Update target data #18
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| name: Update target data | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '00 17 * * 3' | |
| jobs: | |
| update-target-data: | |
| if: ${{ github.repository_owner == 'CDCgov' }} | |
| runs-on: ubuntu-22.04 | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Get Token | |
| id: get_workflow_token | |
| uses: peter-murray/workflow-application-token-action@v4 | |
| with: | |
| application_id: ${{ vars.GH_APP_ID }} | |
| application_private_key: ${{ secrets.GH_APP_KEY }} | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| install-r: false | |
| use-public-rspm: true | |
| - name: Install dependencies | |
| run: | | |
| install.packages(c("argparser", "fs", "readr", "dplyr", "remotes", "RcppTOML")) | |
| remotes::install_github('cdcgov/forecasttools') | |
| shell: Rscript {0} | |
| - name: get updated target data | |
| run: | | |
| Rscript src/get_covid_hosp_data.R --target-data TRUE --base-hub-path "." | |
| env: | |
| NHSN_API_KEY_ID: ${{ secrets.NHSN_API_KEY_ID }} | |
| NHSN_API_KEY_SECRET: ${{ secrets.NHSN_API_KEY_SECRET }} | |
| - name: Check for Changes | |
| id: check_diff | |
| run: | | |
| git diff --exit-code target-data/covid-hospital-admissions.csv || echo "changed=true" >> $GITHUB_ENV | |
| - name: Commit changes | |
| if: env.changed == 'true' | |
| uses: EndBug/add-and-commit@v9 | |
| with: | |
| message: "Update target data" | |
| default_author: github_actions | |
| push: true | |
| new_branch: update-target-data | |
| - name: Create pull request | |
| if: env.changed == 'true' | |
| run: | | |
| gh pr create --base main --head update-target-data --title "Update target data" --body "This PR updates the covid-19 hospital admissions data based on the latest NHSN wednesday data release." | |
| env: | |
| GH_TOKEN: ${{ steps.get_workflow_token.outputs.token }} |