Java Code Examples for org.semanticweb.owlapi.model.OWLLiteral#getLiteral()

private OWLAxiom tr(OWLClass c, OWLAnnotationAssertionAxiom ax) {
	OWLAnnotationProperty p = ax.getProperty();
	if (!ecmap.containsKey(c)) {
		// preserve as-is, exception for labels
		if (p.isLabel()) {
			OWLLiteral lit = (OWLLiteral) ax.getValue();
			String newVal = lit.getLiteral() + " (" + suffix + ")";
			return fac.getOWLAnnotationAssertionAxiom(ax.getProperty(),
					ax.getSubject(), fac.getOWLLiteral(newVal));
		}
		return ax;

	} else {
		// the class is merged - ditch its axioms
		// (in future some may be preserved - syns?)
		// fac.getOWLAnnotationAssertionAxiom(ax.getProperty(), ecmap,
		// ax.getValue());
		return null;
	}
}
 

/*** 
 * @param literal An OWLLiteral
 * @return an optional correctly typed Java object from the OWLLiteral
 */
public static Optional<Object> getTypedLiteralValue(OWLLiteral literal) {
  Object literalValue = null;
  if (literal.isBoolean()) {
    literalValue = literal.parseBoolean();
  } else if (literal.isInteger()) {
    literalValue = literal.parseInteger();
  } else if (literal.isFloat()) {
    literalValue = literal.parseFloat();
  } else if (literal.isDouble()) {
    literalValue = literal.parseDouble();
  } else {
    // This needs to be addressed  by #110
    if (literal.hasLang() && !literal.getLang().startsWith("en")) {
      if (!unknownLanguages.contains(literal.getLang())) {
        unknownLanguages.add(literal.getLang());
        logger.warning("Ignoring *all* literals with unsupported language: \"" + literal.getLang() + "\".");
      }
      return Optional.empty();
    }
    literalValue = literal.getLiteral();
  }
  return Optional.of(literalValue);
}
 

private static String labelFor(OWLClass clazz, OWLOntology ontology) {
  // LabelExtractor is not available in the version of OWLAPI
  // Instead: Use the getAnnotations like we do in getData
  System.out.println("This is unverified. ChEBI parser:");
  System.out.println("LabelExtractor is not available in this OWLAPI v");
  System.out.println("So we extract the label manually. But not sure");
  System.out.println("if this code is correct. Need to check. Pause...");
  System.console().readLine();

  String chebiID = clazz.getIRI().getFragment();
  String label = null;
  for (OWLAnnotation a : clazz.getAnnotations(ontology)) {
    // We got the "if code" below from
    // http://grepcode.com/file/repo1.maven.org/maven2/net.sourceforge.owlapi/owlapi-contract/3.4/uk/ac/manchester/owl/owlapi/tutorial/LabelExtractor.java
    if (a.getProperty().isLabel()) {
      OWLLiteral c = (OWLLiteral) a.getValue();
      label = c.getLiteral();
    }
  }
  // OLD code using LabelExtractor:
  // LabelExtractor le = new LabelExtractor();
  // Set<OWLAnnotation> annotations = clazz.getAnnotations(ontology);
  // for (OWLAnnotation anno : annotations) {
  //   anno.accept(le);
  // }
  // label = le.getResult();

  /* Print out the label if there is one. Else ID */
  if (label != null) {
    return chebiID + "(" + label + ")";
  } else {
    return chebiID;
  }
}
 

private Set<ISynonym> getOBOSynonyms(OWLEntity e, Obo2OWLVocabulary vocabulary, OWLOntology ont) {
	OWLAnnotationProperty synonymProperty = getDataFactory().getOWLAnnotationProperty(vocabulary.getIRI());
	Set<OWLAnnotation> anns = OwlHelper.getAnnotations(e, synonymProperty, ont);
	Set<OWLAnnotationAssertionAxiom> annotationAssertionAxioms = ont.getAnnotationAssertionAxioms(e.getIRI());
	if (anns != null && !anns.isEmpty()) {
		Set<ISynonym> set = new HashSet<ISynonym>();
		for (OWLAnnotation a : anns) {
			if (a.getValue() instanceof OWLLiteral) {
				OWLLiteral val = (OWLLiteral) a.getValue();
				String label = val.getLiteral();
				if (label != null && label.length() > 0) {
					String category = null;
					Set<String> xrefs = null;
					SynonymDetails details = getOBOSynonymDetails(annotationAssertionAxioms, val, synonymProperty);
					if (details != null) {
						category = details.category;
						xrefs = details.xrefs;
					}
					Synonym s = new Synonym(label, vocabulary.getMappedTag(), category, xrefs);
					set.add(s);
				}
			}
		}
		if (!set.isEmpty()) {
			return set;
		}
	}
	return null;
}
 

/**
 * Convenience method to get the first string literal of an
 * annotation property.
 *
 * @param ontology the current ontology
 * @param taxon the subject
 * @param property the property
 * @return null or the label content
 */
protected static String getFirstLiteral(OWLOntology ontology,
		OWLEntity taxon, OWLAnnotationProperty property) {
	Set<OWLAnnotationAssertionAxiom> axioms = ontology.getAnnotationAssertionAxioms(taxon.getIRI());
	for (OWLAnnotationAssertionAxiom axiom : axioms) {
		if (property.equals(axiom.getProperty())) {
			OWLAnnotationValue value = axiom.getValue();
			if (value instanceof OWLLiteral) {
				OWLLiteral literal = (OWLLiteral)value;
				return literal.getLiteral();
			}
		}
	}
	return null;
}
 

public Set<String> getDatabaseIds(OWLClass entity) {
  Set<String> dbAnnotations = new HashSet<>();
  for (OWLAnnotation annotation : entity.getAnnotations(ontology)) {
    if (annotation.getValue() instanceof OWLLiteral) {
      OWLLiteral val = (OWLLiteral) annotation.getValue();
      String value = val.getLiteral();
      if (value.matches(DB_ID_PATTERN)) {
        dbAnnotations.add(value);
      }
    }
  }
  return dbAnnotations;
}
 

public String getOntologyLabel() {
  OWLAnnotationProperty labelProperty =
      factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
  String ontologyLabel = StringUtils.EMPTY;
  for (OWLAnnotation annotation : ontology.getAnnotations()) {
    if (annotation.getProperty().equals(labelProperty)
        && annotation.getValue() instanceof OWLLiteral) {
      OWLLiteral val = (OWLLiteral) annotation.getValue();
      ontologyLabel = val.getLiteral();
    }
  }
  return ontologyLabel;
}
 

public static String renderMarkdown(OWLGraphWrapper g, String baseDir, boolean isIncludeImage) {

		OWLOntology ont = g.getSourceOntology();
		StringBuilder out = new StringBuilder();

		String ontId = g.getOntologyId();

		Set<OWLAnnotation> oAnns = ont.getAnnotations();
		System.err.println("NUM1:"+oAnns.size());

		String title = getVal("title", oAnns);

		out.append("## Ontology: "+title+"\n\n");
		out.append("IRI: "+rurl(ont)+"\n\n");

		String desc = getVal("description", oAnns);
		out.append("### Description\n\n");
		out.append(desc+"\n\n");

		Set<OWLOntology> imports = ont.getImports();
		if (imports.size() > 0) {
			out.append("### Imports\n\n");
			for (OWLOntology im : imports) {
				out.append(" * "+rurl(im)+"\n");
			}
		}
		if (isIncludeImage) {
			String imgFn = baseDir + "/" + ontId + ".png";
			out.append("![]("+imgFn+")\n\n");
		}

		System.err.println("NUM:"+oAnns.size());
		if (oAnns.size() > 0) {
			out.append("### Annotations:\n\n");
			for (OWLAnnotation ann : oAnns) {
				String annLabel = g.getLabelOrDisplayId(ann.getProperty());
				OWLAnnotationValue v = ann.getValue();
				String dv = v.toString();
				if (v instanceof OWLLiteral) {
					OWLLiteral lv = ((OWLLiteral)v);
					dv = lv.getLiteral();
					IRI dt = lv.getDatatype().getIRI();
					//System.out.println("DT = "+dt);
					if (dt.equals(OWL2Datatype.XSD_ANY_URI.getIRI())) {
						dv = href(lv.getLiteral());
					}
				}
				out.append(" * "+href(ann.getProperty().getIRI().toString(),annLabel)+" : "+dv+"\n");
			}
		}

		return out.toString();
	}
 

public IRI getIRIByIdentifier(String id, boolean isAutoResolve) {
	if (isAutoResolve) {
		OWLObject obj = this.getObjectByAltId(id);
		if (obj != null) {
			return ((OWLNamedObject) obj).getIRI();
		}
	}

	// special magic for finding IRIs from a non-standard identifier
	// This is the case for relations (OWLObject properties) with a short hand
	// or for relations with a non identifiers with-out a colon, e.g. negative_regulation
	// we first collect all candidate matching properties in candIRISet.
	Set<IRI> candIRISet = Sets.newHashSet();
	if (!id.contains(":")) {
		final OWLAnnotationProperty shortHand = getDataFactory().getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_OIO_shorthand.getIRI());
		final OWLAnnotationProperty oboIdInOwl = getDataFactory().getOWLAnnotationProperty(Obo2Owl.trTagToIRI(OboFormatTag.TAG_ID.getTag()));
		for (OWLOntology o : getAllOntologies()) {
			for(OWLObjectProperty p : o.getObjectPropertiesInSignature()) {
				// check for short hand or obo ID in owl
				Set<OWLAnnotation> annotations = OwlHelper.getAnnotations(p, o);
				if (annotations != null) {
					for (OWLAnnotation owlAnnotation : annotations) {
						OWLAnnotationProperty property = owlAnnotation.getProperty();
						if ((shortHand != null && shortHand.equals(property)) 
								|| (oboIdInOwl != null && oboIdInOwl.equals(property)))
						{
							OWLAnnotationValue value = owlAnnotation.getValue();
							if (value != null && value instanceof OWLLiteral) {
								OWLLiteral literal = (OWLLiteral) value;
								String shortHandLabel = literal.getLiteral();
								if (id.equals(shortHandLabel)) {
									candIRISet.add(p.getIRI());
								}
							}
						}
					}
				}
			}
		}
	}

	// In the case where we find multiple candidate IRIs, we give priorities for IRIs from BFO or RO ontologies.
	IRI returnIRI = null;
	for (IRI iri: candIRISet) {
		String iriStr = iri.toString();
		if (iriStr.contains("BFO") || iriStr.contains("RO")) {
			returnIRI = iri;
		}
	}

	// If we were not able to find RO/BFO candidate IRIs for id
	if (returnIRI == null) {
		// We return it only if we have only one candidate. 
		if (candIRISet.size() == 1)
			return new ArrayList<IRI>(candIRISet).get(0);
		// This is the unexpected case. Multiple non-RO/BPO properties are mapped to given id and it's not clear what to return.
		else if (candIRISet.size() > 1)
			throw new RuntimeException("Multiple candidate IRIs are found for id: " +  id + ". None of them are from BFO or RO.");
	}
	// If we were able to find the property from RO/BFO, just return it. 
	else {
		return returnIRI;
	}

	// otherwise use the obo2owl method
	Obo2Owl b = new Obo2Owl(getManager()); // re-use manager, creating a new one can be expensive as this is a highly used code path
	b.setObodoc(new OBODoc());
	return b.oboIdToIRI(id);
}
 

@Override
public String visit(OWLLiteral literal) {
	return literal.getLiteral();
}