assertEquals(2504, studyConfiguration.getCohorts().get(defaultCohortId).size()); assertTrue(studyConfiguration.getIndexedFiles().contains(fileIdChr1)); checkLoadedVariants(getVariantStorageEngine().getDBAdaptor(), studyConfiguration, true, false, false, -1); checkLoadedVariants(getVariantStorageEngine().getDBAdaptor(), studyConfiguration, true, false, false, -1);
VariantDBAdaptor dbAdaptor = getVariantStorageEngine().getDBAdaptor(); studyConfiguration = dbAdaptor.getStudyConfigurationManager().getStudyConfiguration(studyConfiguration.getStudyId(), null).first();
StoragePipelineResult etlResult = runDefaultETL(smallInputUri, getVariantStorageEngine(), studyConfiguration, new ObjectMap(VariantStorageEngine.Options.EXTRA_GENOTYPE_FIELDS.key(), extraFields) .append(VariantStorageEngine.Options.TRANSFORM_FORMAT.key(), "avro")
VariantDBAdaptor dbAdaptor = getVariantStorageEngine().getDBAdaptor(); studyConfiguration = dbAdaptor.getStudyConfigurationManager().getStudyConfiguration(studyConfiguration.getStudyId(), null).first();
@Test public void indexWithoutOtherFields() throws Exception { StudyConfiguration studyConfiguration = newStudyConfiguration(); runDefaultETL(smallInputUri, getVariantStorageEngine(), studyConfiguration, new ObjectMap(VariantStorageEngine.Options.EXTRA_GENOTYPE_FIELDS.key(), VariantQueryUtils.NONE) .append(VariantStorageEngine.Options.TRANSFORM_FORMAT.key(), "avro") .append(VariantStorageEngine.Options.ANNOTATE.key(), false) .append(VariantStorageEngine.Options.CALCULATE_STATS.key(), false) ); for (Variant variant : variantStorageEngine.getDBAdaptor()) { assertEquals("GT", variant.getStudy(STUDY_NAME).getFormatAsString()); } }
.append(VariantStorageEngine.Options.ANNOTATE.key(), false); VariantStorageEngine variantStorageEngine = getVariantStorageEngine();
options.putIfAbsent(VariantStorageEngine.Options.ANNOTATE.key(), false); VariantStorageEngine variantStorageManager = getVariantStorageEngine(); VariantDBAdaptor dbAdaptor = variantStorageManager.getDBAdaptor(); StudyConfigurationManager studyConfigurationManager = dbAdaptor.getStudyConfigurationManager(); variantStorageManager = getVariantStorageEngine(); variantStorageManager.getConfiguration().getStorageEngine(variantStorageManager.getStorageEngineId()).getVariant().getOptions() .append(VariantStorageEngine.Options.STUDY.key(), studyConfigurationBatchFile.getStudyName())
@Test @Ignore public void insertVariantIntoSolr() throws Exception { clearDB(DB_NAME); ObjectMap params = new ObjectMap(); StudyConfiguration studyConfiguration = newStudyConfiguration(); params.put(VariantStorageEngine.Options.STUDY.key(), studyConfiguration.getStudyName()); params.put(VariantStorageEngine.Options.TRANSFORM_FORMAT.key(), "json"); params.put(VariantStorageEngine.Options.COMPRESS_METHOD.key(), "gZiP"); params.put(VariantStorageEngine.Options.TRANSFORM_THREADS.key(), 1); params.put(VariantStorageEngine.Options.LOAD_THREADS.key(), 1); params.put(VariantStorageEngine.Options.ANNOTATE.key(), true); runETL(variantStorageEngine, params, true, true, true); VariantDBAdaptor dbAdaptor = getVariantStorageEngine().getDBAdaptor(); VariantSearchManager variantSearchManager = new VariantSearchManager(null, variantStorageEngine.getConfiguration()); // FIXME Collection is not in the configuration any more // variantSearchManager.load(variantStorageEngine.getConfiguration().getSearch().getCollection(), dbAdaptor.iterator()); }