Jupyter won't open or trust notebooks that worked previously

I’m having a problem with both jupyter notebook and just plain jupyter trust, which both seem to have the same underlying issue. Notebooks that were working previously are no longer working. I had updated everything with conda recently, but I tried just totally reinstalling conda (python 3.5) and get the same result.

I’ve found this ipython issue, which is slightly different (different error message), but in any case the solution to that doesn’t solve this. In fact, I tried completely removing my ipython and jupyter profile directories, and nothing changed. I also found this traitlets issue that at least reports the same exception, but that was fixed a few months ago, so it shouldn’t be an issue, right??? Finally, there’s also this issue, but all my directories have the correct permissions and ownership.

If I try to load the notebooks, I see a pop-up saying

Error loading notebook

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

and the log says

[E 13:44:38.278 NotebookApp] Unhandled error in API request
    Traceback (most recent call last):
      File "/home/myuser/anaconda/lib/python3.5/site-packages/traitlets/traitlets.py", line 501, 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 "/home/myuser/anaconda/lib/python3.5/site-packages/notebook/base/handlers.py", line 457, in wrapper
        result = yield gen.maybe_future(method(self, *args, **kwargs))
      File "/home/myuser/anaconda/lib/python3.5/site-packages/tornado/gen.py", line 1008, in run
        value = future.result()
      File "/home/myuser/anaconda/lib/python3.5/site-packages/tornado/concurrent.py", line 232, in result
        raise_exc_info(self._exc_info)
      File "<string>", line 3, in raise_exc_info
      File "/home/myuser/anaconda/lib/python3.5/site-packages/tornado/gen.py", line 282, in wrapper
        yielded = next(result)
      File "/home/myuser/anaconda/lib/python3.5/site-packages/notebook/services/contents/handlers.py", line 124, in get
        path=path, type=type, format=format, content=content,
      File "/home/myuser/anaconda/lib/python3.5/site-packages/notebook/services/contents/filemanager.py", line 358, in get
        model = self._notebook_model(path, content=content)
      File "/home/myuser/anaconda/lib/python3.5/site-packages/notebook/services/contents/filemanager.py", line 318, in _notebook_model
        self.mark_trusted_cells(nb, path)
      File "/home/myuser/anaconda/lib/python3.5/site-packages/notebook/services/contents/manager.py", line 447, in mark_trusted_cells
        trusted = self.notary.check_signature(nb)
      File "/home/myuser/anaconda/lib/python3.5/site-packages/nbformat/sign.py", line 220, in check_signature
        if self.db is None:
      File "/home/myuser/anaconda/lib/python3.5/site-packages/traitlets/traitlets.py", line 529, in __get__
        return self.get(obj, cls)
      File "/home/myuser/anaconda/lib/python3.5/site-packages/traitlets/traitlets.py", line 508, in get
        value = self._validate(obj, dynamic_default())
      File "/home/myuser/anaconda/lib/python3.5/site-packages/nbformat/sign.py", line 127, in _db_default
        self.init_db(db)
      File "/home/myuser/anaconda/lib/python3.5/site-packages/nbformat/sign.py", line 139, in init_db
        )""")
    sqlite3.OperationalError: disk I/O error
[E 13:44:38.289 NotebookApp] {
      "X-Requested-With": "XMLHttpRequest",
      "Referer": "https://localhost:6003/notebooks/MyNotebook.ipynb",
      "Dnt": "1",
      "Connection": "keep-alive",
      "Accept-Encoding": "gzip, deflate, sdch, br",
      "Cookie": "username-localhost-6003=2|1:0|10:1466185422|23:username-localhost-6003|48:NDI5NTg3ZjItMzE4ZS00N2ZjLWEyNjItNjI2OGZlYWNjMWVh|c528ffaedf4e4f72cd802cc1abd197a38d1743cedacd923483208441a870664d",
      "Accept-Language": "en-US,en;q=0.8",
      "Host": "localhost:6003",
      "Accept": "application/json, text/javascript, */*; q=0.01",
      "User-Agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_11_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/51.0.2704.84 Safari/537.36"
    }
[E 13:44:38.289 NotebookApp] 500 GET /api/contents/MyNotebook.ipynb?type=notebook&_=1466185495467 (::1) 346.33ms referer=https://localhost:6003/notebooks/MyNotebook.ipynb

If I try to trust the notebooks from the command line, I see something like this:

> jupyter trust MyNotebook.ipynb
Traceback (most recent call last):
  File "/home/myuser/anaconda/lib/python3.5/site-packages/traitlets/traitlets.py", line 501, 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 "/home/myuser/anaconda/bin/jupyter-trust", line 8, in <module>
    main()
  File "/home/myuser/anaconda/bin/jupyter-trust", line 5, in main
    TrustNotebookApp.launch_instance()
  File "/home/myuser/anaconda/lib/python3.5/site-packages/jupyter_core/application.py", line 267, in launch_instance
    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
  File "/home/myuser/anaconda/lib/python3.5/site-packages/traitlets/config/application.py", line 596, in launch_instance
    app.start()
  File "/home/myuser/anaconda/lib/python3.5/site-packages/nbformat/sign.py", line 416, in start
    self.sign_notebook(notebook_path)
  File "/home/myuser/anaconda/lib/python3.5/site-packages/nbformat/sign.py", line 393, in sign_notebook
    if self.notary.check_signature(nb):
  File "/home/myuser/anaconda/lib/python3.5/site-packages/nbformat/sign.py", line 220, in check_signature
    if self.db is None:
  File "/home/myuser/anaconda/lib/python3.5/site-packages/traitlets/traitlets.py", line 529, in __get__
    return self.get(obj, cls)
  File "/home/myuser/anaconda/lib/python3.5/site-packages/traitlets/traitlets.py", line 508, in get
    value = self._validate(obj, dynamic_default())
  File "/home/myuser/anaconda/lib/python3.5/site-packages/nbformat/sign.py", line 127, in _db_default
    self.init_db(db)
  File "/home/myuser/anaconda/lib/python3.5/site-packages/nbformat/sign.py", line 139, in init_db
    )""")
sqlite3.OperationalError: disk I/O error

Any workaround or fix for this?

[takluyver]

The file it’s trying to open is $(jupyter --data-dir)/nbsignatures.db - try moving that aside and then try again.

Is it possible that your home directory is on an NFS mount? That seems to be the most common cause of issues with sqlite databases. We try to catch these errors and automatically recreate the database file, but maybe we’re missing this one.

[abhimanyu3]

I was getting the error because my disk was full. I moved some of the stuff and its fine now.