def is_sbml_consistent(sbml_document: libsbml.SBMLDocument, check_units=False):
"""Check for SBML validity / consistency
Arguments:
sbml_document: SBML document to check
check_units: Also check for unit-related issues
Returns:
False if problems were detected, otherwise True
"""
if not check_units:
sbml_document.setConsistencyChecks(
libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, False)
has_problems = sbml_document.checkConsistency()
if has_problems:
log_sbml_errors(sbml_document)
logger.warning(
'WARNING: Generated invalid SBML model. Check messages above.')
return not has_problems
def validate_doc(
doc: libsbml.SBMLDocument,
name=None,
log_errors=True,
units_consistency=True,
modeling_practice=True,
internal_consistency=True,
) -> ValidationResult:
"""Validate SBMLDocument.
:param doc: SBMLDocument to check
:param name: identifier or path for report
:param log_errors: boolean flag of errors should be logged
:param units_consistency: boolean flag units consistency
:param modeling_practice: boolean flag modeling practise
:param internal_consistency: boolean flag internal consistency
:return: ValidationResult
"""
if not name:
name = str(doc)
# set the unit checking, similar for the other settings
doc.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY,
units_consistency)
doc.setConsistencyChecks(libsbml.LIBSBML_CAT_MODELING_PRACTICE,
modeling_practice)
# time
current = time.perf_counter()
# all, error, warn
if internal_consistency:
results_internal = _check_consistency(doc, internal_consistency=True)
else:
results_internal = ValidationResult()
results_not_internal = _check_consistency(doc, internal_consistency=False)
# sum up
vresults = ValidationResult.from_results(
[results_internal, results_not_internal])
lines = [
"",
"-" * 80,
str(name),
"{:<25}: {}".format("valid",
str(vresults.is_valid()).upper()),
]
if not vresults.is_perfect():
lines += [
"{:<25}: {}".format("validation error(s)", vresults.error_count),
"{:<25}: {}".format("validation warnings(s)",
vresults.warning_count),
]
lines += [
"{:<25}: {:.3f}".format("check time (s)",
time.perf_counter() - current),
"-" * 80,
"",
]
info = "\n".join(lines)
if vresults.is_valid():
info = bcolors.OKGREEN + info + bcolors.ENDC
else:
info = bcolors.FAIL + info + bcolors.ENDC
info = bcolors.BOLD + info + bcolors.ENDC
# overall validation report
if vresults.is_perfect():
print(info)
else:
if vresults.is_valid():
logging.warning(info)
else:
logging.error(info)
# individual error and warning report
if log_errors:
vresults.log()
return vresults
