Develop Reference

"KeyError: 0" when connecting to MySQL (get_default_isolation_level)

Currently developing for python 3.9.6 with sqlalchemy version 1.4.23 and whenever I use sqlalchemy to connect to a database, I get an error with this stack trace:
Traceback (most recent call last):
File "/mnt/c/Importer/common/db.py", line 106, in db_cur
with engine.connect() as con:
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 3166, in connect
return self._connection_cls(self, close_with_result=close_with_result)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 96, in __init__
else engine.raw_connection()
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 3245, in raw_connection
return self._wrap_pool_connect(self.pool.connect, _connection)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/engine/base.py", line 3212, in _wrap_pool_connect
return fn()
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 307, in connect
return _ConnectionFairy._checkout(self)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 767, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 425, in checkout
rec = pool._do_get()
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/pool/impl.py", line 146, in _do_get
self._dec_overflow()
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__
compat.raise_(
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/util/compat.py", line 207, in raise_
raise exception
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/pool/impl.py", line 143, in _do_get
return self._create_connection()
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 253, in _create_connection
return _ConnectionRecord(self)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 368, in __init__
self.__connect()
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/pool/base.py", line 622, in __connect
pool.dispatch.connect.for_modify(
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/event/attr.py", line 329, in _exec_w_sync_on_first_run
self(*args, **kw)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/event/attr.py", line 343, in __call__
fn(*args, **kw)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/util/langhelpers.py", line 1691, in go
return once_fn(*arg, **kw)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/engine/create.py", line 674, in first_connect
dialect.initialize(c)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/dialects/mysql/base.py", line 2961, in initialize
default.DefaultDialect.initialize(self, connection)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 407, in initialize
self.default_isolation_level = self.get_default_isolation_level(
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/engine/default.py", line 473, in get_default_isolation_level
return self.get_isolation_level(dbapi_conn)
File "/home/jimmy/.local/share/virtualenvs/Importer-0-6a4YAh/lib/python3.9/site-packages/sqlalchemy/dialects/mysql/base.py", line 2720, in get_isolation_level
val = row[0]
KeyError: 0
I can fix the issue by manually changing the file from
val = row[0]
to
val = row['##transaction_isolation']
but I don't want to have to manually change dependency files after installing them. I have tried manually setting the transaction isolation when creating the engine, but that doesn't prevent get_isolation_level() from being called so the error persists. Is sqlalchemy not compatible with python 3.9.6? Does this have anything to do with the mysql server version?

Problem was with the DictCursor being used in the connection. Changing _fetch_type for SELECT ##transaction_isolation to be a tuple instead of a dictionary solved the issue.

Connecting Flask To AWS RDS using Flask-SQLAlchemy

I have been trying to connect my aws RDS database instance to a flask application I have downloaded. I have been following https://medium.com/#rodkey/deploying-a-flask-application-on-aws-a72daba6bb80 and using the flask app on this github to connect to the database https://github.com/inkjet/flask-aws-tutorial. I have set the permissions on my RDS server correctly and have been using the following code to connect to the DB.
# edit the URI below to add your RDS password and your AWS URL
# The other elements are the same as used in the tutorial
# format: (user):(password)#(db_identifier).amazonaws.com:3306/(db_name)
SQLALCHEMY_DATABASE_URI = 'mysql+pymysql://{userName}:{password}#{endpoint}:3306/{dbName}'
# Uncomment the line below if you want to work with a local DB
#SQLALCHEMY_DATABASE_URI = 'sqlite:///test.db'
SQLALCHEMY_POOL_RECYCLE = 3600
WTF_CSRF_ENABLED = True
I am still receiving a timeout error:
{path_to_virt_env}/lib/python3.7/site-packages/flask_sqlalchemy/__init__.py:834: FSADeprecationWarning: SQLALCHEMY_TRACK_MODIFICATIONS adds significant overhead and will be disabled by default in the future. Set it to True or False to suppress this warning.
'SQLALCHEMY_TRACK_MODIFICATIONS adds significant overhead and '
Traceback (most recent call last):
File "{path_to_virt_env}/lib/python3.7/site-packages/pymysql/connections.py", line 583, in connect
**kwargs)
File "/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
socket.timeout: timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2345, in _wrap_pool_connect
return fn()
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 364, in connect
return _ConnectionFairy._checkout(self)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 778, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 495, in checkout
rec = pool._do_get()
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/impl.py", line 140, in _do_get
self._dec_overflow()
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 69, in __exit__
exc_value, with_traceback=exc_tb,
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise_
raise exception
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/impl.py", line 137, in _do_get
return self._create_connection()
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 309, in _create_connection
return _ConnectionRecord(self)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 440, in __init__
self.__connect(first_connect_check=True)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 661, in __connect
pool.logger.debug("Error on connect(): %s", e)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 69, in __exit__
exc_value, with_traceback=exc_tb,
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise_
raise exception
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 656, in __connect
connection = pool._invoke_creator(self)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
return dialect.connect(*cargs, **cparams)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 490, in connect
return self.dbapi.connect(*cargs, **cparams)
File "{path_to_virt_env}/lib/python3.7/site-packages/pymysql/__init__.py", line 94, in Connect
return Connection(*args, **kwargs)
File "{path_to_virt_env}/lib/python3.7/site-packages/pymysql/connections.py", line 325, in __init__
self.connect()
File "{path_to_virt_env}/lib/python3.7/site-packages/pymysql/connections.py", line 630, in connect
raise exc
pymysql.err.OperationalError: (2003, "Can't connect to MySQL server on '{endpoint}' (timed out)")
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "db_create.py", line 4, in <module>
db.create_all()
File "{path_to_virt_env}/lib/python3.7/site-packages/flask_sqlalchemy/__init__.py", line 1039, in create_all
self._execute_for_all_tables(app, bind, 'create_all')
File "{path_to_virt_env}/lib/python3.7/site-packages/flask_sqlalchemy/__init__.py", line 1031, in _execute_for_all_tables
op(bind=self.get_engine(app, bind), **extra)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/sql/schema.py", line 4465, in create_all
ddl.SchemaGenerator, self, checkfirst=checkfirst, tables=tables
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2103, in _run_visitor
with self._optional_conn_ctx_manager(connection) as conn:
File "/usr/local/Cellar/python/3.7.7/Frameworks/Python.framework/Versions/3.7/lib/python3.7/contextlib.py", line 112, in __enter__
return next(self.gen)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2095, in _optional_conn_ctx_manager
with self._contextual_connect() as conn:
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2311, in _contextual_connect
self._wrap_pool_connect(self.pool.connect, None),
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2349, in _wrap_pool_connect
e, dialect, self
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1591, in _handle_dbapi_exception_noconnection
sqlalchemy_exception, with_traceback=exc_info[2], from_=e
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise_
raise exception
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 2345, in _wrap_pool_connect
return fn()
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 364, in connect
return _ConnectionFairy._checkout(self)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 778, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 495, in checkout
rec = pool._do_get()
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/impl.py", line 140, in _do_get
self._dec_overflow()
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 69, in __exit__
exc_value, with_traceback=exc_tb,
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise_
raise exception
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/impl.py", line 137, in _do_get
return self._create_connection()
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 309, in _create_connection
return _ConnectionRecord(self)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 440, in __init__
self.__connect(first_connect_check=True)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 661, in __connect
pool.logger.debug("Error on connect(): %s", e)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 69, in __exit__
exc_value, with_traceback=exc_tb,
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 178, in raise_
raise exception
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/pool/base.py", line 656, in __connect
connection = pool._invoke_creator(self)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
return dialect.connect(*cargs, **cparams)
File "{path_to_virt_env}/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 490, in connect
return self.dbapi.connect(*cargs, **cparams)
File "{path_to_virt_env}/lib/python3.7/site-packages/pymysql/__init__.py", line 94, in Connect
return Connection(*args, **kwargs)
File "{path_to_virt_env}/lib/python3.7/site-packages/pymysql/connections.py", line 325, in __init__
self.connect()
File "{path_to_virt_env}/lib/python3.7/site-packages/pymysql/connections.py", line 630, in connect
raise exc
sqlalchemy.exc.OperationalError: (pymysql.err.OperationalError) (2003, "Can't connect to MySQL server on '{endpoint}' (timed out)")
(Background on this error at: http://sqlalche.me/e/e3q8
If any more information is needed, please let me know!

Based on the comments, the issue was that RDS's public accessibility setting was not enabled.
The solution was to enable it.

Pycharm can not see the Oracle Client, although it is added. Sqlalchemy, Python

I am trying to run my python code in pycharmie, which connects to the database, although it succeeds from the command line, PyCharm returns the following error.
It seems to me that I added all the necessary changes in the pycharma settings to run the Oracle Client.
My_file.py
import sqlalchemy as db
engine = db.create_engine('dialect+driver://user:pass#host:port/db')
connection = enigne.connect()
Error from PyCharm
/home/tymoteusz/Desktop/test/venv/bin/python /home/tymoteusz/Desktop/my_task_sqlalchemy/test_document.py
Traceback (most recent call last):
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2221, in _wrap_pool_connect
return fn()
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 356, in unique_connection
return _ConnectionFairy._checkout(self)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 811, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 543, in checkout
rec = pool._do_get()
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 1239, in _do_get
self._dec_overflow()
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/util/langhelpers.py", line 67, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 277, in reraise
raise value
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 1236, in _do_get
return self._create_connection()
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 361, in _create_connection
return _ConnectionRecord(self)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 488, in __init__
self.__connect(first_connect_check=True)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 690, in __connect
connection = pool._invoke_creator(self)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
return dialect.connect(*cargs, **cparams)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/default.py", line 437, in connect
return self.dbapi.connect(*cargs, **cparams)
cx_Oracle.DatabaseError: DPI-1047: 64-bit Oracle Client library cannot be loaded: "libclntsh.so: cannot open shared object file: No such file or directory". See https://oracle.github.io/odpi/doc/installation.html#linux for help
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/tymoteusz/Desktop/my_task_sqlalchemy/test_document.py", line 6, in <module>
connection = engine.connect()
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2164, in connect
return self._connection_cls(self, **kwargs)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 103, in __init__
else engine.raw_connection()
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2252, in raw_connection
self.pool.unique_connection, _connection
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2225, in _wrap_pool_connect
e, dialect, self
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 1522, in _handle_dbapi_exception_noconnection
util.raise_from_cause(sqlalchemy_exception, exc_info)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 296, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 276, in reraise
raise value.with_traceback(tb)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2221, in _wrap_pool_connect
return fn()
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 356, in unique_connection
return _ConnectionFairy._checkout(self)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 811, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 543, in checkout
rec = pool._do_get()
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 1239, in _do_get
self._dec_overflow()
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/util/langhelpers.py", line 67, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 277, in reraise
raise value
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 1236, in _do_get
return self._create_connection()
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 361, in _create_connection
return _ConnectionRecord(self)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 488, in __init__
self.__connect(first_connect_check=True)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/pool.py", line 690, in __connect
connection = pool._invoke_creator(self)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect
return dialect.connect(*cargs, **cparams)
File "/home/tymoteusz/.local/lib/python3.6/site-packages/sqlalchemy/engine/default.py", line 437, in connect
return self.dbapi.connect(*cargs, **cparams)
sqlalchemy.exc.DatabaseError: (cx_Oracle.DatabaseError) DPI-1047: 64-bit Oracle Client library cannot be loaded: "libclntsh.so: cannot open shared object file: No such file or directory". See https://oracle.github.io/odpi/doc/installation.html#linux for help (Background on this error at: http://sqlalche.me/e/4xp6)
Process finished with exit code 1
How can I solve my problem? Why does the Terminal start the code without returning the error, while PyCharm returns the error related to the Oracle Client Library.
Any help will be appreciated.

If you're doing this on macOS (which I'm guessing from the way you have set DYLD_LIBRARY_PATH) then you need to put the Oracle Instant Client in ~/lib or as described in the cx_Oracle installation instructions https://cx-oracle.readthedocs.io/en/latest/installation.html#install-oracle-instant-client because SIP security on macOS now stops DYLD_LIBRARY_PATH working in sub-shells.
I would also recommend using Instant Client 12.2 unless you actually need to connect to very old DB versions. With 12.2 client you can connect to Oracle DB 10.2 or later.

pymongo.errors.ServerSelectionTimeoutError

What could possibly be the reason of this error? I am using a ubuntu guest server in a windows 10 host system
The entire error is as follows:
` File "train_data.py", line 36, in <module>
update_database.insert_features(features)
File "/pupyl/preprocessing_data/update_database_with_features.py", line 59, in insert_features
self.db_operation.insert_record(records, "train")
File "/pupyl/database_client/database_operations.py", line 33, in insert_record
self.db.train.insert(record)
File "/usr/local/lib/python3.6/site-packages/pymongo/collection.py", line 3161, in insert
check_keys, manipulate, write_concern)
File "/usr/local/lib/python3.6/site-packages/pymongo/collection.py", line 607, in _insert
bypass_doc_val, session)
File "/usr/local/lib/python3.6/site-packages/pymongo/collection.py", line 595, in _insert_one
acknowledged, _insert_command, session)
File "/usr/local/lib/python3.6/site-packages/pymongo/mongo_client.py", line 1242, in _retryable_write
with self._tmp_session(session) as s:
File "/usr/local/lib/python3.6/contextlib.py", line 81, in __enter__
return next(self.gen)
File "/usr/local/lib/python3.6/site-packages/pymongo/mongo_client.py", line 1571, in _tmp_session
s = self._ensure_session(session)
File "/usr/local/lib/python3.6/site-packages/pymongo/mongo_client.py", line 1558, in _ensure_session
return self.__start_session(True, causal_consistency=False)
File "/usr/local/lib/python3.6/site-packages/pymongo/mongo_client.py", line 1511, in __start_session
server_session = self._get_server_session()
File "/usr/local/lib/python3.6/site-packages/pymongo/mongo_client.py", line 1544, in _get_server_session
return self._topology.get_server_session()
File "/usr/local/lib/python3.6/site-packages/pymongo/topology.py", line 427, in get_server_session
None)
File "/usr/local/lib/python3.6/site-packages/pymongo/topology.py", line 199, in _select_servers_loop
self._error_message(selector))
pymongo.errors.ServerSelectionTimeoutError: localhost:27017: [Errno 111] Connection refused
`
train_data.py is as follows, if that helps:
features: Tuple[List[str], List[str], List[str], List[bool], List[str]] = \
extract_features.separation_of_features(parsed_json)
update_database.insert_features(features)

seems like your application is not being able to connect to database, verify if the database is actually running on localhost:27017 and accepting connections
ps: try connecting with mongoshell

Error connecting to DB2 with python/SQLAlchemy: "0x0000" Parameter value "0x0000" is not supported. SQLSTATE=58017

I'm trying to connect to a db2 database via SQLAlchemy using the following script: (Windows 7 x64, Python 3.6 using libraries: ibm_db_sa, and ibm_db_2.0.8a, DB2 on z/OS)
import traceback
import ibm_db_sa
from sqlalchemy import create_engine
from sqlalchemy.ext.automap import automap_base
from sqlalchemy.orm import scoped_session, sessionmaker
if __name__ == '__main__':
try:
Base = automap_base()
connection_string = 'db2+ibm_db://userName:Password#Server.com:6001/DB_0;'
engine = create_engine(connection_string)
session = scoped_session(sessionmaker(autocommit=False,
autoflush=False,
bind=engine))
# reflect the tables
Base.prepare(engine, reflect=True)
base_sa = Base.classes
except Exception as err:
print(traceback.format_exc())
engine.close()
Unfortunately I'm getting the below traceback/error on the Base.prepare(engine, reflect=True) line. This is a proof of concept code to test if I can indeed connect to a db2 database and reflect tables using SQLAlchemy.
I have also tried to run a raw SQL statement instead of reflecting that has had the same outcome:
result = engine.execute(r'SELECT * FROM fooschema.footable;')
TRACEBACK:
Connected to pydev debugger (build 171.4694.67)
Traceback (most recent call last):
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 1122, in _do_get
return self._pool.get(wait, self._timeout)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\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 "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\ibm_db_dbi.py", line 592, in connect
conn = ibm_db.connect(dsn, '', '', conn_options)
SQLCODE=-30073
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 2147, in _wrap_pool_connect
return fn()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 328, in unique_connection
return _ConnectionFairy._checkout(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 766, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 516, in checkout
rec = pool._do_get()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 1138, in _do_get
self._dec_overflow()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\langhelpers.py", line 66, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\compat.py", line 187, in reraise
raise value
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 1135, in _do_get
return self._create_connection()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 333, in _create_connection
return _ConnectionRecord(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 461, in __init__
self.__connect(first_connect_check=True)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 651, in __connect
connection = pool._invoke_creator(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\strategies.py", line 105, in connect
return dialect.connect(*cargs, **cparams)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\default.py", line 393, in connect
return self.dbapi.connect(*cargs, **cparams)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\ibm_db_dbi.py", line 595, in connect
raise _get_exception(inst)
ibm_db_dbi.ProgrammingError: ibm_db_dbi::ProgrammingError: [IBM][CLI Driver] SQL30073N "0x0000" Parameter value "0x0000" is not supported. SQLSTATE=58017\r SQLCODE=-30073
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:/Users/1234567890/Documents/cool_app/db2_is_working.py", line 18, in <module>
Base.prepare(engine, reflect=True)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\ext\automap.py", line 753, in prepare
autoload_replace=False
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\sql\schema.py", line 3840, in reflect
with bind.connect() as conn:
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 2091, in connect
return self._connection_cls(self, **kwargs)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 90, in __init__
if connection is not None else engine.raw_connection()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 2177, in raw_connection
self.pool.unique_connection, _connection)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 2151, in _wrap_pool_connect
e, dialect, self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 1465, in _handle_dbapi_exception_noconnection
exc_info
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\compat.py", line 203, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\compat.py", line 186, in reraise
raise value.with_traceback(tb)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 2147, in _wrap_pool_connect
return fn()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 328, in unique_connection
return _ConnectionFairy._checkout(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 766, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 516, in checkout
rec = pool._do_get()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 1138, in _do_get
self._dec_overflow()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\langhelpers.py", line 66, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\compat.py", line 187, in reraise
raise value
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 1135, in _do_get
return self._create_connection()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 333, in _create_connection
return _ConnectionRecord(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 461, in __init__
self.__connect(first_connect_check=True)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 651, in __connect
connection = pool._invoke_creator(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\strategies.py", line 105, in connect
return dialect.connect(*cargs, **cparams)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\default.py", line 393, in connect
return self.dbapi.connect(*cargs, **cparams)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\ibm_db_dbi.py", line 595, in connect
raise _get_exception(inst)
sqlalchemy.exc.ProgrammingError: (ibm_db_dbi.ProgrammingError) ibm_db_dbi::ProgrammingError: [IBM][CLI Driver] SQL30073N "0x0000" Parameter value "0x0000" is not supported. SQLSTATE=58017\r SQLCODE=-30073
Traceback (most recent call last):
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 1122, in _do_get
return self._pool.get(wait, self._timeout)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\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 "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\ibm_db_dbi.py", line 592, in connect
conn = ibm_db.connect(dsn, '', '', conn_options)
SQLCODE=-30073
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 2147, in _wrap_pool_connect
return fn()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 328, in unique_connection
return _ConnectionFairy._checkout(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 766, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 516, in checkout
rec = pool._do_get()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 1138, in _do_get
self._dec_overflow()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\langhelpers.py", line 66, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\compat.py", line 187, in reraise
raise value
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 1135, in _do_get
return self._create_connection()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 333, in _create_connection
return _ConnectionRecord(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 461, in __init__
self.__connect(first_connect_check=True)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 651, in __connect
connection = pool._invoke_creator(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\strategies.py", line 105, in connect
return dialect.connect(*cargs, **cparams)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\default.py", line 393, in connect
return self.dbapi.connect(*cargs, **cparams)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\ibm_db_dbi.py", line 595, in connect
raise _get_exception(inst)
ibm_db_dbi.ProgrammingError: ibm_db_dbi::ProgrammingError: [IBM][CLI Driver] SQL30073N "0x0000" Parameter value "0x0000" is not supported. SQLSTATE=58017\r SQLCODE=-30073
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "C:/Users/1234567890/Documents/cool_app/db2_is_working.py", line 18, in <module>
Base.prepare(engine, reflect=True)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\ext\automap.py", line 753, in prepare
autoload_replace=False
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\sql\schema.py", line 3840, in reflect
with bind.connect() as conn:
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 2091, in connect
return self._connection_cls(self, **kwargs)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 90, in __init__
if connection is not None else engine.raw_connection()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 2177, in raw_connection
self.pool.unique_connection, _connection)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 2151, in _wrap_pool_connect
e, dialect, self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 1465, in _handle_dbapi_exception_noconnection
exc_info
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\compat.py", line 203, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb, cause=cause)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\compat.py", line 186, in reraise
raise value.with_traceback(tb)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\base.py", line 2147, in _wrap_pool_connect
return fn()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 328, in unique_connection
return _ConnectionFairy._checkout(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 766, in _checkout
fairy = _ConnectionRecord.checkout(pool)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 516, in checkout
rec = pool._do_get()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 1138, in _do_get
self._dec_overflow()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\langhelpers.py", line 66, in __exit__
compat.reraise(exc_type, exc_value, exc_tb)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\util\compat.py", line 187, in reraise
raise value
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 1135, in _do_get
return self._create_connection()
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 333, in _create_connection
return _ConnectionRecord(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 461, in __init__
self.__connect(first_connect_check=True)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\pool.py", line 651, in __connect
connection = pool._invoke_creator(self)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\strategies.py", line 105, in connect
return dialect.connect(*cargs, **cparams)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\sqlalchemy\engine\default.py", line 393, in connect
return self.dbapi.connect(*cargs, **cparams)
File "C:\Users\1234567890\Documents\cool_app\.env\lib\site-packages\ibm_db_dbi.py", line 595, in connect
raise _get_exception(inst)
sqlalchemy.exc.ProgrammingError: (ibm_db_dbi.ProgrammingError) ibm_db_dbi::ProgrammingError: [IBM][CLI Driver] SQL30073N "0x0000" Parameter value "0x0000" is not supported. SQLSTATE=58017\r SQLCODE=-30073
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "C:\Users\1234567890\AppData\Roaming\JetBrains\PyCharm 2017.1.4\helpers\pydev\pydevd.py", line 1591, in <module>
globals = debugger.run(setup['file'], None, None, is_module)
File "C:\Users\1234567890\AppData\Roaming\JetBrains\PyCharm 2017.1.4\helpers\pydev\pydevd.py", line 1018, in run
pydev_imports.execfile(file, globals, locals) # execute the script
File "C:\Users\1234567890\AppData\Roaming\JetBrains\PyCharm 2017.1.4\helpers\pydev\_pydev_imps\_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "C:/Users/1234567890/Documents/cool_app/db2_is_working.py", line 23, in <module>
engine.close()
AttributeError: 'Engine' object has no attribute 'close'

The issue was that I didn't have the correct host/user/password. I resolved the issue by creating a DSN, testing the connection and then using pyodbc to connect. I still haven't been able to get SQLAlchemy to work with the connection but will post a separate question for that.
Update: DB2 on z/OS is currently not supported by SQLAlchemy.

As of Aug, 2020 SqlAlchemy supports IBM_db and I am able to successfully connect and retrieve data on Z/OS
from sqlalchemy import Column, Integer, String, MetaData
from sqlalchemy import create_engine
engine = create_engine("db2+ibm_db://userId:password#host:port/db") #create a database engine
from sqlalchemy.ext.declarative import declarative_base
metadata = MetaData(schema='schemaName')
Base = declarative_base(bind=engine, metadata=metadata)
class Customers(Base):
__tablename__ = 'tableName'
CLIENT_ID = Column(Integer, primary_key=True)
CLIENT_NAME = Column(Integer)
CREATED_BY = Column(String)
from sqlalchemy.orm import sessionmaker
Session = sessionmaker(bind = engine)
session = Session()
result = session.query(Customers).limit(2)
for row in result:
print (row.CLIENT_NAME )