def test_galaxy_workflow_step_failed():
ctx = t_context()
test_artifact = os.path.join(TEST_DATA_DIR, "wf_failed_step.ga")
runnables = for_paths([test_artifact])
with NamedTemporaryFile(prefix="result_json") as json_out:
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"extra_tools": ['$GALAXY_FUNCTIONAL_TEST_TOOLS'],
"test_output_json": json_out.name,
"galaxy_branch": target_galaxy_branch(),
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 1
report = json.load(json_out)
data = report['tests'][0]['data']
assert data['status'] == 'error'
assert data['execution_problem']
invocation_steps = data['invocation_details']['steps']
assert len(invocation_steps) == 2
first_step, second_step = invocation_steps.values()
assert first_step['state'] == 'scheduled'
job = first_step['jobs'][0]
assert job['exit_code'] == 127
assert job['state'] == 'error'
assert second_step['state'] == 'scheduled'
assert second_step['jobs'][0]['state'] == 'paused'
def test_toil_tests():
ctx = t_context()
test_artifact = os.path.join(TEST_DATA_DIR, "int_tool.cwl")
runnables = for_paths([test_artifact])
exit_code = t_runnables(
ctx,
runnables,
engine="toil",
)
assert exit_code == 0
def test_galaxy_workflow_non_data_inputs():
ctx = t_context()
test_artifact = os.path.join(TEST_DATA_DIR, "wf9-int-input.gxwf.yml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": target_galaxy_branch(),
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 0
def test_galaxy_workflow_collection_output_fail():
ctx = t_context()
test_artifact = os.path.join(TEST_DATA_DIR,
"wf7-collection-output-fail.gxwf.yml")
collection_creates_pair = os.path.join(TEST_DATA_DIR,
"collection_creates_pair_2.xml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": target_galaxy_branch(),
"extra_tools": [collection_creates_pair],
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 1
def test_galaxy_wf_tests():
ctx = t_context()
random_lines = os.path.join(PROJECT_TEMPLATES_DIR, "demo",
"randomlines.xml")
cat = os.path.join(PROJECT_TEMPLATES_DIR, "demo", "cat.xml")
test_artifact = os.path.join(TEST_DATA_DIR, "wf1.gxwf.yml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": target_galaxy_branch(),
"extra_tools": [random_lines, cat]
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 0
def test_galaxy_workflow_nested_collection_inputs():
ctx = t_context()
test_artifact = os.path.join(TEST_DATA_DIR,
"wf8-collection-nested-input.gxwf.yml")
collection_cat_pair = os.path.join(TEST_DATA_DIR, "cat_pair.xml")
collection_cat_list = os.path.join(TEST_DATA_DIR, "cat_list.xml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": target_galaxy_branch(),
"extra_tools": [collection_cat_pair, collection_cat_list],
}
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 0
def test_galaxy_workflow_tags():
with NamedTemporaryFile(prefix="data_manager_test_json") as json_out:
ctx = t_context()
test_artifact = os.path.join(TEST_DATA_DIR,
"wf10-tags-and-rules.gxwf.yml")
collection_cat_list = os.path.join(TEST_DATA_DIR, "cat_list.xml")
runnables = for_paths([test_artifact])
kwds = {
"engine": "galaxy",
"no_dependency_resolution": True,
"paste_test_data_paths": False,
"galaxy_branch": "dev",
"extra_tools": [collection_cat_list],
"test_output_json": json_out.name,
}
try:
exit_code = t_runnables(ctx, runnables, **kwds)
assert exit_code == 0
except Exception:
with open(json_out.name, "r") as f:
print(f.read())
raise