Merge pull request #142 from nextstrain/update-case-counts

ingest/fetch-ncov-global-case-counts: Use new endpoint

Author: joverlee521

.github/workflows/update-ncov-case-counts.yaml

@@ -40,6 +40,8 @@ jobs:
       runtime: docker
       run: |
         nextstrain build \
+          --env SLACK_TOKEN \
+          --env SLACK_CHANNELS \
           ingest \
           upload_all_case_counts \
           --config s3_dst="$S3_DST"

ingest/bin/fetch-ncov-global-case-counts

@@ -2,13 +2,13 @@
 set -euo pipefail
 
 # Fetch CSV from Our World in Data
-curl https://covid.ourworldindata.org/data/owid-covid-data.csv \
+curl https://catalog.ourworldindata.org/garden/covid/latest/compact/compact.csv \
     --fail --silent --show-error --location \
     --header 'User-Agent: https://github.com/nextstrain/counts ([email protected])' |
-    # Only keep the date, location, and new_cases columns
-    csvtk cut -f location,date,new_cases |
-    # Rename new_cases to cases
-    csvtk rename -f new_cases -n cases |
+    # Only keep the date, country, and new_cases columns
+    csvtk cut -f country,date,new_cases |
+    # Rename new_cases to cases and country to location
+    csvtk rename -f new_cases,country -n cases,location |
     # Only keep rows that have more than 0 cases
     csvtk filter -f "cases>0" |
     # Remove decimals from case counts