Dockerfile.ub

# FROM kosted/saar-training-jupyterlab:0.0.3
# FROM imansour/maap-esa-jupyterlab:0.0.14
ARG ROOT_CONTAINER=registry.access.redhat.com/ubi9/ubi-init

FROM $ROOT_CONTAINER


LABEL maintainer="Red Hat, Inc."

LABEL com.redhat.component="ubi9-init"
LABEL name="ubi9/ubi9-init"
LABEL version="9.4"
LABEL modifide="2024-10-24"
LABEL modified_by="Islam Mansour"

#label for EULA
LABEL com.redhat.license_terms="https://www.redhat.com/en/about/red-hat-end-user-license-agreements#UBI"

#labels for container catalog
LABEL summary="Provides the latest release of the Red Hat Universal Base Image 9 Init for multi-service containers."
LABEL description="The Universal Base Image Init is designed is designed to run an init system as PID 1 for running multi-services inside a container. This base image is freely redistributable, but Red Hat only supports Red Hat technologies through subscriptions for Red Hat products. This image is maintained by Red Hat and updated regularly."
LABEL io.k8s.display-name="Red Hat Universal Base Image 9 Init"
LABEL io.openshift.expose-services=""

ENV container oci
ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin


# ===============================Custom Start=========================================================================
USER 0

# dnf config-manager isn't available at first, and
# we need it to install the CRB repo below.
RUN dnf -y install 'dnf-command(config-manager)'

# What used to be powertools is now called "CRB".
# We need it for some of the packages installed below.
# https://docs.fedoraproject.org/en-US/epel/
# RUN dnf config-manager --set-enabled crb
RUN dnf -y install \
    https://dl.fedoraproject.org/pub/epel/epel-release-latest-$(rpm -E %rhel).noarch.rpm \
    https://dl.fedoraproject.org/pub/epel/epel-next-release-latest-$(rpm -E %rhel).noarch.rpm
RUN dnf config-manager --enable epel,epel-next
RUN dnf install -y https://download1.rpmfusion.org/free/el/rpmfusion-free-release-9.noarch.rpm
RUN dnf install -y https://download1.rpmfusion.org/nonfree/el/rpmfusion-nonfree-release-9.noarch.rpm

# The --nobest flag is hopefully temporary. Without it we currently hit
# package versioning conflicts around OpenSSL.
RUN dnf update -y \
    && dnf -y --nobest install \
    bash \
    diffutils \
    git \
    git-lfs \
    iproute \
    jq \
    less \
    lsof \
    man \
    nano \
    procps \
    p7zip \
    p7zip-plugins \
    perl-Digest-SHA \
    net-tools \
    openssh-clients \
    rsync \
    socat \
    sudo \
    time \
    vim \
    wget \
    zip \
    stow \
    zlib-devel \
    mediainfo \
    pandoc \
    gfortran \
    gcc \
    bzip2 \
    tini \
  && dnf clean all && rm -rf /var/cache/dnf


# Configure environment
ENV CONDA_DIR=/opt/conda \
    SHELL=/bin/bash \
    LC_ALL=en_US.UTF-8 \
    LANG=en_US.UTF-8 \
    LANGUAGE=en_US.UTF-8
ENV PATH="${CONDA_DIR}/bin:${PATH}" \
    HOME=/root

ENV NB_USER=jovyan
ENV NB_UID=1234
ENV HOME=/home/${NB_USER}

RUN \
    # add user and configure it
    useradd -u 1234 -G wheel,root -d ${HOME} --shell /bin/bash -m ${NB_USER} && \
    mkdir -p ${HOME} && \
    cp -rT /etc/skel ${HOME} && \
    # Setup $PS1 for a consistent and reasonable prompt
    touch /etc/profile.d/udi_prompt.sh && \
    chown 1234 /etc/profile.d/udi_prompt.sh && \
    echo "export PS1='\W \`git branch --show-current 2>/dev/null | sed -r -e \"s@^(.+)@\(\1\) @\"\`$ '" >> /etc/profile.d/udi_prompt.sh && \
    # Copy the global git configuration to user config as global /etc/gitconfig
    # file may be overwritten by a mounted file at runtime
    cp /etc/gitconfig ${HOME}/.gitconfig && \
    chown 1234 ${HOME}/ ${HOME}/.gitconfig  && \
    # Set permissions on /etc/passwd and /home to allow arbitrary users to write
    chgrp -R 0 /home && \
    chmod -R g=u /etc/passwd /etc/group /home

ENV ENV_NAME=base


# Layer cleanup script
# Make clean-layer and fix-permissions executable
COPY resources/scripts/fix-permissions.sh /usr/local/bin/
RUN chmod a+rx /usr/local/bin/fix-permissions.sh \
    && ln -s /usr/local/bin/fix-permissions.sh /usr/local/bin/fix-permissions
    
COPY resources/scripts/clean-layer.sh /usr/local/bin/
RUN chmod a+rx /usr/local/bin/clean-layer.sh \
    && ln -s /usr/local/bin/clean-layer.sh /usr/local/bin/clean-layer


# Enable prompt color in the skeleton .bashrc before creating the default NB_USER
# hadolint ignore=SC2016
RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
   # Add call to conda init script see https://stackoverflow.com/a/58081608/4413446
   echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc


ARG PYTHON_VERSION=3.11

# Download and install Micromamba, and initialize the Conda prefix.
#   <https://github.com/mamba-org/mamba#micromamba>
#   Similar projects using Micromamba:
#     - Micromamba-Docker: <https://github.com/mamba-org/micromamba-docker>
#     - repo2docker: <https://github.com/jupyterhub/repo2docker>
# Install Python, Mamba, and jupyter_core
# Cleanup temporary files and remove Micromamba
# Correct permissions
# Do all this in a single RUN command to avoid duplicating all of the
# files across image layers when the permissions change
COPY initial-condarc "${CONDA_DIR}/.condarc"
WORKDIR /tmp
RUN set -x && \
    arch=$(uname -m) && \
    if [ "${arch}" = "x86_64" ]; then \
        # Should be simpler, see <https://github.com/mamba-org/mamba/issues/1437>
        arch="64"; \
    fi && \
    # https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html#linux-and-macos
    wget --progress=dot:giga -O - \
        "https://micro.mamba.pm/api/micromamba/linux-${arch}/latest" | tar -xvj bin/micromamba && \
    PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && \
    if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && \
    # Install the packages
    ./bin/micromamba install \
        --root-prefix="${CONDA_DIR}" \
        --prefix="${CONDA_DIR}" \
        --yes \
        "${PYTHON_SPECIFIER}" \
        'mamba' \
        'jupyter_core' && \
    rm -rf /tmp/bin/ && \
    # Pin major.minor version of python
    # https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-pkgs.html#preventing-packages-from-updating-pinning
    mamba list --full-name 'python' | tail -1 | tr -s ' ' | cut -d ' ' -f 1,2 | sed 's/\.[^.]*$/.*/' >> "${CONDA_DIR}/conda-meta/pinned" && \
    mamba clean --all -f -y && \
    rm -rf "/home/${NB_USER}/.cache/yarn" 


# Install Jupyter Notebook, Lab, and Hub
# Generate a notebook server config
# Cleanup temporary files
# Correct permissions
# Do all this in a single RUN command to avoid duplicating all of the
# files across image layers when the permissions change
RUN mamba install --quiet --yes \
    'notebook' \
    'jupyterhub' \
    'jupyterlab' \
    'nodejs=20.*' && \
    mamba clean --all -f -y && \
    npm cache clean --force && \
    jupyter notebook --generate-config && \
    jupyter lab clean && \
    clean-layer 

RUN dnf install https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm -y && \
    dnf install -y python3-pip && \
    dnf clean all 

RUN \ 
    mamba install --quiet --yes \
        'altair' \
        'astropy' \
        'beautifulsoup4' \
        'bokeh' \
        'bottleneck' \
        'bqplot' \
        'cartopy' \
        'cloudpickle' \
        'cmake' \
        'cython' \
        'dask-geopandas' \
        'dask-labextension' \
        'dask-sql' \
        'dask' \
        'dill' \
        'entwine' \
        'eoreader' \
        'evidently' \
        'fiona' \
        'gdal' \
        'geopandas' \
        'h5netcdf' \
        'h5py' \
        'ipycytoscape' \
        'ipyleaflet'  \
        'ipyleaflet' \
        'ipympl' \
        'ipympl'\
        'ipyparallel' \
        'ipywidgets' \
        'isce2' \
        'isce3' \
        'jupyter-lsp-python' \
        'jupyter-lsp-r' \
        'jupyter-lsp' \
        'jupyterhub' \
        'jupyterlab_code_formatter' \
        'jupyterlab-drawio' \
        'jupyterlab-git' \
        'jupyterlab-lsp' \
        'jupyterlab-system-monitor' \
        'jupyterlab' \
        'jupytext' \
        'leafmap' \
        'matplotlib-base' \
        'nbclient' \
        'nbdime' \
        'nbformat' \
        'nbqa' \
        'netcdf4' \
        'nikola' \
        'notebook' \
        'numba' \
        'numexpr' \
        'numpy<2' \
        'pandas-profiling' \
        'pandas' \
        'panel' \
        'patsy' \
        'pdal' \
        'pdal' \
        'protobuf' \
        'pygmt' \
        'pyproj' \
        'pyroSAR' \
        'pytables' \
        'python-lsp-server' \
        'python-pdal' \
        'pythreejs' \
        'r-languageserver' \
        'rasterio' \
        'richdem' \
        'rioxarray' \
        'scikit-image' \
        'scikit-learn' \
        'scipy' \
        'seaborn' \
        'shapely' \
        'sqlalchemy' \
        'statsmodels' \
        'sympy' \
        'voila' \
        'widgetsnbextension'\
        'xarray' \
        'xlrd' \
        'zarr' \
  && \
    clean-layer


RUN \
    jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
    pip install --no-cache-dir jupyterlab-novnc jupyterlab-mathjax3 jupyterlab-geojson jupyterlab-katex jupyterlab-fasta jupyterlab-latex && \
    # jupyter lab build -y --dev-build=False --minimize=False && \
    jupyter lab clean -y && \
    npm cache clean --force && \
    clean-layer

# RUN \
#     jupyter nbextension enable --py widgetsnbextension --sys-prefix && \
#     lab_ext_install='jupyter labextension install --no-build '  && \
#     lab_ext_build='jupyter lab build '  && \
#     # Also activate ipywidgets extension for JupyterLab
#     # Check this URL for most recent compatibilities
#     # https://github.com/jupyter-widgets/ipywidgets/tree/master/packages/jupyterlab-manager
#     eval $lab_ext_install \
#         jupyter-matplotlib \
#         @jupyter-widgets/jupyterlab-manager \
#         @bokeh/jupyter_bokeh \
#         @jupyterlab/debugger \
#         plotlywidget \
#         dask-labextension \
#         jupyterlab-chart-editor \
#         @jupyterlab/translation \
#         @jupyterlab/translation-extension \
#         @jupyterlab/hdf5 \
#         @jupyterlab/geojson-extension \
#         @jupyterlab/latex \
#         @jupyterlab/fasta-extension \
#         @jupyterlab/geojson-extension \
#         @jupyterlab/katex-extension \
#         @jupyterlab/mathjax3-extension \
#         @jupyterlab/plugin-playground && \
#     # jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build && \
#     # jupyter labextension install @bokeh/jupyter_bokeh --no-build && \
#     # jupyter labextension install jupyter-matplotlib --no-build && \
#     # jupyter lab build -y && \
#     # jupyter lab clean -y && \
#     eval $lab_ext_build && \
#     jupyter lab clean && \
#     npm cache clean --force && \
#     clean-layer


# Install facets which does not have a pip or conda package at the moment
WORKDIR /tmp
RUN git clone https://github.com/PAIR-code/facets.git && \
    jupyter nbextension install facets/facets-dist/ --sys-prefix && \
    rm -rf /tmp/facets 

# Import matplotlib the first time to build the font cache.
ENV XDG_CACHE_HOME="${HOME}/.cache/"

RUN MPLBACKEND=Agg python -c "import matplotlib.pyplot" 


# # Install pysarpro
# RUN pip install --quiet --no-cache-dir \
#     pysarpro  




WORKDIR /projects
ENV HOME=/projects


#RUN echo ". $CONDA_DIR/etc/profile.d/conda.sh" >> ~/.bashrc && \
#    echo "conda activate base" >> ~/.bashrc

ADD notebooks /projects/
ADD rootfs/root /root/
ADD maap-jupyter-ide/entrypoint.sh /maap-jupyter-ide/entrypoint.sh
# Overwrite & add Labels
LABEL \
    "maintainer"="me@imansour.net" \
    "author"="Islam Mansour" 


#RUN pip install --global-option=build_ext --global-option="-I/usr/include/gdal" GDAL==`gdal-config --version` && \

# We add the script folder and the zip file to be able to unzip the structure of the project
COPY maap-jupyter-ide/scripts/initTemplate.sh /usr/bmap/initTemplate.sh
COPY maap-jupyter-ide/scripts/initCredentials.sh /usr/bmap/initCredentials.sh
COPY maap-jupyter-ide/scripts/Project_template.zip /usr/bmap/Project_template.zip
COPY maap-jupyter-ide/scripts/shareAlgorithm.sh /usr/bmap/shareAlgorithm.sh
COPY maap-jupyter-ide/scripts/.gitlab-ci.yml /usr/bmap/.gitlab-ci.yml
COPY maap-jupyter-ide/scripts/.condarc /usr/bmap/.condarc

# We add the RestClient file
COPY maap-jupyter-ide/scripts/RestClient.py /usr/bmap/RestClient.py
COPY maap-jupyter-ide/scripts/quicklook_raster.py /usr/bmap/quicklook_raster.py
COPY maap-jupyter-ide/scripts/ingestData.py /usr/bmap/ingestData.py
COPY maap-jupyter-ide/scripts/ingestData.sh /usr/bmap/ingestData.sh
COPY maap-jupyter-ide/scripts/maap-s3.py /usr/bmap/maap-s3.py
COPY maap-jupyter-ide/scripts/installLib.sh /usr/bmap/.installLib.sh

RUN chmod a+rwx -R /usr/bmap/

RUN  chmod +x /usr/bmap/initTemplate.sh
RUN  chmod +x /usr/bmap/shareAlgorithm.sh
RUN  chmod +x /usr/bmap/ingestData.sh
RUN  chmod +x /usr/bmap/maap-s3.py

ENV PATH="/usr/bmap/:${PATH}"
ENV PYTHONPATH="/usr/bmap/:${PYTHONPATH}"
ENV PATH="/usr/modules/:${PATH}"
ENV PYTHONPATH="/usr/modules/:${PYTHONPATH}"

#################################
# END OF ESA CUSTOMISATION
#################################


RUN mkdir /.jupyter


    

RUN export PATH="/usr/bmap/:$PATH"
RUN echo "PATH=/opt/conda/bin:${PATH}:/usr/bmap/" >> /etc/environment

RUN chmod a+rwx -R /maap-jupyter-ide/ && chmod a+rwx -R /.jupyter

ENV SHELL="bash"

WORKDIR /projects
EXPOSE 3100

ENTRYPOINT ["/bin/bash", "/maap-jupyter-ide/entrypoint.sh"]

# Julia installation
# Default values can be overridden at build time
# (ARGS are in lower case to distinguish them from ENV)
# Check https://julialang.org/downloads/
ARG julia_version="1.11.1"

# Julia dependencies
# install Julia packages in /opt/julia instead of ${HOME}
ENV JULIA_DEPOT_PATH=/opt/julia \
    JULIA_PKGDIR=/opt/julia \
    JULIA_VERSION="${julia_version}"

WORKDIR /tmp

SHELL ["/bin/bash", "-o", "pipefail", "-c"]
# hadolint ignore=SC2046
RUN set -x && \
    julia_arch=$(uname -m) && \
    julia_short_arch="${julia_arch}" && \
    if [ "${julia_short_arch}" == "x86_64" ]; then \
      julia_short_arch="x64"; \
    fi; \
    julia_installer="julia-${JULIA_VERSION}-linux-${julia_arch}.tar.gz" && \
    julia_major_minor=$(echo "${JULIA_VERSION}" | cut -d. -f 1,2) && \
    mkdir "/opt/julia-${JULIA_VERSION}" && \
    wget -q "https://julialang-s3.julialang.org/bin/linux/${julia_short_arch}/${julia_major_minor}/${julia_installer}" && \
    tar xzf "${julia_installer}" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
    rm "${julia_installer}" && \
    ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia

# Show Julia where conda libraries are \
RUN mkdir /etc/julia && \
    echo "push!(Libdl.DL_LOAD_PATH, \"${CONDA_DIR}/lib\")" >> /etc/julia/juliarc.jl
    
# R packages including IRKernel which gets installed globally.
RUN mamba install --quiet --yes \
    'r-base' \
    'r-caret' \
    'r-crayon' \
    'r-devtools' \
    'r-e1071' \
    'r-forecast' \
    'r-hexbin' \
    'r-htmltools' \
    'r-htmlwidgets' \
    'r-irkernel' \
    'r-nycflights13' \
    'r-randomforest' \
    'r-rcurl' \
    'r-rmarkdown' \
    'r-rodbc' \
    'r-rsqlite' \
    'r-shiny' \
    'r-tidyverse' \
    'rpy2' \
    'unixodbc' \
    'r-terra' \
    'r-rgdal' \
    && clean-layer

# R Pacakges
RUN R -e 'install.packages("raster", repos="https://rspatial.r-universe.dev")' \
    && R -e 'install.packages("fields", repos="http://cran.us.r-project.org")' \
    && R -e 'install.packages("ncdf4", repos="http://cran.us.r-project.org")' \
    && R -e 'install.packages("lubridate", repos="http://cran.us.r-project.org")' \
    && R -e 'install.packages("raster", repos="http://cran.us.r-project.org")' \
    && R -e 'install.packages("dplyr", repos="http://cran.us.r-project.org")' \
    && R -e 'install.packages("ggplot2", repos="http://cran.us.r-project.org")' \
    && R -e 'install.packages("tidyverse", repos="http://cran.us.r-project.org")' \
    && R -e 'install.packages("randomForest", repos="http://cran.us.r-project.org")'\
    && R -e 'install.packages("caret", repos="http://cran.us.r-project.org")'\
    && R -e 'install.packages("reshape2", repos="http://cran.us.r-project.org")'\
    && R -e 'install.packages("rgdal", repos="http://cran.us.r-project.org")' \
    && R -e 'pck<-c("tidyr","raster","ggplot2","randomForest", "caret", "reshape2", "rgdal")' \
    && clean-layer



# Add Julia packages. Only add HDF5 if this is not a test-only build since
# it takes roughly half the entire build time of all of the images on Travis
# to add this one package and often causes Travis to timeout.
#
# Install IJulia as jovyan and then move the kernelspec out
# to the system share location. Avoids problems with runtime UID change not
# taking effect properly on the .local folder in the jovyan home dir.
RUN julia -e 'import Pkg; Pkg.update()' && \
    (test $TEST_ONLY_BUILD || julia -e 'import Pkg; Pkg.add("HDF5")') && \
    julia -e "using Pkg; pkg\"add IJulia\"; pkg\"precompile\"" && \
    # move kernelspec out of home \
    mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/" && \
    chmod -R go+rx "${CONDA_DIR}/share/jupyter" && \
    rm -rf "${HOME}/.local"

# Install pysarpro
RUN pip install --quiet --no-cache-dir \
    pysarpro \
    && clean-layer

# Add starship prompt
# RUN curl -sS https://starship.rs/install.sh | sh -s -- -y 
RUN chown -R 1234:0 /opt ${HOME} /projects
WORKDIR /projects