We Keep Coding

pandas to_sql() gives a SADeprecationWarning

The to_sql() function in pandas is now producing a SADeprecationWarning.
df.to_sql(name=tablename, con=c, if_exists='append', index=False )
[..]/lib/python3.8/site-packages/pandas/io/sql.py:1430: SADeprecationWarning:The Connection.run_callable() method is deprecated and will be removed in a future release. Use a context manager instead. (deprecated since: 1.4)
I was getting this even with df.read_sql() command, when running sql select statements. Changing it to the original df.read_sql_query() that it wraps around, got rid of it. I'm suspecting there would be some linkage there.
So, question is, how to do I write a dataframe table to SQL without it getting deprecated in a future release? What does "use a context manager" mean, how can I implement that?
Versions:
pandas: 1.1.5 | SQLAlchemy: 1.4.0 | pyodbc: 4.0.30 | Python: 3.8.0
Working with a mssql database.
OS: Linux Mint Xfce, 18.04. Using a python virtual environment.
If it matters, connection created like so:
conn_str = r'mssql+pyodbc:///?odbc_connect={}'.format(dbString).strip()
sqlEngine = sqlalchemy.create_engine(conn_str,echo=False, pool_recycle=3600)
c = sqlEngine.connect()
And after the db operation,
c.close()
Doing so keeps the main connection sqlEngine "alive" between api calls and lets me use a pooled connection rather than having to connect anew.

Update: according to the pandas team, this will be fixed in Pandas 1.2.4 which as of the time of writing has not been released yet.
Adding this as an answer since Google led here but the accepted answer is not applicable.
Our surrounding code that uses Pandas does use a context manager:
with get_engine(dbname).connect() as conn:
df = pd.read_sql(stmt, conn, **kwargs)
return df
In my case, this error is being thrown from within pandas itself, not in the surrounding code that uses pandas:
/Users/tommycarpenter/Development/python-indexapi/.tox/py37/lib/python3.7/site-packages/pandas/io/sql.py:1430: SADeprecationWarning: The Engine.run_callable() method is deprecated and will be removed in a future release. Use the Engine.connect() context manager instead. (deprecated since: 1.4)
The snippet from pandas itself is:
def has_table(self, name, schema=None):
return self.connectable.run_callable(
self.connectable.dialect.has_table, name, schema or self.meta.schema
)
I raised an issue: https://github.com/pandas-dev/pandas/issues/40825

You could try...
connection_string = r'mssql+pyodbc:///?odbc_connect={}'.format(dbString).strip()
engine = sqlalchemy.create_engine(connection_string, echo=False, pool_recycle=3600)
with engine.connect() as connection:
df.to_sql(name=tablename, con=connection, if_exists='append', index=False)
This approach uses a ContextManager. The ContextManager of the engine returns a connection and automatically invokes connection.close() on it, see. Read more about ContextManager here. Another useful thing to know is, that a connection is a ContextManager as well and handles transactions for you. This means it begins and ends a transaction and in case of an error it automatically invokes a rollback.

SQLAlchemy Oracle - InvalidRequestError: could not retrieve isolation level

I am having problems accessing tables in an Oracle database over a SQLAlchemy connection. Specifically, I am using Kedro catalog.load('table_name') and getting the error message Table table_name not found. So I decided to test my connection using the method listed in this answer: How to verify SqlAlchemy engine object.
from sqlalchemy import create_engine
engine = create_engine('oracle+cx_oracle://USER:PASSWORD#HOST:PORT/?service_name=SERVICE_NAME')
engine.connect()
Error: InvalidRequestError: could not retrieve isolation level
I have tried explicitly adding an isolation level as explained in the documentation like this:
engine = create_engine('oracle+cx_oracle://USER:PASSWORD#HOST:PORT/?service_name=SERVICE_NAME', execution_options={'isolation_level': 'AUTOCOMMIT'})
and this:
engine.connect().execution_options(isolation_level='AUTOCOMMIT')
and this:
connection = engine.connect()
connection = connection.execution_options(
isolation_level="AUTOCOMMIT"
)
but I get the same error in all cases.

Upgrading from SqlAlchemy 1.3.21 to 1.3.22 solved the problem.

ipython-cypher in Python: cypher.run.Connection object parameter

I'm trying to use ipython-cypher to run Neo4j Cypher queries (and return a Pandas dataframe) in a Python program. I have no trouble forming a connection and running a query when using IPython Notebook, but when I try to run the same query outside of IPython, as per the documentation:
http://ipython-cypher.readthedocs.org/en/latest/introduction.html#usage-out-of-ipython
import cypher
results = cypher.run("MATCH (n)--(m) RETURN n.username, count(m) as neighbors",
"http://XXX.XXX.X.XXX:xxxx")
I get the following error:
neo4jrestclient.exceptions.StatusException: Code [401]: Unauthorized. No permission -- see authorization schemes.
Authorization Required
and
Format: (http|https)://username:password#hostname:port/db/name, or one of dict_keys([])
Now, I was just guessing that that was how I should enter a Connection object as the last parameter, because I couldn't find any additional documentation explaining how to connect to a remote host using Python, and in IPython, I am able to do:
%load_ext cypher
results = %cypher http://XXX.XXX.X.XXX:xxxx MATCH (n)--(m) RETURN n.username,
count(m) as neighbors
Any insight would be greatly appreciated. Thank you.

The documentation has a section for the API. When used outside of IPython and in need to connect to a different host, just using the parameter conn and passing a string should work.
import cypher
results = cypher.run("MATCH (n)--(m) RETURN n.username, count(m) as neighbors",
conn="http://XXX.XXX.X.XXX:xxxx")
But also consider that with the new authentication support in Neo4j 2.2, you need to set the new password before connecting from ipython-cypher. I will fix this as soon as I implement the forcing password change mechanism in neo4jrestclient, the library underneath.

Named Parameters in SQL Queries - cx_Oracle - ORA-01460: unimplemented or unreasonable conversion requested

I have encountered a problem after implementing the named parameters in RAW SQL Queries as per Python DB-API.
Earlier, my code was as follows (and this works fine, both on my DEV Server and my Client's test server)
cursor.execute("SELECT DISTINCT(TAG_STATUS) FROM TAG_HIST WHERE TAG_NBR = '%s' " %(TAG_NBR))
I changed it to the following
cursor.execute("SELECT DISTINCT(TAG_STATUS) FROM TAG_HIST WHERE TAG_NBR = :TAG_NBR " ,{'TAG_NBR':TAG_NBR})
This changed version (with named parameters) works fine on my Development Server
Windows XP Oracle XE
SQL*Plus: Release 11.2.0.2.0
cx_Oracle-5.1.2-11g.win32-py2.7
However, when deployed on my Client's Test Server, it does not.... execution of all queries fail.
Characteristics of my client's server are as follows
Windows Server 2003
Oracle Database 10g Enterprise Edition Release 10.2.0.1.0 - 64bi
cx_Oracle-5.1.2-10g.win32-py2.7
The error that I get is as follows
Traceback (most recent call last):
File "C:/Program Files/App_Logic/..\apps\views.py", line 400, in regularize_TAG
T_cursor.execute("SELECT DISTINCT(TAG_STATUS) FROM TAG_HIST WHERE TAG_NBR = :TAG_NBR " ,{'TAG_NBR':TAG_NBR})
DatabaseError: ORA-01460: unimplemented or unreasonable conversion requested
Appreciate if someone could help me through this issue.
This issue presents itself only when the cx_Oracle code is run inside the Web App (Hosted on Apache).
If i run the same code with named parameters from within the python command line then the query runs just fine.

Here is how this got solved.
I tried typecasting unicode to str and the results were positive.
This one worked for example
T_cursor.execute("SELECT DISTINCT(TAG_STATUS) FROM TAG_HIST WHERE TAG_NBR = :TAG_NBR", {'TAG_NBR': str(TAG_NBR)})
So in effect, unicode was getting mangled by getting encoded into the potentially non-unicode database character set.
To solve that, here is another option
import os
os.environ.update([('NLS_LANG', '.UTF8'),('ORA_NCHAR_LITERAL_REPLACE', 'TRUE'),])
import cx_Oracle
Above guarantees that we are really in UTF8 mode.
Second environment variable one is not an absolute necessity. And AFAIK there is no other way to set these variables (except before running app itself) due the fact that NLS_LANG is
read by OCI libs from the environment.

Sqlite / SQLAlchemy: how to enforce Foreign Keys?

The new version of SQLite has the ability to enforce Foreign Key constraints, but for the sake of backwards-compatibility, you have to turn it on for each database connection separately!
sqlite> PRAGMA foreign_keys = ON;
I am using SQLAlchemy -- how can I make sure this always gets turned on?
What I have tried is this:
engine = sqlalchemy.create_engine('sqlite:///:memory:', echo=True)
engine.execute('pragma foreign_keys=on')
...but it is not working!...What am I missing?
EDIT:
I think my real problem is that I have more than one version of SQLite installed, and Python is not using the latest one!
>>> import sqlite3
>>> print sqlite3.sqlite_version
3.3.4
But I just downloaded 3.6.23 and put the exe in my project directory!
How can I figure out which .exe it's using, and change it?

For recent versions (SQLAlchemy ~0.7) the SQLAlchemy homepage says:
PoolListener is deprecated. Please refer to PoolEvents.
Then the example by CarlS becomes:
engine = create_engine(database_url)
def _fk_pragma_on_connect(dbapi_con, con_record):
dbapi_con.execute('pragma foreign_keys=ON')
from sqlalchemy import event
event.listen(engine, 'connect', _fk_pragma_on_connect)

Building on the answers from conny and shadowmatter, here's code that will check if you are using SQLite3 before emitting the PRAGMA statement:
from sqlalchemy import event
from sqlalchemy.engine import Engine
from sqlite3 import Connection as SQLite3Connection
#event.listens_for(Engine, "connect")
def _set_sqlite_pragma(dbapi_connection, connection_record):
if isinstance(dbapi_connection, SQLite3Connection):
cursor = dbapi_connection.cursor()
cursor.execute("PRAGMA foreign_keys=ON;")
cursor.close()

I now have this working:
Download the latest sqlite and pysqlite2 builds as described above: make sure correct versions are being used at runtime by python.
import sqlite3
import pysqlite2
print sqlite3.sqlite_version # should be 3.6.23.1
print pysqlite2.__path__ # eg C:\\Python26\\lib\\site-packages\\pysqlite2
Next add a PoolListener:
from sqlalchemy.interfaces import PoolListener
class ForeignKeysListener(PoolListener):
def connect(self, dbapi_con, con_record):
db_cursor = dbapi_con.execute('pragma foreign_keys=ON')
engine = create_engine(database_url, listeners=[ForeignKeysListener()])
Then be careful how you test if foreign keys are working: I had some confusion here. When using sqlalchemy ORM to add() things my import code was implicitly handling the relation hookups so could never fail. Adding nullable=False to some ForeignKey() statements helped me here.
The way I test sqlalchemy sqlite foreign key support is enabled is to do a manual insert from a declarative ORM class:
# example
ins = Coverage.__table__.insert().values(id = 99,
description = 'Wrong',
area = 42.0,
wall_id = 99, # invalid fkey id
type_id = 99) # invalid fkey_id
session.execute(ins)
Here wall_id and type_id are both ForeignKey()'s and sqlite throws an exception correctly now if trying to hookup invalid fkeys. So it works! If you remove the listener then sqlalchemy will happily add invalid entries.
I believe the main problem may be multiple sqlite3.dll's (or .so) lying around.

As a simpler approach if your session creation is centralised behind a Python helper function (rather than exposing the SQLA engine directly), you can just issue session.execute('pragma foreign_keys=on') before returning the freshly created session.
You only need the pool listener approach if arbitrary parts of your application may create SQLA sessions against the database.

From the SQLite dialect page:
SQLite supports FOREIGN KEY syntax when emitting CREATE statements for tables, however by default these constraints have no effect on the operation of the table.
Constraint checking on SQLite has three prerequisites:
At least version 3.6.19 of SQLite must be in use
The SQLite libary must be compiled without the SQLITE_OMIT_FOREIGN_KEY or SQLITE_OMIT_TRIGGER symbols enabled.
The PRAGMA foreign_keys = ON statement must be emitted on all connections before use.
SQLAlchemy allows for the PRAGMA statement to be emitted automatically for new connections through the usage of events:
from sqlalchemy.engine import Engine
from sqlalchemy import event
#event.listens_for(Engine, "connect")
def set_sqlite_pragma(dbapi_connection, connection_record):
cursor = dbapi_connection.cursor()
cursor.execute("PRAGMA foreign_keys=ON")
cursor.close()

One-liner version of conny's answer:
from sqlalchemy import event
event.listen(engine, 'connect', lambda c, _: c.execute('pragma foreign_keys=on'))

I had the same problem before (scripts with foreign keys constraints were going through but actuall constraints were not enforced by the sqlite engine); got it solved by:
downloading, building and installing the latest version of sqlite from here: sqlite-sqlite-amalgamation; before this I had sqlite 3.6.16 on my ubuntu machine; which didn't support foreign keys yet; it should be 3.6.19 or higher to have them working.
installing the latest version of pysqlite from here: pysqlite-2.6.0
after that I started getting exceptions whenever foreign key constraint failed
hope this helps, regards

If you need to execute something for setup on every connection, use a PoolListener.

Enforce Foreign Key constraints for sqlite when using Flask + SQLAlchemy.
from flask import Flask
from flask_sqlalchemy import SQLAlchemy
def create_app(config: str=None):
app = Flask(__name__, instance_relative_config=True)
if config is None:
app.config.from_pyfile('dev.py')
else:
logger.debug('Using %s as configuration', config)
app.config.from_pyfile(config)
db.init_app(app)
# Ensure FOREIGN KEY for sqlite3
if 'sqlite' in app.config['SQLALCHEMY_DATABASE_URI']:
def _fk_pragma_on_connect(dbapi_con, con_record): # noqa
dbapi_con.execute('pragma foreign_keys=ON')
with app.app_context():
from sqlalchemy import event
event.listen(db.engine, 'connect', _fk_pragma_on_connect)
Source:
https://gist.github.com/asyd/a7aadcf07a66035ac15d284aef10d458