Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Permission Denied: --NotebookApp.notebook_dir vs --FileContentsManager.root_dir #268

Open
jbaksta opened this issue Mar 29, 2022 · 2 comments
Open

Permission Denied: --NotebookApp.notebook_dir vs --FileContentsManager.root_dir #268

jbaksta opened this issue Mar 29, 2022 · 2 comments
Labels
bug

Comments

@jbaksta
Copy link

jbaksta commented Mar 29, 2022

Bug description

--NotebookApp.notebook_dir vs --FileContentsManager.root_dir getting permission denied.

Expected behaviour

The git operation should occur in --NotebookApp.notebook_dir

Actual behaviour

The git operation is happening in --FileContentsManager.root_dir is passed to starting the JupyterLab instance.
Based on PR #71 and associated issues I found relating to that it seems that it was desired to have the starting directory be the --NotebookApp.notebook_dir, but in my environment, I have notebook_dir set as $HOME, but --FileContentsManager.root_dir=/glade set because that's common root for our shared filesystems, but for demonstrations root_dir could be set to /home

How to reproduce

A minimum jupyterhub installation inside a VM that has the following configuration arguments and the user home directory being /home/$USER:

c.Spawner.args.append('--FileContentsManager.root_dir="/home"')
c.Spawner.args.append('--NotebookApp.notebook_dir="~"')

Your personal set up

  • OS:
    OpenSUSE 15.3
  • Version(s):
# jupyterhub --version
2.2.2

# python --version
Python 3.9.12
  • Full environment 
# packages in environment at /ncar/usr/jupyterhub.hpc.ucar.edu/test:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
aiofiles                  0.7.0                    pypi_0    pypi
aiohttp                   3.8.1            py39h3811e60_0    conda-forge
aiosignal                 1.2.0              pyhd8ed1ab_0    conda-forge
alembic                   1.7.7              pyhd8ed1ab_0    conda-forge
aniso8601                 7.0.0                    pypi_0    pypi
ansimarkup                1.5.0                    pypi_0    pypi
anyio                     3.5.0            py39hf3d152e_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39h7f8727e_0
asttokens                 2.0.5              pyhd3eb1b0_0
async-timeout             4.0.2              pyhd8ed1ab_0    conda-forge
async_generator           1.10                       py_0    conda-forge
asyncssh                  2.10.0                   pypi_0    pypi
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
babel                     2.9.1              pyh44b312d_0    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
batchspawner              1.1.1.dev0               pypi_0    pypi
beautifulsoup4            4.10.0             pyh06a4308_0
bleach                    4.1.0              pyhd8ed1ab_0    conda-forge
blinker                   1.4                        py_1    conda-forge
bokeh                     2.4.2            py39hf3d152e_0    conda-forge
brotli                    1.0.9                he6710b0_2
brotlipy                  0.7.0           py39h3811e60_1003    conda-forge
bzip2                     1.0.8                h7b6447c_0
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2022.3.18            h06a4308_0
certifi                   2021.10.8        py39h06a4308_2
certipy                   0.1.3                      py_0    conda-forge
cffi                      1.15.0           py39h4bc2ebd_0    conda-forge
cfgv                      3.3.1              pyhd8ed1ab_0    conda-forge
chardet                   4.0.0            py39hf3d152e_2    conda-forge
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.1.0            py39hf3d152e_0    conda-forge
cloudpickle               2.0.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.4              pyh9f0ad1d_0    conda-forge
commonmark                0.9.1                      py_0    conda-forge
conda                     4.12.0           py39h06a4308_0
conda-package-handling    1.8.0            py39hb9d737c_0    conda-forge
configurable-http-proxy   4.5.1           node17_h7e777a6_1    conda-forge
coverage                  6.3.2            py39hb9d737c_1    conda-forge
cryptography              36.0.2           py39hd97740a_0    conda-forge
curl                      7.82.0               h7bff187_0    conda-forge
cycler                    0.11.0             pyhd3eb1b0_0
cylc-ext                  0.1.1                    pypi_0    pypi
cylc-flow                 8.0rc2                   pypi_0    pypi
cylc-uiserver             1.0.1                    pypi_0    pypi
cytoolz                   0.11.2           py39h3811e60_1    conda-forge
dask                      2022.3.0           pyhd8ed1ab_0    conda-forge
dask-core                 2022.3.0           pyhd8ed1ab_0    conda-forge
dask-labextension         5.2.0              pyhd8ed1ab_0    conda-forge
dask_labextension         5.2.0                hd8ed1ab_0    conda-forge
dataclasses               0.8                pyh6d0b6a4_7
debugpy                   1.5.1            py39h295c915_0
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecation               2.1.0              pyh9f0ad1d_0    conda-forge
distlib                   0.3.4              pyhd8ed1ab_0    conda-forge
distributed               2022.3.0           pyhd8ed1ab_0    conda-forge
elastic-transport         8.1.0                    pypi_0    pypi
elasticsearch             8.1.1                    pypi_0    pypi
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 0.8.3              pyhd3eb1b0_0
filelock                  3.6.0              pyhd8ed1ab_0    conda-forge
flake8                    4.0.1              pyhd8ed1ab_2    conda-forge
flit-core                 3.6.0              pyhd3eb1b0_0
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.10.4               h0708190_1    conda-forge
frozenlist                1.2.0            py39h7f8727e_0
fsspec                    2022.2.0           pyhd8ed1ab_0    conda-forge
future                    0.18.2           py39h06a4308_1
gettext                   0.21.0               hf68c758_0
giflib                    5.2.1                h7b6447c_0
gitdb                     4.0.7              pyhd3eb1b0_0
gitpython                 3.1.27             pyhd8ed1ab_0    conda-forge
graphene                  2.1.9                    pypi_0    pypi
graphene-tornado          2.6.1                    pypi_0    pypi
graphql-core              2.3.2                    pypi_0    pypi
graphql-relay             2.0.1                    pypi_0    pypi
graphql-ws                0.4.4                    pypi_0    pypi
greenlet                  1.1.2            py39he80948d_1    conda-forge
heapdict                  1.0.1                      py_0    conda-forge
icu                       69.1                 h9c3ff4c_0    conda-forge
identify                  2.4.12             pyhd8ed1ab_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.3           py39hf3d152e_0    conda-forge
importlib_resources       5.2.0              pyhd3eb1b0_1
invoke                    1.7.0              pyhd8ed1ab_0    conda-forge
ipykernel                 6.10.0           py39hef51801_0    conda-forge
ipython                   8.2.0            py39hf3d152e_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                7.7.0              pyhd8ed1ab_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jedi                      0.18.1           py39hf3d152e_0    conda-forge
jinja2                    2.11.3                   pypi_0    pypi
jpeg                      9e                   h7f98852_0    conda-forge
json5                     0.9.5              pyh9f0ad1d_0    conda-forge
jsonschema                4.4.0              pyhd8ed1ab_0    conda-forge
jupyter-packaging         0.12.0             pyhd8ed1ab_0    conda-forge
jupyter-resource-usage    0.6.1              pyhd8ed1ab_0    conda-forge
jupyter-server-mathjax    0.2.5              pyhc268e32_0    conda-forge
jupyter-server-proxy      3.2.1              pyhd8ed1ab_0    conda-forge
jupyter_client            7.2.0              pyhd8ed1ab_0    conda-forge
jupyter_core              4.9.2            py39hf3d152e_0    conda-forge
jupyter_server            1.15.6             pyhd8ed1ab_1    conda-forge
jupyter_telemetry         0.1.0              pyhd8ed1ab_1    conda-forge
jupyterhub                2.2.2                hd8ed1ab_0    conda-forge
jupyterhub-base           2.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab                3.3.2              pyhd8ed1ab_0    conda-forge
jupyterlab-git            0.36.0             pyhd8ed1ab_0    conda-forge
jupyterlab-latex          3.1.0                    pypi_0    pypi
jupyterlab-mathjax3       4.3.0              pyhd8ed1ab_0    conda-forge
jupyterlab-ncar-menu      0.1.1                    pypi_0    pypi
jupyterlab-nvdashboard    0.6.0              pyhd8ed1ab_0    conda-forge
jupyterlab-recents        3.0.1              pyhd8ed1ab_0    conda-forge
jupyterlab-server         2.10.3                   pypi_0    pypi
jupyterlab-sublime        0.4.1                    pypi_0    pypi
jupyterlab-variableinspector 3.0.9              pyhd8ed1ab_0    conda-forge
jupyterlab_code_formatter 1.4.10             pyhd8ed1ab_1    conda-forge
jupyterlab_pygments       0.1.2              pyh9f0ad1d_0    conda-forge
jupyterlab_widgets        1.1.0              pyhd8ed1ab_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.0            py39hf939315_0    conda-forge
krb5                      1.19.3               h3790be6_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libarchive                3.5.2                hccf745f_1    conda-forge
libblas                   3.9.0           13_linux64_openblas    conda-forge
libcblas                  3.9.0           13_linux64_openblas    conda-forge
libcurl                   7.82.0               h7bff187_0    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 11.2.0              h1d223b6_14    conda-forge
libgfortran-ng            11.2.0              h69a702a_14    conda-forge
libgfortran5              11.2.0              h5c6108e_14    conda-forge
libglib                   2.70.2               h174f98d_4    conda-forge
libgomp                   11.2.0              h1d223b6_14    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
liblapack                 3.9.0           13_linux64_openblas    conda-forge
libmamba                  0.22.1               h9c208ef_0    conda-forge
libmambapy                0.22.1           py39h3216e65_0    conda-forge
libmemcached              1.0.18            h17b2bb4_1003    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libsodium                 1.0.18               h36c2ea0_1    conda-forge
libsolv                   0.7.20               h4ff587b_0
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_14    conda-forge
libtiff                   4.3.0                h542a066_3    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libuv                     1.43.0               h7f98852_0    conda-forge
libwebp                   1.2.2                h55f646e_0
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13                 h1bed415_1
libxml2                   2.9.12               h885dcf4_1    conda-forge
libzlib                   1.2.11            h166bdaf_1014    conda-forge
locket                    0.2.0                      py_2    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
lzo                       2.10                 h7b6447c_2
mako                      1.2.0              pyhd8ed1ab_0    conda-forge
mamba                     0.22.1           py39hfa8f2c8_0    conda-forge
markdown                  3.1.1                    pypi_0    pypi
markupsafe                2.0.1                    pypi_0    pypi
matplotlib-base           3.5.1            py39h2fa2bec_0    conda-forge
matplotlib-inline         0.1.3              pyhd8ed1ab_0    conda-forge
mccabe                    0.6.1                      py_1    conda-forge
metomi-isodatetime        1!2.0.2                  pypi_0    pypi
mistune                   0.8.4           py39h3811e60_1005    conda-forge
mock                      4.0.3            py39hf3d152e_2    conda-forge
msgpack-python            1.0.3            py39h1a9c180_0    conda-forge
multidict                 6.0.2            py39h3811e60_0    conda-forge
munkres                   1.1.4                      py_0
nb_conda_kernels          2.3.1            py39hf3d152e_1    conda-forge
nbclassic                 0.3.7              pyhd8ed1ab_0    conda-forge
nbclient                  0.5.13             pyhd8ed1ab_0    conda-forge
nbconvert                 5.6.1                    pypi_0    pypi
nbconvert-pandoc          6.4.5              pyhd8ed1ab_1    conda-forge
nbdime                    3.1.1              pyhd8ed1ab_0    conda-forge
nbformat                  5.2.0              pyhd8ed1ab_0    conda-forge
nbgitpuller               1.1.0              pyhd8ed1ab_0    conda-forge
nbviewer                  1.0.1+265.gd9c5da7          pypi_0    pypi
ncurses                   6.3                  h9c3ff4c_0    conda-forge
nest-asyncio              1.5.4              pyhd8ed1ab_0    conda-forge
newrelic                  7.6.0.173        py39hb9d737c_0    conda-forge
nodeenv                   1.6.0              pyhd8ed1ab_0    conda-forge
nodejs                    17.8.0               h784f1fd_0    conda-forge
nose                      1.3.7                   py_1006    conda-forge
notebook                  6.4.10             pyha770c72_0    conda-forge
notebook-shim             0.1.0              pyhd8ed1ab_0    conda-forge
numpy                     1.22.3           py39h18676bf_0    conda-forge
oauthlib                  3.2.0              pyhd8ed1ab_0    conda-forge
olefile                   0.46               pyh9f0ad1d_1    conda-forge
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1n               h7f8727e_0
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pamela                    1.0.0                      py_0    conda-forge
pandas                    1.4.1            py39hde0f152_0    conda-forge
pandoc                    2.17.1.1             ha770c72_0    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
panel                     0.12.6             pyhd8ed1ab_0    conda-forge
param                     1.12.0             pyh6c4a22f_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
partd                     1.2.0              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h9c3ff4c_0    conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.0.1            py39hae2aec6_2    conda-forge
pip                       22.0.4             pyhd8ed1ab_0    conda-forge
platformdirs              2.5.1              pyhd8ed1ab_0    conda-forge
pre-commit                2.17.0           py39hf3d152e_0    conda-forge
prometheus_client         0.13.1             pyhd8ed1ab_0    conda-forge
promise                   2.3                      pypi_0    pypi
prompt-toolkit            3.0.27             pyha770c72_0    conda-forge
protobuf                  3.19.4                   pypi_0    pypi
psutil                    5.9.0            py39h3811e60_0    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd3eb1b0_0
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycodestyle               2.8.0              pyhd8ed1ab_0    conda-forge
pycosat                   0.6.3           py39h3811e60_1009    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyct                      0.4.6                      py_0    conda-forge
pyct-core                 0.4.6              pyhd3eb1b0_0
pycurl                    7.45.1           py39hd73adbb_0    conda-forge
pydantic                  1.9.0            py39h3811e60_0    conda-forge
pyflakes                  2.4.0              pyhd8ed1ab_0    conda-forge
pygments                  2.11.2             pyhd8ed1ab_0    conda-forge
pyjwt                     2.3.0              pyhd8ed1ab_1    conda-forge
pylibmc                   1.6.1            py39h3811e60_4    conda-forge
pynvml                    11.4.1             pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge
pyrsistent                0.18.1           py39h3811e60_0    conda-forge
pysocks                   1.7.1            py39hf3d152e_4    conda-forge
python                    3.9.12          h9a8a25e_1_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-editor             1.0.4                      py_0    conda-forge
python-json-logger        2.0.1              pyh9f0ad1d_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2022.1             pyhd8ed1ab_0    conda-forge
pyuv                      1.4.0                    pypi_0    pypi
pyviz_comms               2.1.0              pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py39h3811e60_3    conda-forge
pyzmq                     22.3.0           py39h37b5a0c_1    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
reproc                    14.2.4               h295c915_1
reproc-cpp                14.2.4               h295c915_1
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
rich                      12.0.1             pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.17.21          py39h3811e60_0    conda-forge
ruamel.yaml.clib          0.2.6            py39h3811e60_0    conda-forge
ruamel_yaml               0.15.80         py39h3811e60_1006    conda-forge
rx                        1.6.1                    pypi_0    pypi
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                61.2.0           py39hf3d152e_1    conda-forge
simpervisor               0.4                pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     5.0.0              pyhd8ed1ab_0    conda-forge
sniffio                   1.2.0            py39hf3d152e_2    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.1              pyhd3eb1b0_0
sqlalchemy                1.4.32           py39hb9d737c_0    conda-forge
sqlite                    3.37.1               h4ff8645_0    conda-forge
sshspawner                0.1.0                    pypi_0    pypi
stack_data                0.2.0              pyhd3eb1b0_0
statsd                    3.3.0                      py_0    conda-forge
tblib                     1.7.0              pyhd8ed1ab_0    conda-forge
terminado                 0.13.3           py39hf3d152e_0    conda-forge
testpath                  0.6.0              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     1.2.2              pyhd3eb1b0_0
tomlkit                   0.10.1             pyha770c72_0    conda-forge
toolz                     0.11.2             pyhd8ed1ab_0    conda-forge
tornado                   6.1              py39h3811e60_2    conda-forge
tqdm                      4.63.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.1.1              pyhd8ed1ab_0    conda-forge
typing                    3.10.0.0         py39h06a4308_0
typing-extensions         4.1.1                hd8ed1ab_0    conda-forge
typing_extensions         4.1.1              pyha770c72_0    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
ukkonen                   1.0.1            py39h1a9c180_1    conda-forge
urllib3                   1.26.9             pyhd8ed1ab_0    conda-forge
urwid                     2.1.2                    pypi_0    pypi
virtualenv                20.14.0          py39hf3d152e_0    conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.3.2              pyhd8ed1ab_0    conda-forge
werkzeug                  0.12.2                   pypi_0    pypi
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
widgetsnbextension        3.6.0            py39hf3d152e_0    conda-forge
wrapspawner               1.0.1                    pypi_0    pypi
xz                        5.2.5                h516909a_1    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.6.3                he1b5a44_4    conda-forge
yarl                      1.7.2            py39h3811e60_1    conda-forge
zeromq                    4.3.4                h9c3ff4c_1    conda-forge
zict                      2.1.0              pyhd8ed1ab_0    conda-forge
zipp                      3.7.0              pyhd8ed1ab_1    conda-forge
zlib                      1.2.11            h166bdaf_1014    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge
  • Configuration

A basic configuration with the two lines mentioned above:

c.Spawner.args.append('--FileContentsManager.root_dir="/home"')
c.Spawner.args.append('--NotebookApp.notebook_dir="~"')
  • Logs 
$ git clone --depth 1 --branch CSG_tutorial -- https://github.com/dphow/GPU_workshop /home/GPU_workshop
fatal: could not create work tree dir '/home/GPU_workshop': Permission denied
@jbaksta jbaksta added the bug label Mar 29, 2022
@welcome
Copy link

welcome bot commented Mar 29, 2022

Thank you for opening your first issue in this project! Engagement like this is essential for open source projects! 🤗

If you haven't done so already, check out Jupyter's Code of Conduct. Also, please try to follow the issue template as it helps other other community members to contribute more effectively.
welcome
You can meet the other Jovyans by joining our Discourse forum. There is also an intro thread there where you can stop by and say Hi! 👋

Welcome to the Jupyter community! 🎉

@jbaksta
Copy link
Author

jbaksta commented Apr 2, 2022

As a workaround, I attempted to set the environment variable NBGITPULLER_PARENTPATH to relative directory to that of --FileContentsManager.root_dir and that provides me a good ability to do the clone minus the documented way things are expected to work. However, after the git clone operation completes successfully, the redirect attempts to access the repo at the --fileContentsManager.root_dir again and thus shows me a 404 in the tree view.

@pnasrat pnasrat mentioned this issue May 19, 2023
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@jbaksta