Program: 9329
Project: 9329
Buggy source:
@Override public void init() throws ComponentInitException {
  atomicConcepts=new TreeSet<>();
  atomicRoles=new TreeSet<>();
  datatypeProperties=new TreeSet<>();
  individuals=new TreeSet<>();
  df=new OWLDataFactoryImpl();
  manager=OWLManager.createOWLOntologyManager();
  prefixes=new TreeMap<>();
  for (  KnowledgeSource source : sources) {
    if (source instanceof OWLOntologyKnowledgeSource) {
      ontology=((OWLOntologyKnowledgeSource)source).createOWLOntology(manager);
      owlAPIOntologies.add(ontology);
    }
 else {
      throw new ComponentInitException("String_Node_Str" + source.getClass().getName());
    }
    atomicConcepts.addAll(ontology.getClassesInSignature(Imports.INCLUDED));
    atomicRoles.addAll(ontology.getObjectPropertiesInSignature(Imports.INCLUDED));
    datatypeProperties.addAll(ontology.getDataPropertiesInSignature(Imports.INCLUDED));
    individuals.addAll(ontology.getIndividualsInSignature(Imports.INCLUDED));
    OWLDocumentFormat format=manager.getOntologyFormat(ontology);
    if (format != null && format.isPrefixOWLOntologyFormat()) {
      prefixes.putAll(format.asPrefixOWLOntologyFormat().getPrefixName2PrefixMap());
      baseURI=format.asPrefixOWLOntologyFormat().getDefaultPrefix();
      prefixes.remove("String_Node_Str");
    }
  }
  try {
    ontology=manager.createOntology(IRI.create("String_Node_Str"),new HashSet<>(owlAPIOntologies));
    List<OWLOntologyChange> addImports=new ArrayList<>();
    for (    OWLOntology ont : owlAPIOntologies) {
      for (      OWLImportsDeclaration importDeclaration : ont.getImportsDeclarations()) {
        addImports.add(new AddImport(ontology,importDeclaration));
      }
    }
    manager.applyChanges(addImports);
    for (    OWLOntology toRemove : owlAPIOntologies) {
      manager.removeOntology(toRemove);
    }
    owlAPIOntologies=new HashSet<>();
  }
 catch (  OWLOntologyCreationException e1) {
    e1.printStackTrace();
  }
  if (reasoner == null) {
    initBaseReasoner();
  }
  boolean inconsistentOntology=!reasoner.isConsistent();
  if (!inconsistentOntology) {
    reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY,InferenceType.CLASS_ASSERTIONS,InferenceType.OBJECT_PROPERTY_HIERARCHY,InferenceType.DATA_PROPERTY_HIERARCHY,InferenceType.OBJECT_PROPERTY_ASSERTIONS,InferenceType.SAME_INDIVIDUAL);
  }
 else {
    PelletExplanation expGen=new PelletExplanation(ontology);
    System.out.println(expGen.getInconsistencyExplanation());
    reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
    throw new ComponentInitException("String_Node_Str");
  }
  df=manager.getOWLDataFactory();
  initDatatypes();
  Iterator<OWLClass> it=atomicConcepts.iterator();
  while (it.hasNext()) {
    OWLClass cls=it.next();
    if (cls.getIRI().isReservedVocabulary()) {
      it.remove();
    }
  }
  minimizer=new OWLClassExpressionMinimizer(df,this);
  logger.info("String_Node_Str" + reasoner.getReasonerName() + "String_Node_Str"+ reasoner.getClass().getName()+ "String_Node_Str");
}

Fixed version (ground truth):
@Override public void init() throws ComponentInitException {
  atomicConcepts=new TreeSet<>();
  atomicRoles=new TreeSet<>();
  datatypeProperties=new TreeSet<>();
  individuals=new TreeSet<>();
  df=new OWLDataFactoryImpl();
  manager=OWLManager.createOWLOntologyManager();
  prefixes=new TreeMap<>();
  for (  KnowledgeSource source : sources) {
    if (source instanceof OWLOntologyKnowledgeSource) {
      ontology=((OWLOntologyKnowledgeSource)source).createOWLOntology(manager);
      owlAPIOntologies.add(ontology);
    }
 else {
      throw new ComponentInitException("String_Node_Str" + source.getClass().getName());
    }
    atomicConcepts.addAll(ontology.getClassesInSignature(Imports.INCLUDED));
    atomicRoles.addAll(ontology.getObjectPropertiesInSignature(Imports.INCLUDED));
    datatypeProperties.addAll(ontology.getDataPropertiesInSignature(Imports.INCLUDED));
    individuals.addAll(ontology.getIndividualsInSignature(Imports.INCLUDED));
    OWLDocumentFormat format=manager.getOntologyFormat(ontology);
    if (format != null && format.isPrefixOWLOntologyFormat()) {
      prefixes.putAll(format.asPrefixOWLOntologyFormat().getPrefixName2PrefixMap());
      baseURI=format.asPrefixOWLOntologyFormat().getDefaultPrefix();
      prefixes.remove("String_Node_Str");
    }
  }
  manager.getOntologies().stream().map(OWLOntology::getOntologyID).forEach(System.out::println);
  try {
    ontology=manager.createOntology(IRI.generateDocumentIRI(),new HashSet<>(owlAPIOntologies));
    List<OWLOntologyChange> addImports=new ArrayList<>();
    for (    OWLOntology ont : owlAPIOntologies) {
      for (      OWLImportsDeclaration importDeclaration : ont.getImportsDeclarations()) {
        addImports.add(new AddImport(ontology,importDeclaration));
      }
    }
    manager.applyChanges(addImports);
    for (    OWLOntology toRemove : owlAPIOntologies) {
      manager.removeOntology(toRemove);
    }
    owlAPIOntologies=new HashSet<>();
  }
 catch (  OWLOntologyCreationException e1) {
    e1.printStackTrace();
  }
  if (reasoner == null) {
    initBaseReasoner();
  }
  boolean inconsistentOntology=!reasoner.isConsistent();
  if (!inconsistentOntology) {
    reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY,InferenceType.CLASS_ASSERTIONS,InferenceType.OBJECT_PROPERTY_HIERARCHY,InferenceType.DATA_PROPERTY_HIERARCHY,InferenceType.OBJECT_PROPERTY_ASSERTIONS,InferenceType.SAME_INDIVIDUAL);
  }
 else {
    PelletExplanation expGen=new PelletExplanation(ontology);
    System.out.println(expGen.getInconsistencyExplanation());
    reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
    throw new ComponentInitException("String_Node_Str");
  }
  df=manager.getOWLDataFactory();
  initDatatypes();
  Iterator<OWLClass> it=atomicConcepts.iterator();
  while (it.hasNext()) {
    OWLClass cls=it.next();
    if (cls.getIRI().isReservedVocabulary()) {
      it.remove();
    }
  }
  minimizer=new OWLClassExpressionMinimizer(df,this);
  logger.info("String_Node_Str" + reasoner.getReasonerName() + "String_Node_Str"+ reasoner.getClass().getName()+ "String_Node_Str");
}