NIO nullable ByteBuffers

Author: gsvic

src/main/c/custom/tiledb_custom.cxx

@@ -1212,6 +1212,68 @@ extern "C" {
     return jresult;
   }
 
+  SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1set_1buffer_1nullable_1nio(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jstring jarg3, jobject jarg4, jlong jarg5, jobject jarg6, jlong jarg7) {
+    jint jresult = 0 ;
+    tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
+    tiledb_query_t *arg2 = (tiledb_query_t *) 0 ;
+    char *arg3 = (char *) 0 ;
+    void *arg4 = (void *) 0 ;
+    uint64_t *arg5 = (uint64_t *) 0 ;
+    uint8_t *arg6 = (uint8_t *) 0 ;
+    uint64_t *arg7 = (uint64_t *) 0 ;
+    int32_t result;
+
+    (void)jenv;
+    (void)jcls;
+    arg1 = *(tiledb_ctx_t **)&jarg1;
+    arg2 = *(tiledb_query_t **)&jarg2;
+    arg3 = 0;
+    if (jarg3) {
+      arg3 = (char *)jenv->GetStringUTFChars(jarg3, 0);
+      if (!arg3) return 0;
+    }
+    arg4 = *(void **)&jarg4;
+    arg5 = *(uint64_t **)&jarg5;
+    arg6 = *(uint8_t **)&jarg6;
+    arg7 = *(uint64_t **)&jarg7;
+    result = (int32_t)tiledb_query_set_buffer_nullable(arg1,arg2,(char const *)arg3,(void *)jenv->GetDirectBufferAddress(jarg4),arg5,(uint8_t *)jenv->GetDirectBufferAddress(jarg6),arg7);
+    jresult = (jint)result;
+    if (arg3) jenv->ReleaseStringUTFChars(jarg3, (const char *)arg3);
+    return jresult;
+  }
+
+  SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1set_1buffer_1var_1nullable_1nio(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jstring jarg3, jobject jarg4, jlong jarg5, jobject jarg6, jlong jarg7, jobject jarg8, jlong jarg9) {
+      uint64_t * offsets = (uint64_t *)jenv->GetDirectBufferAddress(jarg4);
+      void * values = (void *)jenv->GetDirectBufferAddress(jarg6);
+      uint8_t * validity_bytemap = (uint8_t *)jenv->GetDirectBufferAddress(jarg8);
+
+      jint jresult = 0 ;
+      tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
+      tiledb_query_t *arg2 = (tiledb_query_t *) 0 ;
+      char *arg3 = (char *) 0 ;
+      uint64_t *arg5 = (uint64_t *) 0 ;
+      uint64_t *arg7 = (uint64_t *) 0 ;
+      uint64_t *arg9 = (uint64_t *) 0 ;
+      int32_t result;
+
+      (void)jenv;
+      (void)jcls;
+      arg1 = *(tiledb_ctx_t **)&jarg1;
+      arg2 = *(tiledb_query_t **)&jarg2;
+      arg3 = 0;
+      if (jarg3) {
+        arg3 = (char *)jenv->GetStringUTFChars(jarg3, 0);
+        if (!arg3) return 0;
+      }
+      arg5 = *(uint64_t **)&jarg5;
+      arg7 = *(uint64_t **)&jarg7;
+      arg9 = *(uint64_t **)&jarg9;
+      result = (int32_t)tiledb_query_set_buffer_var_nullable(arg1,arg2,(char const *)arg3, offsets, arg5, values, arg7, validity_bytemap, arg9);
+      jresult = (jint)result;
+      if (arg3) jenv->ReleaseStringUTFChars(jarg3, (const char *)arg3);
+      return jresult;
+    }
+
 
 #ifdef __cplusplus
 }

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

@@ -62,6 +62,7 @@ public class Query implements AutoCloseable {
   private Map<String, Pair<NativeArray, NativeArray>> buffers_;
   private Map<String, Pair<uint64_tArray, uint64_tArray>> buffer_sizes_;
   private Map<String, NativeArray> validityByteMaps_;
+  private Map<String, ByteBuffer> validityByteMapsByteBuffers_;
 
   public Query(Array array, QueryType type) throws TileDBError {
     Context _ctx = array.getCtx();
@@ -83,6 +84,7 @@ public Query(Array array, QueryType type) throws TileDBError {
     this.byteBuffers_ = Collections.synchronizedMap(new HashMap<>());
     this.buffer_sizes_ = Collections.synchronizedMap(new HashMap<>());
     this.validityByteMaps_ = Collections.synchronizedMap(new HashMap<>());
+    this.validityByteMapsByteBuffers_ = Collections.synchronizedMap(new HashMap<>());
   }
 
   public Query(Array array) throws TileDBError {
@@ -604,6 +606,67 @@ public synchronized Query setBufferNullable(
     return this;
   }
 
+  /**
+   * Sets a nullable buffer for a fixed-sized attribute.
+   *
+   * @param attr The attribute name.
+   * @param buffer NativeBuffer to be used for the attribute values.
+   * @param bytemap The byte-map
+   * @exception TileDBError A TileDB exception
+   */
+  public synchronized Query setBufferNullableNIO(String attr, ByteBuffer buffer, ByteBuffer bytemap)
+      throws TileDBError {
+
+    if (buffer.capacity() <= 0) {
+      throw new TileDBError("Number of buffer elements must be >= 1");
+    }
+
+    if (!buffer.isDirect()) {
+      throw new TileDBError(
+          "The ByteBuffer provided is not direct. Please provide a direct buffer (ByteBuffer.allocateDirect(...))");
+    }
+
+    if (!buffer.order().equals(ByteOrder.nativeOrder())) {
+      throw new TileDBError(
+          "The order of the data ByteBuffer should be the same as the native order (ByteOrder.nativeOrder()).");
+    }
+
+    this.byteBuffers_.put(attr, new Pair<>(null, buffer));
+
+    uint64_tArray offsets_array_size = new uint64_tArray(1);
+    uint64_tArray values_array_size = new uint64_tArray(1);
+    uint64_tArray buffer_validity_bytemap_size = new uint64_tArray(1);
+
+    offsets_array_size.setitem(0, BigInteger.valueOf(0));
+    values_array_size.setitem(0, BigInteger.valueOf(buffer.capacity()));
+    buffer_validity_bytemap_size.setitem(0, BigInteger.valueOf(bytemap.capacity()));
+
+    buffer_sizes_.put(attr, new Pair<>(offsets_array_size, values_array_size));
+
+    Pair<uint64_tArray, uint64_tArray> buffer_sizes =
+        new Pair<>(offsets_array_size, values_array_size);
+
+    this.byteBuffers_.put(attr, new Pair<>(null, buffer));
+
+    buffer_sizes_.put(attr, buffer_sizes);
+    validityByteMapsByteBuffers_.put(attr, bytemap);
+
+    // Set the actual TileDB buffer
+    uint64_tArray buffer_size = buffer_sizes.getSecond();
+
+    ctx.handleError(
+        Utils.tiledb_query_set_buffer_nullable_nio(
+            ctx.getCtxp(),
+            queryp,
+            attr,
+            buffer,
+            buffer_size.cast(),
+            bytemap,
+            buffer_validity_bytemap_size.cast()));
+
+    return this;
+  }
+
   /**
    * Sets a nullable buffer for a variable-sized getAttribute.
    *
@@ -681,6 +744,70 @@ public synchronized Query setBufferNullable(
     return this;
   }
 
+  /**
+   * Sets a ByteBuffer buffer for a variable-sized getAttribute.
+   *
+   * @param attr Attribute name
+   * @param offsets Offsets where a new element begins in the data buffer.
+   * @param buffer Buffer vector with elements of the attribute type.
+   * @exception TileDBError A TileDB exception
+   */
+  public synchronized Query setBufferNullableNIO(
+      String attr, ByteBuffer offsets, ByteBuffer buffer, ByteBuffer bytemap) throws TileDBError {
+
+    if (attr.equals(tiledb.tiledb_coords())) {
+      throw new TileDBError("Cannot set coordinate buffer as variable sized.");
+    }
+
+    if (!offsets.order().equals(ByteOrder.nativeOrder()) && offsets.position() > 0) {
+      throw new TileDBError(
+          "The order of the offsets ByteBuffer should be the same as the native order (ByteOrder.nativeOrder()) before values are inserted.");
+    }
+
+    if (!buffer.order().equals(ByteOrder.nativeOrder()) && buffer.position() > 0) {
+      throw new TileDBError(
+          "The order of the data ByteBuffer should be the same as the native order (ByteOrder.nativeOrder()) before values are inserted.");
+    }
+
+    offsets.order(ByteOrder.nativeOrder());
+    buffer.order(ByteOrder.nativeOrder());
+
+    uint64_tArray offsets_array_size = new uint64_tArray(0);
+    uint64_tArray values_array_size = new uint64_tArray(0);
+    uint64_tArray buffer_validity_bytemap_size = new uint64_tArray(0);
+
+    offsets_array_size.setitem(0, BigInteger.valueOf(offsets.capacity()));
+    values_array_size.setitem(0, BigInteger.valueOf(buffer.capacity()));
+    buffer_validity_bytemap_size.setitem(0, BigInteger.valueOf(bytemap.capacity()));
+
+    Pair<uint64_tArray, uint64_tArray> buffer_sizes =
+        new Pair<>(offsets_array_size, values_array_size);
+
+    // Close previous buffers if they exist for this attribute
+    if (buffers_.containsKey(attr)) {
+      Pair<NativeArray, NativeArray> prev_buffers = buffers_.get(attr);
+      prev_buffers.getFirst().close();
+      prev_buffers.getSecond().close();
+    }
+
+    buffer_sizes_.put(attr, buffer_sizes);
+    this.byteBuffers_.put(attr, new Pair(offsets, buffer));
+
+    ctx.handleError(
+        Utils.tiledb_query_set_buffer_var_nullable_nio(
+            ctx.getCtxp(),
+            queryp,
+            attr,
+            offsets,
+            offsets_array_size.cast(),
+            buffer,
+            values_array_size.cast(),
+            bytemap,
+            buffer_validity_bytemap_size.cast()));
+
+    return this;
+  }
+
   /**
    * * Sets a NIO ByteBuffer
    *
@@ -699,7 +826,6 @@ public synchronized Query setBuffer(String attr, long bufferElements) throws Til
     int size = Util.castLongToInt(bufferElements * dt.getNativeSize());
 
     ByteBuffer buffer = ByteBuffer.allocateDirect(size).order(ByteOrder.nativeOrder());
-    ;
 
     this.setBuffer(attr, buffer);
 

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

@@ -202,6 +202,24 @@ public static int tiledb_query_set_buffer_nio(
         SWIGTYPE_p_unsigned_long_long.getCPtr(buffer_size));
   }
 
+  public static int tiledb_query_set_buffer_nullable_nio(
+      SWIGTYPE_p_tiledb_ctx_t ctx,
+      SWIGTYPE_p_tiledb_query_t query,
+      String name,
+      ByteBuffer buffer,
+      SWIGTYPE_p_unsigned_long_long buffer_size,
+      ByteBuffer validity_bytemap,
+      SWIGTYPE_p_unsigned_long_long validity_bytemap_size) {
+    return tiledbJNI.tiledb_query_set_buffer_nullable_nio(
+        SWIGTYPE_p_tiledb_ctx_t.getCPtr(ctx),
+        SWIGTYPE_p_tiledb_query_t.getCPtr(query),
+        name,
+        buffer,
+        SWIGTYPE_p_unsigned_long_long.getCPtr(buffer_size),
+        validity_bytemap,
+        SWIGTYPE_p_unsigned_long_long.getCPtr(validity_bytemap_size));
+  }
+
   public static int tiledb_query_set_buffer_var_nio(
       SWIGTYPE_p_tiledb_ctx_t ctx,
       SWIGTYPE_p_tiledb_query_t query,
@@ -220,6 +238,28 @@ public static int tiledb_query_set_buffer_var_nio(
         SWIGTYPE_p_unsigned_long_long.getCPtr(buffer_val_size));
   }
 
+  public static int tiledb_query_set_buffer_var_nullable_nio(
+      SWIGTYPE_p_tiledb_ctx_t ctx,
+      SWIGTYPE_p_tiledb_query_t query,
+      String name,
+      ByteBuffer offsets,
+      SWIGTYPE_p_unsigned_long_long offsets_size,
+      ByteBuffer buffer,
+      SWIGTYPE_p_unsigned_long_long buffer_size,
+      ByteBuffer validity_bytemap,
+      SWIGTYPE_p_unsigned_long_long validity_bytemap_size) {
+    return tiledbJNI.tiledb_query_set_buffer_var_nullable_nio(
+        SWIGTYPE_p_tiledb_ctx_t.getCPtr(ctx),
+        SWIGTYPE_p_tiledb_query_t.getCPtr(query),
+        name,
+        offsets,
+        SWIGTYPE_p_unsigned_long_long.getCPtr(offsets_size),
+        buffer,
+        SWIGTYPE_p_unsigned_long_long.getCPtr(buffer_size),
+        validity_bytemap,
+        SWIGTYPE_p_unsigned_long_long.getCPtr(validity_bytemap_size));
+  }
+
   public static int tiledb_object_ls(
       SWIGTYPE_p_tiledb_ctx_t ctx, String path, PathCallback callback) {
     return tiledbJNI.tiledb_object_ls_java(

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

@@ -39,6 +39,26 @@ public static final native int tiledb_query_set_buffer_var_nio(
       ByteBuffer jarg6,
       long jarg7);
 
+  public static final native int tiledb_query_set_buffer_nullable_nio(
+      long jarg1,
+      long jarg2,
+      String jarg3,
+      ByteBuffer jarg4,
+      long jarg5,
+      ByteBuffer jarg6,
+      long jarg7);
+
+  public static final native int tiledb_query_set_buffer_var_nullable_nio(
+      long jarg1,
+      long jarg2,
+      String jarg3,
+      ByteBuffer jarg4,
+      long jarg5,
+      ByteBuffer jarg6,
+      long jarg7,
+      ByteBuffer jarg8,
+      long jarg9);
+
   public static final native int tiledb_query_submit_async_java(
       long jarg1,
       SWIGTYPE_p_tiledb_ctx_t jarg1_,