protected void updateCohorts(String studyId, List<String> cohortIds, String sessionId, String status, String message) throws CatalogException { for (String cohortId : cohortIds) { catalogManager.getCohortManager().setStatus(studyId, cohortId, status, message, sessionId); } }
case Cohort.CohortStatus.READY: if (updateStats) { catalogManager.getCohortManager().setStatus(studyFqn, cohortId, Cohort.CohortStatus.INVALID, "", sessionId); break; } else {
newCohorts.put((int) cohort.getUid(), newSampleList.stream().map(Sample::getUid).map(Long::intValue) .collect(Collectors.toSet())); catalogManager.getCohortManager().setStatus(studyStr, cohort.getId(), Cohort.CohortStatus.READY, "", sessionId);
status = Cohort.CohortStatus.NONE; catalogManager.getCohortManager().setStatus(studyConfiguration.getStudyName(), cohortName, status, null, sessionId); logger.debug("Cohort \"{}\" change status from {} to {}", cohort.getId(), cohort.getStats(), Cohort.CohortStatus.READY); catalogManager.getCohortManager().setStatus(studyConfiguration.getStudyName(), cohort.getId(), Cohort.CohortStatus.READY, "Update status from Storage", sessionId); logger.debug("Cohort \"{}\" change status from {} to {}", cohort.getId(), cohort.getStats(), Cohort.CohortStatus.INVALID); catalogManager.getCohortManager().setStatus(studyConfiguration.getStudyName(), cohort.getId(), Cohort.CohortStatus.INVALID, "Update status from Storage", sessionId);
private String updateDefaultCohortStatus(Study study, String status, String sessionId) throws CatalogException { Query query = new Query(CohortDBAdaptor.QueryParams.ID.key(), StudyEntry.DEFAULT_COHORT); Cohort defaultCohort = catalogManager.getCohortManager().get(study.getFqn(), query, new QueryOptions(), sessionId).first(); String prevStatus = defaultCohort.getStatus().getName(); catalogManager.getCohortManager().setStatus(study.getFqn(), defaultCohort.getId(), status, null, sessionId); return prevStatus; }
catalogManager.getCohortManager().setStatus(studyId, cohortId, Cohort.CohortStatus.CALCULATING, "", sessionId);
logger.debug("Default cohort status set to READY"); Cohort defaultCohort = queryResult.first(); catalogManager.getCohortManager().setStatus(study.getFqn(), defaultCohort.getId(), Cohort.CohortStatus.READY, null, sessionId);
@Test public void testResumeCalculateStats() throws Exception { before(); calculateStats(coh[0]); catalogManager.getCohortManager().setStatus(studyId, coh[1], Cohort.CohortStatus.CALCULATING, "", sessionId); Cohort coh1 = catalogManager.getCohortManager().get(studyId, coh[1], null, sessionId).first(); Exception expected = VariantStatsStorageOperation.unableToCalculateCohortCalculating(coh1); try { calculateStats(coh[1]); fail(); } catch (Exception e) { assertThat(e, instanceOf(expected.getClass())); assertThat(e, hasMessage(is(expected.getMessage()))); } calculateStats(coh[1], new QueryOptions(VariantStorageEngine.Options.RESUME.key(), true)); }
files.add(create("platinum/1K.end.platinum-genomes-vcf-NA12880_S1.genome.vcf.gz", true)); files.add(create("platinum/1K.end.platinum-genomes-vcf-NA12881_S1.genome.vcf.gz")); catalogManager.getCohortManager().setStatus(study.getFqn(), cohortName, "READY", "", sessionId);