@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { return mongoDBCollection.nativeQuery().find(parseQuery(query), options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public Iterator nativeIterator(Query query, QueryOptions options) { Bson bson = parseQuery(query); return mongoDBCollection.nativeQuery().find(bson, options).iterator(); }
@Override public DBIterator nativeIterator(Query query, QueryOptions options) throws CatalogDBException { Bson bson = parseQuery(query, false); MongoCursor<Document> iterator = datasetCollection.nativeQuery().find(bson, options).iterator(); return new MongoDBIterator<>(iterator); }
@Override public DBIterator<User> iterator(Query query, QueryOptions options) throws CatalogDBException { Bson bson = parseQuery(query); MongoCursor<Document> iterator = userCollection.nativeQuery().find(bson, options).iterator(); return new MongoDBIterator<>(iterator, userConverter); }
private MongoCursor<Document> getMongoCursor(Query query, QueryOptions options) throws CatalogDBException { Bson bson = parseQuery(query, false); QueryOptions qOptions; if (options != null) { qOptions = new QueryOptions(options); } else { qOptions = new QueryOptions(); } logger.debug("Interpretation query : {}", bson.toBsonDocument(Document.class, MongoClient.getDefaultCodecRegistry())); return interpretationCollection.nativeQuery().find(bson, qOptions).iterator(); }
@Override public Iterator<Variant> iterator(Query query, QueryOptions inputOptions) { Bson bson = parseQuery(query); QueryOptions options = addPrivateExcludeOptions(new QueryOptions(inputOptions)); return new VariantMongoIterator(mongoDBCollection.nativeQuery().find(bson, options).iterator()); }
@Override public Iterator<Variant> iterator(Query query, QueryOptions inputOptions) { Bson bson = parseQuery(query); QueryOptions options = addPrivateExcludeOptions(new QueryOptions(inputOptions)); return new VariantMongoIterator(mongoDBCollection.nativeQuery().find(bson, options).iterator()); }
@Test @Override public void indexWithOtherFieldsExcludeGT() throws Exception { super.indexWithOtherFieldsExcludeGT(); try (VariantMongoDBAdaptor dbAdaptor = getVariantStorageEngine().getDBAdaptor()) { MongoDBCollection variantsCollection = dbAdaptor.getVariantsCollection(); for (Document document : variantsCollection.nativeQuery().find(new Document(), new QueryOptions())) { assertFalse(((Document) document.get(DocumentToVariantConverter.STUDIES_FIELD, List.class).get(0)) .containsKey(GENOTYPES_FIELD)); System.out.println("dbObject = " + document); } } }