def validate_wrapper(
inputs: List[str], input_format: str, input_compression: str, output: str, stream: bool
):
"""
Run KGX validator on an input file to check for Biolink Model compliance.
Parameters
----------
inputs: List[str]
Input files
input_format: str
The input format
input_compression: str
The input compression type
output: str
Path to output file
stream: bool
Whether to parse input as a stream
"""
validate(inputs, input_format, input_compression, output, stream)
def test_validate_streaming():
"""
Test graph validation.
"""
inputs = [
os.path.join(RESOURCE_DIR, 'valid.json'),
]
output = os.path.join(TARGET_DIR, 'validation.log')
errors = validate(inputs=inputs,
input_format='json',
input_compression=None,
output=output,
stream=True)
assert os.path.exists(output)
assert len(errors) == 0
def test_validate_streaming():
"""
Test graph validation.
"""
inputs = [
os.path.join(RESOURCE_DIR, "valid.json"),
]
output = os.path.join(TARGET_DIR, "validation.log")
errors = validate(
inputs=inputs,
input_format="json",
input_compression=None,
output=output,
stream=True,
biolink_release="2.1.0",
)
assert os.path.exists(output)
assert len(errors) == 0
def validate_wrapper(
inputs: List[str],
input_format: str,
input_compression: str,
output: str,
stream: bool,
biolink_release: str = None,
):
"""
Run KGX validator on an input file to check for Biolink Model compliance.
\f
Parameters
----------
inputs: List[str]
Input files
input_format: str
The input format
input_compression: str
The input compression type
output: str
Path to output file
stream: bool
Whether to parse input as a stream
biolink_release: Optional[str]
SemVer version of Biolink Model Release used for validation (default: latest Biolink Model Toolkit version)
"""
errors = []
try:
errors = validate(inputs, input_format, input_compression, output,
stream, biolink_release)
except Exception as ex:
get_logger().error(str(ex))
exit(2)
if errors:
get_logger().error(
"kgx.validate() errors encountered... check the error log")
exit(1)
else:
exit(0)