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mbreskvarmbreskvar
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initial commit for java-jsi-clus-pct-ts
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‎java-jsi-clus-pct-ts/.bumpversion.cfg

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[bumpversion]
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current_version = 0.9.0
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commit = True
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tag = True
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tag_name = java-jsi-clus-pct-ts-{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-pct-ts/.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

‎java-jsi-clus-pct-ts/.gitignore

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target/
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.classpath
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.settings
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.project

‎java-jsi-clus-pct-ts/Dockerfile

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FROM hbpmip/java-base-build:3.5.0-jdk-8-9 as build-java-env
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COPY pom.xml /project/pom.xml
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RUN cp /usr/share/maven/ref/settings-docker.xml /root/.m2/settings.xml \
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&& mvn dependency:resolve
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COPY src/ /project/src
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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 -Dmaven.test.skip=true package site
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FROM hbpmip/java-jsi-clus:latest
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MAINTAINER martin.breskvar@ijs.si
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ENV DOCKER_IMAGE=java-jsi-clus-pct-ts \
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JAVA_CLASSPATH=${JAVA_CLASSPATH}:/usr/share/jars/jsi-clus-pct-ts.jar \
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JAVA_MAINCLASS=eu.humanbrainproject.mip.algorithms.jsi.clus.pct.ts.Entrypoint
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COPY --from=build-java-env /project/target/jsi-clus-pct-ts.jar /usr/share/jars/jsi-clus-pct-ts.jar
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COPY --from=build-java-env /project/target/site/ /var/www/html/
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COPY src/ /src/
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RUN chown -R compute:compute /src/ \
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&& chown -R root:www-data /var/www/html/
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LABEL org.label-schema.build-date=$BUILD_DATE \
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org.label-schema.name="hbpmip/java-jsi-clus-pct-ts" \
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org.label-schema.description="PCT algorithm for time-series prediction" \
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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" \
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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-pct-ts/README.md

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[![DockerHub](https://img.shields.io/badge/docker-hbpmip%2Fjava--jsi--clus--pct--ts-008bb8.svg)](https://hub.docker.com/r/hbpmip/java-jsi-clus-pct-ts/) [![ImageVersion](https://images.microbadger.com/badges/version/hbpmip/java-jsi-clus-pct-ts.svg)](https://hub.docker.com/r/hbpmip/java-jsi-clus-pct-ts/tags "hbpmip/java-jsi-clus-pct-ts image tags") [![ImageLayers](https://images.microbadger.com/badges/image/hbpmip/java-jsi-clus-pct-ts.svg)](https://microbadger.com/#/images/hbpmip/java-jsi-clus-pct-ts "hbpmip/java-jsi-clus-pct-ts on microbadger")
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# hbpmip/java-jsi-clus-pct-ts: Predictive Clustering Trees (PCTs) for time-series prediction from JSI
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Implementation of the Predictive Clustering Trees capable of time-series prediction. http://kt.ijs.si
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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-pct-ts 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_variables: List of target variables
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* PARAM_covariables: List of input variables
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* PARAM_query: Query selecting the data to feed into the algorithm for training
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* MODEL_PARAM_pruned: PCTs can be pruned or not. Use PARAM_pruned=yes to prune and MODEL_PARAM_pruned=no otherwise (default is MODEL_PARAM_pruned=yes)
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* MODEL_PARAM_minobj: Specify minimal number of examples in leaf nodes of the PCT (default is MODEL_PARAM_minobj=2)

‎java-jsi-clus-pct-ts/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-pct-ts/captain.yml

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

‎java-jsi-clus-pct-ts/pom.xml

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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>eu.humanbrainproject.mip.algorithms.jsi</groupId>
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<artifactId>jsi-clus-pct-ts</artifactId>
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<packaging>jar</packaging>
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<version>0.9.0</version><!-- bumpversion -->
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<name>java-jsi-clus-pct-ts</name>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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<jdk.version>1.8</jdk.version>
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<compiler.plugin.version>3.6.2</compiler.plugin.version>
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<jar.plugin.version>3.0.2</jar.plugin.version>
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<surefire.plugin.version>2.19</surefire.plugin.version>
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<site.plugin.version>3.6</site.plugin.version>
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<info.reports.plugin.version>2.9</info.reports.plugin.version>
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<surefire.report.plugin.version>2.20</surefire.report.plugin.version>
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<jxr.plugin.version>2.5</jxr.plugin.version>
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<hadrian.version>0.8.5</hadrian.version>
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<junit.version>5.0.0</junit.version>
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<postgres.version>9.4.1212.jre7</postgres.version>
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<clus.version>1.0.0</clus.version>
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<jsi-clus.version>0.3.8</jsi-clus.version>
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<jackson.version>2.7.0</jackson.version>
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<mip.adapter.version>0.5.3</mip.adapter.version>
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</properties>
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<repositories>
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<repository>
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<id>maven</id>
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<url>https://repo.maven.apache.org/maven2</url>
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<name>Central Maven repository</name>
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</repository>
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<repository>
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<id>opendatagroup</id>
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<url>http://repository.opendatagroup.com/maven</url>
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<name>Repository for Hadrian</name>
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</repository>
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<repository>
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<snapshots>
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<enabled>false</enabled>
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</snapshots>
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<id>bintray-hbpmedical-mip</id>
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<name>bintray</name>
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<url>https://dl.bintray.com/hbpmedical/maven</url>
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</repository>
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</repositories>
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<dependencies>
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<dependency>
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<groupId>eu.humanbrainproject.mip.algorithms</groupId>
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<artifactId>adapter</artifactId>
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<version>${mip.adapter.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.humanbrainproject.mip.algorithms</groupId>
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<artifactId>jsi-clus</artifactId>
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<version>${jsi-clus.version}</version>
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</dependency>
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<dependency>
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<groupId>si.ijs.kt</groupId>
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<artifactId>clus</artifactId>
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<version>${clus.version}</version>
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</dependency>
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-api</artifactId>
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<version>${junit.version}</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>com.opendatagroup</groupId>
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<artifactId>hadrian</artifactId>
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<version>${hadrian.version}</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.postgresql</groupId>
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<artifactId>postgresql</artifactId>
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<version>${postgres.version}</version>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-core</artifactId>
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<version>${jackson.version}</version>
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</dependency>
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</dependencies>
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<build>
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<finalName>${project.artifactId}</finalName>
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<testResources>
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<testResource>
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<directory>src/test/java</directory>
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<includes>
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<include>**/*.csv</include>
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<include>**/*.json</include>
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</includes>
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<filtering>false</filtering>
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</testResource>
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</testResources>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<version>${compiler.plugin.version}</version>
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<configuration>
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<source>${jdk.version}</source>
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<target>${jdk.version}</target>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<version>${jar.plugin.version}</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-plugin</artifactId>
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<version>${surefire.plugin.version}</version>
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<!-- lock down our surefire provider -->
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<dependencies>
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<dependency>
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<groupId>org.junit.platform</groupId>
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<artifactId>junit-platform-surefire-provider</artifactId>
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<version>1.0.0</version>
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</dependency>
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<dependency>
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<groupId>org.junit.jupiter</groupId>
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<artifactId>junit-jupiter-engine</artifactId>
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<version>5.0.0</version>
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</dependency>
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</dependencies>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-site-plugin</artifactId>
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<version>${site.plugin.version}</version>
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</plugin>
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</plugins>
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</build>
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<reporting>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-project-info-reports-plugin</artifactId>
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<version>${info.reports.plugin.version}</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-surefire-report-plugin</artifactId>
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<version>${surefire.report.plugin.version}</version>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jxr-plugin</artifactId>
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<version>${jxr.plugin.version}</version>
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</plugin>
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</plugins>
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</reporting>
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</project>

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