Add tests for migration data fixes

test/unit/data/model/migration_fixes/conftest.py

@@ -0,0 +1,47 @@
+from typing import (
+    Generator,
+    TYPE_CHECKING,
+)
+
+import pytest
+from sqlalchemy import (
+    create_engine,
+    text,
+)
+from sqlalchemy.orm import Session
+
+from galaxy import model as m
+
+if TYPE_CHECKING:
+    from sqlalchemy.engine import Engine
+
+from galaxy.model.unittest_utils.model_testing_utils import (  # noqa: F401 - url_factory is a fixture we have to import explicitly
+    sqlite_url_factory,
+)
+
+
+@pytest.fixture()
+def db_url(sqlite_url_factory):  # noqa: F811
+    return sqlite_url_factory()
+
+
+@pytest.fixture()
+def engine(db_url: str) -> "Engine":
+    return create_engine(db_url)
+
+
+@pytest.fixture
+def session(engine: "Engine") -> Session:
+    return Session(engine)
+
+
+@pytest.fixture(autouse=True)
+def clear_database(engine: "Engine") -> "Generator":
+    """Delete all rows from all tables. Called after each test."""
+    yield
+    with engine.begin() as conn:
+        for table in m.mapper_registry.metadata.tables:
+            # Unless db is sqlite, disable foreign key constraints to delete out of order
+            if engine.name != "sqlite":
+                conn.execute(text(f"ALTER TABLE {table} DISABLE TRIGGER ALL"))
+            conn.execute(text(f"DELETE FROM {table}"))

test/unit/data/model/migration_fixes/test_migrations.py

@@ -0,0 +1,154 @@
+import pytest
+
+from galaxy.model import User
+from galaxy.model.unittest_utils.migration_scripts_testing_utils import (  # noqa: F401 - contains fixtures we have to import explicitly
+    run_command,
+    tmp_directory,
+)
+
+COMMAND = "manage_db.sh"
+
+
+@pytest.fixture(autouse=True)
+def upgrade_database_after_test():
+    """Run after each test for proper cleanup"""
+    yield
+    run_command(f"{COMMAND} upgrade")
+
+
+def test_1cf595475b58(monkeypatch, session, make_user, make_history):
+    # Initialize db and migration environment
+    dburl = str(session.bind.url)
+    monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
+    monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
+    run_command(f"{COMMAND} init")
+
+    # STEP 0: Load pre-migration state
+    run_command(f"{COMMAND} downgrade d619fdfa6168")
+
+    # STEP 1: Load users with duplicate emails
+
+    # Duplicate group 1: users have no histories
+    # Expect: oldest user preserved
+    u1_1 = make_user(email="a")
+    u1_2 = make_user(email="a")
+    u1_3 = make_user(email="a")
+    original_email1 = u1_1.email
+    assert u1_1.email == u1_2.email == u1_3.email
+    assert u1_1.create_time < u1_2.create_time < u1_3.create_time  # u1_1 is oldest user
+
+    # Duplicate group 2: oldest user does NOT have a history, another user has a history
+    # Expect: user with history preserved
+    u2_1 = make_user(email="b")
+    u2_2 = make_user(email="b")
+    u2_3 = make_user(email="b")
+    original_email2 = u2_1.email
+    assert u2_1.email == u2_2.email == u2_3.email
+    assert u2_1.create_time < u2_2.create_time < u2_3.create_time  # u2_1 is oldest user
+
+    make_history(user=u2_2)  # u2_2 has a history
+
+    # Duplicate group 3: oldest user does NOT have a history, 2 users have a history
+    # Expect: oldest user with history preserved
+    u3_1 = make_user(email="c")
+    u3_2 = make_user(email="c")
+    u3_3 = make_user(email="c")
+    original_email3 = u3_1.email
+    assert u3_1.email == u3_2.email == u3_3.email
+    assert u3_1.create_time < u3_2.create_time < u3_3.create_time  # u2_1 is oldest user
+
+    make_history(user=u3_2)  # u3_2 has a history
+    make_history(user=u3_3)  # u3_3 has a history
+
+    # User w/o duplicate email
+    u4 = make_user()
+    original_email4 = u4.email
+
+    # STEP 2: Run migration
+
+    run_command(f"{COMMAND} upgrade 1cf595475b58")
+    session.expire_all()
+
+    # STEP 3: Verify deduplicated results
+
+    # Duplicate group 1:
+    u1_1_fixed = session.get(User, u1_1.id)
+    u1_2_fixed = session.get(User, u1_2.id)
+    u1_3_fixed = session.get(User, u1_3.id)
+
+    # oldest user's email is preserved; the rest are deduplicated
+    assert u1_1.email == original_email1
+    assert u1_1.email != u1_2.email != u1_3.email
+    # deduplicated users are marked as deleted
+    assert u1_1_fixed.deleted is False
+    assert u1_2_fixed.deleted is True
+    assert u1_3_fixed.deleted is True
+
+    # Duplicate group 2:
+    u2_1_fixed = session.get(User, u2_1.id)
+    u2_2_fixed = session.get(User, u2_2.id)
+    u2_3_fixed = session.get(User, u2_3.id)
+
+    # the email of the user with a history is preserved; the rest are deduplicated
+    assert u2_2.email == original_email2
+    assert u2_1.email != u1_2.email != u1_3.email
+    # deduplicated users are marked as deleted
+    assert u2_1_fixed.deleted is True
+    assert u2_2_fixed.deleted is False
+    assert u2_3_fixed.deleted is True
+
+    # Duplicate group 3:
+    u3_1_fixed = session.get(User, u3_1.id)
+    u3_2_fixed = session.get(User, u3_2.id)
+    u3_3_fixed = session.get(User, u3_3.id)
+
+    # the email of the oldest user with a history is preserved; the rest are deduplicated
+    assert u3_2.email == original_email3
+    assert u3_1.email != u3_2.email != u3_3.email
+    # deduplicated users are marked as deleted
+    assert u3_1_fixed.deleted is True
+    assert u3_2_fixed.deleted is False
+    assert u3_3_fixed.deleted is True
+
+    # User w/o duplicate email
+    u4_no_change = session.get(User, u4.id)
+    assert u4_no_change.email == original_email4
+    assert u4_no_change.deleted is False
+
+
+def test_d619fdfa6168(monkeypatch, session, make_user):
+    # Initialize db and migration environment
+    dburl = str(session.bind.url)
+    monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
+    monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
+    run_command(f"{COMMAND} init")
+
+    # STEP 0: Load pre-migration state
+    run_command(f"{COMMAND} downgrade d2d8f51ebb7e")
+
+    # STEP 1: Load users with duplicate usernames
+
+    # Expect: oldest user preserved
+    u1 = make_user(username="a")
+    u2 = make_user(username="a")
+    u3 = make_user(username="a")
+    original_username = u3.username
+    assert u1.username == u2.username == u3.username
+    assert u1.create_time < u2.create_time < u3.create_time  # u3 is newest user
+
+    # STEP 2: Run migration
+    run_command(f"{COMMAND} upgrade d619fdfa6168")
+    session.expire_all()
+
+    # STEP 3: Verify deduplicated results
+    u1_fixed = session.get(User, u1.id)
+    u2_fixed = session.get(User, u2.id)
+    u3_fixed = session.get(User, u3.id)
+
+    # oldest user's username is preserved; the rest are deduplicated
+    assert u3_fixed.username == original_username
+    assert u1.username != u2.username != u3.username
+    # deduplicated users are marked as deleted
+    assert u1_fixed.deleted is True
+    assert u2_fixed.deleted is True
+    assert u3_fixed.deleted is False