chore: update wmg and cellguide fixtures #22407
Workflow file for this run
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name: Push Tests | |
on: | |
pull_request: | |
branches: | |
- "*" | |
push: | |
branches: | |
- "main" | |
workflow_call: | |
env: | |
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
DEPLOYMENT_STAGE: test | |
# Force using BuildKit instead of normal Docker, required so that metadata | |
# is written/read to allow us to use layers of previous builds as cache. | |
DOCKER_BUILDKIT: 1 | |
COMPOSE_DOCKER_CLI_BUILD: 1 | |
DOCKER_REPO: ${{ secrets.ECR_REPO }}/ | |
permissions: | |
id-token: write | |
contents: read | |
jobs: | |
lint: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
runs-on: ubuntu-22.04 | |
steps: | |
- name: Configure AWS Credentials | |
uses: aws-actions/configure-aws-credentials@v4 | |
with: | |
aws-region: us-west-2 | |
role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
role-duration-seconds: 1800 | |
- name: Login to ECR | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ secrets.ECR_REPO }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 2 | |
- uses: actions/setup-python@v5 | |
- name: check backend | |
uses: pre-commit/[email protected] | |
- uses: actions/setup-node@v4 | |
with: | |
node-version-file: "frontend/.nvmrc" | |
cache: "npm" | |
cache-dependency-path: "frontend/package-lock.json" | |
- name: check frontend | |
run: | | |
cd frontend | |
npm ci | |
cp src/configs/local.js src/configs/configs.js | |
npm run lint | |
- uses: 8398a7/action-slack@v3 | |
with: | |
status: ${{ job.status }} | |
fields: repo,commit,author,eventName,workflow,job,mention | |
mention: "here" | |
env: | |
SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
backend-unit-test: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 30 | |
steps: | |
- name: Configure AWS Credentials | |
uses: aws-actions/configure-aws-credentials@v4 | |
with: | |
aws-region: us-west-2 | |
role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
role-duration-seconds: 1800 | |
- name: Login to ECR | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ secrets.ECR_REPO }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 2 | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/[email protected] | |
with: | |
files: | | |
Dockerfile* | |
**/Dockerfile | |
requirements*.txt | |
**/requirements*.txt | |
- name: Check if containers need to be rebuilt | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-rebuild-backend | |
- name: Run unit tests | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-unit-test-backend | |
- name: Upload coverage results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
retention-days: 3 | |
include-hidden-files: true | |
- name: Upload Allure results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: allure-results | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
retention-days: 20 | |
- uses: 8398a7/[email protected] | |
with: | |
status: ${{ job.status }} | |
fields: repo,commit,author,eventName,workflow,job,mention | |
mention: "here" | |
env: | |
SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
backend-wmg-unit-test: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 30 | |
steps: | |
- name: Configure AWS Credentials | |
uses: aws-actions/configure-aws-credentials@v4 | |
with: | |
aws-region: us-west-2 | |
role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
role-duration-seconds: 1800 | |
- name: Login to ECR | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ secrets.ECR_REPO }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 2 | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/[email protected] | |
with: | |
files: | | |
Dockerfile* | |
**/Dockerfile | |
requirements*.txt | |
**/requirements*.txt | |
- name: Check if containers need to be rebuilt | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-rebuild-wmg-backend | |
- name: Run unit tests | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-unit-test-wmg-backend | |
- name: Upload coverage results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
retention-days: 3 | |
include-hidden-files: true | |
- name: Upload Allure results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: allure-results | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
retention-days: 20 | |
- uses: 8398a7/[email protected] | |
with: | |
status: ${{ job.status }} | |
fields: repo,commit,author,eventName,workflow,job,mention | |
mention: "here" | |
env: | |
SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
backend-de-unit-test: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 30 | |
steps: | |
- name: Configure AWS Credentials | |
uses: aws-actions/configure-aws-credentials@v4 | |
with: | |
aws-region: us-west-2 | |
role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
role-duration-seconds: 1800 | |
- name: Login to ECR | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ secrets.ECR_REPO }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 2 | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/[email protected] | |
with: | |
files: | | |
Dockerfile* | |
**/Dockerfile | |
requirements*.txt | |
**/requirements*.txt | |
- name: Check if containers need to be rebuilt | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-rebuild-de-backend | |
- name: Run unit tests | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-unit-test-de-backend | |
- name: Upload coverage results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
retention-days: 3 | |
include-hidden-files: true | |
- name: Upload Allure results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: allure-results | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
retention-days: 20 | |
- uses: 8398a7/[email protected] | |
with: | |
status: ${{ job.status }} | |
fields: repo,commit,author,eventName,workflow,job,mention | |
mention: "here" | |
env: | |
SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
processing-unit-test: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 30 | |
steps: | |
- name: Configure AWS Credentials | |
uses: aws-actions/configure-aws-credentials@v4 | |
with: | |
aws-region: us-west-2 | |
role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
role-duration-seconds: 1800 | |
- name: Login to ECR | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ secrets.ECR_REPO }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 2 | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/[email protected] | |
with: | |
files: | | |
Dockerfile* | |
**/Dockerfile* | |
requirements*.txt | |
**/requirements*.txt | |
- name: Check if containers need to be rebuilt | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-rebuild-processing | |
- name: Run tests in docker-compose | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-unit-test-processing | |
- name: Upload coverage results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
retention-days: 3 | |
include-hidden-files: true | |
- name: Upload Allure results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: allure-results | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
retention-days: 20 | |
include-hidden-files: true | |
- uses: 8398a7/[email protected] | |
with: | |
status: ${{ job.status }} | |
fields: repo,commit,author,eventName,workflow,job,mention | |
mention: "here" | |
env: | |
SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
wmg-processing-unit-test: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 30 | |
steps: | |
- name: Configure AWS Credentials | |
uses: aws-actions/configure-aws-credentials@v4 | |
with: | |
aws-region: us-west-2 | |
role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
role-duration-seconds: 1800 | |
- name: Login to ECR | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ secrets.ECR_REPO }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 2 | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/[email protected] | |
with: | |
files: | | |
Dockerfile* | |
**/Dockerfile* | |
requirements*.txt | |
**/requirements*.txt | |
- name: Check if containers need to be rebuilt | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-rebuild-wmg-processing | |
- name: Run tests in docker-compose | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-unit-test-wmg-processing | |
- name: Upload coverage results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
retention-days: 3 | |
include-hidden-files: true | |
- name: Upload Allure results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: allure-results | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
retention-days: 20 | |
- uses: 8398a7/[email protected] | |
with: | |
status: ${{ job.status }} | |
fields: repo,commit,author,eventName,workflow,job,mention | |
mention: "here" | |
env: | |
SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
cellguide-pipeline-unit-test: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 30 | |
steps: | |
- name: Configure AWS Credentials | |
uses: aws-actions/configure-aws-credentials@v4 | |
with: | |
aws-region: us-west-2 | |
role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
role-duration-seconds: 1800 | |
- name: Login to ECR | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ secrets.ECR_REPO }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 2 | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/[email protected] | |
with: | |
files: | | |
Dockerfile* | |
**/Dockerfile* | |
requirements*.txt | |
**/requirements*.txt | |
- name: Check if containers need to be rebuilt | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-rebuild-cellguide-pipeline | |
- name: Run tests in docker-compose | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-unit-test-cellguide-pipeline | |
- name: Upload coverage results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
retention-days: 3 | |
include-hidden-files: true | |
- name: Upload Allure results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: allure-results | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
retention-days: 20 | |
- uses: 8398a7/[email protected] | |
with: | |
status: ${{ job.status }} | |
fields: repo,commit,author,eventName,workflow,job,mention | |
mention: "here" | |
env: | |
SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
cxg-admin-unit-test: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 30 | |
steps: | |
- name: Configure AWS Credentials | |
uses: aws-actions/configure-aws-credentials@v4 | |
with: | |
aws-region: us-west-2 | |
role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
role-duration-seconds: 1800 | |
- name: Login to ECR | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ secrets.ECR_REPO }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 2 | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/[email protected] | |
with: | |
files: | | |
Dockerfile* | |
**/Dockerfile | |
requirements*.txt | |
**/requirements*.txt | |
- name: Check if containers need to be rebuilt | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-rebuild-backend | |
- name: Run unit tests | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-unit-test-cxg-admin | |
- name: Upload coverage results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
retention-days: 3 | |
include-hidden-files: true | |
- name: Upload Allure results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: allure-results | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
retention-days: 20 | |
- uses: 8398a7/[email protected] | |
with: | |
status: ${{ job.status }} | |
fields: repo,commit,author,eventName,workflow,job,mention | |
mention: "here" | |
env: | |
SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
backend-integration-test: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
runs-on: ubuntu-22.04 | |
timeout-minutes: 30 | |
steps: | |
- name: Configure AWS Credentials | |
uses: aws-actions/configure-aws-credentials@v4 | |
with: | |
aws-region: us-west-2 | |
role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
role-duration-seconds: 1800 | |
- name: Login to ECR | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ secrets.ECR_REPO }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 2 | |
- name: Get changed files | |
id: changed-files | |
uses: tj-actions/[email protected] | |
with: | |
files: | | |
Dockerfile* | |
**/Dockerfile | |
requirements*.txt | |
**/requirements*.txt | |
- name: Check if containers need to be rebuilt | |
if: steps.changed-files.outputs.any_changed == 'true' | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-rebuild-backend | |
- name: Run tests against postgres instance | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make local-integration-test-backend | |
- name: Upload coverage results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: coverage | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/.coverage* | |
retention-days: 3 | |
include-hidden-files: true | |
- name: Upload Allure results as an artifact | |
uses: actions/upload-artifact@v3 | |
with: | |
name: allure-results | |
path: /home/runner/work/single-cell-data-portal/single-cell-data-portal/allure-results | |
retention-days: 20 | |
- uses: 8398a7/[email protected] | |
with: | |
status: ${{ job.status }} | |
fields: repo,commit,author,eventName,workflow,job,mention | |
mention: "here" | |
env: | |
SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK }} | |
if: failure() && (github.ref == 'refs/heads/main' || github.ref == 'refs/heads/staging' || github.ref == 'refs/heads/prod') | |
submit-codecoverage: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
needs: | |
- backend-unit-test | |
- backend-integration-test | |
- backend-wmg-unit-test | |
- wmg-processing-unit-test | |
- processing-unit-test | |
- cellguide-pipeline-unit-test | |
runs-on: ubuntu-22.04 | |
steps: | |
- name: Configure AWS Credentials | |
uses: aws-actions/configure-aws-credentials@v4 | |
with: | |
aws-region: us-west-2 | |
role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }} | |
role-duration-seconds: 1800 | |
- name: Login to ECR | |
uses: docker/login-action@v3 | |
with: | |
registry: ${{ secrets.ECR_REPO }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 2 | |
- uses: actions/download-artifact@v3 | |
with: | |
name: coverage | |
path: . | |
- name: coverage report | |
run: | | |
echo "DOCKER_REPO=${DOCKER_REPO}" > .env.ecr | |
make coverage/report-xml | |
- name: Upload coverage to Codecov | |
uses: codecov/codecov-action@v3 | |
with: | |
token: ${{ secrets.CODECOV_TOKEN }} | |
env_vars: OS,PYTHON | |
files: ./coverage.xml | |
flags: unittests | |
name: codecov-umbrella | |
publish-test-report: | |
if: ${{ ! startsWith(github.head_ref, 'renovate/') }} | |
needs: | |
- backend-unit-test | |
- backend-wmg-unit-test | |
- backend-integration-test | |
- wmg-processing-unit-test | |
- processing-unit-test | |
- cellguide-pipeline-unit-test | |
runs-on: ubuntu-22.04 | |
permissions: | |
contents: write | |
steps: | |
- uses: actions/download-artifact@v3 | |
with: | |
name: allure-results | |
path: allure-results | |
# Checkout gh-pages branch and get Allure result history | |
- name: Get Allure history | |
uses: actions/checkout@v3 | |
if: always() | |
continue-on-error: true | |
with: | |
ref: gh-pages | |
path: gh-pages | |
fetch-depth: 2 | |
# Create test results history as an Allure report | |
- name: Create test results history as an Allure report | |
uses: simple-elf/allure-report-action@master | |
if: always() | |
id: allure-report | |
with: | |
allure_results: allure-results | |
gh_pages: gh-pages | |
allure_report: allure-report | |
allure_history: allure-history | |
# Deploy Allure report to github pages | |
- name: Deploy report to Github Pages | |
if: always() | |
uses: peaceiris/actions-gh-pages@v3 | |
with: | |
github_token: ${{ secrets.GITHUB_TOKEN }} | |
publish_branch: gh-pages | |
publish_dir: allure-history | |
# Output the link to the github page for this current run | |
- name: Post the link to the report in summary | |
run: "echo 'Test Results Dashboard (Run #${{ github.run_number }}): https://chanzuckerberg.github.io/single-cell-data-portal/${{ github.run_number }}' >> $GITHUB_STEP_SUMMARY" |