TASK-4428 - Ability to handle Ext-Tools for OpenCGA

.github/workflows/develop.yml

@@ -13,13 +13,6 @@ jobs:
     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/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
-
   test:
     uses: ./.github/workflows/test-analysis.yml
     needs: deploy-docker-ext-tools

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

@@ -18,5 +18,3 @@ jobs:
     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-ext-tools.yml

@@ -0,0 +1,23 @@
+name: Deploy Docker Ext-Tools
+
+on:
+  push:
+    branches:
+      - develop
+      - release-*
+      - TASK-*
+    paths:
+      - opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile
+  workflow_dispatch:
+
+jobs:
+  build:
+    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@develop
+    needs: build
+    with:
+      cli: python3 ./build/cloud/docker/docker-build.py push --images ext-tools --tag ${{ needs.build.outputs.version }}
+    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
-#on:
-#  schedule:
-#    - cron: '10 1 * * 6'
-#
-#jobs:
-#  test:
-#    uses: ./.github/workflows/test-analysis.yml
-#    secrets: inherit
-#    with:
-#      test_profile: runLongTests,runMediumTests,runShortTests
-#      report_context: development
+
+## Every Saturday at 01:10
+on:
+  schedule:
+    - cron: '10 1 * * 6'
+
+jobs:
+  test:
+    uses: ./.github/workflows/test-analysis.yml
+    secrets: inherit
+    with:
+      test_profile: runLongTests,runMediumTests,runShortTests
+      report_context: development
+
 

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

@@ -3,12 +3,15 @@ name: "Pull Request Merge Workflow"
 on:
   pull_request:
     branches:
-      - "develop"
-      - "release-*"
+      - develop
+      - release-*
     types:
       - closed
 
 jobs:
+  build:
+    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+
   delete-docker:
     uses: opencb/java-common-libs/.github/workflows/delete-docker-hub-workflow.yml@develop
     with:

.github/workflows/release.yml

@@ -12,13 +12,6 @@ jobs:
     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/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
-
   deploy-maven:
     uses: opencb/java-common-libs/.github/workflows/deploy-maven-repository-workflow.yml@develop
     needs: test

.github/workflows/task.yml

@@ -6,7 +6,8 @@ on:
       - TASK-*
   workflow_dispatch:
 
-#WARNING Develop branch needed for prod
+# WARNING Develop branch needed for prod
+
 jobs:
   build:
     uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop

opencga-app/app/cloud/docker/opencga-ext-tools/Dockerfile

@@ -30,4 +30,4 @@ RUN apt-get update -y && DEBIAN_FRONTEND="noninteractive" TZ="Europe/London" apt
     rm -rf /var/lib/apt/lists/* /tmp/* /opt/opencga/signature.tools.lib/.git && \
     strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5
 
-WORKDIR /opt/opencga
+WORKDIR /opt/opencga