Merge pull request #337 from VariantEffect/bugfix/bencap/281/publishe…

…d-score-sets-still-have-tmp-accessions

Refresh Variant URNs Upon Score Set Publication

alembic/manual_migrations/refresh_published_tmp_urns.py

@@ -0,0 +1,33 @@
+import sqlalchemy as sa
+from sqlalchemy.orm import Session, configure_mappers
+
+from mavedb.models import *
+
+from mavedb.lib.score_sets import refresh_variant_urns
+
+from mavedb.models.score_set import ScoreSet
+from mavedb.models.variant import Variant
+
+from mavedb.db.session import SessionLocal
+
+configure_mappers()
+
+
+def do_migration(db: Session):
+    published_score_sets_with_associated_tmp_variants: sa.ScalarResult[str]
+    published_score_sets_with_associated_tmp_variants = db.execute(
+        sa.select(sa.distinct(ScoreSet.urn)).join(Variant).where(ScoreSet.published_date.is_not(None), Variant.urn.like("%tmp:%"))
+    ).scalars()
+
+    for score_set_urn in published_score_sets_with_associated_tmp_variants:
+        refresh_variant_urns(db, db.execute(sa.select(ScoreSet).where(ScoreSet.urn == score_set_urn)).scalar_one())
+
+
+if __name__ == "__main__":
+    db = SessionLocal()
+    db.current_user = None  # type: ignore
+
+    do_migration(db)
+
+    db.commit()
+    db.close()

src/mavedb/lib/score_sets.py

@@ -617,6 +617,21 @@ def create_variants(db, score_set: ScoreSet, variants_data: list[VariantData], b
     return len(score_set.variants)
 
 
+def refresh_variant_urns(db: Session, score_set: ScoreSet):
+    variants = db.execute(select(Variant).where(Variant.score_set_id == score_set.id)).scalars()
+
+    for variant in variants:
+        if not variant.urn:
+            raise ValueError("All variants should have an associated URN.")
+
+        variant_number = variant.urn.split("#")[1]
+        refreshed_urn = f"{score_set.urn}#{variant_number}"
+        variant.urn = refreshed_urn
+        db.add(variant)
+
+    db.commit()
+
+
 def bulk_create_urns(n, score_set, reset_counter=False) -> list[str]:
     start_value = 0 if reset_counter else score_set.num_variants
     parent_urn = score_set.urn

src/mavedb/routers/score_sets.py

@@ -39,6 +39,7 @@
 )
 from mavedb.lib.score_sets import (
     search_score_sets as _search_score_sets,
+    refresh_variant_urns,
 )
 from mavedb.lib.taxonomies import find_or_create_taxonomy
 from mavedb.lib.urns import (
@@ -1034,6 +1035,7 @@ def publish_score_set(
     item.urn = generate_score_set_urn(db, item.experiment)
     item.private = False
     item.published_date = published_date
+    refresh_variant_urns(db, item)
 
     save_to_logging_context({"score_set": item.urn})
 

tests/routers/test_score_set.py

@@ -5,11 +5,13 @@
 
 import jsonschema
 from arq import ArqRedis
+from sqlalchemy import select
 
 from mavedb.lib.validation.urn_re import MAVEDB_TMP_URN_RE
 from mavedb.models.enums.processing_state import ProcessingState
 from mavedb.models.experiment import Experiment as ExperimentDbModel
 from mavedb.models.score_set import ScoreSet as ScoreSetDbModel
+from mavedb.models.variant import Variant as VariantDbModel
 from mavedb.view_models.orcid import OrcidUser
 from mavedb.view_models.score_set import ScoreSet, ScoreSetCreate
 from tests.helpers.constants import (
@@ -593,6 +595,11 @@ def test_publish_score_set(session, data_provider, client, setup_router_db, data
     for key in expected_response:
         assert (key, expected_response[key]) == (key, score_set[key])
 
+    score_set_variants = session.execute(
+        select(VariantDbModel).join(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set["urn"])
+    ).scalars()
+    assert all([variant.urn.startswith("urn:mavedb:") for variant in score_set_variants])
+
 
 def test_publish_multiple_score_sets(session, data_provider, client, setup_router_db, data_files):
     experiment = create_experiment(client)
@@ -625,6 +632,19 @@ def test_publish_multiple_score_sets(session, data_provider, client, setup_route
     assert pub_score_set_3_data["title"] == score_set_3["title"]
     assert pub_score_set_3_data["experiment"]["urn"] == "urn:mavedb:00000001-a"
 
+    score_set_1_variants = session.execute(
+        select(VariantDbModel).join(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set_1["urn"])
+    ).scalars()
+    assert all([variant.urn.startswith("urn:mavedb:") for variant in score_set_1_variants])
+    score_set_2_variants = session.execute(
+        select(VariantDbModel).join(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set_2["urn"])
+    ).scalars()
+    assert all([variant.urn.startswith("urn:mavedb:") for variant in score_set_2_variants])
+    score_set_3_variants = session.execute(
+        select(VariantDbModel).join(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set_3["urn"])
+    ).scalars()
+    assert all([variant.urn.startswith("urn:mavedb:") for variant in score_set_3_variants])
+
 
 def test_cannot_publish_score_set_without_variants(client, setup_router_db):
     experiment = create_experiment(client)
@@ -727,6 +747,11 @@ def test_contributor_can_publish_other_users_score_set(session, data_provider, c
     for key in expected_response:
         assert (key, expected_response[key]) == (key, score_set[key])
 
+    score_set_variants = session.execute(
+        select(VariantDbModel).join(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set["urn"])
+    ).scalars()
+    assert all([variant.urn.startswith("urn:mavedb:") for variant in score_set_variants])
+
 
 def test_admin_cannot_publish_other_user_private_score_set(
     session, data_provider, client, admin_app_overrides, setup_router_db, data_files