Data integration #12

	# This workflow will install pytest, and test validity of data in repo.

	name: Data integration

	on:
	push:
	branches: [ "main" ]
	schedule:
	- cron: '0 0 * * *'

	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v3
	with:
	token: ${{ secrets.NICD_TOKEN }}

	- name: Checkout private tools
	uses: actions/checkout@v3
	with:
	repository: NICD-Wastewater-Genomics/NICD-Freyja-outputs-
	token: ${{ secrets.NICD_TOKEN }}
	path: NICD-Freyja-outputs-

	- name: setup python
	uses: actions/setup-python@v4
	with:
	python-version: 3.9

	- name: Clone
	shell: bash -l {0}
	run: \|
	pip install pandas
	pip install pyarrow
	git config --global user.name "joshuailevy"
	git config --global user.email "joshua.levy16@gmail.com"
	cp NICD-Freyja-outputs-/scripts/NICD_daily_smoothed.csv .
	cp NICD-Freyja-outputs-/scripts/NICD_monthly.csv .
	cp NICD-Freyja-outputs-/scripts/merged_data.tsv .
	python convert_data_format.py

	- name: Push
	run: \|
	if [[($(git status merged_data.tsv --porcelain \| wc -c) -ne 0)]]; then
	git add --all
	git commit -m "automated core data update"
	git push origin main
	else
	echo "no new samples, nothing to do"
	fi

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