Пример #1
0
  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));
  }
Пример #2
0
  private void assertSameConcept(Concept expected, Concept actual, List<String> traversedUrns) {
    String errMsg = String.format("%1$s != %2$s", expected, actual);

    Assert.assertEquals(errMsg, expected, actual);
    Assert.assertEquals(errMsg, expected.getLabel(), actual.getLabel());
    Assert.assertEquals(errMsg, expected.getPreferredLabel(), actual.getPreferredLabel());
    Assert.assertEquals(errMsg, expected.isHref(), actual.isHref());
    Assert.assertEquals(errMsg, expected.getDefinition(), actual.getDefinition());

    // To deal with cycles in the hierarchy
    if (traversedUrns.contains(expected.getUrn())) {
      return;
    } else {
      traversedUrns.add(expected.getUrn());
    }

    assertSameConcept(expected.getBroader(), actual.getBroader(), traversedUrns);
    assertSameConcept(expected.getNarrower(), actual.getNarrower(), traversedUrns);
    assertSameConcept(expected.getRelated(), actual.getRelated(), traversedUrns);
  }