Update from GISAID #1045

	# This is a basic workflow to help you get started with Actions

	name: Update from GISAID

	on:
	repository_dispatch:
	workflow_dispatch:
	schedule:
	# * is a special character in YAML so you have to quote this string
	- cron: "0 5 * * *"

	permissions:
	contents: read
	packages: write

	env:
	REGISTRY: ghcr.io

	# A workflow run is made up of one or more jobs that can run sequentially or in parallel
	jobs:
	# This workflow contains a single job called "build"
	download-aggregate-commit:
	# The type of runner that the job will run on
	runs-on: ubuntu-latest
	environment: production
	permissions:
	contents: "write"

	# Steps represent a sequence of tasks that will be executed as part of the job
	steps:
	- uses: actions/checkout@v3
	with:
	token: ${{ secrets.GITHUB_TOKEN }}
	- name: Download file
	run: curl -u ${{secrets.GISAID_USERNAME}}:${{secrets.GISAID_PW}} https://www.epicov.org/epi3/3p/varsurv02/export/provision.json.xz \| xz -d -T0 > ./provision.json
	working-directory: ./data_processing/
	- name: Setup node
	uses: actions/setup-node@v3
	with:
	node-version: 16.x
	- name: Aggregate
	run: ./aggregate.sh
	working-directory: ./data_processing/
	- name: Copy
	run: cp ./data_processing/aggregated.csv ./api/aggregated.csv
	# https://github.com/actions/checkout#push-a-commit-using-the-built-in-token
	- name: Commit
	run: \|
	git config user.name github-actions
	git config user.email [email protected]
	git add .
	git commit -m "Update data"
	git push

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