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java-jsi-clus-rm initial commit
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‎.circleci/config.yml‎

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name: "Test java-jsi-clus-fr"
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command: |
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PATH=$PATH:/$HOME/.captain/bin/ ./java-jsi-clus-fr/tests/test.sh
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# - run:
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# name: "Build java-jsi-clus-rm"
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# command: |
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# PATH=$PATH:/$HOME/.captain/bin/ ./java-jsi-clus-rm/build.sh
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# - run:
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# name: "Test java-jsi-clus-rm"
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# command: |
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# PATH=$PATH:/$HOME/.captain/bin/ ./java-jsi-clus-rm/tests/test.sh
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- run:
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name: "Build java-jsi-clus-rm"
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command: |
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PATH=$PATH:/$HOME/.captain/bin/ ./java-jsi-clus-rm/build.sh
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- run:
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name: "Test java-jsi-clus-rm"
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command: |
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PATH=$PATH:/$HOME/.captain/bin/ ./java-jsi-clus-rm/tests/test.sh
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- run:
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name: "Build python-jsi-hedwig"
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command: |

‎.gitignore‎

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**/.Rhistory
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*.orig
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.Rproj.user
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/.metadata/
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/.recommenders/

‎build.sh‎

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DOCKER="sudo docker"
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fi
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IMAGES="r-summary-stats r-linear-regression java-rapidminer java-jsi-clus-pct java-jsi-clus-pct-ts java-jsi-clus-fire java-jsi-clus-fr python-jsi-hedwig python-jsi-hinmine"
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IMAGES="r-summary-stats r-linear-regression java-rapidminer java-jsi-clus-pct java-jsi-clus-rm java-jsi-clus-pct-ts java-jsi-clus-fire java-jsi-clus-fr python-jsi-hedwig python-jsi-hinmine"
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commit_id="$(git rev-parse --short HEAD)"
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‎java-jsi-clus-rm/.bumpversion.cfg‎

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[bumpversion]
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current_version = 0.0.1
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commit = True
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tag = True
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tag_name = java-jsi-clus-rm-{new_version}
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parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)
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serialize = {major}.{minor}.{patch}
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[bumpversion:file:pom.xml]
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search = <version>{current_version}</version><!-- bumpversion -->
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replace = <version>{new_version}</version><!-- bumpversion -->
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‎java-jsi-clus-rm/.dockerignore‎

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.git/
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.idea/
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target/
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*~
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.settings
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.project
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deps/rm/
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deps/decompiled/

‎java-jsi-clus-rm/.gitignore‎

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target/
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.classpath
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.settings
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.project

‎java-jsi-clus-rm/Dockerfile‎

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FROM hbpmip/java-base-build:3.5.2-jdk-8-0 as build-java-env
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COPY pom.xml /project/pom.xml
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COPY src/ /project/src
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COPY deps/ /project/deps
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RUN cp /usr/share/maven/ref/settings-docker.xml /root/.m2/settings.xml \
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&& mvn dependency:go-offline
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# Repeating copy of the settings works better. I dunno why.
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RUN cp /usr/share/maven/ref/settings-docker.xml /root/.m2/settings.xml \
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&& mvn package site
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FROM hbpmip/java-mip:0.5.7
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MAINTAINER martin.breskvar@ijs.si
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ENV DOCKER_IMAGE=java-jsi-clus-rm \
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FUNCTION=java-jsi-clus-rm \
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JAVA_CLASSPATH=${JAVA_CLASSPATH}:/opt/weka/props/:/usr/share/jars/jsi-clus-rm-deps.jar:/usr/share/jars/lib/*:/usr/share/jars/Redescription_mining_MW_ConstrainedGen1.jar:/usr/share/jars/CLUSNHMC.jar \
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JAVA_MAINCLASS=eu.humanbrainproject.mip.algorithms.jsi.clus.rm.Entrypoint \
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WEKA_HOME=/opt/weka
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COPY docker/databases-props/ /opt/weka/databases-props/
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COPY --from=build-java-env /project/deps/ /usr/share/jars/
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COPY --from=build-java-env /project/target/jsi-clus-rm-deps.jar /usr/share/jars/jsi-clus-rm-deps.jar
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COPY --from=build-java-env /project/target/site/ /var/www/html/
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COPY src/ /src/
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COPY doc/ /src/doc/
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RUN mkdir -p /opt/weka/props/weka/experiment \
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&& chown -R compute:compute /mip/ /opt/weka/ /usr/share/jars/
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RUN chown -R compute:compute /src/ \
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&& chown -R root:www-data /var/www/html/
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WORKDIR /usr/share/jars
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LABEL org.label-schema.build-date=$BUILD_DATE \
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org.label-schema.name="hbpmip/java-jsi-clus-rm" \
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org.label-schema.description="PCT-based algorithm for Redescription Mining" \
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org.label-schema.url="https://github.com/LREN-CHUV/algorithm-repository" \
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org.label-schema.vcs-type="git" \
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org.label-schema.vcs-url="https://github.com/LREN-CHUV/algorithm-repository.git" \
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org.label-schema.vcs-ref=$VCS_REF \
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org.label-schema.version="$VERSION" \
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org.label-schema.vendor="JSI KT and IRB ZEL" \
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org.label-schema.license="GPLv3" \
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org.label-schema.docker.dockerfile="Dockerfile" \
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org.label-schema.schema-version="1.0"

‎java-jsi-clus-rm/README.md‎

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[![JSI](https://img.shields.io/badge/JSI-KT-AF4C64.svg)](http://kt.ijs.si/)
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[![DockerHub](https://img.shields.io/badge/docker-hbpmip%2Fjava--jsi--clus--rm-008bb8.svg)](https://hub.docker.com/r/hbpmip/java-jsi-clus-rm/)
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[![ImageVersion](https://images.microbadger.com/badges/version/hbpmip/java-jsi-clus-rm.svg)](https://hub.docker.com/r/hbpmip/java-jsi-clus-rm/tags "hbpmip/java-jsi-clus-rm image tags")
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[![ImageLayers](https://images.microbadger.com/badges/image/hbpmip/java-jsi-clus-rm.svg)](https://microbadger.com/#/images/hbpmip/java-jsi-clus-rm "hbpmip/java-jsi-clus-rm on microbadger")
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# hbpmip/java-jsi-clus-rm: Redescription Mining using Predictive Clustering from JSI and IRB
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Implementation of the Redescription mining algorithm based on Predictive Clustering Trees.
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For more details see https://github.com/matmih/CLUS-RM-library.
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## Usage
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```sh
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docker run --rm --env [list of environment variables] hbpmip/java-jsi-clus-rm compute
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```
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where the environment variables are:
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* NODE: name of the node (machine) used for execution
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* JOB_ID: ID of the job.
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* IN_JDBC_DRIVER: org.postgresql.Driver
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* IN_JDBC_URL: URL to the input database, e.g. jdbc:postgresql://db:5432/features
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* IN_JDBC_USER: User for the input database
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* IN_JDBC_PASSWORD: Password for the input database
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* OUT_JDBC_DRIVER: org.postgresql.Driver
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* OUT_JDBC_URL: URL to the output database, jdbc:postgresql://db:5432/woken
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* OUT_JDBC_USER: User for the output database
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* OUT_JDBC_PASSWORD: Password for the output database
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* PARAM_covariables: Attributes contained in the first data view.
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* PARAM_variables: Attributes contained in the second data view.
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* PARAM_query: Query selecting the data to feed into the algorithm for training
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* MODEL_PARAM_minJS: Specify minimal redescription accuracy (measured with Jaccard index) required to return it to the user. Parameter values are contained in [0,1]. (default is MODEL_PARAM_minJS=0.5)
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* MODEL_PARAM_maxPval: Specify maximal redescription p-value required to return it to the user. Parameter values are contained in [0,1]. (default is MODEL_PARAM_maxPval=0.01)
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* MODEL_PARAM_MinSupport: Specify minimal redescription support required to return it to the user. Parameter values are contained in [1,|E|], where |E| denotes number of entities in the dataset. (This parameter MUST be defined by the user and is domain and data dependent).
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* MODEL_PARAM_MaxSupport: Specify maximal redescription support allowed. Parameter values are contained in [1,|E|], where |E| denotes number of entities in the dataset. (default is MODEL_PARAM_MaxSupport = |E|).
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* MODEL_PARAM_numRandomRestarts: Specify the number of random initialization steps performed by the CLUS-RM (the default is MODEL_PARAM_numRandomRestarts = 1).
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* MODEL_PARAM_numIterations: Specify the number of iterations (also called alternations) performed by the CLUS-RM (the default is MODEL_PARAM_numIterations = 10).
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* MODEL_PARAM_numRetRed: Specify the number of redescriptions to be returned by the CLUS-RM (the default is MODEL_PARAM_numRetRed = 50).
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* MODEL_PARAM_attributeImportanceW1: Specify the attribute importance, for attributes contained in view 1, used in constraint-based redescription mining (the default is MODEL_PARAM_attributeImportanceW1 = "none"). Possible values are: "none" - allow redescriptions with any attributes from view1, "suggested" - allow defining combinations of attributes that increase redescription score (redescriptions containing specified attributes are preferred), "soft" - only return redescriptions satisfying at least part of specified constraints to the user (redescriptions satisfying larger portion of constraint set are preferred), "hard" - only return redescriptions satisfying all constraints defined in one constraint set.
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* MODEL_PARAM_attributeImportanceW2: Specify the attribute importance, for attributes contained in view 2, used in constraint-based redescription mining (the default is MODEL_PARAM_attributeImportanceW1 = "none"). Possible values are: "none" - allow redescriptions with any attributes from view2, "suggested" - allow defining combinations of attributes that increase redescription score (redescriptions containing specified attributes are preferred), "soft" - only return redescriptions satisfying at least part of specified constraints to the user (redescriptions satisfying larger portion of constraint set are preferred), "hard" - only return redescriptions satisfying all constraints defined in one constraint set.
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* MODEL_PARAM_importantAttributesW1: defines constraint sets, for attributes contained in view 1, to be used in constraint-based redescription mining (default is MODEL_PARAM_importantAttributesW1=""). Constraints are specified in the format "{a;b;c},{a;d}", where a,b,c,d are some attributes contained in the first view (view1) of the data.
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* MODEL_PARAM_importantAttributesW2: defines constraint sets, for attributes contained in view 2, to be used in constraint-based redescription mining (default is MODEL_PARAM_importantAttributesW1=""). Constraints are specified in the format "{e;f;g},{h;i}", where e,f,g,h,i are some attributes contained in the second view (view2) of the data.

‎java-jsi-clus-rm/build.sh‎

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#!/usr/bin/env bash
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set -o pipefail # trace ERR through pipes
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set -o errtrace # trace ERR through 'time command' and other functions
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set -o errexit ## set -e : exit the script if any statement returns a non-true return value
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get_script_dir () {
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SOURCE="${BASH_SOURCE[0]}"
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while [ -h "$SOURCE" ]; do
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DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
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SOURCE="$( readlink "$SOURCE" )"
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[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
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done
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cd -P "$( dirname "$SOURCE" )"
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pwd
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}
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cd "$(get_script_dir)"
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if [[ $NO_SUDO || -n "$CIRCLECI" ]]; then
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CAPTAIN="captain"
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elif groups $USER | grep &>/dev/null '\bdocker\b'; then
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CAPTAIN="captain"
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else
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CAPTAIN="sudo captain"
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fi
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BUILD_DATE=$(date -Iseconds) \
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VCS_REF=$(git describe --tags --dirty) \
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VERSION=$(git describe --tags --dirty) \
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$CAPTAIN build

‎java-jsi-clus-rm/captain.yml‎

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target_image:
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build: Dockerfile
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image: hbpmip/java-jsi-clus-rm
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pre:
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- echo "Preparing java-jsi-clus-rm"
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post:
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- echo "Finished java-jsi-clus-rm"

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