def test(self, runnables):
"""Test runnable artifacts (workflow or tool)."""
self._check_can_run_all(runnables)
test_cases = [t for tl in map(cases, runnables) for t in tl]
test_results = self._collect_test_results(test_cases)
tests = []
for (test_case, run_response) in test_results:
test_case_data = test_case.structured_test_data(run_response)
tests.append(test_case_data)
test_data = {
'version': '0.1',
'tests': tests,
}
structured_results = StructuredData(data=test_data)
structured_results.calculate_summary_data()
return structured_results
def test(self, runnables):
"""Test runnable artifacts (workflow or tool)."""
self._check_can_run_all(runnables)
test_cases = [t for tl in map(cases, runnables) for t in tl]
test_results = self._collect_test_results(test_cases)
tests = []
for (test_case, run_response) in test_results:
test_case_data = test_case.structured_test_data(run_response)
tests.append(test_case_data)
test_data = {
'version': '0.1',
'tests': tests,
}
structured_results = StructuredData(data=test_data)
structured_results.calculate_summary_data()
return structured_results
def cli(ctx, runnable_identifier, job_path, **kwds):
"""Planemo command for running tools and jobs.
\b
% planemo run cat1-tool.cwl cat-job.json
"""
runnable = for_runnable_identifier(ctx, runnable_identifier, kwds)
is_cwl = runnable.type.is_cwl_artifact
kwds["cwl"] = is_cwl
kwds["execution_type"] = "Run"
if kwds.get("engine", None) is None:
if is_cwl:
kwds["engine"] = "cwltool"
elif kwds.get('galaxy_url', None):
kwds["engine"] = "external_galaxy"
else:
kwds["engine"] = "galaxy"
with engine_context(ctx, **kwds) as engine:
run_result = engine.run(runnable, job_path)
if not run_result.was_successful:
warn("Run failed [%s]" % unicodify(run_result))
elif kwds.get('no_wait'):
info('Run successfully executed - exiting without waiting for results.')
else:
output_json = kwds.get("output_json", None)
outputs_dict = run_result.outputs_dict
if output_json:
with open(output_json, "w") as f:
json.dump(outputs_dict, f)
info('Run completed successfully.')
report_data = StructuredData(data={'tests': [run_result.structured_data()], 'version': '0.1'})
report_data.calculate_summary_data()
return_value = handle_reports_and_summary(ctx, report_data.structured_data, kwds=kwds)
ctx.exit(return_value)