public static Map<EdamUri, Concept> load(String edamPath) throws OWLOntologyCreationException {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntologyFromOntologyDocument(new File(edamPath));
String prefix = ontology.getOntologyID().getOntologyIRI().get().toString();
return ontology
.classesInSignature()
.filter(c -> EdamUri.isEdamUri(c.getIRI().toString(), prefix))
.collect(
Collectors.toMap(
c -> new EdamUri(c.getIRI().toString(), prefix),
c -> {
Concept concept = new Concept();
EntitySearcher.getAnnotations(c, ontology)
.forEachOrdered(
a -> {
if (a.getProperty().isLabel())
concept.setLabel(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty().isDeprecated()) concept.setObsolete(true);
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym")
&& a.getValue().asLiteral().isPresent())
concept.addExactSynonym(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym")
&& a.getValue().asLiteral().isPresent())
concept.addNarrowSynonym(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym")
&& a.getValue().asLiteral().isPresent())
concept.addBroadSynonym(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasDefinition")
&& a.getValue().asLiteral().isPresent())
concept.setDefinition(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty().isComment()
&& a.getValue().asLiteral().isPresent())
concept.setComment(a.getValue().asLiteral().get().getLiteral());
});
if (concept.getLabel().isEmpty())
throw new IllegalStateException(
String.format("Label of concept %s is empty", c.getIRI()));
return concept;
},
(u, v) -> {
throw new IllegalStateException(String.format("Duplicate key %s", u));
},
LinkedHashMap::new));
}
public void actionPerformed(ActionEvent e) {
OWLClass selCls = getOWLClass();
if (selCls == null) {
return;
}
// TODO: Extract this and make less dependent on hierarchy provider
OWLObjectHierarchyProvider<OWLClass> provider =
getOWLModelManager().getOWLHierarchyManager().getOWLClassHierarchyProvider();
Set<OWLClass> clses = new HashSet<>();
for (OWLClass par : provider.getParents(selCls)) {
clses.addAll(provider.getChildren(par));
}
for (Iterator<OWLClass> it = clses.iterator(); it.hasNext(); ) {
OWLClass cls = it.next();
for (OWLOntology ont : getOWLModelManager().getActiveOntologies()) {
if (EntitySearcher.isDefined(cls, ont)) {
it.remove();
break;
}
}
}
if (clses.size() > 1) {
OWLAxiom ax = getOWLDataFactory().getOWLDisjointClassesAxiom(clses);
getOWLModelManager().applyChange(new AddAxiom(getOWLModelManager().getActiveOntology(), ax));
}
// 2) Get the named subs
// try {
// OWLOntology owlOntology = getOWLModelManager().getActiveOntology();
// DisjointAxiomCreator creator = new
// DisjointAxiomCreator(getOWLModelManager().getOWLClassHierarchyProvider(),
// owlOntology,
//
// getOWLModelManager().getActiveOntologies());
//
// getOWLModelManager().applyChanges(creator.getChanges());
// } catch (OWLException ex) {
// logger.error(ex);
// }
}
