Dockerfile

ARG XNAT_VERSION=1.9.1.1
ARG XNAT_ROOT=/data/xnat
ARG XNAT_HOME=/data/xnat/home
# default plugins for AIS
ARG container_service_ver=3.6.2-fat
ARG ldap_auth_ver=1.2.1
ARG ohif_viewer_ver=3.7.0-XNAT-1.8.10
ARG openid_auth_ver=1.3.1-xpl
ARG xsync_ver=1.8.1
ARG batch_launch_ver=0.7.0
ARG jupyterhub_ver=1.3.0

FROM tomcat:9-jdk8 AS build
ARG XNAT_VERSION
ARG XNAT_ROOT
ARG XNAT_HOME
# default plugins for AIS
ARG container_service_ver
ARG ldap_auth_ver
ARG ohif_viewer_ver
ARG openid_auth_ver
ARG xsync_ver
ARG batch_launch_ver
ARG jupyterhub_ver

RUN <<EOT
  apt-get update
  apt-get install -y \
    unzip \
    wget
  rm -rf /var/lib/apt/lists/*
EOT

# Setup XNAT base directory structure
RUN <<EOT
  mkdir -p \
    ${XNAT_ROOT}/archive \
    ${XNAT_ROOT}/build \
    ${XNAT_ROOT}/cache \
    ${XNAT_ROOT}/fileStore \
    ${XNAT_ROOT}/ftp \
    ${XNAT_HOME}/config/auth \
    ${XNAT_HOME}/logs \
    ${XNAT_HOME}/plugins \
    ${XNAT_HOME}/themes \
    ${XNAT_HOME}/work \
    ${XNAT_ROOT}/inbox \
    ${XNAT_ROOT}/pipeline \
    ${XNAT_ROOT}/prearchive
EOT

# Install XNAT web Java application
RUN <<EOT
  rm -rf ${CATALINA_HOME}/webapps/*
  mkdir -p ${CATALINA_HOME}/webapps/ROOT
  wget --no-verbose -P /tmp \
    https://api.bitbucket.org/2.0/repositories/xnatdev/xnat-web/downloads/xnat-web-${XNAT_VERSION}.war
  unzip -o -d ${CATALINA_HOME}/webapps/ROOT /tmp/xnat-web-${XNAT_VERSION}.war
EOT

# Download standard plugins
RUN <<EOT
  wget --no-verbose -P ${XNAT_HOME}/plugins \
    https://api.bitbucket.org/2.0/repositories/xnatdev/container-service/downloads/container-service-${container_service_ver}.jar
  wget --no-verbose -P ${XNAT_HOME}/plugins \
    https://api.bitbucket.org/2.0/repositories/xnatx/ldap-auth-plugin/downloads/ldap-auth-plugin-${ldap_auth_ver}.jar
  wget --no-verbose -P ${XNAT_HOME}/plugins \
    https://api.bitbucket.org/2.0/repositories/icrimaginginformatics/ohif-viewer-xnat-plugin/downloads/ohif-viewer-${ohif_viewer_ver}.jar
  wget --no-verbose -P ${XNAT_HOME}/plugins \
    https://api.bitbucket.org/2.0/repositories/xnatx/openid-auth-plugin/downloads/openid-auth-plugin-${openid_auth_ver}.jar
  wget --no-verbose -P ${XNAT_HOME}/plugins \
    https://api.bitbucket.org/2.0/repositories/xnatdev/xsync/downloads/xsync-plugin-all-${xsync_ver}.jar
  wget --no-verbose -P ${XNAT_HOME}/plugins \
    https://api.bitbucket.org/2.0/repositories/xnatx/xnatx-batch-launch-plugin/downloads/batch-launch-${batch_launch_ver}.jar
  wget --no-verbose -P ${XNAT_HOME}/plugins \
    https://api.bitbucket.org/2.0/repositories/xnatx/xnat-jupyterhub-plugin/downloads/xnat-jupyterhub-plugin-${jupyterhub_ver}.jar  
EOT

FROM tomcat:9-jdk8
ARG XNAT_VERSION
ARG XNAT_ROOT
ARG XNAT_HOME

RUN <<EOT
  apt update
  apt install -y \
    less \
    telnet \
    vim
  rm -rf /var/lib/apt/lists/*
  rm -rf ${CATALINA_HOME}/webapps/*
EOT

COPY --from=build ${CATALINA_HOME}/webapps/ ${CATALINA_HOME}/webapps/
COPY --from=build ${XNAT_ROOT} ${XNAT_ROOT}

RUN <<EOT
  sed -i \
    's/ch.qos.logback.core.rolling.RollingFileAppender/ch.qos.logback.core.ConsoleAppender/' \
    ${CATALINA_HOME}/webapps/ROOT/WEB-INF/classes/logback.xml
EOT

COPY --chmod=0755 ./entrypoint.sh /usr/local/bin/entrypoint.sh
COPY ./xnat-conf.properties ${XNAT_HOME}/config/xnat-conf.properties

ENV XNAT_HOME=${XNAT_HOME} \
    XNAT_VERSION=${XNAT_VERSION} \
    TZ=UTC \
    CATALINA_OPTS="-XX:InitialRAMPercentage=40.0 -XX:MaxRAMPercentage=50.0 -XX:+UseConcMarkSweepGC -XX:-OmitStackTraceInFastThrow -Dxnat.home=${XNAT_HOME}"

LABEL org.opencontainers.image.source https://github.com/australian-imaging-service/xnat-docker-build
LABEL maintainer="AIS Team"

ENTRYPOINT ["entrypoint.sh"]
CMD ["catalina.sh","run"]