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Replace getCoordinates with setBuffer #162

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Merged
merged 1 commit into from
May 20, 2020
Merged

Replace getCoordinates with setBuffer #162

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6 changes: 2 additions & 4 deletions src/main/java/io/tiledb/java/api/Array.java
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Original file line number Diff line number Diff line change
Expand Up @@ -482,8 +482,7 @@ public HashMap<String, Pair> nonEmptyDomain() throws TileDBError {
public Pair getNonEmptyDomainFromIndex(long index) throws TileDBError {
checkIsOpen();
try (Domain domain = schema.getDomain();
NativeArray domainArray =
new NativeArray(ctx, 2 * (int) domain.getRank(), domain.getType())) {
NativeArray domainArray = new NativeArray(ctx, 2, domain.getDimension(index).getType())) {

if (domain.getDimension(index).isVar()) return getNonEmptyDomainVarFromIndex(index);

Expand Down Expand Up @@ -515,8 +514,7 @@ public Pair getNonEmptyDomainFromIndex(long index) throws TileDBError {
public Pair getNonEmptyDomainFromName(String name) throws TileDBError {
checkIsOpen();
try (Domain domain = schema.getDomain();
NativeArray domainArray =
new NativeArray(ctx, 2 * (int) domain.getRank(), domain.getType())) {
NativeArray domainArray = new NativeArray(ctx, 2, domain.getDimension(name).getType())) {

if (domain.getDimension(name).isVar()) return this.getNonEmptyDomainVarFromName(name);

Expand Down
15 changes: 8 additions & 7 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 @@ -174,7 +174,7 @@ public synchronized Query addRange(int dimIdx, Object start, Object end) throws
Datatype dimType;
try (ArraySchema schema = array.getSchema();
Domain domain = schema.getDomain()) {
dimType = domain.getType();
dimType = domain.getDimension(dimIdx).getType();
}

// We use java type check here because we can not tell the difference between unsigned and
Expand Down Expand Up @@ -215,7 +215,7 @@ public synchronized Query addRangeVar(int dimIdx, String start, String end) thro
Datatype dimType;
try (ArraySchema schema = array.getSchema();
Domain domain = schema.getDomain()) {
dimType = domain.getType();
dimType = domain.getDimension(dimIdx).getType();
}

Types.javaTypeCheck(start.getClass(), dimType.javaClass());
Expand Down Expand Up @@ -276,7 +276,7 @@ public synchronized Pair<String, String> getRangeVar(int dimIdx, BigInteger rang
Datatype dimType;
try (ArraySchema schema = array.getSchema();
Domain domain = schema.getDomain()) {
dimType = domain.getType();
dimType = domain.getDimension(dimIdx).getType();
}

Pair<Long, Long> size = this.getRangeVarSize(dimIdx, rangeIdx);
Expand Down Expand Up @@ -325,7 +325,7 @@ public Pair<Object, Object> getRange(int dimIdx, long rangeIdx) throws TileDBErr
Datatype dimType;
try (ArraySchema schema = array.getSchema();
Domain domain = schema.getDomain()) {
dimType = domain.getType();
dimType = domain.getDimension(dimIdx).getType();
}

SWIGTYPE_p_p_void startArrpp = tiledb.new_voidpArray(1);
Expand Down Expand Up @@ -368,7 +368,7 @@ public synchronized Query setBuffer(String attr, NativeArray buffer) throws Tile
try (ArraySchema schema = array.getSchema()) {
try (Domain domain = schema.getDomain()) {
if (attr.equals(tiledb.tiledb_coords())) {
Types.typeCheck(domain.getType(), buffer.getNativeType());
Types.typeCheck(domain.getDimension(attr).getType(), buffer.getNativeType());
} else if (domain.hasDimension(attr)) {
Types.typeCheck(domain.getDimension(attr).getType(), buffer.getNativeType());
} else {
Expand Down Expand Up @@ -429,7 +429,7 @@ public synchronized Query setBuffer(String attr, NativeArray buffer, long buffer
try (ArraySchema schema = array.getSchema()) {
try (Domain domain = schema.getDomain()) {
if (attr.equals(tiledb.tiledb_coords())) {
Types.typeCheck(domain.getType(), buffer.getNativeType());
Types.typeCheck(domain.getDimension(attr).getType(), buffer.getNativeType());
} else if (domain.hasDimension(attr)) {
Types.typeCheck(domain.getDimension(attr).getType(), buffer.getNativeType());
} else {
Expand Down Expand Up @@ -492,7 +492,7 @@ public synchronized Query setBuffer(String attr, NativeArray offsets, NativeArra
try (ArraySchema schema = array.getSchema()) {
try (Domain domain = schema.getDomain()) {
if (attr.equals(tiledb.tiledb_coords())) {
Types.typeCheck(domain.getType(), buffer.getNativeType());
Types.typeCheck(domain.getDimension(attr).getType(), buffer.getNativeType());
} else if (domain.hasDimension(attr)) {
Types.typeCheck(domain.getDimension(attr).getType(), buffer.getNativeType());
} else {
Expand Down Expand Up @@ -748,6 +748,7 @@ public Query setCoordinates(NativeArray buffer) throws TileDBError {
* @return The query result coordinate buffer.
* @exception TileDBError A TileDB exception
*/
@Deprecated
public Object getCoordinates() throws TileDBError {
return getBuffer(tiledb.tiledb_coords());
}
Expand Down
30 changes: 18 additions & 12 deletions src/test/java/io/tiledb/java/api/AsyncTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,10 +42,8 @@ public void test() throws Exception {

public void arrayCreate() throws Exception {
// Create getDimensions
Dimension<Integer> rows =
new Dimension<Integer>(ctx, "rows", Integer.class, new Pair<Integer, Integer>(1, 4), 2);
Dimension<Integer> cols =
new Dimension<Integer>(ctx, "cols", Integer.class, new Pair<Integer, Integer>(1, 4), 2);
Dimension<Integer> rows = new Dimension(ctx, "rows", Integer.class, new Pair(1, 4), 2);
Dimension<Integer> cols = new Dimension(ctx, "cols", Integer.class, new Pair(1, 4), 2);

// Create and set getDomain
Domain domain = new Domain(ctx);
Expand All @@ -65,18 +63,20 @@ public void arrayCreate() throws Exception {
}

public void arrayWrite() throws Exception {
NativeArray d1_data = new NativeArray(ctx, new int[] {1, 2, 2, 4}, Integer.class);
NativeArray d2_data = new NativeArray(ctx, new int[] {1, 1, 2, 3}, Integer.class);

// Prepare cell buffers
NativeArray data = new NativeArray(ctx, new int[] {1, 2, 3, 4}, Integer.class);

NativeArray coords_buff =
new NativeArray(ctx, new int[] {1, 1, 2, 1, 2, 2, 4, 3}, Integer.class);

// Create query
Array array = new Array(ctx, arrayURI, TILEDB_WRITE);
Query query = new Query(array);
query.setLayout(TILEDB_GLOBAL_ORDER);
query.setBuffer("rows", d1_data);
query.setBuffer("cols", d2_data);
query.setBuffer("a", data);
query.setCoordinates(coords_buff);

// Submit query
query.submitAsync();

Expand All @@ -102,9 +102,13 @@ private void arrayRead() throws Exception {
Query query = new Query(array, TILEDB_READ);
query.setLayout(TILEDB_ROW_MAJOR);
query.setBuffer(
"a", new NativeArray(ctx, max_sizes.get("a").getSecond().intValue(), Integer.class));
query.setCoordinates(
"rows",
new NativeArray(ctx, max_sizes.get(TILEDB_COORDS).getSecond().intValue(), Integer.class));
query.setBuffer(
"cols",
new NativeArray(ctx, max_sizes.get(TILEDB_COORDS).getSecond().intValue(), Integer.class));
query.setBuffer(
"a", new NativeArray(ctx, max_sizes.get("a").getSecond().intValue(), Integer.class));

// Submit query with callback
query.submitAsync(new ReadCallback());
Expand All @@ -119,14 +123,16 @@ private void arrayRead() throws Exception {
// Print cell values (assumes all getAttributes are read)
HashMap<String, Pair<Long, Long>> result_el = query.resultBufferElements();

int[] rows = (int[]) query.getBuffer("rows");
int[] cols = (int[]) query.getBuffer("cols");
int[] data = (int[]) query.getBuffer("a");
int[] coords = (int[]) query.getCoordinates();

query.close();
array.close();

Assert.assertTrue(callbackCalled);
Assert.assertArrayEquals(coords, new int[] {1, 1, 2, 1, 2, 2, 4, 3});
Assert.assertArrayEquals(rows, new int[] {1, 2, 2, 4});
Assert.assertArrayEquals(cols, new int[] {1, 1, 2, 3});
Assert.assertArrayEquals(data, new int[] {1, 2, 3, 4});
}

Expand Down
20 changes: 11 additions & 9 deletions src/test/java/io/tiledb/java/api/FragmentsConsolidationTest.java
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Expand Up @@ -112,6 +112,8 @@ public void arrayWrite2() throws Exception {

public void arrayWrite3() throws Exception {
// Prepare cell buffers
NativeArray rows = new NativeArray(ctx, new int[] {1, 3}, Integer.class);
NativeArray cols = new NativeArray(ctx, new int[] {1, 4}, Integer.class);
NativeArray data = new NativeArray(ctx, new int[] {201, 202}, Integer.class);

NativeArray coords = new NativeArray(ctx, new int[] {1, 1, 3, 4}, Integer.class);
Expand All @@ -120,8 +122,9 @@ public void arrayWrite3() throws Exception {
Array array = new Array(ctx, arrayURI, TILEDB_WRITE);
Query query = new Query(array);
query.setLayout(TILEDB_UNORDERED);
query.setBuffer("rows", rows);
query.setBuffer("cols", cols);
query.setBuffer("a", data);
query.setCoordinates(coords);
// Submit query
query.submit();
query.close();
Expand All @@ -140,24 +143,23 @@ private void arrayRead() throws Exception {
query.setLayout(TILEDB_ROW_MAJOR);
query.setSubarray(subarray);
query.setBuffer("a", new NativeArray(ctx, 16, Integer.class));
query.setCoordinates(new NativeArray(ctx, 32, Integer.class));
query.setBuffer("rows", new NativeArray(ctx, 16, Integer.class));
query.setBuffer("cols", new NativeArray(ctx, 16, Integer.class));

// Submit query
query.submit();
// Print cell values (assumes all getAttributes are read)
HashMap<String, Pair<Long, Long>> result_el = query.resultBufferElements();

int[] rows = (int[]) query.getBuffer("rows");
int[] cols = (int[]) query.getBuffer("cols");
int[] data = (int[]) query.getBuffer("a");
int[] coords = (int[]) query.getCoordinates();
query.close();
array.close();

Assert.assertArrayEquals(
coords,
new int[] {
1, 1, 1, 2, 1, 3, 1, 4, 2, 1, 2, 2, 2, 3, 2, 4, 3, 1, 3, 2, 3, 3, 3, 4, 4, 1, 4, 2, 4, 3,
4, 4
});
Assert.assertArrayEquals(rows, new int[] {1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4});
Assert.assertArrayEquals(cols, new int[] {1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4, 1, 2, 3, 4});

Assert.assertArrayEquals(
data,
new int[] {
Expand Down
141 changes: 141 additions & 0 deletions src/test/java/io/tiledb/java/api/HeterogeneousSparseTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,141 @@
/*
* The MIT License (MIT)
*
* Copyright (c) 2020 TileDB, Inc.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/

package io.tiledb.java.api;

import static io.tiledb.java.api.ArrayType.TILEDB_SPARSE;
import static io.tiledb.java.api.Layout.TILEDB_GLOBAL_ORDER;
import static io.tiledb.java.api.Layout.TILEDB_ROW_MAJOR;
import static io.tiledb.java.api.QueryType.TILEDB_READ;
import static io.tiledb.java.api.QueryType.TILEDB_WRITE;

import java.nio.file.Files;
import java.nio.file.Paths;
import org.junit.After;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;

@SuppressWarnings("ALL")
public class HeterogeneousSparseTest {

private Context ctx;
private String arrayURI = "my_sparse_array";

@Before
public void setup() throws Exception {
ctx = new Context();
if (Files.exists(Paths.get(arrayURI))) {
TileDBObject.remove(ctx, arrayURI);
}
}

@After
public void teardown() throws Exception {
if (Files.exists(Paths.get(arrayURI))) {
TileDBObject.remove(ctx, arrayURI);
}
}

@Test
public void testQuickstartSparse() throws Exception {
arrayCreate();
arrayWrite();
arrayRead();
}

public void arrayCreate() throws Exception {
Dimension d1 = new Dimension(ctx, "d1", Datatype.TILEDB_STRING_ASCII, null, null);
Dimension d2 = new Dimension(ctx, "d2", Datatype.TILEDB_INT32, new Pair(0, 100), 2);

// Create and set getDomain
Domain domain = new Domain(ctx);
domain.addDimension(d1).addDimension(d2);

// Add two attributes "a1" and "a2", so each (i,j) cell can store
// a character on "a1" and a vector of two floats on "a2".
Attribute a1 = new Attribute(ctx, "a1", Integer.class);

ArraySchema schema = new ArraySchema(ctx, TILEDB_SPARSE);
schema.setTileOrder(TILEDB_ROW_MAJOR);
schema.setCellOrder(TILEDB_ROW_MAJOR);
schema.setDomain(domain);
schema.addAttribute(a1);

Array.create(arrayURI, schema);
}

public void arrayWrite() throws Exception {
NativeArray d1_data = new NativeArray(ctx, "aabbccddee", Datatype.TILEDB_STRING_ASCII);
NativeArray d1_off = new NativeArray(ctx, new long[] {0, 2, 4, 6, 8}, Datatype.TILEDB_UINT64);
NativeArray d2_data = new NativeArray(ctx, new int[] {1, 4, 9, 10, 12}, Datatype.TILEDB_INT32);

// Prepare cell buffers
NativeArray a1 = new NativeArray(ctx, new int[] {1, 2, 3, 4, 5}, Integer.class);

// Create query
Array array = new Array(ctx, arrayURI, TILEDB_WRITE);
Query query = new Query(array);
query.setLayout(TILEDB_GLOBAL_ORDER);

query.setBuffer("d1", d1_off, d1_data);
query.setBuffer("d2", d2_data);
query.setBuffer("a1", a1);

// Submit query
query.submit();

query.finalizeQuery();
query.close();
array.close();
}

private void arrayRead() throws Exception {
NativeArray d_data = new NativeArray(ctx, 20, Datatype.TILEDB_STRING_ASCII);
NativeArray d_off = new NativeArray(ctx, 20, Datatype.TILEDB_UINT64);

NativeArray d2_data = new NativeArray(ctx, 20, Datatype.TILEDB_INT32);

Query q = new Query(new Array(ctx, arrayURI), TILEDB_READ);
q.setLayout(TILEDB_GLOBAL_ORDER);

q.setBuffer("d1", d_off, d_data);
q.setBuffer("d2", d2_data);

q.addRangeVar(0, "a", "z");

q.submit();

byte[] data = (byte[]) q.getBuffer("d1");
long[] offsets = q.getVarBuffer("d1");
int[] d2 = (int[]) q.getBuffer("d2");

String[] results = new String[offsets.length];

results = Util.bytesToStrings(offsets, data);

Assert.assertArrayEquals(results, new String[] {"aa", "bb", "cc", "dd", "ee"});
Assert.assertArrayEquals(d2, new int[] {1, 4, 9, 10, 12});
}
}
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