Simplify Published Variant MV Indexes

Simplifies the indexes on the published variants materialized view to speed up refresh jobs. Previously, the five indexes on this mv created large amounts of write overhead. Due to the nature of concurrent mv refreshes, this caused jobs to run for huge amounts of time with no sign of finishing. The single simpler unique index on only id fields of the table should result in much lower index maintenance overhead and much quicker mv refreshs.

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 ###