Add spatial #1959
Workflow file for this run
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: Validate pull request | |
| on: | |
| pull_request: | |
| types: [opened, reopened, edited] | |
| jobs: | |
| # BEWARE: GitHub uses Microsoft-style line endings (CRLF) | |
| # instead of Unix-style (LF) interally for things like PR text. | |
| # | |
| # You MUST check for `\r\n` as the line separator instead of `\n` | |
| # in this workflow. | |
| lint-pr-body: | |
| name: Lint pull request body | |
| runs-on: ubuntu-20.04 | |
| concurrency: | |
| group: ${{ github.head_ref }} | |
| cancel-in-progress: true | |
| outputs: | |
| is-staging-na: ${{ steps.extract-staging.outputs.is-staging-na }} | |
| sandbox: ${{ steps.extract-staging.outputs.sandbox }} | |
| is-e2e-box-checked: ${{ steps.check-e2e-checkbox.outcome }} | |
| steps: | |
| - id: install | |
| name: Install requirements | |
| run: |- | |
| sudo apt-get update -y | |
| sudo apt-get install -y pcregrep | |
| - id: extract-staging | |
| name: Check staging URL | |
| run: |- | |
| REGEX="#### Link to staging deployment URL \(or set N\/A\)\s?\r\n(https:\/\/ui-(.+)\.scp-staging\.biomage\.net|https:\/\/ui-(.+)\.staging\.single-cell-platform\.net|N\/A)" | |
| echo "REGEX to test against:" | |
| echo $REGEX | |
| echo "Now looking at regex result:" | |
| URL=$(pcregrep -o1 -M "$REGEX" <<\EOF | |
| ${{ github.event.pull_request.body }} | |
| EOF | |
| ) | |
| IS_STAGING_NA='false' | |
| if [ $URL = 'N/A' ]; then | |
| IS_STAGING_NA='true' | |
| fi | |
| echo "Is staging N/A?" | |
| echo $IS_STAGING_NA | |
| echo "is-staging-na=$IS_STAGING_NA" >> $GITHUB_OUTPUT | |
| echo "Full URL:" | |
| echo $URL | |
| echo "url=$URL" >> $GITHUB_OUTPUT | |
| SANDBOX=$(pcregrep -o2 -M "$REGEX" <<\EOF | |
| ${{ github.event.pull_request.body }} | |
| EOF | |
| ) | |
| echo "Extracted sandbox:" | |
| echo $SANDBOX | |
| echo "sandbox=$SANDBOX" >> $GITHUB_OUTPUT | |
| - id: reach-staging | |
| if: steps.extract-staging.outputs.url != 'N/A' | |
| name: Attempt to reach staging environments | |
| uses: nick-invision/retry@v2 | |
| with: | |
| timeout_seconds: 30 | |
| max_attempts: 5 | |
| retry_on: error | |
| command: curl -f ${{ steps.extract-staging.outputs.url }} | |
| # Add jitter to break up correlated events. | |
| on_retry_command: sleep $[($RANDOM % 10) + 5]s | |
| - id: check-e2e-checkbox | |
| name: Check if E2E testing is checked | |
| continue-on-error: true | |
| run: |- | |
| REGEX="\[[Xx]\] Started end-to-end tests on the latest commit\." | |
| pcregrep -o1 -M "$REGEX" <<\EOF | |
| ${{ github.event.pull_request.body }} | |
| EOF | |
| run-integration-tests: | |
| name: Run integration tests | |
| runs-on: ubuntu-20.04 | |
| needs: lint-pr-body | |
| concurrency: | |
| group: ${{ github.sha }} | |
| steps: | |
| - id: check-e2e-run | |
| name: Check if E2E should run | |
| run: |- | |
| SHOULD_RUN_E2E='true' | |
| SHOULD_CANCEL_E2E='false' | |
| echo "Should E2E cancel?" | |
| if [ "${{ needs.lint-pr-body.outputs.is-staging-na}}" = "false" ] && [ "${{ needs.lint-pr-body.outputs.is-e2e-box-checked }}" != "success" ]; then | |
| SHOULD_CANCEL_E2E='true' | |
| fi | |
| echo $SHOULD_CANCEL_E2E | |
| echo "Should E2E be run?" | |
| if [ "${{ needs.lint-pr-body.outputs.is-staging-na}}" = 'true' ]; then | |
| SHOULD_RUN_E2E='false' | |
| fi | |
| echo $SHOULD_RUN_E2E | |
| echo "should-e2e-cancel=$SHOULD_CANCEL_E2E" >> $GITHUB_OUTPUT | |
| echo "should-e2e-run=$SHOULD_RUN_E2E" >> $GITHUB_OUTPUT | |
| - id: cancel | |
| name: Cancel if staging is not N/A and box is not checked | |
| if: steps.check-e2e-run.outputs.should-e2e-cancel == 'true' | |
| uses: andymckay/[email protected] | |
| - id: install | |
| if: steps.check-e2e-run.outputs.should-e2e-run == 'true' | |
| name: Install requirements | |
| run: |- | |
| sudo apt-get update -y | |
| sudo apt-get install -y pcregrep | |
| - id: extract-commit-details | |
| if: steps.check-e2e-run.outputs.should-e2e-run == 'true' | |
| name: Get details of last commit | |
| run: |- | |
| echo "SHA of latest GitHub branch commit:" | |
| echo ${{ github.event.pull_request.head.sha }} | |
| echo "github_sha=${{ github.event.pull_request.head.sha }}" >> $GITHUB_OUTPUT | |
| REPO_NAME=$(echo $GITHUB_REPOSITORY | awk -F '/' '{print $2}') | |
| echo "Repo name:" | |
| echo $REPO_NAME | |
| echo "repo_name=$REPO_NAME" >> $GITHUB_OUTPUT | |
| - id: extract-integration-test-ref | |
| if: steps.check-e2e-run.outputs.should-e2e-run == 'true' | |
| name: Get integration test ref | |
| run: |- | |
| REGEX="#### Integration test branch\s?\r\n(.+)\s?\r\n" | |
| echo "REGEX to test against:" | |
| echo $REGEX | |
| echo "Now looking at regex result:" | |
| INTEGRATION_TEST_REF=$(pcregrep -o1 -M "$REGEX" <<\EOF | |
| ${{ github.event.pull_request.body }} | |
| EOF | |
| ) | |
| echo "Ref given is $INTEGRATION_TEST_REF, setting it as is." | |
| echo "ref=$INTEGRATION_TEST_REF" >> $GITHUB_OUTPUT | |
| - id: run-integration-test | |
| if: steps.check-e2e-run.outputs.should-e2e-run == 'true' | |
| name: Run integration tests | |
| uses: aurelien-baudet/workflow-dispatch@v2 | |
| with: | |
| workflow: Run end-to-end tests | |
| repo: ${{ github.repository_owner }}/testing | |
| token: ${{ secrets.API_TOKEN_GITHUB }} | |
| ref: ${{ steps.extract-integration-test-ref.outputs.ref }} | |
| inputs: '{ "environment": "staging", "ref": "${{ steps.extract-integration-test-ref.outputs.ref }}", "sandboxId": "${{needs.lint-pr-body.outputs.sandbox}}", "image_sha" : "${{ steps.extract-commit-details.outputs.github_sha }}", "namespace": "${{steps.extract-commit-details.outputs.repo_name}}-${{needs.lint-pr-body.outputs.sandbox}}" }' | |
| - id: get-pr-body | |
| if: failure() | |
| name: Get the current PR body | |
| uses: jwalton/gh-find-current-pr@v1 | |
| with: | |
| state: open | |
| - id: create-unchecked-pr-body | |
| if: failure() | |
| name: Create unchecked PR body | |
| run: |- | |
| UNCHECKED_BODY=$(sed 's/- \[[Xx]\] Started end-to-end tests on the latest commit\./- \[ \] Started end-to-end tests on the latest commit\./' <<\EOF | |
| ${{ steps.get-pr-body.outputs.body }} | |
| EOF | |
| ) | |
| echo "Unchecked PR body" | |
| echo $UNCHECKED_BODY | |
| # This sets multiline strings into the output variable | |
| # See https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#example-of-a-multiline-string | |
| echo "body<<EOF" >> "$GITHUB_OUTPUT" | |
| echo "$UNCHECKED_BODY" >> "$GITHUB_OUTPUT" | |
| echo "EOF" >> "$GITHUB_OUTPUT" | |
| - id: uncheck-integration-checkbox | |
| if: failure() | |
| name: Uncheck the integration checkbox | |
| uses: tzkhan/pr-update-action@v2 | |
| with: | |
| repo-token: ${{ secrets.API_TOKEN_GITHUB }} | |
| head-branch-regex: ${{ github.head_ref }} | |
| lowercase-branch: false | |
| body-template: ${{ steps.create-unchecked-pr-body.outputs.body }} | |
| body-update-action: replace |