unsigned int RenderSBMLDocumentPlugin::checkConsistency() { unsigned int nerrors = 0; unsigned int total_errors = 0; SBMLDocument* doc = static_cast<SBMLDocument *>(this->getParentSBMLObject()); SBMLErrorLog *log = doc->getErrorLog(); unsigned char applicableValidators = doc->getApplicableValidators(); /* determine which validators to run */ bool id = ((applicableValidators & 0x01) == 0x01); bool sbml = ((applicableValidators & 0x02) == 0x02); /* LIST OTHERS HERE */ RenderIdentifierConsistencyValidator id_validator; RenderConsistencyValidator validator; /* LIST OTHERS HERE */ if (id) { id_validator.init(); nerrors = id_validator.validate(*doc); total_errors += nerrors; if (nerrors > 0) { log->add(id_validator.getFailures() ); /* only want to bail if errors not warnings */ if (log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) > 0) { return total_errors; } } } if (sbml) { validator.init(); nerrors = validator.validate(*doc); total_errors += nerrors; if (nerrors > 0) { log->add(validator.getFailures() ); // DO NOT NEED THIS IN LAST CALL // /* only want to bail if errors not warnings */ // if (log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) > 0) // { // return total_errors; // } } } /* ADD OTHERS HERE */ return total_errors; }
int Registry::CheckAndAddSBMLIfGood(SBMLDocument* document) { document->setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false); document->checkConsistency(); SBMLErrorLog* log = document->getErrorLog(); if (log->getNumFailsWithSeverity(2) == 0 && log->getNumFailsWithSeverity(3) == 0) { //It's a valid SBML file. const Model* sbml = document->getModel(); string sbmlname = getNameFromSBMLObject(sbml, "file"); if (sbmlname != MAINMODULE) { while (NewCurrentModule(&sbmlname)) { //Duplicated module name sbmlname += "_"; } } CurrentModule()->LoadSBML(document); if (sbmlname != MAINMODULE) { RevertToPreviousModule(); } return 2; } return 0; }
/* * Performs a set of semantic consistency checks on the document. Query * the results by calling getNumErrors() and getError(). * * @return the number of failed checks (errors) encountered. */ unsigned int SBMLInternalValidator::checkConsistency (bool writeDocument) { unsigned int nerrors = 0; unsigned int total_errors = 0; //if (getLevel() == 3) //{ // logError(L3NotSupported); // return 1; //} /* determine which validators to run */ bool id = ((mApplicableValidators & 0x01) == 0x01); bool sbml = ((mApplicableValidators & 0x02) == 0x02); bool sbo = ((mApplicableValidators & 0x04) == 0x04); bool math = ((mApplicableValidators & 0x08) == 0x08); bool units = ((mApplicableValidators & 0x10) == 0x10); bool over = ((mApplicableValidators & 0x20) == 0x20); bool practice = ((mApplicableValidators & 0x40) == 0x40); /* taken the state machine concept out for now if (LibSBMLStateMachine::isActive()) { units = LibSBMLStateMachine::getUnitState(); } */ IdentifierConsistencyValidator id_validator; ConsistencyValidator validator; SBOConsistencyValidator sbo_validator; MathMLConsistencyValidator math_validator; UnitConsistencyValidator unit_validator; OverdeterminedValidator over_validator; ModelingPracticeValidator practice_validator; SBMLDocument *doc; SBMLErrorLog *log = getErrorLog(); if (writeDocument) { char* sbmlString = writeSBMLToString(getDocument()); log->clearLog(); doc = readSBMLFromString(sbmlString); free (sbmlString); } else { doc = getDocument(); } /* calls each specified validator in turn * - stopping when errors are encountered */ if (id) { id_validator.init(); nerrors = id_validator.validate(*doc); if (nerrors > 0) { unsigned int origNum = log->getNumErrors(); log->add( id_validator.getFailures() ); if (origNum > 0 && log->contains(InvalidUnitIdSyntax) == true) { /* do not log dangling ref */ while (log->contains(DanglingUnitSIdRef) == true) { log->remove(DanglingUnitSIdRef); nerrors--; } total_errors += nerrors; if (nerrors > 0) { if (writeDocument) SBMLDocument_free(doc); return total_errors; } } else if (log->contains(DanglingUnitSIdRef) == false) { total_errors += nerrors; if (writeDocument) SBMLDocument_free(doc); return total_errors; } else { bool onlyDangRef = true; for (unsigned int a = 0; a < log->getNumErrors(); a++) { if (log->getError(a)->getErrorId() != DanglingUnitSIdRef) { onlyDangRef = false; break; } } total_errors += nerrors; if (onlyDangRef == false) { if (writeDocument) SBMLDocument_free(doc); return total_errors; } } } } if (sbml) { validator.init(); nerrors = validator.validate(*doc); total_errors += nerrors; if (nerrors > 0) { log->add( validator.getFailures() ); /* only want to bail if errors not warnings */ if (log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) > 0) { if (writeDocument) SBMLDocument_free(doc); return total_errors; } } } if (sbo) { sbo_validator.init(); nerrors = sbo_validator.validate(*doc); total_errors += nerrors; if (nerrors > 0) { log->add( sbo_validator.getFailures() ); /* only want to bail if errors not warnings */ if (log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) > 0) { if (writeDocument) SBMLDocument_free(doc); return total_errors; } } } if (math) { math_validator.init(); nerrors = math_validator.validate(*doc); total_errors += nerrors; if (nerrors > 0) { log->add( math_validator.getFailures() ); /* at this point bail if any problems * unit checks may crash if there have been math errors/warnings */ if (writeDocument) SBMLDocument_free(doc); return total_errors; } } if (units) { unit_validator.init(); nerrors = unit_validator.validate(*doc); total_errors += nerrors; if (nerrors > 0) { log->add( unit_validator.getFailures() ); /* only want to bail if errors not warnings */ if (log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) > 0) { if (writeDocument) SBMLDocument_free(doc); return total_errors; } } } /* do not even try if there have been unit warnings * changed this as would have bailed */ if (over) { over_validator.init(); nerrors = over_validator.validate(*doc); total_errors += nerrors; if (nerrors > 0) { log->add( over_validator.getFailures() ); /* only want to bail if errors not warnings */ if (log->getNumFailsWithSeverity(LIBSBML_SEV_ERROR) > 0) { if (writeDocument) SBMLDocument_free(doc); return total_errors; } } } if (practice) { practice_validator.init(); nerrors = practice_validator.validate(*doc); if (nerrors > 0) { unsigned int errorsAdded = 0; const std::list<SBMLError> practiceErrors = practice_validator.getFailures(); list<SBMLError>::const_iterator end = practiceErrors.end(); list<SBMLError>::const_iterator iter; for (iter = practiceErrors.begin(); iter != end; ++iter) { if (SBMLError(*iter).getErrorId() != 80701) { log->add( SBMLError(*iter) ); errorsAdded++; } else { if (units) { log->add( SBMLError(*iter) ); errorsAdded++; } } } total_errors += errorsAdded; } } if (writeDocument) SBMLDocument_free(doc); return total_errors; }