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Kubeflow-JupyterLab - Jupyterlab-git is unable to recognize git folder #1314

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Mayurji opened this issue Feb 8, 2024 · 8 comments
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@Mayurji
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Mayurji commented Feb 8, 2024

We have setup a kubeflow environment, where we are running our JupyterLab as part of docker-image(kubeflownotebookswg/jupyter-scipy:v1.7.0). We are able to clone the repository in the JupyterLab, but when we click the git icon on JupyterLab for the cloned repo, we are unable to see branch or changes. It still shows the below message

You are not currently in a Git repository. To use Git, navigate to a local repository, initialize a repository here, or clone an existing repository.

Also looked at the Issue: #179

Modified the --notebook-dir, it still didn't work.

FYI

while cloning the repo in jupyterlab, we see a log on notebook server as follows

E 2024-02-07 12:28:40.798 ServerApp] 500 POST /notebook/project-name/test-git-nb/git/clone?1707308919343
[E 2024-02-08 05:10:26.071 ServerApp] 500 POST /notebook/project-name/test-git-nb/git/show_top_level?1707369025823

Next, we also checked if jupyterlab_git is enabled

` Validating jupyterlab_git...

jupyterlab_git 0.30.1 OK

  • Extension successfully enabled.`
    @jupyterlab/git v0.30.1 enabled OK (python, jupyterlab-git)

How to move forward with this issue?

@Mayurji Mayurji added the bug label Feb 8, 2024
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@Mayurji Mayurji changed the title Kubeflow-JupyterLab - Git folder is not recognized. Kubeflow-JupyterLab - Jupyterlab-git is unable to recognize git folder Feb 9, 2024
@Mayurji
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Mayurji commented Feb 13, 2024

Hi @fcollonval, Can you please look into this issue?

@fcollonval
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Hey @Mayurji

could you run jupyterlab in debug mode jupyter lab --debug and report here the server logs when the errors occur?

Could you also try a more recent version 0.30 is quite old?

@Mayurji
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Mayurji commented Feb 14, 2024

jupyter lab --debug

[D 2024-02-14 14:06:00.807 ServerApp] Searching ['/home/jovyan/.jupyter', '/home/jovyan/.local/etc/jupyter', '/opt/conda/etc/jupyter', '/usr/local/etc/jupyter', '/etc/jupyter'] for config files
[D 2024-02-14 14:06:00.807 ServerApp] Looking for jupyter_config in /etc/jupyter
[D 2024-02-14 14:06:00.808 ServerApp] Looking for jupyter_config in /usr/local/etc/jupyter
[D 2024-02-14 14:06:00.808 ServerApp] Looking for jupyter_config in /opt/conda/etc/jupyter
[D 2024-02-14 14:06:00.808 ServerApp] Looking for jupyter_config in /home/jovyan/.local/etc/jupyter
[D 2024-02-14 14:06:00.808 ServerApp] Looking for jupyter_config in /home/jovyan/.jupyter
[D 2024-02-14 14:06:00.808 ServerApp] Looking for jupyter_server_config in /etc/jupyter
[D 2024-02-14 14:06:00.808 ServerApp] Looking for jupyter_server_config in /usr/local/etc/jupyter
[D 2024-02-14 14:06:00.808 ServerApp] Looking for jupyter_server_config in /opt/conda/etc/jupyter
[D 2024-02-14 14:06:00.809 ServerApp] Looking for jupyter_server_config in /home/jovyan/.local/etc/jupyter
[D 2024-02-14 14:06:00.809 ServerApp] Looking for jupyter_server_config in /home/jovyan/.jupyter
[D 2024-02-14 14:06:00.810 ServerApp] Paths used for configuration of jupyter_server_config: 
        /etc/jupyter/jupyter_server_config.json
[D 2024-02-14 14:06:00.810 ServerApp] Paths used for configuration of jupyter_server_config: 
        /usr/local/etc/jupyter/jupyter_server_config.json
[D 2024-02-14 14:06:00.810 ServerApp] Paths used for configuration of jupyter_server_config: 
        /opt/conda/etc/jupyter/jupyter_server_config.d/jupyter_server_fileid.json
        /opt/conda/etc/jupyter/jupyter_server_config.d/jupyter_server_mathjax.json
        /opt/conda/etc/jupyter/jupyter_server_config.d/jupyter_server_terminals.json
        /opt/conda/etc/jupyter/jupyter_server_config.d/jupyter_server_ydoc.json
        /opt/conda/etc/jupyter/jupyter_server_config.d/jupyterlab.json
        /opt/conda/etc/jupyter/jupyter_server_config.d/jupyterlab_git.json
        /opt/conda/etc/jupyter/jupyter_server_config.d/nbclassic.json
        /opt/conda/etc/jupyter/jupyter_server_config.d/nbdime.json
        /opt/conda/etc/jupyter/jupyter_server_config.d/notebook_shim.json
        /opt/conda/etc/jupyter/jupyter_server_config.json
[D 2024-02-14 14:06:00.811 ServerApp] Paths used for configuration of jupyter_server_config: 
        /home/jovyan/.local/etc/jupyter/jupyter_server_config.json
[D 2024-02-14 14:06:00.811 ServerApp] Paths used for configuration of jupyter_server_config: 
        /home/jovyan/.jupyter/jupyter_server_config.json
[D 2024-02-14 14:06:00.814 ServerApp] Extension package jupyterlab took 0.0000s to import
[D 2024-02-14 14:06:00.816 ServerApp] Extension package jupyter_server_fileid took 0.0020s to import
[D 2024-02-14 14:06:00.817 ServerApp] Extension package jupyter_server_mathjax took 0.0007s to import
[D 2024-02-14 14:06:00.820 ServerApp] Extension package jupyter_server_terminals took 0.0030s to import
[D 2024-02-14 14:06:00.841 ServerApp] Extension package jupyter_server_ydoc took 0.0207s to import
[D 2024-02-14 14:06:00.855 ServerApp] Extension package jupyterlab_git took 0.0134s to import
[D 2024-02-14 14:06:00.855 ServerApp] Extension package nbclassic took 0.0000s to import
[W 2024-02-14 14:06:00.856 ServerApp] A `_jupyter_server_extension_points` function was not found in nbclassic. Instead, a `_jupyter_server_extension_paths` function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.
[D 2024-02-14 14:06:00.856 ServerApp] Extension package nbdime took 0.0000s to import
[D 2024-02-14 14:06:00.857 ServerApp] Extension package notebook_shim took 0.0000s to import
[W 2024-02-14 14:06:00.857 ServerApp] A `_jupyter_server_extension_points` function was not found in notebook_shim. Instead, a `_jupyter_server_extension_paths` function was found and will be used for now. This function name will be deprecated in future releases of Jupyter Server.
[D 2024-02-14 14:06:00.860 FileIdExtension] Config changed: {'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue {'update': {'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}}>}, 'ExtensionApp': {'log_level': 'DEBUG'}}
[D 2024-02-14 14:06:00.860 ServerApp] Config changed: {'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}>}, 'ExtensionApp': {'log_level': 'DEBUG'}}
[I 2024-02-14 14:06:00.861 ServerApp] jupyter_server_fileid | extension was successfully linked.
[D 2024-02-14 14:06:00.863 MathJaxExtension] Config changed: {'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}>}, 'ExtensionApp': {'log_level': 'DEBUG'}}
[D 2024-02-14 14:06:00.864 ServerApp] Config changed: {'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}>}, 'ExtensionApp': {'log_level': 'DEBUG'}}
[I 2024-02-14 14:06:00.864 ServerApp] jupyter_server_mathjax | extension was successfully linked.
[D 2024-02-14 14:06:00.866 TerminalsExtensionApp] Config changed: {'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}>}, 'ExtensionApp': {'log_level': 'DEBUG'}}
[D 2024-02-14 14:06:00.867 ServerApp] Config changed: {'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}>}, 'ExtensionApp': {'log_level': 'DEBUG'}}
[I 2024-02-14 14:06:00.867 ServerApp] jupyter_server_terminals | extension was successfully linked.
[D 2024-02-14 14:06:00.869 YDocExtension] Config changed: {'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}>}, 'ExtensionApp': {'log_level': 'DEBUG'}}
[D 2024-02-14 14:06:00.870 ServerApp] Config changed: {'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}>}, 'ExtensionApp': {'log_level': 'DEBUG'}}
[I 2024-02-14 14:06:00.870 ServerApp] jupyter_server_ydoc | extension was successfully linked.
[D 2024-02-14 14:06:00.873 LabApp] Config changed: {'NotebookApp': {}, 'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}>}, 'ExtensionApp': {'log_level': 'DEBUG'}}
[I 2024-02-14 14:06:00.874 ServerApp] jupyterlab | extension was successfully linked.
[I 2024-02-14 14:06:00.874 ServerApp] jupyterlab_git | extension was successfully linked.
[D 2024-02-14 14:06:00.876 NotebookApp] Config changed: {'NotebookApp': {}, 'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}>}, 'ExtensionApp': {'log_level': 'DEBUG'}}
[I 2024-02-14 14:06:00.877 ServerApp] nbclassic | extension was successfully linked.
[I 2024-02-14 14:06:00.877 ServerApp] nbdime | extension was successfully linked.
[D 2024-02-14 14:06:01.006 ServerApp] Paths used for configuration of jupyter_notebook_config: 
        /home/jovyan/.jupyter/jupyter_notebook_config.json
[D 2024-02-14 14:06:01.006 ServerApp] Paths used for configuration of jupyter_notebook_config: 
        /etc/jupyter/jupyter_notebook_config.json
[D 2024-02-14 14:06:01.006 ServerApp] Paths used for configuration of jupyter_notebook_config: 
        /usr/local/etc/jupyter/jupyter_notebook_config.json
[D 2024-02-14 14:06:01.006 ServerApp] Paths used for configuration of jupyter_notebook_config: 
        /opt/conda/etc/jupyter/jupyter_notebook_config.d/jupyter_server_ydoc.json
        /opt/conda/etc/jupyter/jupyter_notebook_config.d/jupyterlab.json
        /opt/conda/etc/jupyter/jupyter_notebook_config.d/jupyterlab_git.json
        /opt/conda/etc/jupyter/jupyter_notebook_config.d/nbdime.json
        /opt/conda/etc/jupyter/jupyter_notebook_config.json
[D 2024-02-14 14:06:01.006 ServerApp] Paths used for configuration of jupyter_notebook_config: 
        /home/jovyan/.local/etc/jupyter/jupyter_notebook_config.json
[D 2024-02-14 14:06:01.006 ServerApp] Paths used for configuration of jupyter_notebook_config: 
        /home/jovyan/.jupyter/jupyter_notebook_config.json
[I 2024-02-14 14:06:01.007 ServerApp] notebook_shim | extension was successfully linked.
[D 2024-02-14 14:06:01.007 ServerApp] Config changed: {'ExtensionApp': {'log_level': 'DEBUG'}, 'NotebookApp': {}, 'ServerApp': {'log_level': 'DEBUG', 'jpserver_extensions': <LazyConfigValue value={'jupyterlab': True, 'jupyter_server_fileid': True, 'jupyter_server_mathjax': True, 'jupyter_server_terminals': True, 'jupyter_server_ydoc': True, 'jupyterlab_git': True, 'nbclassic': True, 'nbdime': True, 'notebook_shim': True}>}}
[I 2024-02-14 14:06:01.093 ServerApp] notebook_shim | extension was successfully loaded.
[I 2024-02-14 14:06:01.093 FileIdExtension] Configured File ID manager: ArbitraryFileIdManager
[I 2024-02-14 14:06:01.093 FileIdExtension] ArbitraryFileIdManager : Configured root dir: /home/jovyan
[I 2024-02-14 14:06:01.093 FileIdExtension] ArbitraryFileIdManager : Configured database path: /home/jovyan/.local/share/jupyter/file_id_manager.db
[I 2024-02-14 14:06:01.101 FileIdExtension] ArbitraryFileIdManager : Successfully connected to database file.
[I 2024-02-14 14:06:01.101 FileIdExtension] ArbitraryFileIdManager : Creating File ID tables and indices with journal_mode = DELETE
[I 2024-02-14 14:06:01.179 FileIdExtension] Attached event listeners.
[I 2024-02-14 14:06:01.179 ServerApp] jupyter_server_fileid | extension was successfully loaded.
[I 2024-02-14 14:06:01.180 ServerApp] jupyter_server_mathjax | extension was successfully loaded.
[I 2024-02-14 14:06:01.180 ServerApp] jupyter_server_terminals | extension was successfully loaded.
[I 2024-02-14 14:06:01.181 ServerApp] jupyter_server_ydoc | extension was successfully loaded.
[I 2024-02-14 14:06:01.182 LabApp] JupyterLab extension loaded from /opt/conda/lib/python3.11/site-packages/jupyterlab
[I 2024-02-14 14:06:01.182 LabApp] JupyterLab application directory is /opt/conda/share/jupyter/lab
[I 2024-02-14 14:06:01.184 ServerApp] jupyterlab | extension was successfully loaded.
[I 2024-02-14 14:06:01.187 ServerApp] jupyterlab_git | extension was successfully loaded.

  _   _          _      _
 | | | |_ __  __| |__ _| |_ ___
 | |_| | '_ \/ _` / _` |  _/ -_)
  \___/| .__/\__,_\__,_|\__\___|
       |_|
                                                                           
Read the migration plan to Notebook 7 to learn about the new features and the actions to take if you are using extensions.

https://jupyter-notebook.readthedocs.io/en/latest/migrate_to_notebook7.html

Please note that updating to Notebook 7 might break some of your extensions.

[I 2024-02-14 14:06:01.189 ServerApp] nbclassic | extension was successfully loaded.
[D 2024-02-14 14:06:01.221 ServerApp] Using default logger
[D 2024-02-14 14:06:01.221 ServerApp] Using default logger
[D 2024-02-14 14:06:01.221 ServerApp] Using default logger
[D 2024-02-14 14:06:01.221 ServerApp] Using default logger
[D 2024-02-14 14:06:01.221 ServerApp] Using default logger
[D 2024-02-14 14:06:01.221 ServerApp] Using default logger
[I 2024-02-14 14:06:01.222 ServerApp] nbdime | extension was successfully loaded.
[I 2024-02-14 14:06:01.222 ServerApp] The port 8888 is already in use, trying another port.
[I 2024-02-14 14:06:01.222 ServerApp] Serving notebooks from local directory: /home/jovyan
[I 2024-02-14 14:06:01.222 ServerApp] Jupyter Server 2.12.5 is running at:
[I 2024-02-14 14:06:01.222 ServerApp] http://localhost:8889/lab?token=613352800643a7e2267d22f3d0866e0bc80d89b713754995
[I 2024-02-14 14:06:01.222 ServerApp]     http://127.0.0.1:8889/lab?token=613352800643a7e2267d22f3d0866e0bc80d89b713754995
[I 2024-02-14 14:06:01.222 ServerApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[W 2024-02-14 14:06:01.225 ServerApp] No web browser found: Error('could not locate runnable browser').
[C 2024-02-14 14:06:01.225 ServerApp] 
    
    To access the server, open this file in a browser:
        file:///tmp/jupyter_runtime/jpserver-571-open.html
    Or copy and paste one of these URLs:
        http://localhost:8889/lab?token=613352800643a7e2267d22f3d0866e0bc80d89b713754995
        http://127.0.0.1:8889/lab?token=613352800643a7e2267d22f3d0866e0bc80d89b713754995

@Mayurji
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Mayurji commented Feb 14, 2024

We upgraded to different version of jupyterlab-git plugin for instance we tried 0.44 version, 0.31 version, and the latest version as well.

@fcollonval
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fcollonval commented Feb 19, 2024

Thanks @Mayurji

When running JupyterLab in debug mode, could you copy the logs when performing the broken features like cloning or changing the current file browser directory?

In debug mode, the extension will report every git commands executed on the server with their inputs and outputs. With those information, we may get a chance to figure out what is going on.

@Mayurji
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Mayurji commented Feb 20, 2024

@fcollonval, We are running JupyterLab inside a docker image integrated with Kubeflow. So we do see logs on JupyterLab Notebook server as it runs as docker container while cloning the repo as follows

[E 2024-02-20 04:38:00.463 ServerApp] 500 POST /notebook/project-name/nb-test-1/git/clone?1708403777432 (127.0.0.6) 102902.50ms referer=https://kubeflow.dev.net/notebook/project-name/nb-test-1/lab/workspaces/auto-W

What you're requesting is to run jupyterlab in debug mode, which will require us to update docker image. Is my understanding correct?

@fcollonval
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What you're requesting is to run jupyterlab in debug mode, which will require us to update docker image. Is my understanding correct?

Yes this is what is needed to get more information about what is going on.

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