def test_update(test_data_dir, tmpdir, helpers):
crate = ROCrate()
assert not crate.root_dataset["hasPart"]
wf_path = test_data_dir / "test_galaxy_wf.ga"
john = crate.add(Person(crate, '#john', {'name': 'John Doe'}))
file_ = crate.add_file(wf_path)
assert crate.root_dataset["hasPart"] == [file_]
file_["author"] = john
assert isinstance(file_, File)
assert crate.mainEntity is None
wf = crate.add_workflow(wf_path, main=True, lang="galaxy")
assert isinstance(wf, ComputationalWorkflow)
assert wf["author"] is None
assert crate.mainEntity is wf
assert crate.dereference(john.id) is john
assert crate.dereference(file_.id) is wf
assert crate.root_dataset["hasPart"] == [wf]
assert crate.root_dataset.properties()["hasPart"] == [{
"@id":
"test_galaxy_wf.ga"
}]
out_path = tmpdir / "ro_crate_out"
out_path.mkdir()
crate.write_crate(out_path)
json_entities = helpers.read_json_entities(out_path)
helpers.check_wf_crate(json_entities, wf.id)
def make_crate(crate_dir, target_owner, planemo_version):
wf_id = get_wf_id(crate_dir)
planemo_id, planemo_source = get_planemo_id(crate_dir, wf_id)
crate = ROCrate(gen_preview=False)
wf_source = Path(crate_dir) / wf_id
with open(wf_source) as f:
code = json.load(f)
workflow = crate.add_workflow(wf_source,
wf_id,
main=True,
lang="galaxy",
gen_cwl=False)
handle_creator(code, crate, workflow)
workflow["name"] = crate.root_dataset["name"] = get_workflow_name(
crate_dir)
try:
workflow["version"] = code["release"]
except KeyError:
pass
wf_url = f"https://github.com/{target_owner}/{crate_dir.name}"
workflow["url"] = crate.root_dataset["isBasedOn"] = wf_url
try:
crate.root_dataset["license"] = code["license"]
except KeyError:
pass
readme_source = Path(crate_dir) / "README.md"
if readme_source.is_file():
crate.add_file(readme_source, "README.md")
suite = crate.add_test_suite(identifier="#test1")
resource = f"repos/{target_owner}/{crate_dir.name}/actions/workflows/{CI_WORKFLOW.name}"
crate.add_test_instance(suite,
GH_API_URL,
resource=resource,
service="github",
identifier="test1_1")
crate.add_test_definition(suite,
source=planemo_source,
dest_path=planemo_id,
engine="planemo",
engine_version=planemo_version)
crate.metadata.write(crate_dir)
