WIP: Read zarr agglomerate files #1021
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| name: CI Pipeline | |
| on: | |
| push: | |
| branches: | |
| - master | |
| tags: | |
| - '*' | |
| pull_request: | |
| branches: | |
| - '*' | |
| env: | |
| USER_UID: 1001 | |
| USER_GID: 1001 | |
| POSTGRES_URL: "jdbc:postgresql://localhost:5434/webknossos" | |
| POSTGRES_USER: "webknossos_user" | |
| POSTGRES_PASSWORD: "secret_password" | |
| CERTIFICATE: ${{ secrets.CERTIFICATE_FOR_CI_ONLY }} | |
| CERTIFICATE_PUBLIC_KEY: ${{ secrets.CERTIFICATE_PUBLIC_KEY }} | |
| jobs: | |
| frontend-tests: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 5 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 22 | |
| - run: corepack enable | |
| - name: Install frontend dependencies | |
| run: yarn install --immutable | |
| - name: Lint frontend code and check formatting | |
| run: yarn run check-frontend | |
| - name: Typecheck frontend code | |
| run: yarn typecheck | |
| - name: Check for cyclic dependencies in frontend | |
| run: yarn check-cyclic-dependencies | |
| - name: Run frontend tests | |
| run: yarn run vitest run --config vitest_spec.config.ts --coverage.enabled true | |
| - name: Download Coverage Artifacts | |
| # Can not use actions/download-artifact@v4 because it does not support downloading artifacts from other GA runs | |
| run: | | |
| gh_last_success_run_id=$(gh run list --workflow "CI Pipeline" --json conclusion,headBranch,databaseId --branch master --jq 'first(.[] | select(.conclusion | contains("success"))) | .databaseId') | |
| [ -z "$gh_last_success_run_id" ] && echo "No successful run found" && exit 1 || true | |
| gh run download $gh_last_success_run_id -n $ARTIFACT_NAME -D $OUTPUT_DIR | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| ARTIFACT_NAME: vitest-coverage-master | |
| OUTPUT_DIR: coverage-master | |
| - name: 'Report Coverage' | |
| uses: davelosert/vitest-coverage-report-action@v2 | |
| with: | |
| comment-on: none # alternative: pr | |
| json-summary-compare-path: coverage-master/coverage-summary.json | |
| - name: "Upload Coverage" | |
| if: github.ref == 'refs/heads/master' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: vitest-coverage-master | |
| path: coverage | |
| backend-tests: | |
| runs-on: ubuntu-22.04 | |
| if: github.ref != 'refs/heads/master' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 5 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 22 | |
| - run: corepack enable | |
| - uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '21' | |
| - uses: sbt/setup-sbt@v1 | |
| - name: Start Docker Services Postgres, Redis | |
| run: docker compose --file .github/docker-compose.yml up -d postgres redis | |
| - name: Install frontend dependencies | |
| run: yarn install --immutable | |
| - name: "Install System Dependencies" | |
| run: sudo apt-get update && sudo apt-get install -y libdraco-dev libblosc1 | |
| - name: Assert unique evolution numbers | |
| run: tools/postgres/dbtool.js assert-unique-evolution-numbers | |
| - name: Assert schema.sql and evolutions are equal | |
| run: tools/postgres/dbtool.js check-evolutions-schema | |
| - name: Assert that all migrations are mentioned in one migration guide and that they have a reversion counterpart. | |
| run: tools/assert-complete-migrations.sh | |
| - name: Lint backend code and check formatting | |
| run: sbt ";scapegoat; scalafmtCheck; util/scalafmtCheck; webknossosTracingstore/scalafmtCheck; webknossosDatastore/scalafmtCheck" | |
| - name: Run backend unit tests | |
| run: sbt -v "testOnly backend.*" | |
| - name: Start Fossildb for e2e tests | |
| run: docker compose --file .github/docker-compose.yml up -d fossildb | |
| - name: Prepare binaryData folder for e2e tests | |
| run: mkdir -p binaryData/Organization_X && chmod 777 binaryData/Organization_X | |
| - name: Run end-to-end tests | |
| uses: ./.github/actions/retry | |
| with: | |
| run: | | |
| sbt "testOnly e2e.* -- -Dtracingstore.fossildb.address=localhost -Dtracingstore.redis.address=localhost -Ddatastore.redis.address=localhost -Ddatastore.watchFileSystem.enabled=false" | |
| retries: 3 | |
| - name: Assert non-empty e2e files | |
| run: bash -c '[ $(ls -1 frontend/javascripts/test/snapshots/type-check | wc -l) -gt 0 ]' | |
| - name: Check response types of e2e tests | |
| run: yarn tsc | |
| build-smoketest-push: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 5 | |
| - uses: docker/setup-buildx-action@v3 | |
| with: | |
| driver: docker | |
| - name: Start Docker Services Postgres, Redis | |
| run: docker compose --file .github/docker-compose.yml up -d postgres redis | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: 22 | |
| - run: corepack enable | |
| - uses: actions/setup-java@v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '21' | |
| - uses: sbt/setup-sbt@v1 | |
| - name: "Install System Dependencies" | |
| run: sudo apt-get update && sudo apt-get install -y libdraco-dev libblosc1 | |
| - name: "Custom environment variables (Pull Request)" | |
| if: ${{ github.event_name == 'pull_request' }} | |
| run: | | |
| NORMALIZED_BRANCH="${GITHUB_HEAD_REF//[\/-]/_}" | |
| DOCKER_TAG="${NORMALIZED_BRANCH}__${GITHUB_RUN_ID}" | |
| echo "DOCKER_TAG=$DOCKER_TAG" | tee -a "$GITHUB_ENV" | |
| echo "NORMALIZED_BRANCH=$NORMALIZED_BRANCH" | tee -a "$GITHUB_ENV" | |
| echo "CI_BUILD_NUM=$GITHUB_RUN_ID" | tee -a "$GITHUB_ENV" | |
| - name: "Custom environment variables (Not Pull Request)" | |
| if: ${{ github.event_name != 'pull_request' }} | |
| run: | | |
| CI_BRANCH=$(git rev-parse --abbrev-ref HEAD) | |
| NORMALIZED_BRANCH=${CI_BRANCH//[\/-]/_} | |
| DOCKER_TAG="${NORMALIZED_BRANCH}__${GITHUB_RUN_ID}" | |
| echo "DOCKER_TAG=$DOCKER_TAG" | tee -a "$GITHUB_ENV" | |
| if [ "$GITHUB_REF_TYPE" == "branch" ]; then | |
| echo "NORMALIZED_BRANCH=$NORMALIZED_BRANCH" | tee -a "$GITHUB_ENV" | |
| else | |
| CI_TAG=$GITHUB_REF_NAME | |
| echo "CI_TAG=$CI_TAG" | tee -a "$GITHUB_ENV" | |
| echo "NORMALIZED_BRANCH=$CI_TAG" | tee -a "$GITHUB_ENV" | |
| fi | |
| echo "CI_BUILD_NUM=$GITHUB_RUN_ID" | tee -a "$GITHUB_ENV" | |
| - name: Prepare Dependency Folders | |
| run: mkdir -p project/target target ~/.ivy2 ~/.cache/coursier | |
| - name: Install frontend dependencies | |
| run: yarn install --immutable | |
| env: | |
| PUPPETEER_SKIP_CHROMIUM_DOWNLOAD: "true" | |
| - name: Build frontend documentation | |
| run: yarn run docs --project-version "$WK_VERSION" | |
| env: | |
| WK_VERSION: ${{ github.run_id }} | |
| - name: Build webknossos (webpack) | |
| run: yarn build | |
| - name: Build webknossos (sbt) | |
| run: sbt -DfailOnWarning compile stage | |
| - name: Build webknossos-datastore (sbt) | |
| run: sbt -DfailOnWarning "project webknossosDatastore" copyMessages compile stage | |
| - name: Build webknossos-tracingstore (sbt) | |
| run: sbt -DfailOnWarning "project webknossosTracingstore" copyMessages compile stage | |
| - name: Checksum App Dirs | |
| run: find app webknossos-datastore/app webknossos-tracingstore/app -type f -exec md5sum {} \; | sort -k 2 | md5sum > app_checksum.txt | |
| - name: Build webknossos docker image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| file: .github/Dockerfile.webknossos | |
| context: . | |
| push: false | |
| tags: | | |
| scalableminds/webknossos:${{ env.NORMALIZED_BRANCH }} | |
| scalableminds/webknossos:${{ env.DOCKER_TAG }} | |
| outputs: | | |
| type=image | |
| - name: Build webknossos-datastore docker image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| file: .github/Dockerfile.datastore | |
| context: webknossos-datastore | |
| push: false | |
| tags: | | |
| scalableminds/webknossos-datastore:${{ env.NORMALIZED_BRANCH }} | |
| scalableminds/webknossos-datastore:${{ env.DOCKER_TAG }} | |
| outputs: | | |
| type=image | |
| - name: Build webknossos-tracingstore docker image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| file: .github/Dockerfile.tracingstore | |
| context: webknossos-tracingstore | |
| push: false | |
| tags: | | |
| scalableminds/webknossos-tracingstore:${{ env.NORMALIZED_BRANCH }} | |
| scalableminds/webknossos-tracingstore:${{ env.DOCKER_TAG }} | |
| outputs: | | |
| type=image | |
| - name: Start webknossos, datastore and tracingstore for smoke test | |
| run: | | |
| set -e | |
| docker compose --file .github/docker-compose.yml up -d \ | |
| webknossos \ | |
| webknossos-datastore \ | |
| webknossos-tracingstore | |
| - name: Run webknossos smoke test | |
| uses: ./.github/actions/retry | |
| with: | |
| run: curl -v --fail-with-body "http://localhost:9000/api/health" | |
| retries: 20 | |
| retry_delay_seconds: 5 | |
| - name: Run webknossos-datastore smoke test | |
| uses: ./.github/actions/retry | |
| with: | |
| run: curl -v --fail-with-body "http://localhost:9090/data/health" | |
| retries: 20 | |
| retry_delay_seconds: 5 | |
| - name: Run webknossos-tracingstore smoke test | |
| uses: ./.github/actions/retry | |
| with: | |
| run: curl -v --fail-with-body "http://localhost:9050/tracings/health" | |
| retries: 20 | |
| retry_delay_seconds: 5 | |
| - name: Stop webknossos, datastore and tracingstore | |
| run: docker compose --file .github/docker-compose.yml down --volumes --remove-orphans | |
| - uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_USER }} | |
| password: ${{ secrets.DOCKER_PASS }} | |
| - name: Push webknossos image | |
| if: ${{ ! startsWith(github.ref, 'refs/tags/') }} | |
| uses: ./.github/actions/retry | |
| with: | |
| run: docker push "scalableminds/webknossos:${{ env.DOCKER_TAG }}" | |
| retries: 5 | |
| retry_delay_seconds: 10 | |
| - name: Push normalized webknossos image | |
| uses: ./.github/actions/retry | |
| with: | |
| run: docker push "scalableminds/webknossos:${{ env.NORMALIZED_BRANCH }}" | |
| retries: 5 | |
| retry_delay_seconds: 10 | |
| - name: Push webknossos-datastore image | |
| if: ${{ ! startsWith(github.ref, 'refs/tags/') }} | |
| uses: ./.github/actions/retry | |
| with: | |
| run: docker push "scalableminds/webknossos-datastore:${{ env.DOCKER_TAG }}" | |
| retries: 5 | |
| retry_delay_seconds: 10 | |
| - name: Push normalized webknossos-datastore image | |
| uses: ./.github/actions/retry | |
| with: | |
| run: docker push "scalableminds/webknossos-datastore:${{ env.NORMALIZED_BRANCH }}" | |
| retries: 5 | |
| retry_delay_seconds: 10 | |
| - name: Push webknossos-tracingstore image | |
| if: ${{ ! startsWith(github.ref, 'refs/tags/') }} | |
| uses: ./.github/actions/retry | |
| with: | |
| run: docker push "scalableminds/webknossos-tracingstore:${{ env.DOCKER_TAG }}" | |
| retries: 5 | |
| retry_delay_seconds: 10 | |
| - name: Push normalized webknossos-tracingstore image | |
| uses: ./.github/actions/retry | |
| with: | |
| run: docker push "scalableminds/webknossos-tracingstore:${{ env.NORMALIZED_BRANCH }}" | |
| retries: 5 | |
| retry_delay_seconds: 10 | |
| - name: Slack Notification | |
| if: github.ref == 'refs/heads/master' | |
| run: .github/slack-notification.sh | |
| env: | |
| SLACK_NOTIFY_TOKEN: ${{ secrets.SLACK_NOTIFY_TOKEN }} |