Examples with ADD org.molgenis.data.DatabaseAction.ADD used on opensource projects

Example 1 with ADD

use of org.molgenis.data.DatabaseAction.ADD 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");
}