&& StringUtils.isEmpty(projectQR.first().getOrganism().getAssembly())) { objectMap.put(ProjectDBAdaptor.QueryParams.ORGANISM_ASSEMBLY.key(), parameters.getString(ProjectDBAdaptor.QueryParams.ORGANISM_ASSEMBLY.key()));
assertEquals("GRCh38", pr.getOrganism().getAssembly()); assertEquals(-1, pr.getOrganism().getTaxonomyCode()); assertEquals("Homo sapiens", update.first().getOrganism().getScientificName()); assertEquals("", update.first().getOrganism().getCommonName()); assertEquals("GRCh38", update.first().getOrganism().getAssembly()); assertEquals(55, update.first().getOrganism().getTaxonomyCode()); assertEquals("Homo sapiens", update.first().getOrganism().getScientificName()); assertEquals("common", update.first().getOrganism().getCommonName()); assertEquals("GRCh38", update.first().getOrganism().getAssembly()); assertEquals(55, update.first().getOrganism().getTaxonomyCode());
public static void updateProjectMetadata(StudyConfigurationManager scm, Project.Organism organism, int release) throws CatalogException, StorageEngineException { String scientificName = AbstractCellBaseVariantAnnotator.toCellBaseSpeciesName(organism.getScientificName()); scm.lockAndUpdateProject(projectMetadata -> { if (projectMetadata == null) { projectMetadata = new ProjectMetadata(); } projectMetadata.setSpecies(scientificName); projectMetadata.setAssembly(organism.getAssembly()); projectMetadata.setRelease(release); return projectMetadata; }); }