Bump body-parser and express #10
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Build and run unit tests, build data image and run e2e tests | |
| on: push | |
| jobs: | |
| build-and-run-unit-tests: | |
| timeout-minutes: 60 | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 16 | |
| cache: 'npm' | |
| - run: npm ci | |
| - run: APP_ENV=develop npm run ci:build:develop | |
| - run: npm test | |
| check-for-image: | |
| # Run in Sage repo on develop or main branches | |
| # and on all branches in user-owned forks | |
| if: ${{ github.ref_name == 'develop' || github.ref_name == 'main' || github.actor == github.repository_owner }} | |
| timeout-minutes: 5 | |
| runs-on: ubuntu-20.04 | |
| permissions: | |
| packages: read | |
| environment: e2e | |
| env: | |
| ORG_NAME: 'Sage-Bionetworks' | |
| NAMESPACE: ${{ github.repository_owner }} | |
| DATA_IMAGE_NAME: '${{ vars.DB_NAME }}-data-nonmonorepo' | |
| outputs: | |
| DATA_MANIFEST_ID: ${{ steps.get-ids-from-package-json.outputs.DATA_MANIFEST_ID }} | |
| DATA_VERSION: ${{ steps.get-ids-from-package-json.outputs.DATA_VERSION }} | |
| DATA_IMAGE_PATH: ${{ steps.get-ids-from-package-json.outputs.DATA_IMAGE_PATH }} | |
| IMAGE_EXISTS: ${{ steps.check-container-repo.outputs.IMAGE_EXISTS }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: get data image tag, data manifest id, and data version | |
| id: get-ids-from-package-json | |
| env: | |
| PACKAGE_JSON_PATH: 'package.json' | |
| run: | | |
| DATA_MANIFEST_ID=$(jq -r '."data-file"' "${{ env.PACKAGE_JSON_PATH }}") | |
| echo "DATA_MANIFEST_ID=${DATA_MANIFEST_ID}" >> "$GITHUB_OUTPUT" | |
| DATA_VERSION=$(jq -r '."data-version"' "${{ env.PACKAGE_JSON_PATH }}") | |
| echo "DATA_VERSION=${DATA_VERSION}" >> "$GITHUB_OUTPUT" | |
| DATA_IMAGE_TAG="${DATA_MANIFEST_ID}.${DATA_VERSION}" | |
| echo "DATA_IMAGE_TAG=${DATA_IMAGE_TAG}" >> "$GITHUB_OUTPUT" | |
| # GHCR requires image names to be lowercase: https://github.com/orgs/community/discussions/27086 | |
| NAMESPACE_LOWERCASE=$(echo "${{ env.NAMESPACE }}" | tr '[:upper:]' '[:lower:]') | |
| DATA_IMAGE_PATH="ghcr.io/${NAMESPACE_LOWERCASE}/${{ env.DATA_IMAGE_NAME }}:${DATA_IMAGE_TAG}" | |
| echo "DATA_IMAGE_PATH=${DATA_IMAGE_PATH}" >> "$GITHUB_OUTPUT" | |
| - name: login to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: check whether image exists | |
| id: check-container-repo | |
| env: | |
| # https://docs.github.com/en/rest/packages/packages?apiVersion=2022-11-28#list-package-versions-for-a-package-owned-by-an-organization | |
| ORG_PATH: '/orgs/${{ env.ORG_NAME }}/packages/container/${{ env.DATA_IMAGE_NAME }}/versions' | |
| # https://docs.github.com/en/rest/packages/packages?apiVersion=2022-11-28#list-package-versions-for-a-package-owned-by-the-authenticated-user | |
| USER_PATH: '/user/packages/container/${{ env.DATA_IMAGE_NAME }}/versions' | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| DATA_IMAGE_TAG: ${{ steps.get-ids-from-package-json.outputs.DATA_IMAGE_TAG }} | |
| run: | | |
| GH_PATH=$( [[ "${{ env.NAMESPACE }}" == "${{ env.ORG_NAME }}" ]] && echo "${{ env.ORG_PATH }}" || echo "${{ env.USER_PATH }}" ) | |
| # allow error to handle case where gh throws an error when package has not yet been created | |
| set +e | |
| IMAGE_VERSIONS=$(gh api -H "Accept: application/vnd.github+json" -H "X-GitHub-Api-Version: 2022-11-28" "${GH_PATH}") | |
| set -e | |
| PACKAGE_NOT_FOUND=$(echo "${IMAGE_VERSIONS}" | jq '.message? == "Package not found."') | |
| if [[ "${PACKAGE_NOT_FOUND}" == "true" ]]; then | |
| IMAGE_EXISTS="false" | |
| else | |
| IMAGE_EXISTS=$(echo "${IMAGE_VERSIONS}" | jq '[.[] | select(any(.metadata.container.tags[]; . == "${{ env.DATA_IMAGE_TAG }}"))] | length > 0') | |
| fi | |
| echo "IMAGE_EXISTS=${IMAGE_EXISTS}" >> "$GITHUB_OUTPUT" | |
| build-image: | |
| needs: check-for-image | |
| if: ${{ needs.check-for-image.result == 'success' && needs.check-for-image.outputs.IMAGE_EXISTS == 'false' }} | |
| timeout-minutes: 60 | |
| runs-on: ubuntu-20.04 | |
| permissions: | |
| packages: write | |
| environment: e2e | |
| env: | |
| LOCAL_DATA_PATH: './local/data' | |
| LOCAL_TEAM_IMAGES_DIR: './local/data/team_images' | |
| LOCAL_COLLECTIONS_PATH: './scripts/collections.csv' | |
| LOCAL_IMPORT_SCRIPT_PATH: './docker/import-data.sh' | |
| LOCAL_CREATE_INDEXES_PATH: './scripts/mongo-create-Indexes.js' | |
| DATA_VERSION: ${{ needs.check-for-image.outputs.DATA_VERSION }} | |
| DATA_MANIFEST_ID: ${{ needs.check-for-image.outputs.DATA_MANIFEST_ID }} | |
| DATA_IMAGE_PATH: ${{ needs.check-for-image.outputs.DATA_IMAGE_PATH }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| # https://github.com/actions/setup-python/issues/807 | |
| - name: create placeholder requirements.txt file | |
| run: touch ./requirements.txt | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.9' | |
| cache: 'pip' | |
| - name: install synapseclient | |
| run: | | |
| pip install --upgrade synapseclient | |
| - name: download data from synapse | |
| timeout-minutes: 10 | |
| env: | |
| SYNAPSE_AUTH_TOKEN: ${{ secrets.SYNAPSE_AUTH_TOKEN }} | |
| run: | | |
| echo "==> make directory for team images" | |
| mkdir -p "${{ env.LOCAL_TEAM_IMAGES_DIR }}" | |
| echo "==> download manifest file from Synapse" | |
| synapse get --downloadLocation "${{ env.LOCAL_DATA_PATH }}" -v "${{ env.DATA_VERSION }}" "${{ env.DATA_MANIFEST_ID }}" | |
| echo "==> download all files referenced in manifest from Synapse" | |
| cat "${{ env.LOCAL_DATA_PATH }}"/data_manifest.csv | tail -n +2 | while IFS=, read -r id version; do | |
| echo "===> Downloading ${id}.${version}" | |
| synapse get --downloadLocation "${{ env.LOCAL_DATA_PATH }}" -v "${version}" "${id}" | |
| done | |
| echo "==> download team images" | |
| synapse get -r --downloadLocation "${{ env.LOCAL_TEAM_IMAGES_DIR }}/" "${{ vars.TEAM_IMAGES_ID }}" | |
| - name: build image | |
| env: | |
| DOCKERFILE_PATH: './docker/Dockerfile' | |
| run: | | |
| docker build \ | |
| -t "${{ env.DATA_IMAGE_PATH }}" \ | |
| -f "${{ env.DOCKERFILE_PATH }}" \ | |
| --build-arg SOURCE_REPO="https://github.com/${{ github.repository }}" \ | |
| --build-arg DESCRIPTION="${GITHUB_SHA::7}" \ | |
| --build-arg LOCAL_DATA_PATH="${{ env.LOCAL_DATA_PATH }}" \ | |
| --build-arg LOCAL_COLLECTIONS_PATH="${{ env.LOCAL_COLLECTIONS_PATH }}" \ | |
| --build-arg LOCAL_IMPORT_SCRIPT_PATH="${{ env.LOCAL_IMPORT_SCRIPT_PATH }}" \ | |
| --build-arg LOCAL_CREATE_INDEXES_PATH="${{ env.LOCAL_CREATE_INDEXES_PATH }}" \ | |
| . | |
| - name: login to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| # Note: if a new package is created using this workflow, then the package | |
| # visibility will default to the source repository visibility. For example, | |
| # a package created by a workflow in a public repo will also be public. | |
| # Publicly visible container packages are anonymously downloadable. | |
| - name: push to GitHub Container Registry | |
| run: docker push "${{ env.DATA_IMAGE_PATH }}" | |
| run-e2e-tests: | |
| needs: | |
| - check-for-image | |
| - build-image | |
| # always() prevents skipping this job when build-image was skipped | |
| # see https://github.com/actions/runner/issues/491 | |
| if: ${{ always() && needs.check-for-image.result == 'success' && (needs.build-image.result == 'success' || needs.build-image.result == 'skipped')}} | |
| timeout-minutes: 60 | |
| runs-on: ubuntu-20.04 | |
| permissions: | |
| packages: read | |
| environment: e2e | |
| env: | |
| CI: true | |
| DOCKER_COMPOSE_PATH: './docker/docker-compose.yml' | |
| DATA_IMAGE_PATH: ${{ needs.check-for-image.outputs.DATA_IMAGE_PATH }} | |
| DB_USER: ${{ secrets.DB_USER }} | |
| DB_PASS: ${{ secrets.DB_PASS }} | |
| DB_PORT: ${{ vars.DB_PORT }} | |
| DB_NAME: ${{ vars.DB_NAME }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 16 | |
| cache: 'npm' | |
| - name: install dependencies | |
| run: npm ci | |
| - name: install Playwright Browsers | |
| run: npx playwright install --with-deps | |
| - name: login to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: start database, server, and app | |
| run: | | |
| echo "==> start database and data containers" | |
| docker-compose -f "${{ env.DOCKER_COMPOSE_PATH }}" up -d | |
| echo "==> wait for data container to finish seeding database container" | |
| DATA_CONTAINER=$(docker compose -f "${{ env.DOCKER_COMPOSE_PATH }}" ps -a --format '{{.Name}}' mongo-seed) | |
| docker wait "${DATA_CONTAINER}" | |
| echo "==> start server and app in background and wait for server to grab port" | |
| MONGODB_HOST="localhost" MONGODB_PORT="${{ env.DB_PORT }}" APP_ENV="e2e" npm run dev >/dev/null 2>&1 & | |
| sleep 5 | |
| - name: run e2e tests | |
| run: npx playwright test | |
| - name: clean up database, server, and app | |
| run: | | |
| echo "==> stop app" | |
| pid=$(lsof -i :3000 -t) && kill ${pid} | |
| echo "==> stop server" | |
| pid=$(lsof -i :8080 -t) && kill ${pid} | |
| echo "==> stop database" | |
| docker-compose -f "${{ env.DOCKER_COMPOSE_PATH }}" down | |
| - uses: actions/upload-artifact@v4 | |
| if: ${{ !cancelled() }} | |
| with: | |
| name: playwright-report | |
| path: playwright-report/ | |
| retention-days: 5 |