From 08b0e1d9603319157abdf0ee0ed80f938066d067 Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Tue, 6 Aug 2024 17:29:39 +0200
Subject: [PATCH 1/5] Prepare Port Patch Cellbase 5.8.3 -> 6.3.0 #TASK-6647

---
 cellbase-app/pom.xml    | 2 +-
 cellbase-client/pom.xml | 2 +-
 cellbase-core/pom.xml   | 2 +-
 cellbase-lib/pom.xml    | 2 +-
 cellbase-server/pom.xml | 2 +-
 pom.xml                 | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
index b561d3cc62..aed90e9897 100644
--- a/cellbase-app/pom.xml
+++ b/cellbase-app/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.8.3</version>
+        <version>6.3.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
index 96f8c1d062..7424c21bbb 100644
--- a/cellbase-client/pom.xml
+++ b/cellbase-client/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.8.3</version>
+        <version>6.3.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml
index cd396d0e1e..7c74e13d92 100644
--- a/cellbase-core/pom.xml
+++ b/cellbase-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.8.3</version>
+        <version>6.3.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index 15351ef02b..780fc20043 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.8.3</version>
+        <version>6.3.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml
index 101a284617..fe4509c6fc 100644
--- a/cellbase-server/pom.xml
+++ b/cellbase-server/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>5.8.3</version>
+        <version>6.3.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/pom.xml b/pom.xml
index e41d354314..8454cea683 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.opencb.cellbase</groupId>
     <artifactId>cellbase</artifactId>
-    <version>5.8.3</version>
+    <version>6.3.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>CellBase project</name>

From 843bd483f94a2fa8b9cd8b2d8fe3ee425c2fdd4b Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Wed, 18 Sep 2024 09:25:33 +0200
Subject: [PATCH 2/5] CICD: new SDLC Updating version number #TASK-6879

---
 cellbase-app/pom.xml    | 2 +-
 cellbase-client/pom.xml | 2 +-
 cellbase-core/pom.xml   | 2 +-
 cellbase-lib/pom.xml    | 2 +-
 cellbase-server/pom.xml | 2 +-
 pom.xml                 | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
index aed90e9897..adf59c092a 100644
--- a/cellbase-app/pom.xml
+++ b/cellbase-app/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>6.3.0-SNAPSHOT</version>
+        <version>6.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
index 7424c21bbb..977b4b81cd 100644
--- a/cellbase-client/pom.xml
+++ b/cellbase-client/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>6.3.0-SNAPSHOT</version>
+        <version>6.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml
index 7c74e13d92..8fcd89455f 100644
--- a/cellbase-core/pom.xml
+++ b/cellbase-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>6.3.0-SNAPSHOT</version>
+        <version>6.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index 9b4dd7fbe0..a7c4c02dc1 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>6.3.0-SNAPSHOT</version>
+        <version>6.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml
index fe4509c6fc..71cdea12ee 100644
--- a/cellbase-server/pom.xml
+++ b/cellbase-server/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>6.3.0-SNAPSHOT</version>
+        <version>6.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/pom.xml b/pom.xml
index 7d22cff469..380bb87132 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.opencb.cellbase</groupId>
     <artifactId>cellbase</artifactId>
-    <version>6.3.0-SNAPSHOT</version>
+    <version>6.0.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>CellBase project</name>

From 21ed8b04c513b04a49ba7e16812cf945f704628e Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Wed, 18 Sep 2024 09:26:53 +0200
Subject: [PATCH 3/5] CICD: new SDLC Updating branches and version references
 #TASK-6879

---
 .github/workflows/pull-request-approved.yml   | 37 +++++++++++---
 .../workflows/scripts/get-xetabase-branch.sh  | 50 +++++++++++++++++++
 2 files changed, 81 insertions(+), 6 deletions(-)
 create mode 100644 .github/workflows/scripts/get-xetabase-branch.sh

diff --git a/.github/workflows/pull-request-approved.yml b/.github/workflows/pull-request-approved.yml
index eb410c9cba..d339f65b96 100644
--- a/.github/workflows/pull-request-approved.yml
+++ b/.github/workflows/pull-request-approved.yml
@@ -1,15 +1,40 @@
 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:
     types: [ submitted ]
 
 jobs:
-  build:
-    uses: opencb/java-common-libs/.github/workflows/build-java-app-workflow.yml@develop
+  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: |
+          chmod +x ./.github/workflows/scripts/get-xetabase-branch.sh
+          echo "github.event.pull_request.base.ref: ${{ github.event.pull_request.base.ref }}"
+          echo "github.event.pull_request.head.ref: ${{ github.event.pull_request.head.ref }}"
+          xetabase_branch=$(./.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: "Test analysis"
-    uses: ./.github/workflows/test-analysis.yml
-    needs: build
-    secrets: inherit
+    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: ${{ github.event.pull_request.head.ref }}
+    secrets: inherit
\ No newline at end of file
diff --git a/.github/workflows/scripts/get-xetabase-branch.sh b/.github/workflows/scripts/get-xetabase-branch.sh
new file mode 100644
index 0000000000..16ae8c4711
--- /dev/null
+++ 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://$ZETTA_REPO_ACCESS_TOKEN@github.com/zetta-genomics/opencga-enterprise.git" "$input_branch" )" ] ; then
+      echo $input_branch;
+      return 0;
+    fi
+  fi
+
+  # Check if the branch name is "develop" in that case return the same branch name
+  if [[ "$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 - 4))
+    # 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 570346d2d0dc47e4b055ac8290b2657913ba135e Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Wed, 18 Sep 2024 09:27:47 +0200
Subject: [PATCH 4/5] CICD: new SDLC Updating version number #TASK-6879

---
 pom.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 380bb87132..4109da73df 100644
--- a/pom.xml
+++ b/pom.xml
@@ -23,8 +23,8 @@
 
     <properties>
         <pycellbase.version>${project.version}</pycellbase.version>
-        <java-common-libs.version>5.3.0-SNAPSHOT</java-common-libs.version>
-        <biodata.version>3.3.0-SNAPSHOT</biodata.version>
+        <java-common-libs.version>6.0.0-SNAPSHOT</java-common-libs.version>
+        <biodata.version>4.0.0-SNAPSHOT</biodata.version>
 
         <bionetdb.version>0.1.0</bionetdb.version>
         <jetty.version>9.4.51.v20230217</jetty.version>

From 5da999f0e22941df00fa7efe5143c84e692864dc Mon Sep 17 00:00:00 2001
From: JuanfeSanahuja <juanfe.sanahuja@zettagenomics.com>
Date: Thu, 19 Sep 2024 10:18:02 +0200
Subject: [PATCH 5/5] cicd: update version number #TASK-6879

---
 cellbase-app/pom.xml    | 2 +-
 cellbase-client/pom.xml | 2 +-
 cellbase-core/pom.xml   | 2 +-
 cellbase-lib/pom.xml    | 2 +-
 cellbase-server/pom.xml | 2 +-
 pom.xml                 | 2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/cellbase-app/pom.xml b/cellbase-app/pom.xml
index adf59c092a..2877826403 100644
--- a/cellbase-app/pom.xml
+++ b/cellbase-app/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>6.0.0-SNAPSHOT</version>
+        <version>7.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-client/pom.xml b/cellbase-client/pom.xml
index 977b4b81cd..9fc6f72f07 100644
--- a/cellbase-client/pom.xml
+++ b/cellbase-client/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>6.0.0-SNAPSHOT</version>
+        <version>7.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-core/pom.xml b/cellbase-core/pom.xml
index 8fcd89455f..f4659e2759 100644
--- a/cellbase-core/pom.xml
+++ b/cellbase-core/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>6.0.0-SNAPSHOT</version>
+        <version>7.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-lib/pom.xml b/cellbase-lib/pom.xml
index a7c4c02dc1..0c7fbf836f 100644
--- a/cellbase-lib/pom.xml
+++ b/cellbase-lib/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>6.0.0-SNAPSHOT</version>
+        <version>7.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/cellbase-server/pom.xml b/cellbase-server/pom.xml
index 71cdea12ee..d89aa0e106 100644
--- a/cellbase-server/pom.xml
+++ b/cellbase-server/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>org.opencb.cellbase</groupId>
         <artifactId>cellbase</artifactId>
-        <version>6.0.0-SNAPSHOT</version>
+        <version>7.0.0-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 
diff --git a/pom.xml b/pom.xml
index 4109da73df..e6599cd67c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>org.opencb.cellbase</groupId>
     <artifactId>cellbase</artifactId>
-    <version>6.0.0-SNAPSHOT</version>
+    <version>7.0.0-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>CellBase project</name>