Merge branch 'develop' into TASK-2095

.github/workflows/develop.yml

@@ -10,14 +10,13 @@ on:
 jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+    with:
+      maven_opts: -DCELLBASE.WAR.NAME=cellbase -P default-config-test
 
   test:
     uses: ./.github/workflows/test-analysis.yml
     needs: build
     secrets: inherit
-    with:
-      report_context: development
-      report_dir: ${{ github.ref_name }}/cellbase/${{ github.sha }}
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
@@ -32,4 +31,3 @@ jobs:
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base
     secrets: inherit
-

.github/workflows/pull-request-merge.yml

@@ -1,4 +1,4 @@
-name: "Merge Workflow"
+name: "Pull Request Merge Workflow"
 
 on:
   pull_request:
@@ -13,6 +13,4 @@ jobs:
     uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@develop
     with:
       cli: python3 ./build/cloud/docker/docker-build.py delete --images base --tag ${{ github.head_ref }}
-    secrets:
-      DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
-      DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
+    secrets: inherit

.github/workflows/release.yml

@@ -9,32 +9,26 @@ on:
 jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
-
-  test:
-    uses: ./.github/workflows/test-analysis.yml
-    needs: build
-    secrets: inherit
     with:
-      report_context: xetabase
-      report_dir: cellbase
+      maven_opts: -DCELLBASE.WAR.NAME=cellbase
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
-    needs: test
+    needs: build
     with:
       maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
     secrets: inherit
 
   deploy-docker:
     uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
-    needs: test
+    needs: build
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base
     secrets: inherit
 
   deploy-python:
     uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop
-    needs: test
+    needs: build
     with:
       cli: bash ./clients/python/python-build.sh push
       artifact: build-folder

.github/workflows/scripts/get_same_branch.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+BRANCH_NAME=$1
+
+if [[ -z $BRANCH_NAME  ]]; then
+  echo "The first parameter is mandatory and must be a valid branch name."
+  exit 1
+fi
+
+if [[ $BRANCH_NAME != "TASK-"*   ]]; then
+  echo "No need to check dependencies."
+  exit 0
+fi
+
+function install(){
+  local REPO=$1
+  cd /home/runner/work/ || exit 2
+  git clone https://github.com/opencb/"$REPO".git -b "$BRANCH_NAME"
+  if [ -d "./$REPO" ]; then
+    cd "$REPO" || exit 2
+    echo "Branch name $BRANCH_NAME already exists."
+    mvn clean install -DskipTests
+  else
+    echo "$CURRENT Branch is NOT EQUALS $BRANCH_NAME "
+  fi
+}
+
+install "java-common-libs"
+install "biodata"

.github/workflows/task.yml

@@ -5,50 +5,21 @@ on:
     branches:
       - TASK-*
   workflow_dispatch:
-
+    
 jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+    with:
+      maven_opts: -DCELLBASE.WAR.NAME=cellbase -P default-config-test
 
   test:
     uses: ./.github/workflows/test-analysis.yml
     needs: build
     secrets: inherit
-    with:
-      report_context: development
-      report_dir: ${{ github.ref_name }}/cellbase/${{ github.sha }}
 
   deploy-docker:
     uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
     needs: test
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base --tag ${{ github.ref_name }}
     secrets: inherit
-
-  deploy-maven:
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
-    needs: [ build, test ]
-    with:
-      maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
-    if: contains( needs.build.outputs.version ,'TASK')
-    secrets: inherit
-
-  #The following jobs are to see that the previous if does not fail and that the maven deploy is executed because it is true
-  snapshot-version:
-    name: Check SNAPSHOT version
-    needs: [ build, test ]
-    if: contains(needs.build.outputs.version ,'SNAPSHOT')
-    runs-on: ubuntu-22.04
-    steps:
-      - name: test-version-from-check
-        run: echo "Project version is " ${{ needs.build.outputs.version }}
-
-  task-version:
-    name: Check TASK version
-    needs: [ build, test ]
-    if: contains(needs.build.outputs.version ,'TASK')
-    runs-on: ubuntu-22.04
-    steps:
-      - name: test-version-from-check
-        run: echo "Project version is " ${{ needs.build.outputs.version }}
-

.github/workflows/test-analysis.yml

@@ -1,27 +1,11 @@
 name: Build and test the project
+
 on:
   workflow_call:
     secrets:
       SONAR_TOKEN:
         required: true
-      SSH_TESTING_SERVER_HOST:
-        required: true
-      SSH_TESTING_SERVER_PORT:
-        required: true
-      SSH_TESTING_SERVER_USER:
-        required: true
-      SSH_TESTING_SERVER_PASSWORD:
-        required: true
-    inputs:
-      report_dir:
-        type: string
-        required: true
-      report_context:
-        type: string
-        required: true
-env:
-  xb_version: "1.7.0"
-
+
 jobs:
   test:
     name: Test and push Sonar analysis
@@ -41,35 +25,26 @@ jobs:
         with:
           mongodb-version: 6.0
           mongodb-replica-set: rs-test
+      - name: Install dependencies branches
+        run: |
+          if [ -f "./.github/workflows/scripts/get_same_branch.sh" ]; then
+            chmod +x ./.github/workflows/scripts/get_same_branch.sh
+            ./.github/workflows/scripts/get_same_branch.sh ${{ github.ref_name }}
+          else
+             echo "./.github/workflows/scripts/get_same_branch.sh does not exist."
+          fi
       - name: Test and Analyze
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any
           SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-        run: mvn -B verify surefire-report:report -Dcheckstyle.skip org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_cellbase
-      - name: Upload result dir
-        uses: actions/upload-artifact@v3
-        with:
-          name: workdir
-          path: "**/target/site"
-  publish-test:
-    name: Publish test results
-    runs-on: ubuntu-22.04
-    needs: test
-    strategy:
-      matrix:
-        module: ["cellbase-core", "cellbase-app", "cellbase-client", "cellbase-lib", "cellbase-server"]
-    steps:
-      - name: Download result dir
-        uses: actions/download-artifact@v3
-        with:
-          name: workdir
-      - name: Deploy unit tests web recursively to remote
-        uses: garygrossgarten/github-action-scp@release
+        run: mvn -B verify surefire-report:report --fail-never -Dcheckstyle.skip org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_cellbase
+      - name: Publish Test Report
+        uses: scacap/action-surefire-report@v1
+        ## Skip cancelled()
+        ## https://docs.github.com/en/actions/learn-github-actions/expressions#cancelled
+        if: success() || failure()
         with:
-          local: ${{ matrix.module }}/target/site
-          remote: /var/www/html/reports/${{ inputs.report_context }}/${{ env.xb_version }}/${{ inputs.report_dir }}/unit/${{ matrix.module }}
-          host: ${{ secrets.SSH_TESTING_SERVER_HOST}}
-          port: ${{ secrets.SSH_TESTING_SERVER_PORT}}
-          username: ${{ secrets.SSH_TESTING_SERVER_USER }}
-          password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }}
-          concurrency: 2
+          check_name: "Surefire tests report"
+          report_paths: './**/surefire-reports/TEST-*.xml'
+          commit: '${{ github.sha }}'
+          fail_on_test_failures: true

cellbase-app/app/cloud/docker/cellbase-base/Dockerfile

@@ -1,5 +1,6 @@
-## Based on Debian 11 (bullseye)
-FROM openjdk:11-jre
+## Based on Ubuntu 22.04 (jammy)
+## We are now using OpenJDK 8u372 to support "cgroup v2", see https://developers.redhat.com/articles/2023/04/19/openjdk-8u372-feature-cgroup-v2-support#
+FROM eclipse-temurin:8u372-b07-jre-jammy
 
 LABEL org.label-schema.vendor="OpenCB" \
       org.label-schema.name="cellbase-base" \

cellbase-app/src/main/java/org/opencb/cellbase/app/cli/CommandExecutor.java

@@ -18,13 +18,13 @@
 
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.core.config.Configurator;
 import org.opencb.cellbase.client.config.ClientConfiguration;
 import org.opencb.cellbase.core.config.CellBaseConfiguration;
 import org.opencb.cellbase.core.exception.CellBaseException;
 import org.opencb.commons.utils.FileUtils;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.apache.logging.log4j.core.config.Configurator;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -204,5 +204,4 @@ protected void makeDir(Path folderPath) throws IOException {
             Files.createDirectories(folderPath);
         }
     }
-
 }