Merge pull request #180 from TileDB-Inc/victorgiannakouris/ch2662/leverage-nio-bytebuffers-in-tiledb-java

Leverage NIO ByteBuffers in TileDB Java [ch2662]

Author: gsvic

src/main/c/generated/tiledb_wrap.cxx

@@ -7016,6 +7016,34 @@ SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1set_1b
   return jresult;
 }
 
+SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1set_1buffer_1nio(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jstring jarg3, jobject jarg4, jlong jarg5) {
+  void* buffer = (void *)jenv->GetDirectBufferAddress(jarg4);
+
+  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 ;
+  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;
+  result = (int32_t)tiledb_query_set_buffer(arg1,arg2,(char const *)arg3, buffer,arg5);
+  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(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jstring jarg3, jlong jarg4, jlong jarg5, jlong jarg6, jlong jarg7) {
   jint jresult = 0 ;
@@ -9503,6 +9531,34 @@ SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1stats_1dump_1
 }
 
 
+SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1stats_1raw_1dump(JNIEnv *jenv, jclass jcls, jlong jarg1) {
+  jint jresult = 0 ;
+  FILE *arg1 = (FILE *) 0 ;
+  int32_t result;
+  
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(FILE **)&jarg1; 
+  result = (int32_t)tiledb_stats_raw_dump(arg1);
+  jresult = (jint)result; 
+  return jresult;
+}
+
+
+SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1stats_1raw_1dump_1str(JNIEnv *jenv, jclass jcls, jlong jarg1) {
+  jint jresult = 0 ;
+  char **arg1 = (char **) 0 ;
+  int32_t result;
+  
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(char ***)&jarg1; 
+  result = (int32_t)tiledb_stats_raw_dump_str(arg1);
+  jresult = (jint)result; 
+  return jresult;
+}
+
+
 SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1stats_1free_1str(JNIEnv *jenv, jclass jcls, jlong jarg1) {
   jint jresult = 0 ;
   char **arg1 = (char **) 0 ;

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

@@ -28,6 +28,8 @@
 
 import io.tiledb.libtiledb.*;
 import java.math.BigInteger;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Map;
@@ -58,6 +60,7 @@ public class Query implements AutoCloseable {
   private NativeArray subarray;
 
   private Map<String, NativeArray> buffers_;
+  private Map<String, ByteBuffer> byteBuffers_;
   private Map<String, Pair<NativeArray, NativeArray>> var_buffers_;
   private Map<String, Pair<uint64_tArray, uint64_tArray>> buffer_sizes_;
 
@@ -78,6 +81,7 @@ public Query(Array array, QueryType type) throws TileDBError {
     this.querypp = _querypp;
     this.queryp = tiledb.tiledb_query_tpp_value(_querypp);
     this.buffers_ = Collections.synchronizedMap(new HashMap<>());
+    this.byteBuffers_ = Collections.synchronizedMap(new HashMap<>());
     this.var_buffers_ = Collections.synchronizedMap(new HashMap<>());
     this.buffer_sizes_ = Collections.synchronizedMap(new HashMap<>());
   }
@@ -467,6 +471,82 @@ public synchronized Query setBuffer(String attr, NativeArray buffer, long buffer
     return this;
   }
 
+  /**
+   * * Sets a NIO ByteBuffer
+   *
+   * @param attr The attribute
+   * @param bufferElements
+   * @return The NIO ByteBuffer
+   * @throws TileDBError
+   */
+  public synchronized ByteBuffer setBuffer(String attr, long bufferElements) throws TileDBError {
+    if (bufferElements <= 0) {
+      throw new TileDBError("Number of buffer elements must be >= 1");
+    }
+
+    Datatype dt;
+
+    try (ArraySchema schema = array.getSchema()) {
+      try (Domain domain = schema.getDomain()) {
+        if (domain.hasDimension(attr)) {
+          dt = domain.getDimension(attr).getType();
+        } else {
+          try (Attribute attribute = schema.getAttribute(attr)) {
+            dt = attribute.getType();
+          }
+        }
+      }
+    }
+
+    int size = Util.castLongToInt(bufferElements * dt.getNativeSize());
+
+    ByteBuffer buffer = ByteBuffer.allocateDirect(size);
+
+    // Set the byte order to the native system's native order
+    buffer.order(ByteOrder.nativeOrder());
+
+    this.byteBuffers_.put(attr, buffer);
+
+    this.setBuffer(attr, buffer);
+
+    return buffer;
+  }
+
+  /**
+   * * Sets a NIO ByteBuffer
+   *
+   * @param attr The attribute
+   * @param buffer The input NIO ByteBuffer
+   * @return The NIO ByteBuffer
+   * @throws TileDBError
+   */
+  public synchronized ByteBuffer setBuffer(String attr, ByteBuffer buffer) 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())) {
+      // TODO: Add a logger component to Query class and a WARN here
+      buffer.order(ByteOrder.nativeOrder());
+    }
+
+    this.byteBuffers_.put(attr, buffer);
+
+    uint64_tArray values_array_size = new uint64_tArray(1);
+    values_array_size.setitem(0, BigInteger.valueOf(buffer.capacity()));
+
+    ctx.handleError(
+        tiledb.tiledb_query_set_buffer_nio(
+            ctx.getCtxp(), queryp, attr, buffer, values_array_size.cast()));
+
+    return buffer;
+  }
+
   /**
    * Sets a buffer for a variable-sized getAttribute.
    *
@@ -885,6 +965,18 @@ public Object getBuffer(String attr) throws TileDBError {
     }
   }
 
+  /**
+   * Retrieves the ByteBuffer of attribute attr
+   *
+   * @param attr The attribute name
+   * @return The ByteBuffer
+   * @throws TileDBError A TileDB exception
+   */
+  public ByteBuffer getByteBuffer(String attr) throws TileDBError {
+    if (byteBuffers_.containsKey(attr)) return byteBuffers_.get(attr);
+    else throw new TileDBError("ByteBuffer does not exist for attribute: " + attr);
+  }
+
   /**
    * Return an array containing offsets for a variable attribute buffer
    *

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

@@ -29,4 +29,11 @@ public static String[] bytesToStrings(long[] offsets, byte[] data) {
 
     return results;
   }
+
+  public static int castLongToInt(long num) throws TileDBError {
+    if (num > Integer.MAX_VALUE)
+      throw new TileDBError(num + " is larger that the integer max value");
+
+    return (int) num;
+  }
 }

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

@@ -8,6 +8,8 @@
 
 package io.tiledb.libtiledb;
 
+import java.nio.ByteBuffer;
+
 public class tiledb implements tiledbConstants {
   public static SWIGTYPE_p_p_char new_charpArray(int nelements) {
     long cPtr = tiledbJNI.new_charpArray(nelements);
@@ -2131,6 +2133,20 @@ public static int tiledb_query_set_buffer(
         SWIGTYPE_p_unsigned_long_long.getCPtr(buffer_size));
   }
 
+  public static int tiledb_query_set_buffer_nio(
+      SWIGTYPE_p_tiledb_ctx_t ctx,
+      SWIGTYPE_p_tiledb_query_t query,
+      String name,
+      ByteBuffer buffer,
+      SWIGTYPE_p_unsigned_long_long buffer_size) {
+    return tiledbJNI.tiledb_query_set_buffer_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));
+  }
+
   public static int tiledb_query_set_buffer_var(
       SWIGTYPE_p_tiledb_ctx_t ctx,
       SWIGTYPE_p_tiledb_query_t query,
@@ -3155,6 +3171,14 @@ public static int tiledb_stats_dump_str(SWIGTYPE_p_p_char out) {
     return tiledbJNI.tiledb_stats_dump_str(SWIGTYPE_p_p_char.getCPtr(out));
   }
 
+  public static int tiledb_stats_raw_dump(SWIGTYPE_p_FILE out) {
+    return tiledbJNI.tiledb_stats_raw_dump(SWIGTYPE_p_FILE.getCPtr(out));
+  }
+
+  public static int tiledb_stats_raw_dump_str(SWIGTYPE_p_p_char out) {
+    return tiledbJNI.tiledb_stats_raw_dump_str(SWIGTYPE_p_p_char.getCPtr(out));
+  }
+
   public static int tiledb_stats_free_str(SWIGTYPE_p_p_char out) {
     return tiledbJNI.tiledb_stats_free_str(SWIGTYPE_p_p_char.getCPtr(out));
   }

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

@@ -14,5 +14,5 @@ public interface tiledbConstants {
   public static final int TILEDB_OOM = (-2);
   public static final int TILEDB_VERSION_MAJOR = 2;
   public static final int TILEDB_VERSION_MINOR = 0;
-  public static final int TILEDB_VERSION_PATCH = 0;
+  public static final int TILEDB_VERSION_PATCH = 5;
 }

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

@@ -8,6 +8,8 @@
 
 package io.tiledb.libtiledb;
 
+import java.nio.ByteBuffer;
+
 public class tiledbJNI {
 
   static {
@@ -920,6 +922,9 @@ public static final native int tiledb_array_schema_has_attribute(
   public static final native int tiledb_query_set_buffer(
       long jarg1, long jarg2, String jarg3, long jarg4, long jarg5);
 
+  public static final native int tiledb_query_set_buffer_nio(
+      long jarg1, long jarg2, String jarg3, ByteBuffer jarg4, long jarg5);
+
   public static final native int tiledb_query_set_buffer_var(
       long jarg1, long jarg2, String jarg3, long jarg4, long jarg5, long jarg6, long jarg7);
 
@@ -1188,6 +1193,10 @@ public static final native int tiledb_uri_to_path(
 
   public static final native int tiledb_stats_dump_str(long jarg1);
 
+  public static final native int tiledb_stats_raw_dump(long jarg1);
+
+  public static final native int tiledb_stats_raw_dump_str(long jarg1);
+
   public static final native int tiledb_stats_free_str(long jarg1);
 
   public static final native int tiledb_dimension_dump_stdout(long jarg1, long jarg2);