Merge pull request #410 from VariantEffect/maintenance/bencap/rework-indices-on-published-variants-mv

Simplify Published Variant MV Indexes

Author: bencap

alembic/versions/4726e4dddde8_simplify_published_variants_mv_indexes.py

@@ -0,0 +1,72 @@
+"""simplify published variants mv indexes
+
+Revision ID: 4726e4dddde8
+Revises: b85bc7b1bec7
+Create Date: 2025-03-25 10:46:46.641777
+
+"""
+
+from alembic import op
+
+from mavedb.models.published_variant import signature
+
+
+# revision identifiers, used by Alembic.
+revision = "4726e4dddde8"
+down_revision = "b85bc7b1bec7"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(f"idx_{signature}_variant_id", signature)
+    op.drop_index(f"idx_{signature}_variant_urn", signature)
+    op.drop_index(f"idx_{signature}_mapped_variant_id", signature)
+    op.drop_index(f"idx_{signature}_score_set_id", signature)
+    op.drop_index(f"idx_{signature}_score_set_urn", signature)
+
+    op.create_index(
+        f"idx_{signature}_ids",
+        signature,
+        ["mapped_variant_id", "variant_id", "score_set_id"],
+        unique=True,
+    )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(f"idx_{signature}_ids", signature)
+
+    op.create_index(
+        f"idx_{signature}_variant_id",
+        signature,
+        ["variant_id"],
+        unique=False,
+    )
+    op.create_index(
+        f"idx_{signature}_variant_urn",
+        signature,
+        ["variant_urn"],
+        unique=False,
+    )
+    op.create_index(
+        f"idx_{signature}_score_set_id",
+        signature,
+        ["score_set_id"],
+        unique=False,
+    )
+    op.create_index(
+        f"idx_{signature}_score_set_urn",
+        signature,
+        ["score_set_urn"],
+        unique=False,
+    )
+    op.create_index(
+        f"idx_{signature}_mapped_variant_id",
+        signature,
+        ["mapped_variant_id"],
+        unique=True,
+    )
+    # ### end Alembic commands ###

src/mavedb/worker/settings.py

@@ -1,5 +1,6 @@
 import os
 from concurrent import futures
+from datetime import timedelta
 from typing import Callable
 
 from arq.connections import RedisSettings
@@ -26,7 +27,13 @@
 # In UTC time. Depending on daylight savings time, this will bounce around by an hour but should always be very early in the morning
 # for all of the USA.
 BACKGROUND_CRONJOBS: list[CronJob] = [
-    cron(refresh_materialized_views, name="refresh_all_materialized_views", hour=20, minute=0)
+    cron(
+        refresh_materialized_views,
+        name="refresh_all_materialized_views",
+        hour=20,
+        minute=0,
+        keep_result=timedelta(minutes=2).total_seconds(),
+    )
 ]
 
 REDIS_IP = os.getenv("REDIS_IP") or "localhost"