Get new lineages from pango #3460

	name: Get new lineages from pango

	on:
	schedule:
	- cron: '0 0,6,12,18 * * *'

	jobs:
	scheduled_check:
	runs-on: ubuntu-20.04
	defaults:
	run:
	shell: bash
	working-directory: curated_reports_prep

	steps:
	- name: Checkout
	uses: actions/checkout@main
	with:
	repo-token: ${{ secrets.GITHUB_TOKEN }}

	- name: Install python dependencies
	run: python -m pip install --upgrade pip pandas

	- name: process data
	run: \|
	echo "starting update"
	python lineages_hierarchy.py
	python generate_curated_lineages_json.py
	echo "removing log file"
	rm curated_lineages_json.log
	- name: commit if output is different
	run: \|
	echo "running git diff, committing if different"
	if [[($(git status ../web/src/assets/genomics/curated_lineages.json --porcelain \| wc -c) -ne 0)]]; then
	echo "changes were made, adding new lineage info"
	git config --local user.name "$GITHUB_ACTOR"
	git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
	git add ../web/src/assets/genomics/curated_lineages.json
	git add lineages.yml
	git commit -m "updating lineage metadata"
	git push origin master
	else
	echo "no changes were made, doing nothing."
	fi;

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