Ipython: IPython Notebook error: Error loading notebook
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 click on a certain .ipynb file, I get the following error:
An unknown error occurred while loading this notebook. This version can load notebook formats v4 or earlier. See the server log for details.
[E 00:19:41.468 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'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/notebook/base/handlers.py", line 458, in wrapper
result = yield gen.maybe_future(method(self, *args, **kwargs))
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/tornado/gen.py", line 1008, in run
value = future.result()
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/tornado/concurrent.py", line 232, in result
raise_exc_info(self._exc_info)
File "<string>", line 3, in raise_exc_info
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/tornado/gen.py", line 282, in wrapper
yielded = next(result)
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/notebook/services/contents/handlers.py", line 124, in get
path=path, type=type, format=format, content=content,
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/notebook/services/contents/filemanager.py", line 354, in get
model = self._notebook_model(path, content=content)
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/notebook/services/contents/filemanager.py", line 314, in _notebook_model
self.mark_trusted_cells(nb, path)
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/notebook/services/contents/manager.py", line 447, in mark_trusted_cells
trusted = self.notary.check_signature(nb)
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/nbformat/sign.py", line 220, in check_signature
if self.db is None:
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/traitlets/traitlets.py", line 488, in __get__
return self.get(obj, cls)
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/traitlets/traitlets.py", line 467, in get
value = self._validate(obj, dynamic_default())
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/nbformat/sign.py", line 127, in _db_default
self.init_db(db)
File "/opt/local/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/nbformat/sign.py", line 139, in init_db
)""")
sqlite3.DatabaseError: database disk image is malformed
How does one solve this issue?
evanbiederstedt
All 8 comments
The database of notebook signatures got corrupted. To move it out of the way:
cd $(jupyter --data-dir)
mv nbsignatures.db nbsignatures.db.bak # Or just rm it - there's probably no use keeping the corrupt file
We're working on catching the error and doing this automatically in jupyter/nbformat#32.
Once you've done this, all notebooks will be untrusted again. That means that you may have to re-execute them, or manually trust them from the file menu, before some rich output will be displayed.
takluyver
on 23 Jan 2016
My problem was solved with
rm ~/Library/Jupyter/nbsignatures.db
Thanks
evanbiederstedt
on 23 Jan 2016
remove ~/.ipython/profile_default/history_sqlite
This helps for me.
KnightOfTheMoonlight
on 7 Oct 2016
@KnightOfTheMoonlight I think the file is called "history.sqlite" instead of "history_sqlite".
WolfNiu
on 14 Mar 2018
Check the available space in your working environment!!!
I had this error when the server had no space.
cemdede
on 23 Feb 2019
@takluyver I had similar issue and your suggestions did work. Thanks!
sangam-r
on 2 Oct 2019
Check the available space in your working environment!!!
I had this error when the server had no space.
This was my problem too. Thanks for the tip! It worked!
einatlev-ldeo
on 4 May 2020
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.
Cheers!
surgithub
on 13 May 2020
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Most helpful comment
The database of notebook signatures got corrupted. To move it out of the way:
We're working on catching the error and doing this automatically in jupyter/nbformat#32.
Once you've done this, all notebooks will be untrusted again. That means that you may have to re-execute them, or manually trust them from the file menu, before some rich output will be displayed.