Examples with Ontology org.molgenis.ontology.core.meta.Ontology used on opensource projects

Example 1 with Ontology

use of org.molgenis.ontology.core.meta.Ontology in project molgenis by molgenis.

the class OntologyImportServiceIT method verifyOwlAsSystem.

private void verifyOwlAsSystem() {
    // Verify two imported rows (organization and team, as these are interesting examples)
    List<Entity> entities = dataService.findAll("sys_ont_OntologyTerm").collect(Collectors.toList());
    Optional<Entity> organizationOpt = entities.stream().filter(e -> e.getString("ontologyTermName").equals("organization")).findFirst();
    assertTrue(organizationOpt.isPresent());
    Entity organization = organizationOpt.get();
    Optional<Entity> teamOpt = entities.stream().filter(e -> e.getString("ontologyTermName").equals("team")).findFirst();
    assertTrue(teamOpt.isPresent());
    Entity team = teamOpt.get();
    // Verify organization
    assertEquals(organization.getString("ontologyTermIRI"), "http://www.molgenis.org#Organization");
    assertEquals(organization.getString("ontologyTermName"), "organization");
    // verify organization ontologyTermSynonym
    Iterable<Entity> ontologyTermSynonym = organization.getEntities("ontologyTermSynonym");
    List<Entity> termSynonymRefList = new ArrayList<>();
    ontologyTermSynonym.forEach(termSynonymRefList::add);
    assertEquals(termSynonymRefList.size(), 1);
    Entity organizationOntologyTermSynonym = dataService.findOneById("sys_ont_OntologyTermSynonym", termSynonymRefList.get(0).getIdValue());
    assertEquals(organizationOntologyTermSynonym.getString("ontologyTermSynonym"), "organization");
    // verify organization ontology
    Ontology ontology = (Ontology) organization.get("ontology");
    assertEquals(ontology.getOntologyName(), "ontology-small");
    // Verify the team row
    assertEquals(team.getString("ontologyTermIRI"), "http://www.molgenis.org#Team");
    assertEquals(team.getString("ontologyTermName"), "team");
    // verify team dynamic annotations
    Iterable<Entity> dynamicAnnotationItr = team.getEntities("ontologyTermDynamicAnnotation");
    List<Entity> dynamicAnnotations = new ArrayList<>();
    dynamicAnnotationItr.forEach(dynamicAnnotations::add);
    assertEquals(dynamicAnnotations.size(), 2);
    Entity annotationOne = dataService.findOneById("sys_ont_OntologyTermDynamicAnnotation", dynamicAnnotations.get(0).getIdValue());
    assertEquals(annotationOne.getString("label"), "friday:2412423");
    Entity annotationTwo = dataService.findOneById("sys_ont_OntologyTermDynamicAnnotation", dynamicAnnotations.get(1).getIdValue());
    assertEquals(annotationTwo.getString("label"), "molgenis:1231424");
    // verify team ontology
    ontology = (Ontology) team.get("ontology");
    assertEquals(ontology.getOntologyName(), "ontology-small");
}

Example 2 with Ontology

use of org.molgenis.ontology.core.meta.Ontology in project molgenis by molgenis.

the class InformationContentServiceTest method createWordIDF.

@Test
public void createWordIDF() {
    String ontologyIri = "http://www.molgenis.org";
    Ontology ontology = ontologyFactory.create();
    ontology.setOntologyIri(ontologyIri);
    when(dataService.findOne(ONTOLOGY, new QueryImpl<>().eq(OntologyMetaData.ONTOLOGY_IRI, ontologyIri))).thenReturn(ontology);
    when(dataService.count(ONTOLOGY_TERM, new QueryImpl<>().eq(OntologyTermMetaData.ONTOLOGY, ontology))).thenReturn((long) 100);
    QueryRule queryRule = new QueryRule(singletonList(new QueryRule(OntologyTermMetaData.ONTOLOGY_TERM_SYNONYM, Operator.FUZZY_MATCH, "hear")));
    queryRule.setOperator(Operator.DIS_MAX);
    QueryRule finalQuery = new QueryRule(asList(new QueryRule(OntologyTermMetaData.ONTOLOGY, Operator.EQUALS, ontology), new QueryRule(Operator.AND), queryRule));
    when(dataService.count(ONTOLOGY_TERM, new QueryImpl<>(finalQuery))).thenReturn((long) 30);
    QueryRule queryRule2 = new QueryRule(singletonList(new QueryRule(OntologyTermMetaData.ONTOLOGY_TERM_SYNONYM, Operator.FUZZY_MATCH, "impair")));
    queryRule2.setOperator(Operator.DIS_MAX);
    QueryRule finalQuery2 = new QueryRule(asList(new QueryRule(OntologyTermMetaData.ONTOLOGY, Operator.EQUALS, ontology), new QueryRule(Operator.AND), queryRule2));
    when(dataService.count(ONTOLOGY_TERM, new QueryImpl<>(finalQuery2))).thenReturn((long) 10);
    Map<String, Double> expectedWordIDF = informationContentService.createWordIDF("hearing impairment", ontologyIri);
    Assert.assertEquals(expectedWordIDF.get("hear").intValue(), 2);
    Assert.assertEquals(expectedWordIDF.get("impair").intValue(), 3);
}

Example 3 with Ontology

use of org.molgenis.ontology.core.meta.Ontology in project molgenis by molgenis.

the class OntologyImportServiceIT method verifyOboAsSystem.

private void verifyOboAsSystem() {
    List<Entity> ontologies = dataService.findAll("sys_ont_Ontology").collect(Collectors.toList());
    Ontology ontology = (Ontology) ontologies.get(0);
    assertEquals(ontology.getOntologyName(), "ontology-small");
    List<Entity> synonyms = dataService.findAll("sys_ont_OntologyTerm").collect(Collectors.toList());
    verifyOboRow(synonyms, "molgenis ontology core", "http://purl.obolibrary.org/obo/TEMP#molgenis-ontology-core");
    verifyOboRow(synonyms, "molgenis", "http://purl.obolibrary.org/obo/TEMP#molgenis");
    verifyOboRow(synonyms, "Thing", "http://purl.obolibrary.org/obo/TEMP#Thing");
}