Security scan integration

.github/codeql-config.yml

@@ -0,0 +1,12 @@
+name: My CodeQL Analysis
+description: A sample CodeQL analysis
+
+# Ignore the following directories
+paths-ignore:
+  - "charts/**"
+  - "tools/**" 
+  - "src/test/**" 
+
+# # Specify the CodeQL queries to run
+# queries:
+#   - my-query.ql

.github/dependabot.yml

@@ -0,0 +1,17 @@
+version: 2
+updates:
+  # Keep maven dependencies up-to-date
+  - package-ecosystem: maven
+    # Look for `pom.xml`  in the `root` directory
+    directory: "/"
+    # Check the maven registry for updates every day (weekdays)
+    schedule:
+      interval: daily
+    open-pull-requests-limit: 0
+    target-branch: "security-scans-integrations"    
+    # Raise all maven pull requests with custom labels
+    labels:
+      - "dependencies"
+    reviewers:
+      - "hilpitome"
+      - "ekigamba"

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,85 @@
+
+name: "CodeQL Repository scan"
+
+on:
+  push:
+    branches:
+      - security-scans-integration
+
+  #   # Publish `v1.2.3` tags as releases.
+  #   tags:
+  #     - v*
+  pull_request:
+  # schedule:
+  #   - cron: '0 3 * * 1,3'     # CodeQL Scan every Monday and Wednesday at 3 AM UTC
+  # wokflow_dispatch option enables for manual scanning
+  workflow_dispatch:
+
+
+jobs:
+  analyze:
+    name: Analyze 
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'java' ]
+
+
+    steps:
+    - name: Cancel previous workflow runs
+      uses: styfle/[email protected]
+      with:
+        access_token: ${{ github.token }} 
+
+    - name: Checkout repository
+      uses: actions/checkout@v3
+      with:
+       submodules: recursive
+
+    - name: Set up JDK 17
+      uses: actions/setup-java@v1
+      with:
+        java-version: 17
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        queries: security-and-quality, security-extended
+        config-file: ./.github/codeql-config.yml
+
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+    - name: Autobuild Java Code
+      run:  |
+        mvn clean install -DskipTests
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines. 
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"
+        config-file: ./.github/codeql-config.yml

.github/workflows/secrets-scan.yml

@@ -0,0 +1,25 @@
+name: Leaked Secrets Scan
+on:
+  push:
+    branches: 
+      - security-scans-integrations
+  pull_request:    
+  # schedule:
+  #   - cron: '0 3 * * 1,3'   # CodeQL Scan every Monday and Wednesday at 3 AM UTC
+  # # Below is for manual scanning
+  # workflow_dispatch:
+jobs:
+  TruffleHog:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: TruffleHog OSS
+        uses: trufflesecurity/trufflehog@main
+        with:
+          path: ./
+          base: ${{ github.event.repository.default_branch }}
+          head: HEAD
+          extra_args: --debug --only-verified

.github/workflows/trivy-repo-scan.yml

@@ -0,0 +1,129 @@
+name: Trivy Security Scan on HAPI FHIR repository
+on:
+  push:
+    branches:
+      - security-scans-integrations
+  # pull_request:    
+  schedule:
+    - cron: '0 3 * * 1,3'   # CodeQL Scan every Monday and Wednesday at 3 AM UTC
+  # Below is for manual scanning
+  workflow_dispatch:
+
+env:
+  FULL_SUMMARY: ""
+  PATCH_SUMMARY: ""
+
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Cancel previous workflow runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }} 
+
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Run Trivy vulnerability scanner in repo mode - SARIF
+        uses: aquasecurity/trivy-action@master
+        with:
+          scan-type: 'fs'
+          ignore-unfixed: true
+          format: 'sarif'
+          output: 'trivy-repo-results.sarif'          
+
+      - name: Upload Trivy scan results to GitHub Security tab
+        uses: github/codeql-action/upload-sarif@v2
+        with:
+          sarif_file: 'trivy-repo-results.sarif'
+
+      - name: Run Trivy vulnerability scanner in repo mode - JSON (Full)
+        uses: aquasecurity/trivy-action@master
+        with:
+          scan-type: 'fs'
+          format: 'json'
+          output: 'trivy-repo-full-results.json'
+
+      - name: Create summary of trivy issues on Repository Full scan
+        run: |
+          summary=$(jq -r '.Results[] | select(.Vulnerabilities) | .Vulnerabilities | group_by(.Severity) | map({Severity: .[0].Severity, Count: length}) | .[] | [.Severity, .Count] | join(": ")' trivy-repo-full-results.json | awk 'NR > 1 { printf(" | ") } {printf "%s",$0}')
+          if [ -z $summary ]
+          then
+            summary="No vulnerabilities found"
+          fi
+          echo "FULL_SUMMARY=$summary" >> $GITHUB_ENV
+
+      - name: Run Trivy vulnerability scanner in repo mode - JSON (with Patches)
+        uses: aquasecurity/trivy-action@master
+        with:
+          scan-type: 'fs'
+          ignore-unfixed: true
+          format: 'json'
+          output: 'trivy-repo-fixable-results.json'
+
+      - name: Create summary of trivy issues on Repository scan
+        run: |
+          summary=$(jq -r '.Results[] | select(.Vulnerabilities) | .Vulnerabilities | group_by(.Severity) | map({Severity: .[0].Severity, Count: length}) | .[] | [.Severity, .Count] | join(": ")' trivy-repo-fixable-results.json | awk 'NR > 1 { printf(" | ") } {printf "%s",$0}')
+          if [ -z $summary ]
+          then
+            summary="No issues or vulnerability fixes available"
+          fi
+          echo "PATCH_SUMMARY=$summary" >> $GITHUB_ENV
+
+      - name: Generate trivy HTML report on Repository for download
+        uses: aquasecurity/trivy-action@master
+        with:
+          scan-type: 'fs'
+          format: 'template'
+          template: '@/contrib/html.tpl'
+          output: 'trivy-repo-report.html'
+
+      - name: Upload Trivy results as an artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: "trivy-repo-report.html"
+          path: './trivy-repo-report.html'
+          retention-days: 30
+
+      - name: Send Slack Notification
+        uses: slackapi/[email protected]
+        with:
+          payload: |
+            {
+              "text": "Trivy scan results for ${{ github.repository }} repository",
+              "blocks": [
+                {
+                  "type": "section",
+                  "text": {
+                    "type": "mrkdwn",
+                    "text": "TRIVY REPO SCAN RESULTS FOR ${{ github.repository }} REPOSITORY"
+                  }
+                },
+                {
+                  "type": "section",
+                  "text": {
+                    "type": "mrkdwn",
+                    "text": "   Total Vulnerabilities: ${{ env.FULL_SUMMARY }}"
+                  }
+                },
+                {
+                  "type": "section",
+                  "text": {
+                    "type": "mrkdwn",
+                    "text": "   Vulnerabilities with fixes: ${{ env.PATCH_SUMMARY }}"
+                  }
+                },
+                {
+                  "type": "section",
+                  "text": {
+                    "type": "mrkdwn",
+                    "text": "   View HTML result artifact: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}. Artifact is only valid for 30 days."
+                  }
+                }
+              ]
+            }
+        env:
+          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
+          SLACK_WEBHOOK_TYPE: INCOMING_WEBHOOK