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")