add mongo env values #9

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Python application

	on:
	push:
	branches: [ "Refactor_fgi_file_staging_unit_tests" ]
	pull_request:
	branches: [ "Refactor_fgi_file_staging_unit_tests" ]

	permissions:
	contents: read

	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python 3.9
	uses: actions/setup-python@v3
	with:
	python-version: "3.9"
	- name: Install Poetry
	uses: snok/install-poetry@v1
	- name: Install dependencies
	run: \|
	poetry install
	test:
	runs-on: ubuntu-latest
	needs: build
	services:
	mongodb:
	image: mongo
	env:
	MONGO_INITDB_ROOT_USERNAME: root
	MONGO_INITDB_ROOT_PASSWORD: password
	MONGO_INITDB_DATABASE: nmdc
	MONGO_HOST: localhost
	ports:
	- 27017:27017
	options: --health-cmd "mongo --version" --health-interval 10s --health-timeout 5s --health-retries 12
	steps:
	# - uses: actions/checkout@v3
	# - name: Set up Python 3.9
	# uses: actions/setup-python@v3
	# with:
	# python-version: "3.9"
	# - name: Install Poetry
	# uses: snok/install-poetry@v1
	# - name: Install dependencies
	# run: \|
	# poetry install
	- name: Test with pytest
	run: \|
	poetry run pytest

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