specieskey #86

	name: Open Tree of Life tests
	# This workflow runs tests for the OToL-related part of the PhyloNext pipeline
	on: push

	jobs:
	biodiverse-tests:
	name: Run OToL tests
	runs-on: ubuntu-latest
	container:
	image: vmikk/opentree:1.4.0
	volumes:
	- ${{ github.workspace }}:/ott
	steps:

	- name: Check out the repo
	uses: actions/checkout@v3
	with:
	ref: main
	fetch-depth: 1

	# pwd = /__w/PhyloNext/PhyloNext

	- name: Fetching test tree from OToL
	run: \|
	python \
	/__w/PhyloNext/PhyloNext/bin/induced_synth_subtree_from_csv.py \
	--query /__w/PhyloNext/PhyloNext/test_data/Felidae,Canidae_Species_OTT.csv \
	--output_dir $(pwd)/OTT/ \
	--phylo-only \
	--max-age 111

	- name: Verifying results
	run: \|
	ls -l $(pwd)/OTT/

	- name: Check file existence
	id: check_files
	uses: andstor/file-existence-action@v2
	with:
	files: "./OTT/ott_label_dated_tree.tre"
	# `file-existence-action` does not intrpret $(pwd)? -> use relative path

	- name: Files exist?
	if: steps.check_files.outputs.files_exists == 'true'
	run: \|
	echo "Looks good, Labeled and dated phylogenetic tree is in place!"
	exit 0

	- name: Files are missing?
	if: steps.check_files.outputs.files_exists == 'false'
	run: \|
	echo "ERROR! Some files are missing!"
	exit 1

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