Workflow file for this run
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| on: | |
| pull_request: | |
| branches: | |
| - "*" | |
| jobs: | |
| changed_files: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| new_study_dir: ${{ steps.new-dir.outputs.NEW_DIR_LOCATION }} | |
| new_study_name: ${{ steps.new-study.outputs.NEW_STUDY_NAME }} | |
| steps: | |
| - name: Get New Directories Added | |
| id: changed-files-dir-names | |
| uses: tj-actions/changed-files@v38 | |
| with: | |
| dir_names: "true" | |
| - name: Extract Directory Name of New Study | |
| id: new-dir | |
| shell: bash | |
| run: | | |
| echo "NEW_DIR_LOCATION=$( echo ${{ steps.changed-files-dir-names.outputs.added_files }} | awk '{print $1}' )" >> $GITHUB_OUTPUT | |
| - name: Extract New Study Name | |
| id: new-study | |
| shell: bash | |
| run: | | |
| echo "NEW_STUDY_NAME=$( cut -d "/" -f2- <<< ${{ steps.new-dir.outputs.NEW_DIR_LOCATION }} )" >> $GITHUB_OUTPUT | |
| preview: | |
| needs: changed_files | |
| runs-on: ubuntu-latest | |
| container: docker.io/okteto/okteto:2.19.1 | |
| steps: | |
| - name: Checkout Datahub Repository | |
| uses: actions/checkout@v3 | |
| - name: Copy Files to Study Directory | |
| shell: bash | |
| run: | | |
| # mkdir -p study/${{ needs.changed_files.outputs.new_study_name }} | |
| cp -v -R ${{ needs.changed_files.outputs.new_study_dir }} preview_infrastructure/cbioportal-docker-compose/study/${{ needs.changed_files.outputs.new_study_name }} | |
| - name: Context | |
| uses: okteto/context@latest | |
| with: | |
| url: ${{secrets.OKTETO_URL}} | |
| token: ${{ secrets.OKTETO_TOKEN }} | |
| - name: Okteto Build to Import Studies | |
| working-directory: preview_infrastructure/cbioportal-docker-compose | |
| run: | | |
| okteto build --no-cache -t okteto.dev/datahub-cbioportal:okteto-with-volume-mounts cbioportal | |
| - name: Deploy preview environment | |
| uses: okteto/deploy-preview@latest | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| with: | |
| name: pr-${{ github.event.number }}-averyniceday | |
| file: preview_infrastructure/cbioportal-docker-compose/okteto.yml | |
| timeout: 15m | |
| - name: Wait For Response | |
| uses: nev7n/[email protected] | |
| with: | |
| url: 'https://cbioportal-pr-${{ github.event.number }}-averyniceday.cloud.okteto.net/' | |
| responseCode: 200 | |
| timeout: 600000 # 10 minutes | |
| interval: 30000 # 30 seconds | |
| - name: "Activate Namespace" | |
| uses: okteto/namespace@latest | |
| with: | |
| namespace: pr-${{github.event.number}}-averyniceday | |
| - name: Kubectl test | |
| run: | | |
| okteto kubeconfig | |
| kubectl exec -it deployment/cbioportal -- metaImport.py -u http://localhost:8080 -s study/${{needs.changed_files.outputs.new_study_name}}/ -o |