private void compareAndPrintEqualSizedClasses(
OWLClass cl, Set<OWLClass> reasonerSuperClasses, Set<String> superClasses, Jedis idReader)
throws Exception {
// compare each element of these 2 sets
boolean print = false;
for (OWLClass scl : reasonerSuperClasses) {
String sclID = conceptToID(scl.toString(), idReader);
if (!superClasses.contains(sclID)) {
print = true;
System.out.print(cl.toString() + " -e- " + scl.toString());
System.out.print(" , ");
}
}
if (print) System.out.println("\n");
}
private void compareClassificationResults(
OWLOntology ontology, OWLReasoner reasoner, Jedis resultStore, Jedis idReader)
throws Exception {
Set<OWLClass> classes = ontology.getClassesInSignature();
Pipeline resultPipeline = resultStore.pipelined();
double classCount = 0;
int multiplier = 1;
double totalCount = 0;
for (OWLClass cl : classes) {
classCount++;
double classProgress = (classCount / classes.size()) * 100;
Set<OWLClass> reasonerSuperclasses = reasoner.getSuperClasses(cl, false).getFlattened();
// add cl itself to S(X) computed by reasoner. That is missing
// in its result.
reasonerSuperclasses.add(cl);
// adding equivalent classes -- they are not considered if asked for superclasses
Iterator<OWLClass> iterator = reasoner.getEquivalentClasses(cl).iterator();
while (iterator.hasNext()) reasonerSuperclasses.add(iterator.next());
String classToCheckID = conceptToID(cl.toString(), idReader);
List<Response<Double>> responseList = new ArrayList<Response<Double>>();
for (OWLClass scl : reasonerSuperclasses) {
String key = conceptToID(scl.toString(), idReader);
responseList.add(resultPipeline.zscore(key, classToCheckID));
}
resultPipeline.sync();
double hitCount = 0;
for (Response<Double> response : responseList) {
if (response.get() != null) hitCount++;
}
totalCount += (hitCount / reasonerSuperclasses.size());
if (classProgress >= (5 * multiplier)) {
System.out.println(
"% of no. of classes looked at: "
+ classProgress
+ "\tProgress %: "
+ (totalCount / classCount) * 100);
multiplier++;
}
}
double progress = totalCount / classes.size();
System.out.println("\nProgress %: " + (progress * 100));
}
public String[] searchOntology(String term, String ontofilepath, String type) {
OWLAccessorImpl owlapi = new OWLAccessorImpl(new File(ontofilepath));
List<OWLClass> matches = owlapi.retrieveConcept(term);
Iterator<OWLClass> it = matches.iterator();
String[] result = null;
while (it.hasNext()) {
OWLClass c = it.next();
String label = owlapi.getLabel(c);
if (label.compareToIgnoreCase(term) == 0) {
result = new String[3];
result[0] = type;
result[1] =
c.toString()
.replaceFirst("http.*?(?=(PATO|TAO)_)", "")
.replaceFirst("_", ":")
.replaceFirst(">$", "");
result[2] = label;
return result;
}
}
it = matches.iterator();
result = new String[] {"", "", ""};
while (it.hasNext()) {
OWLClass c = it.next();
String label = owlapi.getLabel(c);
result[0] = type;
result[1] +=
c.toString()
.replaceFirst(".*http.*?(?=(PATO|TAO)_)", "")
.replaceFirst("_", ":")
.replaceFirst(">$", "")
+ ";";
result[2] += label + ";";
}
if (result != null) {
result[1] = result[1].replaceFirst(";$", "");
result[2] = result[2].replaceFirst(";$", "");
}
return result;
}
private Set<String> getSuperClasses(OWLReasoner reasoner, OWLClass cl, OWLClass owlThing) {
Set<String> pset = new HashSet<String>();
Set<OWLClass> reasonerSuperClasses = reasoner.getSuperClasses(cl, false).getFlattened();
// add cl itself to S(X) computed by reasoner. That is missing
// in its result.
reasonerSuperClasses.add(cl);
reasonerSuperClasses.add(owlThing);
// adding equivalent classes -- they are not considered if asked for superclasses
Iterator<OWLClass> iterator = reasoner.getEquivalentClasses(cl).iterator();
while (iterator.hasNext()) reasonerSuperClasses.add(iterator.next());
for (OWLClass scl : reasonerSuperClasses) pset.add(scl.toString());
return pset;
}
private void compareAndPrintUnEqualSizedIndividuals(
OWLClass cl,
Set<OWLNamedIndividual> reasonerInstances,
Set<String> computedInstances,
Jedis idReader)
throws Exception {
// compare each element of these 2 sets
boolean print = false;
for (OWLNamedIndividual scl : reasonerInstances) {
String sclID = conceptToID(scl.toString(), idReader);
if (!computedInstances.contains(sclID)) {
print = true;
System.out.print(cl.toString() + " -ne- " + scl.toString());
System.out.print(" , ");
}
computedInstances.remove(sclID);
}
for (String s : computedInstances)
System.out.println("\t -- " + Util.idToConcept(s, idReader) + "(" + s + ")");
System.out.println();
}
/*
* (non-Javadoc)
*
* @see
* org.semanticweb.owlapi.model.OWLClassExpressionVisitor#visit(org.semanticweb
* .owlapi.model.OWLClass)
*/
@Override
public void visit(OWLClass axiom) {
sb.append(print(axiom.toString()));
}
private void rearrangeAndCompareResults(
OWLOntology ontology,
OWLReasoner reasoner,
Jedis resultStore,
Jedis resultStore2,
Jedis idReader)
throws Exception {
new ResultRearranger().initializeAndRearrange();
Set<OWLClass> classes = ontology.getClassesInSignature();
// rearranged results are in DB-1
resultStore.select(1);
double classCount = 0;
int multiplier = 1;
int missCount = 0;
String bottomID = Util.getPackedID(Constants.BOTTOM_ID, EntityType.CLASS);
System.out.println("Comparing Classes... " + classes.size());
OWLClass owlThing = ontology.getOWLOntologyManager().getOWLDataFactory().getOWLThing();
for (OWLClass cl : classes) {
String classID = conceptToID(cl.toString(), idReader);
// REL/Pellet doesn't consider individuals i.e. {a} \sqsubseteq \bottom
// so skipping checking bottom
if (classID.equals(bottomID)) continue;
classCount++;
Set<OWLClass> reasonerSuperClasses = reasoner.getSuperClasses(cl, false).getFlattened();
// add cl itself to S(X) computed by reasoner. That is missing
// in its result.
reasonerSuperClasses.add(cl);
reasonerSuperClasses.add(owlThing);
// adding equivalent classes -- they are not considered if asked for superclasses
Iterator<OWLClass> iterator = reasoner.getEquivalentClasses(cl).iterator();
while (iterator.hasNext()) reasonerSuperClasses.add(iterator.next());
Set<String> superClasses = resultStore.smembers(classID);
if (superClasses.size() == reasonerSuperClasses.size()) {
compareAndPrintEqualSizedClasses(cl, reasonerSuperClasses, superClasses, idReader);
} else {
System.out.println(
"\n"
+ cl.toString()
+ " -- "
+ superClasses.size()
+ ", "
+ reasonerSuperClasses.size());
for (OWLClass scl : reasonerSuperClasses) {
String sclID = conceptToID(scl.toString(), idReader);
if (!superClasses.contains(sclID)) {
System.out.print(cl.toString() + " -ne- " + scl.toString());
System.out.print(" , ");
}
superClasses.remove(sclID);
}
for (String s : superClasses)
System.out.println("\t -- " + Util.idToConcept(s, idReader) + "(" + s + ")");
System.out.println();
missCount++;
}
}
System.out.println("No of classes not equal: " + missCount);
Set<OWLNamedIndividual> individuals = ontology.getIndividualsInSignature();
System.out.println("Rearranging individuals...");
System.out.println("Individuals: " + individuals.size());
System.out.println("Not checking for individuals...");
/*
rearrangeIndividuals(individuals, resultStore, resultStore2, idReader);
int cnt = 0;
for(OWLClass cl : classes) {
Set<OWLNamedIndividual> instances =
reasoner.getInstances(cl, false).getFlattened();
Set<String> computedInstances = resultStore2.smembers(
conceptToID(cl.toString(), idReader));
if(computedInstances.size() == instances.size()) {
compareAndPrintEqualSizedIndividuals(cl, instances, computedInstances, idReader);
}
else {
System.out.println(cl.toString() + " -- " +
computedInstances.size() + " , " + instances.size());
compareAndPrintUnEqualSizedIndividuals(cl, instances, computedInstances, idReader);
cnt++;
}
}
System.out.println("No of classes for which individuals didn't match: " + cnt);
*/
resultStore.select(0);
}