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Posted to notifications@superset.apache.org by GitBox <gi...@apache.org> on 2022/08/10 13:25:49 UTC
[GitHub] [superset] tapanhalani opened a new issue, #21038: "superset db migrate" fails in init-db job
tapanhalani opened a new issue, #21038:
URL: https://github.com/apache/superset/issues/21038
A clear and concise description of what the bug is.
#### How to reproduce the bug
(1.) Successfully installed superset on a managed kubernetes cluster using superset helm chart (v0.7.0) (https://github.com/apache/superset/blob/superset-helm-chart-0.7.0/helm/superset/values.yaml), with docker image version set to `apache/superset:1.5.0`
Database used is postgresql 14.4
(2.) While upgrading the image to 2.0.0 tag, the init-db job is failing with the following logs:
```
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: psycopg2-binary==2.9.1 in /usr/local/lib/python3.8/site-packages (2.9.1)
Requirement already satisfied: redis==3.5.3 in /usr/local/lib/python3.8/site-packages (3.5.3)
WARNING: You are using pip version 21.2.4; however, version 22.2.2 is available.
You should consider upgrading via the '/usr/local/bin/python -m pip install --upgrade pip' command.
Upgrading DB schema...
logging was configured successfully
2022-08-10 11:37:28,958:INFO:superset.utils.logging_configurator:logging was configured successfully
2022-08-10 11:37:28,965:INFO:root:Configured event logger of type <class 'superset.utils.log.DBEventLogger'>
INFO [alembic.runtime.migration] Context impl PostgresqlImpl.
INFO [alembic.runtime.migration] Will assume transactional DDL.
Loaded your LOCAL configuration at [/app/pythonpath/superset_config.py]
Initializing roles...
logging was configured successfully
2022-08-10 11:37:36,904:INFO:superset.utils.logging_configurator:logging was configured successfully
2022-08-10 11:37:36,912:INFO:root:Configured event logger of type <class 'superset.utils.log.DBEventLogger'>
2022-08-10 11:37:40,432:ERROR:flask_appbuilder.security.sqla.manager:Add View Menu Error: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "ab_view_menu_pkey"
DETAIL: Key (id)=(109) already exists.
[SQL: INSERT INTO ab_view_menu (id, name) VALUES (nextval('ab_view_menu_id_seq'), %(name)s) RETURNING ab_view_menu.id]
[parameters: {'name': 'AdvancedDataType'}]
(Background on this error at: http://sqlalche.me/e/13/gkpj)
2022-08-10 11:37:40,506:ERROR:flask_appbuilder.security.sqla.manager:Add View Menu Error: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "ab_view_menu_pkey"
DETAIL: Key (id)=(110) already exists.
[SQL: INSERT INTO ab_view_menu (id, name) VALUES (nextval('ab_view_menu_id_seq'), %(name)s) RETURNING ab_view_menu.id]
[parameters: {'name': 'AdvancedDataType'}]
(Background on this error at: http://sqlalche.me/e/13/gkpj)
2022-08-10 11:37:40,553:ERROR:flask_appbuilder.security.sqla.manager:Creation of Permission View Error: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "ab_view_menu_pkey"
DETAIL: Key (id)=(111) already exists.
[SQL: INSERT INTO ab_view_menu (id, name) VALUES (nextval('ab_view_menu_id_seq'), %(name)s) RETURNING ab_view_menu.id]
[parameters: {'name': 'AdvancedDataType'}]
(Background on this error at: http://sqlalche.me/e/13/gkpj)
2022-08-10 11:37:41,671:ERROR:flask_appbuilder.security.sqla.manager:Creation of Permission View Error: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "ab_permission_view_pkey"
DETAIL: Key (id)=(253) already exists.
[SQL: INSERT INTO ab_permission_view (id, permission_id, view_menu_id) VALUES (nextval('ab_permission_view_id_seq'), %(permission_id)s, %(view_menu_id)s) RETURNING ab_permission_view.id]
[parameters: {'permission_id': 1, 'view_menu_id': 102}]
(Background on this error at: http://sqlalche.me/e/13/gkpj)
Syncing role definition
2022-08-10 11:37:47,781:INFO:superset.security.manager:Syncing role definition
Syncing Admin perms
2022-08-10 11:37:47,921:INFO:superset.security.manager:Syncing Admin perms
Syncing Alpha perms
2022-08-10 11:37:49,060:INFO:superset.security.manager:Syncing Alpha perms
Syncing Gamma perms
2022-08-10 11:37:51,019:INFO:superset.security.manager:Syncing Gamma perms
Loaded your LOCAL configuration at [/app/pythonpath/superset_config.py]
Traceback (most recent call last):
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1256, in _execute_context
self.dialect.do_executemany(
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 912, in do_executemany
cursor.executemany(statement, parameters)
psycopg2.errors.UniqueViolation: duplicate key value violates unique constraint "ab_permission_view_role_pkey"
DETAIL: Key (id)=(639) already exists.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/bin/superset", line 33, in <module>
sys.exit(load_entry_point('apache-superset', 'console_scripts', 'superset')())
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 1128, in __call__
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/flask/cli.py", line 601, in main
return super().main(*args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/flask/cli.py", line 445, in decorator
return __ctx.invoke(f, *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/click/decorators.py", line 26, in new_func
return f(get_current_context(), *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/flask/cli.py", line 445, in decorator
return __ctx.invoke(f, *args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/app/superset/cli/main.py", line 62, in init
security_manager.sync_role_definitions()
File "/app/superset/security/manager.py", line 719, in sync_role_definitions
self.set_role("Gamma", self._is_gamma_pvm)
File "/app/superset/security/manager.py", line 814, in set_role
self.get_session.merge(role)
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/scoping.py", line 163, in do
return getattr(self.registry(), name)(*args, **kwargs)
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 2160, in merge
self._autoflush()
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1633, in _autoflush
util.raise_(e, with_traceback=sys.exc_info()[2])
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
raise exception
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 1622, in _autoflush
self.flush()
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 2540, in flush
self._flush(objects)
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 2682, in _flush
transaction.rollback(_capture_exception=True)
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
compat.raise_(
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
raise exception
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/session.py", line 2642, in _flush
flush_context.execute()
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/unitofwork.py", line 422, in execute
rec.execute(self)
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/unitofwork.py", line 540, in execute
self.dependency_processor.process_saves(uow, states)
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/dependency.py", line 1176, in process_saves
self._run_crud(
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/orm/dependency.py", line 1239, in _run_crud
connection.execute(statement, secondary_insert)
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1011, in execute
return meth(self, multiparams, params)
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/sql/elements.py", line 298, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1124, in _execute_clauseelement
ret = self._execute_context(
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1316, in _execute_context
self._handle_dbapi_exception(
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1510, in _handle_dbapi_exception
util.raise_(
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 182, in raise_
raise exception
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 1256, in _execute_context
self.dialect.do_executemany(
File "/usr/local/lib/python3.8/site-packages/sqlalchemy/dialects/postgresql/psycopg2.py", line 912, in do_executemany
cursor.executemany(statement, parameters)
sqlalchemy.exc.IntegrityError: (raised as a result of Query-invoked autoflush; consider using a session.no_autoflush block if this flush is occurring prematurely)
(psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "ab_permission_view_role_pkey"
DETAIL: Key (id)=(639) already exists.
[SQL: INSERT INTO ab_permission_view_role (id, permission_view_id, role_id) VALUES (nextval('ab_permission_view_role_id_seq'), %(permission_view_id)s, %(role_id)s)]
[parameters: ({'permission_view_id': 192, 'role_id': 4}, {'permission_view_id': 194, 'role_id': 4}, {'permission_view_id': 195, 'role_id': 4}, {'permission_view_id': 198, 'role_id': 4}, {'permission_view_id': 206, 'role_id': 4}, {'permission_view_id': 207, 'role_id': 4}, {'permission_view_id': 209, 'role_id': 4}, {'permission_view_id': 210, 'role_id': 4}, {'permission_view_id': 211, 'role_id': 4}, {'permission_view_id': 213, 'role_id': 4})]
(Background on this error at: http://sqlalche.me/e/13/gkpj)
```
### Environment
(please complete the following information):
- Docker image version: `2.0.0`
- superset version: `1.0`
### Checklist
Make sure to follow these steps before submitting your issue - thank you!
- [x] I have checked the superset logs for python stacktraces and included it here as text if there are any.
- [x] I have reproduced the issue with at least the latest released version of superset.
- [x] I have checked the issue tracker for the same issue and I haven't found one similar.
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[GitHub] [superset] chathawee commented on issue #21038: "superset db migrate" fails in init-db job
Posted by "chathawee (via GitHub)" <gi...@apache.org>.
chathawee commented on issue #21038:
URL: https://github.com/apache/superset/issues/21038#issuecomment-1497162458
Hi all, It might be help you. I have resolved it by checking the max seq id value of ab_permission_view_role table and update nextval(ab_permission_view_role_id_seq) table by using below command.
- SELECT nextval('ab_permission_view_id_seq')
- SELECT currval('ab_permission_view_role_id_seq')
- SELECT max(id) FROM ab_permission_view_role
After update it, the superset init is back to normal.
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Re: [I] "superset db migrate" fails in init-db job [superset]
Posted by "rusackas (via GitHub)" <gi...@apache.org>.
rusackas commented on issue #21038:
URL: https://github.com/apache/superset/issues/21038#issuecomment-1962089491
I'm not sure if this is still an issue in current versions of Superset (3.x). If it is, we can re-open this, or feel free to open a new issue with updated context and a reproducible case using example data. We're no longer supporting Superset 2.x or prior, and it's been a while since this thread saw any activity, so I'm closing this as stale.
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[GitHub] [superset] joaocc commented on issue #21038: "superset db migrate" fails in init-db job
Posted by GitBox <gi...@apache.org>.
joaocc commented on issue #21038:
URL: https://github.com/apache/superset/issues/21038#issuecomment-1271348274
Hi. Has anyone picked up on this? Thx
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[GitHub] [superset] adimyth commented on issue #21038: "superset db migrate" fails in init-db job
Posted by GitBox <gi...@apache.org>.
adimyth commented on issue #21038:
URL: https://github.com/apache/superset/issues/21038#issuecomment-1370629524
Has anyone been able to resolve this yet?
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Re: [I] "superset db migrate" fails in init-db job [superset]
Posted by "rusackas (via GitHub)" <gi...@apache.org>.
rusackas closed issue #21038: "superset db migrate" fails in init-db job
URL: https://github.com/apache/superset/issues/21038
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