v0.0.7 #5
Workflow file for this run
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| name: Publish to Terra | |
| # Publish notebooks and dashboard markdown from the source-of-truth, a GitHub repository, to the | |
| # deployment destination, a Terra workspace. See http://app.terra.bio for more detail. | |
| # | |
| # Only use this workflow for Terra workspaces that are simply mirrors of GitHub repositories, as | |
| # it overwrites assets in Terra-managed storage. | |
| on: | |
| workflow_dispatch: | |
| # Allows manually triggering of workflow on a selected branch via the GitHub Actions tab. | |
| # GitHub blog demo: https://github.blog/changelog/2020-07-06-github-actions-manual-triggers-with-workflow_dispatch/. | |
| release: | |
| types: [published] | |
| env: | |
| # TO REUSE THIS TEMPLATE, change these values to reflect those of your destination Terra workspace. | |
| NAMESPACE: 'uk-biobank-sek' | |
| WORKSPACE: 'ml4h-toolkit-for-machine-learning-on-clinical-data' | |
| WORKSPACE_BUCKET: 'fc-500bd872-4a53-45c9-87d3-39656bd83f85' | |
| jobs: | |
| deploy_to_terra: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.7 | |
| - name: Setup gcloud CLI | |
| uses: google-github-actions/setup-gcloud@v0 | |
| # TO REUSE THIS TEMPLATE, configure auth. | |
| # Step 1: Create a service account and store its key in GitHub as 'TERRA_SECRET' per these instructions: | |
| # https://github.com/google-github-actions/setup-gcloud/blob/master/setup-gcloud/README.md | |
| # https://docs.github.com/en/free-pro-team@latest/actions/reference/encrypted-secrets#creating-encrypted-secrets-for-a-repository | |
| # Step 2: Register the service account with Terra per these instructions | |
| # https://github.com/broadinstitute/terra-tools/tree/master/scripts/register_service_account | |
| # Step 3: Share the destination Terra workspace with the service account, granting it | |
| # "WRITER" access. Also add it to the Authorization Domain for the workspace, if applicable. | |
| with: | |
| version: '290.0.1' | |
| service_account_key: ${{ secrets.TERRA_SECRET }} | |
| export_default_credentials: true | |
| - name: Publish dashboard and notebooks | |
| run: | | |
| # Install the Terra client. | |
| pip install firecloud==0.16.25 | |
| # TO REUSE THIS TEMPLATE, update the code to match your file and directory structure. | |
| # This particular example is based on the structure of https://github.com/verilylifesciences/metis | |
| # Publish the mnist notebook | |
| cd notebooks/ | |
| gsutil cp mnist_survival_analysis_demo.ipynb "gs://${WORKSPACE_BUCKET}/notebooks/" | |
| # Change to the directory holding the workspace assets. | |
| cd terra_featured_workspace/ | |
| # Publish the main notebooks. | |
| gsutil cp image_annotations_demo.ipynb "gs://${WORKSPACE_BUCKET}/notebooks/" | |
| gsutil cp review_model_results_interactive.ipynb "gs://${WORKSPACE_BUCKET}/notebooks/" | |
| gsutil cp review_one_sample_interactive.ipynb "gs://${WORKSPACE_BUCKET}/notebooks/" | |
| # By default, use the SHA of the commit for the version. | |
| VERSION="${{ github.sha }}" | |
| # But for tags, strip the prefix from tag name to use just the tag value as the version. | |
| [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo "${{ github.ref }}" | sed -e 's:refs/tags/::') | |
| # Fill in the setup notebook template. | |
| cat ml4h_setup.ipynb | sed -e s:ml4h.git:ml4h.git@${VERSION}: > ml4h_setup.ipynbWithVersion | |
| # Publish the setup notebook. | |
| gsutil cp ml4h_setup.ipynbWithVersion "gs://${WORKSPACE_BUCKET}/notebooks/ml4h_setup.ipynb" | |
| # Publish the dashboard markdown. | |
| python << EOF | |
| import firecloud.api as fapi | |
| with open('workspace_description.md') as f: | |
| fapi.update_workspace_attributes( | |
| namespace="$NAMESPACE", | |
| workspace="$WORKSPACE", | |
| attrs=[fapi._attr_set(attr='description', value=f.read())]).json() | |
| EOF |