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[Installation]: Docker-compose with Jupyter - SQLite database error
See original GitHub issueInstallation check
- I have read the installation guide.
Installation OS
Linux
Installation Method
Docker
Kubernetes Cluster Type
N/A - Docker
MLRun Kit Helm Chart Version
Issue Description
SQLite error inside jupyter container.
Installation Logs
> 2022-08-16 15:35:54,802 [info] Initializing DB data
jupyter_1 | > 2022-08-16 15:35:54,802 [debug] Waiting for database liveness
jupyter_1 | > 2022-08-16 15:35:54,802 [debug] SQLite DB is used, liveness check not needed
jupyter_1 | > 2022-08-16 15:35:54,849 [info] No projects in DB, assuming latest data version: {'exc': OperationalError('(sqlite3.OperationalError) unable to open database file'), 'latest_data_version': 2}
jupyter_1 | > 2022-08-16 15:35:54,878 [info] No projects in DB, assuming latest data version: {'exc': OperationalError('(sqlite3.OperationalError) unable to open database file'), 'latest_data_version': 2}
jupyter_1 | > 2022-08-16 15:35:54,878 [info] Checking if migration is needed: {'is_migration_from_scratch': True, 'is_schema_migration_needed': True, 'is_data_migration_needed': False, 'is_database_migration_needed': False, 'is_backup_needed': False, 'is_migration_needed': False}
jupyter_1 | > 2022-08-16 15:35:54,879 [info] Creating initial data
jupyter_1 | > 2022-08-16 15:35:54,879 [info] Performing schema migration
jupyter_1 | > 2022-08-16 15:35:54,879 [debug] Performing alembic schema migrations
jupyter_1 | > 2022-08-16 15:35:54,890 [warning] Migrations failed, changing API state: {'state': 'migrations_failed'}
jupyter_1 | Traceback (most recent call last):
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 3208, in _wrap_pool_connect
jupyter_1 | return fn()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 301, in connect
jupyter_1 | return _ConnectionFairy._checkout(self)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 761, in _checkout
jupyter_1 | fairy = _ConnectionRecord.checkout(pool)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 419, in checkout
jupyter_1 | rec = pool._do_get()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/impl.py", line 259, in _do_get
jupyter_1 | return self._create_connection()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 247, in _create_connection
jupyter_1 | return _ConnectionRecord(self)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 362, in __init__
jupyter_1 | self.__connect()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 605, in __connect
jupyter_1 | pool.logger.debug("Error on connect(): %s", e)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__
jupyter_1 | compat.raise_(
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 211, in raise_
jupyter_1 | raise exception
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 599, in __connect
jupyter_1 | connection = pool._invoke_creator(self)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/create.py", line 578, in connect
jupyter_1 | return dialect.connect(*cargs, **cparams)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 584, in connect
jupyter_1 | return self.dbapi.connect(*cargs, **cparams)
jupyter_1 | sqlite3.OperationalError: unable to open database file
jupyter_1 |
jupyter_1 | The above exception was the direct cause of the following exception:
jupyter_1 |
jupyter_1 | Traceback (most recent call last):
jupyter_1 | File "/opt/conda/lib/python3.8/runpy.py", line 194, in _run_module_as_main
jupyter_1 | return _run_code(code, main_globals, None,
jupyter_1 | File "/opt/conda/lib/python3.8/runpy.py", line 87, in _run_code
jupyter_1 | exec(code, run_globals)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/mlrun/api/main.py", line 256, in <module>
jupyter_1 | main()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/mlrun/api/main.py", line 240, in main
jupyter_1 | init_data()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/mlrun/api/initial_data.py", line 65, in init_data
jupyter_1 | _perform_schema_migrations(alembic_util)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/mlrun/api/initial_data.py", line 160, in _perform_schema_migrations
jupyter_1 | alembic_util.init_alembic()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/mlrun/api/utils/db/alembic.py", line 24, in init_alembic
jupyter_1 | alembic.command.upgrade(self._alembic_config, "head")
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/alembic/command.py", line 294, in upgrade
jupyter_1 | script.run_env()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/alembic/script/base.py", line 490, in run_env
jupyter_1 | util.load_python_file(self.dir, "env.py")
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/alembic/util/pyfiles.py", line 97, in load_python_file
jupyter_1 | module = load_module_py(module_id, path)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/alembic/util/compat.py", line 182, in load_module_py
jupyter_1 | spec.loader.exec_module(module)
jupyter_1 | File "<frozen importlib._bootstrap_external>", line 783, in exec_module
jupyter_1 | File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/mlrun/api/migrations_sqlite/env.py", line 82, in <module>
jupyter_1 | run_migrations_online()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/mlrun/api/migrations_sqlite/env.py", line 72, in run_migrations_online
jupyter_1 | with connectable.connect() as connection:
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 3162, in connect
jupyter_1 | return self._connection_cls(self, close_with_result=close_with_result)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 92, in __init__
jupyter_1 | else engine.raw_connection()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 3241, in raw_connection
jupyter_1 | return self._wrap_pool_connect(self.pool.connect, _connection)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 3211, in _wrap_pool_connect
jupyter_1 | Connection._handle_dbapi_exception_noconnection(
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 2061, in _handle_dbapi_exception_noconnection
jupyter_1 | util.raise_(
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 211, in raise_
jupyter_1 | raise exception
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/base.py", line 3208, in _wrap_pool_connect
jupyter_1 | return fn()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 301, in connect
jupyter_1 | return _ConnectionFairy._checkout(self)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 761, in _checkout
jupyter_1 | fairy = _ConnectionRecord.checkout(pool)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 419, in checkout
jupyter_1 | rec = pool._do_get()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/impl.py", line 259, in _do_get
jupyter_1 | return self._create_connection()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 247, in _create_connection
jupyter_1 | return _ConnectionRecord(self)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 362, in __init__
jupyter_1 | self.__connect()
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 605, in __connect
jupyter_1 | pool.logger.debug("Error on connect(): %s", e)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__
jupyter_1 | compat.raise_(
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/util/compat.py", line 211, in raise_
jupyter_1 | raise exception
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/pool/base.py", line 599, in __connect
jupyter_1 | connection = pool._invoke_creator(self)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/create.py", line 578, in connect
jupyter_1 | return dialect.connect(*cargs, **cparams)
jupyter_1 | File "/opt/conda/lib/python3.8/site-packages/sqlalchemy/engine/default.py", line 584, in connect
jupyter_1 | return self.dbapi.connect(*cargs, **cparams)
jupyter_1 | sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) unable to open database file
jupyter_1 | (Background on this error at: http://sqlalche.me/e/14/e3q8)
Additional Information
No response
Issue Analytics
- State:
- Created a year ago
- Comments:9
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From the current log it seems like the API doesn’t have permission to
/home/jovyan/data/breast-cancer-jovyan/111b1248c6084d418408eaa56af7bbce/feature-importance.html. I think I have all the information I need for now, seems like a bug, I’ll verify it locally and will update you how to continue. Thanks @lbonini94@lbonini94 great we have a progress 😃
I think the error you experience now is not related to the error you experienced before, I’ll close this this issue and please open a new one related to the new error. Also if you can please add logs from the API so I could understand better what is going on.