changes to run services in openshift

.github/workflows/sync-cdis-with-pcdc.yml

@@ -0,0 +1,135 @@
+name: Sync from Upstream
+
+on:
+  schedule:
+    - cron: '0 6 * * 1'  # Runs at 06:00 UTC every Monday
+  workflow_dispatch:
+
+jobs:
+  sync-and-create-pr:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+      issues: write
+      actions: read
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.PAT_TOKEN }}
+      - name: Set up Git
+        run: |
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+      - name: Add upstream remote and fetch
+        run: |
+          git remote add upstream https://github.com/uc-cdis/gen3-helm.git
+          git fetch upstream master
+          git fetch origin  # Ensure we have latest origin refs
+
+      - name: Create and push sync branch
+        run: |
+          # Delete existing sync branch if it exists
+          git push origin --delete sync-cdis-pcdc || true
+
+          # Create sync branch from pcdc_dev
+          git checkout -b sync-cdis-pcdc origin/pcdc_dev
+          echo "Created sync-cdis-pcdc branch from pcdc_dev"
+
+      - name: Attempt merge
+        id: merge
+        run: |
+          # Store the current HEAD before merge
+          BEFORE_MERGE=$(git rev-parse HEAD)
+          echo "conflict_branch=false" >> $GITHUB_OUTPUT
+
+          if git merge upstream/master --no-edit; then
+            # Get the HEAD after merge
+            AFTER_MERGE=$(git rev-parse HEAD)
+
+            # Check if the merge actually created any changes
+            if [ "$BEFORE_MERGE" = "$AFTER_MERGE" ]; then
+              echo "merge_success=false" >> $GITHUB_OUTPUT
+              echo "❌ No changes after merge - branches are already up to date"
+              exit 0
+            fi
+
+            # Count actual changes from the merge
+            CHANGES=$(git diff --name-only $BEFORE_MERGE $AFTER_MERGE | wc -l)
+
+
+            # Verify we have actual changes before proceeding
+            if [ "$CHANGES" -eq 0 ]; then
+              echo "merge_success=false" >> $GITHUB_OUTPUT
+              echo "❌ No file changes detected after merge"
+              exit 0
+            fi
+
+            echo "merge_success=true" >> $GITHUB_OUTPUT
+            echo "✅ Merge successful with changes"
+
+          else
+            echo "merge_success=false" >> $GITHUB_OUTPUT
+            echo "conflict_branch=true" >> $GITHUB_OUTPUT
+            echo "❌ Merge conflicts detected"
+          fi
+
+      - name: Push successful merge
+        if: steps.merge.outputs.merge_success == 'true'
+        run: |
+          git push -u origin sync-cdis-pcdc
+          echo "✅ Pushed sync-cdis-pcdc branch"
+
+      - name: Wait for branch to be available
+        if: steps.merge.outputs.merge_success == 'true'
+        run: |
+          echo "Waiting for branch to be available on GitHub..."
+          sleep 10
+
+          # Verify branches exist on GitHub
+          echo "Checking if branches exist on GitHub..."
+          gh api repos/chicagopcdc/gen3-helm/branches/pcdc_dev --jq .name
+          gh api repos/chicagopcdc/gen3-helm/branches/sync-cdis-pcdc --jq .name
+        env:
+          GH_TOKEN: ${{ secrets.PAT_TOKEN }}
+
+      - name: Create Pull Request for successful merge
+        if: steps.merge.outputs.merge_success == 'true'
+        run: |
+          echo "Creating PR with the following details:"
+          echo "Base: pcdc_dev"
+          echo "Head: sync-cdis-pcdc"
+          echo "Files changed: ${{ steps.merge.outputs.files_changed }}"
+
+          # Check if PR already exists
+          if gh pr list --base pcdc_dev --head sync-cdis-pcdc --json number | jq -e '.[0]' > /dev/null; then
+            echo "PR already exists, skipping creation"
+            exit 0
+          fi
+
+          # Create the PR with explicit repository context
+          gh pr create \
+            --repo chicagopcdc/gen3-helm \
+            --base pcdc_dev \
+            --head sync-cdis-pcdc \
+            --title "Sync: Upstream Master into pcdc_dev ($(date -u +%Y-%m-%d))" \
+            --body "This PR automatically syncs changes from upstream/master into the pcdc_dev branch. Files changed: ${{ steps.merge.outputs.files_changed }}"
+        env:
+          GH_TOKEN: ${{ secrets.PAT_TOKEN }}
+
+      - name: Create conflict resolution branch
+        if: steps.merge.outputs.merge_success == 'false' && steps.merge.outputs.conflict_branch == 'true'
+        run: |
+          # Create timestamped branch name
+          TIMESTAMP=$(date -u +%Y%m%d-%H%M%S)
+          CONFLICT_BRANCH="conflict-resolution-${TIMESTAMP}"
+
+          # Create and push conflict resolution branch with unresolved conflicts
+          git checkout -b "$CONFLICT_BRANCH"
+          git push -u origin "$CONFLICT_BRANCH"
+
+          echo "CONFLICT_BRANCH=${CONFLICT_BRANCH}" >> $GITHUB_ENV
+          echo "Created conflict resolution branch: $CONFLICT_BRANCH"

.gitignore

@@ -1,6 +1,29 @@
-postgres.txt
+# --- Folders ---
 **/charts/
 notes/
+CA/
+gen3_scripts/
+gen3_etl/
+_sample-*/
+
+# --- Files ---
 Chart.lock
-.DS_Store
-_sample-*/
+# macOS system file (usually ignored)
+.DS_Store  
+# Helm secrets/values file                                 
+secret-values.yaml                          
+# Environment variables
+.env                                        
+# Instance generated service account or credentials
+credentials.json                            
+temp.yaml
+# Main Helm values file
+/values.yaml                               
+postgres.txt
+# External reference data file for PCDC
+pcdc_data/external/external_reference.json  
+# Script that creates external secrets IAM user
+external_secrets.bash
+secret-gearbox-default-values.yaml
+secret-openshift-gearbox-default-values.yaml
+secret-pcdc-default-values.yaml