Merge branch 'main' into main

.github/workflows/codeql.yml

@@ -0,0 +1,93 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+  schedule:
+    - cron: '27 1 * * 0'
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    # Runner size impacts CodeQL analysis time. To learn more, please see:
+    #   - https://gh.io/recommended-hardware-resources-for-running-codeql
+    #   - https://gh.io/supported-runners-and-hardware-resources
+    #   - https://gh.io/using-larger-runners (GitHub.com only)
+    # Consider using larger runners or machines with greater resources for possible analysis time improvements.
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      # 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:
+        include:
+        - language: javascript-typescript
+          build-mode: none
+        # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
+        # Use `c-cpp` to analyze code written in C, C++ or both
+        # Use 'java-kotlin' to analyze code written in Java, Kotlin or both
+        # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
+        # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
+        # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
+        # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
+        # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+    # If the analyze step fails for one of the languages you are analyzing with
+    # "We were unable to automatically build your code", modify the matrix above
+    # to set the build mode to "manual" for that language. Then modify this step
+    # to build your code.
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+    - if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        exit 1
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/snyk-zap.yml

@@ -0,0 +1,160 @@
+# Define the name of the workflow
+name: snyk-zap
+
+# Define when the workflow should be triggered (on push to a specific branch and pull requests to the master branch)
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+# Define the jobs that will be executed as part of the workflow 
+jobs:
+  # Job to build and push the ZAP Docker image to Docker Hub
+  Snyk-Docker-Image:
+    runs-on:
+      group: ncats-onprem-internal-runners
+
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+      issues: write
+
+    outputs:
+      build_version: ${{ steps.get_build_version.outputs.build_version }}
+
+    steps:
+      # Step 1: Checkout repository
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      # Step 2: Generate Build Version Number
+      - name: Generate Build Version Number
+        id: GET_BUILD_VERSION
+        run: |
+          # Get the last recorded date from the environment variable
+          LAST_DATE=$(date -d "$LAST_BUILD_DATE" +'%Y-%m-%d' 2>/dev/null || echo "")
+      
+          # Get the current date
+          CURRENT_DATE=$(date +'%Y-%m-%d')
+          echo "Last recorded date: $LAST_DATE"
+          echo "Current date: $CURRENT_DATE"
+
+          # Check if it's a new day
+          if [ "$LAST_DATE" != "$CURRENT_DATE" ]; then
+            # Reset BUILDS_TODAY to 0 for the new day
+            BUILDS_TODAY=0
+            echo "Resetting BUILDS_TODAY to 0 for the new day"
+          else
+            # Calculate the number of builds today
+            BUILDS_TODAY=$(seq -f v$GITHUB_RUN_NUMBER.%g $(($GITHUB_RUN_NUMBER - 1)) | wc -l)
+            echo "Incrementing BUILDS_TODAY"
+          fi
+
+          # Store the current date for the next run
+          echo "LAST_BUILD_DATE=$CURRENT_DATE" >> $GITHUB_ENV
+
+          # Generate the build version with the number of builds today
+          BUILD_VERSION_GENERATED=$(date +v%Y.%m%d.$BUILDS_TODAY)
+          echo "Generated Build Version: $BUILD_VERSION_GENERATED"
+          echo "BUILD_VERSION=$BUILD_VERSION_GENERATED" >> $GITHUB_ENV
+          echo "BUILD=true" >> $GITHUB_ENV
+          echo "::set-output name=build_version::$BUILD_VERSION_GENERATED"
+
+      # Step 3: Login to Dockerhub
+      - name: Login to Dockerhub
+        run: docker login -u "${{ secrets.DKRHUB_NCATSSVCDVOPS_USERNAME }}" -p "${{ secrets.DKRHUB_NCATSSVCDVOPS_TOKEN_WRITE }}"
+
+      # # Step 4: Build a Docker image
+      - name: Build a Docker image
+        run: docker build --no-cache -f ./Dockerfile --build-arg BUILD_VERSION=${BUILD_VERSION} -t ncats/pharos-community-data-api:$BUILD_VERSION .
+
+
+      #  # Step 5: Run Snyk to check Docker image for vulnerabilities
+      - name: Run Snyk to check Docker image for vulnerabilities 
+        continue-on-error: true
+        uses: snyk/actions/docker@master
+        id: docker-image-odp-api-python-scan
+        env:
+          SNYK_TOKEN: ${{ secrets.SNYK_CLI }}
+        with:
+          image: ncats/odp-python-api:$BUILD_VERSION
+          args: "--sarif-file-output=snyk.sarif --file=Dockerfile"
+
+      - name: Replace security-severity undefined for license-related findings 
+        run: |
+         sed -i 's/"security-severity": "undefined"/"security-severity": "0"/g' snyk.sarif
+         sed -i 's/"security-severity": "null"/"security-severity": "0"/g' snyk.sarif
+
+      # Step 6: Upload result to GitHub Code Scanning 
+      - name: Upload result to GitHub Code Scanning
+        continue-on-error: true
+        uses: github/codeql-action/upload-sarif@v3
+        with:
+          sarif_file: snyk.sarif
+          category: snyk
+
+      # Step 7: Generate Security Report
+      - name: Generate Security Report
+        uses: rsdmike/[email protected]
+        with:
+            token: ${{ secrets.GITHUB_TOKEN }}
+
+      # Step 8: Uploads artifacts (PDF reports) generated during the workflow to download.
+      - name: Upload Artifacts
+        uses: actions/upload-artifact@v4
+        with: 
+            name: reports
+            path: ./*.pdf
+
+  ZAP-Docker-Scan:
+    needs: Snyk-Docker-Image
+    runs-on:
+      group: ncats-onprem-internal-runners
+
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+      issues: write
+
+    steps:
+      # Step 1: Get BUILD_VERSION from Snyk-Docker-Image job
+      - name: Get BUILD_VERSION from Snyk-Docker-Image job
+        id: get_runner_ip
+        run: |
+          echo "BUILD_VERSION=${{ needs.Snyk-Docker-Image.outputs.build_version }}" >> $GITHUB_ENV
+          echo "::set-output name=runner_ip::$(hostname -I | cut -d' ' -f1)"
+
+      # Step 2: Add the command to start Docker image on port 8080
+      - name: Start Docker image on port 8080
+        continue-on-error: true
+        run: docker run -d -p 8080:8080 ncats/odp-python-api:${{ needs.Snyk-Docker-Image.outputs.build_version }}
+
+      # Step 3: ZAP BASELINE SCAN
+      - name: ZAP base Scan
+        continue-on-error: true
+        uses: zaproxy/[email protected]
+        with:
+          target: 'http://${{ steps.get_runner_ip.outputs.runner_ip }}:8080'
+          docker_name: 'ghcr.io/zaproxy/zaproxy:stable'
+          token: ${{ secrets.GITHUB_TOKEN }}
+          fail_action: false
+
+      # Step 4: Stop and remove the Docker container
+      - name: Stop and remove Docker container
+        run: docker stop $(docker ps -q --filter ancestor=ncats/odp-python-api:$BUILD_VERSION) && docker rm $(docker ps -a -q --filter ancestor=ncats/pharos-community-data-api:$BUILD_VERSION) || true
+
+      # Step 5: Create SARIF file from ZAP results
+      - name: Create SARIF file from ZAP results
+        uses: SvanBoxel/zaproxy-to-ghas@main
+
+      # Step 6: Upload SARIF file to GitHub Code Scanning
+      - name: Upload SARIF file
+        uses: github/codeql-action/upload-sarif@v3
+        with:
+          sarif_file: results.sarif

package.json

@@ -38,7 +38,7 @@
     "csv-parse": "^5.3.3",
     "csv-parser": "^3.0.0",
     "express": "^4.18.2",
-    "fast-xml-parser": "^4.2.4",
+    "fast-xml-parser": "^4.2.5",
     "ts-node": "^10.9.1",
     "typescript": "^4.8.4",
     "typescript-require": "^0.3.0",