Data loss as notebook does not get saved

[asteppke]

With good experiences we are now using the jupyter-collaboration extension (version 2.0.0a4) for a few weeks.

Unfortunately, under some circumstances, and without apparent warnings severe data loss occurs. In this case one opens a notebook in jupyterlab, edits it and it gets automatically saved. This is indicated by the file modification time and the entries in the corresponding jupyterlab logfile:

[I 2023-11-30 17:33:34.155 YDocExtension] Saving the content from room json:notebook:c96e8a68-09a2-4bf8-8a63-92553b34a88f
[I 2023-11-30 17:33:34.157 YDocExtension] Saving file: Rocking comparisons 01.ipynb
[I 2023-11-30 17:33:34.159 ServerApp] Saving Rocking comparisons 01.ipynb

After a break of several hours the connection is re-established to the notebook server, and further editing takes place. Now jupyterlab does not save the changes anymore from here on, any further input does only exist in memory. There is no warning or error from the UI side and if the server is shutdown the notebook does not contain any of the new input.

The logfile indicates a Tornado error but I am not certain if this is related. In any case no save events are logged or take place:

[I 2023-12-01 09:32:00.716 YDocExtension] Content in room json:notebook:452e70df-615e-4442-8ac6-49684152ae7e loaded from the ystore MySQLiteYStore
[I 2023-12-01 09:32:00.916 YDocExtension] Creating FileLoader for: Rocking comparisons 01.ipynb
[I 2023-12-01 09:32:00.916 YDocExtension] Initializing room json:notebook:c96e8a68-09a2-4bf8-8a63-92553b34a88f
[I 2023-12-01 09:32:00.952 YDocExtension] Watching file: Rocking comparisons 01.ipynb
[I 2023-12-01 09:32:01.157 ServerApp] Connecting to kernel bcc63d67-bca9-4d7b-974b-93efd55c863c.
[I 2023-12-01 09:32:01.958 YDocExtension] Out-of-band changes in room json:notebook:c96e8a68-09a2-4bf8-8a63-92553b34a88f
[I 2023-12-01 09:32:01.985 YDocExtension] Content in room json:notebook:c96e8a68-09a2-4bf8-8a63-92553b34a88f loaded from the ystore MySQLiteYStore
[I 2023-12-01 09:32:02.522 ServerApp] Connecting to kernel c15b9221-d24e-4ef8-9fbf-041a4eaa93b7.
[I 2023-12-01 09:32:10.945 ServerApp] Connecting to kernel e72ddd99-54b6-4418-8252-72eaf71e944e.
Task exception was never retrieved
future: <Task finished name='Task-977034' coro=<WebSocketProtocol13.write_message.<locals>.wrapper() done, defined at /applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py:1085> exception=WebSocketClosedError()>
Traceback (most recent call last):
  File "/applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py", line 1087, in wrapper
    await fut
tornado.iostream.StreamClosedError: Stream is closed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py", line 1089, in wrapper
    raise WebSocketClosedError()
tornado.websocket.WebSocketClosedError
Task exception was never retrieved
future: <Task finished name='Task-977053' coro=<WebSocketProtocol13.write_message.<locals>.wrapper() done, defined at /applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py:1085> exception=WebSocketClosedError()>
Traceback (most recent call last):
  File "/applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py", line 1087, in wrapper
    await fut
tornado.iostream.StreamClosedError: Stream is closed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py", line 1089, in wrapper
    raise WebSocketClosedError()
tornado.websocket.WebSocketClosedError
Task exception was never retrieved
future: <Task finished name='Task-977054' coro=<WebSocketProtocol13.write_message.<locals>.wrapper() done, defined at /applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py:1085> exception=WebSocketClosedError()>
Traceback (most recent call last):
  File "/applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py", line 1087, in wrapper
    await fut
tornado.iostream.StreamClosedError: Stream is closed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py", line 1089, in wrapper
    raise WebSocketClosedError()
tornado.websocket.WebSocketClosedError
Task exception was never retrieved
future: <Task finished name='Task-977097' coro=<WebSocketProtocol13.write_message.<locals>.wrapper() done, defined at /applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py:1085> exception=WebSocketClosedError()>
Traceback (most recent call last):
  File "/applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py", line 1087, in wrapper
    await fut
tornado.iostream.StreamClosedError: Stream is closed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py", line 1089, in wrapper
    raise WebSocketClosedError()
tornado.websocket.WebSocketClosedError
Task exception was never retrieved
future: <Task finished name='Task-978193' coro=<WebSocketProtocol13.write_message.<locals>.wrapper() done, defined at /applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py:1085> exception=WebSocketClosedError()>
Traceback (most recent call last):
  File "/applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py", line 1087, in wrapper
    await fut
tornado.iostream.StreamClosedError: Stream is closed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/applications/conda/envs/analysis_edge/lib/python3.11/site-packages/tornado/websocket.py", line 1089, in wrapper
    raise WebSocketClosedError()
tornado.websocket.WebSocketClosedError
[I 2023-12-01 09:32:22.712 YDocExtension] Cleaning room: json:notebook:080a189a-46f5-4518-8a69-bcb92444cf55
[I 2023-12-01 09:32:29.311 ServerApp] Connecting to kernel a16f85d0-dc99-4bcc-af0f-b57b40de73d6.
[I 2023-12-01 09:32:29.372 ServerApp] New client connecting to room: json:notebook:080a189a-46f5-4518-8a69-bcb92444cf55
[I 2023-12-01 09:32:49.042 ServerApp] Connecting to kernel dd32046e-bb57-4acc-8bdb-01c7b8418eba.
[I 2023-12-01 09:33:26.689 YDocExtension] Cleaning room: json:notebook:0b8b95e2-ed0f-41e1-94c4-9842a8c95189
[I 2023-12-01 09:33:26.690 YDocExtension] Cleaning room: json:notebook:e2e164f6-d961-496e-ad72-d7fff497a673
[I 2023-12-01 09:33:26.690 YDocExtension] Cleaning room: json:notebook:3e415acd-0ecc-4cd3-899f-c7cd63b20df6
[I 2023-12-01 09:33:26.690 YDocExtension] Cleaning room: json:notebook:452e70df-615e-4442-8ac6-49684152ae7e
[I 2023-12-01 09:33:26.690 YDocExtension] Cleaning room: JupyterLab:globalAwareness
[I 2023-12-01 09:33:26.690 YDocExtension] Cleaning room: json:notebook:f68c7ace-eb60-4b2d-95d0-2b2aa6d4b202
[I 2023-12-01 09:33:26.690 YDocExtension] Cleaning room: json:notebook:8a1347d4-2c6f-4d29-af3d-3f9441b452db
[I 2023-12-01 09:33:26.690 YDocExtension] Cleaning room: json:notebook:c96e8a68-09a2-4bf8-8a63-92553b34a88f
[I 2023-12-01 09:33:26.690 YDocExtension] Cleaning room: json:notebook:080a189a-46f5-4518-8a69-bcb92444cf55
[I 2023-12-01 09:33:27.688 ServerApp] New client connecting to room: json:notebook:0b8b95e2-ed0f-41e1-94c4-9842a8c95189
[I 2023-12-01 09:33:27.717 ServerApp] New client connecting to room: json:notebook:e2e164f6-d961-496e-ad72-d7fff497a673
[I 2023-12-01 09:33:27.785 ServerApp] New client connecting to room: json:notebook:3e415acd-0ecc-4cd3-899f-c7cd63b20df6
[I 2023-12-01 09:33:27.811 ServerApp] New client connecting to room: json:notebook:452e70df-615e-4442-8ac6-49684152ae7e
[I 2023-12-01 09:33:27.852 ServerApp] New client connecting to room: json:notebook:f68c7ace-eb60-4b2d-95d0-2b2aa6d4b202
[I 2023-12-01 09:33:27.881 ServerApp] New client connecting to room: JupyterLab:globalAwareness
[I 2023-12-01 09:33:27.912 ServerApp] New client connecting to room: json:notebook:8a1347d4-2c6f-4d29-af3d-3f9441b452db
[I 2023-12-01 09:33:27.985 ServerApp] New client connecting to room: json:notebook:c96e8a68-09a2-4bf8-8a63-92553b34a88f
[I 2023-12-01 09:33:28.064 ServerApp] New client connecting to room: json:notebook:080a189a-46f5-4518-8a69-bcb92444cf55
[I 2023-12-01 09:47:26.712 YDocExtension] Cleaning room: JupyterLab:globalAwareness
[I 2023-12-01 09:47:26.714 YDocExtension] Cleaning room: json:notebook:0b8b95e2-ed0f-41e1-94c4-9842a8c95189
[I 2023-12-01 09:47:26.714 YDocExtension] Cleaning room: json:notebook:e2e164f6-d961-496e-ad72-d7fff497a673
[I 2023-12-01 09:47:26.714 YDocExtension] Cleaning room: json:notebook:f68c7ace-eb60-4b2d-95d0-2b2aa6d4b202
[I 2023-12-01 09:47:26.714 YDocExtension] Cleaning room: json:notebook:080a189a-46f5-4518-8a69-bcb92444cf55
[I 2023-12-01 09:47:26.714 YDocExtension] Cleaning room: json:notebook:8a1347d4-2c6f-4d29-af3d-3f9441b452db
[I 2023-12-01 09:47:26.714 YDocExtension] Cleaning room: json:notebook:452e70df-615e-4442-8ac6-49684152ae7e
[I 2023-12-01 09:47:26.714 YDocExtension] Cleaning room: json:notebook:c96e8a68-09a2-4bf8-8a63-92553b34a88f
[I 2023-12-01 09:47:26.714 YDocExtension] Cleaning room: json:notebook:3e415acd-0ecc-4cd3-899f-c7cd63b20df6
[...]

As far as I have observed everything starts out correctly and I do not know who to trigger the behavior explicitly. A disconnect and re-connect to the server after some time does seem to be correlated with it though.

At least a temporary workaround seems to be to explicitly use Save Notebook As... to save the notebook under a new file name, this re-starts the autosave functionality.

How can this be debugged further?

Context

• Linux (RHEL8)
• Chrome
• JupyterLab version 4.0.9
• ystore-database is set to be written to /tmp because the notebook directory is on NFS and this caused troubles in the past

Conda environment

jupyter-collaboration     2.0.0a4                  pypi_0    pypi
jupyter-lsp               2.2.1              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.0              pyhd8ed1ab_0    conda-forge
jupyter_core              5.5.0           py311h38be061_0    conda-forge
jupyter_events            0.9.0              pyhd8ed1ab_0    conda-forge
jupyter_server            2.11.1             pyhd8ed1ab_0    conda-forge
jupyter_server_fileid     0.9.0              pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.4.4              pyhd8ed1ab_1    conda-forge
jupyter_ydoc              1.1.1              pyhd8ed1ab_0    conda-forge
jupyterlab                4.0.9              pyhd8ed1ab_0    conda-forge