From df70872e5d941c6a76327332103ebd9ac3044dc5 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Thu, 20 Jun 2024 12:07:42 +0200
Subject: [PATCH 01/39] test-xetabase-workflow.yml: New workflow to test
 xetabase on pullrequest approve of the libraries #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 93 ++++++++++++++++++++
 1 file changed, 93 insertions(+)
 create mode 100644 .github/workflows/test-xetabase-workflow.yml

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
new file mode 100644
index 000000000..49c4c2af0
--- /dev/null
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -0,0 +1,93 @@
+name: Pull request approve workflow
+
+on:
+  workflow_call:
+    inputs:
+      task:
+        type: string
+        required: true
+      branch:
+        type: string
+        required: true
+
+jobs:
+  test:
+    name: Execute JUnit and Jacoco tests
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Clone OpenCGA Enterprise branch '${{ github.event.inputs.branch }}'
+        uses: actions/checkout@v4
+        with:
+          repository: zetta-genomics/opencga-enterprise
+          ref: ${{ github.event.inputs.branch }}
+          token: ${{ secrets.GH_PRIVATE_TOKEN }}
+          path: opencga-enterprise
+          fetch-depth: "10"
+      - id: get_opencga_branch
+        name: Get OpenCGA branch from 'pom.xml' property
+        run: |
+          pwd
+          chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh
+          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh ${{ github.event.inputs.task }})
+          echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
+      - uses: actions/checkout@v4
+        with:
+          repository: opencb/opencga
+          ref: ${{ steps.get_opencga_branch.outputs.opencga_branch }}
+          path: opencga
+          fetch-depth: '10'
+      - name: Set up JDK 8
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '8'
+          cache: 'maven'
+      - name: Install Samtools
+        run: sudo apt-get install samtools python3-deeptools
+      - name: Start MongoDB v6.0
+        uses: supercharge/mongodb-github-action@1.8.0
+        with:
+          mongodb-version: 6.0
+          mongodb-replica-set: rs-test
+      - name: K8s Tunnel MongoDB
+        run: |
+          wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl
+          chmod +x ./kubectl
+          echo "${{ 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: ${{ secrets.DOCKER_HUB_USER }}
+          password: ${{ secrets.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
+          cd opencga-enterprise
+          ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ github.event.inputs.task }} -c localhost:27018 -H hdp3.1
+      - name: Upload reports results to Github
+        uses: actions/upload-artifact@v4
+        with:
+          name: report-test
+          path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/reports/test
+      - name: Upload log
+        uses: actions/upload-artifact@v4
+        with:
+          name: build-log
+          path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/build.log
+      - name: Upload junit reports to a remote scp server
+        uses: garygrossgarten/github-action-scp@release
+        with:
+          local: opencga-enterprise/reports/test
+          remote: /var/www/html/reports/xetabase/${{ 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 }}
+          concurrency: 2
+
+

From 3f2f4eb710dab9238ead39aee8d47a0a4213d652 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Thu, 20 Jun 2024 12:08:14 +0200
Subject: [PATCH 02/39] test-xetabase-workflow.yml: New workflow to test
 xetabase on pullrequest approve of the libraries #TASK-6399

---
 .github/workflows/scripts/xetabase-branch.sh | 42 ++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 .github/workflows/scripts/xetabase-branch.sh

diff --git a/.github/workflows/scripts/xetabase-branch.sh b/.github/workflows/scripts/xetabase-branch.sh
new file mode 100644
index 000000000..af17f7f12
--- /dev/null
+++ b/.github/workflows/scripts/xetabase-branch.sh
@@ -0,0 +1,42 @@
+#!/bin/bash
+
+# Function to calculate the corresponding branch of Xetabase project
+get_xetabase_branch() {
+  # Input parameter (branch name)
+  input_branch="$1"
+
+  # Check if the branch name is "develop" in that case return the same branch name
+  if [[ "$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"

From 37bfcd14022f33c5f23b6b449148709935f409bd Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Thu, 20 Jun 2024 12:09:42 +0200
Subject: [PATCH 03/39] test-xetabase-workflow.yml: Modify pull_request approve
 workflow to test all Xetabase instead only jcl #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 22 ++++++++++++++-------
 1 file changed, 15 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 329df1be1..c20e61c90 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -5,11 +5,19 @@ on:
     types: [ submitted ]
 
 jobs:
-  build:
-    uses: ./.github/workflows/build-java-app-workflow.yml
-
   test:
-    name: "Run all tests before merging"
-    uses: ./.github/workflows/test-analysis.yml
-    needs: build
-    secrets: inherit
\ No newline at end of file
+    name: Execute JUnit and Jacoco tests
+    runs-on: ubuntu-22.04
+    steps:
+      - id: get_xetabase_branch
+        name: Get current branch for Xetabase from 'pom.xml' property
+        run: |
+          chmod +x ./.github/workflows/scripts/xetabase-branch.sh
+          xetabase_branch=$(./.github/workflows/scripts/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
+      - name: "Run all tests before merging"
+        uses: ./.github/workflows/test-xetabase-workflow.yml
+        with:
+          branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
+          task: ${{ github.event.pull_request.head.ref }}
\ No newline at end of file

From f930213af02064275854e38a3665f4167f0644bf Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Thu, 20 Jun 2024 12:31:42 +0200
Subject: [PATCH 04/39] cicd:clone jcl to exec script in pull request approve
 #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index c20e61c90..ecc007801 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -9,6 +9,8 @@ jobs:
     name: Execute JUnit and Jacoco tests
     runs-on: ubuntu-22.04
     steps:
+      - name: Clone java-common-libs
+        uses: actions/checkout@v4
       - id: get_xetabase_branch
         name: Get current branch for Xetabase from 'pom.xml' property
         run: |

From 9b2e5cf79cc6a5263e05a88da1235d0d0125420f Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Thu, 20 Jun 2024 12:34:25 +0200
Subject: [PATCH 05/39] cicd: fix parenthesi #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index ecc007801..7f80bfed0 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -15,7 +15,7 @@ jobs:
         name: Get current branch for Xetabase from 'pom.xml' property
         run: |
           chmod +x ./.github/workflows/scripts/xetabase-branch.sh
-          xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }}
+          xetabase_branch=$(./.github/workflows/scripts/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
       - name: "Run all tests before merging"

From b5149297841333bdab23748264999675dbf72df9 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Thu, 20 Jun 2024 13:00:11 +0200
Subject: [PATCH 06/39] cicd: debug ./.github/workflows/  #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 7f80bfed0..36defafab 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -11,10 +11,14 @@ jobs:
     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 'pom.xml' property
+        name: "Get current branch for Xetabase from 'pom.xml' property"
         run: |
           chmod +x ./.github/workflows/scripts/xetabase-branch.sh
+          ls ./.github/workflows/scripts/
+          ls ./.github/workflows/
           xetabase_branch=$(./.github/workflows/scripts/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

From f8be19c4ec6154c7fe8ecc03394fb5acf9414531 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 09:42:26 +0200
Subject: [PATCH 07/39] CICD: Added ZETTA_REPO_ACCESS_TOKEN to co xetabase
 #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 49c4c2af0..fa78b2e24 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -1,4 +1,4 @@
-name: Pull request approve workflow
+name: TEST Xetabase and publish report workflow
 
 on:
   workflow_call:
@@ -20,7 +20,7 @@ jobs:
         with:
           repository: zetta-genomics/opencga-enterprise
           ref: ${{ github.event.inputs.branch }}
-          token: ${{ secrets.GH_PRIVATE_TOKEN }}
+          token: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
           path: opencga-enterprise
           fetch-depth: "10"
       - id: get_opencga_branch

From 6cca2db321899bfe48e857b437de5b242a9d3a32 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 09:57:54 +0200
Subject: [PATCH 08/39] cicd: Temporal workflow_dispatch for PR to tests
 #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 36defafab..de45af750 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -1,6 +1,7 @@
 name: Pull request approve workflow
 
 on:
+  workflow_dispatch:
   pull_request_review:
     types: [ submitted ]
 

From 1aa53aa3a12df7d065c2574b246e2b91db435ae7 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 09:59:05 +0200
Subject: [PATCH 09/39] cicd: Delete Temporal workflow_dispatch for PR to tests
 #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index de45af750..36defafab 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -1,7 +1,6 @@
 name: Pull request approve workflow
 
 on:
-  workflow_dispatch:
   pull_request_review:
     types: [ submitted ]
 

From e29adf1e6c06ad520b56c947e4fa6308a84f822d Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 10:07:45 +0200
Subject: [PATCH 10/39] cicd: Temporal call to TASK-6399 yml #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 36defafab..1ee5a1419 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -23,7 +23,7 @@ jobs:
           echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
           echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT
       - name: "Run all tests before merging"
-        uses: ./.github/workflows/test-xetabase-workflow.yml
+        uses: ./.github/workflows/test-xetabase-workflow.yml@TASK-6399
         with:
           branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
           task: ${{ github.event.pull_request.head.ref }}
\ No newline at end of file

From 55e0c2f25e0c418453b718a1e42e3de62a1f9919 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 10:11:00 +0200
Subject: [PATCH 11/39] cicd: Temporal call to TASK-6399 yml #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 1ee5a1419..4169383cf 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -23,7 +23,7 @@ jobs:
           echo "__Xetabase ref:__ \"${xetabase_branch}\"" | tee -a ${GITHUB_STEP_SUMMARY}
           echo "xetabase_branch=${xetabase_branch}" >> $GITHUB_OUTPUT
       - name: "Run all tests before merging"
-        uses: ./.github/workflows/test-xetabase-workflow.yml@TASK-6399
+        uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399
         with:
           branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
           task: ${{ github.event.pull_request.head.ref }}
\ No newline at end of file

From 2083020f3b2ed2035d264a8dcff845d6127b47a2 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 10:43:16 +0200
Subject: [PATCH 12/39] create workflow in develop to test xetabase #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 4169383cf..609bec4ac 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -1,4 +1,5 @@
 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:
   pull_request_review:

From e0d260146f9c5f8e655d1c7be7c8151ccf190121 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 10:52:58 +0200
Subject: [PATCH 13/39] Separate in two jobs to run the tests #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 609bec4ac..f5c6d8a6d 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -6,7 +6,7 @@ on:
     types: [ submitted ]
 
 jobs:
-  test:
+  calculate-xetabase-branch:
     name: Execute JUnit and Jacoco tests
     runs-on: ubuntu-22.04
     steps:
@@ -15,7 +15,7 @@ jobs:
         with:
           fetch-depth: '10'
       - id: get_xetabase_branch
-        name: "Get current branch for Xetabase from 'pom.xml' property"
+        name: "Get current branch for Xetabase from target branch"
         run: |
           chmod +x ./.github/workflows/scripts/xetabase-branch.sh
           ls ./.github/workflows/scripts/
@@ -23,8 +23,11 @@ jobs:
           xetabase_branch=$(./.github/workflows/scripts/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
-      - name: "Run all tests before merging"
-        uses: opencb/java-common-libs/.github/workflows/test-xetabase-workflow.yml@TASK-6399
-        with:
-          branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
-          task: ${{ github.event.pull_request.head.ref }}
\ No newline at end of file
+
+  test:
+    name: "Run all tests before merging"
+    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 }}
\ No newline at end of file

From 606b93ef03e0d71e161e07f80f8cc509ba18b6a1 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 11:01:43 +0200
Subject: [PATCH 14/39] cicd secrets: inherit #TASK-6399

---
 .github/workflows/pull-request-approved.yml  | 3 ++-
 .github/workflows/test-xetabase-workflow.yml | 4 ++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index f5c6d8a6d..e02607698 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -30,4 +30,5 @@ jobs:
     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 }}
\ No newline at end of file
+      task: ${{ github.event.pull_request.head.ref }}
+    secrets: inherit
\ No newline at end of file
diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index fa78b2e24..12e8504ab 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -15,6 +15,10 @@ jobs:
     name: Execute JUnit and Jacoco tests
     runs-on: ubuntu-22.04
     steps:
+      - name: Log inputs
+        run: |
+          echo "__OpenCGA-enterprise branch:__ \"${{ github.event.inputs.branch }}\"" | tee -a $GITHUB_STEP_SUMMARY
+          echo "__Task to test:__ \"${{ github.event.inputs.task }}\"" | tee -a $GITHUB_STEP_SUMMARY
       - name: Clone OpenCGA Enterprise branch '${{ github.event.inputs.branch }}'
         uses: actions/checkout@v4
         with:

From 8014992836d93e82c259478a4c4301f2983627a6 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 12:34:23 +0200
Subject: [PATCH 15/39] cicd create outputs #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index e02607698..36baa148d 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -4,11 +4,17 @@ run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref
 on:
   pull_request_review:
     types: [ submitted ]
+    outputs:
+      version:
+        description: "XetaBase branch to test"
+        value: ${{ jobs.calculate-xetabase-branch.outputs.xetabase_branch }}
 
 jobs:
   calculate-xetabase-branch:
-    name: Execute JUnit and Jacoco tests
+    name: Calculate Xetabase branch
     runs-on: ubuntu-22.04
+    outputs:
+      xetabase_branch: ${{ steps.get_xetabase_branch.outputs.xetabase_branch }}
     steps:
       - name: Clone java-common-libs
         uses: actions/checkout@v4
@@ -23,7 +29,7 @@ jobs:
           xetabase_branch=$(./.github/workflows/scripts/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"
     needs: calculate-xetabase-branch

From 8c8cf8c95c09c06fbc93a0eeb521db94add3716c Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 12:38:14 +0200
Subject: [PATCH 16/39] cicd check bash --version #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 36baa148d..8a32022fa 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -26,6 +26,7 @@ jobs:
           chmod +x ./.github/workflows/scripts/xetabase-branch.sh
           ls ./.github/workflows/scripts/
           ls ./.github/workflows/
+          bash --version
           xetabase_branch=$(./.github/workflows/scripts/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

From f6719a7a5ff185936fbdbeb759c0c25f19b67683 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 12:39:55 +0200
Subject: [PATCH 17/39] cicd check bash --version #TASK-6399

---
 .github/workflows/pull-request-approved.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 8a32022fa..93efbc861 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -4,10 +4,6 @@ run-name: 'Pull request approve workflow ${{ github.event.pull_request.head.ref
 on:
   pull_request_review:
     types: [ submitted ]
-    outputs:
-      version:
-        description: "XetaBase branch to test"
-        value: ${{ jobs.calculate-xetabase-branch.outputs.xetabase_branch }}
 
 jobs:
   calculate-xetabase-branch:

From 26914c71e137a412432514661fc15abde6291476 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 13:25:31 +0200
Subject: [PATCH 18/39] cicd: remove github.event. in inputs #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 12e8504ab..6fceeaa54 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -17,13 +17,13 @@ jobs:
     steps:
       - name: Log inputs
         run: |
-          echo "__OpenCGA-enterprise branch:__ \"${{ github.event.inputs.branch }}\"" | tee -a $GITHUB_STEP_SUMMARY
-          echo "__Task to test:__ \"${{ github.event.inputs.task }}\"" | tee -a $GITHUB_STEP_SUMMARY
-      - name: Clone OpenCGA Enterprise branch '${{ github.event.inputs.branch }}'
+          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: ${{ secrets.ZETTA_REPO_ACCESS_TOKEN }}
           path: opencga-enterprise
           fetch-depth: "10"
@@ -32,7 +32,7 @@ jobs:
         run: |
           pwd
           chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh
-          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh ${{ github.event.inputs.task }})
+          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh ${{ inputs.task }})
           echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
       - uses: actions/checkout@v4
         with:
@@ -72,7 +72,7 @@ jobs:
         run: |
           ln -s opencga opencga-enterprise/opencga-home
           cd opencga-enterprise
-          ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ github.event.inputs.task }} -c localhost:27018 -H hdp3.1
+          ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1
       - name: Upload reports results to Github
         uses: actions/upload-artifact@v4
         with:
@@ -87,7 +87,7 @@ jobs:
         uses: garygrossgarten/github-action-scp@release
         with:
           local: opencga-enterprise/reports/test
-          remote: /var/www/html/reports/xetabase/${{ github.event.inputs.task }}/
+          remote: /var/www/html/reports/xetabase/${{ inputs.task }}/
           host: ${{ secrets.SSH_TESTING_SERVER_HOST}}
           port: ${{ secrets.SSH_TESTING_SERVER_PORT}}
           username: ${{ secrets.SSH_TESTING_SERVER_USER }}

From b4b7a47f23852753aa7e82559227091d232a6c8b Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 13:41:16 +0200
Subject: [PATCH 19/39] cicd: workflow dispatch to test#TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 6fceeaa54..94782ae08 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -9,6 +9,16 @@ on:
       branch:
         type: string
         required: true
+  workflow_dispatch:
+    inputs:
+      task:
+        type: string
+        description: 'Task ID to be tested.'
+        required: true
+      branch:
+        type: string
+        description: 'Branch of opencga-enterprise to be tested and built.'
+        required: true
 
 jobs:
   test:

From 39ec574b58d5b6b8d0023dd8fcea2ce499a33b3c Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 13:44:09 +0200
Subject: [PATCH 20/39] cicd: debug logs added #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 94782ae08..3cf699528 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -80,6 +80,11 @@ jobs:
           password: ${{ secrets.DOCKER_HUB_PASSWORD }}
       - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise
         run: |
+          pwd
+          ls -lrtha 
+          echo "------------------------------------"
+          ls -lrtha /home/runner/work/java-common-libs/java-common-libs
+          echo "------------------------------------"
           ln -s opencga opencga-enterprise/opencga-home
           cd opencga-enterprise
           ./build.sh -t -l runShortTests,runMediumTests,runLongTests -b -s -f -T ${{ inputs.task }} -c localhost:27018 -H hdp3.1

From 3bea1075a79d7b0c305c3e6cb1212988282cc7b1 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 13:49:39 +0200
Subject: [PATCH 21/39] cicd: debug logs added #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 3cf699528..7b14f4829 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -83,10 +83,13 @@ jobs:
           pwd
           ls -lrtha 
           echo "------------------------------------"
-          ls -lrtha /home/runner/work/java-common-libs/java-common-libs
-          echo "------------------------------------"
-          ln -s opencga opencga-enterprise/opencga-home
           cd opencga-enterprise
+          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
       - name: Upload reports results to Github
         uses: actions/upload-artifact@v4

From ae6267643cf5cc16b6e5fd4953f74af94b565e67 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 25 Jun 2024 13:53:17 +0200
Subject: [PATCH 22/39] cicd: debug logs added #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 7b14f4829..54e684b5b 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -9,16 +9,16 @@ on:
       branch:
         type: string
         required: true
-  workflow_dispatch:
-    inputs:
-      task:
-        type: string
-        description: 'Task ID to be tested.'
-        required: true
-      branch:
-        type: string
-        description: 'Branch of opencga-enterprise to be tested and built.'
-        required: true
+#  workflow_dispatch:
+#    inputs:
+#      task:
+#        type: string
+#        description: 'Task ID to be tested.'
+#        required: true
+#      branch:
+#        type: string
+#        description: 'Branch of opencga-enterprise to be tested and built.'
+#        required: true
 
 jobs:
   test:

From 6a7eee58003057ef8f4658639533008cf15be168 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Fri, 28 Jun 2024 10:04:47 +0200
Subject: [PATCH 23/39] cicd: Test level short to fast test upload to report
 server #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 54e684b5b..6f9636314 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -90,7 +90,8 @@ jobs:
           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,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:

From d5b4f38f6164c9684b87157149b972f304efffe3 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Fri, 28 Jun 2024 10:19:20 +0200
Subject: [PATCH 24/39] cicd: Uncomment workflow_dispatch Test level short to
 fast test upload to report server #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 6f9636314..f0f56f3f7 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -9,16 +9,16 @@ on:
       branch:
         type: string
         required: true
-#  workflow_dispatch:
-#    inputs:
-#      task:
-#        type: string
-#        description: 'Task ID to be tested.'
-#        required: true
-#      branch:
-#        type: string
-#        description: 'Branch of opencga-enterprise to be tested and built.'
-#        required: true
+  workflow_dispatch:
+    inputs:
+      task:
+        type: string
+        description: 'Task ID to be tested.'
+        required: true
+      branch:
+        type: string
+        description: 'Branch of opencga-enterprise to be tested and built.'
+        required: true
 
 jobs:
   test:

From 5bb1d4c55600a2c0ccd564e3bbda50812c254036 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Fri, 28 Jun 2024 12:17:23 +0200
Subject: [PATCH 25/39] cicd: fix paths to upload artifacts #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index eab1f53ee..f0e5ad1df 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -103,12 +103,12 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: report-test
-          path: /home/runner/work/testing-environment/testing-environment/opencga-enterprise/reports/test
+          path: /home/runner/work/java-common-libs/java-common-libs/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: /home/runner/work/java-common-libs/java-common-libs/opencga-enterprise/build.log
       - name: Upload junit reports to a remote scp server
         uses: garygrossgarten/github-action-scp@release
         with:

From d4ebf31452cd2c8caf33a0acb28ed96f79a38c71 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Fri, 28 Jun 2024 12:45:13 +0200
Subject: [PATCH 26/39] Added keeper passwords #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 34 ++++++++++++++------
 1 file changed, 24 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index f0e5ad1df..57294ee6a 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -21,10 +21,7 @@ on:
         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:
@@ -32,6 +29,23 @@ jobs:
     name: Execute JUnit and Jacoco tests
     runs-on: ubuntu-22.04
     steps:
+      - name: Retrieve secrets from Keeper
+        id: ksecrets
+        uses: Keeper-Security/ksm-action@master
+        with:
+          keeper-secret-config: ${{ secrets.KEEPER_SM_GH_OPENCB }}
+          secrets: |
+            AZCOPY_SPA_CLIENT_SECRET/field/Secret Value > env:AZCOPY_SPA_CLIENT_SECRET
+            AZCOPY_SPA_APPLICATION_ID/field/Secret Value > env:AZCOPY_SPA_APPLICATION_ID
+            AZCOPY_TENANT_ID/field/Secret Value > env:AZCOPY_TENANT_ID
+            #ZETTA_REPO_ACCESS_TOKEN/field/Secret Value > env:ZETTA_REPO_ACCESS_TOKEN
+            AZURE_KUBE_CONFIG/field/Secret Value > env:AZURE_KUBE_CONFIG
+            DOCKER_HUB_USER/field/Secret Value > env:DOCKER_HUB_USER
+            DOCKER_HUB_PASSWORD/field/Secret Value > env:DOCKER_HUB_PASSWORD
+            SSH_TESTING_SERVER_HOST/field/Secret Value > env:SSH_TESTING_SERVER_HOST
+            SSH_TESTING_SERVER_PORT/field/Secret Value > env:SSH_TESTING_SERVER_PORT
+            SSH_TESTING_SERVER_USER/field/Secret Value > env:SSH_TESTING_SERVER_USER
+            SSH_TESTING_SERVER_PASSWORD/field/Secret Value > env:SSH_TESTING_SERVER_PASSWORD
       - name: Log inputs
         run: |
           echo "__OpenCGA-enterprise branch:__ \"${{ inputs.branch }}\"" | tee -a $GITHUB_STEP_SUMMARY
@@ -74,7 +88,7 @@ jobs:
         run: |
           wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl
           chmod +x ./kubectl
-          echo "${{ secrets.AZURE_KUBE_CONFIG }}" > admin.conf
+          echo "${{ env.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
@@ -83,8 +97,8 @@ 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: ${{ env.DOCKER_HUB_PASSWORD }}
       - name: Run all OpenCB Junit tests, ie. java-common-libs, biodata, cellbase, opencga and opencga-enterprise
         run: |
           pwd
@@ -114,10 +128,10 @@ jobs:
         with:
           local: opencga-enterprise/reports/test
           remote: /var/www/html/reports/xetabase/${{ 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 }}
+          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
 
 

From df6f77b2ffe82780c8ccf33bdbf74fd128bc3676 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Fri, 28 Jun 2024 12:50:53 +0200
Subject: [PATCH 27/39] Added keeper passwords #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 57294ee6a..afa045211 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -38,7 +38,6 @@ jobs:
             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
-            #ZETTA_REPO_ACCESS_TOKEN/field/Secret Value > env:ZETTA_REPO_ACCESS_TOKEN
             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

From 8c9f95802cdcd658edcc091ef7146212db0f8237 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Mon, 1 Jul 2024 11:31:44 +0200
Subject: [PATCH 28/39] cicd: Remove absolute references in Path #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index afa045211..459768a62 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -116,12 +116,12 @@ jobs:
         uses: actions/upload-artifact@v4
         with:
           name: report-test
-          path: /home/runner/work/java-common-libs/java-common-libs/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/java-common-libs/java-common-libs/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:

From 2b5ccecda260326ae715ad249f64dc244a1c4d08 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Mon, 1 Jul 2024 17:15:39 +0200
Subject: [PATCH 29/39] Added get-xetabase-branch.sh #TASK-6399

---
 .github/workflows/pull-request-approved.yml   |  2 +-
 .../workflows/scripts/get-opencga-branch.sh   | 44 +++++++++++++++++++
 ...abase-branch.sh => get-xetabase-branch.sh} |  8 ++++
 .github/workflows/test-xetabase-workflow.yml  |  5 ++-
 4 files changed, 56 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/scripts/get-opencga-branch.sh
 rename .github/workflows/scripts/{xetabase-branch.sh => get-xetabase-branch.sh} (82%)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 93efbc861..5fdf66da6 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -23,7 +23,7 @@ jobs:
           ls ./.github/workflows/scripts/
           ls ./.github/workflows/
           bash --version
-          xetabase_branch=$(./.github/workflows/scripts/xetabase-branch.sh ${{ github.event.pull_request.base.ref }})
+          xetabase_branch=$(./.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
   
diff --git a/.github/workflows/scripts/get-opencga-branch.sh b/.github/workflows/scripts/get-opencga-branch.sh
new file mode 100644
index 000000000..29aa68712
--- /dev/null
+++ b/.github/workflows/scripts/get-opencga-branch.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+
+## Navigate to the root folder where the pom.xml is
+cd "$(dirname "$0")"/../../../ || exit 2
+
+## Use the first argument passed as the branch. If it is not passed, I exit
+if [[ -n $1 ]]; then
+  GIT_BRANCH=$1
+else
+   exit 2
+fi
+
+# If the branch exists in the opencga repository, I return it
+if [ "$(git ls-remote https://github.com/opencb/opencga.git "$GIT_BRANCH" )" ] ; then
+  echo "$GIT_BRANCH";
+  exit 0;
+fi
+
+## Read the opencga version from the pom.xml
+BUILD_VERSION=$(mvn help:evaluate -Dexpression=opencga.version -q -DforceStdout)
+
+## We remove the -SNAPSHOT if it exists
+CLEAN_BUILD_VERSION=$(echo "$BUILD_VERSION" | cut -d "-" -f 1)
+
+## Read the numbers separately to compose the name of the branch
+MAJOR=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 1)
+MINOR=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 2)
+PATCH=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 3)
+
+## it's a HOTFIX. Count the number of points to know if it is a hotfix
+COUNT=$(echo "$CLEAN_BUILD_VERSION" | grep -o '\.' | wc -l )
+if [ "$COUNT" -gt 2 ]; then
+  echo "release-$MAJOR.$MINOR.$PATCH.x"
+  exit 0
+fi
+
+## It's develop branch
+if [[ "$PATCH" ==  "0" ]]; then
+  echo "develop"
+  exit 0
+else #Is release branch
+  echo "release-$MAJOR.$MINOR.x"
+  exit 0
+fi
\ No newline at end of file
diff --git a/.github/workflows/scripts/xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh
similarity index 82%
rename from .github/workflows/scripts/xetabase-branch.sh
rename to .github/workflows/scripts/get-xetabase-branch.sh
index af17f7f12..0be5cb32d 100644
--- a/.github/workflows/scripts/xetabase-branch.sh
+++ b/.github/workflows/scripts/get-xetabase-branch.sh
@@ -5,6 +5,14 @@ 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 [[ "$input_branch" == "develop" ]]; then
     echo "develop"
diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 459768a62..d332ec409 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -62,9 +62,10 @@ jobs:
         run: |
           pwd
           chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh
-          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh ${{ inputs.task }})
+          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-branch.sh ${{ inputs.task }})
           echo "opencga_branch=${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 }}

From 7d6d051929a10ab8306d52494d9b617bdd7e0ef3 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Mon, 1 Jul 2024 17:24:30 +0200
Subject: [PATCH 30/39] Added remove get-opencga-branch.sh #TASK-6399

---
 .../workflows/scripts/get-opencga-branch.sh   | 44 -------------------
 .github/workflows/test-xetabase-workflow.yml  |  4 +-
 2 files changed, 2 insertions(+), 46 deletions(-)
 delete mode 100644 .github/workflows/scripts/get-opencga-branch.sh

diff --git a/.github/workflows/scripts/get-opencga-branch.sh b/.github/workflows/scripts/get-opencga-branch.sh
deleted file mode 100644
index 29aa68712..000000000
--- a/.github/workflows/scripts/get-opencga-branch.sh
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/bin/bash
-
-## Navigate to the root folder where the pom.xml is
-cd "$(dirname "$0")"/../../../ || exit 2
-
-## Use the first argument passed as the branch. If it is not passed, I exit
-if [[ -n $1 ]]; then
-  GIT_BRANCH=$1
-else
-   exit 2
-fi
-
-# If the branch exists in the opencga repository, I return it
-if [ "$(git ls-remote https://github.com/opencb/opencga.git "$GIT_BRANCH" )" ] ; then
-  echo "$GIT_BRANCH";
-  exit 0;
-fi
-
-## Read the opencga version from the pom.xml
-BUILD_VERSION=$(mvn help:evaluate -Dexpression=opencga.version -q -DforceStdout)
-
-## We remove the -SNAPSHOT if it exists
-CLEAN_BUILD_VERSION=$(echo "$BUILD_VERSION" | cut -d "-" -f 1)
-
-## Read the numbers separately to compose the name of the branch
-MAJOR=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 1)
-MINOR=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 2)
-PATCH=$(echo "$CLEAN_BUILD_VERSION" | cut -d "." -f 3)
-
-## it's a HOTFIX. Count the number of points to know if it is a hotfix
-COUNT=$(echo "$CLEAN_BUILD_VERSION" | grep -o '\.' | wc -l )
-if [ "$COUNT" -gt 2 ]; then
-  echo "release-$MAJOR.$MINOR.$PATCH.x"
-  exit 0
-fi
-
-## It's develop branch
-if [[ "$PATCH" ==  "0" ]]; then
-  echo "develop"
-  exit 0
-else #Is release branch
-  echo "release-$MAJOR.$MINOR.x"
-  exit 0
-fi
\ No newline at end of file
diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index d332ec409..411c0ee82 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -61,8 +61,8 @@ jobs:
         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/get-opencga-branch.sh ${{ inputs.task }})
+          chmod +x ./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh
+          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh false)
           echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
       - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}'
         uses: actions/checkout@v4

From 61b806a7df651eea18c891477ed97d5e4f3b83fd Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Mon, 1 Jul 2024 17:46:35 +0200
Subject: [PATCH 31/39] Added log summary step #TASK-6399

---
 .github/workflows/pull-request-approved.yml  | 5 +----
 .github/workflows/test-xetabase-workflow.yml | 5 +++++
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index 5fdf66da6..d96c95627 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -19,10 +19,7 @@ jobs:
       - id: get_xetabase_branch
         name: "Get current branch for Xetabase from target branch"
         run: |
-          chmod +x ./.github/workflows/scripts/xetabase-branch.sh
-          ls ./.github/workflows/scripts/
-          ls ./.github/workflows/
-          bash --version
+          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
diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 411c0ee82..1dbfed69f 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -133,5 +133,10 @@ jobs:
           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
+          
+          
 
 

From 1f896dcdcc3535a58951e414a421a717ccad45d9 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Mon, 1 Jul 2024 17:47:53 +0200
Subject: [PATCH 32/39] cicd: Removed test step in develop.yml #TASK-6399

---
 .github/workflows/develop.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/.github/workflows/develop.yml b/.github/workflows/develop.yml
index 196fc122b..f4d59ed60 100644
--- 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

From af9e16d2ee192734fdc48769439c789e7e3ebab6 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Mon, 1 Jul 2024 21:12:50 +0200
Subject: [PATCH 33/39] cicd: Add debug outputs #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 1dbfed69f..3d01cf422 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -61,6 +61,8 @@ jobs:
         name: Get OpenCGA branch from 'pom.xml' property
         run: |
           pwd
+          ls -lrtha
+          ls -lrtha ./opencga-enterprise
           chmod +x ./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh
           opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh false)
           echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT

From a0861c29c8afefd1665ca364f496efdef562f9cf Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Mon, 1 Jul 2024 21:15:24 +0200
Subject: [PATCH 34/39] cicd: delete param to opencga_branch #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 3d01cf422..0cc013038 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -64,7 +64,7 @@ jobs:
           ls -lrtha
           ls -lrtha ./opencga-enterprise
           chmod +x ./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh
-          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh false)
+          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh)
           echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
       - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}'
         uses: actions/checkout@v4

From 9de5d3c998b7cf23d5e5a3777fc0d08d6ec885bf Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Mon, 1 Jul 2024 21:19:05 +0200
Subject: [PATCH 35/39] cicd: delete param to opencga_branch #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 0cc013038..c4e3e099d 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -65,6 +65,7 @@ jobs:
           ls -lrtha ./opencga-enterprise
           chmod +x ./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh
           opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh)
+          echo "opencga_branch=${opencga_branch}"
           echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
       - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}'
         uses: actions/checkout@v4

From 98d385234221b50c4d732c16ed13cc78bf3dcbc7 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Mon, 1 Jul 2024 21:24:32 +0200
Subject: [PATCH 36/39] cicd:call to xetabase-branch.sh #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index c4e3e099d..950c0b2f6 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -63,8 +63,8 @@ jobs:
           pwd
           ls -lrtha
           ls -lrtha ./opencga-enterprise
-          chmod +x ./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh
-          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/opencga_branch.sh)
+          chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh
+          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh)
           echo "opencga_branch=${opencga_branch}"
           echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
       - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}'

From 75536daaf8c52917cd82cd521221211441742c5c Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 2 Jul 2024 10:39:31 +0200
Subject: [PATCH 37/39] cicd: Change AZURE_KUBE_CONFIG to secrets #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index 950c0b2f6..eab8d1c05 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -91,7 +91,7 @@ jobs:
         run: |
           wget https://dl.k8s.io/release/v1.28.2/bin/linux/amd64/kubectl
           chmod +x ./kubectl
-          echo "${{ env.AZURE_KUBE_CONFIG }}" > admin.conf
+          echo "${{ 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

From 3bfbf9a51afa6d13bd71f492b23aafb082e513f3 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 9 Jul 2024 15:32:54 +0200
Subject: [PATCH 38/39] Rename get-opencga-xetabase-branch.sh reference

---
 .github/workflows/test-xetabase-workflow.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index eab8d1c05..1dfcdc786 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -63,8 +63,8 @@ jobs:
           pwd
           ls -lrtha
           ls -lrtha ./opencga-enterprise
-          chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh
-          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh)
+          chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh
+          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh)
           echo "opencga_branch=${opencga_branch}"
           echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
       - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}'

From 8431eb89a25088057483dc8690c07e59e0b5a08a Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 9 Jul 2024 15:32:54 +0200
Subject: [PATCH 39/39] cicd: Rename get-opencga-xetabase-branch.sh reference
 #TASK-6399

---
 .github/workflows/test-xetabase-workflow.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-xetabase-workflow.yml b/.github/workflows/test-xetabase-workflow.yml
index eab8d1c05..1dfcdc786 100644
--- a/.github/workflows/test-xetabase-workflow.yml
+++ b/.github/workflows/test-xetabase-workflow.yml
@@ -63,8 +63,8 @@ jobs:
           pwd
           ls -lrtha
           ls -lrtha ./opencga-enterprise
-          chmod +x ./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh
-          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/xetabase-branch.sh)
+          chmod +x ./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh
+          opencga_branch=$(./opencga-enterprise/.github/workflows/scripts/get-opencga-xetabase-branch.sh)
           echo "opencga_branch=${opencga_branch}"
           echo "opencga_branch=${opencga_branch}" >> $GITHUB_OUTPUT
       - name: Clone OpenCGA branch '${{ steps.get_opencga_branch.outputs.opencga_branch }}'