public QueryResult<Long> count(Query query, String sessionId) throws CatalogException, StorageEngineException, IOException { return secure(query, new QueryOptions(QueryOptions.EXCLUDE, VariantField.STUDIES), sessionId, engine -> engine.count(query)); }
@Override public Long count(Query query) { try { return variantStorageEngine.count(query).first(); } catch (Exception e) { throw Throwables.propagate(e); } }
QueryResult<Long> result = variantStorageEngine.count(query); System.out.println("Num. results\t" + result.getResult().get(0)); } else if (StringUtils.isNotEmpty(variantQueryCommandOptions.rank)) {
QueryResult<Long> queryResult = variantStorageEngine.count(new Query(VariantQueryParam.GENE.key(), entry.getKey())); System.out.println("queryResult.getDbTime() = " + queryResult.getDbTime()); long count = queryResult.first();
return 0L; Long count = engine.count(finalQuery).first(); long limit = finalQueryOptions.getLong(QueryOptions.LIMIT, Long.MAX_VALUE); long skip = finalQueryOptions.getLong(QueryOptions.SKIP, 0);
public void checkAnnotationSnapshot(VariantStorageEngine variantStorageEngine, String annotationName, String expectedAnnotationName, String expectedId, Query query) throws Exception { int count = 0; for (VariantAnnotation annotation: variantStorageEngine.getAnnotation(annotationName, query, null).getResult()) { assertEquals("an id -- " + expectedId, annotation.getId()); // assertEquals("1", annotation.getAdditionalAttributes().get("opencga").getAttribute().get("release")); assertEquals(expectedAnnotationName, annotation.getAdditionalAttributes().get(GROUP_NAME.key()) .getAttribute().get(VariantField.AdditionalAttributes.ANNOTATION_ID.key())); count++; } assertEquals(count, variantStorageEngine.count(query).first().intValue()); }
long numResults = 0; if (count) { numResults = variantStorageEngine.count(query).first(); } else { try (VariantDBIterator iterator = variantStorageEngine.iterator(query, queryOptions)) {
public void testQueries(VariantStorageEngine variantStorageEngine) throws StorageEngineException { long count = variantStorageEngine.count(new Query()).first(); long partialCount = 0; int batchSize = (int) Math.ceil(count / 10.0); for (int i = 0; i < 10; i++) { partialCount += variantStorageEngine.getAnnotation("v2", null, new QueryOptions(QueryOptions.LIMIT, batchSize) .append(QueryOptions.SKIP, batchSize * i)).getResult().size(); } assertEquals(count, partialCount); for (int chr = 1; chr < 22; chr += 2) { Query query = new Query(VariantQueryParam.REGION.key(), chr + "," + (chr + 1)); count = variantStorageEngine.count(query).first(); partialCount = variantStorageEngine.getAnnotation("v2", query, new QueryOptions()).getResult().size(); assertEquals(count, partialCount); } String consequenceTypes = VariantField.ANNOTATION_CONSEQUENCE_TYPES.fieldName().replace(VariantField.ANNOTATION.fieldName() + ".", ""); for (VariantAnnotation annotation : variantStorageEngine.getAnnotation("v2", null, new QueryOptions(QueryOptions.INCLUDE, consequenceTypes)).getResult()) { assertEquals(1, annotation.getConsequenceTypes().size()); } for (VariantAnnotation annotation : variantStorageEngine.getAnnotation("v2", null, new QueryOptions(QueryOptions.EXCLUDE, consequenceTypes)).getResult()) { assertTrue(annotation.getConsequenceTypes() == null || annotation.getConsequenceTypes().isEmpty()); } // Get annotations from a deleted snapshot thrown.expectMessage("Variant Annotation snapshot \"v1\" not found!"); assertEquals(0, variantStorageEngine.getAnnotation("v1", null, null).getResult().size()); }