Merge pull request #19551 from jdavcs/24.2_migration_edit (1becb2fa) · Commits · NDIP / Galaxy

doc/source/admin/db_migration.md

+6 −1

Original line number	Diff line number	Diff line
		@@ -542,6 +542,12 @@ After that, run the upgrade script: `./manage_db.sh upgrade`. And you're done!

		## Troubleshooting

		### Deadlock detected

		If you see a deadlock error, that may have been caused by a migration script requiring exclusive access
		to a database object, such as a row or a table. To avoid this error, it is recommended to shut down
		all Galaxy processes during database migration.

		### How to handle migrations.IncorrectVersionError

		If you see this error, you'll need to upgrade or downgrade your database before upgrading to
		@@ -552,4 +558,3 @@ is 181. Please see [this issue](https://github.com/galaxyproject/galaxy/issues/1

		#### Please help us improve this page:
		If you encounter any migration-related errors or issues, please [open an issue](https://github.com/galaxyproject/galaxy/issues/new?assignees=&labels=&template=bug_report.md&title=), and we will add the solution with any relevant context to this page.

+16 −4

Original line number	Diff line number	Diff line
		@@ -10,6 +10,7 @@ from alembic import context
		from alembic.script import ScriptDirectory
		from alembic.script.base import Script
		from sqlalchemy import create_engine
		from sqlalchemy.exc import OperationalError

		from galaxy.model import Base
		from galaxy.model.migrations import (
		@@ -111,17 +112,28 @@ def _configure_and_run_migrations_offline(url: str) -> None:
		literal_binds=True,
		dialect_opts={"paramstyle": "named"},
		)
		with context.begin_transaction():
		context.run_migrations()
		_run_migrations()


		def _configure_and_run_migrations_online(url) -> None:
		engine = create_engine(url)
		with engine.connect() as connection:
		context.configure(connection=connection, target_metadata=target_metadata)
		_run_migrations()
		engine.dispose()


		def _run_migrations():
		with context.begin_transaction():
		try:
		context.run_migrations()
		engine.dispose()
		except OperationalError as error:
		if getattr(error.orig, "pgcode", None) == "40P01": # PostgreSQL DeadlockDetected error detected
		msg = """A deadlock has been detected. This may be due to a database
		revision requiring exclusive access to a database object. To avoid this error, it is recommended to
		shut down all Galaxy procesess during database migration."""
		log.error(msg)
		raise


		def _get_url_from_config() -> str:

+18 −2

Original line number	Diff line number	Diff line
		@@ -6,6 +6,11 @@ Create Date: 2024-10-08 14:08:28.418055

		"""

		import logging

		from alembic import op
		from sqlalchemy import text

		from galaxy.model.database_object_names import build_index_name
		from galaxy.model.migrations.util import (
		alter_column,
		@@ -14,6 +19,8 @@ from galaxy.model.migrations.util import (
		transaction,
		)

		log = logging.getLogger(__name__)

		# revision identifiers, used by Alembic.
		revision = "9a5207190a4d"
		down_revision = "a99a5b52ccb8"
		@@ -35,6 +42,15 @@ def upgrade():

		def downgrade():
		with transaction():
		drop_index(index_name, table_name)
		alter_column(table_name, column_name, nullable=True)

		stmt = text("SELECT 1 FROM role GROUP BY name HAVING count(*) > 1")
		has_nonunique_values = op.get_bind().scalar(stmt)
		if not has_nonunique_values:
		drop_index(index_name, table_name)
		create_index(index_name, table_name, [column_name], unique=True)
		else:
		msg = f"""This downgrade requires creating a unique index on the `{table_name}.{column_name}` field.
		This operation cannot proceed due to the existence of non-unique values in that column, which are the result of Galaxy v24.2 (and above)
		operating under normal conditions. The current non-unique index will remain unchanged."""
		log.error(msg)