def test_config_file_missing_required_parameter_is_rejected(tmpdir):
p = tmpdir.mkdir("sub").join("tmp_config.yml")
p.write("something: value")
tmp_config = str(p.dirpath() + "/tmp_config.yml")
with pytest.raises(KeyError) as excinfo:
GalaxyCMDWorkflow.init_from_config_file(tmp_config)
assert 'Missing required parameter \'galaxy_url\'' in str(excinfo.value)
def test_config_file_with_all_required_values_is_accepted(tmpdir):
p = tmpdir.mkdir("sub").join("tmp_config.yml")
p.write("galaxy_url: something\n"
"galaxy_key: something\n"
"history_name: something\n"
"workflow_source: something\n"
"workflow: something\n")
tmp_config = str(p.dirpath() + "/tmp_config.yml")
gflow = GalaxyCMDWorkflow.init_from_config_file(tmp_config)
assert gflow.galaxy_url == "something"
assert gflow.galaxy_key == "something"
assert gflow.history_name == "something"
assert gflow.workflow_source == "something"
assert gflow.workflow == "something"
def gflow():
galaxy_key = os.environ['GALAXY_API_KEY']
galaxy_url = os.environ['GALAXY_URL']
return GalaxyCMDWorkflow.init_from_params(galaxy_url, galaxy_key,
"Test History", "local",
"workflows/galaxy101.ga")
