generate-doi #6
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| name: generate-doi | |
| on: | |
| schedule: | |
| - cron: '0 0 * * 0' # Every Sunday at midnight | |
| workflow_dispatch: | |
| jobs: | |
| get-updated-apps: | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| app_batches: ${{ steps.list_apps.outputs.app_batches }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Check for apps to publish to Zenodo | |
| id: list_apps | |
| run: | | |
| # Get the list of unpublished images from app.json | |
| echo "Get the list of unpublished images..." | |
| export APP_BATCHES=$(python .github/workflows/get-unpublished-apps.py --zenodo_token ${{ secrets.ZENODO_TOKEN }}) | |
| echo "app_batches=${APP_BATCHES}" | |
| echo "app_batches=${APP_BATCHES}" >> $GITHUB_OUTPUT | |
| publish-doi: | |
| needs: get-updated-apps | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 1200 | |
| if: ${{ needs.get-updated-apps.outputs.app_batches != '[]' }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| app_batches: ${{ fromJSON(needs.get-updated-apps.outputs.app_batches) }} | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install requests pyyaml>=6.0.2 | |
| - name : Publish singularity files in batch | |
| shell: bash | |
| run: | | |
| echo "Apps to process: ${{ toJson(matrix.app_batches.apps) }}" | |
| apps_json='${{ toJson(matrix.app_batches.apps) }}' | |
| for app in $(echo "$apps_json" | jq -r '.[]'); do | |
| echo " Processing app: $app with ${#app[@]} apps" | |
| if curl --output /dev/null --silent --head --fail "https://object-store.rc.nectar.org.au/v1/AUTH_dead991e1fa847e3afcca2d3a7041f5d/neurodesk/${app}.simg"; then | |
| # curl --output "$IMAGE_HOME/${app}.simg" "https://object-store.rc.nectar.org.au/v1/AUTH_dead991e1fa847e3afcca2d3a7041f5d/neurodesk/${app}.simg" | |
| echo "Upload container ${app}.simg to Zenodo" | |
| # echo $(find $IMAGE_HOME/${app}.simg) | |
| export DOI_URL=$(python3 .github/workflows/publish-doi.py --container_filepath="https://object-store.rc.nectar.org.au/v1/AUTH_dead991e1fa847e3afcca2d3a7041f5d/neurodesk/${app}.simg" --container_name=${app} --zenodo_token=${{ secrets.ZENODO_TOKEN }} --gh_token=${{ secrets.GITHUB_TOKEN }}) | |
| echo "DOI_URL: $DOI_URL" | |
| else | |
| echo "Container https://object-store.rc.nectar.org.au/v1/AUTH_dead991e1fa847e3afcca2d3a7041f5d/neurodesk/${app}.simg not found. Skipping..." | |
| fi | |
| done |