Added ByteBuffer support for setSubarray()

src/main/c/generated/tiledb_wrap.cxx

@@ -6989,6 +6989,25 @@ SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1set_1s
   return jresult;
 }
 
+SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1set_1subarray_1nio(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jobject jarg3) {
+  void* buffer = (void *)jenv->GetDirectBufferAddress(jarg3);
+
+  jint jresult = 0 ;
+  tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
+  tiledb_query_t *arg2 = (tiledb_query_t *) 0 ;
+  void *arg3 = (void *) 0 ;
+  int32_t result;
+
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(tiledb_ctx_t **)&jarg1;
+  arg2 = *(tiledb_query_t **)&jarg2;
+  arg3 = *(void **)&jarg3;
+  result = (int32_t)tiledb_query_set_subarray(arg1,arg2,buffer);
+  jresult = (jint)result;
+  return jresult;
+}
+
 
 SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1set_1buffer(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jstring jarg3, jlong jarg4, jlong jarg5) {
   jint jresult = 0 ;

src/main/java/io/tiledb/java/api/Query.java

@@ -188,6 +188,17 @@ public synchronized Query setSubarray(NativeArray subarray) throws TileDBError {
     return this;
   }
 
+  /**
+   * Sets a subarray, defined in the order dimensions were added. Coordinates are inclusive.
+   *
+   * @param subarray The targeted subarray.
+   * @exception TileDBError A TileDB exception
+   */
+  public synchronized Query setSubarray(ByteBuffer subarray) throws TileDBError {
+    ctx.handleError(tiledb.tiledb_query_set_subarray_nio(ctx.getCtxp(), queryp, subarray));
+    return this;
+  }
+
   /**
    * Adds a 1D range along a subarray dimension, which is in the form (start, end). The datatype of
    * the range components must be the same as the type of the domain of the array in the query.

src/main/java/io/tiledb/libtiledb/tiledb.java

@@ -2119,6 +2119,12 @@ public static int tiledb_query_set_subarray(
         SWIGTYPE_p_void.getCPtr(subarray));
   }
 
+  public static int tiledb_query_set_subarray_nio(
+      SWIGTYPE_p_tiledb_ctx_t ctx, SWIGTYPE_p_tiledb_query_t query, ByteBuffer subarray) {
+    return tiledbJNI.tiledb_query_set_subarray_nio(
+        SWIGTYPE_p_tiledb_ctx_t.getCPtr(ctx), SWIGTYPE_p_tiledb_query_t.getCPtr(query), subarray);
+  }
+
   public static int tiledb_query_set_buffer(
       SWIGTYPE_p_tiledb_ctx_t ctx,
       SWIGTYPE_p_tiledb_query_t query,

src/main/java/io/tiledb/libtiledb/tiledbJNI.java

@@ -919,6 +919,9 @@ public static final native int tiledb_array_schema_has_attribute(
 
   public static final native int tiledb_query_set_subarray(long jarg1, long jarg2, long jarg3);
 
+  public static final native int tiledb_query_set_subarray_nio(
+      long jarg1, long jarg2, ByteBuffer jarg3);
+
   public static final native int tiledb_query_set_buffer(
       long jarg1, long jarg2, String jarg3, long jarg4, long jarg5);
 

src/test/java/io/tiledb/java/api/QueryTest.java

@@ -304,7 +304,7 @@ public void arrayWithVarAttrWrite() throws Exception {
     }
 
     @Test
-    public void queryTestNIOReadArray() throws Exception {
+    public void queryTestNIOReadArrayRange() throws Exception {
       arrayCreate();
       arrayWrite();
 
@@ -346,6 +346,52 @@ public void queryTestNIOReadArray() throws Exception {
           new int[] {1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4}, d2_result);
     }
 
+    @Test
+    public void queryTestNIOReadArraySubArray() throws Exception {
+      arrayCreate();
+      arrayWrite();
+
+      Array array = new Array(ctx, arrayURI, TILEDB_READ);
+
+      Query query = new Query(array, TILEDB_READ);
+
+      int bufferSize = 4;
+
+      query.setBuffer("rows", bufferSize);
+      query.setBuffer("cols", bufferSize);
+      ByteBuffer d1 = query.getByteBuffer("rows").getSecond();
+      ByteBuffer d2 = query.getByteBuffer("cols").getSecond();
+
+      ByteBuffer subarray = ByteBuffer.allocateDirect(4 * Datatype.TILEDB_INT32.getNativeSize());
+
+      subarray.order(ByteOrder.nativeOrder()).putInt(1).putInt(4).putInt(1).putInt(4);
+
+      query.setSubarray(subarray);
+
+      query.setLayout(TILEDB_ROW_MAJOR);
+
+      int[] d1_result = new int[16];
+      int[] d2_result = new int[16];
+      int idx = 0;
+
+      while (query.getQueryStatus() != QueryStatus.TILEDB_COMPLETED) {
+        query.submit();
+
+        while (d1.hasRemaining() && d2.hasRemaining()) {
+          d1_result[idx] = d1.getInt();
+          d2_result[idx] = d2.getInt();
+          idx++;
+        }
+        d1.clear();
+        d2.clear();
+      }
+
+      Assert.assertArrayEquals(
+          new int[] {1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4}, d1_result);
+      Assert.assertArrayEquals(
+          new int[] {1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4}, d2_result);
+    }
+
     @Test
     public void queryTestNIOReadArrayArbitrarySize() throws Exception {
       arrayCreate();
@@ -361,8 +407,9 @@ public void queryTestNIOReadArrayArbitrarySize() throws Exception {
       ByteBuffer d1 = query.getByteBuffer("rows").getSecond();
       ByteBuffer d2 = query.getByteBuffer("cols").getSecond();
 
-      query.addRange(0, 1, 4);
-      query.addRange(1, 1, 4);
+      ByteBuffer subarray = ByteBuffer.allocateDirect(4 * Datatype.TILEDB_INT32.getNativeSize());
+      subarray.order(ByteOrder.nativeOrder()).putInt(1).putInt(4).putInt(1).putInt(4);
+      query.setSubarray(subarray);
 
       query.setLayout(TILEDB_ROW_MAJOR);
 
@@ -397,9 +444,9 @@ public void arrayReadTest() throws Exception {
       try (Array array = new Array(ctx, arrayURI, TILEDB_READ);
           Query query = new Query(array, TILEDB_READ)) {
 
-        // Slice only rows 1, 2 and cols 2, 3, 4
-        query.addRange(0, 1, 2);
-        query.addRange(1, 2, 4);
+        ByteBuffer subarray = ByteBuffer.allocateDirect(4 * Datatype.TILEDB_INT32.getNativeSize());
+        subarray.order(ByteOrder.nativeOrder()).putInt(1).putInt(2).putInt(2).putInt(4);
+        query.setSubarray(subarray);
         query.setLayout(TILEDB_ROW_MAJOR);
 
         query.setBuffer("rows", 3).setBuffer("cols", 3).setBuffer("a1", 3).setBuffer("a2", 6);
@@ -453,9 +500,9 @@ public void arrayReadTestCustomBufferWithDifferentOrder() throws Exception {
       try (Array array = new Array(ctx, arrayURI, TILEDB_READ);
           Query query = new Query(array, TILEDB_READ)) {
 
-        // Slice only rows 1, 2 and cols 2, 3, 4
-        query.addRange(0, 1, 2);
-        query.addRange(1, 2, 4);
+        ByteBuffer subarray = ByteBuffer.allocateDirect(4 * Datatype.TILEDB_INT32.getNativeSize());
+        subarray.order(ByteOrder.nativeOrder()).putInt(1).putInt(2).putInt(2).putInt(4);
+        query.setSubarray(subarray);
         query.setLayout(TILEDB_ROW_MAJOR);
 
         // Set the opposite byte order from the native system
@@ -523,7 +570,9 @@ public void queryTestNIOSetBufferVarChar() throws Exception {
       ByteBuffer dataBuffer = ByteBuffer.allocateDirect(1000);
 
       Query q = new Query(new Array(ctx, arrayURI), TILEDB_READ);
-      q.addRange(0, 1, 8);
+      ByteBuffer subarray = ByteBuffer.allocateDirect(4 * Datatype.TILEDB_INT32.getNativeSize());
+      subarray.order(ByteOrder.nativeOrder()).putInt(1).putInt(8);
+      q.setSubarray(subarray);
       q.setBuffer("a1", offsetsBuffer, dataBuffer);
       q.submit();