class TestSchemaOrg(unittest.TestCase):
"""Using SchemaOrg Schema to test all functions in biothings_schema
"""
def setUp(self):
# preload biothings schema
PATH = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
self.se = Schema(PATH)
# test list_all_classes
self.clses = self.se.list_all_classes()
# test list_all_properties
self.props = self.se.list_all_properties()
def test_schemaclass_class(self):
""" Test the SchemaClass Class using all classes in BioThings schema"""
# loop through all classes
for _cls in self.clses:
# test get_class
scls = self.se.get_class(_cls.name)
# test describe function
describe = scls.describe()
def test_schemaproperty_class(self):
""" Test the SchemaProperty Class using all classes in BioThings schema
"""
# loop through all properties
for _prop in self.props:
# test get_property
sp = self.se.get_property(_prop.name)
# test describe function
describe = sp.describe()
class TestSchemaClass(unittest.TestCase):
"""Test Schema Validator Class
"""
def setUp(self):
schema_url = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
self.se = Schema(schema_url)
def test_list_all_classes(self):
""" Test list_all_classes function
"""
all_cls = self.se.list_all_classes()
all_cls_names = [_cls.name for _cls in all_cls]
# assert root level Class in all classes
self.assertIn('schema:Thing', all_cls_names)
# assert class "Gene" in all classes
self.assertIn('bts:Gene', all_cls_names)
# class 'ffff' should not be one of the classes
self.assertNotIn('bts:ffff', all_cls_names)
# class name should be curie
self.assertNotIn('Thing', all_cls_names)
# assert type of the class is SchemaClass
self.assertEqual(SchemaClass, type(all_cls[0]))
def test_list_all_properties(self):
""" Test list_all_properties function"""
all_props = self.se.list_all_properties()
all_prop_names = [_prop.name for _prop in all_props]
# assert "name" in all props
self.assertIn('schema:name', all_prop_names)
# property name should be curie
self.assertNotIn('name', all_prop_names)
# assert "ffff" should not be one of the props
self.assertNotIn('bts:ffff', all_prop_names)
# assert type of the property is SchemaProperty
self.assertEqual(SchemaProperty, type(all_props[0]))
def test_get_class(self):
""" Test get_class function"""
scls = self.se.get_class("schema:Gene")
self.assertEqual(SchemaClass, type(scls))
def test_get_property(self):
""" Test get_property function"""
sp = self.se.get_property("ensembl")
self.assertEqual(SchemaProperty, type(sp))
class TestSchemaOrg(unittest.TestCase):
"""Using SchemaOrg Schema to test all functions in biothings_schema
"""
def setUp(self):
# preload schemaorg-only schema
self.se = Schema(base_schema=["schema.org"])
# test list_all_classes
self.clses = self.se.list_all_classes()
# test list_all_properties
self.props = self.se.list_all_properties()
def test_schemaclass_class(self):
""" Test the SchemaClass Class using all classes in Schemaorg schema"""
# loop through all classes
for _cls in self.clses:
# test get_class
scls = self.se.get_class(_cls.name)
# test describe function
describe = scls.describe()
scls = self.se.get_class(_cls.name, output_type="curie")
describe = scls.describe()
scls = self.se.get_class(_cls.name, output_type="uri")
describe = scls.describe()
scls = self.se.get_class(_cls.name, output_type="label")
describe = scls.describe()
def test_schemaproperty_class(self):
""" Test the SchemaProperty Class using all classes in Schemaorg schema
"""
# loop through all properties
for _prop in self.props:
# test get_property
sp = self.se.get_property(_prop.name)
# test describe function
describe = sp.describe()
sp = self.se.get_property(_prop.name, output_type="curie")
# test describe function
describe = sp.describe()
sp = self.se.get_property(_prop.name, output_type="uri")
# test describe function
describe = sp.describe()
sp = self.se.get_property(_prop.name, output_type="label")
# test describe function
describe = sp.describe()
class TestSchemaClass(unittest.TestCase):
"""Test Schema Validator Class
"""
def setUp(self):
schema_file = os.path.join(_CURRENT, 'data',
'extend_from_bioschemas.json')
self.se = Schema(schema_file)
def test_list_all_classes(self):
""" Test list_all_classes function
"""
all_cls = self.se.list_all_classes()
all_cls_names = [_cls.name for _cls in all_cls]
# assert root level Class in all classes
self.assertIn('bioschemas:Gene', all_cls_names)
# class name should be curie
self.assertNotIn('Gene', all_cls_names)
# assert type of the class is SchemaClass
self.assertEqual(SchemaClass, type(all_cls[0]))
def test_list_all_properties(self):
""" Test list_all_properties function"""
all_props = self.se.list_all_properties()
all_prop_names = [_prop.name for _prop in all_props]
# assert "name" in all props
self.assertIn('schema:name', all_prop_names)
# property name should be curie
self.assertNotIn('name', all_prop_names)
# assert "ffff" should not be one of the props
self.assertNotIn('bts:ffff', all_prop_names)
# assert type of the property is SchemaProperty
self.assertEqual(SchemaProperty, type(all_props[0]))
def test_get_class(self):
""" Test get_class function"""
scls = self.se.get_class("bioschemas:Gene")
self.assertEqual(SchemaClass, type(scls))
def test_get_property(self):
""" Test get_property function"""
sp = self.se.get_property("bioschemas:encodesBioChemEntity")
self.assertEqual(SchemaProperty, type(sp))
def timeit():
start = time.time()
PATH = 'https://raw.githubusercontent.com/data2health/schemas/biothings/biothings/biothings_curie_kevin.jsonld'
se = Schema(PATH)
clses = se.list_all_classes()
for _cls in clses:
es_class = {'schema': None, 'name': None, 'clses': None, 'props': []}
es_class['schema'] = _cls.prefix
es_class['name'] = _cls.label
es_class['clses'] = [', '.join(map(str, schemas))
for schemas in _cls.parent_classes]
for prop in _cls.list_properties(group_by_class=False):
info = prop.describe()
_property = {'name': str(prop),
'value_types': [str(_type) for _type in info['range']],
'description': info.get('description')}
es_class['props'].append(_property)
end = time.time()
print(end - start)