Snapshot NHSN data and upload to S3 #19
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| name: Snapshot NHSN data and upload to S3 | |
| on: | |
| schedule: | |
| - cron: "45 17 * * 3" # every Wednesday at 5:45PM UTC == 12:45PM EST | |
| workflow_dispatch: | |
| env: | |
| # Reich lab AWS account number | |
| AWS_ACCOUNT: 312560106906 | |
| permissions: | |
| contents: read | |
| # id-token write required for AWS auth | |
| id-token: write | |
| jobs: | |
| snapshot-nhsn-data: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Set up R 📊 | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 4.4.1 | |
| install-r: true | |
| use-public-rspm: true | |
| extra-repositories: 'https://hubverse-org.r-universe.dev' | |
| - name: install R packages | |
| run: | | |
| Rscript -e "install.packages('RSocrata')" | |
| - name: Get file name | |
| run: echo "FILE_NAME=nhsn-$(date +'%Y-%m-%d').csv" >> $GITHUB_ENV | |
| - name: Snapshot NHSN data | |
| run: Rscript -e "nhsn_data <- RSocrata::read.socrata('https://data.cdc.gov/resource/mpgq-jmmr.csv'); | |
| nhsn_data <- nhsn_data[c('jurisdiction', 'weekendingdate', 'totalconfflunewadm', 'totalconfc19newadm')]; | |
| nhsn_data[['weekendingdate']] <- substr(nhsn_data[['weekendingdate']], 1, 10); | |
| colnames(nhsn_data) <- c('Geographic aggregation', 'Week Ending Date', 'Total Influenza Admissions', 'Total COVID-19 Admissions'); | |
| write.csv(nhsn_data, file = '$FILE_NAME', row.names = FALSE)" | |
| env: | |
| FILE_NAME: ${{ env.FILE_NAME }} | |
| - name: Configure AWS credentials | |
| # request credentials to assume the hub's AWS role via OpenID Connect | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::${{ env.AWS_ACCOUNT }}:role/iddata-github-action | |
| aws-region: us-east-1 | |
| - name: Copy files to cloud storage | |
| run: | | |
| aws s3 cp "./$FILE_NAME" "s3://infectious-disease-data/data-raw/influenza-nhsn/$FILE_NAME" |