I'm working on a java project where i need to use an ontology. I have an ontology on which I can read what is inside through the owl api, but once I want to add a new instance and add dataProperties to it, I'm no more able to read this ontology with my app. And what I find strange is that it's fine with protégé.
The Output is throwing me this error :
Avertissement: StandardWrapperValve[SearchPatient]: Servlet.service() for servlet SearchPatient threw exception
java.util.NoSuchElementException: No value present
at java.util.Optional.get(Optional.java:135)
at model.Ontology.lambda$null$6(Ontology.java:450)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
at model.Ontology.lambda$searchPatient$7(Ontology.java:449)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.ReferencePipeline$Head.forEach(ReferencePipeline.java:580)
at model.Ontology.searchPatient(Ontology.java:449)
at model.Ontology.getPatientInOntology(Ontology.java:144)
at com.mycompany.mavenwebapphadbpm.SearchPatient.processRequest(SearchPatient.java:57)
at com.mycompany.mavenwebapphadbpm.SearchPatient.doGet(SearchPatient.java:91)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.netbeans.modules.web.monitor.server.MonitorFilter.doFilter(MonitorFilter.java:393)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:357)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:260)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:188)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:191)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:168)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:189)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:288)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:206)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:136)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:114)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:838)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:113)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:115)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:55)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:135)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:564)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:544)
at java.lang.Thread.run(Thread.java:748)
I have tried to save as indicated in the OWL API examples so I don't know where my error is.
This is the code i'm using to save the ontology :
onto.saveOntology(onto.getFormat(), man.getOntologyDocumentIRI(onto));
And the code using to add dataProperties :
public ArrayList<AddAxiom> addDataProperties(ArrayList<Info> data, OWLIndividual patient) {
ArrayList<AddAxiom> axioms = new ArrayList<>();
OWLDataFactory df = man.getOWLDataFactory();
for (Info dp : data) {
OWLDataProperty hasProp = df.getOWLDataProperty(IRI.create(owlIRI + "#" + dp.getRelation()));
OWLDataPropertyAssertionAxiom axiom = null;
System.out.println("Relation : " + dp.getRelation() + " valeur : " + dp.getValue());
switch (dp.getType()) {
case "String":
axiom = df.getOWLDataPropertyAssertionAxiom(hasProp, patient, dp.getValue());
break;
case "int":
axiom = df.getOWLDataPropertyAssertionAxiom(hasProp, patient, Integer.parseInt(dp.getValue()));
break;
case "float":
axiom = df.getOWLDataPropertyAssertionAxiom(hasProp, patient, Float.parseFloat(dp.getValue()));
break;
case "boolean":
if (dp.getValue() == null) {
axiom = df.getOWLDataPropertyAssertionAxiom(hasProp, patient, false);
} else {
axiom = df.getOWLDataPropertyAssertionAxiom(hasProp, patient, true);
}
break;
}
AddAxiom addAxiom = new AddAxiom(onto, axiom);
axioms.add(addAxiom);
}
return axioms;
}
[EDIT]
There is the function that uses the method above, and the differents way i used to save the ontology.
Thank You again
public void addPatientIndividual(ArrayList<Info> data, String name) {
OWLDataFactory df = man.getOWLDataFactory();
// Actor's IRI
OWLClass actorIRI = df.getOWLClass(IRI.create(owlIRI + "#Patient"));
// Patient individual
OWLIndividual patient = df.getOWLNamedIndividual(IRI.create(owlIRI + "#" + name));
// Create a link between the class patient and the individual
OWLClassAssertionAxiom type = df.getOWLClassAssertionAxiom(actorIRI, patient);
// Create the axiom corresponding to the link between the patient and the
// individual
AddAxiom axiomType = new AddAxiom(onto, type);
// Add the former link to the ontology
man.applyChange(axiomType);
// Disease individual
OWLIndividual disease = df.getOWLNamedIndividual(owlIRI + "#" + ((Info) data.get(0)).getValue());
// Create the property which is already in the owl the name of the patient to
// the individual
OWLObjectProperty hasDisease = df.getOWLObjectProperty(owlIRI + "#hasDisease");
// Link the disease to the patient
OWLObjectPropertyAssertionAxiom axiomHasDisease = df.getOWLObjectPropertyAssertionAxiom(hasDisease, patient,
disease);
// Create the axiom
AddAxiom addAxiomHasDisease = new AddAxiom(onto, axiomHasDisease);
// Apply the axiom to the ontology
man.applyChange(addAxiomHasDisease);
// Delete the axiom of the disease
data.remove(data.get(0));
for (AddAxiom axiom : addDataProperties(data, patient)) {
man.applyChange(axiom);
}
// Save the ontology
try {
//System.out.println("coucou");
//this.onto.saveOntology(); // PLENTE
//this.getOntology().saveOntology(); // PLENTE
//this.getOntology().saveOntology(this.getOntology().getFormat()); // PLENTE
//manager.saveOntology(onto); // NE FAIS RIENT
//onto.getOWLOntologyManager().saveOntology(onto); // Enregistre puis lecture impossible
//onto.saveOntology(onto.getFormat(), manager.getOntologyDocumentIRI(onto));
//System.out.println(manager.getOntologyDocumentIRI(this.getOntology()));
//System.out.println(owlIRI);
//System.out.println(onto.getOntologyID().getVersionIRI());
//man.saveOntology(onto, onto.getFormat().asPrefixOWLDocumentFormat()); // MARCHE TOUJOURS PAS
//man.saveOntology(onto);
//this.getOntology().saveOntology(); // MARCHE PAS
onto.saveOntology(onto.getFormat(), man.getOntologyDocumentIRI(onto));
System.out.print("Sauvegarde ?????");
} catch (Exception e) {
e.printStackTrace();
System.out.println("-/-/-/-/-/-/-/-/-/-/-/-PLENTE-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-");
}
}
[EDIT] Code for SearchPatient
public Patient searchPatient(String id, OWLReasoner reasoner) {
Patient pat = new Patient();
onto.individualsInSignature().forEach(i -> onto.dataPropertiesInSignature().forEach(p -> {
if (i.getIRI().getRemainder().get().equals(id)) {
pat.setId(id);
Set<OWLLiteral> prop = reasoner.getDataPropertyValues(i, p);
Set<OWLLiteral> values = asUnorderedSet(prop.parallelStream());
for (OWLLiteral v : values) {
if (p.getIRI().getRemainder().get().equals("hasFirstName")) {
pat.setHasFirstName(v.getLiteral());
}
if (p.getIRI().getRemainder().get().equals("hasName")) {
pat.setHasName(v.getLiteral());
}
}
}
}));
return pat;
}
And the code for getPatient
public ArrayList<Patient> getPatientInOntology(OWLReasoner reasoner, String individualName) {
ArrayList<Patient> pats = new ArrayList<>();
//ArrayList<String> liste = new ArrayList<>();
onto.classesInSignature().forEach(c -> {
if (c.getIRI().getFragment().equals(individualName)) {
patient = c;
}
});
// Display all the individual
for (OWLNamedIndividual cls : reasoner.getInstances(patient).getFlattened()) {
//liste.add(cls.getIRI().getRemainder().get());
//pats.add()
//System.out.println("cls : " + cls.getIRI().getRemainder().get());
pats.add(searchPatient(cls.getIRI().getRemainder().get(), reasoner));
}
return pats;
}
