Comments (12)
laurensvdwiel
commented on June 22, 2024
Dear @Johnnywang92 ,
I believe you have not configured the <absolute path > in the docker-compose.yml file.
I have seen that this was incorrectly specified in the installation part of the readme.md, I have changed this to point to the correct line numbers in f7797f0. Can you verify it now works?
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Johnnywang92
commented on June 22, 2024
Thank you for your answer. I tried a lot of times to modify the docker-compose.yml file, and re-run the install script, but still not work.The error message is [ERROR: for metadome_db_1 Cannot create container for service db: b"error while mounting volume with options: type='none' device='</Users/yifanwang/Test/data/meta_data/>' o='bind': no such file or directory"]
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laurensvdwiel
commented on June 22, 2024
Dear @Johnnywang92 ,
The device folders are incorrectly specified in your docker-compose.yml, please remove the '<' and '>'.
Here is an example of my local test docker-compose:
volumes:
data:
driver_opts:
type: none
# Please set the 'device' here to a local folder you are okay with MetaDome to create additional files and folders
device: /usr/data
o: bind
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Johnnywang92
commented on June 22, 2024
Thank you so much Laurens van de Wiel, it worked.
Another error message: sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) FATAL: role "metadom_user" does not exist.
Is that means I need create a user "metadom_user" in mysql?
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laurensvdwiel
commented on June 22, 2024
Dear @Johnnywang92
Is the first command you executed the one specified at https://github.com/cmbi/metadome/blob/master/README.md#first-time-set-up ?
If not, please tear down the existing architecture via the command docker-compose down followed by the command specified in the first time set up: docker-compose run app python install.py
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Johnnywang92
commented on June 22, 2024
Dear @laurensvdwiel
Yes it is. I run the docker-compose run app python install.py for the first time set up.
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laurensvdwiel
commented on June 22, 2024
@cbaakman , could you attempt to replicate this issue?
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cbaakman
commented on June 22, 2024
When I run this on my desktop:
docker-compose run app python install.py
I get the following output:
Creating network "metadome_default" with the default driver
Creating metadome_db_1
Creating metadome_redis_1
Creating metadome_rabbitmq_1
Creating metadome_celery_1
2019-01-11 09:03:36,143 - WARNING - MAILSERVER is not set in default_settings.py
Traceback (most recent call last):
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 1122, in _do_get
return self._pool.get(wait, self._timeout)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/util/queue.py", line 145, in get
raise Empty
sqlalchemy.util.queue.Empty
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 2147, in _wrap_pool_connect
return fn()
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 387, in connect
return _ConnectionFairy._checkout(self)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 766, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 516, in checkout
rec = pool._do_get()
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 1138, in _do_get
self._dec_overflow()
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/util/langhelpers.py", line 66, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 187, in reraise
raise value
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 1135, in _do_get
return self._create_connection()
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 333, in _create_connection
return _ConnectionRecord(self)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 461, in __init__
self.__connect(first_connect_check=True)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 651, in __connect
connection = pool._invoke_creator(self)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/strategies.py", line 105, in connect
return dialect.connect(*cargs, **cparams)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/default.py", line 393, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/usr/local/lib/python3.5/site-packages/psycopg2/__init__.py", line 130, in connect
conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
psycopg2.OperationalError: FATAL: role "metadom_user" does not exist
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "install.py", line 6, in <module>
from metadome.application import app
File "/usr/src/app/metadome/application.py", line 3, in <module>
app = create_app()
File "/usr/src/app/metadome/factory.py", line 72, in create_app
db.create_all()
File "/usr/local/lib/python3.5/site-packages/flask_sqlalchemy/__init__.py", line 963, in create_all
self._execute_for_all_tables(app, bind, 'create_all')
File "/usr/local/lib/python3.5/site-packages/flask_sqlalchemy/__init__.py", line 955, in _execute_for_all_tables
op(bind=self.get_engine(app, bind), **extra)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/sql/schema.py", line 3949, in create_all
tables=tables)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 1928, in _run_visitor
with self._optional_conn_ctx_manager(connection) as conn:
File "/usr/local/lib/python3.5/contextlib.py", line 59, in __enter__
return next(self.gen)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 1921, in _optional_conn_ctx_manager
with self.contextual_connect() as conn:
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 2112, in contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 2151, in _wrap_pool_connect
e, dialect, self)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 1465, in _handle_dbapi_exception_noconnection
exc_info
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 186, in reraise
raise value.with_traceback(tb)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/base.py", line 2147, in _wrap_pool_connect
return fn()
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 387, in connect
return _ConnectionFairy._checkout(self)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 766, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 516, in checkout
rec = pool._do_get()
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 1138, in _do_get
self._dec_overflow()
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/util/langhelpers.py", line 66, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/util/compat.py", line 187, in reraise
raise value
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 1135, in _do_get
return self._create_connection()
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 333, in _create_connection
return _ConnectionRecord(self)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 461, in __init__
self.__connect(first_connect_check=True)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/pool.py", line 651, in __connect
connection = pool._invoke_creator(self)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/strategies.py", line 105, in connect
return dialect.connect(*cargs, **cparams)
File "/usr/local/lib/python3.5/site-packages/sqlalchemy/engine/default.py", line 393, in connect
return self.dbapi.connect(*cargs, **cparams)
File "/usr/local/lib/python3.5/site-packages/psycopg2/__init__.py", line 130, in connect
conn = _connect(dsn, connection_factory=connection_factory, **kwasync)
sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) FATAL: role "metadom_user" does not exist
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cbaakman
commented on June 22, 2024
It looks like "db.create_all" is called twice. Once in the app creation and once in the install procedure.
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laurensvdwiel
commented on June 22, 2024
@cbaakman : is this issue resolved?
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cbaakman
commented on June 22, 2024
Unfortunately not, it's still happening!
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laurensvdwiel
commented on June 22, 2024
Duplicate issue at #69
Am looking into this from my end the coming weeks
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