Fill Value JNI Bindings

src/main/c/generated/tiledb_wrap.cxx

@@ -6068,6 +6068,71 @@ SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1attribute_1du
 }
 
 
+SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1attribute_1set_1fill_1value(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jlong jarg3, jobject jarg4) {
+  jint jresult = 0 ;
+  tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
+  tiledb_attribute_t *arg2 = (tiledb_attribute_t *) 0 ;
+  void *arg3 = (void *) 0 ;
+  uint64_t arg4 ;
+  int32_t result;
+
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(tiledb_ctx_t **)&jarg1; 
+  arg2 = *(tiledb_attribute_t **)&jarg2; 
+  arg3 = *(void **)&jarg3; 
+  {
+    jclass clazz;
+    jmethodID mid;
+    jbyteArray ba;
+    jbyte* bae;
+    jsize sz;
+    int i;
+
+    if (!jarg4) {
+      SWIG_JavaThrowException(jenv, SWIG_JavaNullPointerException, "BigInteger null");
+      return 0;
+    }
+    clazz = jenv->GetObjectClass(jarg4);
+    mid = jenv->GetMethodID(clazz, "toByteArray", "()[B");
+    ba = (jbyteArray)jenv->CallObjectMethod(jarg4, mid);
+    bae = jenv->GetByteArrayElements(ba, 0);
+    sz = jenv->GetArrayLength(ba);
+    arg4 = 0;
+    if (sz > 0) {
+      arg4 = (uint64_t)(signed char)bae[0];
+      for(i=1; i<sz; i++) {
+        arg4 = (arg4 << 8) | (uint64_t)(unsigned char)bae[i];
+      }
+    }
+    jenv->ReleaseByteArrayElements(ba, bae, 0);
+  }
+  result = (int32_t)tiledb_attribute_set_fill_value(arg1,arg2,(void const *)arg3,arg4);
+  jresult = (jint)result; 
+  return jresult;
+}
+
+
+SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1attribute_1get_1fill_1value(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jlong jarg3, jlong jarg4) {
+  jint jresult = 0 ;
+  tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
+  tiledb_attribute_t *arg2 = (tiledb_attribute_t *) 0 ;
+  void **arg3 = (void **) 0 ;
+  uint64_t *arg4 = (uint64_t *) 0 ;
+  int32_t result;
+
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(tiledb_ctx_t **)&jarg1; 
+  arg2 = *(tiledb_attribute_t **)&jarg2; 
+  arg3 = *(void ***)&jarg3; 
+  arg4 = *(uint64_t **)&jarg4; 
+  result = (int32_t)tiledb_attribute_get_fill_value(arg1,arg2,(void const **)arg3,arg4);
+  jresult = (jint)result; 
+  return jresult;
+}
+
+
 SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1domain_1alloc(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2) {
   jint jresult = 0 ;
   tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
@@ -7338,6 +7403,24 @@ SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1get_1l
 }
 
 
+SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1get_1array(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jlong jarg3) {
+  jint jresult = 0 ;
+  tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
+  tiledb_query_t *arg2 = (tiledb_query_t *) 0 ;
+  tiledb_array_t **arg3 = (tiledb_array_t **) 0 ;
+  int32_t result;
+
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(tiledb_ctx_t **)&jarg1; 
+  arg2 = *(tiledb_query_t **)&jarg2; 
+  arg3 = *(tiledb_array_t ***)&jarg3; 
+  result = (int32_t)tiledb_query_get_array(arg1,arg2,arg3);
+  jresult = (jint)result; 
+  return jresult;
+}
+
+
 SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1query_1add_1range(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jlong jarg3, jlong jarg4, jlong jarg5, jlong jarg6) {
   jint jresult = 0 ;
   tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
@@ -9235,6 +9318,36 @@ SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1vfs_1move_1di
 }
 
 
+SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1vfs_1copy_1file(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jstring jarg3, jstring jarg4) {
+  jint jresult = 0 ;
+  tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;
+  tiledb_vfs_t *arg2 = (tiledb_vfs_t *) 0 ;
+  char *arg3 = (char *) 0 ;
+  char *arg4 = (char *) 0 ;
+  int32_t result;
+
+  (void)jenv;
+  (void)jcls;
+  arg1 = *(tiledb_ctx_t **)&jarg1; 
+  arg2 = *(tiledb_vfs_t **)&jarg2; 
+  arg3 = 0;
+  if (jarg3) {
+    arg3 = (char *)jenv->GetStringUTFChars(jarg3, 0);
+    if (!arg3) return 0;
+  }
+  arg4 = 0;
+  if (jarg4) {
+    arg4 = (char *)jenv->GetStringUTFChars(jarg4, 0);
+    if (!arg4) return 0;
+  }
+  result = (int32_t)tiledb_vfs_copy_file(arg1,arg2,(char const *)arg3,(char const *)arg4);
+  jresult = (jint)result; 
+  if (arg3) jenv->ReleaseStringUTFChars(jarg3, (const char *)arg3);
+  if (arg4) jenv->ReleaseStringUTFChars(jarg4, (const char *)arg4);
+  return jresult;
+}
+
+
 SWIGEXPORT jint JNICALL Java_io_tiledb_libtiledb_tiledbJNI_tiledb_1vfs_1open(JNIEnv *jenv, jclass jcls, jlong jarg1, jlong jarg2, jstring jarg3, jint jarg4, jlong jarg5) {
   jint jresult = 0 ;
   tiledb_ctx_t *arg1 = (tiledb_ctx_t *) 0 ;

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

@@ -27,6 +27,7 @@
 import static io.tiledb.java.api.Constants.TILEDB_VAR_NUM;
 
 import io.tiledb.libtiledb.*;
+import java.math.BigInteger;
 
 /**
  * Describes an Attribute of an Array cell.
@@ -260,6 +261,35 @@ public FilterList getFilterList() throws TileDBError {
     return filterlist;
   }
 
+  public void setFillValue(NativeArray value, BigInteger size) throws TileDBError {
+    try {
+      ctx.handleError(
+          tiledb.tiledb_attribute_set_fill_value(
+              ctx.getCtxp(), attributep, value.toVoidPointer(), size));
+    } catch (TileDBError err) {
+      throw err;
+    }
+  }
+
+  public Pair<Object, Long> getFillValue() throws TileDBError {
+
+    try (NativeArray value = new NativeArray(ctx, this.type.getNativeSize(), this.type)) {
+      SWIGTYPE_p_unsigned_long_long size = tiledb.new_ullp();
+      SWIGTYPE_p_p_void v = tiledb.new_voidpArray(1);
+
+      ctx.handleError(tiledb.tiledb_attribute_get_fill_value(ctx.getCtxp(), attributep, v, size));
+
+      Object fillValue;
+      try (NativeArray fillValueArray = new NativeArray(ctx, getType(), v, 1)) {
+        fillValue = fillValueArray.getItem(0);
+      }
+
+      return new Pair(fillValue, tiledb.ullp_value(size));
+    } catch (TileDBError err) {
+      throw err;
+    }
+  }
+
   /** @return A String representation for the Attribute. */
   @Override
   public String toString() {

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

@@ -1652,6 +1652,30 @@ public static int tiledb_attribute_dump(
         SWIGTYPE_p_FILE.getCPtr(out));
   }
 
+  public static int tiledb_attribute_set_fill_value(
+      SWIGTYPE_p_tiledb_ctx_t ctx,
+      SWIGTYPE_p_tiledb_attribute_t attr,
+      SWIGTYPE_p_void value,
+      java.math.BigInteger size) {
+    return tiledbJNI.tiledb_attribute_set_fill_value(
+        SWIGTYPE_p_tiledb_ctx_t.getCPtr(ctx),
+        SWIGTYPE_p_tiledb_attribute_t.getCPtr(attr),
+        SWIGTYPE_p_void.getCPtr(value),
+        size);
+  }
+
+  public static int tiledb_attribute_get_fill_value(
+      SWIGTYPE_p_tiledb_ctx_t ctx,
+      SWIGTYPE_p_tiledb_attribute_t attr,
+      SWIGTYPE_p_p_void value,
+      SWIGTYPE_p_unsigned_long_long size) {
+    return tiledbJNI.tiledb_attribute_get_fill_value(
+        SWIGTYPE_p_tiledb_ctx_t.getCPtr(ctx),
+        SWIGTYPE_p_tiledb_attribute_t.getCPtr(attr),
+        SWIGTYPE_p_p_void.getCPtr(value),
+        SWIGTYPE_p_unsigned_long_long.getCPtr(size));
+  }
+
   public static int tiledb_domain_alloc(
       SWIGTYPE_p_tiledb_ctx_t ctx, SWIGTYPE_p_p_tiledb_domain_t domain) {
     return tiledbJNI.tiledb_domain_alloc(
@@ -2295,6 +2319,16 @@ public static int tiledb_query_get_layout(
         SWIGTYPE_p_tiledb_layout_t.getCPtr(query_layout));
   }
 
+  public static int tiledb_query_get_array(
+      SWIGTYPE_p_tiledb_ctx_t ctx,
+      SWIGTYPE_p_tiledb_query_t query,
+      SWIGTYPE_p_p_tiledb_array_t array) {
+    return tiledbJNI.tiledb_query_get_array(
+        SWIGTYPE_p_tiledb_ctx_t.getCPtr(ctx),
+        SWIGTYPE_p_tiledb_query_t.getCPtr(query),
+        SWIGTYPE_p_p_tiledb_array_t.getCPtr(array));
+  }
+
   public static int tiledb_query_add_range(
       SWIGTYPE_p_tiledb_ctx_t ctx,
       SWIGTYPE_p_tiledb_query_t query,
@@ -3081,6 +3115,15 @@ public static int tiledb_vfs_move_dir(
         new_uri);
   }
 
+  public static int tiledb_vfs_copy_file(
+      SWIGTYPE_p_tiledb_ctx_t ctx, SWIGTYPE_p_tiledb_vfs_t vfs, String old_uri, String new_uri) {
+    return tiledbJNI.tiledb_vfs_copy_file(
+        SWIGTYPE_p_tiledb_ctx_t.getCPtr(ctx),
+        SWIGTYPE_p_tiledb_vfs_t.getCPtr(vfs),
+        old_uri,
+        new_uri);
+  }
+
   public static int tiledb_vfs_open(
       SWIGTYPE_p_tiledb_ctx_t ctx,
       SWIGTYPE_p_tiledb_vfs_t vfs,

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

@@ -13,6 +13,6 @@ public interface tiledbConstants {
   public static final int TILEDB_OK = 0;
   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 = 5;
+  public static final int TILEDB_VERSION_MINOR = 1;
+  public static final int TILEDB_VERSION_PATCH = 2;
 }

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

@@ -795,6 +795,12 @@ public static final native int tiledb_attribute_get_cell_val_num(
 
   public static final native int tiledb_attribute_dump(long jarg1, long jarg2, long jarg3);
 
+  public static final native int tiledb_attribute_set_fill_value(
+      long jarg1, long jarg2, long jarg3, java.math.BigInteger jarg4);
+
+  public static final native int tiledb_attribute_get_fill_value(
+      long jarg1, long jarg2, long jarg3, long jarg4);
+
   public static final native int tiledb_domain_alloc(long jarg1, long jarg2);
 
   public static final native void tiledb_domain_free(long jarg1);
@@ -965,6 +971,8 @@ public static final native int tiledb_query_submit_async(
 
   public static final native int tiledb_query_get_layout(long jarg1, long jarg2, long jarg3);
 
+  public static final native int tiledb_query_get_array(long jarg1, long jarg2, long jarg3);
+
   public static final native int tiledb_query_add_range(
       long jarg1, long jarg2, long jarg3, long jarg4, long jarg5, long jarg6);
 
@@ -1170,6 +1178,9 @@ public static final native int tiledb_vfs_move_file(
   public static final native int tiledb_vfs_move_dir(
       long jarg1, long jarg2, String jarg3, String jarg4);
 
+  public static final native int tiledb_vfs_copy_file(
+      long jarg1, long jarg2, String jarg3, String jarg4);
+
   public static final native int tiledb_vfs_open(
       long jarg1, long jarg2, String jarg3, int jarg4, long jarg5);
 

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

@@ -26,6 +26,7 @@
 
 import static io.tiledb.java.api.Constants.TILEDB_VAR_NUM;
 
+import java.math.BigInteger;
 import org.junit.Assert;
 import org.junit.Test;
 
@@ -59,4 +60,52 @@ public void testAttributeDatatype() throws Exception {
       Assert.assertEquals(Datatype.TILEDB_FLOAT32, a.getType());
     }
   }
+
+  @Test
+  public void testAttributeSetFillValue() throws Exception {
+    try (Context ctx = new Context();
+        Attribute a = new Attribute(ctx, "a2", Datatype.TILEDB_INT32)) {
+
+      NativeArray arr = new NativeArray(ctx, 1, Datatype.TILEDB_INT32);
+
+      arr.setItem(0, 5);
+
+      a.setFillValue(arr, BigInteger.valueOf(arr.getNativeTypeSize() * arr.getSize()));
+
+      Assert.assertEquals(5, a.getFillValue().getFirst());
+      Assert.assertEquals(
+          BigInteger.valueOf(arr.getNativeTypeSize() * arr.getSize()),
+          a.getFillValue().getSecond());
+    }
+
+    try (Context ctx = new Context();
+        Attribute a = new Attribute(ctx, "a2", Datatype.TILEDB_INT64)) {
+
+      NativeArray arr = new NativeArray(ctx, 1, Datatype.TILEDB_INT64);
+
+      arr.setItem(0, 5L);
+
+      a.setFillValue(arr, BigInteger.valueOf(arr.getNativeTypeSize() * arr.getSize()));
+
+      Assert.assertEquals(5L, a.getFillValue().getFirst());
+      Assert.assertEquals(
+          BigInteger.valueOf(arr.getNativeTypeSize() * arr.getSize()),
+          a.getFillValue().getSecond());
+    }
+
+    try (Context ctx = new Context();
+        Attribute a = new Attribute(ctx, "a2", Datatype.TILEDB_CHAR)) {
+
+      NativeArray arr = new NativeArray(ctx, 1, Datatype.TILEDB_CHAR);
+
+      arr.setItem(0, "c");
+
+      a.setFillValue(arr, BigInteger.valueOf(arr.getNativeTypeSize() * arr.getSize()));
+
+      Assert.assertEquals((byte) 'c', a.getFillValue().getFirst());
+      Assert.assertEquals(
+          BigInteger.valueOf(arr.getNativeTypeSize() * arr.getSize()),
+          a.getFillValue().getSecond());
+    }
+  }
 }