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upgrading from 2.2.3 or 2.2.5 to 2.3.2 fails on migration-job

See original GitHub issue

Apache Airflow version

2.3.2 (latest released)

What happened

Upgrade Airflow 2.2.3 or 2.2.5 -> 2.3.2 fails on migration-job.

first time upgrade execution:

Referencing column 'task_id' and referenced column 'task_id' in foreign key constraint 'task_map_task_instance_fkey' are incompatible.")
[SQL: 
CREATE TABLE task_map (
    dag_id VARCHAR(250) COLLATE utf8mb3_bin NOT NULL, 
    task_id VARCHAR(250) COLLATE utf8mb3_bin NOT NULL, 
    run_id VARCHAR(250) COLLATE utf8mb3_bin NOT NULL, 
    map_index INTEGER NOT NULL, 
    length INTEGER NOT NULL, 
    `keys` JSON, 
    PRIMARY KEY (dag_id, task_id, run_id, map_index), 
    CONSTRAINT task_map_length_not_negative CHECK (length >= 0), 
    CONSTRAINT task_map_task_instance_fkey FOREIGN KEY(dag_id, task_id, run_id, map_index) REFERENCES task_instance (dag_id, task_id, run_id, map_index) ON DELETE CASCADE
)
]

after the first failed execution (should be due to the first failed execution):

Can't DROP 'task_reschedule_ti_fkey'; check that column/key exists")
[SQL: ALTER TABLE task_reschedule DROP FOREIGN KEY task_reschedule_ti_fkey[]

What you think should happen instead

The migration-job shouldn’t fail 😉

How to reproduce

Everytime in my environment just need to create a snapshot from last working DB-Snapshot (Airflow Version 2.2.3) and then deploy Airflow 2.3.2. I can update in between to 2.2.5 but ran into the same issue by update to 2.3.2.

Operating System

Debian GNU/Linux 10 (buster) - apache/airflow:2.3.2-python3.8 (hub.docker.com)

Versions of Apache Airflow Providers

apache-airflow-providers-amazon==2.4.0 apache-airflow-providers-celery==2.1.0 apache-airflow-providers-cncf-kubernetes==2.2.0 apache-airflow-providers-docker==2.3.0 apache-airflow-providers-elasticsearch==2.1.0 apache-airflow-providers-ftp==2.0.1 apache-airflow-providers-google==6.2.0 apache-airflow-providers-grpc==2.0.1 apache-airflow-providers-hashicorp==2.1.1 apache-airflow-providers-http==2.0.1 apache-airflow-providers-imap==2.0.1 apache-airflow-providers-microsoft-azure==3.4.0 apache-airflow-providers-mysql==2.1.1 apache-airflow-providers-odbc==2.0.1 apache-airflow-providers-postgres==2.4.0 apache-airflow-providers-redis==2.0.1 apache-airflow-providers-sendgrid==2.0.1 apache-airflow-providers-sftp==2.3.0 apache-airflow-providers-slack==4.1.0 apache-airflow-providers-sqlite==2.0.1 apache-airflow-providers-ssh==2.3.0 apache-airflow-providers-tableau==2.1.4

Deployment

Official Apache Airflow Helm Chart

Deployment details

  • K8s Rev: v1.21.12-eks-a64ea69
  • helm chart version: 1.6.0
  • Database: AWS RDS MySQL 8.0.28

Anything else

Full error Log first execution:

/home/airflow/.local/lib/python3.8/site-packages/airflow/configuration.py:529: DeprecationWarning: The auth_backend option in [api[] has been renamed to auth_backends - the old setting has been used, but please update your config.
  option = self._get_option_from_config_file(deprecated_key, deprecated_section, key, kwargs, section)
/home/airflow/.local/lib/python3.8/site-packages/airflow/configuration.py:356: FutureWarning: The auth_backends setting in [api[] has had airflow.api.auth.backend.session added in the running config, which is needed by the UI. Please update your config before Apache Airflow 3.0.
  warnings.warn(
DB: mysql+mysqldb://airflow:***@test-airflow2-db-blue.fsgfsdcfds76.eu-central-1.rds.amazonaws.com:3306/airflow
Performing upgrade with database mysql+mysqldb://airflow:***@test-airflow2-db-blue.fsgfsdcfds76.eu-central-1.rds.amazonaws.com:3306/airflow
[2022-06-17 12:19:59,724[] {db.py:920} WARNING - Found 33 duplicates in table task_fail.  Will attempt to move them.
[2022-06-17 12:36:18,813[] {db.py:1448} INFO - Creating tables
INFO  [alembic.runtime.migration[] Context impl MySQLImpl.
INFO  [alembic.runtime.migration[] Will assume non-transactional DDL.
INFO  [alembic.runtime.migration[] Running upgrade be2bfac3da23 -> c381b21cb7e4, Create a ``session`` table to store web session data
INFO  [alembic.runtime.migration[] Running upgrade c381b21cb7e4 -> 587bdf053233, Add index for ``dag_id`` column in ``job`` table.
INFO  [alembic.runtime.migration[] Running upgrade 587bdf053233 -> 5e3ec427fdd3, Increase length of email and username in ``ab_user`` and ``ab_register_user`` table to ``256`` characters
INFO  [alembic.runtime.migration[] Running upgrade 5e3ec427fdd3 -> 786e3737b18f, Add ``timetable_description`` column to DagModel for UI.
INFO  [alembic.runtime.migration[] Running upgrade 786e3737b18f -> f9da662e7089, Add ``LogTemplate`` table to track changes to config values ``log_filename_template``
INFO  [alembic.runtime.migration[] Running upgrade f9da662e7089 -> e655c0453f75, Add ``map_index`` column to TaskInstance to identify task-mapping,
and a ``task_map`` table to track mapping values from XCom.
Traceback (most recent call last):
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1705, in _execute_context
    self.dialect.do_execute(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 716, in do_execute
    cursor.execute(statement, parameters)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/cursors.py", line 206, in execute
    res = self._query(query)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/cursors.py", line 319, in _query
    db.query(q)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/connections.py", line 254, in query
    _mysql.connection.query(self, query)
MySQLdb._exceptions.OperationalError: (3780, "Referencing column 'task_id' and referenced column 'task_id' in foreign key constraint 'task_map_task_instance_fkey' are incompatible.")
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
  File "/home/airflow/.local/bin/airflow", line 8, in <module>
    sys.exit(main())
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/__main__.py", line 38, in main
    args.func(args)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/cli/cli_parser.py", line 51, in command
    return func(*args, **kwargs)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/utils/cli.py", line 99, in wrapper
    return f(*args, **kwargs)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/cli/commands/db_command.py", line 82, in upgradedb
    db.upgradedb(to_revision=to_revision, from_revision=from_revision, show_sql_only=args.show_sql_only)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/utils/session.py", line 71, in wrapper
    return func(*args, session=session, **kwargs)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/utils/db.py", line 1449, in upgradedb
    command.upgrade(config, revision=to_revision or 'heads')
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/command.py", line 322, in upgrade
    script.run_env()
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/script/base.py", line 569, in run_env
    util.load_python_file(self.dir, "env.py")
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/util/pyfiles.py", line 94, in load_python_file
    module = load_module_py(module_id, path)
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/util/pyfiles.py", line 110, in load_module_py
    spec.loader.exec_module(module)  # type: ignore
  File "<frozen importlib._bootstrap_external>", line 843, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/migrations/env.py", line 107, in <module>
    run_migrations_online()
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/migrations/env.py", line 101, in run_migrations_online
    context.run_migrations()
  File "<string>", line 8, in run_migrations
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/runtime/environment.py", line 853, in run_migrations
    self.get_context().run_migrations(**kw)
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/runtime/migration.py", line 623, in run_migrations
    step.migration_fn(**kw)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/migrations/versions/0100_2_3_0_add_taskmap_and_map_id_on_taskinstance.py", line 75, in upgrade
    op.create_table(
  File "<string>", line 8, in create_table
  File "<string>", line 3, in create_table
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/operations/ops.py", line 1254, in create_table
    return operations.invoke(op)
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/operations/base.py", line 394, in invoke
    return fn(self, operation)
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/operations/toimpl.py", line 114, in create_table
    operations.impl.create_table(table)
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/ddl/impl.py", line 354, in create_table
    self._exec(schema.CreateTable(table))
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/ddl/impl.py", line 195, in _exec
    return conn.execute(construct, multiparams)
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1200, in execute
    return meth(self, multiparams, params, _EMPTY_EXECUTION_OPTS)
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/sql/ddl.py", line 77, in _execute_on_connection
    return connection._execute_ddl(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1290, in _execute_ddl
    ret = self._execute_context(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1748, in _execute_context
    self._handle_dbapi_exception(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1929, in _handle_dbapi_exception
    util.raise_(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 211, in raise_
    raise exception
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1705, in _execute_context
    self.dialect.do_execute(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 716, in do_execute
    cursor.execute(statement, parameters)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/cursors.py", line 206, in execute
    res = self._query(query)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/cursors.py", line 319, in _query
    db.query(q)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/connections.py", line 254, in query
    _mysql.connection.query(self, query)
sqlalchemy.exc.OperationalError: (MySQLdb._exceptions.OperationalError) (3780, "Referencing column 'task_id' and referenced column 'task_id' in foreign key constraint 'task_map_task_instance_fkey' are incompatible.")
[SQL: 
CREATE TABLE task_map (
    dag_id VARCHAR(250) COLLATE utf8mb3_bin NOT NULL, 
    task_id VARCHAR(250) COLLATE utf8mb3_bin NOT NULL, 
    run_id VARCHAR(250) COLLATE utf8mb3_bin NOT NULL, 
    map_index INTEGER NOT NULL, 
    length INTEGER NOT NULL, 
    `keys` JSON, 
    PRIMARY KEY (dag_id, task_id, run_id, map_index), 
    CONSTRAINT task_map_length_not_negative CHECK (length >= 0), 
    CONSTRAINT task_map_task_instance_fkey FOREIGN KEY(dag_id, task_id, run_id, map_index) REFERENCES task_instance (dag_id, task_id, run_id, map_index) ON DELETE CASCADE
)
]
(Background on this error at: http://sqlalche.me/e/14/e3q8)

Full error Log after first execution (should caused by first execution):


/home/airflow/.local/lib/python3.8/site-packages/airflow/configuration.py:529: DeprecationWarning: The auth_backend option in [api[] has been renamed to auth_backends - the old setting has been used, but please update your config.
  option = self._get_option_from_config_file(deprecated_key, deprecated_section, key, kwargs, section)
/home/airflow/.local/lib/python3.8/site-packages/airflow/configuration.py:356: FutureWarning: The auth_backends setting in [api[] has had airflow.api.auth.backend.session added in the running config, which is needed by the UI. Please update your config before Apache Airflow 3.0.
  warnings.warn(
DB: mysql+mysqldb://airflow:***@test-airflow2-db-blue.cndbtlpttl69.eu-central-1.rds.amazonaws.com:3306/airflow
Performing upgrade with database mysql+mysqldb://airflow:***@test-airflow2-db-blue.cndbtlpttl69.eu-central-1.rds.amazonaws.com:3306/airflow
[2022-06-17 12:41:53,882[] {db.py:1448} INFO - Creating tables
INFO  [alembic.runtime.migration[] Context impl MySQLImpl.
INFO  [alembic.runtime.migration[] Will assume non-transactional DDL.
INFO  [alembic.runtime.migration[] Running upgrade f9da662e7089 -> e655c0453f75, Add ``map_index`` column to TaskInstance to identify task-mapping,
and a ``task_map`` table to track mapping values from XCom.
Traceback (most recent call last):
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1705, in _execute_context
    self.dialect.do_execute(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 716, in do_execute
    cursor.execute(statement, parameters)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/cursors.py", line 206, in execute
    res = self._query(query)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/cursors.py", line 319, in _query
    db.query(q)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/connections.py", line 254, in query
    _mysql.connection.query(self, query)
MySQLdb._exceptions.OperationalError: (1091, "Can't DROP 'task_reschedule_ti_fkey'; check that column/key exists")
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
  File "/home/airflow/.local/bin/airflow", line 8, in <module>
    sys.exit(main())
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/__main__.py", line 38, in main
    args.func(args)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/cli/cli_parser.py", line 51, in command
    return func(*args, **kwargs)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/utils/cli.py", line 99, in wrapper
    return f(*args, **kwargs)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/cli/commands/db_command.py", line 82, in upgradedb
    db.upgradedb(to_revision=to_revision, from_revision=from_revision, show_sql_only=args.show_sql_only)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/utils/session.py", line 71, in wrapper
    return func(*args, session=session, **kwargs)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/utils/db.py", line 1449, in upgradedb
    command.upgrade(config, revision=to_revision or 'heads')
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/command.py", line 322, in upgrade
    script.run_env()
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/script/base.py", line 569, in run_env
    util.load_python_file(self.dir, "env.py")
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/util/pyfiles.py", line 94, in load_python_file
    module = load_module_py(module_id, path)
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/util/pyfiles.py", line 110, in load_module_py
    spec.loader.exec_module(module)  # type: ignore
  File "<frozen importlib._bootstrap_external>", line 843, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/migrations/env.py", line 107, in <module>
    run_migrations_online()
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/migrations/env.py", line 101, in run_migrations_online
    context.run_migrations()
  File "<string>", line 8, in run_migrations
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/runtime/environment.py", line 853, in run_migrations
    self.get_context().run_migrations(**kw)
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/runtime/migration.py", line 623, in run_migrations
    step.migration_fn(**kw)
  File "/home/airflow/.local/lib/python3.8/site-packages/airflow/migrations/versions/0100_2_3_0_add_taskmap_and_map_id_on_taskinstance.py", line 49, in upgrade
    batch_op.drop_index("idx_task_reschedule_dag_task_run")
  File "/usr/local/lib/python3.8/contextlib.py", line 120, in __exit__
    next(self.gen)
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/operations/base.py", line 376, in batch_alter_table
    impl.flush()
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/operations/batch.py", line 111, in flush
    fn(*arg, **kw)
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/ddl/mysql.py", line 155, in drop_constraint
    super(MySQLImpl, self).drop_constraint(const)
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/ddl/impl.py", line 338, in drop_constraint
    self._exec(schema.DropConstraint(const))
  File "/home/airflow/.local/lib/python3.8/site-packages/alembic/ddl/impl.py", line 195, in _exec
    return conn.execute(construct, multiparams)
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1200, in execute
    return meth(self, multiparams, params, _EMPTY_EXECUTION_OPTS)
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/sql/ddl.py", line 77, in _execute_on_connection
    return connection._execute_ddl(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1290, in _execute_ddl
    ret = self._execute_context(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1748, in _execute_context
    self._handle_dbapi_exception(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1929, in _handle_dbapi_exception
    util.raise_(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 211, in raise_
    raise exception
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1705, in _execute_context
    self.dialect.do_execute(
  File "/home/airflow/.local/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 716, in do_execute
    cursor.execute(statement, parameters)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/cursors.py", line 206, in execute
    res = self._query(query)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/cursors.py", line 319, in _query
    db.query(q)
  File "/home/airflow/.local/lib/python3.8/site-packages/MySQLdb/connections.py", line 254, in query
    _mysql.connection.query(self, query)
sqlalchemy.exc.OperationalError: (MySQLdb._exceptions.OperationalError) (1091, "Can't DROP 'task_reschedule_ti_fkey'; check that column/key exists")
[SQL: ALTER TABLE task_reschedule DROP FOREIGN KEY task_reschedule_ti_fkey[]
(Background on this error at: http://sqlalche.me/e/14/e3q8)

Are you willing to submit PR?

  • Yes I am willing to submit a PR!

Code of Conduct

Issue Analytics

  • State:closed
  • Created a year ago
  • Reactions:2
  • Comments:22 (13 by maintainers)

github_iconTop GitHub Comments

3reactions
esthomwcommented, Jul 21, 2022

Hi,

I managed to run migrations with some small manual changes to database before running airflow db upgrade. I was upgrading from 2.2.3 to 2.3.2. The main culprit in that situation was misaligned CHARSET/COLLATE for task_id and dag_id column between multiple tables. Here is the script I used to align those columns:

-- remove foreign key temporarily as it is used by one of modified columns
ALTER TABLE task_reschedule DROP FOREIGN KEY task_reschedule_ti_fkey;

ALTER TABLE task_instance MODIFY task_id VARCHAR(255) CHARACTER SET utf8mb3 COLLATE utf8mb3_bin;
ALTER TABLE task_reschedule MODIFY task_id VARCHAR(255) CHARACTER SET utf8mb3 COLLATE utf8mb3_bin;
ALTER TABLE rendered_task_instance_fields MODIFY task_id VARCHAR(255) CHARACTER SET utf8mb3 COLLATE utf8mb3_bin;
ALTER TABLE rendered_task_instance_fields MODIFY dag_id VARCHAR(255) CHARACTER SET utf8mb3 COLLATE utf8mb3_bin;
ALTER TABLE task_fail MODIFY task_id VARCHAR(255) CHARACTER SET utf8mb3 COLLATE utf8mb3_bin;
ALTER TABLE task_fail MODIFY dag_id VARCHAR(255) CHARACTER SET utf8mb3 COLLATE utf8mb3_bin;

-- reintroduce the key (otherwise migrations should fail)
ALTER TABLE task_reschedule ADD CONSTRAINT task_reschedule_ti_fkey FOREIGN KEY (dag_id, task_id, run_id) REFERENCES task_instance (dag_id, task_id, run_id);
2reactions
michaelosthegecommented, Jul 20, 2022

Thanks, @potiuk from the documentation on sql_engine_collation_for_ids I kew about dag_id, task_id and key, but it did not mention external_executor_id ⚠

Also thank you for clarifying the recommended CHARSET/COLLATION: 👉 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci (as described by the database setup docs) 👉 CHARACTER SET utf8mb3 COLLATE utf8mb3_bin for dag_id, task_id, key, external_executor_id fields

I found the easiest way to fix this is to fix it right in my backup.sql file.

When applying the modified backup.sql some CREATE TABLE failed because dependent tables only got updated later. I believe this is because mysqldump doesn’t DROP TABLE everything at the beginning, but only one by one. Manually doing DROP TABLE for these few tables works.

My recommendation is as usual here: Switch to Postgres.

First things first… If there’s a way to migrate the data I’ll consider it once I recovered from todays incident…

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Triggering DAG from UI Creates 2 DAG runs if the DAG was paused

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mini-scheduler raises AttributeError: 'NoneType' object has no attribute 'keys'