public static void updateProjectMetadata(CatalogManager catalog, StudyConfigurationManager scm, String project, String sessionId) throws CatalogException, StorageEngineException { final Project p = catalog.getProjectManager().get(project, new QueryOptions(QueryOptions.INCLUDE, Arrays.asList( ProjectDBAdaptor.QueryParams.ORGANISM.key(), ProjectDBAdaptor.QueryParams.CURRENT_RELEASE.key())), sessionId) .first(); StorageOperation.updateProjectMetadata(scm, p.getOrganism(), p.getCurrentRelease()); }
studyStr = null; alias = project.getId(); organism = project.getOrganism(); currentRelease = project.getCurrentRelease(); dataStore = getDataStoreByProjectId(catalogManager, projectStr, File.Bioformat.VARIANT, sessionId);
studyInfo.setProjectUid(project.getUid()); studyInfo.setProjectId(project.getId()); studyInfo.setOrganism(project.getOrganism()); String user = catalogManager.getProjectManager().getOwner(project.getUid()); studyInfo.setUserId(user);
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());
&& 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()));