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can't delete file in jupyterlab #1338

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li1311139481 opened this issue Oct 17, 2023 · 11 comments
Open

can't delete file in jupyterlab #1338

li1311139481 opened this issue Oct 17, 2023 · 11 comments
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@li1311139481
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Description

I'm using jupyterlab 4.0.6 in a cluster.
When i want delete a file in jupyterlab. I get an error like this.
image
This error occurs when I try to create and then delete files in jupyterlab, and when I try to delete existing files. I have checked the permissions of these files in the terminal, where I can delete them.
The error message in terminal like this:

[W 2023-10-07 15:04:16.735 ServerApp] delete /zifeng001/ZF065_ovarian_ascites/Junlian/sada.ipynb
[W 2023-10-07 15:04:16.736 ServerApp] 400 DELETE /api/contents/zifeng001/ZF065_ovarian_ascites/Junlian/sada.ipynb?1696662257091 (10.26.20.81): send2trash f`1ailed: [Errno 13] P
ermission denied: b'/cluster/.Trash-1085'
[W 2023-10-07 15:04:16.737 ServerApp] wrote error: "send2trash f`1ailed: [Errno 13] Permission denied: b'/cluster/.Trash-1085'"
    Traceback (most recent call last):
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/send2trash/plat_other.py", line 158, in find_ext_volume_fallback_trash
        check_create(trash_dir)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/send2trash/plat_other.py", line 96, in check_create
        os.makedirs(dir, 0o700)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/os.py", line 225, in makedirs
        mkdir(name, mode)
    PermissionError: [Errno 13] Permission denied: b'/cluster/.Trash-1085'

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/jupyter_server/services/contents/filemanager.py", line 979, in delete_file
        send2trash(os_path)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/send2trash/plat_other.py", line 210, in send2trash
        dest_trash = find_ext_volume_trash(topdir)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/send2trash/plat_other.py", line 169, in find_ext_volume_trash
        trash_dir = find_ext_volume_fallback_trash(volume_root)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/send2trash/plat_other.py", line 161, in find_ext_volume_fallback_trash
        raise TrashPermissionError(e.filename)
    send2trash.exceptions.TrashPermissionError: [Errno 13] Permission denied: b'/cluster/.Trash-1085'

    The above exception was the direct cause of the following exception:

    Traceback (most recent call last):
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/tornado/web.py", line 1713, in _execute
        result = await result
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/jupyter_server/services/contents/handlers.py", line 282, in delete
        await ensure_async(cm.delete(path))
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/jupyter_core/utils/__init__.py", line 184, in ensure_async
        result = await obj
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/jupyter_server/services/contents/manager.py", line 882, in delete
        await self.delete_file(path)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.10/site-packages/jupyter_server/services/contents/filemanager.py", line 981, in delete_file
        raise web.HTTPError(400, "send2trash f`1ailed: %s" % e) from e
    tornado.web.HTTPError: HTTP 400: Bad Request (send2trash f`1ailed: [Errno 13] Permission denied: b'/cluster/.Trash-1085')

Reproduce

I don't know how to reproduce it in other environments. All I did was simply delete a file

Expected behavior

I hope you can help me to solve it, because deleting files in jupyterlab is a very convenient feature

Context

  • Operating System and version: Linux version 3.10.0-514.21.1.el7.x86_64 (builder@kbuilder.dev.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-11) (GCC) ) #1 SMP Thu May 25 17:04:51 UTC 2017
  • Browser and version: Firefox 118.0.1
  • JupyterLab version:
Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
_openmp_mutex             4.5                       2_gnu    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
_r-mutex                  1.0.1               anacondar_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
aiofiles                  22.1.0             pyhd8ed1ab_0    conda-forge
aiosqlite                 0.19.0             pyhd8ed1ab_0    conda-forge
anyio                     3.6.2              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
argon2-cffi-bindings      21.2.0          py310h5764c6d_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
arrow                     1.3.0                    pypi_0    pypi
astroid                   2.12.12                  pypi_0    pypi
asttokens                 2.0.8              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
async-lru                 2.0.4                    pypi_0    pypi
attrs                     22.1.0             pyh71513ae_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
autopep8                  1.6.0              pyhd8ed1ab_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
babel                     2.10.3             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
backports                 1.0                        py_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
binutils_impl_linux-64    2.39                 h6ceecb4_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
bokeh                     2.4.3              pyhd8ed1ab_3    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
brotli                    1.0.9                h166bdaf_7    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
brotli-bin                1.0.9                h166bdaf_7    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
brotlipy                  0.7.0           py310h5764c6d_1004    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
bwidget                   1.9.14               ha770c72_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
bzip2                     1.0.8                h7f98852_4    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
c-ares                    1.18.1               h7f98852_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
cairo                     1.16.0            ha61ee94_1014    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1          py310h255011f_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
colorama                  0.4.5              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
comm                      0.1.4                    pypi_0    pypi
contourpy                 1.0.5           py310hbf28c38_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
cryptography              38.0.2          py310h600f1e7_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
curl                      7.85.0               h2283fc2_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
debugpy                   1.6.3           py310hd8f1fbe_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
dill                      0.3.6              pyhd8ed1ab_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
docstring-to-markdown     0.12               pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
executing                 1.1.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
expat                     2.4.9                h27087fc_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
flake8                    6.0.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
flit-core                 3.7.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
fontconfig                2.14.1               hc2a2eb6_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
fonts-conda-ecosystem     1                             0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
fonts-conda-forge         1                             0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
fonttools                 4.38.0          py310h5764c6d_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
fqdn                      1.5.1                    pypi_0    pypi
freetype                  2.12.1               hca18f0e_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
fribidi                   1.0.10               h36c2ea0_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
gcc_impl_linux-64         12.2.0              hcc96c02_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
gettext                   0.21.1               h27087fc_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
gfortran_impl_linux-64    12.2.0              h55be85b_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
graphite2                 1.3.13            h58526e2_1001    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
gsl                       2.7                  he838d99_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
gxx_impl_linux-64         12.2.0              hcc96c02_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
harfbuzz                  5.3.0                h418a68e_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
icu                       70.1                 h27087fc_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
idna                      3.4                pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
importlib-metadata        4.11.4          py310hff52083_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
importlib_resources       5.10.0             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ipykernel                 6.16.1             pyh210e3f2_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ipympl                    0.9.2              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ipython                   8.5.0              pyh41d4057_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ipython_genutils          0.2.0                      py_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ipywidgets                8.1.1                    pypi_0    pypi
isoduration               20.11.0                  pypi_0    pypi
isort                     5.10.1             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
itables                   1.3.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
jedi                      0.18.1             pyhd8ed1ab_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
jpeg                      9e                   h166bdaf_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
json5                     0.9.5              pyh9f0ad1d_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
jsonpointer               2.4                      pypi_0    pypi
jsonschema                4.17.3             pyhd8ed1ab_0    conda-forge
jupyter-client            8.3.1                    pypi_0    pypi
jupyter-core              5.3.2                    pypi_0    pypi
jupyter-lsp               2.2.0                    pypi_0    pypi
jupyter-server            2.7.3                    pypi_0    pypi
jupyter-server-terminals  0.4.4                    pypi_0    pypi
jupyter_events            0.6.3           py310h06a4308_0  
jupyter_server_fileid     0.9.0              pyhd8ed1ab_0    conda-forge
jupyter_server_ydoc       0.8.0              pyhd8ed1ab_0    conda-forge
jupyter_ydoc              0.2.4           py310h06a4308_0  
jupyterlab                4.0.6                    pypi_0    pypi
jupyterlab-execute-time   3.0.1                    pypi_0    pypi
jupyterlab-lsp            5.0.0rc1                 pypi_0    pypi
jupyterlab-widgets        3.0.9                    pypi_0    pypi
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
jupyterlab_server         2.22.0          py310h06a4308_0  
jupyterthemes             0.20.0                     py_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
kernel-headers_linux-64   2.6.32              he073ed8_15    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
keyutils                  1.6.1                h166bdaf_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
kiwisolver                1.4.4           py310hbf28c38_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
krb5                      1.19.3               h08a2579_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
lazy-object-proxy         1.7.1           py310h5764c6d_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
lcms2                     2.12                 hddcbb42_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ld_impl_linux-64          2.39                 hc81fddc_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
lerc                      4.0.0                h27087fc_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
lesscpy                   0.15.1             pyhd8ed1ab_0    conda-forge
libblas                   3.9.0           16_linux64_openblas    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libbrotlicommon           1.0.9                h166bdaf_7    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libbrotlidec              1.0.9                h166bdaf_7    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libbrotlienc              1.0.9                h166bdaf_7    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libcblas                  3.9.0           16_linux64_openblas    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libcurl                   7.85.0               h2283fc2_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libdeflate                1.14                 h166bdaf_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libedit                   3.1.20191231         he28a2e2_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libev                     4.33                 h516909a_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libffi                    3.4.2                h7f98852_5    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libgcc-devel_linux-64     12.2.0              h3b97bd3_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libgcc-ng                 12.2.0              h65d4601_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libgfortran-ng            12.2.0              h69a702a_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libgfortran5              12.2.0              h337968e_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libglib                   2.74.0               h7a41b64_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libgomp                   12.2.0              h65d4601_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libiconv                  1.17                 h166bdaf_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
liblapack                 3.9.0           16_linux64_openblas    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libnghttp2                1.47.0               hff17c54_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libnsl                    2.0.0                h7f98852_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libopenblas               0.3.21          pthreads_h78a6416_3    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libpng                    1.6.38               h753d276_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libsanitizer              12.2.0              h46fd767_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libsodium                 1.0.18               h36c2ea0_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libsqlite                 3.43.0               h2797004_0    conda-forge
libssh2                   1.10.0               hf14f497_3    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libstdcxx-devel_linux-64  12.2.0              h3b97bd3_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libtiff                   4.4.0                h55922b4_4    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.44.2               h166bdaf_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libwebp-base              1.2.4                h166bdaf_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libxcb                    1.13              h7f98852_1004    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libxml2                   2.10.3               h7463322_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
libzlib                   1.2.13               h166bdaf_4    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
make                      4.3                  hd18ef5c_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
markupsafe                2.1.1           py310h5764c6d_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
matplotlib-base           3.6.1           py310h8d5ebf3_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
mccabe                    0.7.0              pyhd8ed1ab_0    conda-forge
mistune                   2.0.4              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
nbclassic                 0.4.5              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
nbclient                  0.7.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
nbconvert                 7.2.9              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
nbconvert-core            7.2.9              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
nbconvert-pandoc          7.2.9              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
nbformat                  5.7.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
nbresuse                  0.4.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ncurses                   6.4                  hcb278e6_0    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
nodejs                    18.11.0              h8839609_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
notebook                  6.5.1              pyha770c72_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
notebook-shim             0.2.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
numpy                     1.24.2          py310h8deb116_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
openjpeg                  2.5.0                h7d73246_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
openssl                   3.1.3                hd590300_0    conda-forge
overrides                 7.4.0                    pypi_0    pypi
packaging                 21.3               pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pandas                    2.0.1           py310h7cbd5c2_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pandoc                    2.19.2               h32600fe_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pango                     1.50.11              h382ae3d_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
parso                     0.8.3              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pcre2                     10.37                hc3806b6_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pexpect                   4.8.0              pyh9f0ad1d_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pickleshare               0.7.5                   py_1003    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pillow                    9.2.0           py310hbd86126_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pip                       22.3               pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pixman                    0.40.0               h36c2ea0_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
platformdirs              2.5.2              pyhd8ed1ab_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pluggy                    1.0.0           py310hff52083_3    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ply                       3.11                       py_1    conda-forge
prometheus_client         0.15.0             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
prompt-toolkit            3.0.31             pyha770c72_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
psutil                    5.9.3           py310h5764c6d_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pthread-stubs             0.4               h36c2ea0_1001    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pycodestyle               2.10.0             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pycparser                 2.21               pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pydocstyle                6.3.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pyflakes                  3.0.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pylint                    2.15.4                   pypi_0    pypi
pyopenssl                 22.1.0             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pyrsistent                0.18.1          py310h5764c6d_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pysocks                   1.7.1              pyha2e5f31_6    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
python                    3.10.12         hd12c33a_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
python-json-logger        2.0.7              pyhd8ed1ab_0    conda-forge
python-lsp-jsonrpc        1.0.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
python-lsp-server         1.7.2              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
python-lsp-server-base    1.7.2              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    2_cp310    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pytoolconfig              1.2.2              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pytz                      2022.5             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pyyaml                    6.0             py310h5764c6d_4    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
pyzmq                     24.0.1          py310h330234f_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-askpass                 1.1               r42h06615bd_3    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-backports               1.4.1             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-base                    4.2.1                h7880091_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-base64enc               0.1_3           r42h06615bd_1005    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-brew                    1.0_8             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-brio                    1.1.3             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-callr                   3.7.2             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-cli                     3.4.1             r42h7525677_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-codetools               0.2_18            r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-collections             0.3.6             r42h06615bd_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-commonmark              1.8.1             r42h06615bd_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-cpp11                   0.4.3             r42hc72bb7e_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-crayon                  1.5.2             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-curl                    4.3.3             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-cyclocomp               1.1.0           r42hc72bb7e_1005    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-desc                    1.4.2             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-diffobj                 0.3.5             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-digest                  0.6.30            r42h7525677_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-ellipsis                0.3.2             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-evaluate                0.17              r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-fansi                   1.0.3             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-fastmap                 1.1.0             r42h7525677_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-fs                      1.5.2             r42h7525677_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-glue                    1.6.2             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-highr                   0.9               r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-htmltools               0.5.3             r42h7525677_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-httr                    1.4.4             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-jsonlite                1.8.3             r42h06615bd_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-knitr                   1.40              r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-languageserver          0.3.14            r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-lazyeval                0.2.2             r42h06615bd_3    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-lifecycle               1.0.3             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-lintr                   3.0.2             r42hc72bb7e_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-magrittr                2.0.3             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-mime                    0.12              r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-openssl                 2.0.4             r42h1f3e0c5_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-pillar                  1.8.1             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-pkgconfig               2.0.3             r42hc72bb7e_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-pkgload                 1.3.0             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-praise                  1.0.0           r42hc72bb7e_1006    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-processx                3.7.0             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-ps                      1.7.1             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-purrr                   0.3.5             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-r.cache                 0.16.0            r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-r.methodss3             1.8.2             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-r.oo                    1.25.0            r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-r.utils                 2.12.0            r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-r6                      2.5.1             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-rcpp                    1.0.9             r42h7525677_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-rematch2                2.1.2             r42hc72bb7e_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-remotes                 2.4.2             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-repr                    1.1.4             r42h785f33e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-rex                     1.2.1             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-rlang                   1.0.6             r42h7525677_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-roxygen2                7.2.1             r42h7525677_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-rprojroot               2.0.3             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-rstudioapi              0.14              r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-stringdist              0.9.9             r42h06615bd_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-stringi                 1.7.8             r42h30a9eb7_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-stringr                 1.4.1             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-styler                  1.8.0             r42hc72bb7e_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-sys                     3.4.1             r42h06615bd_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-testthat                3.1.5             r42h7525677_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-tibble                  3.1.8             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-utf8                    1.2.2             r42h06615bd_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-vctrs                   0.5.0             r42h7525677_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-waldo                   0.4.0             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-withr                   2.5.0             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-xfun                    0.34              r42h7525677_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-xml2                    1.3.3             r42h044e5c7_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-xmlparsedata            1.0.5             r42hc72bb7e_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
r-yaml                    2.3.6             r42h06615bd_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
readline                  8.2                  h8228510_1    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
rfc3339-validator         0.1.4              pyhd8ed1ab_0    conda-forge
rfc3986-validator         0.1.1              pyh9f0ad1d_0    conda-forge
rope                      1.4.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
sed                       4.8                  he412f7d_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
send2trash                1.8.2                    pypi_0    pypi
setuptools                65.5.0             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
six                       1.16.0             pyh6c4a22f_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
snowballstemmer           2.2.0              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
stack_data                0.5.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
sysroot_linux-64          2.12                he073ed8_15    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
terminado                 0.16.0             pyh41d4057_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
tinycss2                  1.2.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
tk                        8.6.12               h27826a3_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
tktable                   2.10                 hb7b940f_3    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
toml                      0.10.2             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
tomlkit                   0.11.5             pyha770c72_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
tornado                   6.2             py310h5764c6d_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
traitlets                 5.11.2                   pypi_0    pypi
types-python-dateutil     2.8.19.14                pypi_0    pypi
typing                    3.10.0.0           pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
typing-extensions         4.4.0                hd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
typing_extensions         4.4.0              pyha770c72_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
tzdata                    2022e                h191b570_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ujson                     5.5.0           py310hd8f1fbe_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
unicodedata2              14.0.0          py310h5764c6d_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
uri-template              1.3.0                    pypi_0    pypi
urllib3                   1.26.11            pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
wcwidth                   0.2.5              pyh9f0ad1d_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
webcolors                 1.13                     pypi_0    pypi
webencodings              0.5.1                      py_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
websocket-client          1.4.1              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
whatthepatch              1.0.2              pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
widgetsnbextension        4.0.9                    pypi_0    pypi
wrapt                     1.14.1          py310h5764c6d_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-libice               1.0.10               h7f98852_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-libx11               1.7.2                h7f98852_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-libxau               1.0.9                h7f98852_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-libxext              1.3.4                h7f98852_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-libxt                1.2.1                h7f98852_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xorg-xproto               7.0.31            h7f98852_1007    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
xz                        5.2.6                h166bdaf_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
y-py                      0.5.9           py310h52d8a92_0  
yaml                      0.2.5                h7f98852_2    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
yapf                      0.32.0             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
ypy-websocket             0.8.2           py310h06a4308_0  
zeromq                    4.3.4                h9c3ff4c_1    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
zipp                      3.10.0             pyhd8ed1ab_0    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
zlib                      1.2.13               h166bdaf_4    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge
zstd                      1.5.2                h6239696_4    https://mirrors.ustc.edu.cn/anaconda/cloud/conda-forge```
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Any one can help? @JasonWeill told me i should ask the questions at here

@li1311139481
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at the same time. I can't save my notebook. The error message like:
image

[I 2023-11-07 20:03:18.309 ServerApp] Skipped non-installed server(s): bash-language-server, dockerfile-language-server-nodejs, javascript-typescript-la
ngserver, jedi-language-server, julia-language-server, pyright, python-language-server, python-lsp-server, r-languageserver, sql-language-server, texlab
, typescript-language-server, unified-language-server, vscode-css-languageserver-bin, vscode-html-languageserver-bin, vscode-json-languageserver-bin, ya
ml-language-server
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
[I 2023-11-07 20:03:26.745 LabApp] Build is up to date
/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/nbformat/__init__.py:93: MissingIDFieldWarning: Code cell is missing an id f
ield, this will become a hard error in future nbformat versions. You may want to use `normalize()` on your notebooks before validations (available since
 nbformat 5.1.4). Previous versions of nbformat are fixing this issue transparently, and will stop doing so in the future.
  validate(nb)
[W 2023-11-07 20:03:27.061 ServerApp] Notebook zifeng001/ZF067_PAAD/scRNAseq/Frankel_2020_natcancer/ZF067_frankel.ipynb is not trusted
[I 2023-11-07 20:03:29.198 ServerApp] Kernel started: 7590ea66-0e9c-40d5-b1a8-5f13f441f11f
[I 2023-11-07 20:03:29.204 ServerApp] Kernel started: 6d138951-292e-4425-8903-8af799783edf
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
[IPKernelApp] ERROR | Failed to create history session in /tmp/ipython_hist.sqlite. History will not be saved.
Traceback (most recent call last):
  File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/IPython/core/history.py", line 549, in __init__
    self.new_session()
  File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/decorator.py", line 232, in fun
    return caller(func, *(extras + args), **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/IPython/core/history.py", line 60, in only_when_enabled
    return f(self, *a, **kw)
           ^^^^^^^^^^^^^^^^^
  File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/IPython/core/history.py", line 574, in new_session
    cur = conn.execute(
          ^^^^^^^^^^^^^
sqlite3.OperationalError: attempt to write a readonly database
[I 2023-11-07 20:03:30.347 ServerApp] Connecting to kernel 6d138951-292e-4425-8903-8af799783edf.
[I 2023-11-07 20:03:30.408 ServerApp] Connecting to kernel 7590ea66-0e9c-40d5-b1a8-5f13f441f11f.
[I 2023-11-07 20:03:30.446 ServerApp] Connecting to kernel 6d138951-292e-4425-8903-8af799783edf.
[I 2023-11-07 20:03:30.496 ServerApp] Connecting to kernel 6d138951-292e-4425-8903-8af799783edf.
[I 2023-11-07 20:03:32.178 ServerApp] Saving file at /Untitled.ipynb
[I 2023-11-07 20:03:35.108 ServerApp] Saving file at /Untitled.ipynb
[E 2023-11-07 20:03:35.143 ServerApp] Error while saving file: Untitled.ipynb disk I/O error
    Traceback (most recent call last):
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/filemanager.py", line 913, in save
        self.check_and_sign(nb, path)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/manager.py", line 712, in check_and_sign
        self.notary.sign(nb)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/nbformat/sign.py", line 477, in sign
        self.store.store_signature(signature, self.algorithm)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/nbformat/sign.py", line 233, in store_signature
        (n,) = self.db.execute("SELECT Count(*) FROM nbsignatures").fetchone()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    sqlite3.OperationalError: disk I/O error
[W 2023-11-07 20:03:35.147 ServerApp] 500 PUT /api/contents/Untitled.ipynb?1699358615086 (10.26.20.81): Unexpected error while saving file: Untitled.ipynb disk I/O error
[W 2023-11-07 20:03:35.147 ServerApp] wrote error: 'Unexpected error while saving file: Untitled.ipynb disk I/O error'
    Traceback (most recent call last):
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/filemanager.py", line 913, in save
        self.check_and_sign(nb, path)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/manager.py", line 712, in check_and_sign
        self.notary.sign(nb)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/nbformat/sign.py", line 477, in sign
        self.store.store_signature(signature, self.algorithm)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/nbformat/sign.py", line 233, in store_signature
        (n,) = self.db.execute("SELECT Count(*) FROM nbsignatures").fetchone()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    sqlite3.OperationalError: disk I/O error

    The above exception was the direct cause of the following exception:

    Traceback (most recent call last):
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/tornado/web.py", line 1786, in _execute
        result = await result
                 ^^^^^^^^^^^^
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/handlers.py", line 266, in put
        await self._save(model, path)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/handlers.py", line 191, in _save
        model = await ensure_async(self.contents_manager.save(model, path))
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_core/utils/__init__.py", line 189, in ensure_async
        result = await obj
                 ^^^^^^^^^
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/largefilemanager.py", line 133,
 in save
        return await super().save(model, path)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/filemanager.py", line 929, in save
        raise web.HTTPError(500, f"Unexpected error while saving file: {path} {e}") from e
    tornado.web.HTTPError: HTTP 500: Internal Server Error (Unexpected error while saving file: Untitled.ipynb disk I/O error)
[E 2023-11-07 20:03:35.153 ServerApp] {
      "Host": "172.19.247.27:8789",
      "Accept": "*/*",
      "Referer": "http://172.19.247.27:8789/lab",
      "User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:109.0) Gecko/20100101 Firefox/119.0"
    }
[E 2023-11-07 20:03:35.153 ServerApp] 500 PUT /api/contents/Untitled.ipynb?1699358615086 (c5ac8133dec94235a4e0ccc95f9b5582@10.26.20.81) 45.54ms referer=http://172.19.247.27:8789/lab

@li1311139481
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at the same time. I can't save my notebook. The error message like: image

[I 2023-11-07 20:03:18.309 ServerApp] Skipped non-installed server(s): bash-language-server, dockerfile-language-server-nodejs, javascript-typescript-la
ngserver, jedi-language-server, julia-language-server, pyright, python-language-server, python-lsp-server, r-languageserver, sql-language-server, texlab
, typescript-language-server, unified-language-server, vscode-css-languageserver-bin, vscode-html-languageserver-bin, vscode-json-languageserver-bin, ya
ml-language-server
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
[I 2023-11-07 20:03:26.745 LabApp] Build is up to date
/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/nbformat/__init__.py:93: MissingIDFieldWarning: Code cell is missing an id f
ield, this will become a hard error in future nbformat versions. You may want to use `normalize()` on your notebooks before validations (available since
 nbformat 5.1.4). Previous versions of nbformat are fixing this issue transparently, and will stop doing so in the future.
  validate(nb)
[W 2023-11-07 20:03:27.061 ServerApp] Notebook zifeng001/ZF067_PAAD/scRNAseq/Frankel_2020_natcancer/ZF067_frankel.ipynb is not trusted
[I 2023-11-07 20:03:29.198 ServerApp] Kernel started: 7590ea66-0e9c-40d5-b1a8-5f13f441f11f
[I 2023-11-07 20:03:29.204 ServerApp] Kernel started: 6d138951-292e-4425-8903-8af799783edf
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
[IPKernelApp] ERROR | Failed to create history session in /tmp/ipython_hist.sqlite. History will not be saved.
Traceback (most recent call last):
  File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/IPython/core/history.py", line 549, in __init__
    self.new_session()
  File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/decorator.py", line 232, in fun
    return caller(func, *(extras + args), **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/IPython/core/history.py", line 60, in only_when_enabled
    return f(self, *a, **kw)
           ^^^^^^^^^^^^^^^^^
  File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/IPython/core/history.py", line 574, in new_session
    cur = conn.execute(
          ^^^^^^^^^^^^^
sqlite3.OperationalError: attempt to write a readonly database
[I 2023-11-07 20:03:30.347 ServerApp] Connecting to kernel 6d138951-292e-4425-8903-8af799783edf.
[I 2023-11-07 20:03:30.408 ServerApp] Connecting to kernel 7590ea66-0e9c-40d5-b1a8-5f13f441f11f.
[I 2023-11-07 20:03:30.446 ServerApp] Connecting to kernel 6d138951-292e-4425-8903-8af799783edf.
[I 2023-11-07 20:03:30.496 ServerApp] Connecting to kernel 6d138951-292e-4425-8903-8af799783edf.
[I 2023-11-07 20:03:32.178 ServerApp] Saving file at /Untitled.ipynb
[I 2023-11-07 20:03:35.108 ServerApp] Saving file at /Untitled.ipynb
[E 2023-11-07 20:03:35.143 ServerApp] Error while saving file: Untitled.ipynb disk I/O error
    Traceback (most recent call last):
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/filemanager.py", line 913, in save
        self.check_and_sign(nb, path)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/manager.py", line 712, in check_and_sign
        self.notary.sign(nb)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/nbformat/sign.py", line 477, in sign
        self.store.store_signature(signature, self.algorithm)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/nbformat/sign.py", line 233, in store_signature
        (n,) = self.db.execute("SELECT Count(*) FROM nbsignatures").fetchone()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    sqlite3.OperationalError: disk I/O error
[W 2023-11-07 20:03:35.147 ServerApp] 500 PUT /api/contents/Untitled.ipynb?1699358615086 (10.26.20.81): Unexpected error while saving file: Untitled.ipynb disk I/O error
[W 2023-11-07 20:03:35.147 ServerApp] wrote error: 'Unexpected error while saving file: Untitled.ipynb disk I/O error'
    Traceback (most recent call last):
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/filemanager.py", line 913, in save
        self.check_and_sign(nb, path)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/manager.py", line 712, in check_and_sign
        self.notary.sign(nb)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/nbformat/sign.py", line 477, in sign
        self.store.store_signature(signature, self.algorithm)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/nbformat/sign.py", line 233, in store_signature
        (n,) = self.db.execute("SELECT Count(*) FROM nbsignatures").fetchone()
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    sqlite3.OperationalError: disk I/O error

    The above exception was the direct cause of the following exception:

    Traceback (most recent call last):
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/tornado/web.py", line 1786, in _execute
        result = await result
                 ^^^^^^^^^^^^
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/handlers.py", line 266, in put
        await self._save(model, path)
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/handlers.py", line 191, in _save
        model = await ensure_async(self.contents_manager.save(model, path))
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_core/utils/__init__.py", line 189, in ensure_async
        result = await obj
                 ^^^^^^^^^
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/largefilemanager.py", line 133,
 in save
        return await super().save(model, path)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/cluster/facility/hlhuang/miniconda3/envs/jlab/lib/python3.12/site-packages/jupyter_server/services/contents/filemanager.py", line 929, in save
        raise web.HTTPError(500, f"Unexpected error while saving file: {path} {e}") from e
    tornado.web.HTTPError: HTTP 500: Internal Server Error (Unexpected error while saving file: Untitled.ipynb disk I/O error)
[E 2023-11-07 20:03:35.153 ServerApp] {
      "Host": "172.19.247.27:8789",
      "Accept": "*/*",
      "Referer": "http://172.19.247.27:8789/lab",
      "User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64; rv:109.0) Gecko/20100101 Firefox/119.0"
    }
[E 2023-11-07 20:03:35.153 ServerApp] 500 PUT /api/contents/Untitled.ipynb?1699358615086 (c5ac8133dec94235a4e0ccc95f9b5582@10.26.20.81) 45.54ms referer=http://172.19.247.27:8789/lab

a reason for the error may be that the /tmp/ipython_hist.sqlite file is not myself. I do not have permission to edit this file on the computer cluster

@Wh1isper
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Wh1isper commented Nov 19, 2023 •
edited

For cannot delete file

Try setting c.FileContentsManager.delete_to_trash = False or

$jupyter server --FileContentsManager.delete_to_trash=False

About config: https://jupyter-server.readthedocs.io/en/latest/users/configuration.html

I'm guessing it's for the same reason as this comment: #1237 (comment)

For cannot save file

Maybe you are right, the permission.😄

@li1311139481
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@Wh1isper Thank for your reply. Neither issue occurs with Jupyterlab 3.4.8. so now i use Jupyterlab 3.4.8. But i will test $jupyter server --FileContentsManager.delete_to_trash=False to see if works. In the meantime, I'll continue to wait and see if someone can solve the problem of not being able to save files. Thanks your contribution.

@RRosio RRosio mentioned this issue Nov 28, 2023
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@li1311139481
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@Wh1isper I come back. After I updated jupyterlab to 4.0.9. And I found I can save my file.
I also tried to setting Try setting c.FileContentsManager.delete_to_trash = False or $jupyter server --FileContentsManager.delete_to_trash=False. If you edit your ~/.jupyter/jupyter_lab_config.py file. and add a line of c.FileContentsManager.delete_to_trash = False. It worked, I can delete my file. If you use $jupyter server --FileContentsManager.delete_to_trash=False, I can delete my file. But when I restart jupyterlab. I have to use $jupyter server --FileContentsManager.delete_to_trash=False again.

@krassowski
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Should we reopen this issue? While I appreciate that this can be worked around using a configuration setting, it does not appear right that users should need to perform any action for delete to just work.

If this is not a bug in jupyter-server itself, maybe we should reconsider if send2trash is the right library to depend on?

This was referenced Jan 2, 2024
Closed
Open
@li1311139481
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@krassowski Thank you for your attention, and if you think this question is important, please reopen the question. If you want, I'd be happy to help you test whether the changes you make are feasible

@krassowski
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please reopen the question

I would appreciate if you can click the reopen button because I do not have rights on this repo.

I'd be happy to help you test whether the changes you make are feasible

Thank you!

@li1311139481 li1311139481 reopened this Jan 2, 2024
@Wh1isper
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Wh1isper commented Jan 2, 2024 •
edited

If this is not a bug in jupyter-server itself, maybe we should reconsider if send2trash is the right library to depend on?

I've read the related issue and I think Send2Trash should select the Trash folder with right permissions.(Note that Trash has its own structure.)

Also, I was wondering if we cloud have a "restore files/folders from Trash" feature? It seems like we only offer a hidden manual recovery feature. (through Linux Desktop or gio CLI)

Update: I just raised an issue on Send2Trash arsenetar/send2trash#87

@basderonde basderonde mentioned this issue Feb 19, 2024
Open
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@krassowski @Wh1isper @li1311139481