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FROM eclipse-temurin:17 as jre-build
# Create a custom Java runtime
RUN $JAVA_HOME/bin/jlink \
--add-modules ALL-MODULE-PATH \
--strip-debug \
--no-man-pages \
--no-header-files \
--compress=2 \
--output /javaruntime
# Define base image and copy in jlink created minimal Java 17 environment
FROM python:3.10.15-slim
ENV JAVA_HOME=/opt/java/openjdk
ENV PATH "${JAVA_HOME}/bin:${PATH}"
COPY --from=jre-build /javaruntime $JAVA_HOME
# now we have Java 17 and Python 3.9
RUN apt -y update && \
apt -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu && \
mkdir -p /usr/local/app
RUN python3 -m pip install poetry && poetry config cache-dir "/poetry/.cache"
ENV PATH="/root/.poetry/bin:/root/.local/bin:$PATH"
RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
RUN unlink /etc/localtime || true
RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
WORKDIR /usr/local/app
COPY ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
./vcell-server/target/maven-jars/*.jar \
./lib/
# Copy and install pythonVtk
COPY ./pythonVtk/ /usr/local/app/pythonVtk/
RUN cd /usr/local/app/pythonVtk && \
poetry config cache-dir "/poetry/.cache" --local && \
poetry install
COPY ./nativelibs/linux64 ./nativelibs/linux64
COPY ./docker/build/vcell-data.log4j.xml .
ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
serverid=SITE \
dburl="db-url-not-set" \
dbdriver="db-driver-not-set" \
dbuser="db-user-not-set" \
jmshost_int_internal=activemqint \
jmsport_int_internal=61616 \
jmsuser=clientUser \
jmsblob_minsize=100000 \
mongodb_host_internal=mongodb \
mongodb_port_internal=27017 \
mongodb_database=test \
export_baseurl="export-baseurl-not-set" \
simdatadir_external=/path/to/external/simdata/ \
simdataCacheSize="simdataCacheSize-not-set" \
servertype="servertype-not-set" \
s3export_baseURL="s3-export-baseurl-not-set"
ENV dbpswdfile=/run/secrets/dbpswd \
jmspswdfile=/run/secrets/jmspswd \
keystore=/run/secrets/keystorefile \
keystorepswdfile=/run/secrets/keystorepswd
VOLUME /simdata
VOLUME /simdata_secondary
VOLUME /exportdir
EXPOSE 8000
ENTRYPOINT java \
-Xdebug -agentlib:jdwp=transport=dt_socket,address=*:8000,server=y,suspend=n \
-XX:MaxRAMPercentage=80 \
# -XX:+PrintFlagsFinal -XshowSettings:vm \
-Djava.awt.headless=true \
-Dvcell.softwareVersion="${softwareVersion}" \
-Djava.util.logging.manager=org.apache.logging.log4j.jul.LogManager \
-Dlog4j.configurationFile=/usr/local/app/vcell-data.log4j.xml \
-Dvcell.server.id="${serverid}" \
-Dvcell.server.dbConnectURL="${dburl}" \
-Dvcell.server.dbDriverName="${dbdriver}" \
-Dvcell.server.dbUserid="${dbuser}" \
-Dvcell.db.pswdfile="${dbpswdfile}" \
-Dvcell.python.executable=/usr/local/bin/python \
-Dvcell.primarySimdatadir.internal=/simdata \
-Dvcell.secondarySimdatadir.internal=/simdata_secondary \
-Dvcell.n5DataDir.internal=/n5DataDir \
-Dvcell.s3.export.baseURL="${s3export_baseURL}" \
-Dvcell.primarySimdatadir.external="${simdatadir_external}" \
-Dvcell.simdataCacheSize="${simdataCacheSize}" \
-Dvcell.export.baseDir.internal=/exportdir/ \
-Dvcell.export.baseURL="${export_baseurl}" \
-Dvcell.installDir=/usr/local/app \
-Dvcell.jms.int.host.internal="${jmshost_int_internal}" \
-Dvcell.jms.int.port.internal="${jmsport_int_internal}" \
-Dvcell.jms.blobMessageUseMongo=true \
-Dvcell.jms.blobMessageMinSize="${jmsblob_minsize}" \
-Dvcell.jms.user="${jmsuser}" \
-Dvcell.jms.pswdfile="${jmspswdfile}" \
-Dvcellapi.keystore.file="${keystore}" \
-Dvcellapi.keystore.pswdfile="${keystorepswdfile}" \
-Dvcell.mongodb.host.internal=${mongodb_host_internal} \
-Dvcell.mongodb.port.internal=${mongodb_port_internal} \
-Dvcell.mongodb.database=${mongodb_database} \
-cp "./lib/*" cbit.vcell.message.server.data.SimDataServerMain \
"${servertype}"
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