WIP

resolwe_bio/variants/listener_plugin.py

@@ -16,6 +16,7 @@
     VariantAnnotationTranscript,
     VariantCall,
     VariantExperiment,
+    VariantPrimaryKey,
 )
 
 if TYPE_CHECKING:
@@ -116,14 +117,7 @@ def add_variants(
         # database does not returt the ids of the created objects. So first create all
         # the variants and then create the variant calls.
         for variant_data in variants_data:
-            key = {
-                "species": variant_data["species"],
-                "genome_assembly": variant_data["genome_assembly"],
-                "chromosome": variant_data["chromosome"],
-                "position": variant_data["position"],
-                "reference": variant_data["reference"],
-                "alternative": variant_data["alternative"],
-            }
+            key = {key: variant_data[key] for key in VariantPrimaryKey}
             # To reduce the hits to the database use cache for variants.
             key_tuple = tuple(key.values())
             if key_tuple not in variant_cache:
@@ -136,8 +130,11 @@ def add_variants(
                     data=data,
                     sample=sample,
                     quality=variant_data.get("quality"),
+                    depth_norm_quality=variant_data.get("depth_norm_quality"),
+                    unfiltered_allele_depth=variant_data.get("unfiltered_allele_depth"),
                     depth=variant_data.get("depth"),
                     genotype=variant_data.get("genotype"),
+                    genotype_quality=variant_data.get("genotype_quality"),
                     filter=variant_data.get("filter"),
                     experiment=experiment,
                 )
@@ -161,14 +158,7 @@ def add_variants_annotations(
 
         for annotation_data in typed_data:
 
-            key = {
-                "species": annotation_data["species"],
-                "genome_assembly": annotation_data["genome_assembly"],
-                "chromosome": annotation_data["chromosome"],
-                "position": annotation_data["position"],
-                "reference": annotation_data["reference"],
-                "alternative": annotation_data["alternative"],
-            }
+            key = {key: annotation_data[key] for key in VariantPrimaryKey}
             # To reduce the hits to the database use cache for variants.
             key_tuple = tuple(key.values())
             if key_tuple not in variant_cache:

resolwe_bio/variants/migrations/0001_initial.py

@@ -1,4 +1,4 @@
-# Generated by Django 4.2.13 on 2024-05-16 11:48
+# Generated by Django 4.2.11 on 2024-05-21 11:58
 
 from django.conf import settings
 import django.contrib.postgres.fields
@@ -11,8 +11,8 @@ class Migration(migrations.Migration):
     initial = True
 
     dependencies = [
+        ("flow", "0026_create_unaccent_full_text_search_config"),
         migrations.swappable_dependency(settings.AUTH_USER_MODEL),
-        ("flow", "0024_update_sql_entity_methods"),
     ]
 
     operations = [
@@ -134,7 +134,7 @@ class Migration(migrations.Migration):
                         verbose_name="ID",
                     ),
                 ),
-                ("quality", models.FloatField()),
+                ("quality", models.FloatField(blank=True, null=True)),
                 ("depth_norm_quality", models.FloatField(blank=True, null=True)),
                 (
                     "unfiltered_allele_depth",
@@ -146,7 +146,7 @@ class Migration(migrations.Migration):
                     "genotype_quality",
                     models.PositiveIntegerField(blank=True, null=True),
                 ),
-                ("filter", models.CharField(max_length=20)),
+                ("filter", models.CharField(blank=True, max_length=20, null=True)),
                 (
                     "data",
                     models.ForeignKey(
@@ -218,7 +218,7 @@ class Migration(migrations.Migration):
                 (
                     "variant_annotation",
                     models.ForeignKey(
-                        on_delete=django.db.models.deletion.PROTECT,
+                        on_delete=django.db.models.deletion.CASCADE,
                         related_name="transcripts",
                         to="resolwe_bio_variants.variantannotation",
                     ),

resolwe_bio/variants/models.py

@@ -13,7 +13,7 @@
 from resolwe.auditlog.models import AuditModel
 from resolwe.flow.models import Data
 from resolwe.flow.models import Entity as Sample
-from resolwe.permissions.models import PermissionGroup, PermissionInterface
+from resolwe.permissions.models import PermissionInterface
 
 # TODO: sync with the kb, at least the first entry.
 SPECIES_MAX_LENGTH = 50
@@ -38,6 +38,15 @@
 FEATURE_ID_MAX_LENGTH = 200
 FILTER_MAX_LENGTH = 20
 
+VariantPrimaryKey = (
+    "species",
+    "genome_assembly",
+    "chromosome",
+    "position",
+    "reference",
+    "alternative",
+)
+
 
 class Variant(AuditModel):
     """Describe a variant in the database."""
@@ -70,14 +79,7 @@ class Meta:
 
         constraints = [
             models.UniqueConstraint(
-                fields=[
-                    "species",
-                    "genome_assembly",
-                    "chromosome",
-                    "position",
-                    "reference",
-                    "alternative",
-                ],
+                fields=VariantPrimaryKey,
                 name="uniq_composite_key_variants",
             ),
         ]
@@ -177,7 +179,8 @@ class VariantExperiment(AuditModel):
 class VariantCall(AuditModel, PermissionInterface):
     """VariantCall object."""
 
-    def permission_proxy(self) -> str:
+    @classmethod
+    def permission_proxy(cls) -> str:
         """Return the permission proxy name."""
         return "sample"
 

resolwe_bio/variants/serializers.py

@@ -8,11 +8,13 @@
 
 from rest_framework import serializers
 
+from resolwe.flow.serializers.fields import DictRelatedField
 from resolwe.rest.serializers import SelectiveFieldMixin
 
 from resolwe_bio.variants.models import (
     Variant,
     VariantAnnotation,
+    VariantAnnotationTranscript,
     VariantCall,
     VariantExperiment,
 )
@@ -37,9 +39,36 @@ class Meta:
         ]
 
 
+class VariantTranscriptSerializer(SelectiveFieldMixin, serializers.ModelSerializer):
+    """Serializer for VariantAnnotationTranscript objects."""
+
+    class Meta:
+        """Serializer configuration."""
+
+        model = VariantAnnotationTranscript
+        fields = [
+            "id",
+            "variant_annotation_id",
+            "annotation",
+            "annotation_impact",
+            "gene",
+            "protein_impact",
+            "transcript_ids",
+            "canonical",
+        ]
+
+
 class VariantAnnotationSerializer(SelectiveFieldMixin, serializers.ModelSerializer):
     """Serializer for VariantAnnotation objects."""
 
+    transcripts = DictRelatedField(
+        queryset=VariantAnnotationTranscript.objects.all(),
+        serializer=VariantTranscriptSerializer,
+        allow_null=True,
+        required=False,
+        many=True,
+    )
+
     class Meta:
         """Serializer configuration."""
 
@@ -48,17 +77,11 @@ class Meta:
             "id",
             "variant_id",
             "type",
-            "transcripts__annotation",
-            "transcripts__annotation_impact",
-            "transcripts__gene",
-            "transcripts__protein_impact",
-            "transcripts__transcript_ids",
-            "transcripts__canonical",
             "clinical_diagnosis",
             "clinical_significance",
             "dbsnp_id",
             "clinvar_id",
-            "data_id",
+            "transcripts",
         ]
 
 
@@ -89,4 +112,4 @@ class Meta:
         """Serializer configuration."""
 
         model = VariantExperiment
-        fields = ["id", "date", "contributor", "variant_data_source"]
+        fields = ["id", "timestamp", "contributor", "variant_data_source"]