Merge pull request #12 from galaxy-genome-annotation/sed #8

	name: Test

	concurrency:
	group: ci-${{ github.head_ref }}
	cancel-in-progress: true

	on:
	pull_request:
	types: [opened, reopened, synchronize, ready_for_review]
	paths:
	- *.sh
Check failure on line 11 in .github/workflows/test.yml View workflow run for this annotation GitHub Actions / .github/workflows/test.yml Invalid workflow file `You have an error in your yaml syntax on line 11`
	- *.sql
	- Dockerfile

	jobs:
	lint:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v2
	- name: Build container
	run: \|
	docker build -t chado .

	- name: Test Running Container
	run: \|
	container_id=$(docker run -it -e INSTALL_YEAST_DATA=1 -d --name chado chado)

	while true; do
	date

	# Check that it's ready to run
	start_count=$(docker logs $container_id \| grep 'database system is ready to accept connections' \| wc -l)
	if (( start_count > 1 )); then
	break
	fi

	# If it's not output some logs
	docker logs $container_id \| tail

	# And wait a bit
	sleep 5
	done

	# Check that yeast is, in fact loaded.
	docker exec $container_id psql -U postgres -c "select * from organism where common_name = 'yeast' " \| grep '1 row'

	# Dump something useful
	docker exec $container_id psql -U postgres -c "select type_id, count(*) from feature group by type_id ;"

	docker kill $container_id
	docker rm -f $container_id

	# Done!
	exit 0

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