public AggregateIterable<Document> aggregate(List<? extends Bson> operations) { return aggregate(operations, null); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { List<Bson> aggregateList = unwindAndMatchTranscripts(query, options); return mongoDBCollection.nativeQuery().aggregate(aggregateList, options).iterator(); // return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { List<Bson> aggregateList = unwindAndMatchTranscripts(query, options); return mongoDBCollection.nativeQuery().aggregate(aggregateList, options).iterator(); // return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
return userCollection.nativeQuery().aggregate(aggregates, qOptions).iterator();
AggregateIterable<Document> output = mongoDBNativeQuery.aggregate(operations, options); MongoCursor<Document> iterator = output.iterator(); List<T> list = new LinkedList<>();
@Override public void saveAnnotation(String name, ObjectMap options) throws StorageEngineException, VariantAnnotatorException { dbAdaptor.getStudyConfigurationManager().lockAndUpdateProject(project -> { registerNewAnnotationSnapshot(name, variantAnnotator, project); return project; }); String annotationCollectionName = mongoDbAdaptor.getAnnotationCollectionName(name); mongoDbAdaptor.getVariantsCollection() .nativeQuery() .aggregate(Arrays.asList( match(exists(ANNOTATION_FIELD + '.' + ANNOT_ID_FIELD)), project(include( CHROMOSOME_FIELD, START_FIELD, REFERENCE_FIELD, ALTERNATE_FIELD, END_FIELD, TYPE_FIELD, SV_FIELD, RELEASE_FIELD, ANNOTATION_FIELD, CUSTOM_ANNOTATION_FIELD)), out(annotationCollectionName))) .toCollection(); }