Update data sources for CellBase 6.x

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBCollection.java

@@ -131,6 +131,12 @@ public DataResult<Long> count(ClientSession clientSession, Bson query) {
         return endQuery(Collections.emptyList(), l, start);
     }
 
+    public DataResult<Long> estimatedCount() {
+        long start = startQuery();
+        long l = mongoDBNativeQuery.estimatedCount();
+        return endQuery(Collections.emptyList(), l, start);
+    }
+
     public DataResult<?> distinct(String key, Bson query) {
         long start = startQuery();
         List l = new ArrayList<>();

commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBNativeQuery.java

@@ -64,6 +64,10 @@ public long count(ClientSession clientSession, Bson query) {
         }
     }
 
+    public long estimatedCount() {
+        return dbCollection.estimatedDocumentCount();
+    }
+
     public DistinctIterable<Document> distinct(String key) {
         return distinct(key, null, Document.class);
     }
@@ -235,7 +239,11 @@ public <T> MongoDBIterator<T> find(ClientSession clientSession, Bson query, Bson
         Future<Long> countFuture = null;
         if (options != null && options.getBoolean(QueryOptions.COUNT)) {
             ExecutorService executor = Executors.newSingleThreadExecutor();
-            countFuture = executor.submit(() -> count(clientSession, query));
+            if (clientSession == null && (query == null || query.equals(Filters.empty()) || query.toBsonDocument().isEmpty())) {
+                countFuture = executor.submit(this::estimatedCount);
+            } else {
+                countFuture = executor.submit(() -> count(clientSession, query));
+            }
         }
 
         FindIterable<Document> findIterable = null;

commons-datastore/commons-datastore-mongodb/src/test/java/org/opencb/commons/datastore/mongodb/MongoDBCollectionTest.java

@@ -298,6 +298,12 @@ public void testCount1() throws Exception {
         assertEquals("The number must be equals", N, queryResult.getNumMatches());
     }
 
+    @Test
+    public void testEstimatedCount() {
+        DataResult<Long> queryResult = mongoDBCollection.estimatedCount();
+        assertEquals("The number of documents must be equals", N, queryResult.getNumMatches());
+    }
+
     @Test
     public void testDistinct1() throws Exception {
         DataResult<Integer> queryResult = mongoDBCollection.distinct("age", null, Integer.class);