/// <summary>
/// Returns all annotations contained in the manager as DLAnnotationAxiom.
/// </summary>
/// <param name="pfx2ns">If not null, it will be used to transform each prefix found to the full namespace.</param>
/// <returns></returns>
public Dictionary <ARS.EntityKind, List <DL.DLAnnotationAxiom> > getDLAnnotationAxioms(Func <string, string> pfx2ns = null)
{
var dlAnnotatedAxioms = new Dictionary <ARS.EntityKind, List <DL.DLAnnotationAxiom> >();
foreach (var annotKv in _annotatedElements)
{
var kind = ParseSubjectKind(subjectType[annotKv.Key]);
if (!dlAnnotatedAxioms.ContainsKey(kind))
{
dlAnnotatedAxioms.Add(kind, new List <DL.DLAnnotationAxiom>());
}
var dlSubj = CNLTools.DLToFullUri(annotKv.Key, kind, pfx2ns);
foreach (var annotEl in annotKv.Value)
{
var nameToUse = annotEl.Type;
dlAnnotatedAxioms[kind].Add(new DL.DLAnnotationAxiom(null, dlSubj, subjectType[annotKv.Key], CNLTools.DLToFullUri(annotEl.Type, ARS.EntityKind.Role, pfx2ns), annotEl.Language, (string)annotEl.Value));
}
}
return(dlAnnotatedAxioms);
}
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));
}
/// <summary>
/// Loads the W3CAnnotations found in the line. By default the annotationManager is using DL internally if the text you are giving is not in DL, use the inputTranslator argument
/// If the subject of an annotation is a Statement, then the Statement is expected to be written like: "statement where quote is ''"
/// </summary>
/// <param name="line"></param>
/// <param name="append">Decides if the text should be appended to the annotationManager or not</param>
/// <param name="inputTranslator">Used internally to translate for CNL to DL. Use it if the input is not in DL. From ENCNL, the translator is: x => Ontorion.CNL.EN.ENNameingConvention.ToDL(new Ontorion.CNL.EN.EnName() { id = x }, Ontorion.CNL.EN.endict.WordKind.NormalForm).id </param>
/// <returns></returns>
public void loadW3CAnnotationsFromText(string line, bool append = false, Func <string, string> inputTranslator = null)
{
if (String.IsNullOrEmpty(line) || String.IsNullOrWhiteSpace(line) || !line.Contains(":"))
{
return;
}
var localAnnotationManager = new AnnotationManager();
var dp = 0;
if (line.Contains(ANNOTATION_START))
{
dp = line.IndexOf(':') + 1;
}
bool newAnnotationSubjects = false;
var refs = w3cAnnotRg.Matches(line.Substring(dp).Trim());
foreach (Match match in refs)
{
string annotated = match.Groups["annotated"].Value;
string type = match.Groups["type"].Value;
string val = match.Groups["value"].Value;
string kind = match.Groups["annotatedKind"].Value;
// if one of these values are null this means that something went wrong during parsing... someone changed it manually?
// in this case we skip this line.
if (String.IsNullOrWhiteSpace(annotated) || String.IsNullOrWhiteSpace(type) || String.IsNullOrWhiteSpace(val) || String.IsNullOrWhiteSpace(kind))
{
continue;
}
var res = ParseSubjectKind(kind);
annotated = annotated.Trim();
type = type.Trim();
if (inputTranslator != null)
{
if (res != ARS.EntityKind.Statement && !CNLTools.isSurelyDLEntity(annotated, res))
{
annotated = inputTranslator(annotated);
}
if (!CNLTools.isSurelyDLEntity(type, ARS.EntityKind.Role))
{
type = inputTranslator(type);
}
}
// if the subject is a statement, then the annotation manager keeps it internally as: statement with quotes inside (no quotes around!)
if (res == ARS.EntityKind.Statement && annotated.StartsWith("\"") && annotated.EndsWith("\""))
{
annotated = annotated.Substring(1, annotated.Length - 2).Replace("\''", "\"");
}
else if (res == ARS.EntityKind.Statement && !annotated.StartsWith("\"") && !annotated.EndsWith("\"")) //statement should be quoted! If not, continue.
{
continue;
}
if (!localAnnotationManager.ContainsAnnotationSubject(annotated.Trim()))
{
newAnnotationSubjects = true;
}
localAnnotationManager.appendAnnotations(annotated.Trim(), kind.Trim(), new List <W3CAnnotation>()
{
new W3CAnnotation(true)
{
Type = type.Trim(), Value = val.Trim(), Language = match.Groups["language"].Value
}
});
}
if (newAnnotationSubjects && NewAnnotationSubject != null && FireNewSubjectEvent)
{
NewAnnotationSubject(this);
}
if (!append)
{
this.clearAnnotations();
}
appendAnnotations(localAnnotationManager);
if (!append)
{
this.AssumeNotModifiedNow();
}
}
string applyFullUri(string nm)
{
return(CNLTools.DLToFullUri(nm, ARS.EntityKind.Instance, pfx2ns, _defaultNs));
}
