Examples with SemanticTag org.molgenis.data.semantic.SemanticTag used on opensource projects

Example 1 with SemanticTag

use of org.molgenis.data.semantic.SemanticTag in project molgenis by molgenis.

the class UntypedTagService method getTagsForPackage.

@Override
@RunAsSystem
public Iterable<SemanticTag<Package, LabeledResource, LabeledResource>> getTagsForPackage(Package p) {
    Entity packageEntity = dataService.findOne(PACKAGE, new QueryImpl<>().eq(PackageMetadata.ID, p.getId()));
    if (packageEntity == null) {
        throw new UnknownEntityException("Unknown package [" + p.getId() + "]");
    }
    List<SemanticTag<Package, LabeledResource, LabeledResource>> tags = Lists.newArrayList();
    for (Entity tagEntity : packageEntity.getEntities(PackageMetadata.TAGS)) {
        tags.add(SemanticTag.asTag(p, tagEntity));
    }
    return tags;
}

Example 2 with SemanticTag

use of org.molgenis.data.semantic.SemanticTag in project molgenis by molgenis.

the class OntologyTagServiceImpl method getTagsForPackage.

@Override
public Iterable<SemanticTag<Package, OntologyTerm, Ontology>> getTagsForPackage(Package package_) {
    Entity packageEntity = dataService.findOneById(PACKAGE, package_.getId());
    if (packageEntity == null) {
        throw new UnknownEntityException("Unknown package [" + package_.getId() + "]");
    }
    List<SemanticTag<Package, OntologyTerm, Ontology>> tags = Lists.newArrayList();
    for (Entity tagEntity : packageEntity.getEntities(PackageMetadata.TAGS)) {
        tags.add(asTag(package_, tagEntity));
    }
    return tags;
}

Example 3 with SemanticTag

use of org.molgenis.data.semantic.SemanticTag in project molgenis by molgenis.

the class OntologyTagServiceImpl method asTag.

private <SubjectType> SemanticTag<SubjectType, OntologyTerm, Ontology> asTag(SubjectType subjectType, Entity tagEntity) {
    String identifier = tagEntity.getString(TagMetadata.ID);
    Relation relation = asRelation(tagEntity);
    Ontology ontology = asOntology(tagEntity);
    OntologyTerm ontologyTerm = asOntologyTerm(tagEntity);
    if (relation == null || ontologyTerm == null) {
        return null;
    }
    return new SemanticTag<>(identifier, subjectType, relation, ontologyTerm, ontology);
}

Example 4 with SemanticTag

use of org.molgenis.data.semantic.SemanticTag in project molgenis by molgenis.

the class EntityModelWriterTest method testAddStatementsForEntityType.

@Test
public void testAddStatementsForEntityType() {
    Model model = new LinkedHashModel();
    Resource subject = valueFactory.createIRI("http://example.org/subject");
    LabeledResource object = new LabeledResource("http://example.org/object", "object");
    LabeledResource codeSystem = new LabeledResource("ex:object");
    SemanticTag<EntityType, LabeledResource, LabeledResource> tag = new SemanticTag<>("tagId", entityType, Relation.isAssociatedWith, object, codeSystem);
    when(tagService.getTagsForEntity(entityType)).thenReturn(singletonList(tag));
    writer.addStatementsForEntityTags(model, subject, entityType);
    Statement statement = valueFactory.createStatement(subject, TYPE, valueFactory.createIRI("http://example.org/object"));
    assertEquals(newArrayList(model), singletonList(statement));
}

Example 5 with SemanticTag

use of org.molgenis.data.semantic.SemanticTag in project molgenis by molgenis.

the class UntypedTagService method getTagsForEntity.

@Override
@RunAsSystem
public Iterable<SemanticTag<EntityType, LabeledResource, LabeledResource>> getTagsForEntity(EntityType entityType) {
    List<SemanticTag<EntityType, LabeledResource, LabeledResource>> result = new ArrayList<>();
    Entity entity = findEntity(entityType);
    if (entity == null) {
        LOG.warn("No known entity with name " + entityType.getId() + ".");
    } else {
        for (Entity tagEntity : entity.getEntities(EntityTypeMetadata.TAGS)) {
            result.add(SemanticTag.asTag(entityType, tagEntity));
        }
    }
    return result;
}