Merge pull request #15 from reichlab/fix_nhsn_workflow

updates to nhsn workflow

.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 }}