First-time setup: installation issues #42

Johnnywang92 · 2019-01-08T02:51:08Z

when I run the install command on MAC Mojave (Python 2.7.10), get error message as following:

Starting metadome_redis_1 ... done
Starting metadome_rabbitmq_1 ... done
Creating metadome_db_1 ... error

ERROR: for metadome_db_1 Cannot create container for service db: b"error while mounting volume with options: type='none' device='' o='bind': no such file or directory"

ERROR: for db Cannot create container for service db: b"error while mounting volume with options: type='none' device='' o='bind': no such file or directory"
ERROR: Encountered errors while bringing up the project.

Any suggestion?

laurensvdwiel · 2019-01-08T08:15:12Z

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?

Johnnywang92 · 2019-01-09T02:51:17Z

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"]

laurensvdwiel · 2019-01-09T09:36:27Z

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

Johnnywang92 · 2019-01-10T02:04:38Z

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?

laurensvdwiel · 2019-01-10T09:29:06Z

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

Johnnywang92 · 2019-01-11T01:14:29Z

Dear @laurensvdwiel
Yes it is. I run the docker-compose run app python install.py for the first time set up.

laurensvdwiel · 2019-01-11T08:57:32Z

@cbaakman , could you attempt to replicate this issue?

cbaakman · 2019-01-11T09:07:34Z

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

cbaakman · 2019-01-11T09:09:22Z

It looks like "db.create_all" is called twice. Once in the app creation and once in the install procedure.

laurensvdwiel · 2019-07-31T09:46:11Z

@cbaakman : is this issue resolved?

cbaakman · 2019-07-31T11:10:49Z

Unfortunately not, it's still happening!

laurensvdwiel · 2022-04-09T00:34:35Z

Duplicate issue at #69

Am looking into this from my end the coming weeks

Johnnywang92 changed the title ~~install error~~ install error,for db Cannot create container for service db Jan 8, 2019

laurensvdwiel changed the title ~~install error,for db Cannot create container for service db~~ First-time setup: installation issues Jan 10, 2019

laurensvdwiel added the help wanted label Jan 10, 2019

laurensvdwiel assigned cbaakman Jan 11, 2019

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First-time setup: installation issues #42

First-time setup: installation issues #42

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First-time setup: installation issues #42

First-time setup: installation issues #42

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