Dockerfile

FROM ubuntu:focal

LABEL maintainer="Collaboratory Platform <platform@humanbrainproject.eu>"

ARG NB_USER="jovyan"
ARG NB_UID=1000
ARG NB_GID=100

ENV GIT_COMMITTER_NAME=platform@humanbrainproject.eu \
    GIT_COMMITTER_EMAIL=platform@humanbrainproject.eu \
    USER="${NB_USER}" \
    MPLBACKEND=Agg \
    SHELL=/bin/bash \
    SSL_CERT_DIR=/etc/ssl/certs \
    XDG_CACHE_HOME=/tmp/cache/ \
    LAB_IMAGE_NAME=EBRAINS_OFFICIAL

USER root

# Set the Switzerland timezone (necessary to make r-base install noninteractive)
RUN ln -sf /usr/share/zoneinfo/Europe/Zurich /etc/localtime

# Set to noninteractive for install
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update --yes && \
    apt-get install --yes \
    ca-certificates \
    cmake \
    csh \
    curl \
    cython \
    gcc \
    gettext \
    git \
    libnss-wrapper \
    llvm \
    lsof \
    mpich \
    pandoc \
    python-dev \
    python3-venv \
    python3-pip \
    r-base \
    swig \
    unzip \
    vim  && \
    apt-get clean && rm -rf /var/lib/apt/lists/*

# install nodejs
RUN curl -fsSL https://deb.nodesource.com/setup_17.x | bash
RUN apt-get install -y nodejs

# install min texlive (necessary for nb exports)
RUN apt-get update --yes && \
    apt-get install --yes --no-install-recommends \
    texlive-xetex \
    texlive-fonts-recommended \
    texlive-plain-generic && \
    apt-get clean && rm -rf /var/lib/apt/lists/*

# jupyter install in /opt/app-root/ for legacy reasons (previously based on centos base image)
RUN mkdir -p /opt/app-root/etc /opt/app-root/clb/ /opt/app-root/src
COPY base/jupyter_notebook_config.py /opt/app-root/etc/

# folders for drive integration
RUN mkdir -p /mnt/user/
RUN ln -s /mnt/user/drive /opt/app-root/src/drive
RUN ln -s /mnt/user/shared /opt/app-root/src/shared

ENV HOME=/opt/app-root/src/

# install pip packages
COPY base/requirements.txt /tmp
RUN pip install --no-cache-dir -r /tmp/requirements.txt

# fix missing template issue in nbgitpuller: https://github.com/jupyterhub/nbgitpuller/issues/235
# remove this once it has been fixed in project
RUN ln -s /usr/local/lib/python3.8/dist-packages/nbgitpuller/templates/status.html /usr/local/lib/python3.8/dist-packages/notebook/templates/

# disable ipcluster extension
RUN jupyter labextension disable ipcluster \
                              ipyparallel-labextension

# install additional labextensions
RUN jupyter labextension install --no-build \
                             clb-jupyter-ext-query-params@3.2.0 \
                             clb-lab-extension@0.9.2 \
                             ipycanvas@0.12.0
# ipycanvas@0.12.0: Python part installed via spack (py-ipycanvas@0.12.0)

RUN jupyter lab build

RUN jupyter notebook --generate-config
RUN mkdir -p /opt/app-root/src/.ipython/profile_default/startup/ /opt/app-root/src/.local/lib/python3.8/site-packages/ /tmp/cache/

# Preload clb_oauth
RUN echo 'from clb_nb_utils import oauth as clb_oauth' >> /opt/app-root/src/.ipython/profile_default/startup/50-clb-nb-utils.py

# install R kernel
RUN R --slave -e "install.packages('IRkernel')"
RUN R --slave -e "IRkernel::installspec(name = 'ir363', displayname = 'R 3.6.3')"

# fix permissions so NB_USER has permissions to run notebooks and install packages
COPY base/fix-permissions /usr/local/bin/fix-permissions
RUN chmod +x /usr/local/bin/fix-permissions

# copy user setup file
COPY base/user_setup.sh /opt/app-root/etc/
RUN chmod +x /opt/app-root/etc/user_setup.sh

RUN fix-permissions /opt/app-root/ && \
    fix-permissions /tmp/cache/ && \
    fix-permissions /usr/local/share/jupyter/ && \
    fix-permissions /usr/local/etc/jupyter && \
    fix-permissions /usr/local/lib/R/site-library && \
    fix-permissions /usr/etc/jupyter/

# to support OpenShift's arbitrary UIDs
# more info: https://docs.openshift.com/enterprise/3.1/creating_images/guidelines.html
COPY base/passwd.template /tmp/passwd.template
COPY base/group.template /tmp/group.template
COPY base/start-notebook.sh /opt/app-root/etc/
RUN chmod +x /opt/app-root/etc/start-notebook.sh

WORKDIR /opt/app-root/src/

EXPOSE 8080

USER ${NB_UID}

CMD /opt/app-root/etc/start-notebook.sh