TASK-7809 - Upgrade avro version from 1.9.1 to 1.11.4

.github/workflows/develop.yml

@@ -8,21 +8,18 @@ on:
   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:
+      upload_artifact: true
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     with:
       maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
+      cache_key: ${{ needs.test.outputs.cache_key }}
     secrets: inherit
 
   deploy-docker:

.github/workflows/manual-test.yml

@@ -12,11 +12,26 @@ on:
         description: 'The process executes all tests even if some fail.'
         default: false
         required: false
+      upload_artifact:
+        type: boolean
+        description: 'Upload build artifact.'
+        default: false
+        required: false
 
 jobs:
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+    with:
+      needs_hadoop_preparation: false
+      maven_opts: -Dcheckstyle.skip
+      upload_artifact: ${{ inputs.upload_artifact }}
+      dependency_repos: "java-common-libs,biodata"
+    secrets: inherit
+
   test:
     name: JUnit Test
-    runs-on: ubuntu-22.04
+    needs: build
+    runs-on: ${{ vars.UBUNTU_VERSION }}
     steps:
       - uses: actions/checkout@v4
         with:
@@ -34,14 +49,13 @@ jobs:
           chmod +x ./kubectl
           echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf 
           ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27017:27017 --kubeconfig ./admin.conf &
-      - 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: Cache local Maven repository
+        uses: actions/cache/restore@v4
+        with:
+          path: ~/.m2/repository
+          key: ${{ needs.build.outputs.cache_key }}
+          ## Force cache hit to avoid testing with incomplete dependencies
+          fail-on-cache-miss: true
       - name: Test and Analyze
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any

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

@@ -8,4 +8,6 @@ on:
 jobs:
   test:
     uses: ./.github/workflows/test-analysis.yml
-    secrets: inherit
+    secrets: inherit
+    with:
+      upload_artifact: false

.github/workflows/release.yml

@@ -11,12 +11,15 @@ jobs:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
       maven_opts: -DCELLBASE.WAR.NAME=cellbase
+      dependency_repos: "java-common-libs,biodata"
+      upload_artifact: true
 
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: build
     with:
       maven_opts: -Dcheckstyle.skip -DCELLBASE.WAR.NAME=cellbase
+      cache_key: ${{ needs.build.outputs.cache_key }}
     secrets: inherit
 
   deploy-docker:

.github/workflows/task.yml

@@ -7,15 +7,11 @@ on:
   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:
+      upload_artifact: true
 
   deploy-docker:
     uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop

.github/workflows/test-analysis.yml

@@ -2,14 +2,34 @@ name: Build and test the project
 
 on:
   workflow_call:
+    inputs:
+      upload_artifact:
+        type: boolean
+        required: false
+        default: false
+    outputs:
+      cache_key:
+        description: "Cache key used for Maven repository"
+        value: ${{ jobs.build.outputs.cache_key }}
     secrets:
       SONAR_TOKEN:
         required: true
 
 jobs:
+
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+    with:
+      needs_hadoop_preparation: false
+      maven_opts: -Dcheckstyle.skip
+      upload_artifact: ${{ inputs.upload_artifact }}
+      dependency_repos: "java-common-libs,biodata"
+    secrets: inherit
+
   test:
     name: Test and push Sonar analysis
-    runs-on: ubuntu-22.04
+    needs: build
+    runs-on: ${{ vars.UBUNTU_VERSION }}
     steps:
       - uses: actions/checkout@v4
         with:
@@ -26,14 +46,13 @@ jobs:
           chmod +x ./kubectl
           echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf 
           ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27017:27017 --kubeconfig ./admin.conf &
-      - 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: Cache local Maven repository
+        uses: actions/cache/restore@v4
+        with:
+          path: ~/.m2/repository
+          key: ${{ needs.build.outputs.cache_key }}
+          ## Force cache hit to avoid testing with incomplete dependencies
+          fail-on-cache-miss: true
       - name: Test and Analyze
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Needed to get PR information, if any

cellbase-app/src/test/java/org/opencb/cellbase/app/cli/VariantAnnotationCommandExecutorTest.java

@@ -857,8 +857,8 @@ private List<PopulationFrequency> getPopulationFrequency(List<PopulationFrequenc
                     && populationFrequency.getPopulation().equals(populationFrequency1.getPopulation())
                     && populationFrequency.getRefAllele().equals(populationFrequency1.getRefAllele())
                     && populationFrequency.getAltAllele().equals(populationFrequency1.getAltAllele())
-                    && populationFrequency.getAltAlleleFreq().equals(populationFrequency1.getAltAlleleFreq())
-                    && populationFrequency.getRefAlleleFreq().equals(populationFrequency1.getRefAlleleFreq())) {
+                    && populationFrequency.getAltAlleleFreq() == populationFrequency1.getAltAlleleFreq()
+                    && populationFrequency.getRefAlleleFreq() == populationFrequency1.getRefAlleleFreq()) {
                 populationFrequencyList1.add(populationFrequency);
             }
         }

cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantMongoDBAdaptorTest.java

@@ -242,8 +242,8 @@ private List<PopulationFrequency> getPopulationFrequency(List<PopulationFrequenc
                     && populationFrequency.getPopulation().equals(populationFrequency1.getPopulation())
                     && populationFrequency.getRefAllele().equals(populationFrequency1.getRefAllele())
                     && populationFrequency.getAltAllele().equals(populationFrequency1.getAltAllele())
-                    && populationFrequency.getAltAlleleFreq().equals(populationFrequency1.getAltAlleleFreq())
-                    && populationFrequency.getRefAlleleFreq().equals(populationFrequency1.getRefAlleleFreq())) {
+                    && populationFrequency.getAltAlleleFreq() == populationFrequency1.getAltAlleleFreq()
+                    && populationFrequency.getRefAlleleFreq() == populationFrequency1.getRefAlleleFreq()) {
                 populationFrequencyList1.add(populationFrequency);
             }
         }

pom.xml

@@ -44,7 +44,7 @@
         <commons-codec.version>1.13</commons-codec.version>
         <jakarta.xml.bind-api.version>2.3.3</jakarta.xml.bind-api.version>
         <guava.version>19.0</guava.version>
-        <avro.version>1.9.1</avro.version>
+        <avro.version>1.11.4</avro.version>
         <hamcrest.version>1.3</hamcrest.version>
         <htsjdk.version>2.23.0</htsjdk.version>
         <grpc.version>1.48.0</grpc.version>