opencb · juanfeSanahuja · Aug 14, 2024 · Jun 20, 2024 · Jun 20, 2024 · Jun 20, 2024
diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
@@ -10,11 +10,6 @@ jobs:
   build:
     uses: ./.github/workflows/build-java-app-workflow.yml
 
-  test:
-    uses: ./.github/workflows/test-analysis.yml
-    needs: build
-    secrets: inherit
-
   deploy-maven:
     uses: ./.github/workflows/deploy-maven-repository-workflow.yml
     needs: test

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
@@ -6,11 +6,29 @@ on:
     types: [ submitted ]
 
 jobs:
-  build:
-    uses: ./.github/workflows/build-java-app-workflow.yml
-
+  calculate-xetabase-branch:
+    name: Calculate Xetabase branch
+    runs-on: ubuntu-22.04
+    outputs:
+      xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
+    steps:
+      - name: Clone java-common-libs
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: '10'
+      - id: get_xetabase_branch
+        name: "Get current branch for Xetabase from target branch"
+        run: |
+          chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh
+          xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.base.ref }})
+          echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
+          echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT
+
   test:
     name: "Run all tests before merging"
-    uses: ./.github/workflows/test-analysis.yml
-    needs: build
+    needs: calculate-xetabase-branch
+    uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399
+    with:
+      branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }}
+      task: ${{ github.event.pull_request.head.ref }}
     secrets: inherit
diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+# Function to calculate the corresponding branch of Xetabase project
+get_xetabase_branch() {
+  # Input parameter (branch name)
+  input_branch="$1"
+
+  # If the branch begins with 'TASK' and exists in the opencga-enterprise repository, I return it
+  if [[ $input_branch == TASK* ]]; then
+    if [ "$(git ls-remote https://github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then
+      echo "$GIT_BRANCH";
+      exit 0;
+    fi
+  fi
+
+  # Check if the branch name is "develop" in that case return the same branch name
+  if [[ "$input_branch" == "develop" ]]; then
+    echo "develop"
+    return 0
+  fi
+
+  # Check if the branch name starts with "release-" and follows the patterns "release-a.b.x" or "release-a.b.c.x"
+  if [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.x$ ]] || [[ "$input_branch" =~ ^release-([0-9]+)\.([0-9]+)\.([0-9]+)\.x$ ]]; then
+    # Extract the MAJOR part of the branch name
+    MAJOR=${BASH_REMATCH[1]}
+    # Calculate the XETABASE_MAJOR by subtracting 3 from MAJOR
+    XETABASE_MAJOR=$((MAJOR - 3))
+    # Check if the XETABASE_MAJOR is negative
+    if (( XETABASE_MAJOR < 0 )); then
+      echo "Error: 'MAJOR' digit after subtraction results in a negative number."
+      return 1
+    fi
+    # Construct and echo the new branch name
+    echo "release-$XETABASE_MAJOR.${input_branch#release-$MAJOR.}"
+    return 0
+  fi
+
+  # If the branch name does not match any of the expected patterns
+  echo "Error: The branch name is not correct."
+  return 1
+}
+
+# Check if the script receives exactly one argument
+if [ "$#" -ne 1 ]; then
+  echo "Usage: $0 <branch-name>"
+  exit 1
+fi
+
+# Call the function with the input branch name
+get_xetabase_branch "$1"
diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
@@ -19,33 +19,56 @@ on:
         type: string
         description: 'Branch of opencga-enterprise to be tested and built.'
         required: true
+
 env:
-  AZCOPY_SPA_CLIENT_SECRET: ${{ secrets.AZCOPY_SPA_CLIENT_SECRET }}
   AZCOPY_AUTO_LOGIN_TYPE: "SPN"
-  AZCOPY_SPA_APPLICATION_ID: ${{ secrets.AZCOPY_SPA_APPLICATION_ID }}
-  AZCOPY_TENANT_ID: ${{ secrets.AZCOPY_TENANT_ID }}
+
 
 jobs:
   test:
     name: Execute JUnit and Jacoco tests
     runs-on: ubuntu-22.04
     steps:
-      - name: Clone OpenCGA Enterprise branch '${{ github.event.inputs.branch }}'
+      - name: Retrieve secrets from Keeper
+        id: ksecrets
+        uses: Keeper-Security/ksm-action@master
+        with:
+          keeper-secret-config: ${{ secrets.KEEPER_SM_GH_OPENCB }}
+          secrets: |
+            AZCOPY_SPA_CLIENT_SECRET/field/Secret Value > env:AZCOPY_SPA_CLIENT_SECRET
+            AZCOPY_SPA_APPLICATION_ID/field/Secret Value > env:AZCOPY_SPA_APPLICATION_ID
+            AZCOPY_TENANT_ID/field/Secret Value > env:AZCOPY_TENANT_ID
+            AZURE_KUBE_CONFIG/field/Secret Value > env:AZURE_KUBE_CONFIG
+            DOCKER_HUB_USER/field/Secret Value > env:DOCKER_HUB_USER
+            DOCKER_HUB_PASSWORD/field/Secret Value > env:DOCKER_HUB_PASSWORD
+            SSH_TESTING_SERVER_HOST/field/Secret Value > env:SSH_TESTING_SERVER_HOST
+            SSH_TESTING_SERVER_PORT/field/Secret Value > env:SSH_TESTING_SERVER_PORT
+            SSH_TESTING_SERVER_USER/field/Secret Value > env:SSH_TESTING_SERVER_USER
+            SSH_TESTING_SERVER_PASSWORD/field/Secret Value > env:SSH_TESTING_SERVER_PASSWORD
+      - name: Log inputs
+        run: |
+          echo "__OpenCGA-enterprise branch:__ \"${{ inputs.branch }}\"" | tee -a $GITHUB_STEP_SUMMARY
+          echo "__Task to test:__ \"${{ inputs.task }}\"" | tee -a $GITHUB_STEP_SUMMARY
+      - name: Clone OpenCGA Enterprise branch '${{ inputs.branch }}'
         uses: actions/checkout@v4
         with:
           repository: zetta-genomics/opencga-enterprise
-          ref: ${{ github.event.inputs.branch }}
+          ref: ${{ inputs.branch }}
           token: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
           path: opencga-enterprise
           fetch-depth: "10"
       - id: get_opencga_branch
         name: Get OpenCGA branch from 'pom.xml' property
         run: |
           pwd
-          chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh
-          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh ${{ github.event.inputs.task }})
+          ls -lrtha
+          ls -lrtha ./opencga-enterprise
+          chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh
+          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh)
+          echo "opencga_branch=${opencga_branch}"
           echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
-      - uses: actions/checkout@v4
+      - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}'
+        uses: actions/checkout@v4
         with:
           repository: opencb/opencga
           ref: ${{ steps.get_opencga_branch.outputs.opencga_branch }}
@@ -77,32 +100,46 @@ jobs:
       - name: DockerHub login
         uses: docker/login-action@v3
         with:
-          username: ${{ secrets.DOCKER_HUB_USER }}
-          password: ${{ secrets.DOCKER_HUB_PASSWORD }}
+          username: ${{ env.DOCKER_HUB_USER }}
+          password: ${{ env.DOCKER_HUB_PASSWORD }}
       - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise
         run: |
-          ln -s opencga opencga-enterprise/opencga-home
+          pwd
+          ls -lrtha 
+          echo "------------------------------------"
           cd opencga-enterprise
-          ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ github.event.inputs.task }} -c localhost:27018 -H hdp3.1
+          pwd
+          ls -lrtha 
+          echo "------------------------------------"
+          ln -s ../opencga opencga-home
+          echo "------------------------------------"
+          ls -lrtha 
+          #./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1
+          ./build.sh -t -l runShortTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1
       - name: Upload reports results to Github
         uses: actions/upload-artifact@v4
         with:
           name: report-test
-          path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/reports/test
+          path: ./opencga-enterprise/reports/test
       - name: Upload log
         uses: actions/upload-artifact@v4
         with:
           name: build-log
-          path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/build.log
+          path: ./opencga-enterprise/build.log
       - name: Upload junit reports to a remote scp server
         uses: garygrossgarten/github-action-scp@release
         with:
           local: opencga-enterprise/reports/test
-          remote: /var/www/html/reports/xetabase/${{ github.event.inputs.task }}/
-          host: ${{ secrets.SSH_TESTING_SERVER_HOST}}
-          port: ${{ secrets.SSH_TESTING_SERVER_PORT}}
-          username: ${{ secrets.SSH_TESTING_SERVER_USER }}
-          password: ${{ secrets.SSH_TESTING_SERVER_PASSWORD }}
+          remote: /var/www/html/reports/xetabase/${{ inputs.task }}/
+          host: ${{ env.SSH_TESTING_SERVER_HOST}}
+          port: ${{ env.SSH_TESTING_SERVER_PORT}}
+          username: ${{ env.SSH_TESTING_SERVER_USER }}
+          password: ${{ env.SSH_TESTING_SERVER_PASSWORD }}
           concurrency: 2
+      - name: Log summary
+        run: |
+          cat ./opencga-enterprise/build.log | tee -a $GITHUB_STEP_SUMMARY
+
+