New scan workflow + sonar project config file to enable sonarqube scans

.github/scripts/.gitignore

@@ -0,0 +1 @@
+__pycache__/

.github/scripts/repair-scrub-sarif.py

@@ -0,0 +1,58 @@
+#!/usr/bin/env python3
+"""Temporarily repair SARIF generated by nasa-scrub 3.0.
+
+Remove this script once https://github.com/nasa/scrub/issues/118 is fixed and
+the workflow no longer pins an affected nasa-scrub version.
+"""
+
+import argparse
+import json
+from pathlib import Path
+
+
+SARIF_SCHEMA_2_1_0 = "https://json.schemastore.org/sarif-2.1.0.json"
+
+
+def repair_sarif_file(sarif_file: Path) -> bool:
+    with sarif_file.open() as file:
+        sarif = json.load(file)
+
+    changed = False
+    if sarif.get("$schema") != SARIF_SCHEMA_2_1_0:
+        sarif["$schema"] = SARIF_SCHEMA_2_1_0
+        changed = True
+
+    for run in sarif.get("runs", []):
+        tool = run.get("tool")
+        if not isinstance(tool, dict) or "rules" not in tool:
+            continue
+
+        driver = tool.setdefault("driver", {})
+        if "rules" not in driver:
+            driver["rules"] = tool["rules"]
+        elif isinstance(driver["rules"], list) and isinstance(tool["rules"], list):
+            driver["rules"].extend(tool["rules"])
+
+        del tool["rules"]
+        changed = True
+
+    if changed:
+        with sarif_file.open("w") as file:
+            json.dump(sarif, file, indent=2)
+            file.write("\n")
+
+    return changed
+
+
+def main() -> None:
+    parser = argparse.ArgumentParser(description="Repair nasa-scrub SARIF output for SonarQube import.")
+    parser.add_argument("results_dir", type=Path)
+    args = parser.parse_args()
+
+    for sarif_file in args.results_dir.glob("*_stripped.sarif"):
+        if repair_sarif_file(sarif_file):
+            print(f"Repaired {sarif_file}")
+
+
+if __name__ == "__main__":
+    main()

.github/workflows/security-scan.yml

@@ -1,73 +1,174 @@
-name: Security Scan
+# AMMOS OSS Security Scan
+# (internal) docs - https://wiki.jpl.nasa.gov/pages/viewpage.action?spaceKey=AmmosArch&title=Code+Vulnerability+Scanning+Set+Up+for+AMMOS+Open+Source+Software
+name: 'Security Scan'
 
 on:
-  pull_request:
-    branches:
-      - develop
-      - dev-[0-9]+.[0-9]+.[0-9]+
   push:
     branches:
       - develop
     tags:
-      - v*
+      - 'v*'
+  pull_request:
+    branches:
+      - develop
+      - 'dev-[0-9]+.[0-9]+.[0-9]+'
+  schedule:
+    - cron: '42 2 * * 0' # weekly cron scan
   workflow_dispatch:
 
 jobs:
   analyze:
-    name: Analyze
-    runs-on: ubuntu-latest
+    name: Analyze (${{ matrix.language }})
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
     permissions:
-      actions: read
-      contents: write
+      # required for all workflows
       security-events: write
+      # required to fetch internal or private CodeQL packs
+      packages: read
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
 
     strategy:
       fail-fast: false
       matrix:
-        language: ["java", "javascript"]
-
+        include:
+          - language: actions
+            build-mode: none
+          - language: java-kotlin
+            build-mode: autobuild
+          - language: javascript-typescript
+            build-mode: none
+          - language: python
+            build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'rust', 'swift'
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v6
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2
+        with:
+          fetch-depth: 0
+
+      # Add any setup steps before running the `github/codeql-action/init` action.
+      # This includes steps like installing compilers or runtimes (`actions/setup-node`
+      # or others). This is typically only required for manual builds.
+      # - name: Setup runtime (example)
+      #   uses: actions/setup-example@v1
+
+      # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v3
+        uses: github/codeql-action/init@9e0d7b8d25671d64c341c19c0152d693099fb5ba #4.35.5
         with:
           languages: ${{ matrix.language }}
-          queries: +security-extended
-          tools: latest
-      - name: Setup Java
-        uses: actions/setup-java@v5
-        with:
-          distribution: "temurin"
-          java-version: "21"
-      - name: Setup Gradle
-        uses: gradle/actions/setup-gradle@v5
-        with:
-          # This action defaults to matching on "main" and "master" as the branches allowed to write to the cache
-          cache-read-only: ${{ github.ref != 'refs/heads/develop' }}
-      - name: Build
+          build-mode: ${{ matrix.build-mode }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+          # queries: security-extended,security-and-quality
+
+      # If the analyze step fails for one of the languages you are analyzing with
+      # "We were unable to automatically build your code", modify the matrix above
+      # to set the build mode to "manual" for that language. Then modify this step
+      # to build your code.
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+      - name: Run manual build steps
+        if: matrix.build-mode == 'manual'
+        shell: bash
         run: |
-          ./gradlew testClasses
+          echo 'If you are using a "manual" build mode for one or more of the' \
+            'languages you are analyzing, replace this with the commands to build' \
+            'your code, for example:'
+          echo '  make bootstrap'
+          echo '  make release'
+          exit 1
+
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v3
-      - name: NASA Scrub
+        uses: github/codeql-action/analyze@9e0d7b8d25671d64c341c19c0152d693099fb5ba #4.35.5
+        with:
+          category: '/language:${{matrix.language}}'
+          output: ../results
+
+      # This step is required by AMMOS to remove malformed data from the CodeQL output
+      # It may be possible to remove in future iterations
+      - name: Post-Process Output
         run: |
-          python3 -m pip install nasa-scrub
+          python3 -m pip install nasa-scrub==3.0
 
           results_dir=`realpath ${{ github.workspace }}/../results`
           sarif_files=`find $results_dir -name '*.sarif'`
 
           for sarif_file in $sarif_files
           do
-            output_file="$results_dir/$(basename $sarif_file .sarif).scrub"
-            python3 -m scrub.tools.parsers.translate_results $sarif_file $output_file ${{ github.workspace }} scrub
+            output_file="$results_dir/$(basename $sarif_file .sarif)_stripped.sarif"
+
+            python3 -m scrub.tools.parsers.translate_results $sarif_file $output_file ${{ github.workspace }} sarifv2.1.0
           done
 
-          python3 -m scrub.tools.parsers.csv_parser $results_dir
+          # TEMPORARY WORKAROUND: remove this once nasa-scrub emits valid SARIF 2.1.0.
+          # https://github.com/nasa/scrub/issues/118
+          python3 .github/scripts/repair-scrub-sarif.py "$results_dir"
+          # END TEMPORARY WORKAROUND
 
           echo "RESULTS_DIR=$results_dir" >> $GITHUB_ENV
-      - name: Upload Security Scan Results
-        uses: actions/upload-artifact@v7
+
+      # This step makes the analysis artifacts available for download
+      # This can be helpful for debugging and archive purposes
+      - name: Upload Artifacts
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a #v7.0.1
         with:
-          name: Security Scan Results - ${{ matrix.language }}
+          name: codeql-artifacts-${{ matrix.language }}
           path: ${{ env.RESULTS_DIR }}
+
+  sonar:
+    name: Build Java & Run SonarQube Scan
+    needs: analyze
+    runs-on: ubuntu-latest
+    # PRs for forks can't use secrets, can't upload to Sonar
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
+    permissions:
+      actions: read
+      contents: read
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd #v6.0.2
+        with:
+          fetch-depth: 0
+
+      - name: Download CodeQL Artifacts
+        uses: actions/download-artifact@v4
+        with:
+          pattern: codeql-artifacts-*
+          path: codeql-results
+
+      - name: collect stripped .sarif file paths
+        shell: bash
+        run: |
+          echo "downloaded CodeQL artifact files:"
+          find "${{ github.workspace }}/codeql-results" -type f | sort
+
+          sarif_paths="$(find "${{ github.workspace }}/codeql-results" -name '*_stripped.sarif' -type f | paste -sd, -)"
+          echo "sarif paths: $sarif_paths"
+          test -n "$sarif_paths"
+          echo "SARIF_REPORT_PATHS=$sarif_paths" >> "$GITHUB_ENV"
+
+      - name: Setup Java
+        uses: actions/setup-java@v5
+        with:
+          distribution: "temurin"
+          java-version: "21"
+
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@0723195856401067f7a2779048b490ace7a47d7c # 5.0.2
+        with:
+          # This action defaults to matching on "main" and "master" as the branches allowed to write to the cache
+          cache-read-only: ${{ github.ref != 'refs/heads/develop' }}
+
+      # PlanDev Sonar scans are run with the sonarqube gradle plugin instead of the Sonar GH action
+      # this allows discovery + analysis of build artifacts via normal Gradle build process instead of complex Sonar config
+      - name: Build and run Sonar scan
+        env:
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        run: >
+          ./gradlew build sonar
+          -Dsonar.verbose=true
+          -Dsonar.gradle.scanAll=true
+          -Dsonar.sarifReportPaths="${{ env.SARIF_REPORT_PATHS }}"

build.gradle

@@ -1,5 +1,6 @@
 plugins {
   id 'com.github.ben-manes.versions' version '0.47.0'
+  id 'org.sonarqube' version '7.3.0.8198'
 }
 
 task archiveDeployment(type: Tar) {
@@ -21,6 +22,13 @@ configure(subprojects) {
     }())
 }
 
+sonar {
+  properties {
+    property "sonar.projectKey", "NASA-AMMOS_aerie"
+    property "sonar.organization", "nasa-ammos"
+  }
+}
+
 subprojects {
   apply plugin: 'com.github.ben-manes.versions'
 
@@ -42,3 +50,11 @@ subprojects {
     options.addStringOption('Xdoclint:none', '-quiet')
   }
 }
+
+// config for Sonar code scanning - see .github/workflows/security-scan.yml
+sonar {
+  properties {
+    property "sonar.projectKey", "NASA-AMMOS_aerie"
+    property "sonar.organization", "nasa-ammos"
+  }
+}

sonar-project.properties

@@ -0,0 +1,17 @@
+# Project config file for SonarQube scans (run via GH actions)
+
+sonar.projectKey=NASA-AMMOS_aerie
+sonar.organization=nasa-ammos
+
+# name and version displayed in the SonarCloud UI.
+sonar.projectName=plandev
+sonar.projectVersion=4.2.1
+
+# supported python versions
+sonar.python.version=3.7, 3.8, 3.9, 3.10, 3.11, 3.12
+
+# Path of sources to analyze relative to the sonar-project.properties file
+#sonar.sources=.
+
+# Encoding of the source code. Default is default system encoding
+#sonar.sourceEncoding=UTF-8