Validate test data in CI job #55

	on:
	pull_request:
	branches: [ "master", "main" ]

	push:
	branches: [ "master", "main" ]

	jobs:
	check_data_models:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	data_model_file: [
	'PRIMED_phenotype_data_model.json',
	'PRIMED_genotype_data_model.json',
	'PRIMED_GSR_data_model.json'
	]
	name: Check data model
	steps:

	- name: Checkout repository
	uses: actions/checkout@v3

	- name: Setup R
	uses: r-lib/actions/setup-r@v2
	with:
	r-version: "4.2.3"

	- name: Install dependencies
	uses: r-lib/actions/setup-r-dependencies@v2
	with:
	cache-version: 1
	packages: github::UW-GAC/AnvilDataModels, any::sessioninfo
	env:
	GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

	- name: Check ${{ matrix.data_model_file }} file
	run: \|
	AnvilDataModels::json_to_dm("${{ matrix.data_model_file }}")
	shell: Rscript {0}

	check_test_data:
	runs-on: ubuntu-latest
	name: Check test model
	steps:

	- name: Checkout repository
	uses: actions/checkout@v3

	# Install Java to this VM. This Java version and distribution is compatible with Cromwell.
	# This is the same step as used by broadinstitute/cromwell/.github/set_up_cromwell_action.
	- name: Setup JDK
	uses: actions/setup-java@v3
	with:
	distribution: temurin
	java-version: 11

	# Clone the cromwell repo to this VM.
	# This is the same step as used by broadinstitute/cromwell/.github/set_up_cromwell_action,
	# but without a token and into a different directory.
	- name: Clone Cromwell
	uses: actions/checkout@v3
	with:
	repository: broadinstitute/cromwell
	ref: "87"
	path: "cromwell"

	- name: Success!
	run: echo "Success!"

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