diff --git a/.github/workflows/snapshot-nhsn-data.yml b/.github/workflows/snapshot-nhsn-data.yml index efba5b9..f277ebf 100644 --- a/.github/workflows/snapshot-nhsn-data.yml +++ b/.github/workflows/snapshot-nhsn-data.yml @@ -2,7 +2,7 @@ name: Snapshot NHSN data and upload to S3 on: schedule: - - cron: "45 5 * * 3" # every Wednesday at 5:45PM UTC == 12:45PM EST + - cron: "45 17 * * 3" # every Wednesday at 5:45PM UTC == 12:45PM EST workflow_dispatch: env: @@ -34,7 +34,10 @@ jobs: run: echo "FILE_NAME=nhsn-$(date +'%Y-%m-%d').csv" >> $GITHUB_ENV - name: Snapshot NHSN data - run: Rscript -e "nhsn_data <- RSocrata::read.socrata('https://data.cdc.gov/resource/mpgq-jmmr.csv'); + run: Rscript -e "nhsn_data <- RSocrata::read.socrata('https://data.cdc.gov/resource/mpgq-jmmr.csv'); + nhsn_data <- nhsn_data[c("jurisdiction", "weekendingdate", "totalconfflunewadm", "totalconfc19newadm")]; + nhsn_data$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 }}