Dockerfile and other files to construct image for Jupyter lab-hub (old)

.gitignore

@@ -107,3 +107,4 @@ venv.bak/
 # mypy
 .mypy_cache/
 
+/.project

jupyter_docker/Dockerfile

@@ -0,0 +1,105 @@
+# cd <this Dockerfile directory>
+# docker build -t magic-jupyter .
+# Test run:
+# docker run -it --rm -p 8000:8000 -v /home/myuser/docker/jupyterhub:/home magic-jupyter
+# Open browser: "http://localhost:8000"
+#
+# At Magic Server:
+# docker create --network=magic-net --name magic-jupyterhub
+#    -v /srv/docker/magic/data/jupyter:/home
+#    magic-jupyter
+# docker start magic-jupyterhub
+#
+FROM debian:10.3
+
+ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
+
+# Update and install Debian packages
+RUN apt-get update --fix-missing && apt-get install -y wget bzip2 ca-certificates \
+    libglib2.0-0 libxext6 libsm6 libxrender1 libspatialindex-dev \
+    git mercurial subversion
+
+# Install CONDA
+RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
+#    wget --quiet https://repo.continuum.io/archive/Anaconda3-5.3.1-Linux-x86_64.sh -O ~/anaconda.sh && \
+#    wget --quiet https://repo.continuum.io/archive/Anaconda3-2018.12-Linux-x86_64.sh -O ~/anaconda.sh && \
+    wget --quiet https://repo.continuum.io/archive/Anaconda3-2020.02-Linux-x86_64.sh -O ~/anaconda.sh && \
+    /bin/bash ~/anaconda.sh -b -p /opt/conda && \
+    rm ~/anaconda.sh
+
+# "init" for Docker containers
+RUN apt-get install -y curl grep sed dpkg vim && \
+    TINI_VERSION=`curl https://github.com/krallin/tini/releases/latest | grep -o "/v.*\"" | sed 's:^..\(.*\).$:\1:'` && \
+    curl -L "https://github.com/krallin/tini/releases/download/v${TINI_VERSION}/tini_${TINI_VERSION}.deb" > tini.deb && \
+    dpkg -i tini.deb && \
+    rm tini.deb && \
+    apt-get clean
+
+ENV PATH /opt/conda/bin:$PATH
+
+RUN conda install -c conda-forge mpld3 && \
+#    conda install -c conda-forge jupyterlab==0.35.2 && \
+    conda install -c r r-irkernel && \
+    conda install -c r r-essentials && \
+    conda install -c r rpy2
+
+RUN pip install --upgrade pip && \
+#    pip install jupyterlab && \
+    pip install npm webdavclient && \
+    jupyter serverextension enable --py jupyterlab
+
+RUN conda install -c plotly plotly && \
+#    conda install -c conda-forge jupyterhub && \
+    conda update jupyter_core jupyter_client
+
+RUN apt-get install -y software-properties-common gnupg
+
+RUN curl -sL https://deb.nodesource.com/setup_12.x | bash - && \
+    apt-get install -y nodejs && \
+#    jupyter labextension install @jupyterlab/hub-extension && \
+    pip install mapboxgl fiona folium geocoder geopandas geopy googlemaps pyproj pysal rtree shapely telluric
+
+
+# For dashboards, each kernel should run: jupyter nbextension enable jupyter_dashboards --py --sys-prefix
+#RUN conda install -c r rpy2
+
+RUN pip install jupyter_dashboards && jupyter dashboards quick-setup --sys-prefix && \
+    pip install ipywidgets && \
+    jupyter nbextension enable --py --sys-prefix widgetsnbextension && \
+#    jupyter labextension install @jupyter-widgets/[email protected] && \
+#    pip install ipysankeywidget && jupyter nbextension enable --py --sys-prefix ipysankeywidget && \
+    pip install ipyleaflet && jupyter labextension install jupyter-leaflet && \
+#    jupyter labextension install @jupyterlab/geojson-extension && \  ## INCOMPATIBLE WITH JUPYTERLAB_PYVIZ
+    jupyter labextension install @jupyterlab/plotly-extension
+
+RUN conda install -c bokeh bokeh && \
+    jupyter labextension install jupyterlab_bokeh && \
+    conda install -c conda-forge holoviews && \
+    jupyter labextension install @pyviz/jupyterlab_pyviz && \
+    pip install py_d3 altair vega_datasets && \
+    pip install bqplot && jupyter labextension install bqplot && \
+    jupyter labextension install cy-jupyterlab && \
+    pip install ipysigma && \
+    jupyter nbextension enable --py --sys-prefix ipysigma && \
+    jupyter labextension install ipysigma
+
+RUN conda install -c conda-forge cartopy
+RUN pip install pivottablejs
+
+RUN pip install ipylab && \
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager ipylab
+#RUN conda install -c conda-forge ipylab
+
+RUN pip install nexinfosys-client
+
+ADD users.csv /root/users.csv
+ADD create_users.py /root/create_users.py
+ADD init_script.sh /root/init_script.sh
+ADD jupyterhub_config.py /root/jupyterhub_config.py
+RUN ["chmod", "+x", "/root/init_script.sh"]
+
+ENTRYPOINT [ "/usr/bin/tini", "--" ]
+#CMD [ "/bin/bash" ]
+EXPOSE 8000
+CMD ["/root/init_script.sh"]
+#CMD ["jupyter", "notebook", "--port=8000", "--no-browser", "--allow-root", "--ip=0.0.0.0"]

jupyter_docker/README.txt

@@ -0,0 +1,16 @@
+Extracted from the Dockerfile:
+
+Build image:
+
+cd <this Dockerfile directory>
+docker build -t magic-jupyter .
+
+Test run:
+
+docker run -it --rm -p 8000:8000 -v /home/myuser/docker/jupyterhub:/home magic-jupyter
+Open browser: "http://localhost:8000"
+
+At Magic Server:
+
+docker create --network=magic-net --name magic-jupyterhub -v /srv/docker/magic/data/jupyter:/home magic-jupyter
+docker start magic-jupyterhub

jupyter_docker/create_users.py

@@ -0,0 +1,19 @@
+import pandas as pd
+import os
+import sys
+import crypt
+import csv
+
+
+def create_users(file):
+    with open(file, 'r') as csvfile:
+        for row in csv.reader(csvfile, delimiter=','):
+            user = row[0]
+            passw = row[1]
+            pwd = crypt.crypt(passw, crypt.mksalt(crypt.METHOD_SHA512))
+            s = "useradd -m -b /home -p '"+pwd+"' "+user
+            os.system(s)
+
+
+print("Creating users from file: "+sys.argv[1], flush=True)
+create_users(sys.argv[1])

jupyter_docker/init_script.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+python3 /root/create_users.py /root/users.csv
+jupyterhub -f /root/jupyterhub_config.py
+#jupyter labhub