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java-jsi-clus

README.md

JSI DockerHub ImageVersion ImageLayers

hbpmip/java-jsi-clus: Java environment for JSI CLUS algorithms

This image contains support for execution of CLUS software. CLUS contains multiple machine learning algorithms from JSI (http://kt.ijs.si).

Usage

Use this image as part of a multistage build. You need to use this image as the parent image.

Dockerfile

  FROM hbpmip/java-base-build:3.5.2-jdk-8-0 as build-java-env

  COPY pom.xml /project/pom.xml
  RUN cp /usr/share/maven/ref/settings-docker.xml /root/.m2/settings.xml \
      && mvn dependency:resolve

  COPY src/ /project/src

  # Repeating copy of the settings works better. I dunno why.
  RUN cp /usr/share/maven/ref/settings-docker.xml /root/.m2/settings.xml \
      && mvn -Dmaven.test.skip=true package site

  FROM hbpmip/java-jsi-clus:latest

  MAINTAINER <your email>

  ENV DOCKER_IMAGE=my-algo \
      JAVA_CLASSPATH=${JAVA_CLASSPATH}:/usr/share/jars/my-algo.jar \
      JAVA_MAINCLASS=eu.humanbrainproject.mip.algorithms.jsi.clus.YourEntrypoint

  COPY --from=build-java-env /project/target/my-algo.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/

  LABEL org.label-schema.build-date=$BUILD_DATE \
        org.label-schema.name="hbpmip/my-algo" \
        org.label-schema.description="My algorithm" \
        org.label-schema.url="https://github.com/LREN-CHUV/algorithm-repository" \
        org.label-schema.vcs-type="git" \
        org.label-schema.vcs-url="https://github.com/LREN-CHUV/algorithm-repository.git" \
        org.label-schema.vcs-ref=$VCS_REF \
        org.label-schema.version="$VERSION" \
        org.label-schema.vendor="JSI" \
        org.label-schema.license="GPLv3" \
        org.label-schema.docker.dockerfile="Dockerfile" \
        org.label-schema.schema-version="1.0"

Your algorithm will require additional classes and files packaged in my-algo.jar to adapt to the MIP Woken environment and to generate required outputs:

Your class Should extend class Description Required
YourAlgoMeta ClusMeta This class provides metadata of the algorithm. Yes
YourAlgoSerializer ClusGenericSerializer This class serializes your model to PFA. Yes (if algorithm is predictive)
YourAlgoVisualizer ClusVisualizationSerializer This class produces a visualization of your model. No
YourAlgoDescriptiveSerializer ClusDescriptionSerializer This class produces a description of your model which is not predictive. Yes (if algorithm is not predictive)

We also provide a Java library to support the integration:

<repositories>
  <repository>
    <id>bintray-hbpmedical-mip</id>
    <name>bintray</name>
    <url>https://dl.bintray.com/hbpmedical/maven</url>
  </repository>
</repositories>

<dependency>
  <groupId>eu.humanbrainproject.mip.algorithms</groupId>
  <artifactId>jsi-clus</artifactId>
  <version>${mip.jsi-clus.version}</version>
</dependency>