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)
def test_add_test_instance(test_data_dir):
top_dir = test_data_dir / "ro-crate-galaxy-sortchangecase"
wf_path = top_dir / "sort-and-change-case.ga"
crate = ROCrate()
wf = crate.add(ComputationalWorkflow(crate, str(wf_path), wf_path.name))
crate.mainEntity = wf
suite = crate.add_test_suite()
instances = set()
assert crate.dereference(JENKINS) is None
assert crate.dereference(TRAVIS) is None
i1 = crate.add_test_instance(suite, "http://example.com")
assert crate.dereference(JENKINS) is i1.service
assert crate.dereference(TRAVIS) is None
assert i1.url == "http://example.com"
instances.add(i1)
assert instances == set(suite.instance)
i2 = crate.add_test_instance(suite.id, "http://example.com")
assert i2.url == "http://example.com"
instances.add(i2)
assert instances == set(suite.instance)
i3 = crate.add_test_instance(suite, "http://example.com", resource="jobs")
assert i3.url == "http://example.com"
assert i3.resource == "jobs"
instances.add(i3)
assert instances == set(suite.instance)
i4 = crate.add_test_instance(suite, "http://example.com", service="travis")
assert i4.url == "http://example.com"
assert i4.service.id == TRAVIS
assert i4.service is crate.dereference(TRAVIS)
instances.add(i4)
assert instances == set(suite.instance)
i5 = crate.add_test_instance(suite,
"http://example.com",
identifier="test_1_1")
assert i5.url == "http://example.com"
assert i5.id == "#test_1_1"
instances.add(i5)
assert instances == set(suite.instance)
i6 = crate.add_test_instance(suite,
"http://example.com",
name="Test 1 Instance 1")
assert i6.url == "http://example.com"
assert i6.name == "Test 1 Instance 1"
instances.add(i6)
assert instances == set(suite.instance)
