diff --git a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java index 2964443..429d4c1 100644 --- a/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java +++ b/owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java @@ -170,11 +170,12 @@ public void setKbMetdata(KBMetadata kbMetdata) { this.kbMetdata = kbMetdata; } - - private String getShortForm(IRI iri) { - // TODO not great to have a mix of IRI and CURIE - return curieUtil.getCurie(iri.toString()).or(iri.toString()); + if (curieUtil.getCurieMap().isEmpty()) { + return iri.toString(); + } else { + return curieUtil.getCurie(iri.toString()).get(); + } } private void populateLabelsFromOntology(LabelMapper labelMapper, OWLOntology ontology) { @@ -996,9 +997,11 @@ protected String getIdentifier(OWLNamedObject obj) { */ protected OWLClass getOWLClass(String id) { Preconditions.checkNotNull(id); - // TODO not great to have a mix of IRI and CURIE - String iri = curieUtil.getIri(id).or(id); - return getOWLClass(IRI.create(iri)); + if (curieUtil.getCurieMap().isEmpty()) { + return getOWLClass(IRI.create(id)); + } else { + return getOWLClass(IRI.create(curieUtil.getIri(id).get())); + } } /** @@ -1023,9 +1026,11 @@ protected OWLNamedIndividual getOWLNamedIndividual(IRI iri) { */ public OWLNamedIndividual getOWLNamedIndividual(String id) { Preconditions.checkNotNull(id); - // TODO not great to have a mix of IRI and CURIE - String iri = curieUtil.getIri(id).or(id); - return getOWLNamedIndividual(IRI.create(iri)); + if (curieUtil.getCurieMap().isEmpty()) { + return getOWLNamedIndividual(IRI.create(id)); + } else { + return getOWLNamedIndividual(IRI.create(curieUtil.getIri(id).get())); + } } public Attribute getAttribute(String id) {