Merge pull request #1337 from sagely1/AG-1539-surface-uniprot-links-i… #20
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| 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 |