Added setFillValueNullable support and fragment info

Author: gsvic

src/main/c/generated/tiledb_wrap.cxx

@@ -996,6 +996,20 @@ public ArraySchema getSchema() throws TileDBError {
     return _schema;
   }
 
+  /**
+   * Reopens a TileDB array (the array must be already open). This is useful when the array got
+   * updated after it got opened. To sync-up with the updates, the user must either close the array
+   * and open with `tiledb_array_open`, or just use `reopen` without closing. This function will be
+   * generally faster than the former alternative.
+   *
+   * <p>Note: reopening encrypted arrays does not require the encryption key.
+   *
+   * @throws TileDBError
+   */
+  public void reopen() throws TileDBError {
+    ctx.handleError(tiledb.tiledb_array_reopen(ctx.getCtxp(), getArrayp()));
+  }
+
   /** @return The TileDB QueryType enum value that the Array instance. */
   public QueryType getQueryType() {
     return query_type;

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

@@ -290,7 +290,73 @@ public Pair<Object, Long> getFillValue() throws TileDBError {
     }
   }
 
-  public int setNullable(short nullable) throws TileDBError {
+  /**
+   * Sets the default fill value for the input, nullable attribute. This value will be used for the
+   * input attribute whenever querying (1) an empty cell in a dense array, or (2) a non-empty cell
+   * (in either dense or sparse array) when values on the input attribute are missing (e.g., if the
+   * user writes a subset of the attributes in a write operation).
+   *
+   * @param value The fill value to set.
+   * @param size The fill value size in bytes.
+   * @param valid The validity fill value, zero for a null value and non-zero for a valid attribute.
+   * @throws TileDBError
+   */
+  public void setFillValueNullable(NativeArray value, BigInteger size, boolean valid)
+      throws TileDBError {
+
+    try {
+      ctx.handleError(
+          tiledb.tiledb_attribute_set_fill_value_nullable(
+              ctx.getCtxp(),
+              attributep,
+              value.toVoidPointer(),
+              size,
+              valid ? (short) 1 : (short) 0));
+    } catch (TileDBError err) {
+      throw err;
+    }
+  }
+
+  /**
+   * Gets the default fill value for the input, nullable attribute. This value will be used for the
+   * input attribute whenever querying (1) an empty cell in a dense array, or (2) a non-empty cell
+   * (in either dense or sparse array) when values on the input attribute are missing (e.g., if the
+   * user writes a subset of the attributes in a write operation).
+   *
+   * <p>Applicable to both fixed-sized and var-sized attributes.
+   *
+   * @return A pair which contains the fill value and a pair with its size and validity field i.e.
+   *     Pair(5, Pair(4, true))
+   * @throws TileDBError
+   */
+  public Pair<Object, Pair<Long, Boolean>> getFillValueNullable() throws TileDBError {
+
+    try (NativeArray value = new NativeArray(ctx, this.type.getNativeSize(), this.type)) {
+      NativeArray validArr = new NativeArray(ctx, 1, Datatype.TILEDB_UINT8);
+      SWIGTYPE_p_unsigned_long_long size = tiledb.new_ullp();
+      SWIGTYPE_p_p_void v = tiledb.new_voidpArray(1);
+      SWIGTYPE_p_unsigned_char valid = validArr.getUint8_tArray().cast();
+
+      ctx.handleError(
+          tiledb.tiledb_attribute_get_fill_value_nullable(
+              ctx.getCtxp(), attributep, v, size, valid));
+
+      Object fillValue;
+      try (NativeArray fillValueArray = new NativeArray(ctx, getType(), v, 1)) {
+        fillValue = fillValueArray.getItem(0);
+      }
+
+      boolean validBoolean = validArr.getUint8_tArray().getitem(0) == 0 ? false : true;
+
+      return new Pair(fillValue, new Pair(tiledb.ullp_value(size), validBoolean));
+    } catch (TileDBError err) {
+      throw err;
+    }
+  }
+
+  public int setNullable(boolean isNullable) throws TileDBError {
+
+    short nullable = isNullable ? (short) 1 : (short) 0;
 
     try {
       int res;

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

@@ -1628,6 +1628,42 @@ public Query finalizeQuery() throws TileDBError {
     return this;
   }
 
+  /**
+   * Retrieves the number of written fragments. Applicable only to WRITE queries.
+   *
+   * @return The number of written fragments
+   * @throws TileDBError
+   */
+  public long getFragmentNum() throws TileDBError {
+    SWIGTYPE_p_unsigned_int fragmentNum = tiledb.new_uintp();
+    ctx.handleError(tiledb.tiledb_query_get_fragment_num(ctx.getCtxp(), queryp, fragmentNum));
+
+    return tiledb.uintp_value(fragmentNum);
+  }
+
+  /**
+   * Retrieves the URI of the written fragment with the input index. Applicable only to WRITE
+   * queries.
+   *
+   * @return The URI
+   * @throws TileDBError
+   */
+  public String getFragmentURI(BigInteger idx) throws TileDBError {
+    SWIGTYPE_p_p_char uri = tiledb.new_charpp();
+    ctx.handleError(tiledb.tiledb_query_get_fragment_uri(ctx.getCtxp(), queryp, idx, uri));
+
+    return tiledb.charpp_value(uri);
+  }
+
+  public Pair<Long, Long> getFragmentTimestampRange(BigInteger idx) throws TileDBError {
+    SWIGTYPE_p_unsigned_long_long t1 = tiledb.new_ullp();
+    SWIGTYPE_p_unsigned_long_long t2 = tiledb.new_ullp();
+    ctx.handleError(
+        tiledb.tiledb_query_get_fragment_timestamp_range(ctx.getCtxp(), queryp, idx, t1, t2));
+
+    return new Pair(tiledb.ullp_value(t1), tiledb.ullp_value(t2));
+  }
+
   // Default noop async completion callback
   private static class DefaultCallback implements Callback {
     public DefaultCallback() {}

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

@@ -0,0 +1,26 @@
+/* ----------------------------------------------------------------------------
+ * This file was automatically generated by SWIG (http://www.swig.org).
+ * Version 4.0.1
+ *
+ * Do not make changes to this file unless you know what you are doing--modify
+ * the SWIG interface file instead.
+ * ----------------------------------------------------------------------------- */
+
+package io.tiledb.libtiledb;
+
+public class SWIGTYPE_p_p_tiledb_fragment_info_t {
+  private transient long swigCPtr;
+
+  protected SWIGTYPE_p_p_tiledb_fragment_info_t(
+      long cPtr, @SuppressWarnings("unused") boolean futureUse) {
+    swigCPtr = cPtr;
+  }
+
+  protected SWIGTYPE_p_p_tiledb_fragment_info_t() {
+    swigCPtr = 0;
+  }
+
+  protected static long getCPtr(SWIGTYPE_p_p_tiledb_fragment_info_t obj) {
+    return (obj == null) ? 0 : obj.swigCPtr;
+  }
+}

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

@@ -0,0 +1,26 @@
+/* ----------------------------------------------------------------------------
+ * This file was automatically generated by SWIG (http://www.swig.org).
+ * Version 4.0.1
+ *
+ * Do not make changes to this file unless you know what you are doing--modify
+ * the SWIG interface file instead.
+ * ----------------------------------------------------------------------------- */
+
+package io.tiledb.libtiledb;
+
+public class SWIGTYPE_p_tiledb_fragment_info_t {
+  private transient long swigCPtr;
+
+  protected SWIGTYPE_p_tiledb_fragment_info_t(
+      long cPtr, @SuppressWarnings("unused") boolean futureUse) {
+    swigCPtr = cPtr;
+  }
+
+  protected SWIGTYPE_p_tiledb_fragment_info_t() {
+    swigCPtr = 0;
+  }
+
+  protected static long getCPtr(SWIGTYPE_p_tiledb_fragment_info_t obj) {
+    return (obj == null) ? 0 : obj.swigCPtr;
+  }
+}