public string getReasonerName()
{
OWLOntologyManager owlMan = org.semanticweb.owlapi.apibinding.OWLManager.createOWLOntologyManager();
OWLOntology ont = owlMan.createOntology();
OWLReasoner reas = this.createReasoner(ont);
return(reas.getReasonerName());
}
public org.semanticweb.owlapi.reasoner.OWLReasoner createReasoner(OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration config)
{
org.semanticweb.HermiT.Configuration configuration = new org.semanticweb.HermiT.Configuration();
configuration.reasonerProgressMonitor = config.getProgressMonitor();
configuration.throwInconsistentOntologyException = false;
return(new org.semanticweb.HermiT.Reasoner(configuration, ontology));
}
public string getReasonerVersion()
{
OWLOntologyManager owlMan = org.semanticweb.owlapi.apibinding.OWLManager.createOWLOntologyManager();
OWLOntology ont = owlMan.createOntology();
OWLReasoner reas = this.createReasoner(ont);
org.semanticweb.owlapi.util.Version ver = reas.getReasonerVersion();
return(ver.getMajor() + "." + ver.getMinor() + "." + ver.getPatch());
}
public java.util.Set GetConceptChild(OWLOntology ontology)
{
if (this.conceptChild == null)
{
this.conceptChild = GetConcept(ontology).getSubClasses(ontology);
}
return(this.conceptChild);
}
public OWLClass GetConcept(OWLOntology ontology)
{
if (this.concept == null)
{
this.concept = getClass(ontology.getClassesInSignature(), this.conceptKey);
}
return(this.concept);
}
public org.semanticweb.owlapi.reasoner.OWLReasoner createReasoner(OWLOntology ontology)
{
var config = new org.semanticweb.HermiT.Configuration();
config.reasonerProgressMonitor = progrMonitor;
config.throwInconsistentOntologyException = false;
return(new org.semanticweb.HermiT.Reasoner(config, ontology));
}
/// <summary>
/// Searches for reasoners in reasonerDllFolder, instantiate a reasoner and shows the info about this reasoner.
/// </summary>
/// <param name="reasonerDllFolder"></param>
public static void GetOwlInfo(string reasonerDllFolder)
{
manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.createOntology(ontologyIRI);
ReasoningService aa = new ReasoningService(reasonerDllFolder);
OWLReasoner reasoner = aa.reasonerFact.createReasoner(ontology);
Console.WriteLine(aa.reasonerFact.getReasonerName() + " Version:" + aa.reasonerFact.getReasonerVersion() + "\r\n Description:" + aa.reasonerFact.getReasonerDescription());
Console.WriteLine("Press enter to go further...");
Console.ReadLine();
}
public java.util.Set GetConceptParents(OWLOntology ontology)
{
if (this.conceptParent == null)
{
if (GetConcept(ontology) != null) //Si no es una instancia, obtener la clase
{
this.conceptParent = GetConcept(ontology).getSuperClasses(ontology);
}
else
{
//Es una instancia entonces no tiene padres
this.conceptParent = null;
}
}
return(this.conceptParent);
}
private void toolStripButton_load_Click(object sender, EventArgs e)
{
if (Locked)
{
return;
}
OpenFileDialog dialog = new OpenFileDialog();
dialog.Filter = "Ontology Files|*.owl;*.rdf;*.rdfs";
if (dialog.ShowDialog() == DialogResult.OK)
{
OwlManager = new OWLManager();
OwlOntology = new OWLOntology();
initializeOntology(dialog.FileName);
fromOntologyPath = dialog.FileName;
clearLabels();
clearQuery();
initializeLabels();
}
}
public static void Initialize(string ontologyProfilePath)
{
try
{
Manager = OWLManager.createOWLOntologyManager();
//tento řádek je potřebný kvůli nedokonale převedené knihovně z javy, kvůli které se načítá owl parser
[email protected] s = new [email protected]();
// načtení owl souboru, který obsahuje metamodel a který každá vložená báze individuí importuje
byte[] owlResourceUPMM = Properties.Resources.UPMM;
java.io.ByteArrayInputStream upmmInputStream = new java.io.ByteArrayInputStream(owlResourceUPMM);
OWLOntology ontologyUPMM = Manager.loadOntologyFromOntologyDocument(upmmInputStream);
MetamodelIRI = ontologyUPMM.getOntologyID().getOntologyIRI();
Trace.WriteLine("Loaded Metamodel Ontology : " + MetamodelIRI);
// načtení owl báze konkrétního profilu
java.io.File processModel = new java.io.File(ontologyProfilePath);
OWLOntology knowledgeProfile = Manager.loadOntologyFromOntologyDocument(processModel);
ProfileIRI = knowledgeProfile.getOntologyID().getOntologyIRI();
Trace.WriteLine("Loaded Profile Ontology : " + ProfileIRI);
// vytvoření reasoneru nad profilem
Reasoner = new StructuralReasonerFactory().createReasoner(knowledgeProfile, new SimpleConfiguration());
PelletReasoner = new PelletReasonerFactory().createReasoner(knowledgeProfile, new SimpleConfiguration());
//Reasoner = new Reasoner.ReasonerFactory().createReasoner(knowledgeProfile); HermiT
Trace.WriteLine("Reasoner is running!");
DataFactory = Manager.getOWLDataFactory();
}
catch (Exception ex)
{
throw new ApplicationException("Ontology loading failed!", ex);
}
}
/// <summary>
/// proceso para cargar las clases, subclases y axiomas de la ontologia
/// </summary>
private void LoadOWLAPI()
{
//Inicializamos variables
OntologyConcept ontologyConcept = null;
int weigth = 1;
string claseKey = string.Empty;
string claseValor = string.Empty;
//OWLClass _class;
//Se carga la ontologia
string path = url;
java.io.File file = new java.io.File(path);
//Aseguramos una ontologia en el managet
ontology = ontologyManager.loadOntologyFromOntologyDocument(file);
//Creamos el datafactory para obtener los labels de las clases
OWLDataFactory df = ontologyManager.getOWLDataFactory();
OWLAnnotationProperty label = df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
//Obtenemos las clases de la ontologia y las recorremos para obtener las anotaciones
java.util.Set clases = ontology.getClassesInSignature();
for (java.util.Iterator iteratorClases = clases.iterator(); iteratorClases.hasNext();)
{
OWLClass clase = (OWLClass)iteratorClases.next();
List <Anotacion> Anotaciones = new List <Anotacion>();
java.util.Set lit = clase.getAnnotations(ontology, label);
//Se recorren las anotaciones tipo Label
for (java.util.Iterator iteratorAnno = lit.iterator(); iteratorAnno.hasNext();)
{
OWLAnnotation anno = (OWLAnnotation)iteratorAnno.next();
OWLLiteral val = (OWLLiteral)anno.getValue();
string valorAnotacion = string.Empty;
if (val.hasLang("es"))
{
//Se debe hacer un tratamiento a la cadena por los acentos
valorAnotacion = ToAscii(val.getLiteral()).Trim();
}
else
{
valorAnotacion = val.getLiteral().Trim();
}
//Agregar la anotacion a la lista
Anotacion annotemp = new Anotacion(anno.getSignature().ToString(), valorAnotacion, val.getLang());
Anotaciones.Add(annotemp);
//Añadimos la anotacion a la lista de valores a consultar verificando que no este repetido
if (!valores.Contains(valorAnotacion) && !string.IsNullOrEmpty(valorAnotacion))
{
valores.Add(valorAnotacion);
}
//Reportar la anotacion encontrada
Trace.WriteLine(clase.getSignature().ToString() + " -> " + valorAnotacion);
//Almacenamos todas anotaciones en un string para el valor de la clase
claseValor = claseValor + " " + valorAnotacion;
//En caso de tener individuos se almacena en la lista de valores para su búsqueda
Trace.WriteLine("Obteniendo conceptos de los individuos");
string individuoKey = string.Empty;
java.util.Set individuos = clase.getIndividuals(ontology);
for (java.util.Iterator iteratorIndividuos = individuos.iterator(); iteratorIndividuos.hasNext();)
{
OWLIndividual individuo = (OWLIndividual)iteratorIndividuos.next();
java.util.Set litind = individuo.asOWLNamedIndividual().getAnnotations(ontology, df.getRDFSLabel());
//Se recorre las anotaciones tipo Label individuo
for (java.util.Iterator iteratorAnnoind = litind.iterator(); iteratorAnnoind.hasNext();)
{
OWLAnnotation annoind = (OWLAnnotation)iteratorAnnoind.next();
OWLLiteral valind = (OWLLiteral)annoind.getValue();
string valorAnotacionind = string.Empty;
if (valind.hasLang("es"))
{
//Se debe hacer un tratamiento a la cadena por los acentos
valorAnotacionind = ToAscii(valind.getLiteral()).Trim();
}
else
{
valorAnotacionind = valind.getLiteral().Trim();
}
//Agregar la anotacion a la lista
Anotacion annotempind = new Anotacion(annoind.getSignature().ToString(), valorAnotacionind, valind.getLang());
Anotaciones.Add(annotempind);
//Añadimos la anotacion a la lista de valores a consultar verificando que no este repetido
if (!valores.Contains(valorAnotacionind) && !string.IsNullOrEmpty(valorAnotacionind))
{
valores.Add(valorAnotacionind);
}
//Reportar la anotacion encontrada
Trace.WriteLine(clase.getSignature().ToString() + ":" + individuo.getSignature().ToString() + " -> " + valorAnotacionind);
//Almacenamos todas anotaciones en un string para el valor de la clase
claseValor = claseValor + " " + valorAnotacionind;
}
}
//Agregar el concepto a la lista
claseKey = clase.getSignature().ToString();
ontologyConcept = new OntologyConcept(claseKey, claseValor, weigth, clase, clase.getSuperClasses(ontology), clase.getSubClasses(ontology));
ontologyConcept.Anotaciones = Anotaciones;
//Reinicializamos el valor para la nueva clase
claseValor = "";
//Verificar que se obtengan conceptos diferentes. Las claseKey se repiten siempre que aporten anotaciones diferentes
if (!this.concepts.ContainsKey(claseKey) && !this.concepts.ContainsValue(ontologyConcept) && !valores.Contains(ontologyConcept.ConceptValue) && !string.IsNullOrEmpty(ontologyConcept.ConceptValue))
{
this.concepts.Add(claseKey, ontologyConcept);
}
}
}
}
public static string GetOWLXML(CNL.DL.Paragraph para, bool owlXml, string externext, Dictionary <string, string> invUriMappings, AnnotationManager annotMan, string ontologyBase = null, Dictionary <string, Tuple <string, string> > prefixes = null, string defaultGuid = null, Dictionary <string, List <string> > owlOntologyAnnotation = null, string generatedBy = "CogniPy")
{
prefixes = prefixes ?? new Dictionary <string, Tuple <string, string> >();
if (ontologyBase == null)
{
ontologyBase = "http://www.ontorion.com/ontologies/Ontology" + Guid.NewGuid().ToString("N");
}
//var ontologyBase = (ontologyNs ?? "http://www.ontorion.com/ontologies/Ontology" + Guid.NewGuid().ToString("N"));
//if(!String.IsNullOrEmpty(defaultGuid))
// ontologyBase = (ontologyNs ?? "http://www.ontorion.com/ontologies/Ontology" + defaultGuid);
if (!ontologyBase.EndsWith("/") && !ontologyBase.EndsWith("#") && !ontologyBase.Contains("#"))
{
ontologyBase += "#";
}
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
CogniPy.ARS.Transform transform = new CogniPy.ARS.Transform();
transform.InvUriMappings = invUriMappings;
var df = manager.getOWLDataFactory();
ontology = manager.createOntology(IRI.create(ontologyBase));
org.semanticweb.owlapi.vocab.PrefixOWLOntologyFormat owlxmlFormat = null;
if (owlXml)
{
owlxmlFormat = new org.semanticweb.owlapi.io.OWLXMLOntologyFormat();
}
else
{
owlxmlFormat = new org.semanticweb.owlapi.io.RDFXMLOntologyFormat();
}
owlxmlFormat.setDefaultPrefix(ontologyBase);
foreach (var kv in prefixes)
{
owlxmlFormat.setPrefix(kv.Key.Replace("$", "."), kv.Value.Item1); // should we put here the Item2 (the location) and not the inner namespace???
if (!String.IsNullOrEmpty(kv.Value.Item2) && !(kv.Value.Item2.EndsWith(".encnl") || kv.Value.Item2.EndsWith(".encnl#"))) // do not export cnl imports (not in OWL!)
{
// here we need to use Item1 because we cannot export into OWL the specific location of the ontology ---> this is bad practice as in this way we loose the generality of the owl file
// imagine that the location is C://mydirectory/... and I add into an owl file: owl:import "C:/mydirectory/". This mean that only on my computer I will be able to import this file.
// On the other hand if we write owl:import "namespace of the file" there is a good chance that when someone else will open the file, the file will be imported from internet.
var decl = manager.getOWLDataFactory().getOWLImportsDeclaration(OWLPathUriTools.Path2IRI(kv.Value.Item1.TrimEnd('#')));
manager.applyChange(new AddImport(ontology, decl));
}
}
manager.setOntologyFormat(ontology, owlxmlFormat);
if (owlOntologyAnnotation != null)
{
foreach (var keyVal in owlOntologyAnnotation)
{
foreach (string val in keyVal.Value)
{
manager.applyChange(new AddOntologyAnnotation(
ontology,
manager.getOWLDataFactory().getOWLAnnotation(
manager.getOWLDataFactory().getOWLAnnotationProperty(IRI.create(keyVal.Key)),
manager.getOWLDataFactory().getOWLLiteral(val))));
}
}
}
transform.setOWLDataFactory(false, ontologyBase, df, owlxmlFormat, CNL.EN.CNLFactory.lex);
var paraFromAnnotStatements = annotMan.getDLAnnotationAxioms();
var stmts = para.Statements;
foreach (var p in paraFromAnnotStatements)
{
stmts.AddRange(p.Value);
}
var conv = transform.Convert(new CogniPy.CNL.DL.Paragraph(null)
{
Statements = stmts
});
var om = new org.coode.xml.OWLOntologyXMLNamespaceManager(manager, ontology);
foreach (var axiom in conv.axioms)
{
if (axiom.comment != null)
{
var dp = axiom.comment.IndexOf(':');
var x = axiom.comment.Substring(0, dp);
if (x.Trim() == "Namespace")
{
var ontologyIri = axiom.comment.Substring(dp + 1).Trim();
if (ontologyIri.EndsWith("."))
{
ontologyIri = ontologyIri.Substring(0, ontologyIri.Length - 1);
}
if (ontologyIri.StartsWith("\'") && ontologyIri.Length > 2)
{
ontologyIri = ontologyIri.Substring(1, ontologyIri.Length - 2).Replace("\'\'", "\'");
}
manager.removeOntology(ontology);
ontology = manager.createOntology(IRI.create(ontologyIri));
om.setDefaultNamespace(ontologyIri + "#");
transform.setOWLDataFactory(true, ontologyBase, df, owlxmlFormat, CNL.EN.CNLFactory.lex);
}
else if (x.Trim() == "References")
{
var refs = CNLTools.ParseReferences(axiom.comment.Substring(dp));
foreach (Match match in refs)
{
var onto = match.Groups["ont"].Value;
if (onto.StartsWith("\'") && onto.Length > 2)
{
onto = onto.Substring(1, onto.Length - 2).Replace("\'\'", "\'").Trim();
}
if (!string.IsNullOrEmpty(onto))
{
if (onto.ToLower().EndsWith(".encnl"))
{
onto = OWLConverter.PathToIRIString(onto.Substring(0, onto.Length - ".encnl".Length) + externext);
}
var ns = match.Groups["ns"].Value;
if (ns.StartsWith("\'") && ns.Length > 2)
{
ns = ns.Substring(1, ns.Length - 2).Replace("\'\'", "\'").Trim();
}
else
if (string.IsNullOrEmpty(ns))
{
ns = onto;
}
om.setPrefix(match.Groups["pfx"].Value, ns);
owlxmlFormat.setPrefix(match.Groups["pfx"].Value, ns);
var decl = manager.getOWLDataFactory().getOWLImportsDeclaration(OWLPathUriTools.Path2IRI(onto));
manager.applyChange(new AddImport(ontology, decl));
}
}
}
else
{
//manager.applyChange(new AddOntologyAnnotation(
// ontology,
// manager.getOWLDataFactory().getOWLAnnotation(
// manager.getOWLDataFactory().getOWLAnnotationProperty(IRI.create(ontologyBase + x)),
// manager.getOWLDataFactory().getOWLLiteral(axiom.comment.Substring(dp)))));
}
}
else if (axiom.axiom != null)
{
manager.addAxiom(ontology, axiom.axiom);
}
}
foreach (var axiom in conv.additions)
{
manager.addAxiom(ontology, axiom);
}
var ontout = new org.semanticweb.owlapi.io.StringDocumentTarget();
manager.saveOntology(ontology, owlxmlFormat, ontout);
manager.removeOntology(ontology);
var retdoc = new XmlDocument();
retdoc.LoadXml(ontout.toString());
foreach (var elem in retdoc.ChildNodes)
{
if (elem is XmlComment)
{
retdoc.RemoveChild(elem as XmlComment);
}
}
retdoc.AppendChild(retdoc.CreateComment("Generated by " + generatedBy + ", (with support from OwlApi)"));
return(SerializeDoc(retdoc));
}
public org.semanticweb.owlapi.reasoner.OWLReasoner createReasoner(OWLOntology ontology, org.semanticweb.owlapi.reasoner.OWLReasonerConfiguration config)
{
return(new com.clarkparsia.pellet.owlapiv3.PelletReasoner(ontology, config, BufferingMode.BUFFERING));
}
public org.semanticweb.owlapi.reasoner.OWLReasoner createReasoner(OWLOntology ontology)
{
var config = new SimpleConfiguration(progrMonitor);
return(new com.clarkparsia.pellet.owlapiv3.PelletReasoner(ontology, config, BufferingMode.BUFFERING));
}
private void MainForm_Load(object sender, EventArgs e)
{
OwlManager = new OWLManager();
OwlOntology = new OWLOntology();
panel_reasoner.BackColor = Color.Red;
}
