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)