IPython Notebook error: Error loading notebook

Question

Within the past few minutes, I have not been able to access any of the .ipynb files previously created with Python3.4. I go to the subdirectory with these files, enter

ipython3 notebook

When I open a "New" notebook, I get the following error:

Unexpected error while saving file: Untitled1.ipynb database disk image is malformed

I cannot open old notebooks either. I get the error:

An unknown error occurred while loading this notebook. This version can load notebook formats v4 or earlier. See the server log for details.

and within the Terminal, it states

kernels (twice to skip confirmation).
[E 00:30:22.352 NotebookApp] Unhandled error in API request
    Traceback (most recent call last):
      File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/traitlets/traitlets.py", line 460, in get
        value = obj._trait_values[self.name]
    KeyError: 'db'

How can I fix this?

Possibly related to this bug: github.com/ipython/ipython/issues/8294 — anjsimmo
– anjsimmo, Commented Jan 23, 2016 at 5:57

Steven · Accepted Answer · 2018-01-13 18:12:32Z

16

This won't be the issue for everyone, but I got the below error message because the disk was actually full.

An unknown error occurred while loading this notebook. This version can load notebook formats v4 or earlier. See the server log for details.

answered Jan 13, 2018 at 18:12

Steven

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2 Comments

Minstein Over a year ago

me too, my home directory is full in the Linux server

ngDev Over a year ago

Yes, you are right. I had the same issue, my C drive was full. Thank you!

Mike Müller · Accepted Answer · 2016-01-23 05:52:43Z

11

Search for nbsignatures.db. It should be either here:

~/.ipython/profile_default/security/nbsignatures.db

or here:

 ~/Library/Jupyter/nbsignatures.db

The ~ stands for you home directory.

Move this file this to a temporary directory.

Restart your IPython Notebook server.

answered Jan 23, 2016 at 5:52

Mike Müller

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1 Comment

ShanZhengYang Over a year ago

Removing the nbsignatures.db file solved the problem, i.e. rm ~/Library/Jupyter/nbsignatures.db

Moonlight Knight · Accepted Answer · 2016-10-07 17:03:18Z

9

remove ~/.ipython/profile_default/history.sqlite

this helps for me.

answered Oct 7, 2016 at 17:03

Moonlight Knight

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2 Comments

Geoff Over a year ago

This did the trick for me, thanks! I was getting a slightly different error than OP, one which did not include a specific version number: "An unknown error occurred while loading this notebook. This version can load notebook formats or earlier. See the server log for details."

tgrrr Over a year ago

This worked for me with Jupyter for vs code extension. It was generating multiple versions of history.sqlite file. extension: v2022.2.1030672458 Mac: OS 10.15.7 Python: 3.9.7. Error message: "The history saving thread hit an unexpected error (OperationalError('attempt to write a readonly database')).History will not be written to the database."

Raketenolli · Accepted Answer · 2017-01-05 13:56:25Z

5

Since I couldn't find any of the files mentioned in the other answers, I looked for another solution and found this one to work for me:

I solved this problem by changing the ownership of the ~/.local/share/jupyter directory from root to user.

from https://github.com/ipython/ipython/issues/8997

answered Jan 5, 2017 at 13:56

Raketenolli

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jadelord Over a year ago

I had a similar issue. But because the value of the environment variable XDG_DATA_HOME was malformed as /.local/share.

hongkail · Accepted Answer · 2021-04-22 06:09:38Z

4

In my case, my nbsignatures.db was here, after removing it it can operate normally.

~/.local/share/jupyter/nbsignatures.db

Remember to restart your jupyter notebook server. I restarted several times for this to work.

answered Apr 22, 2021 at 6:09

hongkail

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Comments

R Tsch · Accepted Answer · 2020-02-06 16:47:40Z

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Non of the other answers helped in my case.

In the end I simply copied my notebook and renamed the copy. The copy didn't have the error.

answered Feb 6, 2020 at 16:47

R Tsch

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Suresh Kumar · Accepted Answer · 2020-05-13 14:55:19Z

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First run the following in the terminal:

sudo jupyter notebook --allow-root

Then some URL will appear in the terminal, something like:

http://localhost:8888/?token=f2704ecba4c88716337f33e79e13335380e25382603afb80

Finally, copy and paste this URL in a new tab in your browser. Then the jupyter notebook will open in a new tab.

answered May 13, 2020 at 14:55

Suresh Kumar

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