diff --git a/tests/test_validate_cli.py b/tests/test_validate_cli.py index 02362ef0..0ca2b218 100644 --- a/tests/test_validate_cli.py +++ b/tests/test_validate_cli.py @@ -13,11 +13,13 @@ @pytest.fixture +@pytest.mark.slow def runner(): return CliRunner() @pytest.fixture() +@pytest.mark.slow def go_json(): url = 'http://snapshot.geneontology.org/ontology/go-basic.json' file_path = os.path.join(os.getcwd(), 'go-basic.json') @@ -42,7 +44,7 @@ def test_fast_function(): assert True -@pytest.fixture(params=[("goa_cow", "goa"), ("mgi", "MGI"), ("zfin", "ZFIN")], scope='session') +@pytest.fixture(params=[("goa_cow", "goa"), ("goa_chicken", "goa"), ("mgi", "MGI"), ("zfin", "ZFIN")], scope='session') @pytest.mark.slow def gaf_setup(request, runner, go_json): dataset, group = request.param @@ -95,7 +97,7 @@ def test_validate_resulting_gaf(gaf_setup): @pytest.mark.slow def test_validate_gaf(): - dataset = "goa_cow" + dataset = "goa_chicken" group = "goa" ontology_graph = OntologyFactory().create("go", ignore_cache=True) gaf_parser = GafParser(config=assocparser.AssocParserConfig(ontology=ontology_graph)) @@ -113,11 +115,11 @@ def test_validate_gaf(): assert len(results) > 0 for result in results: if hasattr(result, 'subject'): - assert not result.subject.id.startswith("PR:") + assert not result.subject.id.namespace == "PR" assert gpad_parser.version == '2.0' assert len(gpad_results) > 0 for gpad_result in gpad_results: if hasattr(gpad_result, 'subject'): - assert not gpad_result.subject.id.startswith("PR:") + assert not gpad_result.subject.id.namespace == "PR"