Project.Organism organism = new Project.Organism(scientificName, assembly); if (StringUtils.isNumeric(taxonomyCode)) { organism.setTaxonomyCode(Integer.parseInt(taxonomyCode)); organism.setCommonName(assembly);
throw new CatalogException("Can't annotate studies from different databases"); if (!organism.equals(info.getOrganism())) { throw new CatalogException("Can't annotate studies with different organisms");
&& StringUtils.isEmpty(projectQR.first().getOrganism().getScientificName())) { objectMap.put(ProjectDBAdaptor.QueryParams.ORGANISM_SCIENTIFIC_NAME.key(), parameters.getString(ProjectDBAdaptor.QueryParams.ORGANISM_SCIENTIFIC_NAME.key())); && StringUtils.isEmpty(projectQR.first().getOrganism().getCommonName())) { objectMap.put(ProjectDBAdaptor.QueryParams.ORGANISM_COMMON_NAME.key(), parameters.getString(ProjectDBAdaptor.QueryParams.ORGANISM_COMMON_NAME.key())); && projectQR.first().getOrganism().getTaxonomyCode() <= 0) { objectMap.put(ProjectDBAdaptor.QueryParams.ORGANISM_TAXONOMY_CODE.key(), parameters.getInt(ProjectDBAdaptor.QueryParams.ORGANISM_TAXONOMY_CODE.key())); && StringUtils.isEmpty(projectQR.first().getOrganism().getAssembly())) { objectMap.put(ProjectDBAdaptor.QueryParams.ORGANISM_ASSEMBLY.key(), parameters.getString(ProjectDBAdaptor.QueryParams.ORGANISM_ASSEMBLY.key()));
null, null, "GRCh38", null, sessionIdUser).first(); assertEquals("Homo sapiens", pr.getOrganism().getScientificName()); assertEquals("", pr.getOrganism().getCommonName()); 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; }); }