permissions in terminal

JupyterHub
1

Description

For some strange reason if I run the same code in terminal through ssh on my Ubuntu machine and on JupyterLab terminal everything goes fine, but when I run JupyterLab within JupyterHub something changes, I don’t get enough permissions…

Expected behaviour

Here are the commands and response in ssh terminal and in JupyterLab terminal

bioinfo@bioinfo:/var/www/html/scripts$ whoami
bioinfo
bioinfo@bioinfo:/var/www/html/scripts$ groups bioinfo
bioinfo : bioinfo adm cdrom sudo dip plugdev users lpadmin sambashare webmaster fs13-mount-rw
bioinfo@bioinfo:/var/www/html/scripts$ ls -la
total 8
drwxrwxr-x 2 root webmaster 4096 авг  1 18:32 .
dr-xrwxr-x 4 root webmaster 4096 авг  1 18:10 ..
bioinfo@bioinfo:/var/www/html/scripts$ touch 1
bioinfo@bioinfo:/var/www/html/scripts$

Actual behaviour

But under JupyterHub things change:

bioinfo@bioinfo:/var/www/html/scripts$ whoami
bioinfo
bioinfo@bioinfo:/var/www/html/scripts$ groups bioinfo
bioinfo : bioinfo adm cdrom sudo dip plugdev users lpadmin sambashare webmaster fs13-mount-rw
bioinfo@bioinfo:/var/www/html/scripts$ ls -la
total 8
drwxrwxr-x 2 root webmaster 4096 Aug  1 18:32 .
dr-xrwxr-x 4 root webmaster 4096 Aug  1 18:10 ..
bioinfo@bioinfo:/var/www/html/scripts$ touch 1
touch: cannot touch '1': Permission denied

But I don’t get the thing: I’m running commands under the same user, in the same folder. Why would I have different permissions?

Your personal set up

I installed JupyterHub/Lab through pip3.

  • OS: Linux bioinfo 5.4.0-80-generic #90-Ubuntu SMP Fri Jul 9 22:49:44 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

  • Version(s): jupyterhub 1.4.2, python 3.8

  • Full environment 
# paste output of `pip freeze`
$ pip freeze
aiogram==2.14.3
aiohttp==3.7.4.post0
alembic==1.6.5
anyio==3.3.0
APScheduler==3.7.0
apturl==0.5.2
argon2-cffi==20.1.0
async-generator==1.10
async-lru==1.0.2
async-timeout==3.0.1
attrs==21.2.0
Babel==2.9.1
backcall==0.2.0
bcrypt==3.1.7
beautifulsoup4==4.8.2
biopython==1.79
bleach==3.3.1
blinker==1.4
Brlapi==0.7.0
cairocffi==1.2.0
CairoSVG==2.5.2
certifi==2021.5.30
certipy==0.1.3
cffi==1.14.6
chardet==3.0.4
chartkick==0.5.0
cheroot==8.3.0
CherryPy==8.9.1
click==8.0.1
colorama==0.4.3
colour==0.1.5
command-not-found==0.3
ConfigArgParse==0.13.0
cryptography==3.4.7
cssselect2==0.4.1
cupshelpers==1.0
cycler==0.10.0
dbus-python==1.2.16
debugpy==1.4.1
decorator==5.0.9
defer==1.0.6
defusedxml==0.7.1
dill==0.3.4
distro==1.4.0
distro-info===0.23ubuntu1
dnspython==1.16.0
drawSvg==1.8.2
duplicity==0.8.12.0
entrypoints==0.3
et-xmlfile==1.1.0
fasteners==0.14.1
feedparser==5.2.1
filelock==3.0.12
Flask==2.0.1
future==0.18.2
gpg===1.13.1-unknown
gurobipy==9.1.2
html5lib==1.0.1
httplib2==0.14.0
humanfriendly==4.18
humanize==3.10.0
idna==2.8
imageio==2.9.0
ipykernel==6.0.3
ipython==7.25.0
ipython-genutils==0.2.0
ipywidgets==7.6.3
itsdangerous==2.0.1
jaraco.functools==2.0
jedi==0.18.0
Jinja2==3.0.1
joblib==1.0.1
json5==0.9.6
jsonschema==3.2.0
jupyter==1.0.0
jupyter-client==6.1.12
jupyter-console==6.4.0
jupyter-contrib-core==0.3.3
jupyter-contrib-nbextensions==0.5.1
jupyter-core==4.7.1
jupyter-highlight-selected-word==0.2.0
jupyter-latex-envs==1.4.6
jupyter-nbextensions-configurator==0.4.1
jupyter-server==1.10.1
jupyter-telemetry==0.1.0
jupyterhub==1.4.2
jupyterlab==3.0.16
jupyterlab-pygments==0.1.2
jupyterlab-server==2.6.1
jupyterlab-widgets==1.0.0
keyring==18.0.1
kiwisolver==1.3.1
language-selector==0.1
launchpadlib==1.10.13
lazr.restfulclient==0.14.2
lazr.uri==1.0.3
lockfile==0.12.2
logomaker==0.8
louis==3.12.0
lxml==4.5.0
macaroonbakery==1.3.1
Mako==1.1.0
Markdown==3.1.1
MarkupSafe==2.0.1
matplotlib==3.4.2
matplotlib-inline==0.1.2
# Editable install with no version control (misc==0.0.0)
-e /home/bioinfo/lib/misc
mistune==0.8.4
monotonic==1.5
more-itertools==4.2.0
multidict==5.1.0
nbclassic==0.3.1
nbclient==0.5.3
nbconvert==6.1.0
nbformat==5.1.3
nest-asyncio==1.5.1
netifaces==0.10.4
nodejs==0.1.1
notebook==6.4.0
npm==0.1.1
Nuitka==0.6.16.2
numpy==1.21.1
oauthlib==3.1.0
olefile==0.46
onboard==1.4.1
openpyxl==3.0.7
optional-django==0.1.0
packaging==21.0
padme==1.1.1
pamela==1.0.0
pandas==1.3.1
pandocfilters==1.4.3
paramiko==2.6.0
parso==0.8.2
pexpect==4.6.0
pickleshare==0.7.5
Pillow==7.0.0
prometheus-client==0.11.0
prompt-toolkit==3.0.19
protobuf==3.6.1
psutil==5.5.1
ptyprocess==0.7.0
pyaes==1.6.1
pyasn1==0.4.2
pyasn1-modules==0.2.1
pycairo==1.16.2
pycparser==2.20
pycrypto==2.6.1
pycups==1.9.73
pycurl==7.43.0.2
Pygments==2.9.0
PyGObject==3.36.0
PyJWT==1.7.1
pylibacl==0.5.4
-e git+git@github.com:lapotok/pymabs.git@c9c1c29ceb0c6df6756d7fd479f74374939a1a22#egg=pymabs
pymacaroons==0.13.0
-e git+git@github.com:lapotok/pymolbiol.git@71b8bf3ec8a7fc27c8d17d58d3f3b72e3ebfe4f3#egg=pymolbiol
PyNaCl==1.3.0
pyOpenSSL==19.0.0
pyparsing==2.4.6
pyRFC3339==1.1
Pyrogram==1.2.9
pyrsistent==0.18.0
PySocks==1.7.1
pyTelegramBotAPI==3.8.2
python-apt==2.0.0+ubuntu0.20.4.5
python-dateutil==2.7.3
python-debian===0.1.36ubuntu1
python-editor==1.0.4
python-json-logger==2.0.2
python-ldap==3.2.0
pytz==2019.3
pyxattr==0.6.1
pyxdg==0.26
PyYAML==5.3.1
pyzmq==22.1.0
qtconsole==5.1.1
QtPy==1.9.0
rdiff-backup==2.0.0
rdiffweb==2.3.0
regex==2021.7.6
reportlab==3.5.34
repoze.lru==0.7
requests==2.22.0
requests-file==1.5.1
requests-unixsocket==0.2.0
Routes==2.4.1
ruamel.yaml==0.17.10
ruamel.yaml.clib==0.2.6
SecretStorage==2.3.1
selenium==3.141.0
selenium-requests==1.3
Send2Trash==1.7.1
simplejson==3.16.0
six==1.14.0
sniffio==1.2.0
soupsieve==1.9.5
SQLAlchemy==1.3.12
ssh-import-id==5.10
system-service==0.3
systemd-python==234
terminado==0.10.1
testpath==0.5.0
TgCrypto==1.2.2
tinycss2==1.1.0
tldextract==3.1.0
tornado==6.1
torpy==1.1.6
traitlets==5.0.5
typing-extensions==3.10.0.0
tzlocal==2.1
ubuntu-advantage-tools==27.0
ubuntu-drivers-common==0.0.0
ufw==0.36
unattended-upgrades==0.1
unity-scope-calculator==0.1
unity-scope-devhelp==0.1
unity-scope-manpages==0.1
unity-scope-tomboy==0.1
unity-scope-virtualbox==0.1
unity-scope-zotero==0.1
urllib3==1.25.8
usb-creator==0.3.7
wadllib==1.3.3
wcwidth==0.2.5
webencodings==0.5.1
WebOb==1.8.5
websocket-client==1.1.0
Werkzeug==2.0.1
widgetsnbextension==3.5.1
WTForms==2.2.1
xdiagnose==3.8.9
xkit==0.0.0
XlsxWriter==1.1.2
yarl==1.6.3
bioinfo@bioinfo:/var/w
  • Configuration 
# grep -v '\(^#\|^[[:space:]]*$\)' jupyterhub_config.py
c.Spawner.cmd = ["jupyter-labhub"]
c.Spawner.default_url = '/lab'

Thank you in advance!

2

Have you checked your system logs around the time of the error? Do you have any security hardening software running such as AppArmor that might prevent a write which originates from a web server?

Do you have the same problem in other directories, or only this one? For example if you create a directory with the same owner and permissions but under your home directory do you also see the same error?

3

Note that the JupyterLab terminal does not start its terminals as login shells, but as interactive non-login shells (see this explanation of the difference). This means that .bash_profile is not executed for you in the JupyterLab terminal.

Is it possible that some of the configuration that you expect is being loaded by .bash_profile? You can test that by running source ~/.bash_profile in the JupyterLab terminal; if that fixes the problem, then you’ll need to rethink how you lay out your relationship between .bashrc and .bash_profile so that you get the behavior you want in all non-login shells…

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