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release 1.3.0
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‎.env‎

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RDEPOT_PORT=80
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RDEPOT_PORT=8016
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RDEPOT_PORT_SECURE=443
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JAVA_OPTS=
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JAVA_OPTS="-agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=8001"

‎.gitattributes‎

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*.tar.gz filter=lfs diff=lfs merge=lfs -text

‎.gitignore‎

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/bin/
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bin
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.gradle
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.settings
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.project
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.project*
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.classpath
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*.jar
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*.war
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/build/
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/docker/proxy/logs
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/repo/build/
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/repo/bin/
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/docker/app/repository
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.vscode/
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.attach_pid*
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build/tmp
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build/publications
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app/build
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app/bin
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docker/proxy/logs
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repo/build
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repo/bin
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docker/app/repository
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docker/app/new
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.vscode
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.idea
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*.iml
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*.class
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.sts4-cache
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src/integration-test/resources/itestGenerated
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src/integration-test/resources/itestNewFiles
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src/integration-test/resources/itestPackages
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src/integration-test/resources/itestServer
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src/integration-test/resources/itestSourceFiles
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src/integration-test/resources/itestPdf

‎Jenkinsfile‎

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pipeline {
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agent {
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kubernetes {
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yamlFile 'kubernetesPod.yaml'
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defaultContainer 'rdepot-build'
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}
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}
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options {
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buildDiscarder(logRotator(numToKeepStr: '3'))
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}
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environment {
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VERSION = sh(returnStdout: true, script: 'gradle properties -q | grep "baseVersion:" | sed -E "s/baseVersion: (.*)/\\1/g"').trim()
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NS = 'openanalytics'
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REG = '196229073436.dkr.ecr.eu-west-1.amazonaws.com'
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TAG = 'develop'
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DOCKER_BUILDKIT = '1'
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}
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stages {
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stage('build integration test images') {
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matrix {
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axes {
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axis {
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name 'MODULE'
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values 'app', 'repo', 'ldap'
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}
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}
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stages {
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stage('Docker build') {
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steps {
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withOARegistry {
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sh """
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docker build --build-arg BUILDKIT_INLINE_CACHE=1 \
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--cache-from ${env.REG}/${env.NS}/rdepot-${MODULE}-it:${env.TAG} \
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-t ${env.NS}/rdepot-${MODULE}-it:${env.TAG} \
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./src/integration-test/resources/docker/${MODULE}
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"""
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ecrPush "${env.REG}", "${env.NS}/rdepot-${MODULE}-it", "${env.TAG}", '', 'eu-west-1'
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}
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}
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}
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}
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}
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}
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stage('build and test') {
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steps {
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sh "gradle build"
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}
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post {
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success {
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archiveArtifacts 'app/build/libs/rdepot-app-*.war,repo/build/libs/rdepot-repo-*.jar'
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withCredentials([usernamePassword(credentialsId: 'oa-jenkins', usernameVariable: 'OA_NEXUS_USER', passwordVariable: 'OA_NEXUS_PWD')]) {
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sh "gradle publish"
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}
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}
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always {
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publishHTML([
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reportDir: 'build/reports/tests/integrationTest', reportFiles: 'index.html',
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reportName: 'Integration Test Report',
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allowMissing: true, alwaysLinkToLastBuild: true, keepAll: true])
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publishHTML([
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reportDir: 'app/build/reports/tests/test', reportFiles: 'index.html',
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reportName: 'App Test Report',
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allowMissing: true, alwaysLinkToLastBuild: true, keepAll: true])
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publishHTML([
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reportDir: 'repo/build/reports/tests/test', reportFiles: 'index.html',
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reportName: 'Repo Test Report',
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allowMissing: true, alwaysLinkToLastBuild: true, keepAll: true])
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}
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}
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}
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stage('build Docker images and publish') {
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matrix {
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axes {
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axis {
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name 'MODULE'
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values 'app', 'repo'
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}
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}
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stages {
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stage('build Docker images') {
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steps {
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withOARegistry {
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sh """
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docker build --build-arg BUILDKIT_INLINE_CACHE=1 \
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--cache-from ${env.REG}/${env.NS}/rdepot-${MODULE}:${env.VERSION} \
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-t ${env.NS}/rdepot-${MODULE}:${env.VERSION} \
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-t ${env.NS}/rdepot-${MODULE}:latest \
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-f ./docker/build/${MODULE}-standalone/Dockerfile \
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./${MODULE}/build/libs
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"""
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ecrPush "${env.REG}", "${env.NS}/rdepot-${MODULE}", "${env.VERSION}", '', 'eu-west-1'
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ecrPush "${env.REG}", "${env.NS}/rdepot-${MODULE}", "latest", '', 'eu-west-1'
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}
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}
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}
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stage('publish') {
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steps {
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withDockerRegistry([
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credentialsId: "openanalytics-dockerhub",
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url: ""]) {
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sh "docker push ${env.NS}/rdepot-${MODULE}:${env.VERSION}"
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sh "docker push ${env.NS}/rdepot-${MODULE}:latest"
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}
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}
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}
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}
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}
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}
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}
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}

‎Makefile‎

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app:
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rm -rf ./build
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./gradlew build
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cp -f ./build/libs/rdepot*.war ./docker/app/rdepot.war
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repo:
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rm -rf ./repo/build
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cd ./repo && ./gradlew build && cp -f ./build/libs/oa-rdepot-repo*.jar ./../docker/repo/oa-rdepot-repo.jar
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./gradlew build -x test -x integrationTest testClasses #temporary change
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cp -f ./app/build/libs/rdepot-app*application.war ./docker/app/rdepot.war
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cp -f ./app/build/libs/rdepot-app*application.war ./src/integration-test/resources/docker/app/rdepot.war
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repo:
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cp -f ./repo/build/libs/rdepot-repo*application.jar ./docker/repo/rdepot-repo.jar
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cp -f ./repo/build/libs/rdepot-repo*application.jar ./src/integration-test/resources/docker/repo/rdepot-repo.jar
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download:
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curl https://s3-eu-west-1.amazonaws.com/oa-rdepot-build-artifacts/rdepot.war --output ./docker/app/rdepot.war
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curl https://s3-eu-west-1.amazonaws.com/oa-rdepot-build-artifacts/oa-rdepot-repo.jar --output ./docker/repo/oa-rdepot-repo.jar
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curl https://s3-eu-west-1.amazonaws.com/oa-rdepot-build-artifacts/rdepot-repo.jar --output ./docker/repo/rdepot-repo.jar
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rm-app:
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docker-compose stop app
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docker-compose rm -f app
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start-app:
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docker-compose up -d app
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all: app repo
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.PHONY: all test clean repo app download
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.PHONY: all test clean repo app download rm-app start-app

‎README.md‎

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```
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# RDepot
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# R Depot User Guide
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Open Source Enterprise Management of R Repositories
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Currently, R Depot consists of three core components:
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Learn more at https://rdepot.io
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- the RDepot R repository management application (rdepot.war)
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- a database component, preferably Postgres
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- one or more R repositories (instances of oa-rdepot-repo.jar)
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The quickest way to set up a working environment, is by using Docker (preferably on Linux).
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The following prerequisites are needed:
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- docker
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- docker-compose (i.e. by issuing "pip install docker-compose")
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- port 80 is not used (localhost, check for nginx or apache service)
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Please make sure the following files are available:
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- ./docker/app/rdepot.war: downloaded from https://s3-eu-west-1.amazonaws.com/oa-rdepot-build-artifacts/rdepot.war (latest development build)
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- ./docker/repo/oa-rdepot-repo.jar: downloaded from https://s3-eu-west-1.amazonaws.com/oa-rdepot-build-artifacts/oa-rdepot-repo.jar (latest development build)
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The final step is to launch the Docker containers using docker-compose:
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- docker-compose up -d
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One can then go to http://localhost to log in.
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Regarding users and passwords: all passwords are "password" (without ""), because the application is connected by default to "scientists" group of the ForumSys LDAP server (http://www.forumsys.com/tutorials/integration-how-to/ldap/online-ldap-test-server/).
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- user "einstein" is an administrator
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- user "tesla" is a repository maintainer (but not linked to a repository, an administrator has to do that manually)
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- user "galieleo" is a package maintainer (but not linked to a package, a repository maintainer or administrator has to do that manually)
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- user "newton" is a regular user
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To complete an end-to-end flow: R package to R Depot to Repository Server to R client, the following steps are needed:
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- create a repository with (or edit)
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* a repository's publication URI: http://localhost/repo/repositoryName and
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* a server address: http://oa-rdepot-repo:8080/repositoryName
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- submit one or more packages to that repository via the R Depot web interface
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- publish the repository using the green button in the repositories view (if needed)
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- go to the published package page (repositories view, click repository name, click package name)
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- use the install URL shown on the published package page to install the package in R (install.packages("somePackage", repos = c("http://localhost/repo/repositoryName", getOption())))
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To (re)start with fresh database:
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- remove the containers via "docker-compose down -v"
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- start up again using "docker-compose up -d"
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Browse the [RDepot Documentation](https://www.rdepot.io/).
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#### Copyright (c) Copyright of Open Analytics NV, 2010-2018 - Apache 2.0 License
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#### (c) Copyright Open Analytics NV, 2012-2020 - Apache License 2.0

‎WEB-INF/web.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<web-app xmlns="http://java.sun.com/xml/ns/j2ee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd" id="WebApp_ID">
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<display-name>rdepot</display-name>
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<welcome-file-list>
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<welcome-file>index.html</welcome-file>
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<welcome-file>index.htm</welcome-file>
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<welcome-file>index.jsp</welcome-file>
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<welcome-file>default.html</welcome-file>
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<welcome-file>default.htm</welcome-file>
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<welcome-file>default.jsp</welcome-file>
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</welcome-file-list>
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</web-app>

‎WebContent/META-INF/MANIFEST.MF‎

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Manifest-Version: 1.0
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Class-Path:
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‎app/WEB-INF/web.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<web-app xmlns="http://java.sun.com/xml/ns/j2ee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd" id="WebApp_ID">
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<display-name>rdepot-app</display-name>
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<welcome-file-list>
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<welcome-file>index.html</welcome-file>
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<welcome-file>index.htm</welcome-file>
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<welcome-file>index.jsp</welcome-file>
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<welcome-file>default.html</welcome-file>
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<welcome-file>default.htm</welcome-file>
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<welcome-file>default.jsp</welcome-file>
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</welcome-file-list>
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</web-app>

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