Examples with ReferenceGenome uk.ac.bbsrc.tgac.miso.core.data.ReferenceGenome used on opensource projects

Example 1 with ReferenceGenome

use of uk.ac.bbsrc.tgac.miso.core.data.ReferenceGenome in project miso-lims by miso-lims.

the class DefaultReferenceGenomeService method update.

@Override
public long update(ReferenceGenome reference) throws IOException {
    authorizationManager.throwIfNonAdmin();
    ValidationUtils.loadChildEntity(reference::setDefaultScientificName, reference.getDefaultScientificName(), scientificNameService, "defaultScientificNameId");
    ReferenceGenome managed = get(reference.getId());
    validateChange(reference, managed);
    applyChanges(managed, reference);
    return referenceGenomeDao.update(managed);
}

Example 2 with ReferenceGenome

use of uk.ac.bbsrc.tgac.miso.core.data.ReferenceGenome in project miso-lims by miso-lims.

the class DefaultSampleServiceTest method humanReferenceGenome.

private ReferenceGenome humanReferenceGenome() {
    ReferenceGenome referenceGenome = new ReferenceGenomeImpl();
    referenceGenome.setAlias("hg19");
    referenceGenome.setId(1L);
    return referenceGenome;
}

Example 3 with ReferenceGenome

use of uk.ac.bbsrc.tgac.miso.core.data.ReferenceGenome in project miso-lims by miso-lims.

the class Dtos method to.

public static ReferenceGenome to(@Nonnull ReferenceGenomeDto from) {
    ReferenceGenome to = new ReferenceGenomeImpl();
    setLong(to::setId, from.getId(), false);
    setString(to::setAlias, from.getAlias());
    setObject(to::setDefaultScientificName, ScientificName::new, from.getDefaultScientificNameId());
    return to;
}

Example 4 with ReferenceGenome

use of uk.ac.bbsrc.tgac.miso.core.data.ReferenceGenome in project miso-lims by miso-lims.

the class HibernateReferenceGenomeDao method list.

@Override
public List<ReferenceGenome> list() {
    Query query = currentSession().createQuery("from ReferenceGenomeImpl");
    @SuppressWarnings("unchecked") List<ReferenceGenome> records = query.list();
    return records;
}

Example 5 with ReferenceGenome

use of uk.ac.bbsrc.tgac.miso.core.data.ReferenceGenome in project miso-lims by miso-lims.

the class HibernateReferenceGenomeDaoIT method testCreate.

@Test
public void testCreate() throws IOException {
    String alias = "New Reference";
    ReferenceGenome ref = new ReferenceGenomeImpl();
    ref.setAlias(alias);
    long savedId = dao.create(ref);
    clearSession();
    ReferenceGenome saved = (ReferenceGenome) getSessionFactory().getCurrentSession().get(ReferenceGenomeImpl.class, savedId);
    assertEquals(alias, saved.getAlias());
}