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Merged
merged 2 commits into from
Apr 6, 2021
Merged

Victorgiannakouris/java api updates #215

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dc8f711
switch getValiditBytemap to public
gsvic Mar 26, 2021
3eeb5bc
set the correct validity bytemap size
gsvic Mar 30, 2021
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34 changes: 16 additions & 18 deletions src/main/java/io/tiledb/java/api/Query.java
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Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,7 @@ public class Query implements AutoCloseable {
private Map<String, Pair<uint64_tArray, uint64_tArray>> buffer_sizes_;
private Map<String, NativeArray> validityByteMaps_;
private Map<String, ByteBuffer> validityByteMapsByteBuffers_;
private Map<String, uint64_tArray> validityByteMapSizes_;

public Query(Array array, QueryType type) throws TileDBError {
Context _ctx = array.getCtx();
Expand All @@ -85,6 +86,7 @@ public Query(Array array, QueryType type) throws TileDBError {
this.buffer_sizes_ = Collections.synchronizedMap(new HashMap<>());
this.validityByteMaps_ = Collections.synchronizedMap(new HashMap<>());
this.validityByteMapsByteBuffers_ = Collections.synchronizedMap(new HashMap<>());
this.validityByteMapSizes_ = Collections.synchronizedMap(new HashMap<>());
}

public Query(Array array) throws TileDBError {
Expand Down Expand Up @@ -538,23 +540,11 @@ public synchronized Query setBuffer(String attr, NativeArray buffer, long buffer
*
* @param attr The attribute name.
* @param buffer NativeBuffer to be used for the attribute values.
* @param bufferElements The actual number of buffer elements
* @param bytemap The byte-map
* @exception TileDBError A TileDB exception
*/
public synchronized Query setBufferNullable(
String attr, NativeArray buffer, long bufferElements, NativeArray bytemap)
public synchronized Query setBufferNullable(String attr, NativeArray buffer, NativeArray bytemap)
throws TileDBError {
if (bufferElements <= 0) {
throw new TileDBError("Number of buffer elements must be >= 1");
}
if (bufferElements > buffer.getSize()) {
throw new TileDBError(
"Number of elements requested exceeds the number of elements in allocated buffer: "
+ bufferElements
+ " > "
+ buffer.getSize());
}

try (ArraySchema schema = array.getSchema()) {
try (Domain domain = schema.getDomain()) {
Expand All @@ -573,10 +563,10 @@ public synchronized Query setBufferNullable(
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(0l));
values_array_size.setitem(0, BigInteger.valueOf(bufferElements * buffer.getNativeTypeSize()));
buffer_validity_bytemap_size.setitem(
0, BigInteger.valueOf(bytemap.getSize() * bytemap.getNativeTypeSize()));
values_array_size.setitem(0, BigInteger.valueOf(buffer.getNBytes()));
buffer_validity_bytemap_size.setitem(0, BigInteger.valueOf(bytemap.getNBytes()));

Pair<uint64_tArray, uint64_tArray> buffer_sizes =
new Pair<>(offsets_array_size, values_array_size);
Expand All @@ -589,6 +579,7 @@ public synchronized Query setBufferNullable(
buffers_.put(attr, new Pair(null, buffer));
buffer_sizes_.put(attr, buffer_sizes);
validityByteMaps_.put(attr, bytemap);
validityByteMapSizes_.put(attr, buffer_validity_bytemap_size);

// Set the actual TileDB buffer
uint64_tArray buffer_size = buffer_sizes.getSecond();
Expand Down Expand Up @@ -728,6 +719,7 @@ public synchronized Query setBufferNullable(
buffers_.put(attr, new Pair<>(offsets, buffer));
buffer_sizes_.put(attr, buffer_sizes);
validityByteMaps_.put(attr, bytemap);
validityByteMapSizes_.put(attr, buffer_validity_bytemap_size);

ctx.handleError(
tiledb.tiledb_query_set_buffer_var_nullable(
Expand Down Expand Up @@ -1573,9 +1565,15 @@ public long[] getOffsetArray(String bufferName) throws TileDBError {
}

/** @param attribute */
Object getValidityByteMap(String attribute) throws TileDBError {
public short[] getValidityByteMap(String attribute) throws TileDBError {
if (this.validityByteMaps_.containsKey(attribute)) {
return this.validityByteMaps_.get(attribute).toJavaArray();
int nelements =
this.validityByteMapSizes_
.get(attribute)
.getitem(0)
.divide(BigInteger.valueOf(Datatype.TILEDB_UINT8.getNativeSize()))
.intValue();
return (short[]) this.validityByteMaps_.get(attribute).toJavaArray(nelements);
}

throw new TileDBError("Attribute " + attribute + " is not nullable");
Expand Down
28 changes: 14 additions & 14 deletions src/test/java/io/tiledb/java/api/QueryTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1014,8 +1014,8 @@ public void denseArrayWrite() throws Exception {
NativeArray a2Bytemap =
new NativeArray(ctx, new short[] {1, 1, 1, 0}, Datatype.TILEDB_UINT8);

query.setBufferNullable("a1", a1, 4, a1Bytemap);
query.setBufferNullable("a2", a2, 4, a2Bytemap);
query.setBufferNullable("a1", a1, a1Bytemap);
query.setBufferNullable("a2", a2, a2Bytemap);

// Submit query
query.submit();
Expand Down Expand Up @@ -1074,7 +1074,7 @@ public void sparseArrayWrite() throws TileDBError {
new NativeArray(ctx, new short[] {1, 1, 1, 0, 0}, Datatype.TILEDB_UINT8);

query.setBuffer("d1", d_off, d_data);
query.setBufferNullable("a1", a1, 5, a1ByteMap);
query.setBufferNullable("a1", a1, a1ByteMap);
query.setBufferNullable("a2", a2_off, a2_data, a2ByteMap);

// Submit query
Expand Down Expand Up @@ -1112,17 +1112,17 @@ public void denseArrayReadTest() throws Exception {
query.addRange(1, 1, 2);
query.setLayout(TILEDB_ROW_MAJOR);

NativeArray dim1Array = new NativeArray(ctx, 4, Integer.class);
NativeArray dim2Array = new NativeArray(ctx, 4, Integer.class);
NativeArray a1Array = new NativeArray(ctx, 4, Character.class);
NativeArray a1byteMap = new NativeArray(ctx, 4, Datatype.TILEDB_UINT8);
NativeArray a2Array = new NativeArray(ctx, 4, Float.class);
NativeArray a2byteMap = new NativeArray(ctx, 4, Datatype.TILEDB_UINT8);
NativeArray dim1Array = new NativeArray(ctx, 100, Integer.class);
NativeArray dim2Array = new NativeArray(ctx, 100, Integer.class);
NativeArray a1Array = new NativeArray(ctx, 100, Character.class);
NativeArray a1byteMap = new NativeArray(ctx, 100, Datatype.TILEDB_UINT8);
NativeArray a2Array = new NativeArray(ctx, 100, Float.class);
NativeArray a2byteMap = new NativeArray(ctx, 100, Datatype.TILEDB_UINT8);

query.setBuffer("rows", dim1Array);
query.setBuffer("cols", dim2Array);
query.setBufferNullable("a1", a1Array, 4, a1byteMap);
query.setBufferNullable("a2", a2Array, 4, a2byteMap);
query.setBufferNullable("a1", a1Array, a1byteMap);
query.setBufferNullable("a2", a2Array, a2byteMap);

// Submit query
query.submit();
Expand All @@ -1143,8 +1143,8 @@ public void denseArrayReadTest() throws Exception {
byte[] a1 = (byte[]) query.getBuffer("a1");
float[] a2 = (float[]) query.getBuffer("a2");

short[] a1ValidityByteMap = (short[]) query.getValidityByteMap("a1");
short[] a2ValidityByteMap = (short[]) query.getValidityByteMap("a2");
short[] a1ValidityByteMap = query.getValidityByteMap("a1");
short[] a2ValidityByteMap = query.getValidityByteMap("a2");

Assert.assertArrayEquals(new int[] {1, 1, 2, 2}, dim1);
Assert.assertArrayEquals(new int[] {1, 2, 1, 2}, dim2);
Expand Down Expand Up @@ -1249,7 +1249,7 @@ public void sparseArrayReadTest() throws Exception {
NativeArray a2Offsets = new NativeArray(ctx, 5, Datatype.TILEDB_UINT64);
NativeArray a2byteMap = new NativeArray(ctx, 10, Datatype.TILEDB_UINT8);

query.setBufferNullable("a1", a1Array, 5, a1byteMap);
query.setBufferNullable("a1", a1Array, a1byteMap);
query.setBufferNullable("a2", a2Offsets, a2Array, a2byteMap);

// Submit query
Expand Down