SeqvarsQuerySettingsClinvar,
+    SeqvarsQuerySettingsColumns,
     SeqvarsQuerySettingsConsequence,
     SeqvarsQuerySettingsFrequency,
     SeqvarsQuerySettingsGenotype,
@@ -405,6 +405,10 @@ class SeqvarsQuerySettingsFactory(BaseModelFactory):
         "seqvars.tests.factories.SeqvarsQuerySettingsClinvarFactory",
         factory_related_name="querysettings",
     )
+    columns = factory.RelatedFactory(
+        "seqvars.tests.factories.SeqvarsQuerySettingsColumnsFactory",
+        factory_related_name="querysettings",
+    )
 
     class Meta:
         model = SeqvarsQuerySettings
@@ -499,25 +503,28 @@ class Meta:
         model = SeqvarsQuerySettingsClinvar
 
 
+class SeqvarsQuerySettingsColumnsFactory(ColumnsSettingsBaseFactory, BaseModelFactory):
+
+    # We pass in columns=None to prevent creation of a second
+    # ``QuerySettingsColumns``.
+    querysettings = factory.SubFactory(SeqvarsQuerySettingsFactory, columns=None)
+
+    class Meta:
+        model = SeqvarsQuerySettingsColumns
+
+
 class SeqvarsQueryFactory(BaseModelFactory):
 
     rank = 1
     label = factory.Sequence(lambda n: f"query-{n}")
 
     session = factory.SubFactory(CaseAnalysisSessionFactory)
     settings = factory.SubFactory(SeqvarsQuerySettingsFactory)
-    columnsconfig = factory.SubFactory("seqvars.tests.factories.SeqvarsQueryColumnsConfigFactory")
 
     class Meta:
         model = SeqvarsQuery
 
 
-class SeqvarsQueryColumnsConfigFactory(ColumnsSettingsBaseFactory, BaseModelFactory):
-
-    class Meta:
-        model = SeqvarsQueryColumnsConfig
-
-
 class SeqvarsQueryExecutionFactory(BaseModelFactory):
 
     state = SeqvarsQueryExecution.STATE_DONE