Merge pull request #345 from sanger/flags_in_history #927

	# This workflow will build a Java project with Maven
	# For more information see: https://help.github.com/actions/language-and-framework-guides/building-and-testing-java-with-maven

	name: CI

	on:
	push:
	branches: [ devel ]
	pull_request:
	branches: [ devel ]

	jobs:
	build:

	runs-on: ubuntu-latest

	services:
	mysql:
	image: mysql:8.0
	ports:
	- 3306
	env:
	MYSQL_ROOT_PASSWORD: rootpw
	MYSQL_DATABASE: stantest
	MYSQL_USER: stan
	MYSQL_PASSWORD: stanpw

	steps:
	- name: start mysql
	run: \|
	sudo /etc/init.d/mysql start \|\| true
	- name: wait 10s for service
	uses: jakejarvis/wait-action@v0.1.0
	with:
	time: '10s'
	- name: verify mysql from container
	run: \|
	mysql -h 127.0.0.1 -P $MYSQL_PORT -uroot -prootpw -e "SHOW DATABASES"
	env:
	MYSQL_PORT: "${{ job.services.mysql.ports['3306'] }}"
	- uses: actions/checkout@v2
	- name: Set up Java 21
	uses: actions/setup-java@v1
	with:
	java-version: 21
	- name: Build with Maven
	run: mvn -B package --file pom.xml
	env:
	MYSQL_PORT: "${{ job.services.mysql.ports['3306'] }}"
	MYSQL_HOST: localhost
	MYSQL_RW_USER: stan
	MYSQL_RW_PASSWORD: stanpw
	MYSQL_ADMIN_USER: stan
	MYSQL_ADMIN_PASSWORD: stanpw
	MYSQL_DATABASE: stantest
	- name: Run Snyk tests to check for vulnerabilities
	uses: snyk/actions/node@master #Pre-created container
	continue-on-error: true # To make sure that CI run is not blocked on Snyk test failure
	with:
	command: code test
	args: --severity-threshold=high
	env:
	SNYK_TOKEN: ${{ secrets.SNYK_TOKEN }}

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