utoronto nbgitpuller in rstudio tries to pull to /home/jovyan which is ro #2559
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github-project-automation
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moved this to Needs Shaping / Refinement
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Possibly jupyterhub/nbgitpuller#268 |
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{
"NotebookApp": {
"nbserver_extensions": {
"nbgitpuller": true
}
}
}On the user server |
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# The default working directory is the directory from which Jupyter
# server is launched, which is not the same as the root notebook
# directory assuming either --notebook-dir= is used from the
# command line or c.NotebookApp.notebook_dir is set in the jupyter
# configuration. This line assures that all repos are cloned
# relative to server_root_dir/<optional NBGITPULLER_PARENTPATH>,
# so that all repos are always in scope after cloning. Sometimes
# server_root_dir will include things like `~` and so the path
# must be expanded.
repo_parent_dir = os.path.join(os.path.expanduser(self.settings['server_root_dir']),
os.getenv('NBGITPULLER_PARENTPATH', ''))
repo_dir = os.path.join(repo_parent_dir, self.get_argument('targetpath', repo.split('/')[-1])) |
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Hmm ok so cwd of PID 1 which is jupyterhub singleuser is /home/jovyan. So maybe we are not seetting notebook_dir or server_root_dir correctly here. |
volumeMounts:
- mountPath: /home/rstudio
name: home
subPath: pris-2enasrat-40utoronto-2eca
- mountPath: /etc/gitconfig
name: files
subPath: gitconfig
- mountPath: /etc/github/github-app-private-key.pem
name: files
subPath: github-app-private-key.pem
- mountPath: /usr/local/etc/ipython/ipython_kernel_config.json
name: files
subPath: ipython_kernel_config.json
- mountPath: /usr/local/etc/jupyter/jupyter_notebook_config.json
name: files
subPath: jupyter_notebook_config.json
- mountPath: /usr/local/etc/jupyter/jupyter_server_config.json
name: files
subPath: jupyter_server_config.json
- mountPath: /home/jovyan/shared
name: home
readOnly: true
subPath: _shared
workingDir: /home/jovyan |
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@pnasrat yep, #2559 (comment) is the root of the problem. I think we should modify r-common to set workingDir to /home/rstudio. I also felt some deja-vu with this problem, and behold, I had encountered it at UC Berkeley a few years ago and fixed it the exact same way https://github.com/berkeley-dsep-infra/datahub/blob/70447314413e15f41b1e870badae11acaff340c4/deployments/stat20/config/common.yaml#L25 We should add this as a piece of documentation somewhere, but not sure where. |
pnasrat
added a commit
that referenced
this issue
May 22, 2023
|
deployed fix to r-staging and tested via |
github-project-automation
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Ref: https://2i2c.freshdesk.com/a/tickets/726
nbgitpuller doesn’t seem to be working on https://r.datatools.utoronto.ca
For example trying to pull https://github.com/ntaback/learnr_test2 into the hub with
https://r.datatools.utoronto.ca/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2Fntaback%2Flearnr_test2&urlpath=rstudio%2F&branch=main
Throws the error …
This can be worked around by forcing a targetPath
https://r.datatools.utoronto.ca/user/[email protected]/git-pull?repo=https%3A%2F%2Fgithub.com%2Fntaback%2Flearnr_test2.git&urlpath=rstudio%2F&branch=main&redirects=1&targetPath=/home/rstudio/fooThe text was updated successfully, but these errors were encountered: