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_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_local_imports(self):
""" Check the local import behavior """
test_dir = 'issue_260'
# Useful to have an __init__.py available
init_path = env.actual_path(test_dir, '__init__.py')
if not os.path.exists(init_path):
with open(init_path, 'w'):
pass
fp = f'{test_dir}/issue_260a.py'
env.generate_single_file(
fp,
lambda: PythonGenerator(env.input_path(test_dir, 'issue_260a.yaml'
),
importmap=env.import_map,
mergeimports=False).serialize(),
comparator=lambda expected, actual: compare_python(
expected, actual, env.expected_path(fp)),
value_is_returned=True)
fp = f'{test_dir}/issue_260b.py'
env.generate_single_file(
fp,
lambda: PythonGenerator(env.input_path(test_dir, 'issue_260b.yaml'
),
importmap=env.import_map,
mergeimports=False).serialize(),
comparator=lambda expected, actual: compare_python(
expected, actual, env.expected_path(fp)),
value_is_returned=True)
fp = f'{test_dir}/issue_260c.py'
env.generate_single_file(
fp,
lambda: PythonGenerator(env.input_path(test_dir, 'issue_260c.yaml'
),
importmap=env.import_map,
mergeimports=False).serialize(),
comparator=lambda expected, actual: compare_python(
expected, actual, env.expected_path(fp)),
value_is_returned=True)
fp = f'{test_dir}/issue_260.py'
env.generate_single_file(
fp,
lambda: PythonGenerator(env.input_path(test_dir, 'issue_260.yaml'),
importmap=env.import_map,
mergeimports=False).serialize(),
comparator=lambda expected, actual: compare_python(
expected, actual, env.expected_path(fp)),
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_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 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_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_owl(self, name: str) -> Graph:
self.env.generate_single_file(f'{name}.owl',
lambda: OwlSchemaGenerator(env.input_path(f'{name}.yaml'),
importmap=env.import_map).serialize(),
value_is_returned=True, comparator=compare_rdf)
g = Graph()
g.parse(env.expected_path(f'{name}.owl'), format="turtle")
return g
def test_prefix(self):
env.generate_single_file(
'issue112.yuml',
lambda: YumlGenerator(env.input_path('issue_112.yaml')).serialize(
),
value_is_returned=True)
with open(env.expected_path('issue112.yuml')) as f:
url = f.read()
resp = requests.get(url)
self.assertTrue(resp.ok)
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,
expected_path=env.expected_path('foo.py'))
if msg:
self.fail(msg)
def test_inheritence(self):
env.generate_single_file('issue_14.py',
lambda: PythonGenerator(env.input_path('issue_14.yaml')).serialize(),
comparator=lambda exp, act: compare_python(exp, act, self.env.expected_path('issue_14.py')),
filtr=metadata_filter, value_is_returned=True)
# Added test for issue #183, where sex_qualifier disappeared from MixinOwner class
module = compile_python(env.expected_path('issue_14.py'))
subject = module.SubjectRange1(id='sr1',name="SubjectRange1", subject='thing1', object='thing2')
mixin_owner = module.MixinOwner(id='mo1', subject='sr1', name='MixinOwner1', object='thing2', sex_qualifier="ntx")
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=lambda exp, act: compare_python(
exp, act, env.expected_path('importee.py')),
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=lambda exp, act: compare_python(
exp, act, env.expected_path('importer.py')),
value_is_returned=True)
def test_slot_usage_only(self):
""" Slot_usages without parents don't generate slots period. """
env.generate_single_file(
'issue_ttcm_1.py',
lambda: PythonGenerator(env.input_path('issue_tccm',
'resourcedescription.yaml'),
importmap=env.import_map,
mergeimports=True).serialize(),
comparator=lambda exp, act: compare_python(
exp, act, env.expected_path('issue_ttcm_1.py')),
value_is_returned=True)
def test_pattern_1(self):
""" Test the pattern ehnancement """
file = "pattern_1"
env.generate_single_file(f'{self.testdir}/{file}.py',
lambda: PythonGenerator(env.input_path(self.testdir, f'{file}.yaml'),
importmap=env.import_map, mergeimports=False).serialize(),
comparator=lambda exp, act: compare_python(exp, act, self.env.expected_path(f'{self.testdir}/{file}.py')),
value_is_returned=True)
module = compile_python(env.expected_path(self.testdir, f"{file}.py"))
d1 = yaml.load(StringIO(d1_test), yaml.loader.SafeLoader)
dev1 = module.DiskDevice(**d1)
print("HERE")
def test_issue_python_ordering(self):
""" Make sure that types are generated as part of the output """
env.generate_single_file('issue_134.py',
lambda: PythonGenerator(env.input_path('issue_134.yaml')).serialize(),
comparator=compare_python, value_is_returned=True)
module = compile_python(env.expected_path('issue_134.py'))
e = module.E('id:1')
b = module.B('id:2')
e.has_b = b
def output_generator(dirname) -> None:
with open(os.path.join(dirname, 'issue_134.json'), 'w') as f:
f.write(as_json(e))
env.generate_directory('issue_134', lambda dirname: output_generator(dirname) )
def test_enum_import(self):
""" Enum reference isn't getting merged on module import """
# env.generate_single_file('file1.py',
# lambda: PythonGenerator(env.input_path(self.directory, 'file1.yaml'),
# mergeimports=True).serialize(),
# comparator=lambda exp, act: compare_python(exp, act, env.expected_path(self.directory, 'file1.py')),
# value_is_returned=True)
env.generate_single_file(
'file2.py',
lambda: PythonGenerator(env.input_path(self.directory, 'file2.yaml'
),
mergeimports=True).serialize(),
comparator=lambda exp, act: compare_python(
exp, act, env.expected_path(self.directory, 'file2.py')),
value_is_returned=True)
