Hotfix ncrna annotation track color #1361
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| name: Testing | |
| on: [ push, pull_request ] | |
| env: | |
| EMG_CONFIG: ${{ github.workspace }}/client-repo/ci/config.yaml | |
| API_URL: http://localhost:9000/metagenomics/api/v1/ | |
| SEARCH_URL: https://www.ebi.ac.uk/ebisearch/ws/rest/metagenomics_ | |
| DEPLOYMENT_SUBFOLDER: /metagenomics | |
| BASE_URL: http://localhost:9000/metagenomics/ | |
| INTERPRO_URL: http://www.ebi.ac.uk/interpro/ | |
| SEQUENCE_SEARCH_URL: https://wwwdev.ebi.ac.uk/metagenomics/sequence-search/search/phmmer | |
| ENA_URL: https://www.ebi.ac.uk/ena/browser/view/ | |
| CYPRESS_WEBIN_USERNAME: Webin-000 | |
| CYPRESS_WEBIN_PASSWORD: secret | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| services: | |
| mongo: | |
| image: mongo:4.0.6 | |
| ports: | |
| - 27017:27017 | |
| options: --health-cmd="mongo" --health-interval=10s --health-timeout=5s --health-retries=5 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| path: client-repo | |
| - name: 🐍 - Set up Python 3.9 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.9 | |
| - name: 🔧🔬 - Install EMG API | |
| run: | | |
| pip install --user --upgrade pip setuptools | |
| python -V | |
| pip -V | |
| pip install "git+https://github.com/EBI-metagenomics/emgapi@develop#egg=emgcli" | |
| ls -l | |
| - name: Set up db files for API | |
| working-directory: client-repo | |
| run: | | |
| sed -i s#{GITHUB_WORKSPACE}#$GITHUB_WORKSPACE#g ci/config.yaml | |
| cat ci/config.yaml | |
| - name: 🪜 - Setting up Fixtures | |
| working-directory: client-repo | |
| run: | | |
| wget https://fastdl.mongodb.org/tools/db/mongodb-database-tools-ubuntu2204-x86_64-100.6.1.deb | |
| sudo apt install ./mongodb-database-tools-ubuntu2204-x86_64-100.6.1.deb | |
| mongorestore --gzip --archive < ci/testdbs/emg-testdb.mongoarchive | |
| emgcli migrate | |
| mv ci/emg_api_datafiles/results $GITHUB_WORKSPACE/results | |
| - name: ⚙️ - Settings | |
| working-directory: client-repo | |
| env: # Or as an environment variable | |
| MAPS_KEY: ${{ secrets.GOOGLE_MAPS_DEV_KEY }} | |
| run: | | |
| echo "{\"googleMapsKey\": \"$MAPS_KEY\", \"api\": \"$API_URL\"}" > "$(pwd)/config.private.json" | |
| - uses: actions/checkout@v3 | |
| name: 🔬 - Checkout EMG API | |
| with: | |
| repository: 'EBI-Metagenomics/emgapi' | |
| ref: 'develop' | |
| path: emgapi | |
| - name: 🔬 - Start EMG API | |
| run: | | |
| export PYTHONPATH="$PYTHONPATH:${{ github.workspace }}/emgapi/tests/" | |
| echo $PYTHONPATH | |
| emgcli collectstatic --noinput | |
| emgcli check --deploy | |
| cd emgapi | |
| export GUNICORN_CMD_ARGS="--bind 127.0.0.1:8000 --workers=1 --daemon -p emg.pid --error-logfile error.log --access-logfile access.log" | |
| emgdeploy emgcli.wsgi:application | |
| ps aux | grep emgdeploy | |
| cd .. | |
| echo "\ngunicorn v1/" | |
| curl --silent http://localhost:8000/v1/ | |
| - name: 🌎 - Setup NginX | |
| working-directory: client-repo | |
| run: | | |
| sudo chmod 777 /var/log/nginx/* | |
| sudo chmod 777 /var/run/* | |
| sudo chmod 777 /var/run | |
| sed -i s#{GITHUB_WORKSPACE}#$GITHUB_WORKSPACE#g ci/nginx.conf | |
| nginx -c "$(pwd)/ci/nginx.conf" | |
| - name: 📜 - Set up JS Node 16 | |
| uses: actions/setup-node@v3 | |
| with: | |
| node-version: '16' | |
| cache: 'npm' | |
| cache-dependency-path: client-repo/package-lock.json | |
| # TODO: ⚠️ the json generated is not understood by codecov | |
| # TODO: fix 404s for nested URLs – nginx config problem? | |
| - name: 🔧 - Install | |
| working-directory: client-repo | |
| run: | | |
| npm ci | |
| npm run build | |
| npm run coverage:instrument | |
| cp -r dist metagenomics | |
| mv metagenomics /usr/share/nginx/html/metagenomics | |
| cp -r coverage/instrumented/* /usr/share/nginx/html/metagenomics/ | |
| ls /usr/share/nginx/html/metagenomics | |
| echo "=== web index ===" | |
| curl --silent http://localhost:9000/metagenomics/ | |
| env: | |
| SENTRY_AUTH_TOKEN: ${{ secrets.SENTRY_AUTH_TOKEN }} | |
| SENTRY_ORG: ${{ secrets.SENTRY_ORG }} | |
| SENTRY_PROJECT: ${{ secrets.SENTRY_PROJECT }} | |
| - name: 🧹 - ESlint | |
| working-directory: client-repo | |
| run: | | |
| npm run eslint | |
| - name: 🧪 - Testing | |
| uses: cypress-io/github-action@v4 | |
| with: | |
| working-directory: client-repo | |
| browser: chrome | |
| - name: 📉 - Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| directory: ${{ github.workspace }}/client-repo/coverage/ | |
| # TODO: enable sentry when https://github.com/getsentry/action-release/issues/83 is resolved | |
| # - name: Sentry Release | |
| # uses: getsentry/action-release@v1.1.6 | |
| # working-directory: 'client-repo' | |
| # env: | |
| # SENTRY_AUTH_TOKEN: ${{ secrets.SENTRY_AUTH_TOKEN }} | |
| # SENTRY_ORG: ${{ secrets.SENTRY_ORG }} | |
| # SENTRY_PROJECT: ${{ secrets.SENTRY_PROJECT }} | |
| # SENTRY_LOG_LEVEL: 'info' | |
| # with: | |
| # environment: dev | |
| # sourcemaps: './dist/js' | |
| # version: ${{ github.sha }} | |
| - name: 📸 - Failed tests snapshots | |
| uses: actions/upload-artifact@v3 | |
| if: failure() | |
| with: | |
| name: tests-snapshots | |
| path: /home/runner/work/ebi-metagenomics-client/ebi-metagenomics-client/client-repo/cypress/screenshots/ # - name: 📊 - Coverage | |
| - name: 🐞 - Error log | |
| if: failure() | |
| run: | | |
| echo "NGINX error log" | |
| cat /var/log/nginx/error.log | |
| echo "NGINX access log" | |
| cat /var/log/nginx/access.log | |
| - name: 📮 - Slack Notification | |
| uses: rtCamp/action-slack-notify@v2 | |
| continue-on-error: true | |
| if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop' | |
| env: | |
| SLACK_COLOR: "${{ job.status == 'success' && 'good' || 'danger' }}" | |
| SLACK_USERNAME: 'Github Actions API' | |
| SLACK_ICON_EMOJI: ':octocat:' | |
| SLACK_TITLE: 'webkit results in GitHub Actions' | |
| SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }} | |
| SLACK_CHANNEL: '#metagenomics-notify' | |
| MSG_MINIMAL: Actions URL |