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));
}
/** Runs the factory through a standard SISSVoc response XML */
@Test
public void testSISSVocRDF() throws Exception {
// Build our expectation
Concept concept1 = new Concept("urn:concept:1");
Concept concept2 = new Concept("urn:concept:2");
Concept concept3 = new Concept("urn:concept:3");
Concept concept4 = new Concept("urn:concept:4");
NamedIndividual ni1 = new NamedIndividual("urn:ni:1");
NamedIndividual ni2 = new NamedIndividual("urn:ni:2");
NamedIndividual ni3 = new NamedIndividual("urn:ni:3");
concept1.setNarrower(new Concept[] {concept2, concept3, ni2});
concept1.setLabel("LabelConcept1");
concept1.setPreferredLabel("PrefLabelConcept1");
concept2.setBroader(new Concept[] {concept1});
concept2.setRelated(new Concept[] {concept3});
concept2.setLabel("LabelConcept2");
concept2.setPreferredLabel("PrefLabelConcept2");
concept2.setDefinition("DefinitionConcept2");
concept3.setBroader(new Concept[] {concept1});
concept3.setRelated(new Concept[] {concept2});
concept3.setNarrower(new Concept[] {ni1});
concept3.setLabel("LabelConcept3");
concept3.setPreferredLabel("PrefLabelConcept3");
concept4.setNarrower(new Concept[] {ni3});
concept4.setLabel("LabelConcept4");
concept4.setPreferredLabel("PrefLabelConcept4");
concept4.setDefinition("DefinitionConcept4");
ni1.setBroader(new Concept[] {concept3});
ni1.setLabel("LabelNamedIndividual1");
ni1.setPreferredLabel("PrefLabelNamedIndividual1");
ni2.setBroader(new Concept[] {concept1});
ni2.setLabel("LabelNamedIndividual2");
ni2.setPreferredLabel("PrefLabelNamedIndividual2");
ni3.setBroader(new Concept[] {concept4});
ni3.setLabel("LabelNamedIndividual3");
ni3.setPreferredLabel("PrefLabelNamedIndividual3");
Concept[] expectation = new Concept[] {concept1, concept4};
// Build our actual list
String responseXml =
ResourceUtil.loadResourceAsString(
"org/auscope/portal/core/test/responses/sissvoc/SISSVocResponse.xml");
Document responseDoc = DOMUtil.buildDomFromString(responseXml);
Node rdfNode =
(Node)
DOMUtil.compileXPathExpr("rdf:RDF", new VocabNamespaceContext())
.evaluate(responseDoc, XPathConstants.NODE);
ConceptFactory cf = new ConceptFactory();
Concept[] actualConcepts = cf.parseFromRDF(rdfNode);
Assert.assertNotNull(actualConcepts);
assertSameConcept(expectation, actualConcepts, new ArrayList<String>());
}
