Merge 9fb8dd8 into 8ceceac

HISTORY.rst

@@ -32,6 +32,7 @@ End-User Summary
 ================
 
 - Starting with branch of stable version Athenea (VarFish v1).
+- Documenting problem with extra annotations in ``20210728` data release (#450).
 - Documenting problem with extra annotations in ``20210728` data release (#450).
   Includes instructions on how to apply patch to get ``20210728b``.
 - Removing problematic username modification behaviour on login page (#459).
@@ -52,12 +53,12 @@ End-User Summary
 - Added flags `segregates`, `doesnt_segregate` and `no_disease_association` to file export (#502).
 - Adding feature to enable and configure link-out to HGMD (#576).
 - Warning in the case of truncated displayed results (#641).
+- Improving Clinvar filter performance (#635).
 
 Full Change List
 ================
 
 - Starting with branch of stable version Athenea (VarFish v1).
-- Documenting problem with extra annotations in ``20210728` data release (#450).
   Includes instructions on how to apply patch to get ``20210728b``.
 - Removing problematic username modification behaviour on login page (#459).
 - Displaying login page text from settings again (#458).
@@ -78,6 +79,8 @@ Full Change List
 - Converted not cooperative tooltip to standard title on Filter & Display button (#508).
 - Adding feature to enable and configure link-out to HGMD (#576).
 - Warning in the case of truncated displayed results (#641).
+- Improving Clinvar filter performance (#635).
+  Database indices were missing, assumedly because of a Django ``makemigrations`` bug.
 
 ------
 v1.2.0

frequencies/migrations/0009_auto_20220830_0622.py

@@ -0,0 +1,27 @@
+# Generated by Django 3.2.12 on 2022-08-30 06:22
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("frequencies", "0008_alter_mtdb_synonymous"),
+    ]
+
+    operations = [
+        migrations.AddIndex(
+            model_name="helixmtdb",
+            index=models.Index(
+                fields=["release", "chromosome", "start", "reference", "alternative"],
+                name="frequencies_release_a36575_idx",
+            ),
+        ),
+        migrations.AddIndex(
+            model_name="mitomap",
+            index=models.Index(
+                fields=["release", "chromosome", "start", "reference", "alternative"],
+                name="frequencies_release_126cd0_idx",
+            ),
+        ),
+    ]

frequencies/models.py

@@ -1077,6 +1077,12 @@ class HelixMtDb(Coordinates):
     # Site is triallelic
     is_triallelic = models.BooleanField(default=False)
 
+    class Meta:
+        unique_together = ("release", "chromosome", "start", "reference", "alternative")
+        indexes = [
+            models.Index(fields=["release", "chromosome", "start", "reference", "alternative"])
+        ]
+
 
 class MtDb(Coordinates):
     # Allele count
@@ -1105,6 +1111,12 @@ class Mitomap(Coordinates):
     # Allele frequency, i.e. ac/an
     af = models.FloatField()
 
+    class Meta:
+        unique_together = ("release", "chromosome", "start", "reference", "alternative")
+        indexes = [
+            models.Index(fields=["release", "chromosome", "start", "reference", "alternative"])
+        ]
+
 
 #: Information about frequency databases used in ``FrequencyQuery``.
 FREQUENCY_DB_INFO = {

variants/tests/test_views.py

@@ -2921,8 +2921,7 @@ def _base_test_content(self, db):
                 response.context["pop_freqs"]["1000GP"]["Total"]["af"], self.thousand_genomes.af
             )
             self.assertEqual(
-                response.context["clinvar"].pathogenicity_summary,
-                self.clinvar.pathogenicity_summary,
+                response.context["clinvar"].pathogenicity, self.clinvar.pathogenicity,
             )
             self.assertEqual(
                 response.context["knowngeneaa"][0]["alignment"], self.knowngeneaa.alignment