if (!sbmlDocument.hasValidAnnotation()) {
logger.warn("The SBMLDocument element has an invalid rdf:about inside his annotation.");
setRDFAbout(sbmlDocument);
}
Model model = sbmlDocument.getModel();
if (!model.hasValidAnnotation()) {
logger.warn(MessageFormat.format("The model element with metaid = \"{0}\" has an invalid rdf:about = \"{1}\" inside his annotation.", model.getMetaId(), model.getAnnotation().getAbout()));
setRDFAbout(model);
}
if (model.isSetListOfFunctionDefinitions()) {
for (FunctionDefinition functionDefinition : model.getListOfFunctionDefinitions()) {
if (!functionDefinition.hasValidAnnotation()) {
logger.warn("The functionDefinition element '" + functionDefinition.getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(functionDefinition);
}
}
}
if (model.isSetListOfCompartments()) {
for (Compartment compartment : model.getListOfCompartments()) {
if (!compartment.hasValidAnnotation()) {
logger.warn("The compartment '" + compartment.getId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(compartment);
}
}
}
if (model.isSetListOfCompartmentTypes()) {
for (CompartmentType compartmentType : model.getListOfCompartmentTypes()) {
if (!compartmentType.hasValidAnnotation()) {
logger.warn("The compartmentType '" + compartmentType.getId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(compartmentType);
}
}
}
logger.debug("compartments checked");
if (model.isSetListOfConstraints()) {
for (Constraint constraint : model.getListOfConstraints()) {
if (!constraint.hasValidAnnotation()) {
logger.warn("The constraint element '" + constraint.getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(constraint);
}
}
}
if (model.isSetListOfEvents()) {
for (Event event : model.getListOfEvents()) {
if (!event.hasValidAnnotation()) {
logger.warn("The event element '" + event.getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(event);
}
if (event.isSetDelay()) {
if (! event.getDelay().hasValidAnnotation()) {
logger.warn("The delay element '" + event.getDelay().getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(event.getDelay());
}
}
if (event.isSetListOfEventAssignments()) {
for (EventAssignment eventAssignment : event.getListOfEventAssignments()) {
if (!eventAssignment.hasValidAnnotation()) {
logger.warn("The eventAssignment element '" + eventAssignment.getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(eventAssignment);
}
}
}
if (event.isSetTrigger()) {
if (! event.getTrigger().hasValidAnnotation()) {
logger.warn("The trigger element '" + event.getTrigger().getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(event.getTrigger());
}
}
}
}
logger.debug("events checked");
if (model.isSetListOfInitialAssignments()) {
for (InitialAssignment initAssgnt : model.getListOfInitialAssignments()) {
if (!initAssgnt.hasValidAnnotation()) {
logger.warn("The initialAssignment element '" + initAssgnt.getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(initAssgnt);
}
}
}
if (model.isSetListOfParameters()) {
for (Parameter parameter : model.getListOfParameters()) {
if (!parameter.hasValidAnnotation()) {
logger.warn("The parameter element '" + parameter.getId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(parameter);
}
}
}
logger.debug("parameters checked");
if (model.isSetListOfReactions()) {
for (Reaction reaction : model.getListOfReactions()) {
if (!reaction.hasValidAnnotation()) {
logger.warn("The reaction element '" + reaction.getId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(reaction);
}
if (reaction.isSetKineticLaw()) {
KineticLaw kineticLaw = reaction.getKineticLaw();
if (!kineticLaw.hasValidAnnotation()) {
logger.warn("The kineticLaw element '" + kineticLaw.getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(kineticLaw);
}
if (kineticLaw.isSetListOfLocalParameters()) {
for (LocalParameter parameter : kineticLaw.getListOfLocalParameters()) {
if (!parameter.hasValidAnnotation()) {
logger.warn("The local parameter element '" + parameter.getId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(parameter);
}
}
}
}
if (reaction.isSetListOfReactants()) {
for (SpeciesReference reactant : reaction.getListOfReactants()) {
if (!reactant.hasValidAnnotation()) {
logger.warn("The reactant element '" + reactant.getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(reactant);
}
}
}
if (reaction.isSetListOfProducts()) {
for (SpeciesReference product : reaction.getListOfProducts()) {
if (!product.hasValidAnnotation()) {
logger.warn("The product element '" + product.getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(product);
}
}
}
if (reaction.isSetListOfModifiers()) {
for (ModifierSpeciesReference modifier : reaction.getListOfModifiers()) {
if (!modifier.hasValidAnnotation()) {
logger.warn("The modifier element '" + modifier.getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(modifier);
}
}
}
}
}
logger.debug("reactions checked");
if (model.isSetListOfRules()) {
for (Rule rule : model.getListOfRules()) {
if (!rule.hasValidAnnotation()) {
logger.warn("The rule element '" + rule.getMetaId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(rule);
}
}
}
if (model.isSetListOfSpecies()) {
for (Species species : model.getListOfSpecies()) {
if (!species.hasValidAnnotation()) {
logger.warn("The species element '" + species.getId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(species);
}
}
}
if (model.isSetListOfSpeciesTypes()) {
for (Species speciesType : model.getListOfSpecies()) {
if (!speciesType.hasValidAnnotation()) {
logger.warn("The speciesType element '" + speciesType.getId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(speciesType);
}
}
}
logger.debug("species checked");
if (model.isSetListOfUnitDefinitions()) {
for (UnitDefinition unitDefinition : model.getListOfUnitDefinitions()) {
if (!unitDefinition.hasValidAnnotation()) {
logger.warn("The unitDefinition element '" + unitDefinition.getId() + "' has an invalid rdf:about inside his annotation.");
setRDFAbout(unitDefinition);
}