Merge branch 'release-2.12.x' into TASK-5279

.github/workflows/check-junit-test.yml

@@ -51,6 +51,5 @@ jobs:
     uses: ./.github/workflows/test-analysis.yml
     with:
       test_profile: ${{ needs.get_profiles.outputs.profiles }}
-      report_context: development
       mvn_opts: ${{ inputs.mvn_opts }}
     secrets: inherit

.github/workflows/develop.yml

@@ -9,34 +9,26 @@ on:
 
 jobs:
   build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.8.x
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
       maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
 
-  deploy-docker-ext-tools:
-    uses: opencb/java-common-libs/.github/workflows/[email protected]
-    needs: build
-    with:
-      cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }}
-    secrets: inherit
-
   test:
     uses: ./.github/workflows/test-analysis.yml
-    needs: deploy-docker-ext-tools
-    secrets: inherit
+    needs: build
     with:
       test_profile: runShortTests,runMediumTests
-      report_context: development
+    secrets: inherit
 
   deploy-maven:
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.8.x
+    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test
     with:
       maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga
     secrets: inherit
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x
+    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,init

.github/workflows/docker-aws-emr.yml

@@ -8,15 +8,13 @@ on:
 
 jobs:
   build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.8.x
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
       maven_opts: -P storage-hadoop,emr6.1 -Dopencga.war.name=opencga
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
     needs: build
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base,init
     secrets: inherit
-#      DOCKER_HUB_USER: ${{ secrets.DOCKER_HUB_USER }}
-#      DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}

.github/workflows/docker-tools.yml → .github/workflows/docker-ext-tools.yml

@@ -1,4 +1,4 @@
-name: Deploy Docker Tools
+name: Deploy Docker Ext-Tools
 
 on:
   push:
@@ -8,17 +8,14 @@ on:
       - TASK-*
     paths:
       - opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile
-  workflow_dispatch:
 
 jobs:
   build:
-    uses: opencb/java-common-libs/.github/workflows/[email protected]
-    with:
-      maven_opts:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
 
   deploy-docker-ext-tools:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
     needs: build
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }}
-    secrets: inherit
+    secrets: inherit

.github/workflows/long-test-analysis.yml

@@ -1,15 +1,17 @@
 name: Long test for run only on weekend
 
-#Every Saturday at 01:10
+
+## Every Saturday at 01:10
 on:
   schedule:
     - cron: '10 1 * * 6'
+  workflow_dispatch:
 
 jobs:
   test:
     uses: ./.github/workflows/test-analysis.yml
     secrets: inherit
     with:
-      test_profile: runLongTests,runMediumTests,runShortTests
-      report_context: development
+      test_profile: runShortTests,runMediumTests,runLongTests,
+
 

.github/workflows/manual-deploy-docker.yml

@@ -0,0 +1,50 @@
+name: Manual deploy Docker base
+on:
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: "The branch, tag or SHA of the source code to build docker."
+        type: string
+        required: true
+      tag:
+        description: "The tag for the new docker."
+        type: string
+        required: true
+
+jobs:
+  build:
+    name: Build Java app
+    runs-on: ubuntu-22.04
+    outputs:
+      version: ${{ steps.get_project_version.outputs.version }}
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: '10'
+          ref: "${{ inputs.branch }}"
+      - name: Set up JDK 8
+        uses: actions/setup-java@v3
+        with:
+          distribution: 'temurin'
+          java-version: '8'
+          cache: 'maven'
+      - 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 }}
+          fi
+      - name: Maven Build (skip tests)
+        run: mvn -T 2 clean install -DskipTests
+      - uses: actions/upload-artifact@v3
+        with:
+          name: build-folder
+          path: build
+
+
+  deploy-docker:
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
+    needs: build
+    with:
+      cli: python3 ./build/cloud/docker/docker-build.py push --images base,init --tag ${{ inputs.tag }}
+    secrets: inherit

.github/workflows/manual-deploy-ext-tools.yml

@@ -48,3 +48,4 @@ jobs:
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ inputs.tag }}
     secrets: inherit
+

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

@@ -7,12 +7,18 @@ on:
       - "release-*"
     types:
       - closed
+  workflow_dispatch:
 
 jobs:
-  docker-delete:
-    name: Delete TASK Docker image
-    runs-on: ubuntu-22.04
-    steps:
-      - name: "Checkout opencga"
-        uses: actions/checkout@v3
-      - run: python3 ./opencga-app/app/cloud/docker/docker-build.py delete --images base --tag ${{ github.ref_name }} --username ${{ secrets.DOCKER_HUB_USER }} --password ${{ secrets.DOCKER_HUB_PASSWORD }}
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+    with:
+      maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
+
+  delete-docker:
+    uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@develop
+    needs: build
+    with:
+      cli: python3 ./build/cloud/docker/docker-build.py delete --images base --tag ${{ github.head_ref }}
+    secrets: inherit
+

.github/workflows/release.yml

@@ -8,54 +8,38 @@ on:
 
 jobs:
   build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.8.x
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
       maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
 
-  deploy-docker-ext-tools:
-    uses: opencb/java-common-libs/.github/workflows/[email protected]
-    needs: build
-    with:
-      cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }}
-    secrets: inherit
-
-  test:
-    uses: ./.github/workflows/test-analysis.yml
-    needs: deploy-docker-ext-tools
-    secrets: inherit
-    with:
-      test_profile: runShortTests,runMediumTests
-      report_context: xetabase
-
   deploy-maven:
-    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@release-4.8.x
-    needs: test
+    uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
+    needs: build
     with:
       maven_opts: -P storage-hadoop,hdp3.1 -Dopencga.war.name=opencga
     secrets: inherit
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x
-    needs: test
+    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@develop
+    needs: build
     with:
       cli: python3 ./build/cloud/docker/docker-build.py push --images base,init
     secrets: inherit
 
-
-
   deploy-python:
-    uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@release-4.8.x
-    needs: test
+    uses: opencb/java-common-libs/.github/workflows/deploy-python-workflow.yml@develop
+    needs: build
     with:
       cli: ./clients/python/python-build.sh push
       artifact: build-folder
     secrets: inherit
 
   release:
-    uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@release-4.8.x
-    needs: [ build,test ]
+    uses: opencb/java-common-libs/.github/workflows/release-github-workflow.yml@develop
+    needs: [ build, deploy-maven, deploy-docker, deploy-python ]
     with:
       artifact: build-folder
       file: |
         opencga-client-${{ needs.build.outputs.version }}.tar.gz
         clients/R/opencgaR_${{ needs.build.outputs.version }}.tar.gz
+

.github/workflows/scripts/get_same_branch.sh

@@ -0,0 +1,30 @@
+#!/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"
+install "cellbase"

.github/workflows/task.yml

@@ -6,9 +6,11 @@ on:
       - TASK-*
   workflow_dispatch:
 
+# WARNING Develop branch needed for prod
+
 jobs:
   build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@release-4.8.x
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
     with:
       maven_opts: -P storage-hadoop,hdp3.1,RClient,opencga-storage-hadoop-deps -Dopencga.war.name=opencga -Dcheckstyle.skip -pl '!:opencga-storage-hadoop-deps-emr6.1,!:opencga-storage-hadoop-deps-hdp2.6'
 
@@ -18,37 +20,10 @@ jobs:
     secrets: inherit
     with:
       test_profile: runShortTests
-      report_context: development
-
-  deploy-maven:
-    name: Deploy in maven only for renamed versions
-    uses: opencb/java-common-libs/.github/workflows/[email protected]
-    needs: [ build, test ]
-    if: contains( needs.build.outputs.version ,'TASK')
-    secrets: inherit
 
   deploy-docker:
-    uses: opencb/java-common-libs/.github/workflows/deploy-docker-hub-workflow.yml@release-4.8.x
+    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,init --tag ${{ github.ref_name }}
     secrets: inherit
-
-  # The following jobs are to see that the previous 'if' doesn't 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 }}