Dockerfile

# 1. Download ChemAxon Marvin for Debian from https://chemaxon.com/ and save to `./Dockerfile_assets/marvin_linux.deb`
# 2. Obtain license for Marvin and save to `./Dockerfile_assets/chemaxon.license.cxl`
# 3. Copy your Git configuration for accessing GitHub to `./Dockerfile_assets/.gitconfig`. To use SSH to access GitHub,
#    save the following to `./Dockerfile_assets/.gitconfig`.
#
#    [url "ssh://git@github.com/"]
#      insteadOf = https://github.com/
#
# 4. If necessary, copy the SSH keys needed to access GitHub to `./Dockerfile_assets/id_rsa` and `./Dockerfile_assets/id_rsa.pub`.
# 5. If necessary, copy an SSH known hosts file for GitHub to `./Dockerfile_assets/known_hosts`.
# 6. Generate an API token for GitHub, and save it to `./Dockerfile_assets/wc_utils.cfg` in the following format:
#
#    [wc_utils]
#        [[github]]
#            github_api_token = <token>
#
# 7. To test the migration feature, generate an API key for BioPortal and save it to `./Dockerfile_assets/wc_onto.cfg` in the following format:
#
#    [wc_onto]
#        [[bioportal]]
#            key = <key>
#
# 8. Pull the Ubuntu image via `docker pull ubuntu:latest`
# 9. Build with `docker build -f Dockerfile Dockerfile_assets --tag karrlab/obj_tables:latest`7

# Start from Ubuntu (e.g., focal - 20.04)
FROM ubuntu:latest

# metadata
LABEL base_image="ubuntu:20.04"
LABEL version="1.0.13"
LABEL software="ObjTables"
LABEL software.version="1.0.13"
LABEL about.summary="Tools for creating and reusing high-quality spreadsheets"
LABEL about.home="https://objtables.org/"
LABEL about.documentation="https://objtables.org/docs"
LABEL about.license_file="https://github.com/KarrLab/objtables/blob/master/LICENSE"
LABEL about.license="SPDX:MIT"
LABEL about.tags="complex data,spreadsheet,XLSX,reusable,schema,object-relational mapping,CSV,TSV,XLSX,Excel,Python"
LABEL extra.identifiers.biotools="objtables"
LABEL maintainer="Jonathan Karr <karr@mssm.edu>"

# Set default language to UTF-8 US English
ENV TZ=America/New_York \
    DEBIAN_FRONTEND=noninteractive
RUN apt-get update -y \
    && apt-get install --no-install-recommends -y \
        locales \
        tzdata \
    && rm -rf /var/lib/apt/lists/* \
    && locale-gen en_US.UTF-8
ENV LC_ALL=en_US.UTF-8

# Install Git
RUN apt-get update -y \
    && apt-get install --no-install-recommends -y \
        git \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*

# Setup access to GitHub
COPY ./.gitconfig /root/.gitconfig
COPY ./id_rsa /root/.ssh/id_rsa
COPY ./id_rsa.pub /root/.ssh/id_rsa.pub
COPY ./known_hosts /root/.ssh/known_hosts
COPY ./wc_utils.cfg /root/.wc/wc_utils.cfg
RUN apt-get update -y \
    && apt-get install --no-install-recommends -y \
        ssh \
    && chmod 0600 ~/.ssh/id_rsa \
    && chmod 0644 ~/.ssh/id_rsa.pub \
    && eval $(ssh-agent -s) && ssh-add ~/.ssh/id_rsa \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*

# Install Python (e.g., 3.6.9), pip, and setuptools
RUN apt-get update -y \
    && apt-get install --no-install-recommends -y \
        python3 \
        python3-pip \
    && pip3 install -U pip setuptools \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*

# Install GraphViz
RUN apt-get update -y \
    && apt-get install -y --no-install-recommends \
        graphviz \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*

# Install Open Babel 2.4.1
ARG openbabel_version=2.4.1
RUN apt-get update -y \
    && apt-get install --no-install-recommends -y \
        build-essential \
        cmake \
        libcairo2-dev \
        libeigen3-dev \
        libxml2 \
        libxml2-dev \
        tar \
        wget \
        zlib1g-dev \
    \
    && cd /tmp \
    && openbabel_version_dash=$(echo $openbabel_version | sed 's/\./-/g') \
    && wget https://github.com/openbabel/openbabel/archive/openbabel-${openbabel_version_dash}.tar.gz -O /tmp/openbabel-${openbabel_version}.tar.gz \
    && tar -xvvf /tmp/openbabel-${openbabel_version}.tar.gz \
    && cd openbabel-openbabel-${openbabel_version_dash} \
    && mkdir build \
    && cd build \
    && cmake .. \
    && make \
    # && make test \
    && make install \
    && ldconfig \
    && cd / \
    && rm -r /tmp/openbabel-${openbabel_version}.tar.gz \
    && rm -r /tmp/openbabel-openbabel-${openbabel_version_dash} \
    \
    && apt-get remove -y \
        build-essential \
        cmake \
        libcairo2-dev \
        libeigen3-dev \
        libxml2-dev \
        wget \
        zlib1g-dev \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*

# Install Open Babel Python interface
ARG py_openbabel_version=2.4.1
RUN apt-get update -y \
    && apt-get install --no-install-recommends -y \
        build-essential \
        libpython3-dev \
        swig \
    \
    && pip3 install openbabel==${py_openbabel_version} \
    \
    && apt-get remove -y \
          build-essential \
          libpython3-dev \
          swig \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*

# Install ChemAxon Marvin (e.g., 20.6)
COPY ./marvin_linux.deb /tmp/
COPY ./chemaxon.license.cxl /tmp/
RUN apt-get update -y \
    && apt-get install --no-install-recommends -y \
        default-jdk \
        default-jre \
    \
    && mkdir ~/.chemaxon \
    && mv /tmp/chemaxon.license.cxl ~/.chemaxon/license.cxl \
    && dpkg -i /tmp/marvin_linux.deb \
    \
    && rm /tmp/marvin_linux.deb \
    && apt-get autoremove -y \
    && rm -rf /var/lib/apt/lists/*
ENV JAVA_HOME=/usr/lib/jvm/default-java \
    CLASSPATH=${CLASSPATH}:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar

# Install ObjTables
RUN pip3 install obj_tables[grammar,math,sci,chem,bio,revisioning,viz,web]

# Set entry point
ENTRYPOINT ["obj-tables"]
CMD []

# Test ObjTables
ARG test=1
COPY ./wc_onto.cfg /root/.wc/wc_onto.cfg
RUN if [ "$test" = "1" ]; then \
      apt-get update -y \
      && apt-get install --no-install-recommends -y \
          build-essential \
          libpython3-dev \
       \
       && cd / \
       && git clone https://github.com/KarrLab/obj_tables.git \
       && cd /obj_tables \
       && pip3 install pytest \
       && pip3 install -r tests/requirements.txt \
       && python3 -m pytest tests/ \
       \
       && cd / \
       && rm -r obj_tables \
       && apt-get remove -y \
           build-essential \
           libpython3-dev \
       && apt-get autoremove -y \
       && rm -rf /var/lib/apt/lists/*; \
     fi