public static Parts Split(string uri)
{
return(new OwlName()
{
iri = IRI.create(uri)
}.Split());
}
public IRI getIRIFromId(string qname, EntityKind makeFor)
{
if (InvUriMappings.ContainsKey(qname))
{
return(IRI.create(InvUriMappings[qname]));
}
else
{
DlName dl = new DlName()
{
id = qname
};
var dlp = dl.Split();
if (InvUriMappings.ContainsKey(dlp.name) && dlp.term == ns2pfx(IRI.create(InvUriMappings[dlp.name]).getNamespace()))
{
return(IRI.create(InvUriMappings[dlp.name]));
}
else
{
return(owlNameingConvention.FromDL(new DlName()
{
id = qname
}, lex, pfx2ns, makeFor).iri);
}
}
}
public DlName ToDL(string uri, ARS.EntityKind makeFor)
{
var owlName = new CogniPy.ARS.OwlName()
{
iri = IRI.create(uri)
};
return(owlNameingConvention.ToDL(owlName, lex, ns2pfx, makeFor));
}
public OwlName Combine()
{
string sep = "";
if (!ns.EndsWith("/") && !ns.EndsWith("#") && !ns.Contains("#"))
{
sep = "#";
}
if (name.Contains("/") && ns.EndsWith("/"))
{
ns = ns.Substring(0, ns.Length - 1) + "#";
}
return(new OwlName()
{
iri = IRI.create(ns + sep + encodedName)
});
}
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);
}
}
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));
}
static public string IRI2Path(IRI iri)
{
return(iri.toURI().toString().Replace('\\', '/'));
}
static public IRI Path2IRI(string fileName)
{
return(IRI.create(fileName.Replace('\\', '/')));
}
/// <summary>Creates an array of RDF triples for the given graph.</summary>
/// <remarks>Creates an array of RDF triples for the given graph.</remarks>
/// <param name="graph">the graph to create RDF triples for.</param>
internal virtual void GraphToRDF(string graphName,
JObject graph
)
{
// 4.2)
IList <Quad> triples = new List <Quad>();
// 4.3)
var subjects = graph.GetKeys();
// Collections.sort(subjects);
foreach (var id in subjects)
{
if (JsonLdUtils.IsRelativeIri(id))
{
continue;
}
var node = (JObject)graph[id];
var properties = new JArray(node.GetKeys());
properties.SortInPlace();
foreach (string property in properties)
{
var localProperty = property;
JArray values;
// 4.3.2.1)
if ("@type".Equals(localProperty))
{
values = (JArray)node["@type"];
localProperty = JsonLdConsts.RdfType;
}
else
{
// 4.3.2.2)
if (JsonLdUtils.IsKeyword(localProperty))
{
continue;
}
// 4.3.2.3)
if (localProperty.StartsWith("_:") && !api.opts.GetProduceGeneralizedRdf())
{
continue;
}
// 4.3.2.4)
if (JsonLdUtils.IsRelativeIri(localProperty))
{
continue;
}
values = (JArray)node[localProperty];
}
Node subject;
if (id.IndexOf("_:") == 0)
{
subject = new BlankNode(id);
}
else
{
subject = new IRI(id);
}
// RDF predicates
Node predicate;
if (localProperty.StartsWith("_:"))
{
predicate = new BlankNode(localProperty);
}
else
{
predicate = new IRI(localProperty);
}
foreach (var item in values)
{
// convert @list to triples
if (JsonLdUtils.IsList(item))
{
var list = (JArray)((JObject)item)["@list"];
Node last = null;
var firstBNode = nil;
if (!list.IsEmpty())
{
last = ObjectToRDF(list[list.Count - 1]);
firstBNode = new BlankNode(api.GenerateBlankNodeIdentifier());
}
triples.Add(new Quad(subject, predicate, firstBNode, graphName));
for (var i = 0; i < list.Count - 1; i++)
{
var @object = ObjectToRDF(list[i]);
triples.Add(new Quad(firstBNode, first, @object, graphName));
Node restBNode = new BlankNode(api.GenerateBlankNodeIdentifier
());
triples.Add(new Quad(firstBNode, rest, restBNode, graphName));
firstBNode = restBNode;
}
if (last != null)
{
triples.Add(new Quad(firstBNode, first, last, graphName));
triples.Add(new Quad(firstBNode, rest, nil, graphName));
}
}
else
{
// convert value or node object to triple
var @object = ObjectToRDF(item);
if (@object != null)
{
triples.Add(new Quad(subject, predicate, @object, graphName));
}
}
}
}
}
this[graphName] = triples;
}
private IRI decode_IRI()
{
push("IRI");
bool decoded = true;
int s0 = index;
var e0 = new List<Rule>();
Rule rule;
decoded = false;
if (!decoded)
{
{
var e1 = new List<Rule>();
int s1 = index;
decoded = true;
if (decoded)
{
bool f1 = true;
int c1 = 0;
for (int i1 = 0; i1 < 1 && f1; i1++)
{
rule = decode_scheme();
if ((f1 = rule != null))
{
e1.Add(rule);
c1++;
}
}
decoded = c1 == 1;
}
if (decoded)
{
bool f1 = true;
int c1 = 0;
for (int i1 = 0; i1 < 1 && f1; i1++)
{
rule = decode_StringValue(":");
if ((f1 = rule != null))
{
e1.Add(rule);
c1++;
}
}
decoded = c1 == 1;
}
if (decoded)
{
bool f1 = true;
int c1 = 0;
for (int i1 = 0; i1 < 1 && f1; i1++)
{
rule = decode_ihier_part();
if ((f1 = rule != null))
{
e1.Add(rule);
c1++;
}
}
decoded = c1 == 1;
}
if (decoded)
{
bool f1 = true;
int c1 = 0;
for (int i1 = 0; i1 < 1 && f1; i1++)
{
decoded = false;
if (!decoded)
{
{
var e2 = new List<Rule>();
int s2 = index;
decoded = true;
if (decoded)
{
bool f2 = true;
int c2 = 0;
for (int i2 = 0; i2 < 1 && f2; i2++)
{
rule = decode_StringValue("?");
if ((f2 = rule != null))
{
e2.Add(rule);
c2++;
}
}
decoded = c2 == 1;
}
if (decoded)
{
bool f2 = true;
int c2 = 0;
for (int i2 = 0; i2 < 1 && f2; i2++)
{
rule = decode_iquery();
if ((f2 = rule != null))
{
e2.Add(rule);
c2++;
}
}
decoded = c2 == 1;
}
if (decoded)
e1.AddRange(e2);
else
index = s2;
}
}
if (decoded)
c1++;
f1 = decoded;
}
decoded = true;
}
if (decoded)
{
bool f1 = true;
int c1 = 0;
for (int i1 = 0; i1 < 1 && f1; i1++)
{
decoded = false;
if (!decoded)
{
{
var e2 = new List<Rule>();
int s2 = index;
decoded = true;
if (decoded)
{
bool f2 = true;
int c2 = 0;
for (int i2 = 0; i2 < 1 && f2; i2++)
{
rule = decode_StringValue("#");
if ((f2 = rule != null))
{
e2.Add(rule);
c2++;
}
}
decoded = c2 == 1;
}
if (decoded)
{
bool f2 = true;
int c2 = 0;
for (int i2 = 0; i2 < 1 && f2; i2++)
{
rule = decode_ifragment();
if ((f2 = rule != null))
{
e2.Add(rule);
c2++;
}
}
decoded = c2 == 1;
}
if (decoded)
e1.AddRange(e2);
else
index = s2;
}
}
if (decoded)
c1++;
f1 = decoded;
}
decoded = true;
}
if (decoded)
e0.AddRange(e1);
else
index = s1;
}
}
rule = null;
if (decoded)
rule = new IRI(text.Substring(s0, index - s0), e0);
else
index = s0;
pop("IRI", decoded, index - s0);
return (IRI)rule;
}
public IRI(IRI rule)
: base(rule.spelling, rule.rules)
{
}