@Test @Transactional(propagation = Propagation.REQUIRES_NEW) public void testLoadAllReferenceGenomes() throws IOException { registerTestReference(); Reference g38 = EntityHelper.createG38Reference(referenceGenomeManager.createReferenceId()); referenceGenomeManager.create(g38); List<Reference> loaded = referenceGenomeManager.loadAllReferenceGenomes(); Assert.assertFalse(loaded.isEmpty()); Assert.assertEquals(1, loaded.stream().filter(r -> r.getGeneFile() != null && r.getGeneFile().getId() != null && r.getGeneFile().getName() != null).count()); }
@Transactional(propagation = Propagation.SUPPORTS) public List<Reference> loadAllReferenceGenomes() { return loadAllReferenceGenomes(null); }
ReferenceGenomeManager implements SecuredEntityManager { @Transactional(propagation = Propagation.SUPPORTS) public List<Reference> loadAllReferenceGenomes() { return loadAllReferenceGenomes(null); } }
ReferenceGenomeManager implements SecuredEntityManager { @Transactional(propagation = Propagation.SUPPORTS) public List<Reference> loadAllReferenceGenomes() { return loadAllReferenceGenomes(null); }  }
ReferenceGenomeManager implements SecuredEntityManager { @Transactional(propagation = Propagation.SUPPORTS) public List<Reference> loadAllReferenceGenomes() { return loadAllReferenceGenomes(null); }  @Transactional(propagation = Propagation.REQUIRED) Long createReferenceId(); @Transactional(propagation = Propagation.REQUIRED) Reference create(final Reference reference); @Transactional(propagation = Propagation.REQUIRED) void delete(final Reference reference); @Transactional(propagation = Propagation.REQUIRED) Reference load(final Long referenceId); @Transactional(propagation = Propagation.REQUIRED) Reference loadReferenceGenomeByBioItemId(final Long dataItemId); @Transactional(propagation = Propagation.SUPPORTS) List<Reference> loadAllReferenceGenomes(); @Transactional(propagation = Propagation.REQUIRED) List<Reference> loadAllReferenceGenomes(String referenceName); @Transactional(propagation = Propagation.SUPPORTS) Chromosome loadChromosome(final Long chromosomeId); @Transactional(propagation = Propagation.SUPPORTS) List<Chromosome> loadChromosomes(final Long referenceId); @Transactional(propagation = Propagation.SUPPORTS) List<BaseEntity> loadAllFile(final Long referenceId); @Transactional(propagation = Propagation.SUPPORTS) Reference getOnlyReference(final Long referenceId); @Transactional(propagation = Propagation.REQUIRED) Reference updateReferenceGeneFileId(long referenceId, Long geneFileId); @Transactional(propagation = Propagation.REQUIRED) Reference updateSpecies(long referenceId, String speciesVersion); @Transactional(propagation = Propagation.SUPPORTS) boolean isRegistered(Long id); @Transactional(propagation = Propagation.REQUIRED) List<BiologicalDataItem> getReferenceAnnotationFiles(Long referenceId); @Transactional(propagation = Propagation.REQUIRED) Reference updateReferenceAnnotationFile(Long referenceId, Long annotationFileBiologicalItemId,
                                                   Boolean remove); @Transactional(propagation = Propagation.REQUIRED) Species registerSpecies(Species species); @Transactional(propagation = Propagation.SUPPORTS) List<Species> loadAllSpecies(); @Transactional(propagation = Propagation.SUPPORTS) Species loadSpeciesByVersion(String version); @Transactional(propagation = Propagation.REQUIRED) Species unregisterSpecies(String speciesVersion); @Override @Transactional(propagation = Propagation.REQUIRED) AbstractSecuredEntity changeOwner(Long id, String owner); @Override AclClass getSupportedClass(); }
ReferenceGenomeManager implements SecuredEntityManager { @Transactional(propagation = Propagation.SUPPORTS) public List<Reference> loadAllReferenceGenomes() { return loadAllReferenceGenomes(null); }  @Transactional(propagation = Propagation.REQUIRED) Long createReferenceId(); @Transactional(propagation = Propagation.REQUIRED) Reference create(final Reference reference); @Transactional(propagation = Propagation.REQUIRED) void delete(final Reference reference); @Transactional(propagation = Propagation.REQUIRED) Reference load(final Long referenceId); @Transactional(propagation = Propagation.REQUIRED) Reference loadReferenceGenomeByBioItemId(final Long dataItemId); @Transactional(propagation = Propagation.SUPPORTS) List<Reference> loadAllReferenceGenomes(); @Transactional(propagation = Propagation.REQUIRED) List<Reference> loadAllReferenceGenomes(String referenceName); @Transactional(propagation = Propagation.SUPPORTS) Chromosome loadChromosome(final Long chromosomeId); @Transactional(propagation = Propagation.SUPPORTS) List<Chromosome> loadChromosomes(final Long referenceId); @Transactional(propagation = Propagation.SUPPORTS) List<BaseEntity> loadAllFile(final Long referenceId); @Transactional(propagation = Propagation.SUPPORTS) Reference getOnlyReference(final Long referenceId); @Transactional(propagation = Propagation.REQUIRED) Reference updateReferenceGeneFileId(long referenceId, Long geneFileId); @Transactional(propagation = Propagation.REQUIRED) Reference updateSpecies(long referenceId, String speciesVersion); @Transactional(propagation = Propagation.SUPPORTS) boolean isRegistered(Long id); @Transactional(propagation = Propagation.REQUIRED) List<BiologicalDataItem> getReferenceAnnotationFiles(Long referenceId); @Transactional(propagation = Propagation.REQUIRED) Reference updateReferenceAnnotationFile(Long referenceId, Long annotationFileBiologicalItemId,
                                                   Boolean remove); @Transactional(propagation = Propagation.REQUIRED) Species registerSpecies(Species species); @Transactional(propagation = Propagation.SUPPORTS) List<Species> loadAllSpecies(); @Transactional(propagation = Propagation.SUPPORTS) Species loadSpeciesByVersion(String version); @Transactional(propagation = Propagation.REQUIRED) Species unregisterSpecies(String speciesVersion); @Override @Transactional(propagation = Propagation.REQUIRED) AbstractSecuredEntity changeOwner(Long id, String owner); @Override AclClass getSupportedClass();  }