def validate(config, path, input_type, output_dir, record_size):
os.makedirs(output_dir, exist_ok=True)
validator = Validator(record_size)
t = get_transformer(get_type(path))()
t.parse(path)
# t = load_transformer(path, input_type)
validator.validate(t.graph)
for error_type, failures in validator.error_dict.items():
filename = error_type.replace(' ', '_') + '.log'
with click.open_file(os.path.join(output_dir, filename), 'a+') as f:
f.write('--- {} ---\n'.format(datetime.now()))
for t in failures:
if len(t) == 2:
n, message = t
if message is not None:
f.write('node({}):\t{}\n'.format(n, message))
else:
f.write('node({})\n'.format(n))
elif len(t) == 3:
u, v, message = t
if message is not None:
f.write('edge({}, {}):\t{}\n'.format(u, v, message))
else:
f.write('edge({}, {})\n'.format(u, v))
if validator.error_dict == {}:
click.echo('No errors found')
else:
for key, value in validator.error_dict.items():
click.echo('{} - {}'.format(key, len(value)))
def test_validator_good():
"""
A fake test to establish a success condition for validation
"""
G = nx.MultiDiGraph()
G.add_node('UniProtKB:P123456',
id='UniProtKB:P123456',
name='fake',
category=['Protein'])
G.add_node('UBERON:0000001',
id='UBERON:0000001',
name='fake',
category=['NamedThing'])
G.add_node('UBERON:0000002',
id='UBERON:0000002',
name='fake',
category=['NamedThing'])
G.add_edge('UBERON:0000001',
'UBERON:0000002',
association_id='UBERON:0000001-part_of-UBERON:0000002',
relation='RO:1',
edge_label='part_of',
subject='UBERON:0000001',
object='UBERON:0000002')
validator = Validator(verbose=True)
e = validator.validate(G)
assert len(e) == 0
def test_validate_json():
"""
Validate against a valid representative Biolink Model compliant JSON
"""
json_file = os.path.join(resource_dir, 'valid.json')
jt = JsonTransformer()
jt.parse(json_file)
validator = Validator()
e = validator.validate(jt.graph)
assert len(e) == 0
def test_validator_bad():
"""
A fake test to establish a fail condition for validation
"""
G = nx.MultiDiGraph()
G.add_node('x', foo=3)
G.add_node('ZZZ:3', nosuch=1)
G.add_edge('x', 'y', baz=6)
validator = Validator(verbose=True)
e = validator.validate(G)
assert len(e) > 0
def test_validator_bad():
"""
fake test
"""
G = nx.MultiDiGraph()
G.add_node('x', foo=3)
G.add_node('ZZZ:3', nosuch=1)
G.add_edge('x', 'y', baz=6)
validator = Validator()
validator.validate(G)
write_errors(validator)
assert not validator.ok()
def test_validator_rdf():
"""
use test files
"""
cwd = os.path.abspath(os.path.dirname(__file__))
resdir = os.path.join(cwd, 'resources')
src_path = os.path.join(resdir, 'monarch', 'biogrid_test.ttl')
t = ObanRdfTransformer()
t.parse(src_path, input_format="turtle")
validator = Validator()
validator.validate(t.graph)
write_errors(validator)
def test_validator_bad():
"""
fake test
"""
G = nx.MultiDiGraph()
G.add_node('x', foo=3)
G.add_node('ZZZ:3', nosuch=1)
G.add_edge('x', 'y', baz=6)
validator = Validator()
validator.validate(G)
write_errors(validator)
# TODO: status is True when it should be False
assert not validator.ok()
def test_validator_good():
"""
fake test
"""
print("Creating fake test graph...")
G = nx.MultiDiGraph()
G.add_node('UniProtKB:P123456', name='fake')
G.add_edge('UBERON:0000001',
'UBERON:0000002',
relation='RO:1',
edge_label='part_of')
validator = Validator()
#print("PM={}".format(validator.prefix_manager.prefixmap))
validator.validate(G)
write_errors(validator)
assert validator.ok() == 0
def test_validate_edge_properties(query):
required_properties = Validator.get_required_edge_properties()
e = Validator.validate_edge_properties(query[0], query[1], query[2],
required_properties)
assert (len(e) == 0) == query[3]
def test_get_all_prefixes(prefix):
prefixes = Validator.get_all_prefixes()
assert prefix in prefixes
def test_validate_edge_label(query):
e = Validator.validate_edge_label(query[0], query[1], query[2])
assert (len(e) == 0) == query[3]
def test_validate_categories(query):
e = Validator.validate_categories(query[0], query[1])
assert (len(e) == 0) == query[2]
def test_validate_edge_property_values(query):
e = Validator.validate_edge_property_values(query[0], query[1], query[2])
assert (len(e) == 0) == query[3]
def test_get_required_edge_properties(property):
properties = Validator.get_required_edge_properties()
assert property in properties
def test_validate_node_property_types(query):
e = Validator.validate_node_property_types(query[0], query[1])
assert (len(e) == 0) == query[2]