Snapshot NHSN data and upload to S3 #9

	name: Snapshot NHSN data and upload to S3

	on:
	schedule:
	- cron: "45 5 * * 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');
	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"

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