mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-11-04 23:43:20 +08:00
John Davis
b57ec18991
- Do not explicitly import fixtures (a little duplication is safer/cleaner) - Move dangerous fixture into module to prevent accidental usage from other modules - Ensure only one database is used for all tests in module
401 lines
14 KiB
Python
401 lines
14 KiB
Python
from typing import (
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Generator,
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TYPE_CHECKING,
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)
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import pytest
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from sqlalchemy import (
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select,
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text,
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)
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from galaxy import model as m
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from galaxy.model import (
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GroupRoleAssociation,
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User,
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UserGroupAssociation,
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UserRoleAssociation,
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)
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from galaxy.model.unittest_utils.migration_scripts_testing_utils import run_command
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if TYPE_CHECKING:
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from sqlalchemy.engine import Engine
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COMMAND = "manage_db.sh"
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@pytest.fixture(autouse=True)
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def clear_database(engine: "Engine") -> "Generator":
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"""Delete all rows from all tables. Called after each test."""
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yield
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with engine.begin() as conn:
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for table in m.mapper_registry.metadata.tables:
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# Unless db is sqlite, disable foreign key constraints to delete out of order
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if engine.name != "sqlite":
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conn.execute(text(f"ALTER TABLE {table} DISABLE TRIGGER ALL"))
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conn.execute(text(f"DELETE FROM {table}"))
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@pytest.fixture(autouse=True)
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def upgrade_database_after_test():
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"""Run after each test for proper cleanup"""
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yield
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run_command(f"{COMMAND} upgrade")
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def test_1cf595475b58(monkeypatch, session, make_user, make_history):
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# Initialize db and migration environment
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dburl = str(session.bind.url)
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monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
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monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
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run_command(f"{COMMAND} init")
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# STEP 0: Load pre-migration state
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run_command(f"{COMMAND} downgrade d619fdfa6168")
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# STEP 1: Load users with duplicate emails
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# Duplicate group 1: users have no histories
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# Expect: oldest user preserved
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u1_1 = make_user(email="a")
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u1_2 = make_user(email="a")
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u1_3 = make_user(email="a")
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original_email1 = u1_1.email
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assert u1_1.email == u1_2.email == u1_3.email
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assert u1_1.create_time < u1_2.create_time < u1_3.create_time # u1_1 is oldest user
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# Duplicate group 2: oldest user does NOT have a history, another user has a history
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# Expect: user with history preserved
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u2_1 = make_user(email="b")
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u2_2 = make_user(email="b")
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u2_3 = make_user(email="b")
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original_email2 = u2_1.email
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assert u2_1.email == u2_2.email == u2_3.email
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assert u2_1.create_time < u2_2.create_time < u2_3.create_time # u2_1 is oldest user
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make_history(user=u2_2) # u2_2 has a history
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# Duplicate group 3: oldest user does NOT have a history, 2 users have a history
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# Expect: oldest user with history preserved
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u3_1 = make_user(email="c")
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u3_2 = make_user(email="c")
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u3_3 = make_user(email="c")
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original_email3 = u3_1.email
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assert u3_1.email == u3_2.email == u3_3.email
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assert u3_1.create_time < u3_2.create_time < u3_3.create_time # u2_1 is oldest user
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make_history(user=u3_2) # u3_2 has a history
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make_history(user=u3_3) # u3_3 has a history
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# User w/o duplicate email
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u4 = make_user()
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original_email4 = u4.email
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# STEP 2: Run migration
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run_command(f"{COMMAND} upgrade")
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session.expire_all()
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# STEP 3: Verify deduplicated results
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# Duplicate group 1:
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u1_1_fixed = session.get(User, u1_1.id)
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u1_2_fixed = session.get(User, u1_2.id)
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u1_3_fixed = session.get(User, u1_3.id)
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# oldest user's email is preserved; the rest are deduplicated
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assert u1_1.email == original_email1
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assert u1_1.email != u1_2.email != u1_3.email
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# deduplicated users are marked as deleted
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assert u1_1_fixed.deleted is False
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assert u1_2_fixed.deleted is True
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assert u1_3_fixed.deleted is True
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# Duplicate group 2:
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u2_1_fixed = session.get(User, u2_1.id)
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u2_2_fixed = session.get(User, u2_2.id)
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u2_3_fixed = session.get(User, u2_3.id)
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# the email of the user with a history is preserved; the rest are deduplicated
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assert u2_2.email == original_email2
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assert u2_1.email != u1_2.email != u1_3.email
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# deduplicated users are marked as deleted
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assert u2_1_fixed.deleted is True
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assert u2_2_fixed.deleted is False
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assert u2_3_fixed.deleted is True
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# Duplicate group 3:
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u3_1_fixed = session.get(User, u3_1.id)
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u3_2_fixed = session.get(User, u3_2.id)
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u3_3_fixed = session.get(User, u3_3.id)
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# the email of the oldest user with a history is preserved; the rest are deduplicated
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assert u3_2.email == original_email3
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assert u3_1.email != u3_2.email != u3_3.email
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# deduplicated users are marked as deleted
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assert u3_1_fixed.deleted is True
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assert u3_2_fixed.deleted is False
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assert u3_3_fixed.deleted is True
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# User w/o duplicate email
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u4_no_change = session.get(User, u4.id)
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assert u4_no_change.email == original_email4
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assert u4_no_change.deleted is False
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def test_d619fdfa6168(monkeypatch, session, make_user):
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# Initialize db and migration environment
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dburl = str(session.bind.url)
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monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
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monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
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run_command(f"{COMMAND} init")
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# STEP 0: Load pre-migration state
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run_command(f"{COMMAND} downgrade d2d8f51ebb7e")
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# STEP 1: Load users with duplicate usernames
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# Expect: oldest user preserved
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u1 = make_user(username="a")
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u2 = make_user(username="a")
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u3 = make_user(username="a")
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original_username = u3.username
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assert u1.username == u2.username == u3.username
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assert u1.create_time < u2.create_time < u3.create_time # u3 is newest user
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# STEP 2: Run migration
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run_command(f"{COMMAND} upgrade")
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session.expire_all()
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# STEP 3: Verify deduplicated results
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u1_fixed = session.get(User, u1.id)
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u2_fixed = session.get(User, u2.id)
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u3_fixed = session.get(User, u3.id)
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# oldest user's username is preserved; the rest are deduplicated
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assert u3_fixed.username == original_username
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assert u1.username != u2.username != u3.username
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# deduplicated users are marked as deleted
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assert u1_fixed.deleted is True
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assert u2_fixed.deleted is True
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assert u3_fixed.deleted is False
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def test_349dd9d9aac9(monkeypatch, session, make_user, make_role, make_user_role_association):
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# Initialize db and migration environment
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dburl = str(session.bind.url)
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monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
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monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
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run_command(f"{COMMAND} init")
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# Load pre-migration state
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run_command(f"{COMMAND} downgrade 1cf595475b58")
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# Load duplicate records
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u1, u2 = make_user(), make_user()
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r1, r2 = make_role(), make_role()
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make_user_role_association(user=u1, role=r1)
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make_user_role_association(user=u1, role=r2)
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make_user_role_association(user=u1, role=r2) # duplicate
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make_user_role_association(user=u2, role=r1)
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make_user_role_association(user=u2, role=r1) # duplicate
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# Verify duplicates
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assert len(u1.roles) == 3
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assert len(u2.roles) == 2
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all_associations = session.execute(select(UserRoleAssociation)).all()
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assert len(all_associations) == 5
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# Run migration
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run_command(f"{COMMAND} upgrade")
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session.expire_all()
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# Verify clean data
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assert len(u1.roles) == 2
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assert len(u2.roles) == 1
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all_associations = session.execute(select(UserRoleAssociation)).all()
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assert len(all_associations) == 3
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def test_56ddf316dbd0(monkeypatch, session, make_user, make_group, make_user_group_association):
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# Initialize db and migration environment
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dburl = str(session.bind.url)
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monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
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monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
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run_command(f"{COMMAND} init")
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# Load pre-migration state
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run_command(f"{COMMAND} downgrade 1fdd615f2cdb")
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# Load duplicate records
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u1, u2 = make_user(), make_user()
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g1, g2 = make_group(), make_group()
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make_user_group_association(user=u1, group=g1)
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make_user_group_association(user=u1, group=g2)
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make_user_group_association(user=u1, group=g2) # duplicate
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make_user_group_association(user=u2, group=g1)
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make_user_group_association(user=u2, group=g1) # duplicate
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# Verify duplicates
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assert len(u1.groups) == 3
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assert len(u2.groups) == 2
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all_associations = session.execute(select(UserGroupAssociation)).all()
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assert len(all_associations) == 5
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# Run migration
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run_command(f"{COMMAND} upgrade")
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session.expire_all()
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# Verify clean data
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assert len(u1.groups) == 2
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assert len(u2.groups) == 1
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all_associations = session.execute(select(UserGroupAssociation)).all()
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assert len(all_associations) == 3
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def test_9ef6431f3a4e(monkeypatch, session, make_group, make_role, make_group_role_association):
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# Initialize db and migration environment
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dburl = str(session.bind.url)
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monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
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monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
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run_command(f"{COMMAND} init")
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# Load pre-migration state
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run_command(f"{COMMAND} downgrade 13fe10b8e35b")
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# Load duplicate records
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g1, g2 = make_group(), make_group()
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r1, r2 = make_role(), make_role()
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make_group_role_association(group=g1, role=r1)
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make_group_role_association(group=g1, role=r2)
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make_group_role_association(group=g1, role=r2) # duplicate
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make_group_role_association(group=g2, role=r1)
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make_group_role_association(group=g2, role=r1) # duplicate
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# Verify duplicates
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assert len(g1.roles) == 3
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assert len(g2.roles) == 2
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all_associations = session.execute(select(GroupRoleAssociation)).all()
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assert len(all_associations) == 5
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# Run migration
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run_command(f"{COMMAND} upgrade")
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session.expire_all()
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# Verify clean data
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assert len(g1.roles) == 2
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assert len(g2.roles) == 1
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all_associations = session.execute(select(GroupRoleAssociation)).all()
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assert len(all_associations) == 3
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def test_1fdd615f2cdb(monkeypatch, session, make_user, make_role, make_user_role_association):
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# Initialize db and migration environment
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dburl = str(session.bind.url)
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monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
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monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
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run_command(f"{COMMAND} init")
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# Load pre-migration state
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run_command(f"{COMMAND} downgrade 349dd9d9aac9")
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# Load records w/nulls
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ura1 = make_user_role_association(user=make_user(), role=make_role())
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ura2 = make_user_role_association(user=make_user(), role=make_role())
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ura3 = make_user_role_association(user=make_user(), role=make_role())
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ura1.user_id = None
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ura2.role_id = None
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ura3.user_id = None
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ura3.role_id = None
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session.add_all([ura1, ura2, ura3])
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session.commit()
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# Load record w/o nulls
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make_user_role_association(user=make_user(), role=make_role())
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# Verify data
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all_associations = session.execute(select(UserRoleAssociation)).all()
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assert len(all_associations) == 4
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# Run migration
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run_command(f"{COMMAND} upgrade")
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session.expire_all()
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# Verify clean data
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all_associations = session.execute(select(UserRoleAssociation)).all()
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assert len(all_associations) == 1
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def test_13fe10b8e35b(monkeypatch, session, make_user, make_group, make_user_group_association):
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# Initialize db and migration environment
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dburl = str(session.bind.url)
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monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
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monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
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run_command(f"{COMMAND} init")
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# Load pre-migration state
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run_command(f"{COMMAND} downgrade 56ddf316dbd0")
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# Load records w/nulls
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uga1 = make_user_group_association(user=make_user(), group=make_group())
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uga2 = make_user_group_association(user=make_user(), group=make_group())
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uga3 = make_user_group_association(user=make_user(), group=make_group())
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uga1.user_id = None
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uga2.group_id = None
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uga3.user_id = None
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uga3.group_id = None
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session.add_all([uga1, uga2, uga3])
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session.commit()
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# Load record w/o nulls
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make_user_group_association(user=make_user(), group=make_group())
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# Verify data
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all_associations = session.execute(select(UserGroupAssociation)).all()
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assert len(all_associations) == 4
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# Run migration
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run_command(f"{COMMAND} upgrade")
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session.expire_all()
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# Verify clean data
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all_associations = session.execute(select(UserGroupAssociation)).all()
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assert len(all_associations) == 1
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def test_25b092f7938b(monkeypatch, session, make_group, make_role, make_group_role_association):
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# Initialize db and migration environment
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dburl = str(session.bind.url)
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monkeypatch.setenv("GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION", dburl)
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monkeypatch.setenv("GALAXY_INSTALL_CONFIG_OVERRIDE_INSTALL_DATABASE_CONNECTION", dburl)
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run_command(f"{COMMAND} init")
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# Load pre-migration state
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run_command(f"{COMMAND} downgrade 9ef6431f3a4e")
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# Load records w/nulls
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gra1 = make_group_role_association(group=make_group(), role=make_role())
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gra2 = make_group_role_association(group=make_group(), role=make_role())
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gra3 = make_group_role_association(group=make_group(), role=make_role())
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gra1.group_id = None
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gra2.role_id = None
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gra3.group_id = None
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gra3.role_id = None
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session.add_all([gra1, gra2, gra3])
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session.commit()
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# Load record w/o nulls
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make_group_role_association(group=make_group(), role=make_role())
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# Verify data
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all_associations = session.execute(select(GroupRoleAssociation)).all()
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assert len(all_associations) == 4
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# Run migration
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run_command(f"{COMMAND} upgrade")
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session.expire_all()
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# Verify clean data
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all_associations = session.execute(select(GroupRoleAssociation)).all()
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assert len(all_associations) == 1
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