TASK-2270

.github/workflows/build-test.yml

@@ -0,0 +1,72 @@
+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
+
+env:
+  xb_version: "1.5.0"
+
+jobs:
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+
+  test:
+    name: Test and push Sonar analysis
+    runs-on: ubuntu-22.04
+    needs: build
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: '0'
+      - name: Set up JDK 11
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '11'
+          cache: 'maven'
+      - name: Install Samtools
+        run: sudo apt-get install samtools
+      - 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  org.sonarsource.scanner.maven:sonar-maven-plugin:sonar -Dsonar.projectKey=opencb_biodata
+      - 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: [ "biodata-tools","biodata-models" ]
+    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
+        with:
+          local: ${{ matrix.module }}/target/site
+          remote: /var/www/html/reports/development/${{ env.xb_version }}/${{ github.ref_name }}/biodata/${{ github.sha }}/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

.github/workflows/develop.yml

@@ -7,44 +7,14 @@ on:
       - release-*
 
 jobs:
-  build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
-
-  sonar:
-    uses: opencb/java-common-libs/.github/workflows/sonar-analysis-workflow.yml@develop
-    needs: build
-    with:
-      sonarProjectKey: opencb_biodata
+  test:
+    uses: opencb/biodata/.github/workflows/build-test.yml@develop
     secrets:
       SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-  test:
-    name: Test biodata
-    runs-on: ubuntu-20.04
-    needs: build
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: '10'
-      - name: Set up JDK 8
-        uses: actions/setup-java@v3
-        with:
-          distribution: 'temurin'
-          java-version: '8'
-          cache: 'maven'
-      - name: Install Samtools
-        run: sudo apt-get install samtools
-      - name: Run tests with Maven
-        run: mvn -T 2 clean install -DskipTests
-#        run: mvn surefire-report:report
-#      - name: Deploy tests web recursively to remote
-#        uses: garygrossgarten/github-action-scp@release
-#        with:
-#          local: biodata-tools/target
-#          remote: /mnt/data/opencb/biodata/tests/${{ needs.build.outputs.version }}/${{ github.ref_name }}/${{ github.sha }}
-#          host: ${{ secrets.SSH_SWDEV_IP }}
-#          username: ${{ secrets.SSH_SWDEV_USER }}
-#          password: ${{ secrets.SSH_SWDEV_PASSWORD }}
+      SSH_TESTING_SERVER_HOST: ${{ secrets.SSH_TESTING_SERVER_HOST}}
+      SSH_TESTING_SERVER_PORT: ${{ secrets.SSH_TESTING_SERVER_PORT}}
+      SSH_TESTING_SERVER_USER: ${{ secrets.SSH_TESTING_SERVER_USER }}
+      SSH_TESTING_SERVER_PASSWORD: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }}
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop

.github/workflows/release.yml

@@ -6,38 +6,14 @@ on:
       - '*'
 
 jobs:
-  build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
-
-  sonar:
-    uses: opencb/java-common-libs/.github/workflows/sonar-analysis-workflow.yml@develop
-    needs: build
-    with:
-      sonarProjectKey: opencb_biodata
+  test:
+    uses: opencb/biodata/.github/workflows/build-test.yml@develop
     secrets:
       SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-  test:
-    name: Test biodata
-    runs-on: ubuntu-20.04
-    needs: build
-    strategy:
-      matrix:
-        mongodb: ["4.2"]
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: '10'
-      - name: Set up JDK 8
-        uses: actions/setup-java@v3
-        with:
-          distribution: 'temurin'
-          java-version: '8'
-          cache: 'maven'
-      - name: Install Samtools
-        run: sudo apt-get install samtools
-      - name: Run tests with Maven
-        run: mvn -T 2 clean install -DskipTests
+      SSH_TESTING_SERVER_HOST: ${{ secrets.SSH_TESTING_SERVER_HOST}}
+      SSH_TESTING_SERVER_PORT: ${{ secrets.SSH_TESTING_SERVER_PORT}}
+      SSH_TESTING_SERVER_USER: ${{ secrets.SSH_TESTING_SERVER_USER }}
+      SSH_TESTING_SERVER_PASSWORD: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }}
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
@@ -50,4 +26,4 @@ jobs:
 
   release:
     uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop
-    needs: deploy-maven
+    needs: test

.github/workflows/task.yml

@@ -1,37 +1,16 @@
-name: Push biodata develop
+name: Push biodata task
 
 on:
   push:
     branches:
       - TASK-*
 
 jobs:
-  build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
-
-  sonar:
-    uses: opencb/java-common-libs/.github/workflows/sonar-analysis-workflow.yml@develop
-    needs: build
-    with:
-      sonarProjectKey: opencb_biodata
+  test:
+    uses: opencb/biodata/.github/workflows/build-test.yml@develop
     secrets:
       SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
-
-  test:
-    name: Test biodata
-    runs-on: ubuntu-20.04
-    needs: build
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          fetch-depth: '10'
-      - name: Set up JDK 8
-        uses: actions/setup-java@v3
-        with:
-          distribution: 'temurin'
-          java-version: '8'
-          cache: 'maven'
-      - name: Install Samtools
-        run: sudo apt-get install samtools
-      - name: Run tests and create report with Maven
-        run: mvn -T 2 clean install -DskipTests
+      SSH_TESTING_SERVER_HOST: ${{ secrets.SSH_TESTING_SERVER_HOST}}
+      SSH_TESTING_SERVER_PORT: ${{ secrets.SSH_TESTING_SERVER_PORT}}
+      SSH_TESTING_SERVER_USER: ${{ secrets.SSH_TESTING_SERVER_USER }}
+      SSH_TESTING_SERVER_PASSWORD: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }}

pom.xml

@@ -251,6 +251,45 @@
                 <artifactId>maven-surefire-plugin</artifactId>
                 <version>3.0.0-M7</version>
             </plugin>
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>0.8.8</version>
+                <executions>
+                    <execution>
+                        <id>default-prepare-agent</id>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>default-report</id>
+                        <goals>
+                            <goal>report</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>default-check</id>
+                        <goals>
+                            <goal>check</goal>
+                        </goals>
+                        <configuration>
+                            <rules>
+<!--                                <rule>-->
+<!--                                    <element>BUNDLE</element>-->
+<!--                                    <limits>-->
+<!--                                        <limit>-->
+<!--                                            <counter>COMPLEXITY</counter>-->
+<!--                                            <value>COVEREDRATIO</value>-->
+<!--                                            <minimum>0.60</minimum>-->
+<!--                                        </limit>-->
+<!--                                    </limits>-->
+<!--                                </rule>-->
+                            </rules>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
 
@@ -259,7 +298,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-surefire-report-plugin</artifactId>
-                <version>3.0.0-M7</version>
+                <version>3.0.0-M8</version>
             </plugin>
         </plugins>
     </reporting>