@Test public void testGetAllVariants() { long numResults = count(null); assertEquals(NUM_VARIANTS, numResults); }
@Test public void rank_gene() throws Exception { QueryResult<Map<String, Object>> queryResult_rank = rank(40, new Query(), "gene", false); System.out.println(new ObjectMapper().writerWithDefaultPrettyPrinter().writeValueAsString(queryResult_rank)); assertEquals(40, queryResult_rank.getNumResults()); for (Map<String, Object> map : queryResult_rank.getResult()) { Long variantQueryResult = count(new Query(GENE.key(), map.get("id"))); assertEquals((variantQueryResult).intValue(), ((Number) map.get("count")).intValue()); } }
@Test public void rank_ct() throws Exception { int limit = 20; QueryResult<Map<String, Object>> queryResult_rank = rank(limit, new Query(), "ct", false); System.out.println(new ObjectMapper().writerWithDefaultPrettyPrinter().writeValueAsString(queryResult_rank)); assertEquals(limit, queryResult_rank.getNumResults()); for (Map<String, Object> map : queryResult_rank.getResult()) { Long variantQueryResult = count(new Query(ANNOT_CONSEQUENCE_TYPE.key(), map.get("id"))); assertEquals((variantQueryResult).intValue(), ((Number) map.get("count")).intValue()); } }
@Test public void testGetAllVariants_filterNoFile() { // FILTER Query query = new Query(FILTER.key(), "PASS"); long numResults = count(query); assertEquals(NUM_VARIANTS, numResults); query.append(FILTER.key(), "NO_PASS"); assertEquals(0, count(query).longValue()); // FILTER+STUDY query = new Query(STUDY.key(), studyConfiguration.getStudyId()).append(FILTER.key(), "PASS"); numResults = count(query); assertEquals(NUM_VARIANTS, numResults); query.append(FILTER.key(), "NO_PASS"); assertEquals(0, count(query).longValue()); }
@Test public void testGetAllVariants_fileNotFound() { VariantQueryException e = VariantQueryException.missingStudyForFile("-1", Collections.singletonList(studyConfiguration.getStudyName())); thrown.expectMessage(e.getMessage()); thrown.expect(e.getClass()); count(new Query(FILE.key(), -1)); // assertEquals("There is no file with ID -1", 0, numResults); }
@Test public void testGetAllVariants_files() { Query query = new Query(FILE.key(), fileId); long numResults = count(query); assertEquals(NUM_VARIANTS, numResults); query = new Query(FILE.key(), fileId).append(STUDY.key(), studyConfiguration.getStudyId()); numResults = count(query); assertEquals(NUM_VARIANTS, numResults); query = new Query().append(STUDY.key(), studyConfiguration.getStudyId()); numResults = count(query); assertEquals(NUM_VARIANTS, numResults); }
@Test public void testGetAllVariants_Negatedstudies() { // query = new Query(STUDY.key(), NOT + studyConfiguration.getStudyId()); // numResults = count(query); // assertEquals(0, numResults); Query query = new Query(STUDY.key(), NOT + studyConfiguration.getStudyName()); long numResults = count(query); assertEquals(0, numResults); }
@Test public void testGetAllVariants_filter() { Query query; long numResults; // FILTER+FILE query = new Query(FILE.key(), fileId).append(FILTER.key(), "PASS"); numResults = count(query); assertEquals(NUM_VARIANTS, numResults); query.append(FILTER.key(), "NO_PASS"); assertEquals(0, count(query).longValue()); // FILTER+FILE+STUDY query = new Query(FILE.key(), fileId).append(STUDY.key(), studyConfiguration.getStudyId()).append(FILTER.key(), "PASS"); numResults = count(query); assertEquals(NUM_VARIANTS, numResults); query.append(FILTER.key(), "NO_PASS"); assertEquals(0, count(query).longValue()); }
assertEquals(combinedKeywordsOr, count(query).intValue()); query = new Query(ANNOT_PROTEIN_KEYWORD.key(), "Complete proteome;Transmembrane helix"); assertEquals(combinedKeywordsAnd, count(query).intValue()); query = new Query(ANNOT_PROTEIN_KEYWORD.key(), "Complete proteome;!Transmembrane helix"); assertEquals(combinedKeywordsAndNot, count(query).intValue());
@Test public void testGetAllVariants_studies() { Query query = new Query(STUDY.key(), studyConfiguration.getStudyName()); long numResults = count(query); assertEquals(allVariants.getNumResults(), numResults); query = new Query(STUDY.key(), studyConfiguration.getStudyId()); numResults = count(query); assertEquals(allVariants.getNumResults(), numResults); }
numResults = count(new Query(STATS_MAF.key(), STUDY_NAME + ":cohort1>0.2")); assertEquals(expectedCount, numResults); numResults = count(new Query(STATS_MAF.key(), "1:10>0.2")); assertEquals(expectedCount, numResults); numResults = count(new Query(STATS_MAF.key(), STUDY_NAME + ":10>0.2")); assertEquals(expectedCount, numResults); queryResult = query(new Query(STATS_MAF.key(), "1:cohort1>0.2"), null);