@Test public void testGetAllVariants_returnedFiles1() { testGetAllVariants_returnedFiles1(false); }
query = new Query(); if (studyConfiguration1 == null) { clearDB(DB_NAME); studyConfiguration1 = new StudyConfiguration(1, "Study1"); studyConfiguration2 = new StudyConfiguration(2, "Study2"); studyConfiguration3 = new StudyConfiguration(3, "Study3"); ObjectMap options = getExtraOptions() .append(VariantStorageEngine.Options.STUDY_TYPE.key(), SampleSetType.CONTROL_SET) .append(VariantStorageEngine.Options.CALCULATE_STATS.key(), true) .append(VariantStorageEngine.Options.ANNOTATE.key(), false); URI file1Uri = getResourceUri("1000g_batches/" + fileName1); runDefaultETL(file1Uri, variantStorageEngine, studyConfiguration1, options); assertEquals(500, studyConfiguration1.getCohorts().get(studyConfiguration1.getCohortIds().get(StudyEntry.DEFAULT_COHORT)).size()); file1 = studyConfiguration1.getFileIds().get(UriUtils.fileName(file1Uri)); URI file2Uri = getResourceUri("1000g_batches/" + fileName2); runDefaultETL(file2Uri, variantStorageEngine, studyConfiguration1, options); assertEquals(1000, studyConfiguration1.getCohorts().get(studyConfiguration1.getCohortIds().get(StudyEntry.DEFAULT_COHORT)).size()); file2 = studyConfiguration1.getFileIds().get(UriUtils.fileName(file2Uri)); URI file3Uri = getResourceUri("1000g_batches/" + fileName3); runDefaultETL(file3Uri, variantStorageEngine, studyConfiguration2, options); assertEquals(500, studyConfiguration2.getCohorts().get(studyConfiguration2.getCohortIds().get(StudyEntry.DEFAULT_COHORT)).size()); file3 = studyConfiguration2.getFileIds().get(UriUtils.fileName(file3Uri)); URI file4Uri = getResourceUri("1000g_batches/" + fileName4); runDefaultETL(file4Uri, variantStorageEngine, studyConfiguration2, options);
.map(StudyEntry::getFiles) .flatMap(Collection::stream) .filter(fileEntry -> sameVariant(variant, fileEntry.getCall())) .map(FileEntry::getFileId) .collect(Collectors.toSet());
.map(StudyEntry::getFiles) .flatMap(Collection::stream) .filter(fileEntry -> sameVariant(variant, fileEntry.getCall())) .map(FileEntry::getFileId) .anyMatch(fileName1::equals)) {
@Test public void testGetAllVariants_returnedFiles1_implicit() { testGetAllVariants_returnedFiles1(true); }