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pudo / dataset

Easy-to-use data handling for SQL data stores with support for implicit table creation, bulk loading, and transactions.
https://dataset.readthedocs.org/
MIT License
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Can't connect to MySQL server on 'localhost' #294

Closed PlatonB closed 5 years ago

PlatonB commented 5 years ago

elementary OS 5.0 Python 3.6.7

Is it possible to solve this problem without configs editing?

db = dataset.connect(f'mysql+mysqlconnector://platon:<password>@localhost:3306{db_path}')

Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/mysql/connector/connection_cext.py", line 179, in _open_connection
    self._cmysql.connect(**cnx_kwargs)
_mysql_connector.MySQLInterfaceError: Can't connect to MySQL server on 'localhost' (111)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/base.py", line 2262, in _wrap_pool_connect
    return fn()
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 303, in unique_connection
    return _ConnectionFairy._checkout(self)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 760, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 492, in checkout
    rec = pool._do_get()
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/impl.py", line 139, in _do_get
    self._dec_overflow()
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
    compat.reraise(exc_type, exc_value, exc_tb)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/util/compat.py", line 129, in reraise
    raise value
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/impl.py", line 136, in _do_get
    return self._create_connection()
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 308, in _create_connection
    return _ConnectionRecord(self)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 437, in __init__
    self.__connect(first_connect_check=True)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 639, in __connect
    connection = pool._invoke_creator(self)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/strategies.py", line 114, in connect
    return dialect.connect(*cargs, **cparams)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/default.py", line 451, in connect
    return self.dbapi.connect(*cargs, **cparams)
  File "/usr/local/lib/python3.6/dist-packages/mysql/connector/__init__.py", line 172, in connect
    return CMySQLConnection(*args, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/mysql/connector/connection_cext.py", line 78, in __init__
    self.connect(**kwargs)
  File "/usr/local/lib/python3.6/dist-packages/mysql/connector/abstracts.py", line 736, in connect
    self._open_connection()
  File "/usr/local/lib/python3.6/dist-packages/mysql/connector/connection_cext.py", line 182, in _open_connection
    sqlstate=exc.sqlstate)
mysql.connector.errors.DatabaseError: 2003 (HY000): Can't connect to MySQL server on 'localhost' (111)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/platon/_0_Диссертация/00_Скрипты/create_database.py", line 41, in <module>
    db_path = create_database('/home/platon/_0_Диссертация/SQL_test/ALL.chr1_GRCh38.genotypes.20170504.vcf.gz', 130, [0, 1, 2])
  File "/home/platon/_0_Диссертация/00_Скрипты/create_database.py", line 31, in create_database
    table.insert(dict(zip(col_names, cells)))
  File "/usr/local/lib/python3.6/dist-packages/dataset/table.py", line 79, in insert
    row = self._sync_columns(row, ensure, types=types)
  File "/usr/local/lib/python3.6/dist-packages/dataset/table.py", line 265, in _sync_columns
    columns = self.columns
  File "/usr/local/lib/python3.6/dist-packages/dataset/table.py", line 53, in columns
    if not self.exists:
  File "/usr/local/lib/python3.6/dist-packages/dataset/table.py", line 41, in exists
    return self.name in self.db
  File "/usr/local/lib/python3.6/dist-packages/dataset/database.py", line 147, in __contains__
    return normalize_table_name(table_name) in self.tables
  File "/usr/local/lib/python3.6/dist-packages/dataset/database.py", line 142, in tables
    return self.inspect.get_table_names(schema=self.schema)
  File "/usr/local/lib/python3.6/dist-packages/dataset/database.py", line 75, in inspect
    return Inspector.from_engine(self.executable)
  File "/usr/local/lib/python3.6/dist-packages/dataset/database.py", line 63, in executable
    self.local.conn = self.engine.connect()
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/base.py", line 2193, in connect
    return self._connection_cls(self, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/base.py", line 103, in __init__
    else engine.raw_connection()
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/base.py", line 2293, in raw_connection
    self.pool.unique_connection, _connection
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/base.py", line 2266, in _wrap_pool_connect
    e, dialect, self
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/base.py", line 1536, in _handle_dbapi_exception_noconnection
    util.raise_from_cause(sqlalchemy_exception, exc_info)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/util/compat.py", line 383, in raise_from_cause
    reraise(type(exception), exception, tb=exc_tb, cause=cause)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/util/compat.py", line 128, in reraise
    raise value.with_traceback(tb)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/base.py", line 2262, in _wrap_pool_connect
    return fn()
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 303, in unique_connection
    return _ConnectionFairy._checkout(self)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 760, in _checkout
    fairy = _ConnectionRecord.checkout(pool)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 492, in checkout
    rec = pool._do_get()
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/impl.py", line 139, in _do_get
    self._dec_overflow()
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
    compat.reraise(exc_type, exc_value, exc_tb)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/util/compat.py", line 129, in reraise
    raise value
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/impl.py", line 136, in _do_get
    return self._create_connection()
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 308, in _create_connection
    return _ConnectionRecord(self)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 437, in __init__
    self.__connect(first_connect_check=True)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/pool/base.py", line 639, in __connect
    connection = pool._invoke_creator(self)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/strategies.py", line 114, in connect
    return dialect.connect(*cargs, **cparams)
  File "/usr/local/lib/python3.6/dist-packages/sqlalchemy/engine/default.py", line 451, in connect
    return self.dbapi.connect(*cargs, **cparams)
  File "/usr/local/lib/python3.6/dist-packages/mysql/connector/__init__.py", line 172, in connect
    return CMySQLConnection(*args, **kwargs)
  File "/usr/local/lib/python3.6/dist-packages/mysql/connector/connection_cext.py", line 78, in __init__
    self.connect(**kwargs)
  File "/usr/local/lib/python3.6/dist-packages/mysql/connector/abstracts.py", line 736, in connect
    self._open_connection()
  File "/usr/local/lib/python3.6/dist-packages/mysql/connector/connection_cext.py", line 182, in _open_connection
    sqlstate=exc.sqlstate)
sqlalchemy.exc.DatabaseError: (mysql.connector.errors.DatabaseError) 2003 (HY000): Can't connect to MySQL server on 'localhost' (111)
(Background on this error at: http://sqlalche.me/e/4xp6)
PlatonB commented 5 years ago

The issue is also reproduced on Fedora 30 Silverblue.

stefanw commented 5 years ago

Please read the link in your stack trace, quick googling leads to this SO question. Very likely has nothing to do with dataset.

PlatonB commented 5 years ago

@stefanw I cannot ask users of my programs to google and/or edit configs. It would be desirable to have a ready-to-use solution.

stefanw commented 5 years ago

I cannot ask users of my programs to google and/or edit configs.

Can ask you though?

Again: your mysql setup seems to be borked. This has nothing to do with dataset.