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java-mip

README.md

CHUV License DockerHub ImageVersion ImageLayers

hbpmip/java-mip: Adapt the base Java image to the MIP environment

This image provides a Java environment compatible with MIP. This base image provides the basic tools and library to execute a statistical or machine-learning Java algorithm in the runtime environment provided by MIP Algorithm Factory / Woken.

It provides the following features:

  • The compute user is used to run the Java programs
  • Directories /data/in and /data/out are intended to store the incoming files and outgoing files for the computations. They can be mounted on an external filesystem.
  • The environment variables COMPUTE_IN and COMPUTE_OUT can be used to locate those folders from the Java programs.
  • In the /src directory you should place all scripts and libraries used to perform the computation.
  • If you run the container with the export command and mount /data/out to a local directory, the source files will be copied to that local directory.
  • If you run the container with the serve command, a web server will run and display any content located in /var/www/html/. You should place in this folder the documentation for the container.
  • If you run the container with the export-docs command and mount /data/out to a local directory, the documentation will be copied to that local directory.
  • If you run the container with the shell command, an interactive shell will start.

Usage

Use this image as the parent image to adapt a Java-based algorithm to the MIP platform:

Dockerfile

  FROM hbpmip/java-base-build:3.6.0-jdk-11-0 as build-java-env

  COPY pom.xml /project/pom.xml
  COPY src/ /project/src

  # Repeating the file copy works better. I dunno why.
  RUN cp /usr/share/maven/ref/settings-docker.xml /root/.m2/settings.xml \
      && mvn package assembly:single site

  FROM hbpmip/java-mip:0.5.11

  MAINTAINER <your email>

  ENV DOCKER_IMAGE=hbpmip/my-algo:1.0.0 \
      JAVA_CLASSPATH=/usr/share/jars/my-algo.jar \
      JAVA_MAINCLASS=org.myorg.myalgo.Main \
      JAVA_ARGS=--verbose

  COPY --from=build-java-env /project/target/my-algo-jar-with-dependencies.jar /usr/share/jars/my-algo.jar
  COPY --from=build-java-env /project/target/site/ /var/www/html/
  COPY src/ /src/

  RUN chown -R compute:compute /src/ \
      && chown -R root:www-data /var/www/html/

See also

You may want to use one of the following specialised images for your algorithm instead:

Summary of commands:

  • Run the main computations

      mkdir -p in out && docker run --rm -v $(pwd)/in:/data/in -v $(pwd)/out:/data/out <image name> compute

  • Export the documentation to the ./doc directory

      docker run --rm -v /data/out:./doc <image name> export-docs

  • Interactive shell

      docker run -i -t --rm <image name> shell

  • Quick documentation accessible at http://localhost:7777/ and sources at http://localhost:7777/src/ Stop the server using Ctrl+C from the command line.

      docker run -d --rm -p 7777:80 <image name> serve

  • Export the sources to the ./src directory

      mkdir -p src && docker run --rm -v $(pwd)/src:/data/out <image name> export

  • Export the documentation to the ./doc directory

      mkdir -p doc && docker run --rm -v $(pwd)/doc:/data/out <image name> export-docs

Useful environment variables:

  • COMPUTE_IN: the directory containing the input files
  • COMPUTE_OUT: the output directory to use to store the output files
  • COMPUTE_TMP: the directory to use to store temporary files
  • SRC: the directory containing the sources
  • JAVA_CLASSPATH: the Java classpath
  • JAVA_MAINCLASS: the main class of the Java application
  • JAVA_ARGS: arguments to pass to the main class