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jaserud
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- port to es7
- remove circle CI - added jenkins pipeline - updated dockerfile
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10 files changed

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-165
lines changed

10 files changed

+193
-165
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‎.circleci/config.yml

-56
This file was deleted.

‎.mvn/wrapper/maven-wrapper.properties

+4-4
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@@ -1,6 +1,6 @@
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#
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# Copyright (c) 2018. The Ontario Institute for Cancer Research. All rights reserved.
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#
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# Copyright (c) 2020. The Ontario Institute for Cancer Research. All rights reserved.
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#
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# This program is free software: you can redistribute it and/or modify
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# it under the terms of the GNU Affero General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
@@ -13,7 +13,7 @@
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#
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# You should have received a copy of the GNU Affero General Public License
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# along with this program. If not, see <http://www.gnu.org/licenses/>.
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#
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#
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#
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distributionUrl=https://repo1.maven.org/maven2/org/apache/maven/apache-maven/3.5.3/apache-maven-3.5.3-bin.zip
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distributionUrl=https://repo1.maven.org/maven2/org/apache/maven/apache-maven/3.6.3/apache-maven-3.6.3-bin.zip

‎Dockerfile

+23-27
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@@ -1,36 +1,32 @@
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FROM openjdk:8u121-jdk-alpine
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FROM openjdk:11-jdk as builder
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ARG MAVEN_VERSION=3.5.4
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ARG SHA=ce50b1c91364cb77efe3776f756a6d92b76d9038b0a0782f7d53acf1e997a14d
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ARG BASE_URL=https://apache.osuosl.org/maven/maven-3/${MAVEN_VERSION}/binaries
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# Build song-server jar
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COPY . /srv
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WORKDIR /srv
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RUN ./mvnw clean package -DskipTests
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RUN apk add --no-cache curl tar bash \
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&& mkdir -p /usr/share/maven /usr/share/maven/ref \
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&& curl -fsSL -o /tmp/apache-maven.tar.gz ${BASE_URL}/apache-maven-${MAVEN_VERSION}-bin.tar.gz \
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&& echo "${SHA} /tmp/apache-maven.tar.gz" | sha256sum -c - \
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&& tar -xzf /tmp/apache-maven.tar.gz -C /usr/share/maven --strip-components=1 \
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&& rm -f /tmp/apache-maven.tar.gz \
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&& ln -s /usr/share/maven/bin/mvn /usr/bin/mvn
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15-
WORKDIR /usr/src/app
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FROM openjdk:11-jre as server
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# Paths
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ENV APP_HOME /srv/rollcall
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ENV APP_LOGS $APP_HOME/logs
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ENV JAR_FILE /srv/rollcall/rollcall.jar
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# copy just the pom.xml and install dependencies for caching
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COPY pom.xml .
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RUN mvn verify clean --fail-never
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COPY --from=builder /srv/target/rollcall-*.jar $JAR_FILE
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ENV APP_USER rollcall
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ENV APP_UID 9999
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ENV APP_GID 9999
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COPY . .
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RUN useradd -r -u $APP_UID $APP_USER \
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&& mkdir -p $APP_HOME $APP_LOGS \
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&& chown -R $APP_UID:$APP_GID $APP_HOME \
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&& chown -R $APP_UID:$APP_GID $APP_LOGS
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RUN mkdir -p /srv/rollcall/install \
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&& mkdir -p /srv/rollcall/exec \
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&& mvn package -Dmaven.test.skip=true \
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&& mv /usr/src/app/target/rollcall-*-SNAPSHOT.jar /srv/rollcall/install/ROLLCALL.jar \
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&& mv /usr/src/app/src/main/resources/scripts/run.sh /srv/rollcall/exec/run.sh
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USER $APP_USER
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# setup required environment variables
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ENV ROLLCALL_INSTALL_PATH /srv/rollcall
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# start ego server
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WORKDIR $ROLLCALL_INSTALL_PATH
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CMD $ROLLCALL_INSTALL_PATH/exec/run.sh
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WORKDIR $APP_HOME
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CMD java -Dlog.path=$APP_LOGS \
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-jar $JAR_FILE \
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--spring.config.location=classpath:/application.yml

‎Jenkinsfile

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@@ -1,2 +1,102 @@
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@Library(value="oicr", changelog=false) _
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rollcall{}
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import groovy.json.JsonOutput
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def version = "UNKNOWN"
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def commit = "UNKNOWN"
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pipeline {
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agent {
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kubernetes {
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label 'rollcall-executor'
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yaml """
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apiVersion: v1
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kind: Pod
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spec:
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containers:
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- name: jdk
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tty: true
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image: openjdk:11
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env:
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- name: DOCKER_HOST
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value: tcp://localhost:2375
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- name: helm
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image: alpine/helm:2.12.3
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command:
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- cat
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tty: true
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- name: docker
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image: docker:18-git
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tty: true
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volumeMounts:
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- mountPath: /var/run/docker.sock
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name: docker-sock
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- name: dind-daemon
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image: docker:18.06-dind
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securityContext:
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privileged: true
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volumeMounts:
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- name: docker-graph-storage
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mountPath: /var/lib/docker
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volumes:
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- name: docker-sock
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hostPath:
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path: /var/run/docker.sock
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type: File
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- name: docker-graph-storage
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emptyDir: {}
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"""
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}
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}
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stages {
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stage('Prepare') {
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steps {
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script {
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commit = sh(returnStdout: true, script: 'git describe --always').trim()
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}
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script {
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version = readMavenPom().getVersion()
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}
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}
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}
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stage('Test') {
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steps {
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container('jdk') {
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sh "./mvnw test package"
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}
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}
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}
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stage('Build & Publish Develop') {
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when {
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branch "develop"
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}
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steps {
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container('docker') {
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withCredentials([usernamePassword(credentialsId:'OvertureDockerHub', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
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sh 'docker login -u $USERNAME -p $PASSWORD'
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}
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sh "docker build --network=host -f Dockerfile . -t overture/rollcall:edge -t overture/rollcall:${commit}"
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sh "docker push overture/rollcall:edge"
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sh "docker push overture/rollcall:${commit}"
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}
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}
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}
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stage('Release & tag') {
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when {
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branch "master"
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}
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steps {
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container('docker') {
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withCredentials([usernamePassword(credentialsId: 'OvertureBioGithub', passwordVariable: 'GIT_PASSWORD', usernameVariable: 'GIT_USERNAME')]) {
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sh "git tag ${version}"
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sh "git push https://${GIT_USERNAME}:${GIT_PASSWORD}@github.com/overture-stack/rollcall --tags"
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}
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withCredentials([usernamePassword(credentialsId:'OvertureDockerHub', usernameVariable: 'USERNAME', passwordVariable: 'PASSWORD')]) {
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sh 'docker login -u $USERNAME -p $PASSWORD'
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}
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sh "docker build --network=host -f Dockerfile . -t overture/rollcall:latest -t overture/rollcall:${version}"
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sh "docker push overture/rollcall:${version}"
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sh "docker push overture/rollcall:latest"
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}
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}
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}
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}
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}

‎pom.xml

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<groupId>bio.overture</groupId>
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<artifactId>rollcall</artifactId>
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<version>1.0.0-SNAPSHOT</version>
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<version>2.0.0-SNAPSHOT</version>
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<packaging>jar</packaging>
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2929
<name>rollcall</name>
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101101
<dependency>
102102
<groupId>org.elasticsearch</groupId>
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<artifactId>elasticsearch</artifactId>
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<version>6.3.1</version>
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<version>7.5.2</version>
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</dependency>
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<dependency>
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<groupId>org.elasticsearch.client</groupId>
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<artifactId>elasticsearch-rest-high-level-client</artifactId>
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<version>6.3.1</version>
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<version>7.5.2</version>
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</dependency>
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<dependency>
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<groupId>org.elasticsearch.client</groupId>
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<artifactId>transport</artifactId>
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<version>6.3.1</version>
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</dependency>
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<dependency>
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<groupId>org.elasticsearch.plugin</groupId>
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<artifactId>transport-netty4-client</artifactId>
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<version>6.3.1</version>
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<artifactId>elasticsearch-rest-client</artifactId>
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<version>7.5.2</version>
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</dependency>
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<!-- Swagger -->
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145140
<scope>test</scope>
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</dependency>
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143+
<!-- JAXB -->
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<dependency>
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<groupId>org.glassfish.jaxb</groupId>
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<artifactId>jaxb-runtime</artifactId>
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<version>2.4.0-b180830.0438</version>
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</dependency>
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</dependencies>
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150151
<build>

‎src/main/java/bio/overture/rollcall/config/ElasticsearchConfig.java

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import org.apache.http.HttpHost;
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import org.elasticsearch.client.RestClient;
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import org.elasticsearch.client.RestHighLevelClient;
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import org.elasticsearch.client.transport.TransportClient;
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import org.elasticsearch.common.settings.Settings;
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import org.elasticsearch.common.transport.TransportAddress;
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import org.elasticsearch.transport.client.PreBuiltTransportClient;
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import org.springframework.beans.factory.annotation.Value;
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import org.springframework.context.annotation.Bean;
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import org.springframework.context.annotation.Configuration;
@@ -35,16 +31,12 @@
3531
@Configuration
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public class ElasticsearchConfig {
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38-
private static final String CLUSTER_NAME = "cluster.name";
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@Value("${elasticsearch.host}")
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private String host;
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@Value("${elasticsearch.port}")
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private int port;
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46-
@Value("${elasticsearch.cluster-name}")
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private String clusterName;
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@Bean
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@SneakyThrows
@@ -55,14 +47,4 @@ public RestHighLevelClient restClient() {
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)
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);
5749
}
58-
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@Bean
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@SneakyThrows
61-
public TransportClient transportClient() {
62-
return new PreBuiltTransportClient(Settings.builder()
63-
.put(CLUSTER_NAME, clusterName)
64-
.build())
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.addTransportAddress(new TransportAddress(InetAddress.getByName(host), port));
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}
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}

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