Merge branch 'master' of github.com:molgenis/molgenis-service-armadil…

…lo into fix/migrate-minio-skip-rds

.circleci/config.yml

@@ -0,0 +1,89 @@
+# Java Gradle CircleCI 2.0 configuration file
+#
+# Check https://circleci.com/docs/2.0/language-java/ for more details
+#
+version: 2.1
+
+jobs:
+  build:
+    docker:
+      # specify the version you desire here
+      - image: gradle:jdk17-focal
+
+    working_directory: ~/repo
+    resource_class: large
+
+    environment:
+      # Customize the JVM maximum heap limit
+      JVM_OPTS: -Xmx3200m
+      GRADLE_OPTS: "-Dorg.gradle.daemon=false -Dorg.gradle.workers.max=2"
+      TERM: dumb
+
+    steps:
+      - checkout
+
+      # Download and cache dependencies
+      - restore_cache:
+          keys:
+            - v1-dependencies-{{ checksum "build.gradle" }}
+            # fallback to using the latest cache if no exact match is found
+            - v1-dependencies-
+
+      - run: ./gradlew dependencies
+
+      - save_cache:
+          paths:
+            - ~/.gradle
+          key: v1-dependencies-{{ checksum "build.gradle" }}
+
+      # run tests!
+      - run:
+          name: update package manager
+          command: apt-get update
+
+      - run:
+          name: add packages for docker cli install
+          command: apt-get -y install gnupg lsb-release curl
+
+      - run:
+          name: update packages again
+          command: apt-get update
+
+      - run:
+          name: set repo keys for docker packages
+          command: curl -fsSL https://download.docker.com/linux/ubuntu/gpg | gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
+
+      - run:
+          name: add repo for docker packages
+          command: echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null
+
+      - run:
+          name: update package manager again
+          command: apt-get update
+
+      - run:
+          name: Install Docker client
+          command: apt-get -y install docker-ce docker-ce-cli containerd.io
+
+      - setup_remote_docker:
+          version: 19.03.13
+          docker_layer_caching: true
+
+      - run:
+          name: Sign in to docker
+          command: docker login -u $DOCKER_USER -p $DOCKER_PASS
+
+      - run:
+          name: Setup git
+          command: |
+            git config --global --add safe.directory '*'
+            git config user.email "[email protected]"
+            git config user.name "molgenis-jenkins"
+            git config url.https://.insteadOf git://
+
+      - run:
+          name: build, test, push docker
+          command: |
+            ./gradlew build test jacocoMergedReport sonarqube release dockerPush \
+            -Dsonar.login=${SONAR_TOKEN} -Dsonar.organization=molgenis -Dsonar.host.url=https://sonarcloud.io \
+            -Dorg.ajoberstar.grgit.auth.username=${GITHUB_TOKEN} -Dorg.ajoberstar.grgit.auth.password

.gitignore

@@ -1,5 +1,12 @@
 .DS_Store
 
+#gradle
+.gradle
+build/
+!gradle-wrapper.jar
+out
+dist
+
 ### STORAGE ###
 data/user-*
 data/system

Dockerfile

@@ -0,0 +1,7 @@
+FROM eclipse-temurin:17-jdk-focal
+ENV SPRING_PROFILES_ACTIVE development
+VOLUME /data
+ARG JAR_FILE
+EXPOSE 8080
+COPY ${JAR_FILE} /app.jar
+ENTRYPOINT ["java","-Djava.security.egd=file:/dev/./urandom","-jar","/app.jar"]