def test_issue_113(self): """ Make sure that types are generated as part of the output """ env.generate_single_file( 'issue_113.py', lambda: PythonGenerator(env.input_path('issue_113.yaml') ).serialize(), comparator=lambda exp, act: compare_python(exp, act, 'issue_113.py' ), value_is_returned=True) module = compile_python(env.expected_path('issue_113.py')) example = module.TestClass(test_attribute_2="foo") assert hasattr(example, "test_attribute_2") assert hasattr(example, "test_attribute_1") example.wiible = "foo" example.test_attribute_1 = "foo" example.test_attribute_2 = "foo" env.generate_single_file( 'issue_113.json', lambda: PythonGenerator(env.input_path('issue_113.yaml') ).serialize(), comparator=lambda exp, act: compare_python(exp, act, 'issue_113.py' ), value_is_returned=True) def output_generator(dirname) -> None: with open(os.path.join(dirname, 'issue_113.json'), 'w') as f: f.write(as_json(example)) env.generate_directory('issue_113', lambda dirname: output_generator(dirname))
def test_local_imports(self): """ Check the local import behavior """ dir = 'issue_260' # Useful to have an __init__.py available init_path = env.actual_path(dir, '__init__.py') if not os.path.exists(init_path): with open(init_path, 'w'): pass env.generate_single_file('issue_260/issue_260a.py', lambda: PythonGenerator(env.input_path(dir, 'issue_260a.yaml'), importmap=env.import_map, mergeimports=False).serialize(), comparator=compare_python, value_is_returned=True) env.generate_single_file('issue_260/issue_260b.py', lambda: PythonGenerator(env.input_path(dir, 'issue_260b.yaml'), importmap=env.import_map, mergeimports=False).serialize(), comparator=compare_python, value_is_returned=True) env.generate_single_file('issue_260/issue_260c.py', lambda: PythonGenerator(env.input_path(dir, 'issue_260c.yaml'), importmap=env.import_map, mergeimports=False).serialize(), comparator=compare_python, value_is_returned=True) env.generate_single_file('issue_260/issue_260.py', lambda: PythonGenerator(env.input_path(dir, 'issue_260.yaml'), importmap=env.import_map, mergeimports=False).serialize(), comparator=compare_python, value_is_returned=True)
def test_minimal_model(self): """ Test to make the absolute minimal model work """ YAMLGenerator(env.input_path('issue_tccm', 'minimalmodel.yaml'), mergeimports=False, log_level=logging.INFO).serialize(validateonly=True) env.make_testing_directory(env.expected_path('issue_tccm')) for generator in Generator.__subclasses__(): if not generator.__module__.startswith('linkml.generators'): pass elif not generator.directory_output: env.generate_single_file( [ 'issue_tccm', 'minimalmodel.' + generator.valid_formats[0] ], lambda: generator(env.input_path('issue_tccm', 'minimalmodel.yaml'), importmap=env.import_map, mergeimports=False, emit_metadata=False).serialize(), value_is_returned=True) else: env.generate_directory( ['issue_tccm', generator.__name__], lambda d: generator( env.input_path('issue_tccm', 'minimalmodel.yaml'), importmap=env.import_map, mergeimports=False, emit_metadata=False).serialize(directory=d))
def _do_test(self, tfn): env.generate_single_file(f'{tfn}.yaml', lambda: YAMLGenerator(env.input_path(f'{tfn}.yaml'), log_level=INFO).serialize(), filtr=yaml_filter, value_is_returned=True) env.generate_single_file(f'{tfn}.context.jsonld', lambda: ContextGenerator(env.input_path(f'{tfn}.yaml')).serialize(), filtr=ldcontext_metadata_filter, value_is_returned=True)
def test_domain_slots(self): """ Subsets need to be imported as well """ CsvGenerator(env.input_path('issue_38.yaml'), log_level=DEFAULT_LOG_LEVEL, importmap=env.input_path( 'biolink-model-importmap.json')).serialize() # We never get here if the imports fails self.assertEqual(True, True)
def test_issue_368(self): """ Make sure that types are generated as part of the output """ env.generate_single_file( 'issue_368_imports.py', lambda: PythonGenerator(env.input_path('issue_368_imports.yaml'), mergeimports=False).serialize(), comparator=lambda exp, act: compare_python( exp, act, self.env.expected_path('issue_368_imports.py')), value_is_returned=True) env.generate_single_file( 'issue_368.py', lambda: PythonGenerator(env.input_path('issue_368.yaml'), mergeimports=False).serialize(), comparator=lambda exp, act: compare_python( exp, act, self.env.expected_path('issue_368.py')), value_is_returned=True) with open(env.expected_path('issue_368.py')) as f: python = f.read() has_imports = False for line in python.split("\n"): if line.startswith("from . issue_368_imports"): imps = line.replace("from . issue_368_imports import ", "").split(", ") assert 'SampleEnum' in imps assert 'ParentClass' in imps has_imports = True assert has_imports module = compile_python(env.expected_path('issue_368.py')) enum_inst = module.SampleEnum("pva") # EnumInstanceImpl example = module.SampleClass(slot_1="pva") assert hasattr(example, "slot_1") assert example.slot_1.code.text == enum_inst.code.text assert str(example.slot_1) == "pva: PVA description" def dump_and_load(dumper: Callable, sfx: str) -> None: fname = env.actual_path(f'issue_368_1.{sfx}') dumper(example, fname) with open(fname) as f: print(f'\n----- {sfx} -----') print(f.read()) dump_and_load(json_dumper.dump, 'json') dump_and_load(yaml_dumper.dump, 'yaml') env.generate_single_file( 'issue_368.context.jsonld', lambda: ContextGenerator(env.input_path('issue_368.yaml'), emit_metadata=False).serialize(), filtr=ldcontext_metadata_filter, value_is_returned=True) dump_and_load( lambda obj, fname: rdf_dumper.dump( obj, fname, env.expected_path("issue_368.context.jsonld")), 'ttl')
def test_python_import(self): """ Import generates for biolink-model """ python = PythonGenerator( env.input_path('issue_38.yaml'), importmap=env.input_path( 'biolink-model-importmap.json')).serialize() msg = validate_python(python) if msg: self.fail(msg)
def test_local_imports(self): """ Make sure there is a '.' on a local import in python """ env.generate_single_file('importee.py', lambda: PythonGenerator(env.input_path('issue_tccm', 'importee.yaml'), importmap=env.import_map, mergeimports=False).serialize(), comparator=compare_python, value_is_returned=True) env.generate_single_file('importer.py', lambda: PythonGenerator(env.input_path('issue_tccm', 'importer.yaml'), importmap=env.import_map, mergeimports=False).serialize(), comparator=compare_python, value_is_returned=True)
def test_issue_167b_python(self): """ Annotations python example """ env.generate_single_file('issue_167b.py', lambda: PythonGenerator(env.input_path('issue_167b.yaml'), importmap=env.import_map, emit_metadata=False).serialize(), comparator=lambda exp, act: compare_python(exp, act, self.env.expected_path('issue_167b.py')), value_is_returned=True) env.generate_single_file('issue_167b2.py', lambda: PythonGenerator(env.input_path('issue_167b.yaml'), importmap=env.import_map, mergeimports=False, emit_metadata=False).serialize(), comparator=lambda exp, act: compare_python(exp, act, self.env.expected_path('issue_167b_nomerged.py')), value_is_returned=True)
def test_issue_120(self): """ Courses not inlining """ env.generate_single_file( 'issue_120.py', lambda: PythonGenerator(env.input_path('issue_120.yaml') ).serialize(), value_is_returned=True, comparator=compare_python) env.generate_single_file( 'issue_120.json', lambda: JsonSchemaGenerator(env.input_path('issue_120.yaml') ).serialize(), value_is_returned=True)
def test_issue_121(self): """ Make sure that types are generated as part of the output """ env.generate_single_file('issue_121.py', lambda: PythonGenerator(env.input_path('issue_121.yaml')).serialize(), comparator=compare_python, value_is_returned=True) with open(env.expected_path('issue_121.py')) as f: python= f.read() has_includes = False for line in python.split("\n"): if line.startswith("from includes.types"): assert line == "from includes.types import String" has_includes = True assert has_includes module = compile_python(env.expected_path('issue_121.py')) example = module.Biosample(depth="test") assert hasattr(example, "depth") assert example.depth == "test" example2 = module.ImportedClass() def output_generator(dirname) -> None: with open(os.path.join(dirname, 'issue_121_1.json'), 'w') as f: f.write(as_json(example)) with open(os.path.join(dirname, 'issue_121_2.json'), 'w') as f: f.write(as_json(example2)) env.generate_directory('issue_121', lambda dirname: output_generator(dirname))
def test_domain_slots(self): """ has_phenotype shouldn't appear in the UML graph """ yuml = YumlGenerator(env.input_path('issue_12.yaml')).serialize() self.assertEqual('http://yuml.me/diagram/nofunky;dir:TB/class/[BiologicalEntity]++- ' 'required thing 0..1>[PhenotypicFeature],[BiologicalEntity]', yuml) resp = requests.get(yuml) self.assertTrue(resp.ok)
def test_multiple_postinit(self): """ Generate postinit code for a multi-occurring element """ env.generate_single_file( 'issue_44.py', lambda: PythonGenerator(env.input_path('issue_44.yaml'), emit_metadata=False).serialize(), value_is_returned=True)
def test_issue_50(self): env.generate_single_file( 'issue_84.py', lambda: PythonGenerator(env.input_path('issue_84.yaml')).serialize( ), comparator=compare_python, value_is_returned=True)
def test_issue_80(self): """ Make sure that types are generated as part of the output """ env.generate_single_file( 'issue_80.py', lambda: PythonGenerator(env.input_path('issue_80.yaml')).serialize( ), comparator=lambda exp, act: compare_python( exp, act, self.env.expected_path('issue_80.py')), value_is_returned=True) module = compile_python(env.expected_path('issue_80.py')) example = module.Person("http://example.org/person/17", "Fred Jones", 43) # Create output for various forms def output_generator(dirname) -> None: with open(os.path.join(dirname, 'issue_80.json'), 'w') as f: f.write(as_json(example)) context = os.path.join(dirname, 'issue_80.context.jsonld') with open(context, 'w') as f: f.write( ContextGenerator( env.input_path('issue_80.yaml')).serialize()) with open(os.path.join(dirname, 'issue_80.ttl'), 'w') as f: f.write( as_rdf( example, contexts=context).serialize(format="turtle").decode()) env.generate_directory('issue_80', lambda dirname: output_generator(dirname))
def test_no_inverse_domain(self): with self.assertRaises(ValueError) as e: env.generate_single_file('issue_18_error3.yaml', lambda: as_yaml(SchemaLoader(env.input_path('issue_18_error3.yaml')).resolve()), value_is_returned=True) self.assertEqual("Unable to determine the range of slot `s1'. Its inverse (s2) has no declared domain", str(e.exception).strip())
def test_issue_167b_json(self): env.generate_single_file( 'issue_167b.json', lambda: JSONLDGenerator(env.input_path('issue_167b.yaml'), importmap=env.import_map).serialize(), filtr=json_metadata_filter, value_is_returned=True)
def test_inverse_mismatch(self): """ Test error detection when inverses don't match """ with self.assertRaises(ValueError) as e: env.generate_single_file('issue_18_error1.yaml', lambda: as_yaml(SchemaLoader(env.input_path('issue_18_error1.yaml')).resolve()), value_is_returned=True) self.assertEqual('Slot s1.inverse (s2) does not match slot s2.inverse (s3)', str(e.exception).strip())
def test_issue_167b_rdf(self): env.generate_single_file( 'issue_167b.ttl', lambda: RDFGenerator(env.input_path('issue_167b.yaml'), importmap=env.import_map).serialize(), comparator=compare_rdf, value_is_returned=True)
def test_slot_subclass(self): """ Test slot domain as superclass of parent """ env.generate_single_file( 'issue_56_good.py', lambda: PythonGenerator(env.input_path('issue_56_good.yaml') ).serialize(), comparator=compare_python, value_is_returned=True) with self.assertRaises(Exception) as e: env.generate_single_file( 'issue_56_bad.py', lambda: PythonGenerator(env.input_path('issue_56_bad.yaml') ).serialize(), comparator=compare_python, value_is_returned=True)
def test_contained_constructor(self): test_name = 'issue_355' """ Make sure that types are generated as part of the output """ env.generate_single_file(f'{test_name}.py', lambda: PythonGenerator(env.input_path(f'{test_name}.yaml')).serialize(), comparator=lambda exp, act: compare_python(exp, act, self.env.expected_path(f'{test_name}.py')), value_is_returned=True) module = compile_python(env.expected_path(f'{test_name}.py')) c = module.Container(module.Containee('11111', "Glaubner's disease")) self.assertEqual('''entry: '11111': id: '11111' value: Glaubner's disease''', as_yaml(c).strip()) c = module.Container({'22222': dict(id='22222', value='Phrenooscopy')}) self.assertEqual('''entry: '22222': id: '22222' value: Phrenooscopy''', as_yaml(c).strip()) alt_object = YAMLRoot() alt_object.id = '33333' alt_object.value = 'test' c = module.Container(alt_object) self.assertEqual('''entry: '33333': id: '33333' value: test''', as_yaml(c).strip()) c = module.Container([dict(id='44444', value="Gracken's curse")]) self.assertEqual('''entry: '44444': id: '44444' value: Gracken's curse''', as_yaml(c).strip())
def test_multi_domains(self): with self.redirect_logstream() as logger: env.generate_single_file('issue_18_warning1.yaml', lambda: as_yaml(SchemaLoader(env.input_path('issue_18_warning1.yaml'), logger=logger).resolve()), filtr=yaml_filter, value_is_returned=True) self.assertIn('Slot s2.inverse (s1), has multi domains (c1, c2) Multi ranges not yet implemented', logger.result)
def test_issue_371(self): """ Infer a model from a CSV """ CLS = 'my_class' obj = infer_model(env.input_path('issue_371.csv'), sep=',', class_name=CLS) print(yaml.dump(obj, default_flow_style=False, sort_keys=False)) assert len(obj['classes'][CLS]['slots']) == 4 assert obj['slots']['age']['range'] == 'integer' assert obj['slots']['name']['range'] == 'string'
def test_issue_167b_python(self): """ Annotations python example """ env.generate_single_file( 'issue_167b.py', lambda: PythonGenerator(env.input_path('issue_167b.yaml'), importmap=env.import_map).serialize(), comparator=compare_python, value_is_returned=True)
def test_issue_167(self): """ Test extensions to the four basic types """ env.generate_single_file( 'issue_167.yaml', lambda: as_yaml( SchemaLoader(env.input_path('issue_167.yaml')).resolve()), value_is_returned=True, filtr=yaml_filter)
def test_issue_177_dup(self): env.generate_single_file( 'issue_177_error.yaml', lambda: as_yaml( SchemaLoader(env.input_path('issue_177_error.yaml')).resolve() ), value_is_returned=True, filtr=yaml_filter)
def test_context(self): """ Test no context in the argument""" self.assertIn( '''"@context": [ [ "https://w3id.org/biolink/biolinkml/context.jsonld" ],''', JSONLDGenerator(env.input_path('issue_332.yaml')).serialize())
def test_namespace(self): context = "https://biolink.github.io/biolink-model/context.jsonld" env.generate_single_file( 'issue_namespace.ttl', lambda: RDFGenerator(env.input_path('issue_namespace.yaml') ).serialize(context=context), comparator=compare_rdf, value_is_returned=True)
def test_dictionary_name(self): """ Allow dictionaries w/ explicit keys or identifiers through as long as they match """ yaml = env.generate_single_file(['issue_tccm', 'explicit_key_id.yaml'], lambda: YAMLGenerator(env.input_path('issue_tccm', 'explicit_key_id.yaml'), importmap=env.import_map, mergeimports=False, emit_metadata=False).serialize(), value_is_returned = True) print(yaml)
def test_prefix(self): env.generate_single_file( 'issue_107.py', lambda: PythonGenerator(env.input_path('issue_107.yaml') ).serialize(), comparator=lambda exp, act: compare_python( exp, act, self.env.expected_path('issue_107.py')), value_is_returned=True)