fix: properly interpret Optional[] in seqvars types and API (#1789) (#…

…1790)
varfish-org · Jul 12, 2024 · 36da785 · 36da785
1 parent 69bae65
commit 36da785
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Showing 7 changed files with 124 additions and 61 deletions.
diff --git a/backend/seqvars/migrations/0003_seqvarsquerysettings_predefinedquery.py b/backend/seqvars/migrations/0003_seqvarsquerysettings_predefinedquery.py
@@ -0,0 +1,24 @@
+# Generated by Django 3.2.25 on 2024-07-12 04:39
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("seqvars", "0002_auto_20240708_1305"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="seqvarsquerysettings",
+            name="predefinedquery",
+            field=models.ForeignKey(
+                blank=True,
+                null=True,
+                on_delete=django.db.models.deletion.PROTECT,
+                to="seqvars.seqvarspredefinedquery",
+            ),
+        ),
+    ]
diff --git a/backend/seqvars/models.py b/backend/seqvars/models.py
@@ -522,7 +522,6 @@ def clone_with_presetsset(
             status=self.STATUS_DRAFT,
         )
 
-        old_uuid_to_new_obj = {}
         for key in (
             "seqvarsquerypresetsfrequency_set",
             "seqvarsquerypresetsvariantprio_set",
@@ -722,11 +721,16 @@ class SeqvarsQuerySettings(BaseModel):
     #: The presets set version that this ``QuerySettings`` is based on.
     #:
     #: This information is used for computing differences between the presets and the
-    #: effective query settings.
+    #: effective query settings (together with ``predefinedquery``).
     presetssetversion = models.ForeignKey(
         SeqvarsQueryPresetsSetVersion, on_delete=models.PROTECT, null=True, blank=True
     )
 
+    #: The predefined query that this ``QuerySettings`` is based on.
+    predefinedquery = models.ForeignKey(
+        SeqvarsPredefinedQuery, on_delete=models.PROTECT, null=True, blank=True
+    )
+
     def __str__(self):
         return f"SeqvarsQuerySettings '{self.sodar_uuid}'"
 

diff --git a/backend/seqvars/serializers.py b/backend/seqvars/serializers.py
@@ -769,6 +769,8 @@ class SeqvarsQuerySettingsSerializer(BaseModelSerializer):
 
     #: Serialize ``presetssetversion`` as its ``sodar_uuid``.
     presetssetversion = serializers.ReadOnlyField(source="presetssetversion.sodar_uuid")
+    #: Serialize ``predefinedquery`` as its ``sodar_uuid``.
+    predefinedquery = serializers.ReadOnlyField(source="predefinedquery.sodar_uuid")
 
     #: Serialize ``genotype`` as its ``sodar_uuid``.
     genotype = serializers.ReadOnlyField(source="genotype.sodar_uuid")
@@ -798,6 +800,7 @@ class Meta:
         fields = BaseModelSerializer.Meta.fields + [
             "session",
             "presetssetversion",
+            "predefinedquery",
             "genotype",
             "quality",
             "consequence",

diff --git a/backend/varfish/spectacular_utils.py b/backend/varfish/spectacular_utils.py
@@ -11,15 +11,15 @@
 
 def pydantic_to_json_schema(schema_arg: typing.Any) -> typing.Dict[str, typing.Any]:
     """Convert a Python/pydantic schema to a JSON schema."""
-    if type(schema_arg) is type(int) or type(schema_arg) is type(float):
+    if schema_arg is int or schema_arg is float:
         return {
             "type": "number",
         }
-    elif type(schema_arg) is type(str):
+    elif schema_arg is str:
         return {
             "type": "string",
         }
-    elif type(schema_arg) is type(None):
+    elif schema_arg is type(None):
         return {
             "type": "null",
         }

diff --git a/backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml b/backend/varfish/tests/drf_openapi_schema/varfish_api_schema.yaml
@@ -6951,7 +6951,7 @@ components:
                 default: null
             title: SeqvarsGenotypePresets
             type: object
-          - type: number
+          - type: 'null'
           default:
             choice: null
         quality:
@@ -7176,7 +7176,7 @@ components:
                 title: Frequency
             title: GnomadNuclearFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         gnomad_genomes:
           oneOf:
           - description: Settings for gnomAD nuclear frequency filtering.
@@ -7211,7 +7211,7 @@ components:
                 title: Frequency
             title: GnomadNuclearFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         gnomad_mitochondrial:
           oneOf:
           - description: Settings for gnomAD mitochondrial frequency filtering.
@@ -7240,7 +7240,7 @@ components:
                 title: Frequency
             title: GnomadMitochondrialFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         helixmtdb:
           oneOf:
           - description: Settings for HelixMtDb frequency filtering.
@@ -7269,7 +7269,7 @@ components:
                 title: Frequency
             title: HelixmtDbFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         inhouse:
           oneOf:
           - description: Settings for in-house frequency filtering.
@@ -7304,7 +7304,7 @@ components:
                 title: Carriers
             title: InhouseFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         sodar_uuid:
           type: string
           format: uuid
@@ -7591,6 +7591,10 @@ components:
           type: string
           format: uuid
           readOnly: true
+        predefinedquery:
+          type: string
+          format: uuid
+          readOnly: true
         genotype:
           $ref: '#/components/schemas/SeqvarsQuerySettingsGenotype'
         quality:
@@ -8527,7 +8531,7 @@ components:
                 default: null
             title: SeqvarsGenotypePresets
             type: object
-          - type: number
+          - type: 'null'
           default:
             choice: null
         quality:
@@ -8994,7 +8998,7 @@ components:
                 title: Frequency
             title: GnomadNuclearFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         gnomad_genomes:
           oneOf:
           - description: Settings for gnomAD nuclear frequency filtering.
@@ -9029,7 +9033,7 @@ components:
                 title: Frequency
             title: GnomadNuclearFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         gnomad_mitochondrial:
           oneOf:
           - description: Settings for gnomAD mitochondrial frequency filtering.
@@ -9058,7 +9062,7 @@ components:
                 title: Frequency
             title: GnomadMitochondrialFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         helixmtdb:
           oneOf:
           - description: Settings for HelixMtDb frequency filtering.
@@ -9087,7 +9091,7 @@ components:
                 title: Frequency
             title: HelixmtDbFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         inhouse:
           oneOf:
           - description: Settings for in-house frequency filtering.
@@ -9122,7 +9126,7 @@ components:
                 title: Carriers
             title: InhouseFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         sodar_uuid:
           type: string
           format: uuid
@@ -9586,6 +9590,10 @@ components:
           type: string
           format: uuid
           readOnly: true
+        predefinedquery:
+          type: string
+          format: uuid
+          readOnly: true
         genotype:
           type: string
           format: uuid
@@ -9627,6 +9635,7 @@ components:
       - genotype
       - locus
       - phenotypeprio
+      - predefinedquery
       - presetssetversion
       - quality
       - session
@@ -9727,6 +9736,10 @@ components:
           type: string
           format: uuid
           readOnly: true
+        predefinedquery:
+          type: string
+          format: uuid
+          readOnly: true
         genotype:
           $ref: '#/components/schemas/SeqvarsQuerySettingsGenotype'
         quality:
@@ -9752,6 +9765,7 @@ components:
       - genotype
       - locus
       - phenotypeprio
+      - predefinedquery
       - presetssetversion
       - quality
       - session
@@ -9795,7 +9809,7 @@ components:
                 title: Frequency
             title: GnomadNuclearFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         gnomad_genomes:
           oneOf:
           - description: Settings for gnomAD nuclear frequency filtering.
@@ -9830,7 +9844,7 @@ components:
                 title: Frequency
             title: GnomadNuclearFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         gnomad_mitochondrial:
           oneOf:
           - description: Settings for gnomAD mitochondrial frequency filtering.
@@ -9859,7 +9873,7 @@ components:
                 title: Frequency
             title: GnomadMitochondrialFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         helixmtdb:
           oneOf:
           - description: Settings for HelixMtDb frequency filtering.
@@ -9888,7 +9902,7 @@ components:
                 title: Frequency
             title: HelixmtDbFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         inhouse:
           oneOf:
           - description: Settings for in-house frequency filtering.
@@ -9923,7 +9937,7 @@ components:
                 title: Carriers
             title: InhouseFrequencySettings
             type: object
-          - type: number
+          - type: 'null'
         sodar_uuid:
           type: string
           format: uuid
@@ -10427,7 +10441,7 @@ components:
     strList:
       type: array
       items:
-        type: number
+        type: string
   securitySchemes:
     basicAuth:
       type: http