bgruening / docker-jupyter-notebook Goto Github PK

DEBUG:root:Host IP determined to be 172.17.0.1

INFO:requests.packages.urllib3.connectionpool:Starting new HTTPS connection (1): 172.17.0.1
---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
<ipython-input-1-f806ba0d650b> in <module>()
----> 1 handle = open(get(2), 'r')

/home/jovyan/py/galaxy.py in get(dataset_id, history_id)
    115     history_id = history_id or os.environ['HISTORY_ID']
    116 
--> 117     gi = get_galaxy_connection(history_id=history_id)
    118 
    119     file_path = '/import/%s' % dataset_id

/home/jovyan/py/galaxy.py in get_galaxy_connection(history_id)
     92     ### Fail ###
     93     msg = "Could not connect to a galaxy instance on %s. Please contact your SysAdmin for help with this error" % url
---> 94     raise Exception(msg)
     95 
     96 

Exception: Could not connect to a galaxy instance on http://172.17.0.1:None. Please contact your SysAdmin for help with this error

[TrustNotebookApp] Writing notebook-signing key to /home/jovyan/.local/share/jupyter/notebook_secret
Signing notebook: /import/ipython_galaxy_notebook.ipynb
[E 07:40:41.105 NotebookApp] Exception while loading config file /home/jovyan/.jupyter/jupyter_notebook_config.py
    Traceback (most recent call last):
      File "/opt/conda/lib/python3.4/site-packages/traitlets/config/application.py", line 535, in _load_config_files
        config = loader.load_config()
      File "/opt/conda/lib/python3.4/site-packages/traitlets/config/loader.py", line 432, in load_config
        self._read_file_as_dict()
      File "/opt/conda/lib/python3.4/site-packages/traitlets/config/loader.py", line 464, in _read_file_as_dict
        py3compat.execfile(conf_filename, namespace)
      File "/opt/conda/lib/python3.4/site-packages/ipython_genutils/py3compat.py", line 185, in execfile
        exec(compiler(f.read(), fname, 'exec'), glob, loc)
      File "/home/jovyan/.jupyter/jupyter_notebook_config.py", line 20, in <module>
        """ % {'CORS_ORIGIN': os.environ['CORS_ORIGIN'], 'WS_CORS_ORIGIN': 'ws://%s' % os.environ['CORS_ORIGIN'].split('://')[1]}
    IndexError: list index out of range
[I 07:40:41.113 NotebookApp] Writing notebook server cookie secret to /home/jovyan/.local/share/jupyter/runtime/notebook_cookie_secret
[W 07:40:41.144 NotebookApp] ipywidgets package not installed.  Widgets are unavailable.
[I 07:40:41.173 NotebookApp] Serving notebooks from local directory: /import
[I 07:40:41.174 NotebookApp] 0 active kernels 
[I 07:40:41.174 NotebookApp] The IPython Notebook is running at: http://localhost:8888/
[I 07:40:41.174 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

""" % {'CORS_ORIGIN': os.environ['CORS_ORIGIN'], 'WS_CORS_ORIGIN': 'ws://%s' % os.environ['CORS_ORIGIN'].split('://')[1]}

$ jupyter kernelspec list
Available kernels:
  ruby         /home/jovyan/.ipython/kernels/ruby
  bash         /home/jovyan/.local/share/jupyter/kernels/bash
  ir           /opt/conda/share/jupyter/kernels/ir
  julia-0.5    /opt/conda/share/jupyter/kernels/julia-0.5
  python3      /opt/conda/share/jupyter/kernels/python3
  python2      /usr/local/share/jupyter/kernels/python2

[TrustNotebookApp] ERROR | Notebook missing: /import/ipython_galaxy_notebook.ipynb
[I 14:41:39.906 NotebookApp] Writing notebook server cookie secret to /home/jovyan/.local/share/jupyter/runtime/notebook_cookie_secret
[W 14:41:40.269 NotebookApp] All authentication is disabled.  Anyone who can connect to this server will be able to run code.
[W 2021-04-30 14:41:41.436 LabApp] 'allow_origin' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-04-30 14:41:41.439 LabApp] 'ip' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-04-30 14:41:41.439 LabApp] 'port' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-04-30 14:41:41.439 LabApp] 'allow_credentials' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-04-30 14:41:41.439 LabApp] 'allow_origin' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-04-30 14:41:41.439 LabApp] 'allow_root' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-04-30 14:41:41.439 LabApp] 'base_url' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-04-30 14:41:41.440 LabApp] 'token' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-04-30 14:41:41.440 LabApp] 'tornado_settings' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[W 2021-04-30 14:41:41.440 LabApp] 'tornado_settings' has moved from NotebookApp to ServerApp. This config will be passed to ServerApp. Be sure to update your config before our next release.
[I 2021-04-30 14:41:41.455 LabApp] JupyterLab extension loaded from /opt/conda/lib/python3.8/site-packages/jupyterlab
[I 2021-04-30 14:41:41.455 LabApp] JupyterLab application directory is /opt/conda/share/jupyter/lab
[I 14:41:41.865 NotebookApp] [Jupytext Server Extension] Deriving a JupytextContentsManager from LargeFileManager
[I 14:41:41.869 NotebookApp] Serving notebooks from local directory: /import
[I 14:41:41.869 NotebookApp] Jupyter Notebook 6.2.0 is running at:
[I 14:41:41.869 NotebookApp] http://36c4117dfe7e:8888/gie_proxy/jupyter/ipython/
[I 14:41:41.869 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[I 14:41:41.880 NotebookApp] 302 GET /gie_proxy/jupyter/ipython/login?next=%2Fgie_proxy%2Fjupyter%2Fipython%2Ftree (172.17.0.1) 2.090000ms
[W 14:41:42.192 NotebookApp] 404 GET /gie_proxy/jupyter/ipython/notebooks/ipython_galaxy_notebook.ipynb (172.17.0.1): No such file or directory: ipython_galaxy_notebook.ipynb
[W 14:41:42.218 NotebookApp] 404 GET /gie_proxy/jupyter/ipython/notebooks/ipython_galaxy_notebook.ipynb (172.17.0.1) 27.870000ms referer=http://212.189.205.57/plugins/interactive_environments/jupyter/show?image_tag=quay.io%2Fbgruening%2Fdocker-jupyter-notebook%3Alatest&dataset_id=f2db41e1fa331b3e&additional_dataset_ids=

#!/bin/bash

# The IPython image starts as privileged user.
# The parent Galaxy server is mounting data into /import with the same
# permissions as the Galaxy server is running on.
# In case of 1450 as UID and GID we are fine, because our preconfigured ipython
# user owns this UID/GID.
# (1450 is the user id the Galaxy-Docker Image is using)
# If /import is not owned by 1450 we need to create a new user with the same
# UID/GID as /import and make everything accessible to this new user.
#
# In the end the IPython Server is started as non-privileged user. Either
# with the UID 1450 (preconfigured jupyter user) or a newly created 'galaxy' user
# with the same UID/GID as /import.

export PATH=/home/jovyan/.local/bin:$PATH

python /get_notebook.py

if [ ! -f /import/ipython_galaxy_notebook.ipynb ]; then
    cp /home/$NB_USER/notebook.ipynb /import/ipython_galaxy_notebook.ipynb
    chown $NB_USER /import/ipython_galaxy_notebook.ipynb
fi

jupyter trust /import/ipython_galaxy_notebook.ipynb
##/monitor_traffic.sh &
jupyter notebook --no-browser