build: refactor circleci so sonar shows latest test results again AND…

… remove formatcheck precommit hook (#3224)

* build: refactor so sonar shows latest test results again

* small changes

* small fixes

* make gradle cache build javascript so it doesn't build again on test

* make javascript build caching properly so step is skipped if files not touchedf

* remove formatcheck, we only should do apply

* move checkformat to build step

* fix that javascript build should go before resources are processed into jar

* merge prepare and build to save some overhead

* merge prepare and build to save some overhead

* merge prepare and build to save some overhead

* remove unused docker in build phase

* fix

* move format to the build instead of test otherwise build repeats

* simplify

.circleci/config.yml

@@ -6,11 +6,17 @@ version: 2
 orbs:
   slack: circleci/[email protected]
 jobs:
-  prepare:
+  build:
     docker:
     # specify the version you desire here
     - image: molgenis/ci-build:latest
     working_directory: ~/repo
+    resource_class: large
+
+    environment:
+      JVM_OPTS: -Xmx3200m
+      GRADLE_OPTS: "-Dorg.gradle.daemon=false -Dorg.gradle.workers.max=2"
+      TERM: dumb
 
     steps:
     - checkout
@@ -33,50 +39,20 @@ jobs:
         - ~/.gradle
         key: v1-dependencies-{{ checksum "build.gradle" }}
 
-    - 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, todo, move to molgenisci user
         command: |
           git config --global --add safe.directory '*'
           git config user.email "[email protected]"
           git config user.name "mswertz"
           git config url.https://.insteadOf git://
-    - persist_to_workspace:
-          root: .
-          paths:
-              - .
-
-  build:
-    docker:
-    - image: molgenis/ci-build:latest
-    - image: postgres:15-alpine
-      environment:
-        POSTGRES_USER: postgres
-        POSTGRES_PASSWORD: postgres
-        POSTGRES_DB: postgres
-    working_directory: ~/repo
-
-    # The resource_class feature allows configuring CPU and RAM resources for each job. Different resource classes are available for different executors. https://circleci.com/docs/2.0/configuration-reference/#resourceclass
-    resource_class: large
-
-    environment:
-      JVM_OPTS: -Xmx3200m
-      GRADLE_OPTS: "-Dorg.gradle.daemon=false -Dorg.gradle.workers.max=2"
-      TERM: dumb
 
-    steps:
-    - attach_workspace:
-        at: ~/repo
+    - run:
+        name: build jar and compile test classes and export 'ci' config
+        command: |
+          ./gradlew clean testClasses shadowJar ci
+          export $( cat build/ci.properties | xargs )
 
-    - run: ./gradlew clean assemble testClasses ci
-
     - persist_to_workspace:
         root: .
         paths:
@@ -106,14 +82,10 @@ jobs:
         command: docker login -u $DOCKER_USER -p $DOCKER_PASS
 
     - run:
-        name: push emx2 docker images
+        name: push emx2 docker images and helm for the preview
         command: |
           echo "PR number: ${CIRCLE_PULL_REQUEST##*/}"
-          ./gradlew -s jacocoMergedReport --no-daemon shadowJar dockerPush helmPublishMainChart ci sonar -x test -x :apps:buildJavascript -x :apps:checkFormat -x :apps:testJavaScript \
-          -Dorg.ajoberstar.grgit.auth.username=${GITHUB_TOKEN} -Dorg.ajoberstar.grgit.auth.password \
-          -Dsonar.login=${SONAR_TOKEN} -Dsonar.organization=molgenis -Dsonar.host.url=https://sonarcloud.io -Dsonar.verbose=true \
-          -Dsonar.pullrequest.key=${CIRCLE_PULL_REQUEST##*/} -Dsonar.pullrequest.branch=${CIRCLE_BRANCH}
-          export $( cat build/ci.properties | xargs )
+          ./gradlew -s --no-daemon dockerPush helmPublishMainChart
 
     - run:
         name: push ssr-catalogue docker images
@@ -173,7 +145,13 @@ jobs:
 
     - run: psql -h 127.0.0.1 -p 5432 -U postgres < .docker/initdb.sql
 
-    - run: ./gradlew test --no-daemon
+    - run:
+        name: Run tests, merge test results using jacoco and push test results to sonar
+        command: |
+          ./gradlew test jacocoMergedReport sonar -x apps:format -x apps:buildJavaScript  --no-daemon \
+          -Dorg.ajoberstar.grgit.auth.username=${GITHUB_TOKEN} -Dorg.ajoberstar.grgit.auth.password \
+          -Dsonar.login=${SONAR_TOKEN} -Dsonar.organization=molgenis -Dsonar.host.url=https://sonarcloud.io -Dsonar.verbose=true \
+          -Dsonar.pullrequest.key=${CIRCLE_PULL_REQUEST##*/} -Dsonar.pullrequest.branch=${CIRCLE_BRANCH}
       
     - run:
         name: Save test results
@@ -208,23 +186,17 @@ jobs:
         command: docker login -u $DOCKER_USER -p $DOCKER_PASS
 
     - run:
-        name: release, push docker, push python
+        name: release, push release docker, push release python
         command: |
           export $( cat build/ci.properties | xargs )
-          ./gradlew -s jacocoMergedReport --no-daemon shadowJar dockerPush helmPublishMainChart release -x test -x :apps:buildJavascript -x :apps:checkFormat -x :apps:testJavaScript  \
-          -Dorg.ajoberstar.grgit.auth.username=${GITHUB_TOKEN} -Dorg.ajoberstar.grgit.auth.password \
-          -Dsonar.login=${SONAR_TOKEN} -Dsonar.organization=molgenis -Dsonar.host.url=https://sonarcloud.io -Dsonar.verbose=true
+          ./gradlew -s --no-daemon dockerPush helmPublishMainChart release
           if [[ "$TAG_NAME" == *"SNAPSHOT"* ]]; then
             docker build apps/nuxt3-ssr/ -t molgenis/ssr-catalogue-snapshot:latest -t molgenis/ssr-catalogue-snapshot:${TAG_NAME}
             docker push molgenis/ssr-catalogue-snapshot --all-tags
           else
             docker build apps/nuxt3-ssr/ -t molgenis/ssr-catalogue:latest -t molgenis/ssr-catalogue:${TAG_NAME}
             docker push molgenis/ssr-catalogue --all-tags
           fi
-        environment:
-          MOLGENIS_POSTGRES_USER: molgenis
-          MOLGENIS_POSTGRES_PASS: molgenis
-          MOLGENIS_POSTGRES_URI: jdbc:postgresql://localhost/molgenis
 
     - run: 
         name: update rug server
@@ -254,10 +226,7 @@ workflows:
   version: 2
   build_and_test_and_preview_or_release:
     jobs:
-      - prepare
-      - build:
-          requires:
-            - prepare
+      - build
       - preview:
           requires:
             - build