def test_error_paths(self):
""" Test various loader error situations"""
fn = env.input_path('loadererror1.yaml')
with self.assertRaises(ValueError,
msg="Unknown slot domain should fail") as e:
SchemaLoader(fn).resolve()
self.assertIn('loadererror1.yaml", line 11, col 13', str(e.exception))
fn = env.input_path('loadererror2.yaml')
with self.assertRaises(ValueError, msg="No Type URI") as e:
SchemaLoader(fn).resolve()
self.assertIn('type "string" does not declare a URI', str(e.exception))
fn = env.input_path('loadererror2a.yaml')
with self.assertRaises(ValueError,
msg="Optional key slot should fail") as e:
SchemaLoader(fn).resolve()
self.assertIn('slot: s1 - key and identifier slots cannot be optional',
str(e.exception))
fn = env.input_path('loadertest1.yaml')
schema = SchemaLoader(fn).resolve()
self.assertEqual('string', schema.slots['s1'].range)
fn = env.input_path('loadererror4.yaml')
with self.assertRaises(ValueError,
msg="Default prefix is not defined") as e:
SchemaLoader(fn).resolve()
self.assertIn('loadererror4.yaml", line 6, col 17', str(e.exception))
def test_load_raw_file(self):
""" Test loading a data file """
self._verify_schema1_content(
load_raw_schema(env.input_path('schema1.yaml')), 'schema1')
# Verify that we can't pass source_file parameters when we've got a directory name
with self.assertRaises(AssertionError):
load_raw_schema(env.input_path('schema1.yaml'),
source_file_size=117)
def test_missing_type_uri(self):
""" A type with neither a typeof or uri is an error """
fn = env.input_path('loadererror10.yaml')
with self.assertRaises(ValueError,
msg="A non-typeof type has to have a URI") as e:
_ = SchemaLoader(fn).resolve()
self.assertIn('loadererror10.yaml", line 12, col 3', str(e.exception))
fn = env.input_path('loaderpass11.yaml')
_ = SchemaLoader(fn).resolve()
def test_representation_errors(self):
""" Test misformed schema elements """
fn = env.input_path('typeerror1.yaml')
with self.assertRaises(ValueError):
SchemaLoader(fn)
fn = env.input_path('typeerror2.yaml')
with self.assertRaises(ValueError):
SchemaLoader(fn)
fn = env.input_path('typeerror3.yaml')
with self.assertRaises(ValueError):
SchemaLoader(fn)
fn = env.input_path('typeerror4.yaml')
with self.assertRaises(ValueError):
SchemaLoader(fn)
def test_dupcheck_loader(self):
""" Make sure the duplicate checker finds duplicates """
with open(env.input_path('yaml1.yaml')) as f:
y1 = yaml.safe_load(f)
self.assertEqual(17, y1['f1'])
with open(env.input_path('yaml1.yaml')) as f:
with self.assertRaises(ValueError):
yaml.load(f, DupCheckYamlLoader)
with open(env.input_path('yaml2.yaml')) as f:
with self.assertRaises(ValueError):
yaml.load(f, DupCheckYamlLoader)
with open(env.input_path('schema1.yaml')) as f:
s1 = yaml.load(f, DupCheckYamlLoader)
self.assertEqual('schema1', s1['name'])
def test_default_range(self):
""" Validate default slot range settings """
schema = SchemaLoader(env.input_path('resolver1.yaml')).resolve()
self.assertEqual({
's1': 't1',
's2': 't2'
}, {slot.name: slot.range
for slot in schema.slots.values()})
schema = SchemaLoader(env.input_path('resolver2.yaml')).resolve()
self.assertEqual({
's1': 'string',
's2': 't2'
}, {slot.name: slot.range
for slot in schema.slots.values()})
def test_multi_key(self):
""" Multiple keys are not supported """
fn = env.input_path('loadererror6.yaml')
with self.assertRaises(
ValueError, msg='Multiple keys/identifiers not allowed') as e:
_ = SchemaLoader(fn).resolve()
self.assertIn('multiple keys/identifiers not allowed',
str(e.exception))
fn = env.input_path('loadererror7.yaml')
with self.assertRaises(ValueError,
msg="Two or more keys are not allowed") as e:
_ = SchemaLoader(fn).resolve()
self.assertIn('multiple keys/identifiers not allowed',
str(e.exception))
def test_empty_range(self):
""" A type must have either a base or a parent """
fn = env.input_path('loadererror5.yaml')
with self.assertRaises(ValueError,
msg="Range error should be raised") as e:
_ = SchemaLoader(fn).resolve()
self.assertIn('loadererror5.yaml", line 9, col 3', str(e.exception))
def test_undefined_subset(self):
""" Throw an error on an undefined subset reference """
fn = env.input_path('loadererror11.yaml')
with self.assertRaises(ValueError,
msg="Subset references must be valid") as e:
_ = SchemaLoader(fn).resolve()
self.assertIn('loadererror11.yaml", line 22, col 16', str(e.exception))
def test_as_yaml(self):
""" Test the YAML output representation """
schema = self.fix_schema_metadata(
load_raw_schema(env.input_path('schema4.yaml')))
env.eval_single_file(env.expected_path('schema4.yaml'),
as_yaml(schema),
filtr=lambda s: s)
def test_multi_schemas(self):
""" Test multiple schemas in the same file """
def check_types(s: SchemaDefinition) -> None:
output = env.expected_path('schema4.json')
if not os.path.exists(output):
with open(output, 'w') as f:
f.write(
as_json(
JsonObj(
**{
k: as_dict(loads(as_json(v)))
for k, v in s.types.items()
})))
with open(output) as f:
expected = as_dict(load(f))
self.assertEqual(
expected,
{k: as_dict(loads(as_json(v)))
for k, v in s.types.items()})
s.types = None
self._verify_schema1_content(
load_raw_schema(env.input_path('schema4.yaml')), 'schema4',
check_types)
def test_uri_and_curie(self):
""" Compile a model of URI's and Curies and then test the various types """
self.single_file_generator('py',
PythonGenerator,
filtr=metadata_filter,
comparator=compare_python)
# Check that the interpretations are correct
self.single_file_generator(
'jsonld',
ContextGenerator,
filtr=ldcontext_metadata_filter,
comparator=lambda expected, actual: compare_rdf(
expected, actual, fmt="json-ld"))
self.single_file_generator('json',
JSONLDGenerator,
filtr=json_metadata_filter)
module = compile_python(env.expected_path(self.model_name + '.py'))
curie_obj = module.C1("ex:obj1",
hasCurie="ex:curie",
hasURI="http://example.org/test/uri",
hasNcName="A123",
id2="ex:id2")
instance_jsonld = loads('{ "ex": "http://example.org/test/inst#" }')
g = as_rdf(
curie_obj,
[env.input_path(self.model_name + '.jsonld'), instance_jsonld])
env.eval_single_file(env.expected_path('uriandcurie.ttl'),
g.serialize(format='ttl').decode(), lambda s: s,
compare_rdf)
def test_multi_usages_3(self):
""" Illegal alias usage """
with self.assertRaises(ValueError) as e:
schema = SchemaLoader(
env.input_path('multi_usages_3.yaml')).resolve()
self.assertIn(
'Class: "child_class1" - alias not permitted in slot_usage slot: foo',
str(e.exception))
def test_mergeerror1(self):
""" Test conflicting definitions path """
fn = env.input_path('mergeerror1.yaml')
with self.assertRaises(ValueError) as ve:
SchemaLoader(fn)
self.assertEqual(
"Conflicting URIs (http://example.org/schema2, http://example.org/schema1) for item: c1",
str(ve.exception))
def test_pred_types(self):
self.env.generate_single_file(
'owl2.owl',
lambda: OwlSchemaGenerator(env.input_path('owl2.yaml'),
importmap=env.import_map).serialize(),
filtr=filtr,
comparator=compare_rdf,
value_is_returned=True)
def test_multi_usages_2(self):
""" Slot usage chain with starting alias """
schema = SchemaLoader(env.input_path('multi_usages_2.yaml')).resolve()
self._eval_expected(schema, 's1', 'value', 'root_class', None, None, 'string')
self._eval_expected(schema, 'child_class1_s1', 'value', 'child_class1', 's1', 's1', 'boolean')
self._eval_expected(schema, 'child_class2_s1', 'value', 'child_class2', 'child_class1_s1', 's1', 'integer')
self._eval_expected(schema, 'child_class3_s1', 'value', 'child_class3', 'child_class2_s1', 's1', 'integer')
env.eval_single_file(env.expected_path('multi_usages_2.yaml'), as_yaml(schema), filtr=yaml_filter)
def test_key_and_id(self):
""" A slot cannot be both a key and an identifier """
fn = env.input_path('loadererror8.yaml')
with self.assertRaises(
ValueError,
msg="A slot cannot be both a key and identifier") as e:
_ = SchemaLoader(fn).resolve()
self.assertIn(
'A slot cannot be both a key and identifier at the same time',
str(e.exception))
fn = env.input_path('loadererror9.yaml')
with self.assertRaises(
ValueError,
msg="A slot cannot be both a key and identifier") as e:
_ = SchemaLoader(fn).resolve()
self.assertIn(
'A slot cannot be both a key and identifier at the same time',
str(e.exception))
def test_type_uri(self):
""" Validate type URI's and the fact that they aren't inherited """
schema = SchemaLoader(env.input_path('resolver2.yaml')).resolve()
self.assertEqual(
{
'string': 'xsd:string',
't1': 'xsd:string',
't2': 'xsd:int',
't3': 'xsd:string'
}, {t.name: t.uri
for t in schema.types.values()})
def test_importmap(self):
""" Test the importmap parameter """
fn = env.input_path('import_test_1.yaml')
importmap = {
"http://example.org/import_test_2": "import_test_2",
"loc/imp3": "import_test_3",
"base:import_test_4": "http://example.org/import_test_4",
"http://example.org/import_test_4": "import_test_4",
"types": "http://w3id.org/biolink/biolinkml/types"
}
self.env.generate_single_file(
'import_test_1.json',
lambda: as_json(SchemaLoader(fn, importmap=importmap).resolve()),
filtr=json_metadata_filter)
def test_element_slots(self):
""" Test all element slots and their inheritence """
schema = SchemaLoader(env.input_path('resolver3.yaml')).resolve()
x = {
k: v
for k, v in as_dict(schema.slots['s1']).items()
if v is not None and v != []
}
outfile = env.expected_path('resolver3.json')
if not os.path.exists(outfile):
with open(outfile, 'w') as f:
f.write(as_json(JsonObj(**x)))
with open(outfile) as f:
expected = as_dict(load(f))
self.assertEqual(expected, x)
def eval_synopsis(self,
base_name: str,
source: Optional[str] = None) -> None:
schema = SchemaLoader(source if source else env.input_path(base_name +
'.yaml'),
importmap=env.import_map)
schema.resolve()
self.summary = schema.synopsis.summary()
self.env.generate_single_file(
base_name + '.errs',
lambda: '\n'.join(schema.synopsis.errors()),
value_is_returned=True)
self.env.generate_single_file(base_name + '.synopsis',
lambda: self.summary,
value_is_returned=True)
def test_slot_class_paths(self):
""" Test for aliased slot name, class identifier path and slot type path """
gen = GeneratorTest(env.input_path('ownalltest.yaml'))
gen.sort_class_slots = True
self.assertEqual(['s1', 's5', 's6', 's2', 's3', 's4'], [
gen.aliased_slot_name(s.name)
for s in gen.all_slots(cast(ClassDefinitionName, 'c4'))
])
self.assertEqual(['s5', 's1', 's6', 's2', 's3', 's4'], [
gen.aliased_slot_name(s)
for s in gen.all_slots(cast(ClassDefinitionName, 'c5'))
])
self.assertEqual(
{
'c4_s1': ['int'],
'c4_s5': ['Bool', 'T5'],
'c4_s6': ['int', 'C1S1', 'C2S1', 'C3S1', 'C4S1'],
's2': ['int', 'C1S1'],
's3': ['int', 'T2', 'T3'],
's4': ['Bool']
}, {
s.name: gen.slot_range_path(s)
for s in gen.all_slots(cast(ClassDefinitionName, 'c4'))
})
self.assertEqual(
{
'c4_s5': ['Bool', 'T5'],
'c5_s1': ['int'],
'c5_s6': ['str'],
's2': ['int', 'C1S1'],
's3': ['int', 'T2', 'T3'],
's4': ['Bool']
}, {
s.name: gen.slot_range_path(s)
for s in gen.all_slots(cast(ClassDefinitionName, 'c5'))
})
self.assertEqual({
's1': ['int'],
's3': ['int', 'T2', 'T3']
}, {
s.name: gen.slot_range_path(s)
for s in gen.all_slots(cast(ClassDefinitionName, 'c1'))
})
def test_visitors(self):
""" Test the generator visitor functions """
gen = GeneratorTest(env.input_path('generator1.yaml'))
gen.serialize()
self.assertEqual(expected1, gen.visited)
gen.visit_all_class_slots = False
gen.serialize()
self.assertEqual(expected2, gen.visited)
gen.visit_all_class_slots = True
gen.visits_are_sorted = True
gen.serialize()
self.assertEqual(expected3, gen.visited)
gen.visits_are_sorted = False
gen.sort_class_slots = True
gen.serialize()
self.assertEqual(expected4, gen.visited)
gen.sort_class_slots = False
gen.visit_class_return = False
gen.serialize()
self.assertEqual(expected5, gen.visited)
def test_import_from_url(self):
""" Validate namespace bindings """
shex = ShExGenerator(env.input_path('import_test_l2.yaml')).serialize()
self.assertEqual(
"""BASE <http://example.org/l2/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX l1: <http://example.org/l1/>
PREFIX base: <http://example.org/b/>
l1:Int xsd:integer
base:String xsd:string
base:BaseClass CLOSED {
( $base:BaseClass_tes base:base_slot @base:String ? ;
rdf:type [ base:BaseClass ] ?
)
}
l1:L1Class (
CLOSED {
( $l1:L1Class_tes ( l1:l1_slot1 @base:String ? ;
l1:l1_slot2 @l1:Int ?
) ;
rdf:type [ l1:L1Class ] ?
)
} OR @<L2Class>
)
<L2Class> CLOSED {
( $<L2Class_tes> ( &l1:L1Class_tes ;
rdf:type [ l1:L1Class ] ? ;
<l2_slot1> @base:String ? ;
<l2_slot2> @l1:Int ?
) ;
rdf:type [ <L2Class> ] ?
)
}""", shex.strip())
def test_inherited_slot(self):
""" Validate default slot range settings """
schema = SchemaLoader(env.input_path('inherited_slots.yaml')).resolve()
self.assertTrue('same as' in schema.classes['named thing'].slots)
def test_name_from_sourcefile(self):
""" Test no identifier at all """
with self.assertRaises(ValueError):
load_raw_schema(env.input_path('schema5.yaml'))
def test_own_slots(self):
""" Test the generator own_slots and all_slots helper functions """
gen = GeneratorTest(env.input_path('ownalltest.yaml'))
gen.sort_class_slots = True
self.assertEqual(
['s6'],
[s.name for s in gen.own_slots(cast(ClassDefinitionName, 'at1'))])
self.assertEqual(
['s6'],
[s.name for s in gen.all_slots(cast(ClassDefinitionName, 'at1'))])
self.assertEqual(['s6'], [
s.name for s in gen.all_slots(cast(ClassDefinitionName, 'at1'),
cls_slots_first=True)
])
self.assertEqual(
['s5', 's6'],
[s.name for s in gen.own_slots(cast(ClassDefinitionName, 'm2'))])
self.assertEqual(
['s5', 's6'],
[s.name for s in gen.all_slots(cast(ClassDefinitionName, 'm2'))])
self.assertEqual(['s5', 's6'], [
s.name for s in gen.all_slots(cast(ClassDefinitionName, 'm2'),
cls_slots_first=True)
])
self.assertEqual(
['s4'],
[s.name for s in gen.own_slots(cast(ClassDefinitionName, 'm1'))])
self.assertEqual(
['s4'],
[s.name for s in gen.all_slots(cast(ClassDefinitionName, 'm1'))])
self.assertEqual(['s4'], [
s.name for s in gen.all_slots(cast(ClassDefinitionName, 'm1'),
cls_slots_first=True)
])
self.assertEqual(
['s1', 's3'],
[s.name for s in gen.own_slots(cast(ClassDefinitionName, 'c1'))])
self.assertEqual(
['s1', 's3'],
[s.name for s in gen.all_slots(cast(ClassDefinitionName, 'c1'))])
self.assertEqual(['s1', 's3'], [
s.name for s in gen.all_slots(cast(ClassDefinitionName, 'c1'),
cls_slots_first=True)
])
self.assertEqual(
['s2', 's4'],
[s.name for s in gen.own_slots(cast(ClassDefinitionName, 'c2'))])
self.assertEqual(
['s1', 's2', 's3', 's4'],
[s.name for s in gen.all_slots(cast(ClassDefinitionName, 'c2'))])
self.assertEqual(['s2', 's4', 's1', 's3'], [
s.name for s in gen.all_slots(cast(ClassDefinitionName, 'c2'),
cls_slots_first=True)
])
self.assertEqual(
['s5', 's6'],
[s.name for s in gen.own_slots(cast(ClassDefinitionName, 'c3'))])
self.assertEqual(
['s1', 's2', 's3', 's4', 's5', 's6'],
[s.name for s in gen.all_slots(cast(ClassDefinitionName, 'c3'))])
self.assertEqual(['s5', 's6', 's2', 's4', 's1', 's3'], [
s.name for s in gen.all_slots(cast(ClassDefinitionName, 'c3'),
cls_slots_first=True)
])
self.assertEqual(
['c4_s1', 'c4_s5', 'c4_s6'],
[s.name for s in gen.own_slots(cast(ClassDefinitionName, 'c4'))])
self.assertEqual(
['c4_s1', 'c4_s5', 'c4_s6', 's2', 's3', 's4'],
[s.name for s in gen.all_slots(cast(ClassDefinitionName, 'c4'))])
self.assertEqual(['c4_s1', 'c4_s5', 'c4_s6', 's2', 's4', 's3'], [
s.name for s in gen.all_slots(cast(ClassDefinitionName, 'c4'),
cls_slots_first=True)
])
self.assertEqual(
['c5_s1', 'c5_s6'],
[s.name for s in gen.own_slots(cast(ClassDefinitionName, 'c5'))])
self.assertEqual(
['c4_s5', 'c5_s1', 'c5_s6', 's2', 's3', 's4'],
[s.name for s in gen.all_slots(cast(ClassDefinitionName, 'c5'))])
self.assertEqual(['c5_s1', 'c5_s6', 'c4_s5', 's2', 's4', 's3'], [
s.name for s in gen.all_slots(cast(ClassDefinitionName, 'c5'),
cls_slots_first=True)
])
def test_load_text(self):
""" Test loading straight text """
with open(env.input_path('schema1.yaml')) as f:
self._verify_schema1_content(
load_raw_schema(f.read(), 'schema1.yaml',
"Mon Dec 31 11:25:38 2018", 76), 'schema1')
def test_orphan_slot_usage(self):
""" Make sure an orphan slot_usage works """
# The bug is that this goes into an endless loop
output_dir = env.temp_file_path('slottest')
GolrSchemaGenerator(env.input_path('orphan_slot_usage.yaml')).serialize(directory=output_dir)
def test_as_json(self):
schema = self.fix_schema_metadata(
load_raw_schema(env.input_path('schema6.yaml')))
env.eval_single_file(env.expected_path('schema6.json'),
as_json(schema),
filtr=lambda s: s)
