[IPython-dev] rubbish null bytes at the end of ipynb file

Gregor Thalhammer gregor.thalhammer at gmail.com
Tue Jan 21 09:15:05 EST 2014


Am 20.01.2014 um 21:37 schrieb Matthias BUSSONNIER <bussonniermatthias at gmail.com>:

> Hi, 
> 
> Le 20 janv. 2014 à 17:59, Gregor Thalhammer a écrit :
> 
>> Dear developers,
>> 
>> sometimes it happens to me that at the very end of my notebook files null bytes (0x00) are appended (I observed between 2 and several hundreds) . The notebook files fail to load ('bad request') the next time. Also nbconvert fails:
>> ...
>>  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/IPython/nbformat/reader.py", line 44, in parse_json
>>    raise NotJSONError(("Notebook does not appear to be JSON: %r" % s)[:77] + "...")
>> NotJSONError: Notebook does not appear to be JSON: u'{\n "metadata": {\n  "name": ""\n },\n...
>> 
> 
> This is **really** weird. 
> 
> Could you open an issue on github ? 
> 
> Notebook are written in 
> 	IPython/html/services/notebooks/filenbmanager.py ~L243. 
> 
> You can try to have a check with a retry to get warn 'on write' when this happen to narrow the issue. 
> Problem is that we do use std lib to write JSON, so this should never happened.

Dear Matthias,

thanks for the hint. I opened an issue #4841.
I had a look at the ipython source and can confirm that this should not happen, since saving a notebook essentially only uses the standard json module + encode().
To debug this: How to start a notebook server from a ipython shell (ideally from the source directory) so that I can use pdb for interactive debugging?

Gregor

> -- 
> M
> 
>> Luckily such an file can be resurrected by deleting the null bytes.
>> This only happens sometimes, but with a file containing a lot of inline pylab figures (png) and heavy recreating of figures this happens quite often.
>> 
>> What could I do to localize the root of this problem?
>> 
>> I am using recent ipython from git, with python 2.7 on osx 10.9.
>> 
>> thanks for your help
>> Gregor
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