Possible setup problem
xiaochuanyu opened this issue · 3 comments
Not sure if this is a setup problem but I followed the instructions from README and ran into the following error logged in jupyte whilst opening any notebook:
[IPKernelApp] WARNING | Unknown error in handling startup files:
Consequently, I get the following when trying to use %%sql:
ERROR:root:Cell magic `%%sql` not found.
Using jupyter notebook --debug did not produce additional info.
I'm using OSX with brew installed python.
~ jupyter --version
4.2.1
~ ipython2 --version
5.2.2
~ ipython3 --version
5.1.0
~ python3 --version
Python 3.5.2
~ python2 --version
Python 2.7.12
I have no other plugins/extensions installed.
What version of python/jupyer/ipython works with this extension?
Hey! Thanks for the notice. I ran into that problem when I installed it on a Mac recently. Do you have pandas and SQLAlchemy installed?
Here's a way to get a clearer error message:
• Find this file /usr/local/lib/python2.7/site-packages/IPython/core/shellapp.py (this is the directory mine is in, but just find the appropriate shellapp.py file.
• add import traceback to the top of the file
• Find this line: self.log.warning("Unknown error in handling startup files:")
• add these lines under the previous line:
self.log.warning(e)
self.log.warning(traceback.format_exc())
This will produce clear error messages and allow you to debug more effectively.
If you need any further assistance, please drop another message here and I'll get back to you. It's unfortunate that IPython doesn't produce clearer error messages, but the above lines should get you some clarity.
The reason for the cryptic WARNING | Unknown error in handling startup files: error is because when you load a startup file in IPython, the file /usr/local/lib/python2.7/site-packages/IPython/core/shellapp.py is supposed to log the errors that any startup files produces, but it doesn't.
So I actually modified shellapp.py as follows:
try:
for fname in sorted(startup_files):
self._exec_file(fname)
except:
self.log.warning("Unknown error in handling startup files:")
raise # added this
The stacktrace I got is:
[IPKernelApp] WARNING | Unknown error in handling startup files:
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 174, in _run_module_as_main
"__main__", fname, loader, pkg_name)
File "/usr/local/Cellar/python/2.7.12_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/usr/local/lib/python2.7/site-packages/ipykernel/__main__.py", line 3, in <module>
app.launch_new_instance()
File "/usr/local/lib/python2.7/site-packages/traitlets/config/application.py", line 657, in launch_instance
app.initialize(argv)
File "<decorator-gen-120>", line 2, in initialize
File "/usr/local/lib/python2.7/site-packages/traitlets/config/application.py", line 87, in catch_config_error
return method(app, *args, **kwargs)
File "/usr/local/lib/python2.7/site-packages/ipykernel/kernelapp.py", line 461, in initialize
self.init_code()
File "/usr/local/lib/python2.7/site-packages/IPython/core/shellapp.py", line 263, in init_code
self._run_startup_files()
File "/usr/local/lib/python2.7/site-packages/IPython/core/shellapp.py", line 355, in _run_startup_files
self._exec_file(fname)
File "/usr/local/lib/python2.7/site-packages/IPython/core/shellapp.py", line 328, in _exec_file
raise_exceptions=True)
File "/usr/local/lib/python2.7/site-packages/IPython/core/interactiveshell.py", line 2481, in safe_execfile
self.compile if kw['shell_futures'] else None)
File "/usr/local/lib/python2.7/site-packages/IPython/utils/py3compat.py", line 289, in execfile
builtin_mod.execfile(filename, *where)
File "/Users/xyu/.ipython/profile_default/startup/sqlcell_app.py", line 3, in <module>
from SQLCell.sqlcell import sql, __KERNEL_VARS__
File "/Users/xyu/.ipython/profile_default/startup/SQLCell/sqlcell.py", line 27, in <module>
from .tasks.params import __SQLCell_GLOBAL_VARS__, unique_db_id, engine, application_name
File "/Users/xyu/.ipython/profile_default/startup/SQLCell/tasks/params.py", line 14, in <module>
engine = create_engine(driver+'://'+username+':'+password+'@'+host+':'+port+'/'+default_db+application_name)
TypeError: cannot concatenate 'str' and 'NoneType' objects
It seems one of those variables must be None but was not expected.
I then added a print as follows:
print([driver, username, password, host, port, default_db, application_name]) # added this
create_engine(driver+'://'+username+':'+password+'@'+host+':'+port+'/'+default_db+application_name)
Running ipython2 produces:
['postgresql', None, None, 'localhost', '5432', 'phUsers', '?application_name=jupyter92dc4d16-3827-4da2-b569-08c47c484ec4']
... same stacktrace as above printed ...
So username and password are None.
Tracing their origin to SQLCell/engines/engine_config.py, I see the following:
username = os.getenv('DB_USERNAME')
password = os.getenv('DB_PASSWORD')
So I guess I was supposed to define those environment variables?
Yes, you can define those variables in your .bash_profile or you can utilize the ENGINE param as noted here on the readme page.
Note that you can also use the declare-engines flag to store your connection string info.
Let me know if that helps.