Merge branch 'release-5.x.x' into TASK-6879

opencb · Sep 16, 2024 · 1e042b9 · 1e042b9
2 parents afde81c + 864b1d4
commit 1e042b9
Show file tree

Hide file tree

Showing 10 changed files with 81 additions and 42 deletions.
diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
@@ -16,18 +16,25 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: '10'
+          ## This is important to avoid the error in the next step: "fatal: repository 'https://github.com/zetta-genomics/opencga-enterprise.git/' not found"
+          persist-credentials: false
       - 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 "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}"
+          echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}"
+          echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}"
+          xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh ${{ github.event.pull_request.head.ref }})
           echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
           echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT
+        env:
+          ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
 
   test:
     name: "Run all tests before merging"
     needs: calculate-xetabase-branch
-    uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399
+    uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop
     with:
       branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }}
       task: ${{ github.event.pull_request.head.ref }}

diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh
@@ -1,15 +1,16 @@
 #!/bin/bash
-
+set -e
+set -x
 # 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;
+    if [ "$(git ls-remote "https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then
+      echo $input_branch;
+      return 0;
     fi
   fi
 
@@ -40,11 +41,6 @@ get_xetabase_branch() {
   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-pull-request-approved.yml b/.github/workflows/test-pull-request-approved.yml
@@ -0,0 +1,48 @@
+name: Pull request approve workflow
+run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref }} -> ${{ github.event.pull_request.base.ref }} by @${{ github.actor }}'
+
+on:
+  push:
+    branches:
+      - TASK-*
+
+
+jobs:
+  calculate-xetabase-branch:
+    name: Calculate Xetabase branch
+    runs-on: ubuntu-22.04
+    outputs:
+      xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
+    steps:
+      - name: Clone java-common-libs
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: '10'
+          ## This is important to avoid the error in the next step: "fatal: repository 'https://github.com/zetta-genomics/opencga-enterprise.git/' not found"
+          persist-credentials: false
+      - id: get_xetabase_branch
+        name: "Get current branch for Xetabase from target branch"
+        run: |
+          if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/opencb/opencga.git "TASK-6807" )" ] ; then
+           echo "OPENCGA TASK-6807 branch";
+          fi
+          
+          if [ "$( git ls-remote https://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git "$input_branch" )" ] ; then
+            echo "Here it is TASK-6807 branch";
+          fi
+          chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh
+          echo "secrets.ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}" | tee -a ${GITHUB_STEP_SUMMARY}
+          xetabase_branch=$(./.github/workflows/scripts/get-xetabase-branch.sh "TASK-6807" )
+          echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
+          echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT
+        env:
+          ZETTA_REPO_ACCESS_TOKEN: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
+
+  test:
+    name: "Run all tests before merging"
+    needs: calculate-xetabase-branch
+    uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@develop
+    with:
+      branch: ${{ needs.calculate-xetabase-branch.outputs.xetabase_branch }}
+      task: TASK-6807
+    secrets: inherit
diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
@@ -20,10 +20,6 @@ on:
         description: 'Branch of opencga-enterprise to be tested and built.'
         required: true
 
-env:
-  AZCOPY_AUTO_LOGIN_TYPE: "SPN"
-
-
 jobs:
   test:
     name: Execute JUnit and Jacoco tests
@@ -35,16 +31,13 @@ jobs:
         with:
           keeper-secret-config: ${{ secrets.KEEPER_SM_GH_OPENCB }}
           secrets: |
-            AZCOPY_SPA_CLIENT_SECRET/field/Secret Value > env:AZCOPY_SPA_CLIENT_SECRET
-            AZCOPY_SPA_APPLICATION_ID/field/Secret Value > env:AZCOPY_SPA_APPLICATION_ID
-            AZCOPY_TENANT_ID/field/Secret Value > env:AZCOPY_TENANT_ID
             AZURE_KUBE_CONFIG/field/Secret Value > env:AZURE_KUBE_CONFIG
             DOCKER_HUB_USER/field/Secret Value > env:DOCKER_HUB_USER
             DOCKER_HUB_PASSWORD/field/Secret Value > env:DOCKER_HUB_PASSWORD
-            SSH_TESTING_SERVER_HOST/field/Secret Value > env:SSH_TESTING_SERVER_HOST
-            SSH_TESTING_SERVER_PORT/field/Secret Value > env:SSH_TESTING_SERVER_PORT
-            SSH_TESTING_SERVER_USER/field/Secret Value > env:SSH_TESTING_SERVER_USER
-            SSH_TESTING_SERVER_PASSWORD/field/Secret Value > env:SSH_TESTING_SERVER_PASSWORD
+            SSH_TESTING_SERVER_HOST/field/Secret Value > env:SSH_HOST
+            SSH_TESTING_SERVER_PORT/field/Secret Value > env:SSH_PORT
+            SSH_TESTING_SERVER_USER/field/Secret Value > env:SSH_USER
+            SSH_TESTING_SERVER_PASSWORD/field/Secret Value > env:SSH_PASS
       - name: Log inputs
         run: |
           echo "__OpenCGA-enterprise branch:__ \"${{ inputs.branch }}\"" | tee -a $GITHUB_STEP_SUMMARY
@@ -93,15 +86,20 @@ jobs:
           chmod +x ./kubectl
           echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf
           ./kubectl -n cellbase-db port-forward services/cellbase-rs0-svc 27018:27017 --kubeconfig ./admin.conf &
-      - name: Install Azure AZCOPY
-        uses: kheiakiyama/install-azcopy-action@v1
-        with:
-          version: 'v10'
       - name: DockerHub login
         uses: docker/login-action@v3
         with:
           username: ${{ env.DOCKER_HUB_USER }}
           password: ${{ env.DOCKER_HUB_PASSWORD }}
+      - name: Install sshpass
+        run: sudo apt-get install sshpass
+      - name: Add SSH Host to known_hosts
+        run: |
+          mkdir -p ~/.ssh
+          ssh-keyscan -p ${{ env.SSH_PORT }} ${{ env.SSH_HOST }} >> ~/.ssh/known_hosts
+        env:
+          SSH_HOST: ${{ env.SSH_HOST }}
+          SSH_PORT: ${{ env.SSH_PORT }}
       - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise
         run: |
           cd opencga-enterprise
@@ -117,16 +115,6 @@ jobs:
         with:
           name: build-log
           path: ./opencga-enterprise/build.log
-      - name: Upload junit reports to a remote scp server
-        uses: garygrossgarten/github-action-scp@release
-        with:
-          local: opencga-enterprise/reports/test
-          remote: /var/www/html/reports/xetabase/${{ 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

diff --git a/commons-datastore/commons-datastore-core/pom.xml b/commons-datastore/commons-datastore-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons-datastore</artifactId>
-        <version>5.2.1-SNAPSHOT</version>
+        <version>5.2.2-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/commons-datastore/commons-datastore-mongodb/pom.xml b/commons-datastore/commons-datastore-mongodb/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons-datastore</artifactId>
-        <version>5.2.1-SNAPSHOT</version>
+        <version>5.2.2-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/commons-datastore/commons-datastore-solr/pom.xml b/commons-datastore/commons-datastore-solr/pom.xml
@@ -22,7 +22,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons-datastore</artifactId>
-        <version>5.2.1-SNAPSHOT</version>
+        <version>5.2.2-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/commons-datastore/pom.xml b/commons-datastore/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons</artifactId>
-        <version>5.2.1-SNAPSHOT</version>
+        <version>5.2.2-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/commons-lib/pom.xml b/commons-lib/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.commons</groupId>
         <artifactId>commons</artifactId>
-        <version>5.2.1-SNAPSHOT</version>
+        <version>5.2.2-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.opencb.commons</groupId>
     <artifactId>commons</artifactId>
-    <version>5.2.1-SNAPSHOT</version>
+    <version>5.2.2-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>OpenCB commons project</name>